Photofragment imaging study of the CH2CCH2OH radical intermediate of the OH+allene reaction

International Nuclear Information System (INIS)

Raman, Arjun S.; Justine Bell, M.; Lau, K.-C.; Butler, Laurie J.

2007-01-01

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 2 CCH 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 2 CCH 2 OH photofragments, a spin-orbit branching ratio for Cl( 2 P 1/2 ):Cl( 2 P 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 2 CCH 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 2 CCH 2 OH radical intermediate to the three most important product channels for the OH+allene reaction expected from this radical intermediate: formaldehyde+C 2 H 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 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

Photofragment imaging study of the CH2CCH2OH radical intermediate of the OH +allene reaction

Science.gov (United States)

Raman, Arjun S.; Justine Bell, M.; Lau, Kai-Chung; Butler, Laurie J.

2007-10-01

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 CH2CCH2OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl +CH2CCH2OH photofragments, a spin-orbit branching ratio for Cl(P1/22):Cl(P3/22) 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 CH2CCH2OH 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 CH2CCH2OH radical intermediate to the three most important product channels for the OH +allene reaction expected from this radical intermediate: formaldehyde+C2H3, 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+CH3 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.

On intermediate structures in heavy ion reactions

International Nuclear Information System (INIS)

Rotter, I.

1977-01-01

The conceptions of the nuclear reaction theory are reinvestigated on the basis of the continuum shell model. The correlation of the resonance states via the continuum can lead to intermediate structures in the cross section. (Auth.)

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

Science.gov (United States)

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 reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.

Comparative TEA for Indirect Liquefaction Pathways to Distillate-Range Fuels via Oxygenated Intermediates

Energy Technology Data Exchange (ETDEWEB)

Tan, Eric; Snowden-Swan, Lesley J.; Talmadge, Michael; Dutta, Abhijit; Jones, Susanne; Ramasamy, Karthikeyan; Gray, Michael; Dagle, Robert; Padmaperuma, Asanga; Gerber, Mark; Sahir, Asad; Tao, Ling; Zhang, Yanan

2017-03-03

This paper presents a comparative techno-economic analysis of five conversion pathways from biomass to gasoline-, jet-, and diesel-range hydrocarbons via indirect liquefaction with specific focus on pathways utilizing oxygenated intermediates (derived either via thermochemical or biochemical conversion steps). The four emerging pathways of interest are compared with one conventional pathway (Fischer-Tropsch) for the production of the hydrocarbon blendstocks. The processing steps of the four emerging pathways include: biomass-to-syngas via indirect gasification, gas cleanup, conversion of syngas to alcohols/oxygenates, followed by conversion of alcohols/oxygenates to hydrocarbon blendstocks via dehydration, oligomerization, and hydrogenation. We show that the emerging pathways via oxygenated intermediates have the potential to be cost competitive with the conventional Fischer-Tropsch process. The evaluated pathways and the benchmark process generally exhibit similar fuel yields and carbon conversion efficiencies. The resulting minimum fuel selling prices are comparable to the benchmark at approximately $3.60 per gallon-gasoline equivalent, with potential for two new pathways to be more economically competitive. Additionally, the coproduct values can play an important role in the economics of the processes with oxygenated intermediates derived via syngas fermentation. Major cost drivers for the integrated processes are tied to achievable fuel yields and conversion efficiency of the intermediate steps, i.e., the production of oxygenates/alcohols from syngas and the conversion of oxygenates/alcohols to hydrocarbon fuels.

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

Science.gov (United States)

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 60 min with an electrical energy per order (EEO) of 10.77 kWh m(-3) at an initial concentration of 200 μg L(-1) and a relative inlet pressure pin=0.35 MPa. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

Transfer and breakup reactions at intermediate energies

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase

NARCIS (Netherlands)

Ridder, L.; Mulholland, A.; Rietjens, I.M.C.M.; Vervoort, J.

1999-01-01

The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the

Reaction-transport simulations of non-oxidative methane conversion with continuous hydrogen removal: Homogeneous-heterogeneous methane reaction pathways

International Nuclear Information System (INIS)

Li, Lin; Borry, Richard W.; Iglesia, Enrique

2000-01-01

Detailed kinetic-transport models were used to explore thermodynamic and kinetic barriers in the non-oxidative conversion of CH4 via homogeneous and homogeneous-heterogeneous pathways and the effects of continuous hydrogen removal and of catalytic sites on attainable yields of useful C2-C10 products. The homogeneous kinetic model combines separately developed models for low-conversion pyrolysis and for chain growth to form large aromatics and carbon. The H2 formed in the reaction decreases CH4 pyrolysis rates and equilibrium conversions and it favors the formation of lighter products. The removal of H2 along tubular reactors with permeable walls increases reaction rates and equilibrium CH4 conversions. C2-C10 yields reach values greater than 90 percent at intermediate values of dimensionless transport rates (delta=1-10), defined as the ratio hydrogen transport and methane conversion rates. Homogeneous reactions require impractical residence times, even with H2 removal, because of slow initiation and chain transfer rates. The introduction of heterogeneous chain initiation pathways using surface sites that form methyl radicals eliminates the induction period without influencing the homogeneous product distribution. Methane conversion, however, occurs predominately in the chain transfer regime, within which individual transfer steps and the formation of C2 intermediates become limited by thermodynamic constraints. Catalytic sites alone cannot overcome these constraints. Catalytic membrane reactors with continuous H2 removal remove these thermodynamic obstacles and decrease the required residence time. Reaction rates become limited by homogeneous reactions of C2 products to form C6+ aromatics. Higher delta values lead to subsequent conversion of the desired C2-C10 products to larger polynuclear aromatics. We conclude that catalytic methane pyrolysis at the low temperatures required for restricted chain growth and the elimination of thermodynamics constraints via

Mechanisms for the inversion of chirality: Global reaction route mapping of stereochemical pathways in a probable chiral extraterrestrial molecule, 2-aminopropionitrile

International Nuclear Information System (INIS)

Kaur, Ramanpreet; Vikas

2015-01-01

2-Aminopropionitrile (APN), a probable candidate as a chiral astrophysical molecule, is a precursor to amino-acid alanine. Stereochemical pathways in 2-APN are explored using Global Reaction Route Mapping (GRRM) method employing high-level quantum-mechanical computations. Besides predicting the conventional mechanism for chiral inversion that proceeds through an achiral intermediate, a counterintuitive flipping mechanism is revealed for 2-APN through chiral intermediates explored using the GRRM. The feasibility of the proposed stereochemical pathways, in terms of the Gibbs free-energy change, is analyzed at the temperature conditions akin to the interstellar medium. Notably, the stereoinversion in 2-APN is observed to be more feasible than the dissociation of 2-APN and intermediates involved along the stereochemical pathways, and the flipping barrier is observed to be as low as 3.68 kJ/mol along one of the pathways. The pathways proposed for the inversion of chirality in 2-APN may provide significant insight into the extraterrestrial origin of life

Reaction pathways for catalytic gas-phase oxidation of glycerol over mixed metal oxides

Energy Technology Data Exchange (ETDEWEB)

Suprun, W.; Glaeser, R.; Papp, H. [Leipzig Univ. (Germany). Inst. of Chemical Technology

2011-07-01

Glycerol as a main by-product from bio-diesel manufacture is a cheap raw material with large potential for chemical or biochemical transformations to value-added C3-chemicals. One possible way of glycerol utilization involves its catalytic oxidation to acrylic acid as an alternative to petrochemical routes. However, this catalytic conversion exhibits various problems such as harsh reaction conditions, severe catalyst coking and large amounts of undesired by-products. In this study, the reaction pathways for gas-phase conversion of glycerol over transition metal oxides (Mo, V und W) supported on TiO{sub 2} and SiO{sub 2} were investigated by two methods: (i) steady state experiments of glycerol oxidation and possible reactions intermediates, i.e., acrolein, 3-hydroxy propionaldehyde and acetaldehyde, and (ii) temperature-programmed surface reaction (TPSR) studies of glycerol conversion in the presence and in the absence of gas-phase oxygen. It is shown that the supported W-, V and Mo-oxides possess an ability to catalyze the oxidation of glycerol to acrylic acid. These investigations allowed us to gain a deeper insight into the reaction mechanism. Thus, based on the obtained results, three possible reactions pathways for the selective oxidation of glycerol to acrylic acid on the transition metal-containing catalysts are proposed. The major pathways in presence of molecular oxygen are a fast successive destructive oxidation of glycerol to CO{sub x} and the dehydration of glycerol to acrolein which is a rate-limiting step. (orig.)

Fission in intermediate energy heavy ion reactions

International Nuclear Information System (INIS)

Wilhelmy, J.B.; Begemann-Blaich, M.; Blaich, T.; Boissevain, J.; Fowler, M.M.; Gavron, A.; Jacak, B.V.; Lysaght, P.S.; Britt, H.C.; Fields, D.J.; Hansen, L.F.; Lanier, R.G.; Massoletti, D.J.; Namboodiri, M.M.; Remington, B.A.; Sangster, T.C.; Struble, G.L.; Webb, M.L.; Chan, Y.D.; Dacai, A.; Harmon, A.; Leyba, J.; Pouliot, J.; Stokstad, R.G.; Hansen, O.; Levine, M.J.; Thorn, C.E.; Trautmann, W.; Dichter, B.; Kaufman, S.; Videbaek, F.; Fraenkel, Z.; Mamane, G.; Cebra, D.; Westfall, G.D.

1989-01-01

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

Fission in intermediate energy heavy ion reactions

International Nuclear Information System (INIS)

Wilhelmy, J.B.; Begemann-Blaich, M.; Blaich, T.

1989-01-01

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

Nucleon charge-exchange reactions at intermediate energy

Energy Technology Data Exchange (ETDEWEB)

Alford, W.P. [Western Ontario Univ., London, ON (Canada). Dept. of Physics]|[TRIUMF, Vancouver, BC (Canada); Spicer, B.M. [Melbourne Univ., Parkville, VIC (Australia). School of Physics

1997-12-31

An historical review of the development of ideas pertaining to Gamow-Teller giant resonances is given, and a description of the emergence of techniques for the study of charge exchange reactions - particularly the technical advances which yielded the recent volume of new date. The present status of charge exchange reactions is reviewed and assessed. Evidence is presented from the {sup 14}C(p,n) reaction for the dominance of the spin-isospin component of the nucleon-nucleon interaction in intermediate energy reactions. In (p,n) reactions the Gamow-Teller giant resonance dominates the spectra, with higher multipoles contributing. By contrast, in (n,p) reactions in the heavier nuclei, the Gamow-Teller transitions are substantially Pauli-blocked and the spin dipole resonance dominates, with contributions from higher multipoles. Discussions of the multipole decomposition process, used to obtain from the data the contributions of the different multipoles, and the contributions of the multipoles, are given. 226 refs., 19 figs.

Nucleon charge-exchange reactions at intermediate energy

International Nuclear Information System (INIS)

Alford, W.P.; Spicer, B.M.

1997-01-01

An historical review of the development of ideas pertaining to Gamow-Teller giant resonances is given, and a description of the emergence of techniques for the study of charge exchange reactions - particularly the technical advances which yielded the recent volume of new date. The present status of charge exchange reactions is reviewed and assessed. Evidence is presented from the 14 C(p,n) reaction for the dominance of the spin-isospin component of the nucleon-nucleon interaction in intermediate energy reactions. In (p,n) reactions the Gamow-Teller giant resonance dominates the spectra, with higher multipoles contributing. By contrast, in (n,p) reactions in the heavier nuclei, the Gamow-Teller transitions are substantially Pauli-blocked and the spin dipole resonance dominates, with contributions from higher multipoles. Discussions of the multipole decomposition process, used to obtain from the data the contributions of the different multipoles, and the contributions of the multipoles, are given

Photocatalytic degradation of metoprolol tartrate in suspensions of two TiO2-based photocatalysts with different surface area. Identification of intermediates and proposal of degradation pathways

International Nuclear Information System (INIS)

Abramović, Biljana; Kler, Sanja; Šojić, Daniela; Laušević, Mila; Radović, Tanja; Vione, Davide

2011-01-01

Highlights: ► Kinetics and efficiency of photocatalytic degradation of the β 1 -blocker metoprolol tartrate (MET). ► Two TiO 2 specimens employed. ► Faster degradation of MET, but slower mineralization, obtained with the TiO 2 specimen having lower surface area. ► Photocatalytic transformation pathways of MET including mineralization. - Abstract: This study investigates the efficiency of the photocatalytic degradation of metoprolol tartrate (MET), a widely used β 1 -blocker, in TiO 2 suspensions of Wackherr's “Oxyde de titane standard” and Degussa P25. The study encompasses transformation kinetics and efficiency, identification of intermediates and reaction pathways. In the investigated range of initial concentrations (0.01–0.1 mM), the photocatalytic degradation of MET in the first stage of the reaction followed approximately a pseudo-first order kinetics. The TiO 2 Wackherr induced a significantly faster MET degradation compared to TiO 2 Degussa P25 when relatively high substrate concentrations were used. By examining the effect of ethanol as a scavenger of hydroxyl radicals (·OH), it was shown that the reaction with ·OH played the main role in the photocatalytic degradation of MET. After 240 min of irradiation the reaction intermediates were almost completely mineralized to CO 2 and H 2 O, while the nitrogen was predominantly present as NH 4 + . Reaction intermediates were studied in detail and a number of them were identified using LC–MS/MS (ESI+), which allowed the proposal of a tentative pathway for the photocatalytic transformation of MET as a function of the TiO 2 specimen.

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

Directory of Open Access Journals (Sweden)

Yiran Huang

Full Text Available Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

Photocatalytic degradation of metoprolol tartrate in suspensions of two TiO{sub 2}-based photocatalysts with different surface area. Identification of intermediates and proposal of degradation pathways

Energy Technology Data Exchange (ETDEWEB)

Abramovic, Biljana, E-mail: biljana.abramovic@dh.uns.ac.rs [Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg D. Obradovica 3, 21000 Novi Sad (Serbia); Kler, Sanja, E-mail: sanja.kler@dh.uns.ac.rs [Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg D. Obradovica 3, 21000 Novi Sad (Serbia); Sojic, Daniela, E-mail: daniela.sojic@dh.uns.ac.rs [Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg D. Obradovica 3, 21000 Novi Sad (Serbia); Lausevic, Mila, E-mail: milal@tmf.bg.ac.rs [Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11120 Belgrade (Serbia); Radovic, Tanja, E-mail: tradovic@tmf.bg.ac.rs [Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11120 Belgrade (Serbia); Vione, Davide, E-mail: davide.vione@unito.it [Dipartimento di Chimica Analitica, Universita di Torino, Via Pietro Giuria 5, 10125 Torino (Italy)

2011-12-30

Highlights: Black-Right-Pointing-Pointer Kinetics and efficiency of photocatalytic degradation of the {beta}{sub 1}-blocker metoprolol tartrate (MET). Black-Right-Pointing-Pointer Two TiO{sub 2} specimens employed. Black-Right-Pointing-Pointer Faster degradation of MET, but slower mineralization, obtained with the TiO{sub 2} specimen having lower surface area. Black-Right-Pointing-Pointer Photocatalytic transformation pathways of MET including mineralization. - Abstract: This study investigates the efficiency of the photocatalytic degradation of metoprolol tartrate (MET), a widely used {beta}{sub 1}-blocker, in TiO{sub 2} suspensions of Wackherr's 'Oxyde de titane standard' and Degussa P25. The study encompasses transformation kinetics and efficiency, identification of intermediates and reaction pathways. In the investigated range of initial concentrations (0.01-0.1 mM), the photocatalytic degradation of MET in the first stage of the reaction followed approximately a pseudo-first order kinetics. The TiO{sub 2} Wackherr induced a significantly faster MET degradation compared to TiO{sub 2} Degussa P25 when relatively high substrate concentrations were used. By examining the effect of ethanol as a scavenger of hydroxyl radicals ({center_dot}OH), it was shown that the reaction with {center_dot}OH played the main role in the photocatalytic degradation of MET. After 240 min of irradiation the reaction intermediates were almost completely mineralized to CO{sub 2} and H{sub 2}O, while the nitrogen was predominantly present as NH{sub 4}{sup +}. Reaction intermediates were studied in detail and a number of them were identified using LC-MS/MS (ESI+), which allowed the proposal of a tentative pathway for the photocatalytic transformation of MET as a function of the TiO{sub 2} specimen.

Criegee Intermediates: What Direct Production and Detection Can Teach Us About Reactions of Carbonyl Oxides

Science.gov (United States)

Taatjes, Craig A.

2017-05-01

The carbonyl oxide intermediates in the ozonolysis of alkenes, often known as Criegee intermediates, are potentially important reactants in Earth's atmosphere. For decades, careful analysis of ozonolysis systems was employed to derive an understanding of the formation and reactions of these species. Recently it has proved possible to synthesize at least some of these intermediates separately from ozonolysis, and hence to measure their reaction kinetics directly. Direct measurements have allowed new or more detailed understanding of each type of gas-phase reaction that carbonyl oxides undergo, often acting as a complement to highly detailed ozonolysis experiments. Moreover, the use of direct characterization methods to validate increasingly accurate theoretical investigations can enhance their impact well beyond the set of specific reactions that have been measured. Reactions that initiate particles or fuel their growth could be a new frontier for direct measurements of Criegee intermediate chemistry.

Combustion kinetics and reaction pathways

Energy Technology Data Exchange (ETDEWEB)

Klemm, R.B.; Sutherland, J.W. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01

This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.

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

Directory of Open Access Journals (Sweden)

Samuel Hernández Anzaldo

2016-06-01

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

Reaction between peroxynitrite and boronates: EPR spin-trapping, HPLC analyses, and quantum mechanical study of the free radical pathway

Science.gov (United States)

Sikora, Adam; Zielonka, Jacek; Lopez, Marcos; Dybala-Defratyka, Agnieszka; Joseph, Joy; Marcinek, Andrzej; Kalyanaraman, Balaraman

2013-01-01

Recently we showed that peroxynitrite (ONOO−) reacts directly and rapidly with aromatic and aliphatic boronic acids (k ≈ 106 M−1s−1). Product analyses and substrate consumption data indicated that ONOO− reacts stoichiometrically with boronates, yielding the corresponding phenols as the major product (~85–90%), and the remaining products (10–15%) were proposed to originate from free radical intermediates (phenyl and phenoxyl radicals). Here we investigated in detail the minor, free radical pathway of boronate reaction with ONOO−. The electron paramagnetic resonance (EPR) spin-trapping technique was used to characterize the free radical intermediates formed from the reaction between boronates and ONOO−. Using 2-methyl-2-nitrosopropane (MNP) and 5-diethoxyphosphoryl-5-methyl-1-pyrroline-N-oxide (DEPMPO) spin traps, phenyl radicals were trapped and detected. Although phenoxyl radicals were not detected, the positive effects of molecular oxygen, and inhibitory effects of hydrogen atom donors (acetonitrile, and 2-propanol) and general radical scavengers (GSH, NADH, ascorbic acid and tyrosine) on the formation of phenoxyl radical-derived nitrated product, suggest that phenoxyl radical was formed as the secondary species. We propose that the initial step of the reaction involves the addition of ONOO− to the boron atom in boronates. The anionic intermediate undergoes both heterolytic (major pathway) and homolytic (minor pathway) cleavage of the peroxy (O-O) bond to form phenol and nitrite as a major product (via a non-radical mechanism), or a radical pair PhB(OH)2O•−…•NO2 as a minor product. It is conceivable that phenyl radicals are formed by the fragmentation of PhB(OH)2O•− radical anion. According to the DFT quantum mechanical calculations, the energy barrier for the dissociation of PhB(OH)2O•− radical anion to form phenyl radicals is only a few kcal/mol, suggesting rapid and spontaneous fragmentation of PhB(OH)2O•− radical anion

Comparative techno-economic analysis and process design for indirect liquefaction pathways to distillate-range fuels via biomass-derived oxygenated intermediates upgrading: Liquid Transportation Fuel Production via Biomass-derived Oxygenated Intermediates Upgrading

Energy Technology Data Exchange (ETDEWEB)

Tan, Eric C. D. [National Renewable Energy Laboratory, Golden CO USA; Snowden-Swan, Lesley J. [Pacific Northwest National Laboratory, Richland WA USA; Talmadge, Michael [National Renewable Energy Laboratory, Golden CO USA; Dutta, Abhijit [National Renewable Energy Laboratory, Golden CO USA; Jones, Susanne [Pacific Northwest National Laboratory, Richland WA USA; Ramasamy, Karthikeyan K. [Pacific Northwest National Laboratory, Richland WA USA; Gray, Michel [Pacific Northwest National Laboratory, Richland WA USA; Dagle, Robert [Pacific Northwest National Laboratory, Richland WA USA; Padmaperuma, Asanga [Pacific Northwest National Laboratory, Richland WA USA; Gerber, Mark [Pacific Northwest National Laboratory, Richland WA USA; Sahir, Asad H. [National Renewable Energy Laboratory, Golden CO USA; Tao, Ling [National Renewable Energy Laboratory, Golden CO USA; Zhang, Yanan [National Renewable Energy Laboratory, Golden CO USA

2016-09-27

This paper presents a comparative techno-economic analysis (TEA) of five conversion pathways from biomass to gasoline-, jet-, and diesel-range hydrocarbons via indirect liquefaction with specific focus on pathways utilizing oxygenated intermediates. The four emerging pathways of interest are compared with one conventional pathway (Fischer-Tropsch) for the production of the hydrocarbon blendstocks. The processing steps of the four emerging pathways include: biomass to syngas via indirect gasification, gas cleanup, conversion of syngas to alcohols/oxygenates followed by conversion of alcohols/oxygenates to hydrocarbon blendstocks via dehydration, oligomerization, and hydrogenation. Conversion of biomass-derived syngas to oxygenated intermediates occurs via three different pathways, producing: 1) mixed alcohols over a MoS2 catalyst, 2) mixed oxygenates (a mixture of C2+ oxygenated compounds, predominantly ethanol, acetic acid, acetaldehyde, ethyl acetate) using an Rh-based catalyst, and 3) ethanol from syngas fermentation. This is followed by the conversion of oxygenates/alcohols to fuel-range olefins in two approaches: 1) mixed alcohols/ethanol to 1-butanol rich mixture via Guerbet reaction, followed by alcohol dehydration, oligomerization, and hydrogenation, and 2) mixed oxygenates/ethanol to isobutene rich mixture and followed by oligomerization and hydrogenation. The design features a processing capacity of 2,000 tonnes/day (2,205 short tons) of dry biomass. The minimum fuel selling prices (MFSPs) for the four developing pathways range from $3.40 to $5.04 per gasoline-gallon equivalent (GGE), in 2011 US dollars. Sensitivity studies show that MFSPs can be improved with co-product credits and are comparable to the commercial Fischer-Tropsch benchmark ($3.58/GGE). Overall, this comparative TEA study documents potential economics for the developmental biofuel pathways via mixed oxygenates.

INTERMEDIATE STAGES OF REACTIONS FORMING CARBIDES OF TITANIUM, ZIRCONIUM, VANADIUM, NIOBIUM, AND TANTALIUM

Science.gov (United States)

intermediate and final products, and also during the calculation of approximate heat values of their formation, the passage of the reaction is confirmed...for obtaining TiC, and ZrC through the stage of intermediate oxides Ti2O3, Ti3O5, TiO and Zr2O3, ZrO, respectively and also for the reaction of...forming carbides of V (from V2O3 + 5C), of Nb and Ta (from Nb2O5 + 7C and Ta205 + 7C) through the stage of intermediate oxides VO, V4O and TaO2, Ta4O. The

Quantum Chemical Investigation of the Transition States and Intermediates for the Reaction of the Nitrosonium Ion with the Pentaammineazidocobalt(III) Ion.

Science.gov (United States)

Rotzinger, François P

2016-12-19

The water exchange reaction on Co(NH 3 ) 5 OH 2 3+ was investigated with various density functionals and basis sets. A Gibbs activation energy (ΔG ⧧ ) agreeing with experiment was obtained with the long-range-corrected functionals ωB97X-D3 and LC-BOP-LRD, SMD hydration, and modified Karlsruhe def2-TZVP basis sets. This computational technique was then applied to the reaction of NO + with Co(NH 3 ) 5 N 3 2+ . All of the possible pathways were investigated, NO + attack at the terminal N of Co(NH 3 ) 5 N 3 2+ via the E and the Z isomers of the transition states, and NO + attack at the bound N of azide, also via both isomers. The most favorable pathway proceeds via the attack at the bound N via the Z isomer. This leads to the intermediate with an oxatetrazole ligand bound to Co(III) at the N in the 3-position, Co(NH 3 ) 5 (cycl-N 4 O) 3+ , which undergoes N 2 elimination to yield the Co(NH 3 ) 5 N 2 O 3+ intermediate. The subsequent substitution of N 2 O by water follows the I d mechanism with retention of the configuration. No evidence for the existence of the square-pyramidal pentacoordinated intermediate Co(NH 3 ) 5 3+ was found. All of the investigated intermediates, Co(NH 3 ) 5 N 2 3+ , Co(NH 3 ) 5 [E-N(N 2 )(NO)] 3+ , Co(NH 3 ) 5 (E-ON 4 ) 3+ , Co(NH 3 ) 5 ON 2 3+ , Co(NH 3 ) 5 (cycl-N 4 O) 3+ , and Co(NH 3 ) 5 N 2 O 3+ , exhibit short lifetimes of less than ∼60 μs and react via the I d mechanism.

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

International Nuclear Information System (INIS)

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

1988-05-01

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

Reaction pathway and oxidation mechanisms of dibutyl phthalate by persulfate activated with zero-valent iron

Energy Technology Data Exchange (ETDEWEB)

Li, Huanxuan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); Wan, Jinquan, E-mail: ppjqwan@scut.edu.cn [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Ma, Yongwen [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Wang, Yan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China)

2016-08-15

This study investigated reaction pathway and oxidation mechanisms of dibutyl phthalate (DBP) by persulfate (PS) activated with zero-valent iron (ZVI). The DBP degradation was studied at three pH values (acidic, neutral and basic) in the presence of different organic scavengers. Using a chemical probe method, both sulfate radical (SO{sub 4}·{sup −}) and hydroxyl radical (·OH) were found to be primary oxidants at pH 3.0 and pH 7.0, respectively while ·OH was the major specie to oxidize DBP at pH 11.0. A similar result was found in an experiment of Electron Spin Resonance spin-trapping where in addition to ·OH, superoxide radical (O{sub 2}·{sup −}) was detected at pH 11.0. The transformation of degradation products including dimethyl phthalate (DMP), diethyl phthalate (DEP), phthalic anhydride, and acetophenone exhibited diverse variation during the reaction processes. The phthalic anhydride concentration appeared to be maximum at all pHs. Another eleven intermediate products were also found at pH 3.0 by GC–MS and HPLC analysis, and their degradation mechanisms and pathways were proposed. It was suggested that dealkylation, hydroxylation, decarboxylation and hydrogen extraction were the dominant degradation mechanisms of DBP at pH 3.0. - Highlights: • Both SO{sub 4}{sup −}· and ·OH were found to be the major active species at pH 3.0 and pH 7.0. • ·OH and ·O2– were the primary oxidants pH 11.0. • The intermediate products were investigated as well as the degradation pathway. • Dealkylation, hydroxylation, decarboxylation, H-extraction were the major mechanisms.

27Al MAS NMR spectroscopic identification of reaction intermediates in the carbothermal reduction and nitridation of alumina

International Nuclear Information System (INIS)

Jung, Woo-Sik; Chae, Seen-Ae

2010-01-01

The reaction intermediates in the carbothermal reduction and nitridation (CRN) reaction of γ-Al 2 O 3 were identified by 27 Al magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. This identification ruled out the possibility of a reaction mechanism involving the gaseous reaction intermediates. In the CRN reaction of γ-Al 2 O 3 , AlO 4 units were converted to AlN stepwise via AlN x O 4-x (x = 1, 2, 3) intermediates, while AlO 6 units were more slowly converted to AlN than AlO 4 units and the NMR peaks of partially nitridated AlO 6 units were not detected. The NMR peak intensities of partially nitridated AlO 4 units became weaker with increasing reaction temperature.

Manganese-Oxygen Intermediates in O-O Bond Activation and Hydrogen-Atom Transfer Reactions.

Science.gov (United States)

Rice, Derek B; Massie, Allyssa A; Jackson, Timothy A

2017-11-21

Biological systems capitalize on the redox versatility of manganese to perform reactions involving dioxygen and its derivatives superoxide, hydrogen peroxide, and water. The reactions of manganese enzymes influence both human health and the global energy cycle. Important examples include the detoxification of reactive oxygen species by manganese superoxide dismutase, biosynthesis by manganese ribonucleotide reductase and manganese lipoxygenase, and water splitting by the oxygen-evolving complex of photosystem II. Although these enzymes perform very different reactions and employ structurally distinct active sites, manganese intermediates with peroxo, hydroxo, and oxo ligation are commonly proposed in catalytic mechanisms. These intermediates are also postulated in mechanisms of synthetic manganese oxidation catalysts, which are of interest due to the earth abundance of manganese. In this Account, we describe our recent efforts toward understanding O-O bond activation pathways of Mn III -peroxo adducts and hydrogen-atom transfer reactivity of Mn IV -oxo and Mn III -hydroxo complexes. In biological and synthetic catalysts, peroxomanganese intermediates are commonly proposed to decay by either Mn-O or O-O cleavage pathways, although it is often unclear how the local coordination environment influences the decay mechanism. To address this matter, we generated a variety of Mn III -peroxo adducts with varied ligand environments. Using parallel-mode EPR and Mn K-edge X-ray absorption techniques, the decay pathway of one Mn III -peroxo complex bearing a bulky macrocylic ligand was investigated. Unlike many Mn III -peroxo model complexes that decay to oxo-bridged-Mn III Mn IV dimers, decay of this Mn III -peroxo adduct yielded mononuclear Mn III -hydroxo and Mn IV -oxo products, potentially resulting from O-O bond activation of the Mn III -peroxo unit. These results highlight the role of ligand sterics in promoting the formation of mononuclear products and mark an important

Synthetic routes to some isotopically labelled intermediates for diterpenoid biosynthesis

International Nuclear Information System (INIS)

Dawson, R.M.; Godfrey, I.M.; Hogg, R.W.; Knox, J.R.

1989-01-01

The exo-15-hydrogen of ent-kaurene can be exchanged through a reversible ene reaction in a convenient and efficient procedure which has the potential for giving high specific activity 3 H-labelling. Copalol, the (Z)-double bond stereoisomer, and the allylic alcohol isomers ent-manool and ent-epimanool have been obtained through divergent synthetic pathways involving a 15,16-bisnor ketone intermediate. These pathways have also allowed the four compounds to be obtained with 14 C-labelling. A method, involving a Wittig reaction to form a vinyl bromide intermediate, has been developed for obtaining copalol, as the trityl ether derivative, with stereospecific isotopic labelling of one or the other of the hydrogens of the exocyclic methylene group. 27 refs., figs

On light cluster production in nucleon induced reactions at intermediate energy

Energy Technology Data Exchange (ETDEWEB)

Lacroix, D.; Blideanu, V.; Durand, D

2004-09-01

A dynamical model dedicated to nucleon induced reaction between 30-150 MeV is presented. It considers different stages of the reaction: the approaching phase, the in-medium nucleon-nucleon collisions, the cluster formation and the secondary de-excitation process. The notions of influence area and phase-space exploration during the reaction are introduced. The importance of the geometry of the reaction and of the conservation laws are underlined. The model is able to globally reproduce the absolute cross sections for the emission of neutron and light charged particles for proton and neutron induced reactions on heavy and intermediate mass targets ({sup 56}Fe and {sup 208}Pb). (authors)

On light cluster production in nucleon induced reactions at intermediate energy

International Nuclear Information System (INIS)

Lacroix, D.; Blideanu, V.; Durand, D.

2004-09-01

A dynamical model dedicated to nucleon induced reaction between 30-150 MeV is presented. It considers different stages of the reaction: the approaching phase, the in-medium nucleon-nucleon collisions, the cluster formation and the secondary de-excitation process. The notions of influence area and phase-space exploration during the reaction are introduced. The importance of the geometry of the reaction and of the conservation laws are underlined. The model is able to globally reproduce the absolute cross sections for the emission of neutron and light charged particles for proton and neutron induced reactions on heavy and intermediate mass targets ( 56 Fe and 208 Pb). (authors)

Laccase-catalyzed removal of the antimicrobials chlorophene and dichlorophen from water: Reaction kinetics, pathway and toxicity evaluation.

Science.gov (United States)

Shi, Huanhuan; Peng, Jianbiao; Li, Jianhua; Mao, Liang; Wang, Zunyao; Gao, Shixiang

2016-11-05

As active agents in cleaning and disinfecting products, antimicrobials have been widely spread in the environment and have drawn extensive attention as potential threats to the ecological system and human health. In this study, the laccase-catalyzed removal of two emerging antimicrobials, chlorophene (CP) and dichlorophen (DCP), was investigated under simulated environmental conditions. Intrinsic reaction kinetics showed that the removal of CP and DCP followed second-order reaction kinetics, first-order with respect to both the enzyme and the substrate concentration. It was also found that fulvic acid could suppress the transformation of CP and DCP by reversing the oxidation reactions through its action as a scavenger of the free radical intermediates produced from reactions between laccase and the substrates. Several reaction products were identified by a quadrupole time-of-flight mass spectrometer, and detailed reaction pathways were proposed. For both CP and DCP, direct polymerization was the principal pathway, and the coupling patterns were further corroborated based on molecular modeling. The nucleophilic substitution of chlorine by the hydroxyl group was observed, and further oxidation products capable of coupling with each other were also found. Additionally, toxicity evaluation tests using Scenedesmus obliquus confirmed that the toxicity of CP and DCP was effectively eliminated during the reaction processes. Copyright © 2016 Elsevier B.V. All rights reserved.

The concern of emergence of multi-station reaction pathways that might make stepwise the mechanism of the 1,3-dipolar cycloadditions of azides and alkynes

Science.gov (United States)

Mohtat, Bita; Siadati, Seyyed Amir; Khalilzadeh, Mohammad Ali; Zareyee, Daryoush

2018-03-01

After hot debates on the concerted or stepwise nature of the mechanism of the catalyst-free 1,3-dipolar cycloadditions (DC)s, nowadays, it is being believed that for the reaction of each dipole and dipolarophile, there is a possibility that the reaction mechanism becomes stepwise, intermediates emerge, and the reaction becomes non-stereospecific. Yield of even minimal amounts of unwanted side products or stereoisomers as impurities could bring many troubles like difficult purification steps. In this project, we have made attempts to study all probable reaction channels of the azide cycloadditions with two functionalized alkynes, in order to answer this question: "is there any possibility that intermediates evolve in the catalyst-free click 1,3-DC reaction of azide-alkynes?". During the calculations, several multi-station reaction pathways supporting the stepwise and concerted mechanisms were detected. Also, the born-oppenheimer molecular dynamic (BOMD) simulation was used to find trustable geometries which could be emerged during the reaction coordinate.

Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid.

Science.gov (United States)

Medrano, María; Fuertes, Miguel Ángel; Valbuena, Alejandro; Carrillo, Pablo J P; Rodríguez-Huete, Alicia; Mateu, Mauricio G

2016-11-30

Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.

A Networks Approach to Modeling Enzymatic Reactions.

Science.gov (United States)

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

Macroscopic/microscopic simulation of nuclear reactions at intermediate energies

International Nuclear Information System (INIS)

Lacroix, D.; Van Lauwe, A.; Durand, D.

2003-01-01

An event generator, HIPSE (Heavy-Ion Phase-Space Exploration), dedicated to the description of nuclear collisions in the intermediate energy range is presented. The model simulates events for reactions close to the fusion barrier (5-10 MeV/A) up to higher energy (100 MeV/A) and it gives access to the phase-space explored during the collision. The development of HIPSE has been largely influenced by experimental observations. We have separated the reaction into 4 steps: contact, fragment formation, chemical freeze-out, and in-flight deexcitation. HIPSE will be useful for a study of various mechanisms such as neck fragmentation or multi-fragmentation

Reaction Intermediate Analogues as Bisubstrate Inhibitors of Pantothenate Synthetase

OpenAIRE

Xu, Zhixiang; Yin, Wei; Martinelli, Leonardo K.; Evans, Joanna; Chen, Jinglei; Yu, Yang; Wilson, Daniel J.; Mizrahi, Valerie; Qiao, Chunhua; Aldrich, Courtney C.

2014-01-01

The biosynthesis of pantothenate, the core of coenzyme A (CoA), has been considered an attractive target for the development of antimicrobial agents since this pathway is essential in prokaryotes, but absent in mammals. Pantothenate synthetase, encoded by the gene panC, catalyzes the final condensation of pantoic acid with β–alanine to afford pantothenate via an intermediate pantoyl adenylate. We describe the synthesis and biochemical characterization of five PanC inhibitors that mimic the in...

Reaction Pathways in Catechol/Primary Amine Mixtures: A Window on Crosslinking Chemistry.

Directory of Open Access Journals (Sweden)

Juan Yang

Full Text Available Catechol chemistry is used as a crosslinking tool abundantly in both natural organisms (e.g. mussels, sandcastle worms and synthetic systems to achieve the desired mechanical properties. Despite this abundance and success, the crosslinking chemistry is still poorly understood. In this study, to simplify the system, yet to capture the essential chemistry, model compounds 4-methyl catechol and propylamine are used. The reaction of 4-methyl catechol (2 mM with propylamine (6 mM is carried out in the presence of NaIO4 (2 mM in 10 mM Na2CO3 aqueous solution. A variety of spectroscopic/spectrometric and chromatographic methods such as 1H NMR, LC-MS, and UV-VIS are used to track the reaction and identify the products/intermediates. It is found that the crosslinking chemistry of a catechol and an amine is both fast and complicated. Within five minutes, more than 60 products are formed. These products encompass 19 different masses ranging from molecular weight of 179 to 704. By combining time-dependent data, it is inferred that the dominant reaction pathways: the majority is formed via aryloxyl-phenol coupling and Michael-type addition, whereas a small fraction of products is formed via Schiff base reactions.

Photocatalytic mineralization of codeine by UV-A/TiO{sub 2}—Kinetics, intermediates, and pathways

Energy Technology Data Exchange (ETDEWEB)

Kuo, Chin-Sheng [Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan, ROC (China); Lin, Cheng-Fang, E-mail: cflin@ntu.edu.tw [Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan, ROC (China); Hong, Pui-Kwan Andy [Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT 84112 (United States)

2016-01-15

Highlights: • Codeine was completely removed in 30 min under irradiated UV-A/TiO{sub 2}. • Codeine was mineralized in 90 min with near complete N conversion to NH{sub 4}{sup +} and NO{sub 3}{sup −}. • Morphine was authenticated and four others were identified as intermediates. • Degradation proceeded via ipso-substitution and hydroxylation of the aromatic ring. - Abstract: This study investigated the photocatalytic degradation of codeine by UV-irradiated TiO{sub 2}. The degradation kinetics was determined under varied conditions including the TiO{sub 2} loading, codeine concentration, and pH. Codeine and several reaction intermediates including morphine were identified and tracked during degradation using HPLC/MS–MS technique, along with TOC and IC measurements. Specifically, removal of 100 μg/L of spike codeine was complete in 3 min by contact with a 0.1 g/L suspension of TiO{sub 2} under UV irradiation at pH 7. The degradation kinetics of codeine was first-order with respect to both the catalyst TiO{sub 2} and the reactant codeine, with enhanced reaction rates with increasing pH up to pH 9. Mineralization of codeine was possible upon prolonged contact; near complete mineralization of 10 mg/L of codeine was achieved in 90 min with 0.1 g/L TiO{sub 2} under irradiation at pH 5, during which the organic nitrogen was converted to NH{sub 3}-N (74%) and NO{sub 3}-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.

Organotrichlorogermane synthesis by the reaction of elemental germanium, tetrachlorogermane and organic chloride via dichlorogermylene intermediate.

Science.gov (United States)

Okamoto, Masaki; Asano, Takuya; Suzuki, Eiichi

2004-08-07

Organotrichlorogermanes were synthesized by the reaction of elemental germanium, tetrachlorogermane and organic chlorides, methyl, propyl, isopropyl and allyl chlorides. Dichlorogermylene formed by the reaction of elemental germanium with tetrachlorogermane was the reaction intermediate, which was inserted into the carbon-chlorine bond of the organic chloride to give organotrichlorogermane. When isopropyl or allyl chloride was used as an organic chloride, organotrichlorogermane was formed also in the absence of tetrachlorogermane. These chlorides were converted to hydrogen chloride, which subsequently reacted with elemental germanium to give the dichlorogermylene intermediate. The reaction of elemental germanium, tetrachlorogermane and organic chlorides provides a simple and easy method for synthesizing organotrichlorogermanes, and all the raw materials are easily available.

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

Science.gov (United States)

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

2015-02-25

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

Formation of Reactive Intermediates, Color, and Antioxidant Activity in the Maillard Reaction of Maltose in Comparison to d-Glucose.

Science.gov (United States)

Kanzler, Clemens; Schestkowa, Helena; Haase, Paul T; Kroh, Lothar W

2017-10-11

In this study, the Maillard reaction of maltose and d-glucose in the presence of l-alanine was investigated in aqueous solution at 130 °C and pH 5. The reactivity of both carbohydrates was compared in regards of their degradation, browning, and antioxidant activity. In order to identify relevant differences in the reaction pathways, the concentrations of selected intermediates such as 1,2-dicarbonyl compounds, furans, furanones, and pyranones were determined. It was found, that the degradation of maltose predominantly yields 1,2-dicarbonyls that still carry a glucosyl moiety and thus subsequent reactions to HMF, furfural, and 2-acetylfuran are favored due to the elimination of d-glucose, which is an excellent leaving group in aqueous solution. Consequently, higher amounts of these heterocycles are formed from maltose. 3-deoxyglucosone and 3-deoxygalactosone represent the only relevant C 6 -1,2-dicarbonyls in maltose incubations and are produced in nearly equimolar amounts during the first 60 min of heating as byproducts of the HMF formation.

Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

Science.gov (United States)

Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2016-02-01

Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.

Compound nuclei, binary decay, and multifragmentation in intermediate-energy heavy-ion reactions

International Nuclear Information System (INIS)

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

1988-07-01

Hot compound nuclei, frequently produced in intermediate-energy reactions through a variety of processes, are shown to be an important and at times dominant source of complex fragments. 13 refs., 12 figs

Intermediate energy heavy ion reactions. A program for CELSIUS

International Nuclear Information System (INIS)

Jakobsson, B.

1986-02-01

The accelerator system under construction in Uppsala with the ECR-source + the K equals 200 synchrocyclotron + the CELSIUS synchrotron ring for storage, cooling and acceleration opens up possibilities for a very fruitful heavy ion physics program. Some recently obtained results and some recent ideas on intermediate energy reactions are discussed and speculations are made about some experiments where the unconventional qualities of CELSIUS beams could be utilized. (author)

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

International Nuclear Information System (INIS)

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

2014-01-01

This study deals with the parahydrogenation of the symmetric substrate acetylene dicarboxylic acid catalyzed by a Rh(I) complex bearing the chelating diphosphine dppb (1,4-bis(diphenylphosphino)butane). The two magnetically equivalent protons of the product yield a hyperpolarized emission signal in the 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

Fragment mass distribution of proton-induced spallation reaction with intermediate energy

International Nuclear Information System (INIS)

Fan Sheng; Ye Yanlin; Xu Chuncheng; Chen Tao; Sobolevsky, N.M.

2000-01-01

The test of part benchmark of SHIELD code is finished. The fragment cross section and mass distribution and excitation function of the residual nuclei from proton-induced spallation reaction on thin Pb target with intermediate energy have been calculated by SHIELD code. And the results are in good agreement with measured data. The fragment mass distribution of the residual nuclei from proton-induced spallation reaction on thick Pb target with incident energy 1.6 GeV have been simulated

A few aspects of intermediate energy heavy ion reactions

International Nuclear Information System (INIS)

Guet, C.

1982-10-01

Some aspects of reactions induced by intermediate energy heavy ions, with a special emphasis of 85 MeV/nucleon 12 C data, are discussed and compared to low energy and relativistic energy features. Transition from mean field to independant nucleon picture is advocated by an increase of nuclear transparency illuminated by reaction cross section estimations. Projectile-like fragment distributions, while demonstrating a typical high energy fragmentation behaviour, exhibit low energy regime distortions. Light fragments, associated to large parallel momentum transfer may result from total explosion. Proton emission is investigated and discussed in terms of opposite models such as thermal equilibrium and nucleon-nucleon scattering. First pion production data are well explained by single nucleon-nucleon inelastic scattering

One-step simultaneous differential scanning calorimetry-FTIR microspectroscopy to quickly detect continuous pathways in the solid-state glucose/asparagine Maillard reaction.

Science.gov (United States)

Hwang, Deng-Fwu; Hsieh, Tzu-Feng; Lin, Shan-Yang

2013-01-01

The stepwise reaction pathway of the solid-state Maillard reaction between glucose (Glc) and asparagine (Asn) was investigated using simultaneous differential scanning calorimetry (DSC)-FTIR microspectroscopy. The color change and FTIR spectra of Glc-Asn physical mixtures (molar ratio = 1:1) preheated to different temperatures followed by cooling were also examined. The successive reaction products such as Schiff base intermediate, Amadori product, and decarboxylated Amadori product in the solid-state Glc-Asn Maillard reaction were first simultaneously evidenced by this unique DSC-FTIR microspectroscopy. The color changed from white to yellow-brown to dark brown, and appearance of new IR peaks confirmed the formation of Maillard reaction products. The present study clearly indicates that this unique DSC-FTIR technique not only accelerates but also detects precursors and products of the Maillard reaction in real time.

Oxidative degradation of atenolol by heat-activated persulfate: Kinetics, degradation pathways and distribution of transformation intermediates.

Science.gov (United States)

Miao, Dong; Peng, Jianbiao; Zhou, Xiaohuan; Qian, Li; Wang, Mengjie; Zhai, Li; Gao, Shixiang

2018-05-17

Atenolol (ATL) has been widely detected in wastewater and aquatic environment. Although satisfactory removal of ATL from wastewater could be achieved, the mineralization ratio is usually low, which may result in the accumulation of its transformation products in the effluent and cause additional ecological risk to the environment. The aim of this study is to explore the effectiveness of heat activated persulfate (PS) in the removal of ATL from wastewater. Influencing factors including temperature, PS dosage, solution pH, existence of NO 3 - , Cl - , HCO 3 - and Suwannee river fulvic acid (SRFA) were examined. Complete removal of ATL was achieved within 40 min at pH 7.0 and 70 °C by using 0.5 mM PS. Inhibitive effects of HCO 3 - and FA had been observed on ATL oxidation, which was increased with the increase of their concentration. Sulfate radical (SO 4 - ) was determined as the main reactive species by quenching experiment. Eight intermediates produced in ATL degradation were identified, and four degradation pathways were proposed based on the analysis of mass spectrum and frontier electron densities. The distribution of major intermediates was influenced by reaction temperature. Hydroxylation intermediates and deamidation intermediate were the most prominent at 50 °C and 60 °C, respectively. All intermediates were completely degraded in 40 min except P134 at 70 °C. Effective removal of TOC (74.12%) was achieved with 0.5 mM PS, pH 7.0 and 70 °C after 240 min. The results proved that heat activation of PS is a promising method to remove organic pollutants in wastewater. Copyright © 2018 Elsevier Ltd. All rights reserved.

Isovector couplings for nucleon charge-exchange reactions at intermediate energies

International Nuclear Information System (INIS)

Love, W.G.; Nakayama, K.; Franey, M.A.

1987-01-01

The isovector parts of the effective nucleon-nucleon interaction are studied by examination of the reaction /sup 14/C(p,n) at intermediate energies near zero momentum transfer with use of recently developed G-matrix and free--t-matrix interactions. The spin-independent coupling (V/sub tau/) exhibits a strong energy and density dependence which, in the case of the G matrix based on the Bonn potential, significantly improves the agreement between calculated values of chemical bondV/sub σ//sub tau//V/sub tau/chemical bond 2 at q = 0 and those recently extracted from the reaction /sup 14/C

A mechanistic study on the reaction pathways leading to benzene and naphthalene in cellulose vapor phase cracking

International Nuclear Information System (INIS)

Norinaga, Koyo; Yang, Huamei; Tanaka, Ryota; Appari, Srinivas; Iwanaga, Keita; Takashima, Yuka; Kudo, Shinji; Shoji, Tetsuya; Hayashi, Jun-ichiro

2014-01-01

The reaction pathways leading to aromatic hydrocarbons such as benzene and naphthalene in gas-phase reactions of multi-component mixtures derived from cellulose fast pyrolysis were studied both experimentally and numerically. A two-stage tubular reactor was used for evaluating the reaction kinetics of secondary vapor phase cracking of the nascent pyrolysates at temperature ranging from 400 to 900 °C, residence time from 0.2 to 4.3 s, and at 241 kPa. The products of alkyne and diene were identified from the primary pyrolysis of cellulose even at low temperature range 500–600 °C. These products include acetylene, propyne, propadiene, vinylacetylene, and cyclopentadiene. Experiments were also numerically validated by a detailed chemical kinetic model consisting of more than 8000 elementary step-like reactions with over 500 chemical species. Acceptable capabilities of the kinetic model in predicting concentration profiles of the products enabled us to assess reaction pathways leading to benzene and naphthalene via the alkyne and diene from primary pyrolysates of cellulose. C 3 alkyne and diene are primary precursors of benzene at 650 °C, while combination of ethylene and vinylacetylene produces benzene dominantly at 850 °C. Cyclopentadiene is a prominent precursor of naphthalene. Combination of acetylene with propyne or allyl radical leads to the formation of cyclopentadiene. Furan and acrolein are likely important alkyne precursors in cellulose pyrolysis at low temperature, whereas dehydrogenations of olefins are major route to alkyne at high temperatures. - Highlights: • Analytical pyrolysis experiments provided data for kinetic modeling. • Detailed chemical kinetic model was used and evaluated. • Alkyne and diene were important intermediates for aromatic hydrocarbon formation. • Reaction pathways leading to aromatic hydrocarbons were proposed

Hydrozirconation of lithium alkynylselenolate anions. Generation and reactions of alpha-zirconated vinyl selenide intermediates

Science.gov (United States)

Dabdoub; Begnini; Guerrero; Baroni

2000-01-14

Lithium alkynylselenolate anions react completely with 1.0 equiv of Cp(2)Zr(H)Cl in THF at room temperature to give exclusively the alpha-zirconated vinylselenolate intermediates 23-27, which by treatment with an alkyl halide afforded the alpha-zirconated vinyl alkylselenide intermediates 29-33. Reaction of 29-33 with butyltellurenyl bromide results in the formation of ketene telluro(seleno) acetals 35-39 with total control of the regio- and stereochemistry. The synthetic utility of the ketene telluro(seleno) acetals obtained here was demonstrated by reaction of 36 with butyllithium. This promotes the exclusive and stereospecific removal of the tellurium moiety and enables formation of the corresponding selenium-containing allylic alcohol of type 44, alpha-(alkylseleno)-alpha,beta-unsaturated aldehyde 45, ester 46, or carboxylic acid 47, after reaction with different types of electrophiles.

A paradigm shift for radical SAM reactions: The organometallic intermediate Ω is central to catalysis.

Science.gov (United States)

Byer, Amanda S; Yang, Hao; McDaniel, Elizabeth C; Kathiresan, Venkatesan; Impano, Stella; Pagnier, Adrien; Watts, Hope; Denler, Carly; Vagstad, Anna; Piel, Jörn; Duschene, Kaitlin S; Shepard, Eric M; Shields, Thomas P; Scott, Lincoln G; Lilla, Edward A; Yokoyama, Kenichi; Broderick, William E; Hoffman, Brian M; Broderick, Joan B

2018-06-28

Radical S-adenosyl-L-methionine (SAM) en-zymes comprise a vast superfamily catalyzing diverse reactions essential to all life through ho-molytic SAM cleavage to liberate the highly-reactive 5-deoxyadenosyl radical (5-dAdo•). Our recent observation of a catalytically compe-tent organometallic intermediate Ω that forms dur-ing reaction of the radical SAM (RS) enzyme py-ruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an in-termediate under a variety of mixing order condi-tions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double reso-nance spectroscopy establish that Ω involves an Fe-C5 bond between 5-dAdo• and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (co-enzyme B12) cofactor used to initiate radical reac-tions via a 5'-dAdo• intermediate. Generation of a 5'-dAdo• intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However coenzyme B12 is involved in enzymes catalyzing of only a small number (~12) of distinct reactions, while the RS superfamily has more than 100,000 distinct se-quences and over 80 reaction types character-ized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

International Nuclear Information System (INIS)

Wang Zhan-Feng; Liu Yu-Ru; Wang Peng-Ye; Xie Ping

2017-01-01

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson–Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA–RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP. (paper)

Photocatalytic degradation of paracetamol: intermediates and total reaction mechanism.

Science.gov (United States)

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

2012-12-01

The advanced oxidation of paracetamol (PAM) promoted by TiO(2)/UV system in aqueous medium was investigated. Monitoring this reaction by HPLC and TOC, it was demonstrated that while oxidation of paracetamol is quite efficient under these conditions, its mineralization is not complete. HPLC indicated the formation of hydroquinone, benzoquinone, p-aminophenol and p-nitrophenol in the reaction mixtures. Further evidence of p-nitrophenol formation was obtained following the reaction by UV-vis spectroscopy. Continuous monitoring by IR spectroscopy demonstrated the breaking of the aromatic amide present in PAM and subsequent formation of several aromatic intermediate compounds such as p-aminophenol and p-nitrophenol. These aromatic compounds were eventually converted into trans-unsaturated carboxylic acids. Based on these experimental results, an alternative deacylation mechanism for the photocatalytic oxidation of paracetamol is proposed. Our studies also demonstrated IR spectroscopy to be a useful technique to investigate oxidative mechanisms of pharmaceutical compounds. Copyright © 2012 Elsevier B.V. All rights reserved.

Confirmation of the reaction pathway for obtaining 1-(stearamidoethyl-2-hepta-decyl-2-i midazoline

Directory of Open Access Journals (Sweden)

Ružić Nenad Lj.

2002-01-01

Full Text Available 2-lmidazolines are components of many products, used in industry and households. 1-(Stearamidoethyl-2-heptadecyl-2-imidazoline is a surface active compound, which after quaternization with dimethyl sulfate, is used in lubricants, detergents, shampoos, softeners and cosmetics products. Due to its importance, it was essential to establish the exact reaction pathway for obtaining this compound. Diethylene triamine and stearic acid were used as the starting components. Using titrimetric analysis, and IR and 1H NMR spectros-copic analysis, as well as UV-Vis spectrophotometry it was established that the main intermediate was the 1,3-diamide bis(stearamidoethylamine. Earlier investigations conducted by some authors, using exclusively titrimetric analysis, showed that the main intermediate was the 1,2-diamide. In this paper it was proved that the assumption of these authors that salicylaldehiyde would react only with the primary and not the secondary amine groups was wrong. 1,2-Diamide is the main product of the hydrolysis of 1-(stearamido-ethyl-2-heptadecyl-2-imidazoline. It was shown, in this paper that the reaction of diethylene triamine with stearic acid in xylene at the reflux temperature, yields the salt of 1-(stearamidoethyl-2-heptadecyl-2-imidazoline and stearic acid.

Novel pathway of SO2 oxidation in the atmosphere: reactions with monoterpene ozonolysis intermediates and secondary organic aerosol

Science.gov (United States)

Ye, Jianhuai; Abbatt, Jonathan P. D.; Chan, Arthur W. H.

2018-04-01

Ozonolysis of monoterpenes is an important source of atmospheric biogenic secondary organic aerosol (BSOA). While enhanced BSOA formation has been associated with sulfate-rich conditions, the underlying mechanisms remain poorly understood. In this work, the interactions between SO2 and reactive intermediates from monoterpene ozonolysis were investigated under different humidity conditions (10 % vs. 50 %). Chamber experiments were conducted with ozonolysis of α-pinene or limonene in the presence of SO2. Limonene SOA formation was enhanced in the presence of SO2, while no significant changes in SOA yields were observed during α-pinene ozonolysis. Under dry conditions, SO2 primarily reacted with stabilized Criegee intermediates (sCIs) produced from ozonolysis, but at 50 % RH heterogeneous uptake of SO2 onto organic aerosol was found to be the dominant sink of SO2, likely owing to reactions between SO2 and organic peroxides. This SO2 loss mechanism to organic peroxides in SOA has not previously been identified in experimental chamber studies. Organosulfates were detected and identified using an electrospray ionization-ion mobility spectrometry-high-resolution time-of-flight mass spectrometer (ESI-IMS-TOF) when SO2 was present in the experiments. Our results demonstrate the synergistic effects between BSOA formation and SO2 oxidation through sCI chemistry and SO2 uptake onto organic aerosol and illustrate the importance of considering the chemistry of organic and sulfur-containing compounds holistically to properly account for their reactive sinks.

Degradation of γ-HCH spiked soil using stabilized Pd/Fe0 bimetallic nanoparticles: Pathways, kinetics and effect of reaction conditions

International Nuclear Information System (INIS)

Singh, Ritu; Misra, Virendra; Mudiam, Mohana Krishna Reddy; Chauhan, Lalit Kumar Singh; Singh, Rana Pratap

2012-01-01

Highlights: ► This study explores the potential of CMC-Pd/nFe 0 to degrade γ-HCH in spiked soil. ► Sorption–desorption characteristics and partitioning of γ-HCH is investigated. ► Three degradation pathways has been proposed and discussed. ► γ-HCH degradation mechanism and kinetics is elucidated. ► Activation energy reveals that γ-HCH degradation is a surface mediated reaction. - Abstract: This study investigates the degradation pathway of gamma-hexachlorocyclohexane (γ-HCH) in spiked soil using carboxymethyl cellulose stabilized Pd/Fe 0 bimetallic nanoparticles (CMC-Pd/nFe 0 ). GC–MS analysis of γ-HCH degradation products showed the formation of pentachlorocyclohexene, tri- and di-chlorobenzene as intermediate products while benzene was formed as the most stable end product. On the basis of identified intermediates and final products, degradation pathway of γ-HCH has been proposed. Batch studies showed complete γ-HCH degradation at a loading of 0.20 g/L CMC-Pd/nFe 0 within 6 h of incubation. The surface area normalized rate constant (k SA ) was found to be 7.6 × 10 −2 L min −1 m −2 . CMC-Pd/nFe 0 displayed ∼7-fold greater efficiency for γ-HCH degradation in comparison to Fe 0 nanoparticles (nFe 0 ), synthesized without CMC and Pd. Further studies showed that increase in CMC-Pd/nFe 0 loading and reaction temperature facilitates γ-HCH degradation, whereas a declining trend in degradation was noticed with the increase in pH, initial γ-HCH concentration and in the presence of cations. The data on activation energy (33.7 kJ/mol) suggests that γ-HCH degradation is a surface mediated reaction. The significance of the study with respect to remediation of γ-HCH contaminated soil using CMC-Pd/nFe 0 has been discussed.

Kynurenine pathway metabolites and enzymes involved in redox reactions.

Science.gov (United States)

González Esquivel, D; Ramírez-Ortega, D; Pineda, B; Castro, N; Ríos, C; Pérez de la Cruz, V

2017-01-01

Oxido-reduction reactions are a fundamental part of the life due to support many vital biological processes as cellular respiration and glucose oxidation. In the redox reactions, one substance transfers one or more electrons to another substance. An important electron carrier is the coenzyme NAD + , which is involved in many metabolic pathways. De novo biosynthesis of NAD + is through the kynurenine pathway, the major route of tryptophan catabolism, which is sensitive to redox environment and produces metabolites with redox capacity, able to alter biological functions that are controlled by redox-responsive signaling pathways. Kynurenine pathway metabolites have been implicated in the physiology process and in the physiopathology of many diseases; processes that also share others factors as dysregulation of calcium homeostasis, mitochondrial dysfunction, oxidative stress, inflammation and cell death, which impact the redox environment. This review examines in detail the available evidence in which kynurenine pathway metabolites participate in redox reactions and their effect on cellular redox homeostasis, since the knowledge of the main factors and mechanisms that lead to cell death in many neurodegenative disorders and other pathologies, such as mitochondrial dysfunction, oxidative stress and kynurenines imbalance, will allow to develop therapies using them as targets. This article is part of the Special Issue entitled 'The Kynurenine Pathway in Health and Disease'. Copyright © 2016 Elsevier Ltd. All rights reserved.

Adsorption and Photocatalytic Decomposition of the β-Blocker Metoprolol in Aqueous Titanium Dioxide Suspensions: Kinetics, Intermediates, and Degradation Pathways

Directory of Open Access Journals (Sweden)

Violette Romero

2013-01-01

Full Text Available This study reports the photocatalytic degradation of the β-blocker metoprolol (MET using TiO2 suspended as catalyst. A series of photoexperiments were carried out by a UV lamp, emitting in the 250–400 nm range, providing information about the absorption of radiation in the photoreactor wall. The influence of the radiation wavelength on the MET photooxidation rate was investigated using a filter cutting out wavelengths shorter than 280 nm. Effects of photolysis and adsorption at different initial pH were studied to evaluate noncatalytic degradation for this pharmaceutical. MET adsorption onto titania was fitted to two-parameter Langmuir isotherm. From adsorption results it appears that the photocatalytic degradation can occur mainly on the surface of TiO2. MET removed by photocatalysis was 100% conditions within 300 min, while only 26% was achieved by photolysis at the same time. TiO2 photocatalysis degradation of MET in the first stage of the reaction followed approximately a pseudo-first-order model. The major reaction intermediates were identified by LC/MS analysis such as 3-(propan-2-ylaminopropane-1,2-diol or 3-aminoprop-1-en-2-ol. Based on the identified intermediates, a photocatalytic degradation pathway was proposed, including the cleavage of side chain and the hydroxylation addition to the parent compounds.

Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

International Nuclear Information System (INIS)

Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas; Goulding, Celia W.

2014-01-01

The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully

Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

Energy Technology Data Exchange (ETDEWEB)

Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas [UC Irvine, 2212 Natural Sciences I, Irvine, CA 92697 (United States); Goulding, Celia W., E-mail: celia.goulding@uci.edu [UC Irvine, 2212 Natural Sciences I, Irvine, CA 92697 (United States); UC Irvine, 2302 Natural Sciences I, Irvine, CA 92697 (United States)

2014-04-01

The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully

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

Energy Technology Data Exchange (ETDEWEB)

Rajagopalan, S., E-mail: rajagopalan78@hotmail.com [Indira Gandhi Centre for Atomic Research, Materials Science Group (India); Asthalter, T., E-mail: t.asthalter@web.de [Universität Stuttgart, Institute of Physical Chemistry (Germany); Rabe, V.; Laschat, S. [Universität Stuttgart, Institute of Organic Chemistry (Germany)

2016-12-15

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

Why do alpha-beta parallel proteins, like flavodoxins, form misfolded off-pathway intermediates?

NARCIS (Netherlands)

Nabuurs, S.M.

2009-01-01

The question: “Why do α-β parallel proteins, like flavodoxins, form misfolded off-pathway
intermediates?" is the main subject of this thesis. A. vinelandii apoflavodoxin is chosen as protein
of interest as it is a representative of α-β parallel proteins, which are widely prevalent in

Minimum Energy Pathways for Chemical Reactions

Science.gov (United States)

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

1995-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.

Combustion modeling and kinetic rate calculations for a stoichiometric cyclohexane flame. 1. Major reaction pathways.

Science.gov (United States)

Zhang, Hongzhi R; Huynh, Lam K; Kungwan, Nawee; Yang, Zhiwei; Zhang, Shaowen

2007-05-17

The Utah Surrogate Mechanism was extended in order to model a stoichiometric premixed cyclohexane flame (P = 30 Torr). Generic rates were assigned to reaction classes of hydrogen abstraction, beta scission, and isomerization, and the resulting mechanism was found to be adequate in describing the combustion chemistry of cyclohexane. Satisfactory results were obtained in comparison with the experimental data of oxygen, major products and important intermediates, which include major soot precursors of C2-C5 unsaturated species. Measured concentrations of immediate products of fuel decomposition were also successfully reproduced. For example, the maximum concentrations of benzene and 1,3-butadiene, two major fuel decomposition products via competing pathways, were predicted within 10% of the measured values. Ring-opening reactions compete with those of cascading dehydrogenation for the decomposition of the conjugate cyclohexyl radical. The major ring-opening pathways produce 1-buten-4-yl radical, molecular ethylene, and 1,3-butadiene. The butadiene species is formed via beta scission after a 1-4 internal hydrogen migration of 1-hexen-6-yl radical. Cascading dehydrogenation also makes an important contribution to the fuel decomposition and provides the exclusive formation pathway of benzene. Benzene formation routes via combination of C2-C4 hydrocarbon fragments were found to be insignificant under current flame conditions, inferred by the later concentration peak of fulvene, in comparison with benzene, because the analogous species series for benzene formation via dehydrogenation was found to be precursors with regard to parent species of fulvene.

A multi-pathway model for photosynthetic reaction center

International Nuclear Information System (INIS)

Qin, M.; Shen, H. Z.; Yi, X. X.

2016-01-01

Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments.

Synthesized TiO{sub 2}/ZSM-5 composites used for the photocatalytic degradation of azo dye: Intermediates, reaction pathway, mechanism and bio-toxicity

Energy Technology Data Exchange (ETDEWEB)

Zhou, Kefu; Hu, Xin-Yan [College of the Environment and Ecology, Xiamen University, Xiamen (China); Chen, Bor-Yann; Hsueh, Chung-Chuan [Department of Chemical and Materials Engineering, National I-Lan University, I-Lan, Taiwan (China); Zhang, Qian [Department of Environmental Engineering, National Taiwan University, Taipei, Taiwan (China); Wang, Jiajie; Lin, Yu-Jung [College of the Environment and Ecology, Xiamen University, Xiamen (China); Chang, Chang-Tang, E-mail: ctchang73222@gmail.com [Department of Environmental Engineering, National I-Lan University, I-Lan, Taiwan (China)

2016-10-15

Highlights: • The major photo-catalytic degradation pathway of azo-dye was elaborated according to the identification of by-products from GC–MS and IC analysis. • Comparative assessment on characteristics of abiotic and biotic dye decolorization was analyzed. • EDTA (hole scavengers) and t-BuOH (radical scavengers) were used to determine the main active oxidative species in the system. • The toxicity effects of degradation intermediates of Reactive Black 5 (RB5) on the cellular respiratory activity were assessed. - Abstract: In this study, a one-step solid dispersion method was used to synthesize titanium dioxide (TiO{sub 2})/Zeolite Socony Mobil-5 (ZSM-5) composites with substantially reduced time and energy consumption. A degradation efficiency of more than 95% was achieved within 10 min using 50% PTZ (synthesized TiO{sub 2}/ZSM-5 composites with TiO{sub 2} contents of 50 wt% loaded on ZSM-5) at pH 7 and 25 °C. The possible degradation pathway of azo-dye Reactive Black 5 (RB5) was investigated using gas chromatography–mass spectrometry and ion chromatography (IC). The bonds between the N atoms and naphthalene groups are likely attacked first and cleaved by hydroxyl radicals, ultimately resulting in the decolorization and mineralization of the azo dye. A comparative assessment of the characteristics of abiotic and biotic dye decolorization was completed. In addition, the toxicity effects of the degradation intermediates of azo-dye RB5 on cellular respiratory activity were analyzed. The bio-toxicity results showed that the decay rate constants of CO{sub 2} production from the azo-dye RB5 samples at different degradation times increased initially and subsequently decreased, indicating that intermediates of higher toxicity could adhere to the catalyst surface and gradually destroyed by further photocatalytic oxidation. Additionally, EDTA (hole scavengers) and t-BuOH (radical scavengers) were used to detect the main active oxidative species in the system

Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

Science.gov (United States)

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-04-10

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.

Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

Directory of Open Access Journals (Sweden)

Xue Zhang

2015-04-01

Full Text Available As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs and polychlorinated biphenyls (PCBs are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD. Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

Science.gov (United States)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

Identifying Reaction Pathways and their Environments

DEFF Research Database (Denmark)

Maronsson, Jon Bergmann

Finding the mechanisms and estimating the rate of chemical reactions is an essential part of modern research of atomic scale systems. In this thesis, the application of well established methods for reaction rates and paths to important systems for hydrogen storage is considered before developing...... extensions to further identify the reaction environment for a more accurate rate. Complex borohydrides are materials of high hydrogen storage capacity and high thermodynamic stability (too high for hydrogen storage). In an effort to gain insight into the structural transitions of two such materials, Ca(BH4......-interstitial defects. In good agreement with the experiments, C3-type rotations activate at lower temperature than C2-type rotations. In order to investigate the environment of reaction pathways, a method for finding the ridge between first order saddle points on a multidimensional surface was developed...

Intermediates detected by visible spectroscopy during the reaction of nitrite with deoxyhemoglobin: the effect of nitrite concentration and diphosphoglycerate.

Science.gov (United States)

Nagababu, Enika; Ramasamy, Somasundaram; Rifkind, Joseph M

2007-10-16

The reaction of nitrite with deoxyhemoglobin (deoxyHb) results in the reduction of nitrite to NO, which binds unreacted deoxyHb forming Fe(II)-nitrosylhemoglobin (Hb(II)NO). The tight binding of NO to deoxyHb is, however, inconsistent with reports implicating this reaction with hypoxic vasodilation. This dilemma is resolved by the demonstration that metastable intermediates are formed in the course of the reaction of nitrite with deoxyHb. The level of intermediates is quantitated by the excess deoxyHb consumed over the concentrations of the final products formed. The dominant intermediate has a spectrum that does not correspond to that of Hb(III)NO formed when NO reacts with methemoglobin (MetHb), but is similar to metHb resulting in the spectroscopic determinations of elevated levels of metHb. It is a delocalized species involving the heme iron, the NO, and perhaps the beta-93 thiol. The putative role for red cell reacted nitrite on vasodilation is associated with reactions involving the intermediate. (1) The intermediate is less stable with a 10-fold excess of nitrite and is not detected with a 100-fold excess of nitrite. This observation is attributed to the reaction of nitrite with the intermediate producing N2O3. (2) The release of NO quantitated by the formation of Hb(II)NO is regulated by changes in the distal heme pocket as shown by the 4.5-fold decrease in the rate constant in the presence of 2,3-diphosphoglycerate. The regulated release of NO or N2O3 as well as the formation of the S-nitroso derivative of hemoglobin, which has also been reported to be formed from the intermediates generated during nitrite reduction, should be associated with any hypoxic vasodilation attributed to the RBC.

A board game to assist pharmacy students in learning metabolic pathways.

Science.gov (United States)

Rose, Tyler M

2011-11-10

To develop and evaluate a board game designed to increase students' enjoyment of learning metabolic pathways; their familiarity with pathway reactions, intermediates, and regulation; and, their understanding of how pathways relate to one another and to selected biological conditions. The board game, entitled Race to Glucose, was created as a team activity for first-year pharmacy students in the biochemistry curriculum. A majority of respondents agreed that the game was helpful for learning regulation, intermediates, and interpathway relationships but not for learning reactions, formation of energetic molecules, or relationships, to biological conditions. There was a significant increase in students' scores on game-related examination questions (68.8% pretest vs. 81.3% posttest), but the improvement was no greater than that for examination questions not related to the game (12.5% vs. 10.9%). First-year pharmacy students considered Race to Glucose to be an enjoyable and helpful tool for learning intermediates, regulation, and interpathway relationships.

Multifragmentation in intermediate energy 129Xe-induced heavy-ion reactions

International Nuclear Information System (INIS)

Tso, Kin.

1996-05-01

The 129 Xe-induced reactions on nat Cu, 89 Y, 165 Ho, and 197 Au at bombarding energies of E/A = 40 ampersand 60 MeV have been studied theoretically and experimentally in order to establish the underlying mechanism of multifragmentation at intermediate energy heavy-Ion collisions. Nuclear disks formed in central heavy-ion collisions, as simulated by means of Boltzmann-like kinetic equations, break up into several fragments due to a new kind of Rayleigh-like surface instability. A sheet of liquid, stable in the limit of non-interacting surfaces, is shown to become unstable due to surface-surface interactions. The onset of this instability is determined analytically. A thin bubble behaves like a sheet and is susceptible to the surface instability through the crispation mode. The Coulomb effects associated with the depletion of charges in the central cavity of nuclear bubbles are investigated. The onset of Coulomb instability is demonstrated for perturbations of the radial mode. Experimental intermediate-mass-fragment multiplicity distributions for the 129 Xe-induced reactions are shown to be binomial at each transverse energy. From these distributions, independent of the specific target, an elementary binary decay probability p can be extracted that has a thermal dependence. Thus it is inferred that multifragmentation is reducible to a combination of nearly independent emission processes. If sequential decay is assumed, the increase of p with transverse energy implies a contraction of the emission time scale. The sensitivity of p to the lower Z threshold in the definition of intermediate-mass-fragments points to a physical Poisson simulations of the particle multiplicities show that the weak auto-correlation between the fragment multiplicity and the transverse energy does not distort a Poisson distribution into a binomial distribution. The effect of device efficiency on the experimental results has also been studied

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

Science.gov (United States)

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

2008-11-25

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

Reactions and reaction intermediates on iron surfaces--1. Methanol, ethanol, and isopropanol on Fe(100). 2. Hydrocarbons and carboxylic acids

Energy Technology Data Exchange (ETDEWEB)

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

1980-09-01

Temperature-programed desorption and ESCA showed that the alcohols formed alkoxy intermediates on Fe(100) surfaces at room temperature, but that the methoxy and ethoxy species were much more stable than the isopropoxy intermediate. The alkoxy species reacted above 400/sup 0/K by decomposing into carbon monoxide and hydrogen, hydrogenation to alcohol, and scission of C-C and C-O bonds with hydrogenation of the hydrocarbon fragments. Ethylene, acetylene, and cis-2-butene formed stable, unidentified surface species. Methyl chloride formed stable surface methyl groups which decomposed into hydrogen and surface carbide at 475/sup 0/K. Formic and acetic acids yielded stable carboxylate intermediates which decomposed above 490/sup 0/K to hydrogen, carbon monoxide, and carbon dioxide. The studies suggested that the alkoxy surface species may be important intermediates in the Fischer-Tropsch reaction on iron.

Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment.

Directory of Open Access Journals (Sweden)

Ruijuan Qu

Full Text Available 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.

Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment

Science.gov (United States)

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

Serpentinization reaction pathways: implications for modeling approach

Energy Technology Data Exchange (ETDEWEB)

Janecky, D.R.

1986-01-01

Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.

Anodic Cyclization Reactions and the Mechanistic Strategies That Enable Optimization.

Science.gov (United States)

Feng, Ruozhu; Smith, Jake A; Moeller, Kevin D

2017-09-19

Oxidation reactions are powerful tools for synthesis because they allow us to reverse the polarity of electron-rich functional groups, generate highly reactive intermediates, and increase the functionality of molecules. For this reason, oxidation reactions have been and continue to be the subject of intense study. Central to these efforts is the development of mechanism-based strategies that allow us to think about the reactive intermediates that are frequently central to the success of the reactions and the mechanistic pathways that those intermediates trigger. For example, consider oxidative cyclization reactions that are triggered by the removal of an electron from an electron-rich olefin and lead to cyclic products that are functionalized for further elaboration. For these reactions to be successful, the radical cation intermediate must first be generated using conditions that limit its polymerization and then channeled down a productive desired pathway. Following the cyclization, a second oxidation step is necessary for product formation, after which the resulting cation must be quenched in a controlled fashion to avoid undesired elimination reactions. Problems can arise at any one or all of these steps, a fact that frequently complicates reaction optimization and can discourage the development of new transformations. Fortunately, anodic electrochemistry offers an outstanding opportunity to systematically probe the mechanism of oxidative cyclization reactions. The use of electrochemical methods allows for the generation of radical cations under neutral conditions in an environment that helps prevent polymerization of the intermediate. Once the intermediates have been generated, a series of "telltale indicators" can be used to diagnose which step in an oxidative cyclization is problematic for less successful transformation. A set of potential solutions to address each type of problem encountered has been developed. For example, problems with the initial

Trapping and Characterization of a Reaction Intermediate in Carbapenem Hydrolysis by B. cereus Metallo-β-lactamase

Science.gov (United States)

Tioni, Mariana F.; Llarrull, Leticia I.; Poeylaut-Palena, Andrés A.; Martí, Marcelo A.; Saggu, Miguel; Periyannan, Gopal R.; Mata, Ernesto G.; Bennett, Brian; Murgida, Daniel H.; Vila, Alejandro J.

2009-01-01

Metallo-β-lactamases hydrolyze most β-lactam antibiotics. The lack of a successful inhibitor for them is related to the previous failure to characterize a reaction intermediate with a clinically useful substrate. Stopped-flow experiments together with rapid freeze-quench EPR and Raman spectroscopies were used to characterize the reaction of Co(II)-BcII with imipenem. These studies show that Co(II)-BcII is able to hydrolyze imipenem both in the mono- and dinuclear forms. In contrast to the situation met for penicillin, the species that accumulates during turnover is an enzyme-intermediate adduct in which the β-lactam bond has already been cleaved. This intermediate is a metal-bound anionic species, with a novel resonant structure, that is stabilized by the metal ion at the DCH or Zn2 site. This species has been characterized based on its spectroscopic features. This represents a novel, previously unforeseen intermediate, that is related to the chemical nature of carbapenems, as confirmed by the finding of a similar intermediate for meropenem. Since carbapenems are the only substrates cleaved by B1, B2 and B3 lactamases, the identification of this intermediate could be exploited as a first step towards the design of transition state based inhibitors for all three classes of metallo-β-lactamases. PMID:18980308

Developmentally programmed DNA deletion in Tetrahymena thermophila by a transposition-like reaction pathway.

Science.gov (United States)

Saveliev, S V; Cox, M M

1996-01-01

We provide a molecular description of key intermediates in the deletion of two internal eliminated sequences (IES elements), the M and R regions, during macronuclear development in Tetrahymena thermophila. Using a variety of PCR-based methods in vivo, double-strand breaks are detected that are generated by hydrolytic cleavage and correspond closely to the observed chromosomal junctions left behind in the macronuclei. The breaks exhibit a temporal and structural relationship to the deletion reaction that provides strong evidence that they are intermediates in the deletion pathway. Breaks in the individual strands are staggered by 4 bp, producing a four nucleotide 5' extension. Evidence is presented that breaks do not occur simultaneously at both ends. The results are most consistent with a deletion mechanism featuring initiation by double-strand cleavage at one end of the deleted element, followed by transesterification to generate the macronuclear junction on one DNA strand. An adenosine residue is found at all the nucleophilic 3' ends used in the postulated transesterification step. Evidence for the transesterification step is provided by detection of a 3' hydroxyl that would be liberated by such a step at a deletion boundary where no other DNA strand ends are detected. Images PMID:8654384

Photodegradation of lambda-cyhalothrin and cypermethrin in aqueous solution as affected by humic acid and/or copper: intermediates and degradation pathways.

Science.gov (United States)

Xie, Jimin; Wang, Pingli; Liu, Jun; Lv, Xiaomeng; Jiang, Deli; Sun, Cheng

2011-11-01

The influence of coexisting humic acids (HA) or Cu²⁺ on the photodegradation of pesticides lambda-cyhalothrin (λ-CHT) and cypermethrin (CPM) in aqueous solution was studied under xenon lamp irradiation. The removal efficiency of pesticides λ-CHT and CPM were enhanced in the presence of either Cu²⁺ or HA but restrained in the presence of both Cu²⁺ and HA. The photodegradation of λ-CHT and CPM followed first-order reaction kinetics. The photodegradation intermediates of λ-CHT and CPM were determined using gas chromatography/mass spectrometry. Possible photodegradation pathways included decarboxylation, ester bond cleavage, dechlorination, and phenyl group removal. Copyright © 2011 SETAC.

Transesterification of Jatropha curcas oil glycerides: Theoretical and experimental studies of biodiesel reaction

Energy Technology Data Exchange (ETDEWEB)

Neyda C. Om Tapanes; Donato A. Gomes Aranda; Jose W. de Mesquita Carneiro; Octavio A. Ceva Antunes [Universidade Federal do Rio de Janeiro, Rio de Janeiro (Brazil). Laboratorio GREENTEC

2008-08-15

Vegetal oil, also known as triglycerides, is a mixture of fatty acid triesters of glycerol. In the triglycerides alkyl chains of Jatropha curcas oil, predominate the palmitic, oleic and linoleic fatty acids. The process usually used to convert these triglycerides to biodiesel is called transesterification. The overall process is a sequence of three equivalent, consecutive and reversible reactions, in which di- and monoglycerides are formed as intermediates. Semi-empirical AM1 molecular orbital calculations were used to investigate the reaction pathways of base-catalyzed transesterification of glycerides of palmitic, oleic and linoleic acid. The most probable pathway and the rate determining-step of the reactions were estimated from the molecular orbital calculations. Our results suggest the formation of only one tetrahedral intermediate, which in a subsequent step rearranges to form the products. The rate determining-step is the break of this tetrahedral intermediate. 27 refs., 6 figs., 4 tabs.

Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

Science.gov (United States)

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

1994-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

Central collisions in intermediate energy heavy-ion reactions

International Nuclear Information System (INIS)

Wong, C.Y.

1979-01-01

The critical collisions in intermediate energy heavy-ion reactions are examined from both a microscopic and macroscopic viewpoint. In the microscopic description the proper tool is the extended TDHF approximation involving both the mean field and the particle collisions. To understand the underlying physics, the effect of the mean field and the effect of particle collisions are studied separately. It is found that th sudden increase in the density of the overlapping region can cause the volcano effect, leading to the complete disintegration of one of the nuclei. The self-consistent mean field also gives rise to the bunching instability when the two Fermi spheres of the colliding nucleons separate. The collision between nucleons, on the other hand, leads to irreversible dissipation, thermalization, and the possibility of a hydrodynamical description of the dynamics. Next is studied the dynamics of central collisions using the hydrodynamical description for many combinations of targets and projectiles at different energies. The formation of shock waves, sidesplash, and the complete disintegration of the whole nucleus are examined. Nuclear viscosity is found to affect the angular distribution of the reaction products and also the maximum compression ratio achieved during the collision. 28 references

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

Science.gov (United States)

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

2009-01-01

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

Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogues

Science.gov (United States)

Lietzan, Adam D.; St. Maurice, Martin

2014-01-01

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

A kinetic model for the glucose/glycine Maillard reaction pathways

NARCIS (Netherlands)

Martins, S.I.F.S.; Boekel, van M.A.J.S.

2005-01-01

A comprehensive kinetic model for the glucose/glycine Maillard reaction is proposed based on an approach called multiresponse kinetic modelling. Special attention was paid to reactants, intermediates and end products: -fructose, N-(1-deoxy--fructos-1-yl)-glycine (DFG), 1-deoxy-2,3-hexodiulose and

Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

Energy Technology Data Exchange (ETDEWEB)

Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

2013-09-15

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

International Nuclear Information System (INIS)

Ovacik, Meric A.; Androulakis, Ioannis P.

2013-01-01

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy

Stepwise radical cation Diels-Alder reaction via multiple pathways.

Science.gov (United States)

Shimizu, Ryo; Okada, Yohei; Chiba, Kazuhiro

2018-01-01

Herein we disclose the radical cation Diels-Alder reaction of aryl vinyl ethers by electrocatalysis, which is triggered by an oxidative SET process. The reaction clearly proceeds in a stepwise fashion, which is a rare mechanism in this class. We also found that two distinctive pathways, including "direct" and "indirect", are possible to construct the Diels-Alder adduct.

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

Science.gov (United States)

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

2015-01-01

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

Coincidence measurements of intermediate mass fragments produced in /sup 32/S-induced reactions on Ag at E/A = 22.5 MeV

International Nuclear Information System (INIS)

Fields, D.J.; Lynch, W.G.; Nayak, T.K.

1986-01-01

Single- and two-particle inclusive cross sections for the production of light nuclei and intermediate mass fragments, 3< or =Z< or =24, were measured at angles well beyond the grazing angle for /sup 32/S-induced reactions on Ag at 720 MeV. Information about fragment multiplicities and reaction dynamics was extracted from measurements of light particles, intermediate mass fragments, and targetlike residues in coincidence with intermediate mass fragments. Incomplete linear momentum transfer and non-compound-particle emission are important features of collisions producing intermediate mass fragments. About half of the incident kinetic energy in these collisions is converted into internal excitation. The mean multiplicity of intermediate mass fragments is of the order of 1. Particle correlations are strongly enhanced in the plane which contains the intermediate mass fragment and the beam axis

Inclusive quasielastic neutrino reactions in 12C and 16O at intermediate energies

International Nuclear Information System (INIS)

Singh, S.K.; Oset, E.

1993-01-01

Inclusive quasielastic neutrino (antineutrino) reactions on 12 C and 16 O at intermediate energies (50< E<400 MeV) are studied to investigate the effects of the nuclear medium on the total cross section and the energy spectrum of the outgoing leptons. The calculations are done in the local density approximation and various nuclear effects like Pauli blocking, Fermi motion, and strong-interaction renormalizations due to the presence of nucleons are taken into account. The corrections due to Coulomb effects are included which have been hitherto neglected in inclusive reactions. The results presented here are applicable to the inclusive reactions with neutrino beams planned to look for neutrino oscillations in the Los Alamos experiments or the experiments with underground detectors looking for atmospheric or solar flare neutrinos

Pathways for the reaction of the butadiene radical cation, [C{sub 4}H{sub 6}]{sup {sm{underscore}bullet}+}, with ethylene

Energy Technology Data Exchange (ETDEWEB)

Hofmann, M.; Schaefer, H.F. III

1999-11-04

The Diels-Alder (DA) reaction, a [4+2] cycloaddition used to build six membered rings, is one of the most valuable cycloadditions in organic chemistry. In cases where the ene does not add to the diene (even with the help of Lewis acids which may reduce the electron density of one reactant by complexation) one electron oxidation (by an oxidizing agent or by photoinduced electron transfer (PET)) may accelerate the reaction. Reaction pathways for the addition of ethylene, 1, to butadiene radical cation, 2, involving H-shifts have been investigated at the coupled cluster UCCSD(T)/DZP//UMP2(fc)/DZP + ZPE level of theory. Activation energies are relatively low for [1,2]- (10.0 kcal mol{sup {minus}1}, TS-4/20) and [1,5]-hydrogen shifts (7.7 kcal mol{sup {minus}1}, TS-4/26) but are relatively high for [1,4]-(33.8 kcal mol{sup {minus}1}, TS-4/14) and [1,3]-H shifts (e.g., 42.2 kcal mol{sup {minus}1}, TS-12/13; 57.2 kcal mol{sup {minus}1}, TS-16/21). Several rearrangement reactions have been found to occur below the energy limit of separated 1 + 2. The cyclopentenyl cation, [C{sub 5}{sub 7}]{sup +}, 18, experimentally observed as reaction product of the butadiene radical cation, 2, and ethylene, 1, in the gas phase may origin from various reaction pathways. The following reaction sequence has been identified as the lowest in energy path from 1 + 2 to 18 with all relative energies ({Delta}E{degree}) of transition structures below that of 1 + 2: (a) ethylene adds to the butadiene radical cation to form an open-chain distonic intermediate, that undergoes a [1,5]-H shift to the 1,4-hexadiene radical cation; (b) intramolecular [2+1] cycloaddition to methyl-cyclopenta-1,3-diyl intermediates, which can interconvert through a bicyclo[2.1.0]pentane radical cation; (c) [1,2]-H shift to the 3-methyl cyclopentene radical cation; (d) methyl radical loss to give cyclopenten-3-yl cation. Along this reaction pathway, {Delta}H{sup 298} is below that of 1 + 2; max. ({Delta}G{sup 298} by

(γ,2n) reactions in complexe nuclei at intermediate energies

International Nuclear Information System (INIS)

Pinheiro Filho, J. de D.

1976-01-01

The Monte Carlo Method has been used in the intranuclear cascade model for the calculation of the cross sections of the (γ,2n) reactions in complex nuclei 9 Be, 12 C, 16 O, 59 Co, 103 Rh, 127 I, 197 Au and 209 Bi at intermediate energies (200MeV-1000MeV). The initial photon-interaction via the photomesonic and quasi-deuteron mechanisms have been taken into account. The nuclear model used was a degenerate Fermi gas of nucleons, and the Pauli exclusion principle was considered in all secondary interactions. To improve accuracy in the results of the calculations, 30000 cascades have been followed for each target nucleus at a given incident photon energy. The probabilities of the various (γ,2n) reactions, as well as the correspondent cross section obtained, are summarized in tables and graphs. New data on the cross sections of the 59 Co (γ,2n) and 209 Bi (γ,2n) reactions at photon energies between 300 MeV and 1000MeV are also reported. These measurements were obtained with the Bremsstrahlung beams of the Frascati 1 GeV Electron Synchrotron. A comparison between all existing data in the literature on the (γ,2n) reaction cross sections and the estimates by the Monte Carlo Method, is presented. (Author) [pt

Calculation for fission decay from heavy ion reactions at intermediate energies

International Nuclear Information System (INIS)

Blaich, T.; Begemann-Blaich, M.; Fowler, M.M.; Wilhelmy, J.B.; Britt, H.C.; Fields, D.J.; Hansen, L.F.; Namboodiri, M.N.; Sangster, T.C.; Fraenkel, Z.

1992-01-01

A detailed deexcitation calculation is presented for target residues resulting from intermediate-energy heavy ion reactions. The model involves an intranuclear cascade, subsequent fast nucleon emission, and final decay by statistical evaporation including fission. Results are compared to data from bombardments with Fe and Nb projectiles on targets of Ta, Au, and Th at 100 MeV/nucleon. The majority of observable features are reproduced with this simple approach, making obvious the need for involving new physical phenomena associated with multifragmentation or other collective dissipation mechanisms

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

Science.gov (United States)

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 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.

[Intermediate energy studies of polarization transfer, polarized deuteron scattering, and (p,π+-) reactions: Rapporteur's report

International Nuclear Information System (INIS)

Moss, J.M.

1985-01-01

An overview of intermediate energy (80 to 1000 MeV) study contributions to the International Polarization Symposium in Osaka, Japan, August 1985 is presented in this report. Contributions fall into three categories: polarization transfer, polarized deuteron scattering and polarized (p,π +- ) reactions

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

KAUST Repository

Wang, Zhandong

2017-11-28

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

KAUST Repository

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah; Wang, Heng; Sioud, Salim; Raji, Misjudeen; Kohse-Hö inghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R.; Sarathy, Mani

2017-01-01

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.

Electrophilic properties of patulin. Adduct structures and reaction pathways with 4-bromothiophenol and other model nucleophiles.

Science.gov (United States)

Fliege, R; Metzler, M

2000-05-01

The mycotoxin patulin (PAT) is believed to exert its cytotoxic and chromosome-damaging effects by forming covalent adducts with essential cellular thiols. Since the chemical structures of such adducts are unknown to date, we have studied the reaction of PAT and its O-acetylated derivative with the monofunctional thiol model compound 4-bromothiophenol (BTP), which was chosen due to analytical advantages. By means of analytical and preparative high-performance liquid chromatography, 16 adducts of PAT and 3 adducts of acetyl-PAT were isolated and their chemical structures elucidated by (1)H and (13)C NMR, IR, and UV spectroscopy. Time course studies and analysis of daughter product formation from isolated intermediate adducts led to a detailed scheme for the reaction of PAT with BTP. The structures of adducts of PAT formed with other model nucleophiles, e. g., the aliphatic thiol 2-mercaptoethanol and the aromatic amine 4-bromoaniline, were also elucidated and found to corroborate the reaction scheme. In addition, one further reaction pathway was observed with 2-mercaptoethanol, which appears to be independent from those found for BTP. Our study with model nucleophiles provides insights into the electrophilic reactivity of PAT and proved to be useful for the structure elucidation of PAT adducts with biological nucleophiles of toxicological relevance, as will be reported by Fliege and Metzler [(2000) Chem. Res. Toxicol. 13, 373-381].

Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A: Kinetics, reaction pathways, and formation of brominated by-products

Energy Technology Data Exchange (ETDEWEB)

Ji, Yuefei [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China); Kong, Deyang [Nanjing Institute of Environmental Science, Ministry of Environmental Protection of PRC, Nanjing 210042 (China); Lu, Junhe, E-mail: jhlu@njau.edu.cn [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China); Jin, Hao; Kang, Fuxing; Yin, Xiaoming; Zhou, Quansuo [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China)

2016-08-05

Highlights: • Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A. • Phenolic moiety was the reactive site for sulfate radical attack. • Pathways include β-scission, oxidation, debromination and coupling reactions. • Brominated disinfection by-products were found during TBBPA degradation. • Humic acid inhibited TBBPA degradation but promoted DBPs formation. - Abstract: Degradation of tetrabromobisphenol A (TBBPA), a flame retardant widely spread in the environment, in Co(II) catalyzed peroxymonosulfate (PMS) oxidation process was systematically explored. The second-order-rate constant for reaction of sulfate radical (SO{sub 4}{sup ·−}) with TBBPA was determined to be 5.27 × 10{sup 10} M{sup −1} s{sup −1}. Apparently, degradation of TBBPA showed first-order kinetics to the concentrations of both Co(II) and PMS. The presence of humic acid (HA) and bicarbonate inhibited TBBPA degradation, most likely due to their competition for SO{sub 4}{sup ·−}. Degradation of TBBPA was initiated by an electron abstraction from one of the phenolic rings. Detailed transformation pathways were proposed, including β-scission of isopropyl bridge, phenolic ring oxidation, debromination and coupling reactions. Further oxidative degradation of intermediates in Co(II)/PMS process yielded brominated disinfection by-products (Br-DBPs) such as bromoform and brominated acetic acids. Evolution profile of Br-DBPs showed an initially increasing and then decreasing pattern with maximum concentrations occurring around 6–10 h. The presence of HA enhanced the formation of Br-DBPs significantly. These findings reveal potentially important, but previously unrecognized, formation of Br-DBPs during sulfate radical-based oxidation of bromide-containing organic compounds that may pose toxicological risks to human health.

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates**

Science.gov (United States)

Draksharapu, Apparao; Angelone, Davide; Quesne, Matthew G; Padamati, Sandeep K; Gómez, Laura; Hage, Ronald; Costas, Miquel; Browne, Wesley R; de Visser, Sam P

2015-01-01

FeIII–hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme FeIII–hypohalite intermediates of possible relevance to iron halogenases. We show that FeIII-OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the FeIII-OCl, and ultimately FeIV=O, species and provide indirect evidence for a short-lived FeII-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases. PMID:25663379

An unexpected reaction pathway in the synthesis of the ABCE framework of strychnine-type alkaloids - A multidisciplinary study

Science.gov (United States)

Šoral, Michal; Markus, Jozef; Doháňošová, Jana; Šoralová, Stanislava; Dvoranová, Dana; Chyba, Andrej; Moncol, Ján; Berkeš, Dušan; Liptaj, Tibor

2017-01-01

Acid-catalyzed cyclization of spirocyclic 1‧-benzyl-2‧-(prop-2-en-1-yl)spiro[indole-3,3‧-pyrrolidine]-5‧-one (1) was performed. The pentacyclic product of Povarov-like imino-Diels-Alder reaction was isolated in high yield instead of expected tetracyclic aza-Prins intermediate. The unusual exotic alkaloid-type structure of the resulting molecule 2 was unambiguously confirmed by a detailed NMR analysis using a set of 2D NMR spectra including an INADEQUATE experiment. The relative configuration of 2 was predicted from the synthesis mechanism and DFT geometry calculations and independently confirmed using NOESY and residual dipolar coupling (RDC) assisted NMR analysis in stretched crosslinked polystyrene gels. The reversibility of the cycloaddition in aprotic solvents was observed. A new reaction pathway yielding a rare 6-5-5-5 tetracyclic spiroindoline 3 was suggested. The relative configuration within the tetracyclic framework was ultimately proved using Single-crystal X-ray diffraction analysis of compound 4.

Multifragmentation in intermediate energy ¹²⁹Xe-induced heavy-ion reactions

Energy Technology Data Exchange (ETDEWEB)

Tso, Kin [Univ. of California, Berkeley, CA (United States)

1996-05-01

The ¹²⁹Xe-induced reactions on ^natCu, ⁸⁹Y, ¹⁶⁵Ho, and ¹⁹⁷Au at bombarding energies of E/A = 40 & 60 MeV have been studied theoretically and experimentally in order to establish the underlying mechanism of multifragmentation at intermediate energy heavy-Ion collisions. Nuclear disks formed in central heavy-ion collisions, as simulated by means of Boltzmann-like kinetic equations, break up into several fragments due to a new kind of Rayleigh-like surface instability. A sheet of liquid, stable in the limit of non-interacting surfaces, is shown to become unstable due to surface-surface interactions. The onset of this instability is determined analytically. A thin bubble behaves like a sheet and is susceptible to the surface instability through the crispation mode. The Coulomb effects associated with the depletion of charges in the central cavity of nuclear bubbles are investigated. The onset of Coulomb instability is demonstrated for perturbations of the radial mode. Experimental intermediate-mass-fragment multiplicity distributions for the ¹²⁹Xe-induced reactions are shown to be binomial at each transverse energy. From these distributions, independent of the specific target, an elementary binary decay probability p can be extracted that has a thermal dependence. Thus it is inferred that multifragmentation is reducible to a combination of nearly independent emission processes. If sequential decay is assumed, the increase of p with transverse energy implies a contraction of the emission time scale. The sensitivity of p to the lower Z threshold in the definition of intermediate-mass-fragments points to a physical Poisson simulations of the particle multiplicities show that the weak auto-correlation between the fragment multiplicity and the transverse energy does not distort a Poisson distribution into a binomial distribution. The effect of device efficiency on the experimental results has also been studied.

Macromolecular crowding compacts unfolded apoflavodoxin and causes severe aggregation of the off-pathway intermediate during apoflavodoxin folding

NARCIS (Netherlands)

Engel, R.; Westphal, A.H.; Huberts, D.; Nabuurs, S.M.; Lindhoud, S.; Visser, A.J.W.G.; Mierlo, van C.P.M.

2008-01-01

To understand how proteins fold in vivo, it is important to investigate the effects of macromolecular crowding on protein folding. Here, the influence of crowding on in vitro apoflavodoxin folding, which involves a relatively stable off-pathway intermediate with molten globule characteristics, is

The Intermediate Velocity Source in the 40Ca + 197Au Reaction at 35 AMeV

International Nuclear Information System (INIS)

Planeta, R.; Sosin, Z.; Hachaj, P.

2001-01-01

The creation of hot Ca-like fragments and the emission of intermediate velocity particles was studied in the 40 Ca+ 197 Au reaction at 35 AMeV. For peripheral collisions the primary projectile-like fragment was reconstructed using the AMPHORA 4π detector system. The particle distributions are compared with the predictions of a Monte Carlo code which calculates the nucleon transfer and clustering probabilities according to the system density of states. The velocity distributions of charged particles projected on the beam direction can be explained if emissions from the hot projectile-like fragment and the target-like fragment are supplemented by an emission from an intermediate velocity source located between them. The properties of the intermediate velocity source are properly described, including the 2 D/ 3 T/ 3 He effect. (author)

Specialized reactions: reactions at intermediate energies: Baryon--nucleus collisions, 150 MeV--1 GeV

International Nuclear Information System (INIS)

Igo, G.

1974-01-01

The high energy collision approximation proposed by Glauber to describe experimental data at the upper end of the intermediate range is reviewed. Some aspects of the model which limit its validity are outlined. Elastic scattering of protons from light nuclei is discussed in the framework of the Glauber model. For data in the energy region near 200 MeV, the plane wave impulse approximation (PWIA) and the distorted wave impulse approximation (DWIA) are applied. Quasielastic scattering is treated by considering (p,p') and (p,2p) reactions with light nuclei. A short discussion of the high resolution spectrometer facility at LAMPF and the SPES 1 facility at Saturne is given. (46 figures, 3 tables, 102 references) (U.S.)

Progress in applyiong the FKK multistep reaction theory to intermediate-energy data evaluation

International Nuclear Information System (INIS)

Chadwick, M.B.; Young, P.G.

1994-01-01

Recent developments to the physics modeling in the FKK-GNASH code system are reviewed. We describe modifications to include a linking of multistep direct and multistep compound processes, which are important when the incident energy is less than about 30 MeV. A model for multiple preequilibrium emission is given, and compared with experimental measurements of proton reactions on 90 Zr at 160 MeV. We also give some preliminary observations concerning FKK calculations which use both normal and non-normal DWBA matrix elements. We describe the application of the FKK-GNASH code to a range of nuclear data applications, including intermediate energy reactions of importance in the accelerator transmutation of waste, and fast neutron and proton cancer radiation treatment. We outline areas where further work is needed for the accurate modeling of nuclear reactions using the FKK theory

Glucose and Fructose to Platform Chemicals: Understanding the Thermodynamic Landscapes of Acid-Catalysed Reactions Using High-Level ab Initio Methods

Energy Technology Data Exchange (ETDEWEB)

Assary, Rajeev S.; Kim, Taijin; Low, John; Greeley, Jeffrey P.; Curtiss, Larry A.

2012-12-28

Molecular level understanding of acid-catalysed conversion of sugar molecules to platform chemicals such as hydroxy-methyl furfural (HMF), furfuryl alcohol (FAL), and levulinic acid (LA) is essential for efficient biomass conversion. In this paper, the high-level G4MP2 method along with the SMD solvation model is employed to understand detailed reaction energetics of the acid-catalysed decomposition of glucose and fructose to HMF. Based on protonation free energies of various hydroxyl groups of the sugar molecule, the relative reactivity of gluco-pyranose, fructo-pyranose and fructo-furanose are predicted. Calculations suggest that, in addition to the protonated intermediates, a solvent assisted dehydration of one of the fructo-furanosyl intermediates is a competing mechanism, indicating the possibility of multiple reaction pathways for fructose to HMF conversion in aqueous acidic medium. Two reaction pathways were explored to understand the thermodynamics of glucose to HMF; the first one is initiated by the protonation of a C2–OH group and the second one through an enolate intermediate involving acyclic intermediates. Additionally, a pathway is proposed for the formation of furfuryl alcohol from glucose initiated by the protonation of a C2–OH position, which includes a C–C bond cleavage, and the formation of formic acid. The detailed free energy landscapes predicted in this study can be used as benchmarks for further exploring the sugar decomposition reactions, prediction of possible intermediates, and finally designing improved catalysts for biomass conversion chemistry in the future.

Permanganate oxidation of α-amino acids: kinetic correlations for the nonautocatalytic and autocatalytic reaction pathways.

Science.gov (United States)

Perez-Benito, Joaquin F

2011-09-08

The reactions of permanganate ion with seven α-amino acids in aqueous KH(2)PO(4)/K(2)HPO(4) buffers have been followed spectrophotometrically at two different wavelengths: 526 nm (decay of MnO(4)(-)) and 418 nm (formation of colloidal MnO(2)). All of the reactions studied were autocatalyzed by colloidal MnO(2), with the contribution of the autocatalytic reaction pathway decreasing in the order glycine > l-threonine > l-alanine > l-glutamic acid > l-leucine > l-isoleucine > l-valine. The rate constants corresponding to the nonautocatalytic and autocatalytic pathways were obtained by means of either a differential rate law or an integrated one, the latter requiring the use of an iterative method for its implementation. The activation parameters for the two pathways were determined and analyzed to obtain statistically significant correlations for the series of reactions studied. The activation enthalpy of the nonautocatalytic pathway showed a strong, positive dependence on the standard Gibbs energy for the dissociation of the protonated amino group of the α-amino acid. Linear enthalpy-entropy correlations were found for both pathways, leading to isokinetic temperatures of 370 ± 21 K (nonautocatalytic) and 364 ± 28 K (autocatalytic). Mechanisms in agreement with the experimental data are proposed for the two reaction pathways.

RhoA/ROCK Signaling Pathway Mediates Shuanghuanglian Injection-Induced Pseudo-allergic Reactions.

Science.gov (United States)

Han, Jiayin; Zhao, Yong; Zhang, Yushi; Li, Chunying; Yi, Yan; Pan, Chen; Tian, Jingzhuo; Yang, Yifei; Cui, Hongyu; Wang, Lianmei; Liu, Suyan; Liu, Jing; Deng, Nuo; Liang, Aihua

2018-01-01

Background: Shuanghuanglian injection (SHLI) is a famous Chinese medicine used as an intravenous preparation for the treatment of acute respiratory tract infections. In the recent years, the immediate hypersensitivity reactions induced by SHLI have attracted broad attention. However, the mechanism involved in these reactions has not yet been elucidated. The present study aims to explore the characteristics of the immediate hypersensitivity reactions induced by SHLI and deciphers the role of the RhoA/ROCK signaling pathway in these reactions. Methods: SHLI-immunized mice or naive mice were intravenously injected (i.v.) with SHLI (600 mg/kg) once, and vascular leakage in the ears was evaluated. Passive cutaneous anaphylaxis test was conducted using sera collected from SHLI-immunized mice. Naive mice were administered (i.v.) with a single dose of 150, 300, or 600 mg/kg of SHLI, and vascular leakage, histamine release, and histopathological alterations in the ears, lungs, and intestines were tested. In vitro , human umbilical vein endothelial cell (HUVEC) monolayer was incubated with SHLI (0.05, 0.1, or 0.15 mg/mL), and the changes in endothelial permeability and cytoskeleton were observed. Western blot analysis was performed and ROCK inhibitor was employed to investigate the contribution of the RhoA/ROCK signaling pathway in SHLI-induced hypersensitivity reactions, both in HUVECs and in mice. Results: Our results indicate that SHLI was able to cause immediate dose-dependent vascular leakage, edema, and exudates in the ears, lungs, and intestines, and histamine release in mice. These were pseudo-allergic reactions, as SHLI-specific IgE was not elicited during sensitization. In addition, SHLI induced reorganization of actin cytoskeleton and disrupted the endothelial barrier. The administration of SHLI directly activated the RhoA/ROCK signaling pathway both in HUVECs and in the ears, lungs, and intestines of mice. Fasudil hydrochloride, a ROCK inhibitor, ameliorated the

Synthesis and reactions of deuterated 2-(alkylimino)-3-nitrosooxazolidines, 3-alkly-1-(2-hydroxyethyl)-1-nitrosoureas, and related compounds as possible intermediates in the aqueous decomposition of 3-alkyl-1-(2-chloroethyl)-1-nitrosoureas

International Nuclear Information System (INIS)

Lown, J.W.; Chauhan, S.M.S.

1981-01-01

Decomposition of 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea-α-d 2 (CCNU-α-d 2 ) (7) in pH 7.2 phosphate buffer or of CINO-α-d 2 (9) or CHNU-α-d 2 (8) with the addition of chloride ion gives rise to the same spectrum of products, including deuterium-free acetaldehyde (29), a mixture of the two deuterio-2-chloroethanols, 2-hydroxy-2,2-dideuterioethyl cyclohexyl carbamates, and vinyl chloride containing one deuterium (i.e., opposite the results obtained in the corresponding reaction of BCNU-α-d 4 ). The products were identified and the number and position of the deuterium labels determined by GC/MS. The results are interpreted in terms of two decomposition pathways for CCNU. The first decomposition pathway operating for CCNU is via an intermediate-2-chloroethanediazohydroxide or the equivalent 2-chloroethyl cation in agreement with the results of other workers. The second pathway may involve reversible conversion of CCNU-α-d 2 (7) to CINO-α-d 2 (9) and then ring opening of the latter to CHNU-α-d 2 (8). Independent decomposition of 8 provides evidence for its conversion to a 1.1-dideuterio-2-hydroxyethanediazohydroxide (41) leading to the isolated carbamates 36 and 44. The intermediacy of species 41 may account for the formation of 2-hydroxyethylated nucleosides observed when (2-chloroethyl)nitrosoureas react with DNA. An alternative ring-opening reaction of 9 leads to a 2-hydroxydiazoethyl cyclohexylcarbamate species (37), elimination of which and attack by halide ion may account for the vinyl halide species formed. Further evidence in support of these competing pathways employing additional specifically deuterated intermediates is described and discussed

Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

DEFF Research Database (Denmark)

Jin, Biao; Rolle, Massimo

2016-01-01

The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework ...

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

DEFF Research Database (Denmark)

Rasmussen, Dominik Bjørn; Christensen, Jakob Munkholt; Temel, Burcin

2015-01-01

Unprecedented insight into the carbonylation of dimethyl ether over Mordenite is provided through the identification of ketene (CH2CO) as a reaction intermediate. The formation of ketene is predicted by detailed DFT calculations and verified experimentally by the observation of doubly deuterated ...

Organometallic copper I, II or III species in an intramolecular dechlorination reaction

KAUST Repository

Poater, Albert

2013-03-15

The present paper gives insight into an intramolecular dechlorination reaction involving Copper (I) and an ArCH2Cl moiety. The discussion of the presence of a CuIII organometallic intermediate becomes a challenge, and because of the lack of clear experimental detection of this proposed intermediate, and due to the computational evidence that it is less stable than other isomeric species, it can be ruled out for the complex studied here. Our calculations are completely consistent with the key hypothesis of Karlin et al. that TMPA-CuI is the substrate of intramolecular dechlorination reactions as well as the source to generate organometallic species. However the organometallic character of some intermediates has been refused because computationally these species are less stable than other isomers. Thus this study constitutes an additional piece towards the full understanding of a class of reaction of biological relevance. Further, the lack of high energy barriers and deep energy wells along the reaction pathway explains the experimental difficulties to trap other intermediates. © Springer-Verlag Berlin Heidelberg 2013.

On the characterization of intermediates in the isodesmic aggregation pathway of hen lysozyme at alkaline pH.

Directory of Open Access Journals (Sweden)

Vijay Kumar Ravi

Full Text Available Protein aggregation leading to formation of amyloid fibrils is a symptom of several diseases like Alzheimer's, type 2 diabetes and so on. Elucidating the poorly understood mechanism of such phenomena entails the difficult task of characterizing the species involved at each of the multiple steps in the aggregation pathway. It was previously shown by us that spontaneous aggregation of hen-eggwhite lysozyme (HEWL at room temperature in pH 12.2 is a good model to study aggregation. Here in this paper we investigate the growth kinetics, structure, function and dynamics of multiple intermediate species populating the aggregation pathway of HEWL at pH 12.2. The different intermediates were isolated by varying the HEWL monomer concentration in the 300 nM-0.12 mM range. The intermediates were characterized using techniques like steady-state and nanosecond time-resolved fluorescence, atomic force microscopy and dynamic light scattering. Growth kinetics of non-fibrillar HEWL aggregates were fitted to the von Bertalanffy equation to yield a HEWL concentration independent rate constant (k = (6.6 ± 0.6 × 10(-5 s(-1. Our results reveal stepwise changes in size, molecular packing and enzymatic activity among growing HEWL aggregates consistent with an isodesmic aggregation model. Formation of disulphide bonds that crosslink the monomers in the aggregate appear as a unique feature of this aggregation. AFM images of multiple amyloid fibrils emanating radially from amorphous aggregates directly confirmed that on-pathway fibril formation was feasible under isodesmic polymerization. The isolated HEWL aggregates are revealed as polycationic protein nanoparticles that are robust at neutral pH with ability to take up non-polar molecules like ANS.

Bridge mediated two-electron transfer reactions: Analysis of stepwise and concerted pathways

International Nuclear Information System (INIS)

Petrov, E.G.; May, V.

2004-01-01

A theory of nonadiabatic donor (D)-acceptor (A) two-electron transfer (TET) mediated by a single regular bridge (B) is developed. The presence of different intermediate two-electron states connecting the reactant state D -- BA with the product state DBA -- results in complex multiexponential kinetics. The conditions are discussed at which a reduction to two-exponential as well as single-exponential kinetics becomes possible. For the latter case the rate K TET is calculated, which describes the bridge-mediated reaction as an effective two-electron D-A transfer. In the limit of small populations of the intermediate TET states D - B - A, DB -- A, D - BA - , and DB - A - , K TET is obtained as a sum of the rates K TET (step) and K TET (sup) . The first rate describes stepwise TET originated by transitions of a single electron. It starts at D -- BA and reaches DBA -- via the intermediate state D - BA - . These transitions cover contributions from sequential as well as superexchange reactions all including reduced bridge states. In contrast, a specific two-electron superexchange mechanism from D -- BA to DBA -- defines K TET (sup) . An analytic dependence of K TET (step) and K TET (sup) on the number of bridging units is presented and different regimes of D-A TET are studied

Graph-representation of oxidative folding pathways

Directory of Open Access Journals (Sweden)

Kaján László

2005-01-01

Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.A.

Probing the Catalytic Mechanism of S-Ribosylhomocysteinase (LuxS) with Catalytic Intermediates and Substrate Analogues

Energy Technology Data Exchange (ETDEWEB)

Gopishetty, Bhaskar; Zhu, Jinge; Rajan, Rakhi; Sobczak, Adam J.; Wnuk, Stanislaw F.; Bell, Charles E.; Pei, Dehua; (OSU); (FIU)

2009-05-12

S-Ribosylhomocysteinase (LuxS) cleaves the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of the type II bacterial quorum sensing molecule (AI-2). The catalytic mechanism of LuxS comprises three distinct reaction steps. The first step involves carbonyl migration from the C1 carbon of ribose to C2 and the formation of a 2-ketone intermediate. The second step shifts the C=O group from the C2 to C3 position to produce a 3-ketone intermediate. In the final step, the 3-ketone intermediate undergoes a {beta}-elimination reaction resulting in the cleavage of the thioether bond. In this work, the 3-ketone intermediate was chemically synthesized and shown to be chemically and kinetically competent in the LuxS catalytic pathway. Substrate analogues halogenated at the C3 position of ribose were synthesized and reacted as time-dependent inhibitors of LuxS. The time dependence was caused by enzyme-catalyzed elimination of halide ions. Examination of the kinetics of halide release and decay of the 3-ketone intermediate catalyzed by wild-type and mutant LuxS enzymes revealed that Cys-84 is the general base responsible for proton abstraction in the three reaction steps, whereas Glu-57 likely facilitates substrate binding and proton transfer during catalysis.

Angular dependences of the tensor analyzing powers in the dd→3Hen reaction at intermediate energies

International Nuclear Information System (INIS)

Ladygin, V.P.; Ladygina, N.B.

2002-01-01

The tensor analyzing powers A yy , A xx , and A xz in the dd→ 3 Hen reaction at intermediate energies are considered in the framework of the one-nucleon-exchange approximation. Their strong sensitivity to the 3 He and deuteron spin structure at short distances is shown

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

Science.gov (United States)

Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

2013-01-01

Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

On the deduction of chemical reaction pathways from measurements of time series of concentrations.

Science.gov (United States)

Samoilov, Michael; Arkin, Adam; Ross, John

2001-03-01

We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system. (c) 2001 American Institute of Physics.

Intermediate and high energy nuclear reactions at the hadronic structural level

Energy Technology Data Exchange (ETDEWEB)

Slowinski, B [Institute of Physics, Warsaw, University of Technology, Poland, Institute of Atomic Energy, Swierk, (Poland)

1997-12-31

Form tens of MeV to several hundred of GeV is stretched out quite a large interval of energy when the interaction between hadrons (for instance, pion/nucleon-nucleus and nucleus-nucleus reactions) can be described by the considerably simplified way with still acceptable accuracy. This happens because in this energy region hadrons (i.e. pions, nucleons etc.) remain quasiparticles of nuclear matter mostly without revealing any internal structure, their de Broglie`s wavelength is much shorter as compared to the average intranuclear nucleon`s distance, and the energy transfers in the reaction are, on the average, significantly greater than the binding energy of nucleons inside nuclei. Consequently an approach to the analysis of these phenomena based on simple geometric and probabilistic considerations is justifiable, especially for many practical purposes, in particular, for shielding and dosimetric estimations, material behaviour prediction, as well as for the approximate evaluation of electronuclear breeding effects in different composites of target materials, for nuclear passivation problems and so on. In this work basic physical reasons of such a simplified picture of intermediate and high energy nuclear reactions are presented. The most usual phenomenological models of hadronic multiple emission/production and recent results of the cascade evaporation type models, are also discussed. 2 figs.

Competing retention pathways of uranium upon reaction with Fe(II)

Science.gov (United States)

Massey, Michael S.; Lezama-Pacheco, Juan S.; Jones, Morris E.; Ilton, Eugene S.; Cerrato, José M.; Bargar, John R.; Fendorf, Scott

2014-10-01

Biogeochemical retention processes, including adsorption, reductive precipitation, and incorporation into host minerals, are important in contaminant transport, remediation, and geologic deposition of uranium. Recent work has shown that U can become incorporated into iron (hydr)oxide minerals, with a key pathway arising from Fe(II)-induced transformation of ferrihydrite, (Fe(OH)3·nH2O) to goethite (α-FeO(OH)); this is a possible U retention mechanism in soils and sediments. Several key questions, however, remain unanswered regarding U incorporation into iron (hydr)oxides and this pathway's contribution to U retention, including: (i) the competitiveness of U incorporation versus reduction to U(IV) and subsequent precipitation of UO2; (ii) the oxidation state of incorporated U; (iii) the effects of uranyl aqueous speciation on U incorporation; and, (iv) the mechanism of U incorporation. Here we use a series of batch reactions conducted at pH ∼7, [U(VI)] from 1 to 170 μM, [Fe(II)] from 0 to 3 mM, and [Ca] at 0 or 4 mM coupled with spectroscopic examination of reaction products of Fe(II)-induced ferrihydrite transformation to address these outstanding questions. Uranium retention pathways were identified and quantified using extended X-ray absorption fine structure (EXAFS) spectroscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. Analysis of EXAFS spectra showed that 14-89% of total U was incorporated into goethite, upon reaction with Fe(II) and ferrihydrite. Uranium incorporation was a particularly dominant retention pathway at U concentrations ⩽50 μM when either uranyl-carbonato or calcium-uranyl-carbonato complexes were dominant, accounting for 64-89% of total U. With increasing U(VI) and Fe(II) concentrations, U(VI) reduction to U(IV) became more prevalent, but U incorporation remained a functioning retention pathway. These findings highlight the potential importance of U(V) incorporation within iron

Identification and characterization of monoclonal antibodies specific for macrophages at intermediate stages in the tumoricidal activation pathway

International Nuclear Information System (INIS)

Paulnock, D.M.; Lambert, L.E.

1990-01-01

Macrophage activation for tumor cell killing is a multistep pathway in which responsive macrophages interact sequentially with priming and triggering stimuli in the acquisition of full tumoricidal activity. A number of mediators have been identified which have activating capability, including in particular IFN-gamma and bacterial LPS. Although the synergistic functional response of normal macrophages to sequential incubation with these activation signals has been well-established, characterization of the intermediate stages in the activation pathway has been difficult. We have developed a model system for examination of various aspects of macrophage activation, through the use of the murine macrophage tumor cell line, RAW 264.7. These cells, like normal macrophages, exhibit a strict requirement for interaction with both IFN-gamma and LPS in the development of tumor cytolytic activity. In addition, these cells can be stably primed by the administration of gamma-radiation. In the studies reported here, we have used RAW 264.7 cells treated with IFN-gamma alone or with IFN-gamma plus LPS to stimulate the production of rat mAb probes recognizing cell surface changes occurring during the activation process. In this way we have identified three Ag associated with intermediate stages of the activation process. One Ag, TM-1, is expressed on RAW 264.7 cells primed by IFN-gamma or gamma-radiation. This surface Ag thus identifies cells at the primed cell intermediate stage of the tumoricidal activation pathway regardless of the mechanism of activation. A second Ag, TM-2, is expressed on IFN-treated RAW 264.7 cells but not on RAW 264.7 cells primed with gamma-radiation alone. Expression of this Ag can be induced by treatment of irradiated cells with IFN-gamma, but is not induced by IFN-gamma treatment of a noncytolytic cell line, WEHI-3

Reactivity of Single-Walled Carbon Nanotubes in the Diels-Alder Cycloaddition Reaction: Distortion-Interaction Analysis along the Reaction Pathway.

Science.gov (United States)

Li, Yingzi; Osuna, Sílvia; Garcia-Borràs, Marc; Qi, Xiaotian; Liu, Song; Houk, Kendall N; Lan, Yu

2016-08-26

Diels-Alder cycloaddition is one of the most powerful tools for the functionalization of single-walled carbon nanotubes (SWCNTs). Density functional theory at the B3-LYP level of theory has been used to investigate the reactivity of different-diameter SWCNTs (4-9,5) in Diels-Alder reactions with 1,3-butadiene; the reactivity was found to decrease with increasing SWCNT diameter. Distortion/interaction analysis along the whole reaction pathway was found to be a better way to explore the reactivity of this type of reaction. The difference in interaction energy along the reaction pathway is larger than that of the corresponding distortion energy. However, the distortion energy plots for these reactions show the same trend. Therefore, the formation of the transition state can be determined from the interaction energy. A lower interaction energy leads to an earlier transition state, which indicates a lower activation energy. The computational results also indicate that the original distortion of the SWCNTs leads to an increase in the reactivity of the SWCNTs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway.

Science.gov (United States)

Guntaka, Naga Sandhya; Healy, Alan R; Crawford, Jason M; Herzon, Seth B; Bruner, Steven D

2017-10-20

Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway

Energy Technology Data Exchange (ETDEWEB)

Guntaka, Naga Sandhya; Healy, Alan R.; Crawford, Jason M.; Herzon, Seth B.; Bruner, Steven D. (Yale); (Florida); (Yale-MED)

2017-09-08

Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.

Exploring the Reaction Pathways of Bioglycerol Hydrodeoxygenation to Propene over Molybdena-Based Catalysts.

Science.gov (United States)

Zacharopoulou, Vasiliki; Vasiliadou, Efterpi S; Lemonidou, Angeliki A

2018-01-10

The one-step reaction of glycerol with hydrogen to form propene selectively is a particularly challenging catalytic pathway that has not yet been explored thoroughly. Molybdena-based catalysts are active and selective to C-O bond scission; propene is the only product in the gas phase under the standard reaction conditions, and further hydrogenation to propane is impeded. Within this context, this work focuses on the exploration of the reaction pathways and the investigation of various parameters that affect the catalytic performance, such as the role of hydrogen on the product distribution and the effect of the catalyst pretreatment step. Under a hydrogen atmosphere, propene is produced primarily via 2-propenol, whereas under an inert atmosphere propanal and glycerol dissociation products are formed mainly. The reaction most likely proceeds through a reverse Mars-van Krevelen mechanism as partially reduced Mo species drive the reaction to the formation of the desired product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Springloaded Metal-Ligand Mesocate Allows Access to Trapped Intermediates of Self-Assembly.

Science.gov (United States)

Bogie, Paul M; Holloway, Lauren R; Lyon, Yana; Onishi, Nicole C; Beran, Gregory J O; Julian, Ryan R; Hooley, Richard J

2018-04-02

A strained, "springloaded" Fe 2 L 3 iminopyridine mesocate shows highly variable reactivity upon postassembly reaction with competitive diamines. The strained assembly is reactive toward transimination in minutes at ambient temperature and allows observation of kinetically trapped intermediates in the self-assembly pathway. When diamines are used that can only form less favored cage products upon full equilibration, trapped ML 3 fragments with pendant, "hanging" NH 2 groups are selectively formed instead. Slight variations in diamine structure have large effects on the product outcome: less rigid diamines convert the mesocate to more favored self-assembled cage complexes under mild conditions and allow observation of heterocomplex intermediates in the displacement pathway. The mesocate allows control of equilibrium processes and direction of product outcomes via small, iterative changes in added subcomponent structure and provides a method of accessing metal-ligand cage structures not normally observed in multicomponent Fe-iminopyridine self-assembly.

A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion.

Directory of Open Access Journals (Sweden)

Mériam Ben Hamida-Rebaï

Full Text Available Small G-proteins of the superfamily Ras function as molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs. Large conformational changes accompany the exchange reaction, and our understanding of the mechanism is correspondingly incomplete. However, much knowledge has been derived from structural studies of blocked or inactive mutant GEFs, which presumably closely represent intermediates in the exchange reaction and yet which are by design incompetent for carrying out the nucleotide exchange reaction. In this study we have used comparative modelling to recreate an exchange-competent form of a late, pre-GDP-ejection intermediate species in Arf1, a well-characterized small G-protein. We extensively characterized three distinct models of this intermediate using molecular dynamics simulations, allowing us to address ambiguities related to the mutant structural studies. We observed in particular the unfavorable nature of Mg2+ associated forms of the complex and the establishment of closer Arf1-GEF contacts in its absence. The results of this study shed light on GEF-mediated activation of this small G protein and on predicting the fate of the Mg ion at a critical point in the exchange reaction. The structural models themselves furnish additional targets for interfacial inhibitor design, a promising direction for exploring potentially druggable targets with high biological specificity.

Reaction of iminopropadienones with amines--formation of zwitterionic intermediates, ketenes, and ketenimines.

Science.gov (United States)

Veedu, Rakesh Naduvile; Kokas, Okanya J; Couturier-Tamburelli, Isabelle; Koch, Rainer; Aycard, Jean-Pierre; Borget, Fabien; Wentrup, Curt

2008-10-09

Five aryliminopropadienones 4a- d have been synthesized by flash vacuum thermolysis (FVT) by using two different precursors in each case. These compounds were deposited at 50 K at a pressure of ca. 10(-6) mbar together with three different nucleophiles, namely, trimethylamine (TMA), dimethylamine (DMA), and diethylamine (DEA), in order to study their reactions as neat solids during warm-up by FTIR spectroscopy. The reaction with TMA showed that a zwitterionic species (5 and/or 6) was formed in all the cases. With DMA and DEA, an alpha-oxoketenimine and/or an imidoylketene (7 and 8 or 9 and 10) was formed as the final product. In addition, several bands were observed, which can be assigned to zwitterionic intermediates (11 or 12). Optimized structures and vibrational spectra for all products were calculated at the B3LYP/6-31G(d) level of theory by using the polarizable continuum model (epsilon = 5).

Nitric oxide formation from the reaction of nitrite with carp and rabbit hemoglobin at intermediate oxygen saturations

DEFF Research Database (Denmark)

Jensen, Frank Bo

2008-01-01

The nitrite reductase activity of deoxyhemoglobin has received much recent interest because the nitric oxide produced in this reaction may participate in blood flow regulation during hypoxia. The present study used spectral deconvolution to characterize the reaction of nitrite with carp and rabbit...... hemoglobin at different constant oxygen tensions that generate the full range of physiological relevant oxygen saturations. Carp is a hypoxia-tolerant species with very high hemoglobin oxygen affinity, and the high R-state character and low redox potential of the hemoglobin is hypothesized to promote...... NO generation from nitrite. The reaction of nitrite with deoxyhemoglobin leads to a 1 : 1 formation of nitrosylhemoglobin and methemoglobin in both species. At intermediate oxygen saturations, the reaction with deoxyhemoglobin is clearly favored over that with oxyhemoglobin, and the oxyhemoglobin reaction...

Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

Energy Technology Data Exchange (ETDEWEB)

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

1993-12-01

Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

Role of Intermediate Filaments in Vesicular Traffic

Directory of Open Access Journals (Sweden)

Azzurra Margiotta

2016-04-01

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

Chemical pathways for the formation of ammonia in Hanford wastes

Energy Technology Data Exchange (ETDEWEB)

Stock, L.M.; Pederson, L.R.

1997-09-01

This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence.

Chemical pathways for the formation of ammonia in Hanford wastes

International Nuclear Information System (INIS)

Stock, L.M.; Pederson, L.R.

1997-09-01

This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence

Uranium fluoride chemistry. Part 1. The gas phase reaction of uranium hexafluoride with alcohols

International Nuclear Information System (INIS)

Schnautz, N.G.; Venter, P.J.

1992-01-01

The reaction between uranium hexafluoride (UF 6 ) and simple alcohols in the gas phase was observed to proceed by way of three possible reaction pathways involving dehydration, deoxygenative fluorination, and ether formation. These reactions can best be explained by assuming that alcohols first react with UF 6 to afford the alkoxy uranium pentafluoride intermediate ROUF 5 , which reacts further to give the dehydration, deoxygenative fluorination, and ether products. In each of the above three reaction pathways, UF 6 is transformed to UOF 4 , which being as reactive toward alcohols as UF 6 , reacts further with the alcohol in question to finally afford the unreactive uranyl fluoride (UO 2 F 2 ). 6 refs., 2 tabs

Angular dependences of the tensor analyzing powers in the dd → 3Hen reaction at intermediate energies

International Nuclear Information System (INIS)

Ladygin, V.P.; Ladygina, N.B.; )

2002-01-01

The tensor analyzing powers A yy , A xx , and A xz in the dd → 3 Hen reaction at intermediate energies are considered in the framework of the one-nucleon-exchange approximation. Their strong sensitivity to the 3 He and deuteron spin structure at short distances is shown [ru

Exploration of the Singlet O2 Oxidation of 8-Oxoguanine by Guided-Ion Beam Scattering and Density Functional Theory: Changes of Reaction Intermediates, Energetics, and Kinetics upon Protonation/Deprotonation and Hydration.

Science.gov (United States)

Sun, Yan; Lu, Wenchao; Liu, Jianbo

2017-02-09

8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) is one of the most common DNA lesions resulting from reactive oxygen species and ionizing radiation, and is involved in mutagenesis, carcinogenesis, and cell death. Notably, 8-oxodGuo is more reactive toward singlet (a 1 Δ g ) O 2 than the undamaged guanosine, and the lesions arising from the secondary oxidation of 8-oxodGuo are more mutagenic. Herein the 1 O 2 oxidation of free base 8-oxoguanine (8-oxoG) was investigated at different initial conditions including protonated [8-oxoG + H] + , deprotonated [8-oxoG - H] - , and their monohydrates. Experiment was carried out on a guided-ion beam scattering tandem mass spectrometer. Measurements include the effects of collision energy (E col ) on reaction cross sections over a center-of-mass E col range from 0.1 to 0.5 eV. The aim of this study is to quantitatively probe the sensitivity of the early stage of 8-oxoG oxidation to ionization and hydration. Density functional theory and Rice-Ramsperger-Kassel-Marcus calculations were performed to identify the intermediates and the products along reaction pathways and locate accessible reaction potential energy surfaces, and to rationalize reaction outcomes from energetic and kinetic points of view. No product was observed for the reaction of [8-oxoG + H] + ·W 0,1 (W = H 2 O) because insurmountable barriers block the addition of 1 O 2 to reactant ions. Neither was [8-oxoG - H] - reactive with 1 O 2 , in this case due to the rapid decay of transient intermediates to starting reactants. However, the nonreactivity of [8-oxoG - H] - was inverted by hydration; as a result, 4,5-dioxetane of [8-oxoG - H] - was captured as the main oxidation product. Reaction cross section for [8-oxoG - H] - ·W + 1 O 2 decreases with increasing E col and becomes negligible above 0.3 eV, indicating that the reaction is exothermic and has no barriers above reactants. The contrasting oxidation behaviors of [8-oxoG + H] + ·W 0,1 and [8-oxoG - H] - ·W 0

Surface-Activated Coupling Reactions Confined on a Surface.

Science.gov (United States)

Dong, Lei; Liu, Pei Nian; Lin, Nian

2015-10-20

Chemical reactions may take place in a pure phase of gas or liquid or at the interface of two phases (gas-solid or liquid-solid). Recently, the emerging field of "surface-confined coupling reactions" has attracted intensive attention. In this process, reactants, intermediates, and products of a coupling reaction are adsorbed on a solid-vacuum or a solid-liquid interface. The solid surface restricts all reaction steps on the interface, in other words, the reaction takes place within a lower-dimensional, for example, two-dimensional, space. Surface atoms that are fixed in the surface and adatoms that move on the surface often activate the surface-confined coupling reactions. The synergy of surface morphology and activity allow some reactions that are inefficient or prohibited in the gas or liquid phase to proceed efficiently when the reactions are confined on a surface. Over the past decade, dozens of well-known "textbook" coupling reactions have been shown to proceed as surface-confined coupling reactions. In most cases, the surface-confined coupling reactions were discovered by trial and error, and the reaction pathways are largely unknown. It is thus highly desirable to unravel the mechanisms, mechanisms of surface activation in particular, of the surface-confined coupling reactions. Because the reactions take place on surfaces, advanced surface science techniques can be applied to study the surface-confined coupling reactions. Among them, scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) are the two most extensively used experimental tools. The former resolves submolecular structures of individual reactants, intermediates, and products in real space, while the latter monitors the chemical states during the reactions in real time. Combination of the two methods provides unprecedented spatial and temporal information on the reaction pathways. The experimental findings are complemented by theoretical modeling. In particular, density

Surface Interrogation Scanning Electrochemical Microscopy for a Photoelectrochemical Reaction: Water Oxidation on a Hematite Surface.

Science.gov (United States)

Kim, Jae Young; Ahn, Hyun S; Bard, Allen J

2018-03-06

To understand the pathway of a photoelectrochemical (PEC) reaction, quantitative knowledge of reaction intermediates is important. We describe here surface interrogation scanning electrochemical microscopy for this purpose (PEC SI-SECM), where a light pulse to a photoactive semiconductor film at a given potential generates intermediates that are then analyzed by a tip generated titrant at known times after the light pulse. The improvements were demonstrated for photoelectrochemical water oxidation (oxygen evolution) reaction on a hematite surface. The density of photoactive sites, proposed to be Fe 4+ species, on a hematite surface was successfully quantified, and the photoelectrochemical water oxidation reaction dynamics were elucidated by time-dependent redox titration experiments. The new configuration of PEC SI-SECM should find expanded usage to understand and investigate more complicated PEC reactions with other materials.

Broadband Microwave Study of Reaction Intermediates and Products Through the Pyrolysis of Oxygenated Biofuels

Science.gov (United States)

Abeysekera, Chamara; Hernandez-Castillo, Alicia O.; Fritz, Sean; Zwier, Timothy S.

2017-06-01

The rapidly growing list of potential plant-derived biofuels creates a challenge for the scientific community to provide a molecular-scale understanding of their combustion. Development of accurate combustion models rests on a foundation of experimental data on the kinetics and product branching ratios of their individual reaction steps. Therefore, new spectroscopic tools are necessary to selectively detect and characterize fuel components and reactive intermediates generated by pyrolysis and combustion. Substituted furans, including furanic ethers, are considered second-generation biofuel candidates. Following the work of the Ellison group, an 8-18 GHz microwave study was carried out on the unimolecular and bimolecular decomposition of the smallest furanic ether, 2-methoxy furan, and it`s pyrolysis intermediate, the 2-furanyloxy radical, formed in a high-temperature pyrolysis source coupled to a supersonic expansion. Details of the experimental setup and analysis of the spectrum of the radical will be discussed.

Intermediates and the folding of proteins L and G

Energy Technology Data Exchange (ETDEWEB)

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.

Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

International Nuclear Information System (INIS)

Lee, Yuan-Pern

2015-01-01

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

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

Science.gov (United States)

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

A Western Blot-based Investigation of the Yeast Secretory Pathway Designed for an Intermediate-Level Undergraduate Cell Biology Laboratory

Science.gov (United States)

Hood-DeGrenier, Jennifer K.

2008-01-01

The movement of newly synthesized proteins through the endomembrane system of eukaryotic cells, often referred to generally as the secretory pathway, is a topic covered in most intermediate-level undergraduate cell biology courses. An article previously published in this journal described a laboratory exercise in which yeast mutants defective in…

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

Science.gov (United States)

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

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

International Nuclear Information System (INIS)

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 σ(700)-meson exchange in γγ→ππ 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 γΝ-Δ transition; pion photoproduction and the γΝ-Δ 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 γ, π 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 Ν → Νγ and Δ → γΝ transition form factors; electroproduction studies of the Ν → Δ transition at bates and CEBAF

Direct single-molecule dynamic detection of chemical reactions.

Science.gov (United States)

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Angular distributions of intermediate mass fragments emitted in 30 MeV/u 40Ar induced reactions

International Nuclear Information System (INIS)

Gou Quanbu; Zhu Yongtai; Xu Hushan; Wei Zhiyong; Lu Jun; Zhang Yuhu; Wang Qi; Li Songlin; Wu Zhongli

1999-01-01

The angular distributions of intermediate mass fragments with charge numbers from 3 to 24 emitted in 30 MeV/u 40 Ar + 58,64 Ni and 115 In reactions over an angular range of 5 degree-140 degree have been measured. In different angular region an exponential distribution function dσ/dΩ = N exp(-θ/α) was used to fit the measured angular distributions. The decay factor α which can be connected with the interaction time τ and the factor N which is related to the intensity of the emission sources have been extracted. The relationship of α(Z) and N(Z) with Z for different reaction systems and different angular regions has been discussed. The different behavior of dσ/dΩ, α(Z), and N(Z) for the three studied reaction systems exists mainly in the middle and backward angular regions. The dependencies of angular distributions on isospin and the size of reaction systems have also been discussed

Angular dependences of the tensor analyzing powers in the dd -> sup 3 Hen reaction at intermediate energies

CERN Document Server

Ladygin, V P

2002-01-01

The tensor analyzing powers A sub y sub y , A sub x sub x , and A sub x sub z in the dd -> sup 3 Hen reaction at intermediate energies are considered in the framework of the one-nucleon-exchange approximation. Their strong sensitivity to the sup 3 He and deuteron spin structure at short distances is shown

Reaction pathways of the dissociation of methylal: A DFT study

Energy Technology Data Exchange (ETDEWEB)

Frey, H -M; Beaud, P; Gerber, T; Mischler, B; Radi, P P; Tzannis, A -P [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1999-08-01

Schemata for modelling combustion processes do not yet include reaction rates for oxygenated fuels like methylal (DMM) which is considered as an additive or replacement for diesel due to its low sooting propensity. Density functional theory (DFT) studies of the possible reaction pathways for different dissociation steps of methylal are presented. Cleavage of a hydrogen bond to the methoxy group or the central carbon atom were simulated at the BLYP/6-311++G{sup **} level of theory. The results are compared to the experiment when dissociating and/or ionising DMM with femtosecond pulses. (author) 1 fig., 1 tab., 1 ref.

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

International Nuclear Information System (INIS)

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

1982-01-01

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

Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

International Nuclear Information System (INIS)

Osborn, David L.

2017-01-01

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low temperature combustion and the oxidation of volatile organic compounds in earth’s atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization make characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, while master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.

Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

Science.gov (United States)

Osborn, David L.

2017-05-01

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low-temperature combustion and in the oxidation of volatile organic compounds in Earth's atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization makes characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, and master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.

Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

International Nuclear Information System (INIS)

Jin, Biao; Rolle, Massimo

2016-01-01

The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces the multi-element isotope data observed in previous experimental studies. Furthermore, it precisely captures the dual element isotope trends characteristic of different reaction pathways as well as their range of variation consistent with observed bulk isotope fractionation. It was also possible to directly validate the model capability to predict the evolution of position-specific isotope ratios with available experimental data. Therefore, the approach is useful both for a mechanism-based evaluation of experimental results and as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. - Highlights: • Mechanism-based, position-specific isotope modeling of micropollutants degradation. • Simultaneous description of concentration and primary and secondary isotope effects. • Key features of the model are demonstrated with three illustrative examples. • Model as a tool to explore reaction mechanisms and to design experiments. - We propose a modeling approach incorporating mechanistic information and

Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography.

Science.gov (United States)

Samara, Nadine L; Gao, Yang; Wu, Jinjun; Yang, Wei

2017-01-01

Structures of enzyme-substrate/product complexes have been studied for over four decades but have been limited to either before or after a chemical reaction. Recently using in crystallo catalysis combined with X-ray diffraction, we have discovered that many enzymatic reactions in nucleic acid metabolism require additional metal ion cofactors that are not present in the substrate or product state. By controlling metal ions essential for catalysis, the in crystallo approach has revealed unprecedented details of reaction intermediates. Here we present protocols used for successful studies of Mg 2+ -dependent DNA polymerases and ribonucleases that are applicable to analyses of a variety of metal ion-dependent reactions. © 2017 Elsevier Inc. All rights reserved.

Reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma

Science.gov (United States)

Zhao, Yuefeng; Wang, Chao; Li, Li; Wang, Lijuan; Pan, Jie

2018-03-01

In this work, a two-dimensional fluid model is built up to numerically investigate the reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma. The calculation results indicate that the electron collisions with CH4 are the key pathways to produce the neutral particles CH2 and CH as well as the charged particles e and CH3+. CH3, H2, H, C2H2, and C2H4 primarily result from the reactions between the neutral particles and CH4. The charge transfer reactions are the significant pathways to produce CH4+, C2H2+, and C2H4+. As to the neutral species CH and H and the charged species CH3+, the reactions between themselves and CH4 contribute to substantial losses of these particles. The ways responsible for losing CH3, H2, C2H2, and C2H4 are CH3 + H → CH4, H2 + CH → CH2 + H, CH4+ + C2H2 → C2H2+ + CH4, and CH4+ + C2H4 → C2H4+ + CH4, respectively. Both electrons and C2H4+ are consumed by the dissociative electron-ion recombination reactions. The essential reaction pathways of losing CH4+ and C2H2+ are the charge transfer reactions.

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

Science.gov (United States)

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

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

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

Energy Technology Data Exchange (ETDEWEB)

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

1992-10-01

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

Photochemical transformation of phenylurea herbicides in surface waters: a model assessment of persistence, and implications for the possible generation of hazardous intermediates.

Science.gov (United States)

Fabbri, Debora; Minella, Marco; Maurino, Valter; Minero, Claudio; Vione, Davide

2015-01-01

This work models the phototransformation kinetics in surface waters of five phenylurea herbicides (diuron, fenuron, isoproturon, metoxuron and chlortoluron), for which important photochemical parameters are available in the literature (direct photolysis quantum yields and reaction rate constants with ·OH, CO3(-·) and the triplet states of chromophoric dissolved organic matter, (3)CDOM*). Model calculations suggest that isoproturon and metoxuron would be the least photochemically persistent and diuron the most persistent compound. Reactions with ·OH and (3)CDOM* would be the main phototransformation pathways for all compounds in the majority of environmental conditions. Reaction with CO3(-) could be important in waters with low dissolved organic carbon (DOC), while direct photolysis would be negligible for fenuron, quite important for chlortoluron, and somewhat significant for the other compounds. The direct photolysis of metoxuron and diuron is known to increase toxicity, and such a photoreaction pathway would be enhanced at intermediate DOC values (1-4 mg C L(1)). The reaction between phenylureas and ·OH is known to produce toxic intermediates, differently from (3)CDOM*. Therefore, the shift of reactivity from ·OH to (3)CDOM* with increasing DOC could reduce the environmental impact of photochemical transformation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Theoretical investigation of the gas-phase reactions of CrO(+) with ethylene.

Science.gov (United States)

Scupp, Thomas M; Dudley, Timothy J

2010-01-21

The potential energy surfaces associated with the reactions of chromium oxide cation (CrO(+)) with ethylene have been characterized using density functional, coupled-cluster, and multireference methods. Our calculations show that the most probable reaction involves the formation of acetaldehyde and Cr(+) via a hydride transfer involving the metal center. Our calculations support previous experimental hypotheses that a four-membered ring intermediate plays an important role in the reactivity of the system. We have also characterized a number of viable reaction pathways that lead to other products, including ethylene oxide. Due to the experimental observation that CrO(+) can activate carbon-carbon bonds, a reaction pathway involving C-C bond cleavage has also been characterized. Since many of the reactions involve a change in the spin state in going from reactants to products, locations of these spin surface crossings are presented and discussed. The applicability of methods based on Hartree-Fock orbitals is also discussed.

II. The intermediate velocity source in the 40Ca+40Ca reaction at Elab=35 AMeV

International Nuclear Information System (INIS)

Sosin, Z.; Planeta, R.; Ciszek, T.

2001-01-01

The shape of the velocity distributions of charged particles projected on the beam direction can be explained if emissions from the hot projectile-like fragment and the target-like fragment are supplemented by an emission from an intermediate velocity source located between them. The creation of this source is predicted by a two-stage reaction model where, in the second stage, some of the nucleons identified in the first stage as participants form a group of clusters located in the region between the colliding nuclei. The cluster coalescence process is governed on the average by the maximum value of entropy, although its fluctuations are also significant. The properties of the intermediate velocity source are precisely described, including the isotopic composition of the emitted particles. (orig.)

Intermediate structure and threshold phenomena

International Nuclear Information System (INIS)

Hategan, Cornel

2004-01-01

The Intermediate Structure, evidenced through microstructures of the neutron strength function, is reflected in open reaction channels as fluctuations in excitation function of nuclear threshold effects. The intermediate state supporting both neutron strength function and nuclear threshold effect is a micro-giant neutron threshold state. (author)

Delineating neurotrophin-3 dependent signaling pathways underlying sympathetic axon growth along intermediate targets.

Science.gov (United States)

Keeler, Austin B; Suo, Dong; Park, Juyeon; Deppmann, Christopher D

2017-07-01

Postganglionic sympathetic neurons detect vascular derived neurotrophin 3 (NT3) via the axonally expressed receptor tyrosine kinase, TrkA, to promote chemo-attraction along intermediate targets. Once axons arrive to their final target, a structurally related neurotrophic factor, nerve growth factor (NGF), also acts through TrkA to promote final target innervation. Does TrkA signal differently at these different locales? We previously found that Coronin-1 is upregulated in sympathetic neurons upon exposure to NGF, thereby endowing the NGF-TrkA complex with new signaling capabilities (i.e. calcium signaling), which dampens axon growth and branching. Based on the notion that axons do not express functional levels of Coronin-1 prior to final target innervation, we developed an in vitro model for axon growth and branching along intermediate targets using Coro1a -/- neurons grown in NT3. We found that, similar to NGF-TrkA, NT3-TrkA is capable of inducing MAPK and PI3K in the presence or absence of Coronin-1. However, unlike NGF, NT3 does not induce calcium release from intracellular stores. Using a combination of pharmacology, knockout neurons and in vitro functional assays, we suggest that the NT3-TrkA complex uses Ras/MAPK and/or PI3K-AKT signaling to induce axon growth and inhibit axon branching along intermediate targets. However, in the presence of Coronin-1, these signaling pathways lose their ability to impact NT3 dependent axon growth or branching. This is consistent with a role for Coronin-1 as a molecular switch for axon behavior and suggests that Coronin-1 suppresses NT3 dependent axon behavior. Copyright © 2017 Elsevier Inc. All rights reserved.

Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study.

Science.gov (United States)

Bykov, Dmytro; Plog, Matthias; Neese, Frank

2014-01-01

In this article, we consider, in detail, the second half-cycle of the six-electron nitrite reduction mechanism catalyzed by cytochrome c nitrite reductase. In total, three electrons and four protons must be provided to reach the final product, ammonia, starting from the HNO intermediate. According to our results, the first event in this half-cycle is the reduction of the HNO intermediate, which is accomplished by two PCET reactions. Two isomeric radical intermediates, HNOH(•) and H2NO(•), are formed. Both intermediates are readily transformed into hydroxylamine, most likely through intramolecular proton transfer from either Arg114 or His277. An extra proton must enter the active site of the enzyme to initiate heterolytic cleavage of the N-O bond. As a result of N-O bond cleavage, the H2N(+) intermediate is formed. The latter readily picks up an electron, forming H2N(+•), which in turn reacts with Tyr218. Interestingly, evidence for Tyr218 activity was provided by the mutational studies of Lukat (Biochemistry 47:2080, 2008), but this has never been observed in the initial stages of the overall reduction process. According to our results, an intramolecular reaction with Tyr218 in the final step of the nitrite reduction process leads directly to the final product, ammonia. Dissociation of the final product proceeds concomitantly with a change in spin state, which was also observed in the resonance Raman investigations of Martins et al. (J Phys Chem B 114:5563, 2010).

Pyrite formation and mineral transformation pathways upon sulfidation of ferric hydroxides depend on mineral type and sulfide concentration

NARCIS (Netherlands)

Peiffer, Stefan; Behrends, Thilo; Hellige, Katrin; Larese-Casanova, Philip; Wan, Moli; Pollok, Kilian

2015-01-01

The reaction of ferric (hydr)oxides with dissolved sulfide does not lead to the instantaneous production of thermodynamically stable products but can induce a variety of mineral transformations including the formation of metastable intermediates. The importance of the various transformation pathways

Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds.

Science.gov (United States)

Dondi, Daniele; Merli, Daniele; Albini, Angelo; Zeffiro, Alberto; Serpone, Nick

2012-05-01

When a chemical system is submitted to high energy sources (UV, ionizing radiation, plasma sparks, etc.), as is expected to be the case of prebiotic chemistry studies, a plethora of reactive intermediates could form. If oxygen is present in excess, carbon dioxide and water are the major products. More interesting is the case of reducing conditions where synthetic pathways are also possible. This article examines the theoretical modeling of such systems with random-generated chemical networks. Four types of random-generated chemical networks were considered that originated from a combination of two connection topologies (viz., Poisson and scale-free) with reversible and irreversible chemical reactions. The results were analyzed taking into account the number of the most abundant products required for reaching 50% of the total number of moles of compounds at equilibrium, as this may be related to an actual problem of complex mixture analysis. The model accounts for multi-component reaction systems with no a priori knowledge of reacting species and the intermediates involved if system components are sufficiently interconnected. The approach taken is relevant to an earlier study on reactions that may have occurred in prebiotic systems where only a few compounds were detected. A validation of the model was attained on the basis of results of UVC and radiolytic reactions of prebiotic mixtures of low molecular weight compounds likely present on the primeval Earth.

Intermediate resonance excitation in the {gamma}p->p{pi}{sup 0}{pi}{sup 0} reaction

Energy Technology Data Exchange (ETDEWEB)

Ahrens, J. [Institut fuer Kernphysik, Universitaet Mainz, D-55099 Mainz (Germany); Altieri, S. [INFN, Sezione di Pavia, I-27100 Pavia (Italy); Dipartimento di Fisica Nucleare e Teorica, Universita di Pavia, I-27100 Pavia (Italy); Annand, J.R.M. [Department of Physics and Astronomy, University of Glasgow (United Kingdom)] (and others)

2005-09-29

The helicity dependence of the total cross section for the {gamma}->p->->p{pi}{sup 0}{pi}{sup 0} reaction has been measured for the first time at incident photon energies from 400 to 800 MeV. The measurement, performed at the tagged photon beam facility of the MAMI accelerator in Mainz, used the large acceptance detector DAPHNE and a longitudinally polarized frozen-spin target. This channel is found to be excited predominantly when the photon and proton have a parallel spin orientation, most likely due to the intermediate production of the D{sub 13}(1520) resonance. However, the contribution of the antiparallel spin configuration, arising from other reaction mechanisms, is also not negligible. This result gives important new information to resolve the existing model discrepancies in the identification of the nucleon resonances contributing to this channel.

Copper-Catalyzed Oxidative Reaction of β-Keto Sulfones with Alcohols via C-S Bond Cleavage: Reaction Development and Mechanism Study.

Science.gov (United States)

Du, Bingnan; Wang, Wenmin; Wang, Yang; Qi, Zhenghang; Tian, Jiaqi; Zhou, Jie; Wang, Xiaochen; Han, Jianlin; Ma, Jing; Pan, Yi

2018-02-16

A Cu-catalyzed cascade oxidative radical process of β-keto sulfones with alcohols has been achieved by using oxygen as an oxidant. In this reaction, β-keto sulfones were converted into sulfinate esters under the oxidative conditions via cleavage of C-S bond. Experimental and computational studies demonstrate that a new pathway is involved in this reaction, which proceeds through the formation of the key four-coordinated Cu II intermediate, O-O bond homolysis induced C-S bond cleavage and Cu-catalyzed esterification to form the final products. This reaction provides a new strategy to sulfonate esters and enriches the research content of C-S bond cleavage and transformations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen oxidation mechanisms on Ni/yttria stabilized zirconia anodes: Separation of reaction pathways by geometry variation of pattern electrodes

Science.gov (United States)

Doppler, M. C.; Fleig, J.; Bram, M.; Opitz, A. K.

2018-03-01

Nickel/yttria stabilized zirconia (YSZ) electrodes are affecting the overall performance of solid oxide fuel cells (SOFCs) in general and strongly contribute to the cell resistance in case of novel metal supported SOFCs in particular. The electrochemical fuel conversion mechanisms in these electrodes are, however, still only partly understood. In this study, micro-structured Ni thin film electrodes on YSZ with 15 different geometries are utilized to investigate reaction pathways for the hydrogen electro-oxidation at Ni/YSZ anodes. From electrodes with constant area but varying triple phase boundary (TPB) length a contribution to the electro-catalytic activity is found that does not depend on the TPB length. This additional activity could clearly be attributed to a yet unknown reaction pathway scaling with the electrode area. It is shown that this area related pathway has significantly different electrochemical behavior compared to the TPB pathway regarding its thermal activation, sulfur poisoning behavior, and H2/H2O partial pressure dependence. Moreover, possible reaction mechanisms of this reaction pathway are discussed, identifying either a pathway based on hydrogen diffusion through Ni with water release at the TPB or a path with oxygen diffusion through Ni to be a very likely explanation for the experimental results.

Photolysis of nonylphenol ethoxylates: the determination of the degradation kinetics and the intermediate products.

Science.gov (United States)

Chen, Ling; Zhou, Hai-Yun; Deng, Qin-Ying

2007-06-01

The photolysis of nonylphenol ethoxylates with an average oligomers length of ten ethoxylate units (NPEO(10)) in aqueous solution under UV, as well as the influence of humic acid (HA) on the photolysis was studied. A 125W high-pressure mercury lamp was employed as the light source. The intermediate products from the photolysis were determined by LC-MS. The results indicated that NPEO(10) underwent direct photolysis upon exposed to UV. The degradation pathway was complex. Besides the generally proposed degradation pathway of ethylene oxide (EO) side chains shortening, the oxidation of alkyl chain and EO chain led to intermediates having both a carboxylated (as well as carbonylated) ethoxylate and alkyl chain of varying lengths. The hydrogenation of benzene ring was also detected. The kinetics data showed that the first order reaction kinetics could be well used to describe the kinetics of NPEO(10) degradation. In the presence of dissolved organic matter by HA addition, the performance of NPEO(10) photodegradation was reduced. The photolysis rate decreased with increased HA concentration.

Temperature-Dependent Rate Coefficients for the Reaction of CH2OO with Hydrogen Sulfide.

Science.gov (United States)

Smith, Mica C; Chao, Wen; Kumar, Manoj; Francisco, Joseph S; Takahashi, Kaito; Lin, Jim Jr-Min

2017-02-09

The reaction of the simplest Criegee intermediate CH 2 OO with hydrogen sulfide was measured with transient UV absorption spectroscopy in a temperature-controlled flow reactor, and bimolecular rate coefficients were obtained from 278 to 318 K and from 100 to 500 Torr. The average rate coefficient at 298 K and 100 Torr was (1.7 ± 0.2) × 10 -13 cm 3 s -1 . The reaction was found to be independent of pressure and exhibited a weak negative temperature dependence. Ab initio quantum chemistry calculations of the temperature-dependent reaction rate coefficient at the QCISD(T)/CBS level are in reasonable agreement with the experiment. The reaction of CH 2 OO with H 2 S is 2-3 orders of magnitude faster than the reaction with H 2 O monomer. Though rates of CH 2 OO scavenging by water vapor under atmospheric conditions are primarily controlled by the reaction with water dimer, the H 2 S loss pathway will be dominated by the reaction with monomer. The agreement between experiment and theory for the CH 2 OO + H 2 S reaction lends credence to theoretical descriptions of other Criegee intermediate reactions that cannot easily be probed experimentally.

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

Science.gov (United States)

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

Kinetics and reaction mechanism for aminolysis of benzyl 4-pyridyl carbonate in H2O: Effect of modification of nucleofuge from 2-pyridyl oxide to 4-pyridyl oxide on reactivity and reaction mechanism

International Nuclear Information System (INIS)

Kang, Ji Sun; Um, Ikhwan

2012-01-01

Pseudo-first-order rate constants k amine have been measured spectrophotometrically for the reactions of benzyl 4-pyridyl carbonate 6 with a series of alicyclic secondary amines in H 2 O at 25.0.deg.C. The plots of k amine vs. [amine] curve upward, indicating that the reactions proceed through a stepwise mechanism with two intermediates, a zwitterionic tetrahedral intermediate T ± and its deprotonated form T - . This contrasts to the report that the corresponding reactions of benzyl 2-pyridyl carbonate 5 proceed through a forced concerted pathway. The k amine values for the reactions of 6 have been dissected into the second-order rate constant Kk 2 and the third order rate constant Kk 3 . The Brφnsted-type plots are linear with β nuc = 0.94 and 1.18 for Kk 2 and Kk 3 , respectively. The Kk 2 for the reaction of 6 is smaller than the second-order rate constant k N for the corresponding reaction of 5, although 4-pyridyl oxide in 6 is less basic and a better nucleofuge than 2-pyridyl oxide in 5

Back-reactions, short-circuits, leaks and other energy wasteful reactions in biological electron transfer: redox tuning to survive life in O(2).

Science.gov (United States)

Rutherford, A William; Osyczka, Artur; Rappaport, Fabrice

2012-03-09

The energy-converting redox enzymes perform productive reactions efficiently despite the involvement of high energy intermediates in their catalytic cycles. This is achieved by kinetic control: with forward reactions being faster than competing, energy-wasteful reactions. This requires appropriate cofactor spacing, driving forces and reorganizational energies. These features evolved in ancestral enzymes in a low O(2) environment. When O(2) appeared, energy-converting enzymes had to deal with its troublesome chemistry. Various protective mechanisms duly evolved that are not directly related to the enzymes' principal redox roles. These protective mechanisms involve fine-tuning of reduction potentials, switching of pathways and the use of short circuits, back-reactions and side-paths, all of which compromise efficiency. This energetic loss is worth it since it minimises damage from reactive derivatives of O(2) and thus gives the organism a better chance of survival. We examine photosynthetic reaction centres, bc(1) and b(6)f complexes from this view point. In particular, the evolution of the heterodimeric PSI from its homodimeric ancestors is explained as providing a protective back-reaction pathway. This "sacrifice-of-efficiency-for-protection" concept should be generally applicable to bioenergetic enzymes in aerobic environments. Copyright © 2012 Federation of European Biochemical Societies. All rights reserved.

One-Pot Conversion of Carbohydrates into Furan Derivatives via Furfural and 5-Hydroxylmethylfurfural as Intermediates.

Science.gov (United States)

Liu, Bing; Zhang, Zehui

2016-08-23

Recently, there has been growing interest in the transformation of renewable biomass into value-added fuels and chemicals. The catalytic conversion of naturally abundant carbohydrates can generate two-important furan chemicals: 5-hydroxymethylfurfural (HMF) from C6 carbohydrates and furfural from C5 carbohydrates. Both HMF and furfural have received great interest as precursors in the synthesis of commodity chemicals and liquid fuels. In recent years, a trend has emerged to integrate sequential catalytic processes involving multistep reactions for the direct one-pot transformation of carbohydrates into the aimed fuels and chemicals. One-pot reactions have remarkably unique and environmentally friendly benefits, including the fact that isolation and purification of intermediate compounds can be avoided. Herein, the present article aims to review recent advances in the one-pot conversion of carbohydrates into furan derivatives via furfural and HMF as intermediates. Special attention will be paid to the catalytic systems, mechanistic insight, reaction pathways, and catalyst stability. It is expected that this review will guide researchers to develop effective catalytic systems for the one-pot transformation of carbohydrates into furan derivatives. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermediate-energy nuclear chemistry workshop

International Nuclear Information System (INIS)

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

Intermediate-energy nuclear chemistry workshop

Energy Technology Data Exchange (ETDEWEB)

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.

Neutron-proton bremsstrahlung from intermediate energy heavy-ion reactions as a probe of the nuclear symmetry energy?

International Nuclear Information System (INIS)

Yong, G.-C.; Li Baoan; Chen Liewen

2008-01-01

Hard photons from neutron-proton bremsstrahlung in intermediate energy heavy-ion reactions are examined as a potential probe of the nuclear symmetry energy within a transport model. Effects of the symmetry energy on the yields and spectra of hard photons are found to be generally smaller than those due to the currently existing uncertainties of both the in-medium nucleon-nucleon cross sections and the photon production probability in the elementary process pn→pnγ. Very interestingly, nevertheless, the ratio of hard photon spectra R 1/2 (γ) from two reactions using isotopes of the same element is not only approximately independent of these uncertainties but also quite sensitive to the symmetry energy. For the head-on reactions of 132 Sn + 124 Sn and 112 Sn + 112 Sn at E beam /A=50 MeV, for example, the R 1/2 (γ) displays a rise up to 15% when the symmetry energy is reduced by about 20% at ρ=1.3ρ 0 which is the maximum density reached in these reactions

Homoaromatics as intermediates in the substitution reactions of 1,2,4,5-tetrazines with ammonia and hydrazine

International Nuclear Information System (INIS)

Counotte-Potman, A.D.

1981-01-01

This thesis describes some nucleophilic substitution reactions between the red 1,2,4,5-tetrazines and hydrazine-hydrate or ammonia. Special attention was paid to the occurrence of the Ssub(N) (ANRORC) mechanism in these substitution reactions. This mechanism comprises a sequence of reactions, involving the Addition of a Nucleopile to a heteroaromatic species, followed by a Ring-Opening and Ring Closure reaction to the substitution product. 3-Alkyl(aryl)-1,2,4,5-tetrazines were found to undergo a Chichibabin hydrazination into 6-hydrazino-3-alkyl(aryl)-1,2,4,5-tetrazines on treatment with hydrazine-hydrate. The first step in this reaction sequence was the formation of a homoaromatic sigma-adduct. Subsequently an open-chain intermediate was observed by NMR, on raising the temperature. Finally the hydrazino compound is formed by ring closure. This reaction sequence can be considered as an Ssub(N)(ANRORC) process. With 15 N-labelled hydrazine, only part of the label was found to be built in the 1,2,4,5-tetrazine ring of the 6-hydrazino compounds. This is the first example of a reaction in which both the hydrazino compound with the 15 N-label in the ring and with the 15 N-label in the exocyclic hydrazino group are formed according to the Ssub(N)(ANRORC) mechanism. (Auth.)

Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

Science.gov (United States)

Dateo, Christopher E.; Walch, Stephen P.

2002-01-01

As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.

Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway.

Science.gov (United States)

Ries, Marco I; Ali, Hazrat; Lankhorst, Peter P; Hankemeier, Thomas; Bovenberg, Roel A L; Driessen, Arnold J M; Vreeken, Rob J

2013-12-27

Metabolic profiling and structural elucidation of novel secondary metabolites obtained from derived deletion strains of the filamentous fungus Penicillium chrysogenum were used to reassign various previously ascribed synthetase genes of the roquefortine/meleagrin pathway to their corresponding products. Next to the structural characterization of roquefortine F and neoxaline, which are for the first time reported for P. chrysogenum, we identified the novel metabolite roquefortine L, including its degradation products, harboring remarkable chemical structures. Their biosynthesis is discussed, questioning the exclusive role of glandicoline A as key intermediate in the pathway. The results reveal that further enzymes of this pathway are rather unspecific and catalyze more than one reaction, leading to excessive branching in the pathway with meleagrin and neoxaline as end products of two branches.

DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals

DEFF Research Database (Denmark)

Chen, Xiulai; Gao, Cong; Guo, Liang

2018-01-01

, and pathway optimization at the systems level, offers a conceptual and technological framework to exploit potential pathways, modify existing pathways and create new pathways for the optimal production of desired chemicals. Here, we summarize recent progress of DCEO biotechnology and examples of its......Chemical synthesis is a well established route for producing many chemicals on a large scale, but some drawbacks still exist in this process, such as unstable intermediates, multistep reactions, complex process control, etc. Biobased production provides an attractive alternative to these challenges......, but how to make cells into efficient factories is challenging. As a key enabling technology to develop efficient cell factories, design-construction-evaluation-optimization (DCEO) biotechnology, which incorporates the concepts and techniques of pathway design, pathway construction, pathway evaluation...

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.

Science.gov (United States)

Dailey, Harry A; Dailey, Tamara A; Gerdes, Svetlana; Jahn, Dieter; Jahn, Martina; O'Brian, Mark R; Warren, Martin J

2017-03-01

The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized. Copyright © 2017 American Society for Microbiology.

Vapor-Phase Hydrodeoxygenation of Guaiacol to Aromatics over Pt/HBeta: Identification of the Role of Acid Sites and Metal Sites on the Reaction Pathway

Energy Technology Data Exchange (ETDEWEB)

Nie, Lei [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Peng, Bo [Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Zhu, Xinli [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China

2018-02-05

Hydrodeoxygenation of guaiacol, a phenolic compound derived from lignin fraction of biomass, over a Pt/HBeta catalyst at 350 °C and atmospheric pressure produces benzene, toluene, xylenes, and C9+ aromatics with yield of 42%, 29%, 12%, and 5%, respectively. Reaction pathways for conversion of two functional groups (hydroxyl and methoxyl) over the bifunctional catalyst were studied. Both guaiacol and intermediate products (catechol and cyclopentanone) were fed onto zeolite HBeta and Pt/SiO2 to identify the individual role of acid site and metal site. Acid sites (mainly Brønsted acid site, BAS) catalyze transalkylation and dehydroxylation reactions in sequence, producing phenol, cresols and xylenols as the major products at high conversion. Pt sites catalyze demethylation reaction resulting in catechol as the primary product, which can either be deoxygenated to phenol followed by phenol to benzene, or decarbonylated to cyclopentanone and further to butane. The close proximity of Pt and BAS in bifunctional Pt/HBeta enables both transalkylation and deoxygenation reactions with inhibited demethylation and decarbonylation reactions, producing aromatics as major final products with a total yield > 85%. Both activity and stability of bifunctional Pt/HBeta during hydrodeoxygenation of guaiacol is improved compared to HBeta and Pt/SiO2. The addition of water to the feed further improves the activity and stability via hydrolysis of O-CH3 bond of guaiacol on BAS and removing coke around Pt.

Using Physical Organic Chemistry To Shape the Course of Electrochemical Reactions.

Science.gov (United States)

Moeller, Kevin D

2018-05-09

While organic electrochemistry can look quite different to a chemist not familiar with the technique, the reactions are at their core organic reactions. As such, they are developed and optimized using the same physical organic chemistry principles employed during the development of any other organic reaction. Certainly, the electron transfer that triggers the reactions can require a consideration of new "wrinkles" to those principles, but those considerations are typically minimal relative to the more traditional approaches needed to manipulate the pathways available to the reactive intermediates formed downstream of that electron transfer. In this review, three very different synthetic challenges-the generation and trapping of radical cations, the development of site-selective reactions on microelectrode arrays, and the optimization of current in a paired electrolysis-are used to illustrate this point.

Does shoe heel design influence ground reaction forces and knee moments during maximum lunges in elite and intermediate badminton players?

Directory of Open Access Journals (Sweden)

Wing-Kai Lam

Full Text Available Lunge is one frequently executed movement in badminton and involves a unique sagittal footstrike angle of more than 40 degrees at initial ground contact compared with other manoeuvres. This study examined if the shoe heel curvature design of a badminton shoe would influence shoe-ground kinematics, ground reaction forces, and knee moments during lunge.Eleven elite and fifteen intermediate players performed five left-forward maximum lunge trials with Rounded Heel Shoe (RHS, Flattened Heel Shoe (FHS, and Standard Heel Shoes (SHS. Shoe-ground kinematics, ground reaction forces, and knee moments were measured by using synchronized force platform and motion analysis system. A 2 (Group x 3 (Shoe ANOVA with repeated measures was performed to determine the effects of different shoes and different playing levels, as well as the interaction of two factors on all variables.Shoe effect indicated that players demonstrated lower maximum vertical loading rate in RHS than the other two shoes (P < 0.05. Group effect revealed that elite players exhibited larger footstrike angle, faster approaching speed, lower peak horizontal force and horizontal loading rates but higher vertical loading rates and larger peak knee flexion and extension moments (P < 0.05. Analysis of Interactions of Group x Shoe for maximum and mean vertical loading rates (P < 0.05 indicated that elite players exhibited lower left maximum and mean vertical loading rates in RHS compared to FHS (P < 0.01, while the intermediate group did not show any Shoe effect on vertical loading rates.These findings indicate that shoe heel curvature would play some role in altering ground reaction force impact during badminton lunge. The differences in impact loads and knee moments between elite and intermediate players may be useful in optimizing footwear design and training strategy to minimize the potential risks for impact related injuries in badminton.

Fenton degradation of Cartap hydrochloride: identification of the main intermediates and the degradation pathway.

Science.gov (United States)

Tian, Kaixun; Ming, Cuixiang; Dai, Youzhi; Honore Ake, Kouassi Marius

2015-01-01

The advanced oxidation of Cartap hydrochloride (Cartap) promoted by the Fenton system in an aqueous medium was investigated. Based on total organic carbon, chemical oxygen demand and high-performance liquid chromatography, the oxidation of Cartap is quite efficient by the Fenton system. Its long chain is easily destroyed, but the reaction does not proceed to complete mineralization. Ion chromatography detection indicated the formation of acetic acid, propionic acid, formic acid, nitrous acid and sulfuric acid in the reaction mixtures. Further evidence of nitrogen monoxide and sulfur dioxide formation was obtained by using a flue gas analyzer. Monitoring by gas chromatograph-mass spectrometer demonstrated the formation of oxalic acid, ethanol, carbon dioxide, and L-alanine ethylamide. Based on these experimental results, plausible degradation pathways for Cartap mineralization in an aqueous medium by the Fenton system are proposed.

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

KAUST Repository

Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin

2016-01-01

To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

KAUST Repository

Kuwahara, Hiroyuki

2016-04-29

To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

The role of grain boundaries and transient porosity increase as fluid pathways for reaction front propagation

Science.gov (United States)

Jonas, Laura; John, Timm; Geisler, Thorsten; Putnis, Andrew

2013-04-01

The pseudomorphic replacement of Carrara marble by calcium phosphates was studied as a model system to examine the influence of different fluid pathways for reaction front propagation induced by fluid-rock interaction. In this model system, the grain boundaries present in the rock and the transient porosity structures developing throughout the replacement reaction enable the reaction front to progress further into the rock as well as to the center of each single grain until complete transformation. Hydrothermal treatment of the marble using phosphate bearing solutions at temperature levels of 150° C and 200° C for different durations lead to the formation of two product phases which were identified as hydroxyapatite [Ca5(PO4)3OH] as well as β-tricalcium phosphate [β-Ca3(PO4)2] (β-TCP). The formation of β-TCP was probably favored by the presence of ~0.6wt.% of Mg in the parent phase. Completely transformed single grains show a distinctive zoning, both in composition and texture. Whereas areas next to the grain boundary consist of nearly pure hydroxyapatite and show a coarse porosity, areas close to the center of the single grains show a high amount of β-TCP and a very fine porous microstructure. If F was added as an additional solution component, the formation of β-TCP was avoided and up to 3wt.% of F were incorporated into the product apatite. The use of the isotope 18O as a chronometer for the replacement reaction makes it possible to reconstruct the chronological development of the calcium phosphate reaction front. Raman analysis revealed that the incorporation of 18O in the PO4 tetrahedron of hydroxyapatite results in the development of distinct profiles in the calcium phosphate reaction front perpendicular to the grain boundaries of the marble. Through the use of the 18O chronometer, it is possible to estimate and compare the time effectiveness of the different fluid pathways in this model system. The results show that the grain boundaries serve as a

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

Science.gov (United States)

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

Time-resolved resonance fluorescence spectroscopy for study of chemical reactions in laser-induced plasmas.

Science.gov (United States)

Liu, Lei; Deng, Leimin; Fan, Lisha; Huang, Xi; Lu, Yao; Shen, Xiaokang; Jiang, Lan; Silvain, Jean-François; Lu, Yongfeng

2017-10-30

Identification of chemical intermediates and study of chemical reaction pathways and mechanisms in laser-induced plasmas are important for laser-ablated applications. Laser-induced breakdown spectroscopy (LIBS), as a promising spectroscopic technique, is efficient for elemental analyses but can only provide limited information about chemical products in laser-induced plasmas. In this work, time-resolved resonance fluorescence spectroscopy was studied as a promising tool for the study of chemical reactions in laser-induced plasmas. Resonance fluorescence excitation of diatomic aluminum monoxide (AlO) and triatomic dialuminum monoxide (Al 2 O) was used to identify these chemical intermediates. Time-resolved fluorescence spectra of AlO and Al 2 O were used to observe the temporal evolution in laser-induced Al plasmas and to study their formation in the Al-O 2 chemistry in air.

The Azomethine Ylide Route to Amine C–H Functionalization: Redox-Versions of Classic Reactions and a Pathway to New Transformations

Science.gov (United States)

2016-01-01

Conspectus Redox-neutral methods for the functionalization of amine α-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 α-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 α-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 α-C–H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-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

The azomethine ylide route to amine C-H functionalization: redox-versions of classic reactions and a pathway to new transformations.

Science.gov (United States)

Seidel, Daniel

2015-02-17

Conspectus Redox-neutral methods for the functionalization of amine α-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 α-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 α-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 α-C-H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-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

Dealkylation of alkylbenzenes: a significant pathway in the toluene, o-, m-, p-xylene + OH reaction.

Science.gov (United States)

Noda, Jun; Volkamer, Rainer; Molina, Mario J

2009-09-03

The OH-radical initiated oxidation of a series of monocyclic aromatic hydrocarbons (benzene, toluene, o-, m-, and p-xylene) in the presence of oxygen and NO(x) was investigated in a flowtube coupled with a chemical ionization mass spectrometer (CIMS). OH-radical addition to the aromatic ring--the major reaction pathway--has previously been shown to have a particular sensitivity to experimental conditions. This is the first flowtube study that demonstrates the atmospheric relevance of product yields from the OH-addition channel on the millisecond time scale (35-75 ms); the phenol yield from benzene and cresol yields from toluene are found to be 51.0 +/- 4.3% and 17.7 +/- 2.1%, in excellent agreement with previous studies under close to atmospheric conditions. We further report unambiguous experimental evidence that dealkylation is a novel and significant pathway for toluene and o-, m-, and p-xylene oxidation. At 150 Torr of O2 partial pressure, toluene is found to dealkylate with a yield of 5.4 +/- 1.2% phenol; similarly, m-, o-, and p-xylene dealkylate with yields of 11.2 +/- 3.8%, 4.5 +/- 3.2%, and 4.3 +/- 3.1% cresol, respectively. A dealkylation mechanism via OH-addition in the ipso position is feasible (DeltaH = -9 kcal/mol for phenol formation from toluene) but does not lend itself easily to explain the significant isomer effect observed among xylenes; instead an alternative mechanism is presented that can explain this isomer effect and forms phenol and likely epoxide type products with identical m/z (indistinguishable in our CIMS analysis) via a carbene-type intermediate. Dealkylation adds to the atmospheric production of phenol- and likely epoxide-type products, with aldehydes as expected co-products, and helps improve the carbon balance in the initial stages of aromatic oxidation.

Reaction pathways of model compounds of biomass-derived oxygenates on Fe/Ni bimetallic surfaces

Science.gov (United States)

Yu, Weiting; Chen, Jingguang G.

2015-10-01

Controlling the activity and selectivity of converting biomass-derivatives to fuels and valuable chemicals is critical for the utilization of biomass feedstocks. There are primarily three classes of non-food competing biomass, cellulose, hemicellulose and lignin. In the current work, glycolaldehyde, furfural and acetaldehyde are studied as model compounds of the three classes of biomass-derivatives. Monometallic Ni(111) and monolayer (ML) Fe/Ni(111) bimetallic surfaces are studied for the reaction pathways of the three biomass surrogates. The ML Fe/Ni(111) surface is identified as an efficient surface for the conversion of biomass-derivatives from the combined results of density functional theory (DFT) calculations and temperature programmed desorption (TPD) experiments. A correlation is also established between the optimized adsorption geometry and experimental reaction pathways. These results should provide helpful insights in catalyst design for the upgrading and conversion of biomass.

Engineering the spatial organization of metabolic pathways

DEFF Research Database (Denmark)

Albertsen, Line; Maury, Jerome; Bach, Lars Stougaard

One of the goals of metabolic engineering is to optimize the production of valuable metabolites in cell factories. In this context, modulating the gene expression and activity of enzymes are tools that have been extensively used. Another approach that is gaining interest is the engineering...... of the spatial organization of biosynthetic pathways. Several natural systems for ensuring optimal spatial arrangement of biosynthetic enzymes exist. Sequentially acting enzymes can for example be positioned in close proximity by attachment to cellular structures, up-concentration in membrane enclosed organelles...... or assembly into large complexes. The vision is that by positioning sequentially acting enzymes in close proximity, the cell can accelerate reaction rates and thereby prevent loss of intermediates through diffusion, degradation or competing pathways. The production of valuable metabolites in cell factories...

Extending the Kawai-Kerman-McVoy Statistical Theory of Nuclear Reactions to Intermediate Structure via Doorways

International Nuclear Information System (INIS)

Arbanas, Goran; Bertulani, C.A.; Dean, D.J.; Kerman, A.K.; Roche, K.J.

2011-01-01

Kawai, Kerman, and McVoy have shown that a statistical treatment of many open channels that are coupled by direct reactions leads to modifications of the Hauser- Feshbach expression for energy-averaged cross section (Ann. of Phys. 75 (1973) 156). The energy averaging interval for this cross section is on the order of the width of single particle resonances, 1MeV, revealing only a gross structure in the cross section. When the energy-averaging interval is decreased down to a width of a doorway state 0.1 MeV, a so-called intermediate structure may be observed in cross sections. We extend the Kawai-Kerman-McVoy theory into the intermediate structure by leveraging a theory of doorway states developed by Feshbach, Kerman, and Lemmer (Ann. of Phys. 42 (1967) 230). As a byproduct of the extension, an alternative derivation of the central result of the Kawai-Kerman-McVoy theory is suggested. We quantify the effect of the approximations used in derivation by performing numerical computations for a large set of compound nuclear states.

Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

DEFF Research Database (Denmark)

Nielsen, Jens Bredal

1997-01-01

Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

Diclofenac degradation in water by FeCeOx catalyzed H2O2: Influencing factors, mechanism and pathways.

Science.gov (United States)

Chong, Shan; Zhang, Guangming; Zhang, Nan; Liu, Yucan; Huang, Ting; Chang, Huazhen

2017-07-15

The degradation of diclofenac in a like Fenton system, FeCeO x -H 2 O 2 , was studied in details. The influencing factors, reaction kinetics, reaction mechanism and degradation pathways of diclofenac were investigated. The optimum conditions were at a solution pH of 5.0, H 2 O 2 concentration of 3.0mmol/L, diclofenac initial concentration of 0.07mmol/L, FeCeO x dosage of 0.5g/L, and 84% degradation of diclofenac was achieved within 40min. The kinetics of FeCeO x catalyzed H 2 O 2 process involved adsorption-dominating and degradation-dominating stages and fitted pseudo-second order model and pseudo-first order model, respectively. Singlet oxygen 1 O 2 was the primary intermediate oxidative species in the degradation process; superoxide radical anion O 2 - also participated in the reaction. The surface cerium and iron sites and the oxygen vacancies in the FeCeO x catalyst were proposed to play an important role in H 2 O 2 decomposition and active species generation. The detected intermediates were identified as hydroxylated derivatives (m/z of 310, 326 and 298), quinone imine compounds (m/z of 308, 278 and 264) and hydroxyl phenylamine (m/z of 178). The majority intermediates were hydroxylated derivatives and the minority was hydroxyl phenylamine. The degradation pathways were proposed to involve hydroxylation, decarboxylation, dehydrogenation and CN bond cleavage. Copyright © 2017 Elsevier B.V. All rights reserved.

Catalytic effect of KF-846 on the reforming of the primary intermediates from the co-pyrolysis of pubescens and LDPE

International Nuclear Information System (INIS)

Liu, Wen-wu; Hu, Chang-wei; Tong, Dong-mei; Yang, Yu; Li, Gui-ying; Zhu, Liang-fang; Tang, Jin-Qiang

2014-01-01

Highlights: • Reforming reactions were inhibited by H 2 , decrease of acidity and low temperature. • There was a synergistic effect on producing hydrogen between Ni and Mo. • The lattice oxygen over catalyst employed might transfer into the intermediates. • Co-pyrolysis, low temperature and N 2 could restrain oxygen transfer to some extent. - Abstract: Co-pyrolysis is regarded as an effective approach to upgrade the quality of pyrolysis products. In this work the activity of KF-846 was evaluated by co-pyrolysis of pubescens and low density polyethylene under different experimental conditions including catalytic mode, pyrolytic atmosphere and temperature, etc. The results showed that the fresh KF-846 exerted strong effects of cyclization, aromatization, hydrogen transfer and vapor-catalytic reforming reactions on the primary intermediates from the co-pyrolysis. The hydrogen-rich gases indicated a synergistic effect between Ni and Mo over KF-846 on producing hydrogen. More importantly, the reforming reactions might be inhibited to some extent by H 2 atmosphere, the low temperature and the decrease of acidity over catalyst. Furthermore, it was deduced that the oxygen over the lattice of catalyst or some intermediates might transfer into other intermediates, possibly resulting in more products with high oxygen content, but it was presumed that the low temperature, co-pyrolysis process and N 2 atmosphere could repress the trend to a certain degree. The mass and energy balance of co-pyrolysis were analyzed, and the main reaction pathways were also proposed. The interference in pyrolysis by regulating the catalytic mode, pyrolytic atmosphere and temperature, acidity over catalyst might posses a certain guiding significance for the pyrolytic technology and the design/selection of catalysts employed

Cross-Aldol Reaction of Activated Carbonyls with Nitrosocarbonyl Intermediates: Stereoselective Synthesis toward α-Hydroxy-β-amino Esters and Amides.

Science.gov (United States)

Mallik, Sumitava; Bhajammanavar, Vinod; Ramakrishna, Isai; Baidya, Mahiuddin

2017-07-21

A practical and flexible strategy toward α-hydroxy-β-amino esters and amides, which are important biological motifs, based on an organocatalytic cross-aldol reaction of in situ-generated nitrosocarbonyl intermediates followed by hydrogenation is presented. The protocol features operational simplicity, high yields, a wide substrate scope, and high regio- and diastereoselectivity profiles. The utility of this method was showcased through the synthesis of bestatin analogues and indole formation.

First-principles calculated decomposition pathways for LiBH4 nanoclusters

Science.gov (United States)

Huang, Zhi-Quan; Chen, Wei-Chih; Chuang, Feng-Chuan; Majzoub, Eric H.; Ozoliņš, Vidvuds

2016-05-01

We analyze thermodynamic stability and decomposition pathways of LiBH4 nanoclusters using grand-canonical free-energy minimization based on total energies and vibrational frequencies obtained from density-functional theory (DFT) calculations. We consider (LiBH4)n nanoclusters with n = 2 to 12 as reactants, while the possible products include (Li)n, (B)n, (LiB)n, (LiH)n, and Li2BnHn; off-stoichiometric LinBnHm (m ≤ 4n) clusters were considered for n = 2, 3, and 6. Cluster ground-state configurations have been predicted using prototype electrostatic ground-state (PEGS) and genetic algorithm (GA) based structural optimizations. Free-energy calculations show hydrogen release pathways markedly differ from those in bulk LiBH4. While experiments have found that the bulk material decomposes into LiH and B, with Li2B12H12 as a kinetically inhibited intermediate phase, (LiBH4)n nanoclusters with n ≤ 12 are predicted to decompose into mixed LinBn clusters via a series of intermediate clusters of LinBnHm (m ≤ 4n). The calculated pressure-composition isotherms and temperature-pressure isobars exhibit sloping plateaus due to finite size effects on reaction thermodynamics. Generally, decomposition temperatures of free-standing clusters are found to increase with decreasing cluster size due to thermodynamic destabilization of reaction products.

Measuring protection of aromatic wine thiols from oxidation by competitive reactions vs wine preservatives with ortho-quinones.

Science.gov (United States)

Nikolantonaki, Maria; Magiatis, Prokopios; Waterhouse, Andrew L

2014-11-15

Quinones are central intermediates in wine oxidation that can degrade the quality of wine by reactions with varietal thiols, such as 3-sulfanylhexanol, decreasing desirable aroma. Protection by wine preservatives (sulphur dioxide, glutathione, ascorbic acid and model tannin, phloroglucinol) was assessed by competitive sacrificial reactions with 4-methyl-1,2-benzoquinone, quantifying products and ratios by HPLC-UV-MS. Regioselectivity was assessed by product isolation and identification by NMR spectroscopy. Nucleophilic addition reactions compete with two electron reduction of quinones by sulphur dioxide or ascorbic acid, and both routes serve as effective quenching pathways, but minor secondary products from coupled redox reactions between the products and reactants are also observed. The wine preservatives were all highly reactive and thus all very protective against 3-sulfanylhexanol loss to the quinone, but showed only additive antioxidant effects. Confirmation of these reaction rates and pathways in wine is needed to assess the actual protective action of each tested preservative. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular weight growth in Titan's atmosphere: branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes.

Science.gov (United States)

Kirk, Benjamin B; Savee, John D; Trevitt, Adam J; Osborn, David L; Wilson, Kevin R

2015-08-28

The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.

Computational Chemical Kinetics for the Reaction of Criegee Intermediate CH2OO with HNO3 and Its Catalytic Conversion to OH and HCO.

Science.gov (United States)

Raghunath, P; Lee, Yuan-Pern; Lin, M C

2017-05-25

The kinetics and mechanisms for the reaction of the Criegee intermediate CH 2 OO with HNO 3 and the unimolecular decomposition of its reaction product CH 2 (O)NO 3 are important in atmospheric chemistry. The potential-energy profile of the reactions predicted with the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ method shows that the initial association yields a prereaction complex that isomerizes by H migration to yield excited intermediate nitrooxymethyl hydroperoxide NO 3 CH 2 OOH* with internal energy ∼44 kcal mol -1 . A fragmentation of this excited intermediate produces CH 2 (O)NO 3 + OH with its transition state located 5.0 kcal mol -1 below that of the reactants. Further decomposition of CH 2 (O)NO 3 produces HCO + HNO 3 , forming a catalytic cycle for destruction of CH 2 OO by HNO 3 . The rate coefficients and product-branching ratios were calculated in the temperature range 250-700 K at pressure 20-760 Torr (N 2 ) using the variational-transition-state and Rice-Ramsperger-Kassel-Marcus (RRKM) theories. The predicted total rate coefficient for reaction CH 2 OO + HNO 3 at 295 K, 5.1 × 10 -10 cm 3 molecule -1 s -1 , agrees satisfactorily with the experimental value, (5.4 ± 1.0) × 10 -10 cm 3 molecule -1 s -1 . The predicted branching ratios at 295 K are 0.21 for the formation of NO 3 CH 2 OOH and 0.79 for CH 2 (O)NO 3 + OH at a pressure of 40 Torr (N 2 ), and 0.79 for the formation of NO 3 CH 2 OOH and 0.21 for CH 2 (O)NO 3 + OH at 760 Torr (N 2 ). This new catalytic conversion of CH 2 OO to HCO + OH by HNO 3 might have significant impact on atmospheric chemistry.

Fluid flow pathways through the oceanic crust: reaction permeability and isotopic tracing

Science.gov (United States)

McCaig, Andrew; Castelain, Teddy; Klein, Frieder

2013-04-01

It is generally assumed that the dominant means of creating permeability in ocean floor hydrothermal systems is fracturing, induced either by cooling or by tectonic stress. Here we show textural evidence that metamorphic reactions can create a hierarchy of permeable pathways through gabbroic rocks similar to a fracture hierarchy. Isotopic microsampling shows that just as with fractures, most flow occurs through the larger channelways, and that even at the microscale, flow can be extremely heterogeneous with alteration affecting only certain minerals in the framework, leaving others untouched. Reaction permeability is created in three ways; dissolution creating open porosity, microcracking due to volume increase reactions involving olivine, and expansion of water due to rapid heating in dyke margins, particularly when intruded into brecciated rocks. Our data comes from IODP Hole U1309D, which was drilled to 1400 mbsf in the footwall of the Atlantis Massif detachment fault at the Mid-Atlantic Ridge 30°N. The core is composed of gabbroic rocks interlayered with olivine rich troctolites, with several basalt/diabase sills in the top 130 m. The dominant alteration occurred in the greenschist facies, at depths at least 1 km below seafloor, and decreases in intensity downhole. Whole rock oxygen isotope values range from +5.5 permil to +1.5 permil, indicating variable degrees of interaction with seawater at temperatures generally > 250 °C. Gabbroic rocks and diabases exhibit a range of Sr isotope ratios from MORB values (0.70261) to intermediate ratios (0.70429). Microsampling shows that amphiboles are often more radiogenic than coexisting plagioclase and can sometimes be isotopically altered in the same rock as completely unaltered primary minerals. Large (10 cm) amphibole-filled vugs show values ranging up to 0.708, close to seawater. In some cases however the secondary minerals are virtually unaltered indicating low fluid fluxes in pervasive alteration. SEM textures in

Process Design and Economics for the Conversion of Lignocellulosic Biomass to Hydrocarbons via Indirect Liquefaction. Thermochemical Research Pathway to High-Octane Gasoline Blendstock Through Methanol/Dimethyl Ether Intermediates

Energy Technology Data Exchange (ETDEWEB)

Tan, E. C. D.; Talmadge, M.; Dutta, A.; Hensley, J.; Schaidle, J.; Biddy, M.; Humbird, D.; Snowden-Swan, L. J.; Ross, J.; Sexton, D.; Yap, R.; Lukas, J.

2015-03-01

This report was developed as part of the U.S. Department of Energy’s Bioenergy Technologies Office’s (BETO’s) efforts to enable the development of technologies for the production of infrastructure-compatible, cost-competitive liquid hydrocarbon fuels from lignocellulosic biomass feedstocks. The research funded by BETO is designed to advance the state of technology of biomass feedstock supply and logistics, conversion, and overall system sustainability. It is expected that these research improvements will be made within the 2022 timeframe. As part of their involvement in this research and development effort, the National Renewable Energy Laboratory and the Pacific Northwest National Laboratory investigate the economics of conversion pathways through the development of conceptual biorefinery process models and techno-economic analysis models. This report describes in detail one potential conversion process for the production of high-octane gasoline blendstock via indirect liquefaction of biomass. The processing steps of this pathway include the conversion of biomass to synthesis gas or syngas via indirect gasification, gas cleanup, catalytic conversion of syngas to methanol intermediate, methanol dehydration to dimethyl ether (DME), and catalytic conversion of DME to high-octane, gasoline-range hydrocarbon blendstock product. The conversion process configuration leverages technologies previously advanced by research funded by BETO and demonstrated in 2012 with the production of mixed alcohols from biomass. Biomass-derived syngas cleanup via reforming of tars and other hydrocarbons is one of the key technology advancements realized as part of this prior research and 2012 demonstrations. The process described in this report evaluates a new technology area for the downstream utilization of clean biomass-derived syngas for the production of high-octane hydrocarbon products through methanol and DME intermediates. In this process, methanol undergoes dehydration to

Kinetics of the glucose/glycine Maillard reaction pathways: influences of pH and reactant initial concentrations

NARCIS (Netherlands)

Martins, S.I.F.S.; Boekel, van M.A.J.S.

2005-01-01

A previously proposed kinetic model for the glucose/glycine Maillard reaction pathways has been validated by changing the initial pH (4.8, 5.5, 6.0, 6.8 and 7.5) of the reaction and reactant initial concentrations (1:2 and 2:1 molar ratios were compared to the 1:1 ratio). The model consists of 10

Sequential reduction–oxidation for photocatalytic degradation of tetrabromobisphenol A: Kinetics and intermediates

International Nuclear Information System (INIS)

Guo, Yaoguang; Lou, Xiaoyi; Xiao, Dongxue; Xu, Lei; Wang, Zhaohui; Liu, Jianshe

2012-01-01

Highlights: ► Sequential photocatalytic reduction–oxidation degradation of TBBPA was firstly examined. ► Different atmospheres were found to have significant effect on debromination reaction. ► A possible sequential photocatalytic reduction–oxidation pathway was proposed. - Abstract: C-Br bond cleavage is considered as a key step to reduce their toxicities and increase degradation rates for most brominated organic pollutants. Here a sequential reduction/oxidation strategy (i.e. debromination followed by photocatalytic oxidation) for photocatalytic degradation of tetrabromobisphenol A (TBBPA), one of the most frequently used brominated flame retardants, was proposed on the basis of kinetic analysis and intermediates identification. The results demonstrated that the rates of debromination and even photodegradation of TBBPA strongly depended on the atmospheres, initial TBBPA concentrations, pH of the reaction solution, hydrogen donors, and electron acceptors. These kinetic data and byproducts identification obtained by GC–MS measurement indicated that reductive debromination reaction by photo-induced electrons dominated under N 2 -saturated condition, while oxidation reaction by photoexcited holes or hydroxyl radicals played a leading role when air was saturated. It also suggested that the reaction might be further optimized for pretreatment of TBBPA-contaminated wastewater by a two-stage reductive debromination/subsequent oxidative decomposition process in the UV-TiO 2 system by changing the reaction atmospheres.

Does shoe heel design influence ground reaction forces and knee moments during maximum lunges in elite and intermediate badminton players?

Science.gov (United States)

Lam, Wing-Kai; Ryue, Jaejin; Lee, Ki-Kwang; Park, Sang-Kyoon; Cheung, Jason Tak-Man; Ryu, Jiseon

2017-01-01

Lunge is one frequently executed movement in badminton and involves a unique sagittal footstrike angle of more than 40 degrees at initial ground contact compared with other manoeuvres. This study examined if the shoe heel curvature design of a badminton shoe would influence shoe-ground kinematics, ground reaction forces, and knee moments during lunge. Eleven elite and fifteen intermediate players performed five left-forward maximum lunge trials with Rounded Heel Shoe (RHS), Flattened Heel Shoe (FHS), and Standard Heel Shoes (SHS). Shoe-ground kinematics, ground reaction forces, and knee moments were measured by using synchronized force platform and motion analysis system. A 2 (Group) x 3 (Shoe) ANOVA with repeated measures was performed to determine the effects of different shoes and different playing levels, as well as the interaction of two factors on all variables. Shoe effect indicated that players demonstrated lower maximum vertical loading rate in RHS than the other two shoes (P badminton lunge. The differences in impact loads and knee moments between elite and intermediate players may be useful in optimizing footwear design and training strategy to minimize the potential risks for impact related injuries in badminton.

Bioorthogonal Cycloadditions with Sub-Millisecond Intermediates.

Science.gov (United States)

Qing, Yujia; Pulcu, Gökçe Su; Bell, Nicholas A W; Bayley, Hagan

2018-01-26

Tetrazine- and sydnone-based click reactions have emerged as important bioconjugation strategies with fast kinetics and N 2 or CO 2 as the only byproduct. Mechanistic studies of these reactions have focused on the initial rate-determining cycloaddition steps. The subsequent N 2 or CO 2 release from the bicyclic intermediates has been approached mainly through computational studies, which have predicted lifetimes of femtoseconds. In the present study, bioorthogonal cycloadditions involving N 2 or CO 2 extrusion have been examined experimentally at the single-molecule level by using a protein nanoreactor. At the resolution of this approach, the reactions appeared to occur in a single step, which places an upper limit on the lifetimes of the intermediates of about 80 μs, which is consistent with the computational work. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The adsorption and reaction of halogenated volatile organic compounds (VOC's) on metal oxides. 1998 annual progress report

International Nuclear Information System (INIS)

Goodman, D.W.; Haw, J.F.; Lunsford, J.

1998-01-01

'The goal of the research is to elucidate the properties of the materials responsible for the activation of halocarbons and the nature of the intermediates formed in the dissociative adsorption of this class of compounds. This information is essential for interpreting and predicting stoichiometric and catalytic pathways for the safe destruction of halocarbon pollutants. The specific objectives are: (1) to study the adsorption and reactivity of chloromethanes and chloroethanes on metal oxides; (2) to identify the reaction intermediates using spectroscopic methods; and (3) to develop kinetic models for the reaction of these halocarbons with oxide surfaces. This report summarizes work after 20 months of a 36-month project. Emphasis has been placed understanding the surfaces phases, as well as the bulk phases that are present during the reactions of chlorinated hydrocarbons with strongly basic metal oxides. Most of the research has been carried out with carbon tetrachloride.'

A Density Functional Theory Study on the Reaction Mechanism of Terpinolene with O{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Kim, Hahkjoon [Duksung Women' s University, Seoul (Korea, Republic of)

2016-02-15

The energies of chemical species involved in the early stage of the reaction of terpinolene with ozone were calculated to understand the oxidation mechanism of terpinolene with atmospheric O{sub 2} and NO determined experimentally. All the quantum calculations for geometry optimization and frequency calculations in this study were carried out using B3LYP with the 6-31G(d,p) basis (Gaussian 03 software package). In conclusion, quantum chemical calculations were performed to obtain the relative energies and energy barriers for the early stage of the reaction pathways of terpinolene with ozone. The branching ratio for pathways 3 and 4 determined experimentally is in qualitative agreement with the current calculations. The results of these calculations are important for assessing the relative stabilities of the intermediates in the reaction of terpinolene with ozone although detailed RRKM calculations are still needed to fully understand the branching ratios of the final products.

The major/minor concept: dependence of the selectivity of homogeneously catalyzed reactions on reactivity ratio and concentration ratio of the intermediates.

Science.gov (United States)

Schmidt, Thomas; Dai, Zhenya; Drexler, Hans-Joachim; Hapke, Marko; Preetz, Angelika; Heller, Detlef

2008-07-07

The homogeneously catalyzed asymmetric hydrogenation of prochiral olefins with cationic Rh(I) complexes is one of the best-understood selection processes. For some of the catalyst/substrate complexes, experimental proof points out the validation of the major/minor principle; the concentration-deficient minor substrate complex, which has very high reactivity, yields the excess enantiomer. As exemplified by the reaction system of [Rh(dipamp)(MeOH)2]+/methyl (Z)-alpha-acetamidocinnamate (dipamp=1,2-bis((o-methoxyphenyl)phenylphosphino)ethane), all six of the characteristic reaction rate constants have been previously identified. Recently, it was found that the major substrate complex can also yield the major enantiomer (lock-and-key principle). The differential equation system that results from the reaction sequence can be solved numerically for different hydrogen partial pressures by including the known equilibrium constants. The result displays the concentration-time dependence of all species that exist in the catalytic cycle. On the basis of the known constants as well as further experimental evidence, this work focuses on the examination of all principal possibilities resulting from the reaction sequence and leading to different results for the stereochemical outcome. From the simulation, the following conclusions can be drawn: 1) When an intermediate has extreme reactivity, its stationary concentration can become so small that it can no longer be the source of product selectivity; 2) in principle, the major/minor and lock-and-key principles can coexist depending on the applied pressure; 3) thermodynamically determined intermediate ratios can be completely converted under reaction conditions for a selection process; and 4) the increase in enantioselectivity with increasing hydrogen partial pressure, a phenomenon that is experimentally proven but theoretically far from being well-understood, can be explained by applying both the lock-and-key as well as the major

Bonding pathways of high-pressure chemical transformations

International Nuclear Information System (INIS)

Hu Anguang; Zhang Fan

2013-01-01

A three-stage bonding pathway towards high-pressure chemical transformations from molecular precursors or intermediate states has been identified by first-principles simulations. With the evolution of principal stress tensor components in the response of chemical bonding to compressive loading, the three stages can be defined as the van der Waals bonding destruction, a bond breaking and forming reaction, and equilibrium of new bonds. The three-stage bonding pathway leads to the establishment of a fundamental principle of chemical bonding under compression. It reveals that during high-pressure chemical transformation, electrons moving away from functional groups follow anti-addition, collision-free paths to form new bonds in counteracting the local stress confinement. In applying this principle, a large number of molecular precursors were identified for high-pressure chemical transformations, resulting in new materials. (fast track communication)

Density functional theory study on water-gas-shift reaction over molybdenum disulfide

DEFF Research Database (Denmark)

Shi, X. R.; Wang, Shengguang; Hu, J.

2009-01-01

. The pathway for water-gas-shift reaction on both terminations has been carefully studied where the most favorable reaction path precedes the redox mechanism, namely the reaction takes place as follows: CO + H2O --> CO + OH + H --> CO + O + 2H --> CO2 + H-2. The most likely reaction candidates for the formate......Density functional theory calculations have been carried out to investigate the adsorption of reaction intermediates appearing during water-gas-shift reaction at the sulfur covered MoS2 (1 0 0)surfaces, Mo-termination with 37.5% S coverage and S-termination with 50% S coverage using periodic slabs...... species HCOO formation is the surface CO2 reaction with H as a side reaction of CO2 desorption on S-termination with 50% S coverage. The formed HCOO species will react further with adsorbed hydrogen yielding H2COO followed by breaking its C-O bond to form the surface CH2O and O species....

Traumatic Brain Injury Pathophysiology and Treatments: Early, Intermediate, and Late Phases Post-Injury

Science.gov (United States)

Algattas, Hanna; Huang, Jason H.

2014-01-01

Traumatic Brain Injury (TBI) affects a large proportion and extensive array of individuals in the population. While precise pathological mechanisms are lacking, the growing base of knowledge concerning TBI has put increased emphasis on its understanding and treatment. Most treatments of TBI are aimed at ameliorating secondary insults arising from the injury; these insults can be characterized with respect to time post-injury, including early, intermediate, and late pathological changes. Early pathological responses are due to energy depletion and cell death secondary to excitotoxicity, the intermediate phase is characterized by neuroinflammation and the late stage by increased susceptibility to seizures and epilepsy. Current treatments of TBI have been tailored to these distinct pathological stages with some overlap. Many prophylactic, pharmacologic, and surgical treatments are used post-TBI to halt the progression of these pathologic reactions. In the present review, we discuss the mechanisms of the pathological hallmarks of TBI and both current and novel treatments which target the respective pathways. PMID:24381049

Electrochemical mineralization pathway of quinoline by boron-doped diamond anodes.

Science.gov (United States)

Wang, Chunrong; Ma, Keke; Wu, Tingting; Ye, Min; Tan, Peng; Yan, Kecheng

2016-04-01

Boron-doped diamond anodes were selected for quinoline mineralization, and the resulting intermediates, phenylpropyl aldehyde, phenylpropionic acid, and nonanal were identified and followed during quinoline oxidation by gas chromatography-mass spectrometry and high-performance liquid chromatography. The evolutions of formic acid, acetic acid, oxalic acid, NO2(-), NO3(-), and NH4(+) were quantified. A new reaction pathway for quinoline mineralization by boron-doped diamond anodes has been proposed, where the pyridine ring in quinoline is cleaved by a hydroxyl radical giving phenylpropyl aldehyde and NH4(+). Phenylpropyl aldehyde is quickly oxidized into phenylpropionic acid, and the benzene ring is cleaved giving nonanal. This is further oxidized to formic acid, acetic acid, and oxalic acid. Finally, these organic intermediates are mineralized to CO2 and H2O. NH4(+) is also oxidized to NO2(-) and on to NO3(-). The results will help to gain basic reference for clearing intermediates and their toxicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reaction of H2 with O2 in Excited Electronic States: Reaction Pathways and Rate Constants.

Science.gov (United States)

Pelevkin, Alexey V; Loukhovitski, Boris I; Sharipov, Alexander S

2017-12-21

Comprehensive quantum chemical analysis with the use of the multireference state-averaged complete active space self-consistent field approach was carried out to study the reactions of H 2 with O 2 in a 1 Δ g , b 1 Σ g + , c 1 Σ u - , and A' 3 Δ u electronically excited states. The energetically favorable reaction pathways and possible intersystem crossings have been revealed. The energy barriers were refined employing the extended multiconfiguration quasi-degenerate second-order perturbation theory. It has been shown that the interaction of O 2 (a 1 Δ g ) and O 2 (A' 3 Δ u ) with H 2 occurs through the H-abstraction process with relatively low activation barriers that resulted in the formation of the HO 2 molecule in A″ and A' electronic states, respectively. Meanwhile, molecular oxygen in singlet sigma states (b 1 Σ g + and c 1 Σ u - ) was proved to be nonreactive with respect to the molecular hydrogen. Appropriate rate constants for revealed reaction and quenching channels have been estimated using variational transition-state theory including corrections for the tunneling effect, possible nonadiabatic transitions, and anharmonicity of vibrations for transition states and reactants. It was demonstrated that the calculated reaction rate constant for the H 2 + O 2 (a 1 Δ g ) process is in reasonable agreement with known experimental data. The Arrhenius approximations for these processes have been proposed for the temperature range T = 300-3000 K.

Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

Science.gov (United States)

Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

2007-01-01

A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

Isoporphyrin Intermediate in Heme Oxygenase Catalysis

Science.gov (United States)

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

2008-01-01

Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the α-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin π-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of α-meso-phenylheme-IX, α-meso-(p-methylphenyl)-mesoheme-III, and α-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 α-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 α-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

The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism.

Science.gov (United States)

Igamberdiev, Abir U; Kleczkowski, Leszek A

2018-01-01

Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

Intermediate behaviour of reaction mechanisms in 27Al + 63Cu collisions at 13.4 MeV/nucleon

International Nuclear Information System (INIS)

Bougault, R.

1983-09-01

This experiment aimed to investigate the nuclear reaction mechanisms in the energy transition region between 10 and 20 MeV/Nucleon. So, collisions between 27 Al (projectile) and 63 Cu (target) were studied for a bombarding energy of 13.4 MeV/nucleon. For that purpose, projectile-like fragments were detected at the grazing angle (thetasub(g)) for that system by a spectrometer and an E-ΔE telescope. A second telescope was set at various angles for light particle detection; both inclusive and coincident measurements were performed. Isotope production at angle thetasub(g) cannot be clearly explained neither by inelastic transfers nor by ''cold'' projectile fragmentation. This production seems rather to occur through an intermediate process where the Al nucleus is slowed down, and excited, and then dissociates. Moreover, kinematical correlations between fragments show evidence for a mechanism where the projectile is splitted after picking up some nucleons to the target. Finally, light particles are shown to araise essentially from a fusion-like system thermalized at T=3,5 MeV; such a temperature may be considered as an intermediate value [fr

Study of the optimal reaction conditions for assay of the mouse alternative complement pathway

NARCIS (Netherlands)

Dijk, H. van; Rademaker, P.M.; Klerx, J.P.A.M.; Willers, J.M.M.

1985-01-01

The optimal reaction conditions for hemolytic assay of alternative complement pathway activity in mouse serum were investigated. A microtiter system was used, in which a number of 7.5×106 rabbit erythrocytes per test well appeared to be optimal. Rabbit erythrocytes were superior as target cells over

Surface intermediates on metal electrodes at high temperatures

DEFF Research Database (Denmark)

Zachau-Christiansen, Birgit; Jacobsen, Torben; Bay, Lasse

1998-01-01

The mechanisms widely conceived for the O(2)-reduction or H(2)-oxidation reactions in SOFC's involve intermediate O/H species adsorbed on the electrode surface. The presence of these intermediates is investigated by linear sweep voltammetry. In air at moderate temperatures (500 degrees C) Pt...

Theoretical study of the decomposition pathways and products of C5- perfluorinated ketone (C5 PFK)

Energy Technology Data Exchange (ETDEWEB)

Fu, Yuwei; Wang, Xiaohua, E-mail: xhw@mail.xjtu.edu.cn, E-mail: mzrong@mail.xjtu.edu.cn; Li, Xi; Yang, Aijun; Wu, Yi; Rong, Mingzhe, E-mail: xhw@mail.xjtu.edu.cn, E-mail: mzrong@mail.xjtu.edu.cn [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 XianNing West Road, Xi’an, Shaanxi Province 710049 (China); Han, Guohui; Lu, Yanhui [Pinggao Group Co. Ltd., Pingdingshan, Henan Province 467001 (China)

2016-08-15

Due to the high global warming potential (GWP) and increasing environmental concerns, efforts on searching the alternative gases to SF{sub 6}, which is predominantly used as insulating and interrupting medium in high-voltage equipment, have become a hot topic in recent decades. Overcoming the drawbacks of the existing candidate gases, C5- perfluorinated ketone (C5 PFK) was reported as a promising gas with remarkable insulation capacity and the low GWP of approximately 1. Experimental measurements of the dielectric strength of this novel gas and its mixtures have been carried out, but the chemical decomposition pathways and products of C5 PFK during breakdown are still unknown, which are the essential factors in evaluating the electric strength of this gas in high-voltage equipment. Therefore, this paper is devoted to exploring all the possible decomposition pathways and species of C5 PFK by density functional theory (DFT). The structural optimizations, vibrational frequency calculations and energy calculations of the species involved in a considered pathway were carried out with DFT-(U)B3LYP/6-311G(d,p) method. Detailed potential energy surface was then investigated thoroughly by the same method. Lastly, six decomposition pathways of C5 PFK decomposition involving fission reactions and the reactions with a transition states were obtained. Important intermediate products were also determined. Among all the pathways studied, the favorable decomposition reactions of C5 PFK were found, involving C-C bond ruptures producing Ia and Ib in pathway I, followed by subsequent C-C bond ruptures and internal F atom transfers in the decomposition of Ia and Ib presented in pathways II + III and IV + V, respectively. Possible routes were pointed out in pathway III and lead to the decomposition of IIa, which is the main intermediate product found in pathway II of Ia decomposition. We also investigated the decomposition of Ib, which can undergo unimolecular reactions to give the

Intermediate nuclear structure for 2ν2β decay of 48Ca studied by (p, n) and (n, p) reactions at 300 MeV

International Nuclear Information System (INIS)

Sakai, H.; Yako, K.

2009-01-01

The two neutrino double beta (2ν2β) decay proceeds through a sequence of Gamow-Teller (GT) transitions, namely from the parent nucleus to the intermediate nucleus and then from the intermediate nucleus to the final daughter nucleus. The nuclear matrix element M 2ν for the 2ν2β - decay thus consists of the 2β - decay matrix elements for the parent nucleus decay and the 2β - decay matrix elements for the intermediate nucleus decay. These 2β - decay matrix elements can be studied experimentally through the (p, n) reaction for the parent nucleus decay and the (n, p) reaction for the intermediate nucleus decay. The 2ν2β-decay nucleus, 4 8C a is studied. The charge exchange (p, n) and (n, p) measurements at 300 MeV were performed using the neutron time-of-flight facility and the (n,p) facility, respectively, at RCNP. The (p, n) measurement on 4 8C a and the (n,p) measurement on 4 8T i provided us, for the first time, reliable B(GT - ) and B(GT + ) strength distributions up to high excitation energy of 30 MeV of the intermediate nucleus 4 8S c. The multipole decomposition analysis was applied to the angular distributions of the cross section spectra to extract the ΔL = 0 components, which are used to deduce B(GT ± ). Figure shows the double differential cross Nb sections for 4 8C a(p, n)4 8S c (left panel) and 4 8T i(n,p)4 8S c (right panel) reactions. The histograms show the results of the multi-pole decomposition analyses. It is very surprising to find sizable amount of ΔL = 0 yield, i.e. B(GT + ) strength in the highly excited energy region (> 10 MeV). The obtained B(GT ± ) distribution in 4 8S c as well as corresponding nuclear matrix elements M 2ν are compared with theoretical shell model calculation. In this talk, new results will be presented and their implication to the nuclear matrix elements for the 2ν2β-decay will be discussed (author)

Reaction pathway towards formation of cobalt single chain magnets and nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Balaji, G.; Desilva, Rohini M.; Palshin, V. [Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806 (United States); Desilva, N. [Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 (United States); Palmer, G. [Department of Biochemistry and Cell Biology, Rice University, MS 140, 6100 Main street, Houston, TX 77251 (United States); Kumar, Challa S.S.R., E-mail: ckumar1@lsu.ed [Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806 (United States)

2010-03-15

With the advent of molecular magnets the quest for suitable high density magnetic storage materials has fuelled further research in this area. Here in this report, we present a detailed mechanistic investigation of thermal decomposition of cyclopentadienyl cobalt [CoCp(CO){sub 2}] precursor where Cp is the cyclopentadienyl moiety. The reaction revealed the formation of cobalt nanoparticles (Co-NPs) through an isolable reaction intermediate characterized as a Single Chain Magnet (SCM), [Co(Cp){sub 2}]{sub 2}CoCl{sub 4} (1). The SQUID magnetic measurements showed the presence of very strong antiferromagnetic interactions between Co{sup 2+} ions. The zero-field cooled (ZFC) and field cooled (FC) magnetization curves branch out below 5 K and there is evidence for frequency dependent complex susceptibility along with a maximum observed around 2.5 K. The optical studies indicated that the Co{sup 2+} d-d transition is influenced by the polarity of the solvents. The cobalt nanoparticles (Co-NPs) were obtained, either directly from 1 or from its precursor. They are spherical in shape with a mean size 15 nm, have fcc crystal structure and were found to be ferromagnetic at room temperature.

A Western blot-based investigation of the yeast secretory pathway designed for an intermediate-level undergraduate cell biology laboratory.

Science.gov (United States)

Hood-Degrenier, Jennifer K

2008-01-01

The movement of newly synthesized proteins through the endomembrane system of eukaryotic cells, often referred to generally as the secretory pathway, is a topic covered in most intermediate-level undergraduate cell biology courses. An article previously published in this journal described a laboratory exercise in which yeast mutants defective in two distinct steps of protein secretion were differentiated using a genetic reporter designed specifically to identify defects in the first step of the pathway, the insertion of proteins into the endoplasmic reticulum (Vallen, 2002). We have developed two versions of a Western blotting assay that serves as a second way of distinguishing the two secretory mutants, which we pair with the genetic assay in a 3-wk laboratory module. A quiz administered before and after students participated in the lab activities revealed significant postlab gains in their understanding of the secretory pathway and experimental techniques used to study it. A second survey administered at the end of the lab module assessed student perceptions of the efficacy of the lab activities; the results of this survey indicated that the experiments were successful in meeting a set of educational goals defined by the instructor.

Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

Science.gov (United States)

Jin, Biao; Rolle, Massimo

2016-04-01

Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M

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

International Nuclear Information System (INIS)

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

2015-01-01

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH 2 OO and anti/syn-CH 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 2 OO and anti-CH 3 C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH 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 3 C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH 3 group by the terminal O atom producing CH 2 C(H)O–OH. At 298 K, the intramolecular insertion process in CH 2 OO was found to be 600 times faster than the commonly assumed ring-closing reaction

Reactivity of Criegee Intermediates toward Carbon Dioxide.

Science.gov (United States)

Lin, Yen-Hsiu; Takahashi, Kaito; Lin, Jim Jr-Min

2018-01-04

Recent theoretical work by Kumar and Francisco suggested that the high reactivity of Criegee intermediates (CIs) could be utilized for designing efficient carbon capture technologies. Because the anti-CH 3 CHOO + CO 2 reaction has the lowest barrier in their study, we chose to investigate it experimentally. We probed anti-CH 3 CHOO with its strong UV absorption at 365 nm and measured the rate coefficient to be ≤2 × 10 -17 cm 3 molecule -1 s -1 at 298 K, which is consistent with our theoretical value of 2.1 × 10 -17 cm 3  molecule -1 s -1 at the QCISD(T)/CBS//B3LYP/6-311+G(2d,2p) level but inconsistent with their results obtained at the M06-2X/aug-cc-pVTZ level, which tends to underestimate the barrier heights. The experimental result indicates that the reaction of a Criegee intermediate with atmospheric CO 2 (400 ppmv) would be inefficient (k eff < 0.2 s -1 ) and cannot compete with other decay processes of Criegee intermediates like reactions with water vapor (∼10 3 s -1 ) or thermal decomposition (∼10 2 s -1 ).

Stabilization of the second oxyanion intermediate by 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase of the menaquinone pathway: spectroscopic evidence of the involvement of a conserved aspartic acid.

Science.gov (United States)

Chen, Minjiao; Jiang, Ming; Sun, Yueru; Guo, Zu-Feng; Guo, Zhihong

2011-07-05

1,4-Dihydroxy-2-naphthoyl-coenzyme A (DHNA-CoA) synthase, or MenB, catalyzes an intramolecular Claisen condensation involving two oxyanion intermediates in the biosynthetic pathway of menaquinone, an essential respiration electron transporter in many microorganisms. Here we report the finding that the DHNA-CoA product and its analogues bind and inhibit the synthase from Escherichia coli with significant ultraviolet--visible spectral changes, which are similar to the changes induced by deprotonation of the free inhibitors in a basic solution. Dissection of the structure--affinity relationships of the inhibitors identifies the hydroxyl groups at positions 1 (C1-OH) and 4 (C4-OH) of DHNA-CoA or their equivalents as the dominant and minor sites, respectively, for the enzyme--ligand interaction that polarizes or deprotonates the bound ligands to cause the observed spectral changes. In the meantime, spectroscopic studies with active site mutants indicate that C4-OH of the enzyme-bound DHNA-CoA interacts with conserved polar residues Arg-91, Tyr-97, and Tyr-258 likely through a hydrogen bonding network that also includes Ser-161. In addition, site-directed mutation of the conserved Asp-163 to alanine causes a complete loss of the ligand binding ability of the protein, suggesting that the Asp-163 side chain is most likely hydrogen-bonded to C1-OH of DHNA-CoA to provide the dominant polarizing effect. Moreover, this mutation also completely eliminates the enzyme activity, strongly supporting the possibility that the Asp-163 side chain provides a strong stabilizing hydrogen bond to the tetrahedral oxyanion, which takes a position similar to that of C1-OH of the enzyme-bound DHNA-CoA and is the second high-energy intermediate in the intracellular Claisen condensation reaction. Interestingly, both Arg-91 and Tyr-97 are located in a disordered loop forming part of the active site of all available DHNA-CoA synthase structures. Their involvement in the interaction with the small

Surface Intermediates on Metal Electrodes at High Temperature

DEFF Research Database (Denmark)

Zachau-Christiansen, Birgit; Jacobsen, Torben; Bay, Lasse

1997-01-01

The mechanisms widely suggested for the O2-reduc-tion or H2-oxidation SOFC reactions involve inter-mediate O/H species adsorbed on the electrode surface. The presence of these intermediates is investigated by linear sweep voltammetry. In airat moderate temperatures (500øC) Pt in contact with YSZ...

Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP.

Science.gov (United States)

Alvarado, Omar; Jaña, Gonzalo; Delgado, Eduardo J

2012-08-01

In this study the formation of the lactyl-thiamin diphosphate intermediate (L-ThDP) is addressed using density functional theory calculations at X3LYP/6-31++G(d,p) level of theory. The study includes potential energy surface scans, transition state search, and intrinsic reaction coordinate calculations. Reactivity is analyzed in terms of Fukui functions. The results allow to conclude that the reaction leading to the formation of L-ThDP occurs via a concerted mechanism, and during the nucleophilic attack on the pyruvate molecule, the ylide is in its AP form. The calculated activation barrier for the reaction is 19.2 kcal/mol, in agreement with the experimental reported value.

Role of interference of states of intermediate nuclei in exchange processes

International Nuclear Information System (INIS)

Belyaeva, T.L.; Zelenskaya, N.S.; Teplov, I.B.

1982-01-01

Role of interference of intermediate nucleus states for exchange processes in reactions with alpha particles on 11 B, 7 Li and 6 Li light nuclei was investigated when considering exactly the process dynamics in the method of distorted waves with a finite interaction radius. The process dynamics, in particular, the overlapping degree of wave functions of bound states and interaction potentials, affects considerably the reaction cross section in the rections with alpha particles on nuclei of 1p shell. If in the reaction selection rules permit the excitation of components of intermediate system states with maximum values of #betta# 1 and #betta# 2 orbital moments at the given N 1 and N 2 , the contribution of such components to the cross section will be determining. When components of intermediate system states with maximum #betta# 1 (or #betta# 2 ) are forbidden with selection rules, several intermediate states can have approximately similar overlapping integrals

Methane coupling reaction in an oxy-steam stream through an OH radical pathway by using supported alkali metal catalysts

KAUST Repository

Liang, Yin

2014-03-24

A universal reaction mechanism involved in the oxidative coupling of methane (OCM) is demonstrated under oxy-steam conditions using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from a H 2O-O2 reaction followed by C-H activation in CH 4 with an OH radical. Thus, the presence of water enhances both the CH4 conversion rate and the C2 selectivity. This OH radical pathway that is selective for the OCM was observed for the catalyst without Mn, which suggests clearly that Mn is not the essential component in a selective OCM catalyst. The experiments with different catalyst compositions revealed that the OH.-mediated pathway proceeded in the presence of catalysts with different alkali metals (Na, K) and different oxo anions (W, Mo). This difference in catalytic activity for OH radical generation accounts for the different OCM selectivities. As a result, a high C2 yield is achievable by using Na2WO4/SiO2, which catalyzes the OH.-mediated pathway selectively. Make it methane: A universal reaction mechanism involved in the oxidative coupling of methane is demonstrated under oxy-stream conditions by using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from an H2O-O2 reaction, followed by C-H activation in CH4 with an OH radical. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Primary photodissociation pathways of epichlorohydrin and analysis of the C-C bond fission channels from an O(3P)+allyl radical intermediate

International Nuclear Information System (INIS)

FitzPatrick, Benjamin L.; Alligood, Bridget W.; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim Jr-Min

2010-01-01

This study initially characterizes the primary photodissociation processes of epichlorohydrin, c-(H 2 COCH)CH 2 Cl. The three dominant photoproduct channels analyzed are c-(H 2 COCH)CH 2 +Cl, c-(H 2 COCH)+CH 2 Cl, and C 3 H 4 O+HCl. In the second channel, the c-(H 2 COCH) photofission product is a higher energy intermediate on C 2 H 3 O global potential energy surface and has a small isomerization barrier to vinoxy. The resulting highly vibrationally excited vinoxy radicals likely dissociate to give the observed signal at the mass corresponding to ketene, H 2 CCO. The final primary photodissociation pathway HCl+C 3 H 4 O evidences a recoil kinetic energy distribution similar to that of four-center HCl elimination in chlorinated alkenes, so is assigned to production of c-(H 2 COC)=CH 2 ; the epoxide product is formed with enough vibrational energy to isomerize to acrolein and dissociate. The paper then analyzes the dynamics of the C 3 H 5 O radical produced from C-Cl bond photofission. When the epoxide radical photoproduct undergoes facile ring opening, it is the radical intermediate formed in the O( 3 P)+allyl bimolecular reaction when the O atom adds to an end C atom. We focus on the HCO+C 2 H 4 and H 2 CO+C 2 H 3 product channels from this radical intermediate in this report. Analysis of the velocity distribution of the momentum-matched signals from the HCO+C 2 H 4 products at m/e=29 and 28 shows that the dissociation of the radical intermediate imparts a high relative kinetic energy, peaking near 20 kcal/mol, between the products. Similarly, the energy imparted to relative kinetic energy in the H 2 CO+C 2 H 3 product channel of the O( 3 P)+allyl radical intermediate also peaks at high-recoil kinetic energies, near 18 kcal/mol. The strongly forward-backward peaked angular distributions and the high kinetic energy release result from tangential recoil during the dissociation of highly rotationally excited nascent radicals formed photolytically in this experiment

Primary photodissociation pathways of epichlorohydrin and analysis of the C-C bond fission channels from an O(3P)+allyl radical intermediate

Science.gov (United States)

FitzPatrick, Benjamin L.; Alligood, Bridget W.; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim-Min, Jr.

2010-09-01

This study initially characterizes the primary photodissociation processes of epichlorohydrin, c-(H2COCH)CH2Cl. The three dominant photoproduct channels analyzed are c-(H2COCH)CH2+Cl, c-(H2COCH)+CH2Cl, and C3H4O+HCl. In the second channel, the c-(H2COCH) photofission product is a higher energy intermediate on C2H3O global potential energy surface and has a small isomerization barrier to vinoxy. The resulting highly vibrationally excited vinoxy radicals likely dissociate to give the observed signal at the mass corresponding to ketene, H2CCO. The final primary photodissociation pathway HCl+C3H4O evidences a recoil kinetic energy distribution similar to that of four-center HCl elimination in chlorinated alkenes, so is assigned to production of c-(H2COC)=CH2; the epoxide product is formed with enough vibrational energy to isomerize to acrolein and dissociate. The paper then analyzes the dynamics of the C3H5O radical produced from C-Cl bond photofission. When the epoxide radical photoproduct undergoes facile ring opening, it is the radical intermediate formed in the O(P3)+allyl bimolecular reaction when the O atom adds to an end C atom. We focus on the HCO+C2H4 and H2CO+C2H3 product channels from this radical intermediate in this report. Analysis of the velocity distribution of the momentum-matched signals from the HCO+C2H4 products at m/e=29 and 28 shows that the dissociation of the radical intermediate imparts a high relative kinetic energy, peaking near 20 kcal/mol, between the products. Similarly, the energy imparted to relative kinetic energy in the H2CO+C2H3 product channel of the O(P3)+allyl radical intermediate also peaks at high-recoil kinetic energies, near 18 kcal/mol. The strongly forward-backward peaked angular distributions and the high kinetic energy release result from tangential recoil during the dissociation of highly rotationally excited nascent radicals formed photolytically in this experiment. The data also reveal substantial branching to an HCCH+H3

Flavin-N5 Covalent Intermediate in a Nonredox Dehalogenation Reaction Catalyzed by an Atypical Flavoenzyme.

Science.gov (United States)

Dai, Yumin; Kizjakina, Karina; Campbell, Ashley C; Korasick, David A; Tanner, John J; Sobrado, Pablo

2018-01-04

The flavin-dependent enzyme 2-haloacrylate hydratase (2-HAH) catalyzes the conversion of 2-chloroacrylate, a major component in the manufacture of acrylic polymers, to pyruvate. The enzyme was expressed in Escherichia coli, purified, and characterized. 2-HAH was shown to be monomeric in solution and contained a non-covalent, yet tightly bound, flavin adenine dinucleotide (FAD). Although the catalyzed reaction was redox-neutral, 2-HAH was active only in the reduced state. A covalent flavin-substrate intermediate, consistent with the flavin-acrylate iminium ion, was trapped with cyanoborohydride and characterized by mass spectrometry. Small-angle X-ray scattering was consistent with 2-HAH belonging to the succinate dehydrogenase/fumarate reductase family of flavoproteins. These studies establish 2-HAH as a novel noncanonical flavoenzyme. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions.

Science.gov (United States)

Netto, Luis Eduardo S; de Oliveira, Marcos Antonio; Tairum, Carlos A; da Silva Neto, José Freire

2016-01-01

Thiol-disulfide exchange reactions are highly reversible, displaying nucleophilic substitutions mechanism (S(N)2 type). For aliphatic, low molecular thiols, these reactions are slow, but can attain million times faster rates in enzymatic processes. Thioredoxin (Trx) proteins were the first enzymes described to accelerate thiol-disulfide exchange reactions and their high reactivity is related to the high nucleophilicity of the attacking thiol. Substrate specificity in Trx is achieved by several factors, including polar, hydrophobic, and topological interactions through a groove in the active site. Glutaredoxin (Grx) enzymes also contain the Trx fold, but they do not share amino acid sequence similarity with Trx. A conserved glutathione binding site is a typical feature of Grx that can reduce substrates by two mechanisms (mono and dithiol). The high reactivity of Grx enzymes is related to the very acid pK(a) values of reactive Cys that plays roles as good leaving groups. Therefore, although distinct oxidoreductases catalyze similar thiol–disulfide exchange reactions, their enzymatic mechanisms vary. PDI and DsbA are two other oxidoreductases, but they are involved in disulfide bond formation, instead of disulfide reduction, which is related to the oxidative environment where they are found. PDI enzymes and DsbC are endowed with disulfide isomerase activity, which is related with their tetra-domain architecture. As illustrative description of specificity in thiol-disulfide exchange, redox aspects of transcription activation in bacteria, yeast, and mammals are presented in an evolutionary perspective. Therefore, thiol-disulfide exchange reactions play important roles in conferring specificity to pathways, a required feature for signaling.

Heterogeneous reaction of particulate chlorpyrifos with NO3 radicals: Products, pathways, and kinetics

Science.gov (United States)

Li, Nana; Zhang, Peng; Yang, Bo; Shu, Jinian; Wang, Youfeng; Sun, Wanqi

2014-08-01

Chlorpyrifos is a typical chlorinated organophosphorus pesticide. The heterogeneous reaction of chlorpyrifos particles with NO3 radicals was investigated using a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and a real-time atmospheric gas analysis mass spectrometer. Chlorpyrifos oxon, 3,5,6-trichloro-2-pyridinol, O,O-diethyl O-hydrogen phosphorothioate, O,O-diethyl ester thiophosphoric acid, diethyl hydrogen phosphate and a phosphinyl disulfide compound were identified as the main degradation products. The heterogeneous reaction pathways were proposed and their kinetic processes were investigated via a mixed-phase relative rate method. The observed effective rate constant is 3.4 ± 0.2 × 10-12 cm3 molecule-1 s-1.

Catalytic Hydrotreatment of Fast Pyrolysis Oil : Model Studies on Reaction Pathways for the Carbohydrate Fraction

NARCIS (Netherlands)

Wildschut, J.; Arentz, J.; Rasrendra, C. B.; Venderbosch, R. H.; Heeres, H. J.

2009-01-01

Fast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250-400 degrees C, 100-200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon-like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions

Theoretical study on keto-enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional theory

Science.gov (United States)

Fukuyoshi, Shuichi; Nakayoshi, Tomoki; Takahashi, Ohgi; Oda, Akifumi

2017-03-01

In order to elucidate the reason why glutamic acid residues have lesser racemisation reactivity than asparaginic acid, we investigated the racemisation energy barrier of piperidinedione, which is the presumed intermediate of the isomerisation reaction of L-Glu to D-Glu, by density functional theory calculations. In two-water-molecule-assisted racemisation, the activation barrier for keto-enol isomerisation was 28.1 kcal/mol. The result showed that the activation barrier for the racemisation of glutamic acid residues was not different from that for the racemisation of aspartic acid residues. Thus, glutamic acid residues can possibly cause the racemisation reaction if the cyclic intermediate stably exists.

Unprecedented Carbonato Intermediates in Cyclic Carbonate Synthesis Catalysed by Bimetallic Aluminium(Salen) Complexes.

Science.gov (United States)

Castro-Osma, José A; North, Michael; Offermans, Willem K; Leitner, Walter; Müller, Thomas E

2016-04-21

The mechanism by which [Al(salen)]2 O complexes catalyse the synthesis of cyclic carbonates from epoxides and carbon dioxide in the absence of a halide cocatalyst has been investigated. Density functional theory (DFT) studies, mass spectrometry and (1) H NMR, (13) C NMR and infrared spectroscopies provide evidence for the formation of an unprecedented carbonato bridged bimetallic aluminium complex which is shown to be a key intermediate for the halide-free synthesis of cyclic carbonates from epoxides and carbon dioxide. Deuterated and enantiomerically-pure epoxides were used to study the reaction pathway. Based on the experimental and theoretical results, a catalytic cycle is proposed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secondary Interactions Arrest the Hemiaminal Intermediate To Invert the Modus Operandi of Schiff Base Reaction: A Route to Benzoxazinones.

Science.gov (United States)

Patel, Ketan; Deshmukh, Satej S; Bodkhe, Dnyaneshwar; Mane, Manoj; Vanka, Kumar; Shinde, Dinesh; Rajamohanan, Pattuparambil R; Nandi, Shyamapada; Vaidhyanathan, Ramanathan; Chikkali, Samir H

2017-04-21

Discovered by Hugo Schiff, condensation between amine and aldehyde represents one of the most ubiquitous reactions in chemistry. This classical reaction is widely used to manufacture pharmaceuticals and fine chemicals. However, the rapid and reversible formation of Schiff base prohibits formation of alternative products, of which benzoxazinones are an important class. Therefore, manipulating the reactivity of two partners to invert the course of this reaction is an elusive target. Presented here is a synthetic strategy that regulates the sequence of Schiff base reaction via weak secondary interactions. Guided by the computational models, reaction between 2,3,4,5,6-pentafluoro-benzaldehyde with 2-amino-6-methylbenzoic acid revealed quantitative (99%) formation of 5-methyl-2-(perfluorophenyl)-1,2-dihydro-4H-benzo[d][1,3]oxazin-4-one (15). Electron donating and electron withdrawing ortho-substituents on 2-aminobenzoic acid resulted in the production of benzoxazinones 9-36. The mode of action was tracked using low temperature NMR, UV-vis spectroscopy, and isotopic ( 18 O) labeling experiments. These spectroscopic mechanistic investigations revealed that the hemiaminal intermediate is arrested by the hydrogen-bonding motif to yield benzoxazinone. Thus, the mechanistic investigations and DFT calculations categorically rule out the possibility of in situ imine formation followed by ring-closing, but support instead hydrogen-bond assisted ring-closing to prodrugs. This unprecedented reaction represents an interesting and competitive alternative to metal catalyzed and classical methods of preparing benzoxazinone.

Singlet channel coupling in deuteron elastic scattering at intermediate energies

International Nuclear Information System (INIS)

Al-Khalili, J.S.; Tostevin, J.A.; Johnson, R.C.

1990-01-01

Intermediate energy deuteron elastic scattering is investigated in a three-body model incorporating relativistic kinematics. The effects of deuteron breakup to singlet spin intermediate states, on the elastic scattering observables for the 58 Ni(d vector, d) 58 Ni reaction at 400 and 700 MeV, are studied quantitatively. The singlet-breakup contributions to the elastic amplitude are estimated within an approximate two-step calculation. The calculation makes an adiabatic approximation in the intermediate states propagator which allows the use of closure over the np intermediate states continuum. The singlet channel coupling is found to produce large effects on the calculated reaction tensor analysing power A yy , characteristic of a dynamically induced second-rank tensor interaction. By inspection of the calculated breakup amplitudes we show this induced interaction to be of the T L tensor type. (orig.)

Kinetic evidence for the formation of discrete 1,4-dehydrobenzene intermediates. Trapping by inter- and intramolecular hydrogen atom transfer and observation of high-temperature CIDNP

Energy Technology Data Exchange (ETDEWEB)

Lockhart, Thomas P. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States); Comita, Paul B. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States); Bergman, Robert G. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States)

1981-07-01

Upon heating, alkyl-substituted cis-1,2-diethynyl olefins undergo cyclization to yield reactive 1,4-dehydrobenzenes; the products isolated may be derived from either unimolecular or bimolecular reactions of the intermediate. (Z)-4,5-Diethynyl-4-octene (4) undergoes rearrangement to yield 2,3-di-n-propyl-1,4-dehydrobenzene (17). Solution pyrolysis of 4 in inert aromatic solvents produces three unimolecular products, (Z)-dodeca-4,8-diyn-6-ene (7), benzocyclooctene (9), and o-allyl-n-propylbenzene (10), in high yield. When 1,4-cyclohexadiene is added to the pyrolysis solution as a trapping agent, high yields of the reduced product o-di-n-propylbenzene (12) are obtained. The kinetics of solution pyrolysis of 4 in the presence and absence of trapping agent establish that 2,3-di-n-propyl-1,4-dehydrobenzene is a discrete intermediate on the pathway leading to products. When the reaction was run in the heated probe of an NMR spectrometer, CIDNP was observed in 10. This observation, along with kinetic and chemical trapping evidence, indicates the presence of two additional intermediates, formed from 17 by sequential intramolecular [1,5] hydrogen transfer, on the pathway to products. The observation of CIDNP, coupled with the reactivity exhibited by 17 and the other two intermediates, implicate a biradical description of these molecules. Biradical 17 has been estimated to have a lifetime of about 10^-9 s at 200°C and to lie in a well of about 5 kcal/mol with respect to the lowest energy unimolecular pathway ([1,5] hydrogen transfer). Ring opening (expected to be the lowest energy process for 1,4-dehydrobenzenes in which intramolecular hydrogen transfer is unlikely) to the isomeric diethynyl olefin 7 appears to have an activation enthalpy of about 10 kcal/moL Upon thermal reaction in the gas phase (400°C) or in solution in inert solvents (Z)-hexa-2,3-diethyl-1,5-diyn-3-ene (5) rearranges in good yield to the isomeric diethynyl olefin (Z)-deca-3,7-diyn-5-ene (8

Oxidation of nonylphenol and octylphenol by manganese dioxide: Kinetics and pathways

International Nuclear Information System (INIS)

Lu, Zhijiang; Gan, Jay

2013-01-01

Due to their potent estrogenicity and ubiquitous occurrence, non-ionic surfactant metabolites nonylphenol (NP) and octylphenol (OP) are of significant concern. Abiotic chemical oxidation by naturally abundant metal oxides may be an important route of their environmental attenuation, but is poorly understood. We investigated the reaction kinetics and pathways of NP and OP with MnO 2 . At pH 5.5 and 100 mg/L δ-MnO 2 , 92, 84 and 76% of 4-n-NP, 4-tert-OP and technical nonylphenol (tNP) was transformed in 90 min, respectively. A further experiment using a Mn-containing soil and Mn-removed soil confirmed that soil MnO 2 caused NP removal. Multiple reaction products, including hydroquinone, hydroxylated products, dimers and trimers were identified through fragmentation analysis by GC–MS/MS and UPLC–MS/MS, allowing the construction of tentative pathways. This study suggested that abiotic oxidation by MnO 2 may contribute to the dissipation of tNP, 4-n-NP, 4-tert-OP and their analogues in the natural environment. Highlights: •The oxidation of nonylphenol and octylphenol by manganese dioxide was efficient and pH dependent. •The importance of soil MnO 2 was further confirmed by experiment using Mn-containing soil. •The reaction in environment is substantially slower than with synthetic MnO 2 . •The oxidation was inhibited by metal ions and enhanced by humic acids. •Reaction pathway is proposed based on reaction intermediates identified. -- Naturally occurring MnO 2 may contribute significantly to the attenuation of nonylphenol and octylphenol in soil, water and sediment

Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

Directory of Open Access Journals (Sweden)

Shinichi Yamabe

2014-01-01

Full Text Available Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p SCRF=(PCM, solvent = 1,2-ethanediol optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H2N–NH2 and (H2O8. A ready reaction channel of acetone → acetone hydrazine (Me2C=N–NH2 was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N2 extrusion step from the isopropyl diimine intermediate (Me2C(H–N=N–H. Two base-catalyzed reactions were investigated by models of the ketone, H2N–NH2 and OH−(H2O7. Here, ketones are acetone and acetophenone. While routes of the ketone → hydrazone → diimine are similar, those from the diimines are different. From the isopropyl diimine, the N2 extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenylethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.

Mechanism of ({sup 14}N, {sup 12}B) reactions at intermediate energy leading to large spin-polarization of {sup 12}B

Energy Technology Data Exchange (ETDEWEB)

Mitsuoka, Shin-ichi [Osaka Univ., Ibaraki (Japan). Research Center for Nuclear Physics; Shimoda, Tadashi; Miyatake, Hiroari [and others

1996-05-01

To study mechanisms of the ({sup 14}N, {sup 12}B) reactions at intermediate energies, double differential cross section and nuclear spin-polarization of the {sup 12}B projectile-like fragments have been measured as a function of longitudinal momentum in the angular range of 0deg - 9deg. Large spin-polarization of the reaction products {sup 12}B has been observed in the {sup 9}Be({sup 14}N, {sup 12}B) reaction at 39.3 MeV/u. The momentum distributions at forward angles exhibit characteristic features which can not be understood by the current projectile fragmentation picture. It is shown that by assuming the existence of direct two-proton transfer process in addition to the fragmentation process, both the cross section and polarization of {sup 12}B fragments are successfully explained. The target and incident energy dependence of the momentum distribution are also explained reasonably. (author)

Approach to photocatalysis at the molecular level. Design of photocatalysts, detection of intermediate species, and reaction mechanisms

Energy Technology Data Exchange (ETDEWEB)

Anpo, Masakazu [Department of Applied Chemistry, University of Osaka Prefecture, Gakuen-cho, Sakai, Osaka (Japan)

1995-08-01

The characterization of the Cu{sup +}/ZSM-5 catalysts prepared via reduction of ion-exchanged Cu{sup 2+}/ZSM-5 samples and highly dispersed Ti-oxide catalysts anchored on Vycor glass has been undertaken by in-situ photoluminescence, EPR, XAFS (XANES and FT-EXAFS), and FT-IR spectroscopy. UV-irradiation of the Cu{sup +}/ZSM-5 catalyst in the presence of NO leads to the direct photocatalytic decomposition of NO into N{sub 2} and O{sub 2} at normal temperatures. UV-irradiation of the highly dispersed anchored Ti-oxide catalyst in the presence of CO{sub 2} and H{sub 2}O also leads to the evolution of CH{sub 4}, CO, and CH{sub 3}OH at normal temperatures. The clarification of the coordination structure of the active surface sites and the direct detection of the reaction precursors and intermediate species in these photocatalytic systems contributed significantly in characterizing the molecular scale reaction mechanisms. Based on these results, the design of highly concentrated and efficient photocatalysts has successfully been achieved by application of the sol-gel method

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

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Trong-Nghia [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi (Viet Nam); Putikam, Raghunath; Lin, M. C., E-mail: chemmcl@emory.edu [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China)

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.

The deterioration of intermediate moisture foods

Science.gov (United States)

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.

Novel Reagents for Multi-Component Reactions

Science.gov (United States)

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

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

Biomimicry Promotes the Efficiency of a 10-Step Sequential Enzymatic Reaction on Nanoparticles, Converting Glucose to Lactate.

Science.gov (United States)

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L; Lata, James P; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M; Bergkvist, Magnus; Sherwood, Robert W; Zhang, Sheng; Travis, Alexander J

2017-01-02

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An NPF transporter exports a central monoterpene indole alkaloid intermediate from the vacuole

DEFF Research Database (Denmark)

Payne, Richard; Xu, Deyang; Foureau, Emilien

2017-01-01

Plants sequester intermediates of metabolic pathways into different cellular compartments, but the mechanisms by which these molecules are transported remain poorly understood. Monoterpene indole alkaloids, a class of specialized metabolites that includes the anticancer agent vincristine, antimal......Plants sequester intermediates of metabolic pathways into different cellular compartments, but the mechanisms by which these molecules are transported remain poorly understood. Monoterpene indole alkaloids, a class of specialized metabolites that includes the anticancer agent vincristine...

Steady-state isotopic transient kinetic analysis investigation of CO-O2 and CO-NO reactions over a commercial automotive catalyst

International Nuclear Information System (INIS)

Oukaci, R.; Blackmond, D.G.; Goodwin, J.G. Jr.; Gallaher, G.R.

1992-01-01

In this paper, steady-state isotopic transient kinetic analysis (SSITKA) is used to study two model reactions, CO oxidation and CO-NO reactions, on a typical formulation of a three-way auto-catalyst. Under steady-state conditions, abrupt switches in the isotopic composition of CO ( 12 C 16 O/ 13 C 18 O) were carried out to produce isotopic transients in both labeled reactants and products. Along with the determination of the average surface lifetimes and concentrations of reaction intermediates, an analysis of the transient responses along the carbon reaction pathway indicated that the distribution of active sites for the formation of CO 2 was bimodal for both reactions. Furthermore, relatively few surface sites contributed to the overall reaction rate

Reactions of neopentane and neohexane on platinum/Y-zeolite and platinum/silica catalysts

Energy Technology Data Exchange (ETDEWEB)

Foger, K.; Anderson, J.R.

1978-10-13

The hydrocracking/hydroisomerization reaction of 20:1 hydrogen/neopentane at 455-625/sup 0/K was studied on platinum-exchanged sodium, calcium, and lanthanum Y zeolites and Aerosil-supported platinum of 1-20 nm average platinum particle size, by analysis of the product distribution, ESCA, and temperature-programed desorption. The results suggested that the reaction occurs only on platinum and that it proceeds by two parallel pathways which have different activation energies and whose relative proportion depends on the particle size. One pathway is the conventionally accepted one on low-index crystallite facets; the other proceeds on single-surface platinum atoms of low coordination (corner or edge atoms) which become more abundant at lower crystallite size. In both cases, the adsorbed intermediate may undergo either isomerization or hydrogenolysis; the selectivity depends on the hydrogen partial pressure and the relative strength of adsorption of hydrogen and neopentane. Neohexane isomerization selectivity on the same catalysts is consistent with a carbonium ion mechanism on a dual-function catalyst.

Mechanistic Insights into the Unique Role of Copper in CO2 Electroreduction Reactions.

Science.gov (United States)

Liu, Shan Ping; Zhao, Ming; Gao, Wang; Jiang, Qing

2017-01-20

Cu demonstrates a unique capability towards CO 2 electroreduction that can close the anthropogenic carbon cycle; however, its reaction mechanism remains elusive, owing to the obscurity of the solid-liquid interface on Cu surfaces where electrochemical reactions occur. Using a genetic algorithm method in addition to density functional theory, we explicitly identify the configuration of a water bilayer on Cu(2 1 1) and build electrochemical models. These enable us to reveal a mechanistic picture for CO 2 electroreduction, finding the key intermediates CCO* for the C 2 H 4 pathway and CH* for the CH 4 pathway, which rationalize a series of experimental observations. Furthermore, we find that the interplay between the Cu surfaces, carbon monomers, and water network (but not the binding of CO*) essentially determine the unique capability of Cu towards CO 2 electroreduction, proposing a new and effective descriptor for exploiting optimal catalysts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reaction mechanism for the free-edge oxidation of soot by O 2

KAUST Repository

Raj, Abhijeet

2012-11-01

The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.

Reaction mechanism for the free-edge oxidation of soot by O 2

KAUST Repository

Raj, Abhijeet; da Silva, Gabriel; Chung, Suk-Ho

2012-01-01

The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.

Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

Science.gov (United States)

Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

2007-10-31

Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.

Desaturation reactions catalyzed by soluble methane monooxygenase.

Science.gov (United States)

Jin, Y; Lipscomb, J D

2001-09-01

Soluble methane monooxygenase (MMO) is shown to be capable of catalyzing desaturation reactions in addition to the usual hydroxylation and epoxidation reactions. Dehydrogenated products are generated from MMO-catalyzed oxidation of certain substrates including ethylbenzene and cyclohexadienes. In the reaction of ethylbenzene, desaturation of ethyl C-H occurred along with the conventional hydroxvlations of ethyl and phenyl C-Hs. As a result, styrene is formed together with ethylphenols and phenylethanols. Similarly, when 1,3- and 1,4-cyclohexadienes were used as substrates, benzene was detected as a product in addition to the corresponding alcohols and epoxides. In all cases, reaction conditions were found to significantly affect the distribution among the different products. This new activity of MMO is postulated to be associated with the chemical properties of the substrates rather than fundamental changes in the nature of the oxygen and C-H activation chemistries. The formation of the desaturated products is rationalized by formation of a substrate cationic intermediate, possibly via a radical precursor. The cationic species is then proposed to partition between recombination (alcohol formation) and elimination (alkene production) pathways. This novel function of MMO indicates close mechanistic kinship between the hydroxylation and desaturation reactions catalyzed by the nonheme diiron clusters.

In situ loading of well-dispersed silver nanoparticles on nanocrystalline magnesium oxide for real-time monitoring of catalytic reactions by surface enhanced Raman spectroscopy.

Science.gov (United States)

Zhang, Kaige; Li, Gongke; Hu, Yuling

2015-10-28

The surface-enhanced Raman spectroscopy (SERS) technique is of great importance for insight into the transient reaction intermediates and mechanistic pathways involved in heterogeneously catalyzed chemical reactions under actual reaction conditions, especially in water. Herein, we demonstrate a facile method for in situ synthesis of nanocrystalline magnesium oxide-Ag(0) (nano MgO-Ag(0)) hybrid nanomaterials with dispersed Ag nanoparticles (Ag NPs) on the surface of nanocrystalline magnesium oxide (nano MgO) via Sn(2+) linkage and reduction. As a benefit from the synergy effect of nano MgO and Ag NPs, the nano MgO-Ag(0) exhibited both excellent SERS and catalytic activities for the reduction of 4-nitrothiophenol in the presence of NaBH4. The nano MgO-Ag(0) was used for real-time monitoring of the catalytic reaction process of 4-nitrothiophenol to 4-aminothiophenol in an aqueous medium by observing the SERS signals of the reactant, intermediate and final products. The intrinsic reaction kinetics and reaction mechanism of this reaction were also investigated. This SERS-based synergy technique provides a novel approach for quantitative in situ monitoring of catalytic chemical reaction processes.

AAPH-mediated antioxidant reactions of secoisolariciresinol and SDG.

Science.gov (United States)

Hosseinian, Farah S; Muir, Alister D; Westcott, Neil D; Krol, Ed S

2007-02-21

Secoisolariciresinol (SECO ) is the major lignan found in flaxseed (Linum usitatissimum L.) and is present in a polymer that contains secoisolariciresinol diglucoside (SDG ). SECO, SDG and the polymer are known to have a number of health benefits, including reduction of serum cholesterol levels, delay in the onset of type II diabetes and decreased formation of breast, prostate and colon cancers. The health benefits of SECO and SDG may be partially attributed to their antioxidant properties. To better understand their antioxidant properties, SECO and SDG were oxidized using 2,2'-azobis(2-amidinopropane), an in vitro model of radical scavenging. The major lignan radical-scavenging oxidation products and their formation over time were determined. SDG was converted to four major products, which were the result of a phenoxyl radical intermediate. One of these products, a dimer of SDG, decomposed under the reaction conditions to form two of the other major products, and . SECO was converted to five major products, two of which were also the result of a phenoxyl radical intermediate. The remaining products were the result of an unexpected alkoxyl radical intermediate. The phenol oxidation products were stable under the reaction conditions, whereas two of the alcohol oxidation products decomposed. In general, only one phenol group on the lignans was oxidized, suggesting that the number of phenols per molecule may not predict radical scavenging antioxidant ability of lignans. Finally, SECO is a superior antioxidant to SDG, and it may be that the additional alcohol oxidation pathway contributes to its greater antioxidant ability.

Formation of N-nitrosodimethylamine (NDMA) from reaction of monochloramine: a new disinfection by-product.

Science.gov (United States)

Choi, Junghoon; Valentine, Richard L

2002-02-01

Studies have been conducted specifically to investigate the hypothesis that N-nitrosodimethylamine (NDMA) can be produced by reactions involving monochloramine. Experiments were conducted using dimethylamine (DMA) as a model precursor. NDMA was formed from the reaction between DMA and monochloramine indicating that it should be considered a potential disinfection by-product. The formation of NDMA increased with increased monochloramine concentration and showed maximum in yield when DMA was varied at fixed monochloramine concentrations. The mass spectra of the NDMA formed from DMA and 15N isotope labeled monochloramine (15NH2Cl) showed that the source of one of the nitrogen atoms in the nitroso group in NDMA was from monochloramine. Addition of 0.05 and 0.5 mM of preformed monochloramine to a secondarily treated wastewater at pH 7.2 also resulted in the formation of 3.6 and 111 ng/L of NDMA, respectively, showing that this is indeed an environmentally relevant NDMA formation pathway. The proposed NDMA formation mechanism consists of (i) the formation of 1,1-dimethylhydrazine (UDMH) intermediate from the reaction of DMA with monochloramine followed by, (ii) the oxidation of UDMH by monochloramine to NDMA, and (iii) the reversible chlorine transfer reaction between monochloramine and DMA which is parallel to (i). We conclude that reactions involving monochloramine in addition to classical nitrosation reactions are potentially important pathways for NDMA formation.

Low energy ion-molecule reactions

International Nuclear Information System (INIS)

Farrar, J.M.

1986-01-01

The authors work during the past year has focused on several problems in the condensation reactions of C + and CH 3 + with small molecules, particularly hydrocarbons. Their emphasis has been on understanding the dynamics of collision complex formation and isomerization of transient intermediates along the reaction coordinate. In many ionic reactions, intermediates having non-classical valence structures may be nearly as stable as their classical analogs, in contrast with neutral systems where the non-classical structures are much less stable. The C + + NH 3 system shows this behavior, indicating that the non-classical HCNH 2 + structure formed by insertion of C + into the N-H bond serves as a precursor to the products. N-H bond cleavage in this intermediate to form HCNH + occurs over a large barrier and occurs more readily than the 1,2 hydrogen atom shift to form the classical H 2 C = NH + intermediate. Their experimental kinetic energy distribution for this channel is consistent with the presence of a large exit channel barrier. Their recently published work on C + + H 2 O also demonstrates this phenomenon. The CHOH + hydroxycarbene cation serves as the initial intermediate and isomerization to the classical H 2 CO + cation is competitive with O-H or C-H cleavage to yield the formyl, HCO + , or isoformyl, COH + , cations. They have also completed studies on the reactions of C + with O 2 , CH 3 OH, HCN, and the two-carbon containing hydrocarbons ethane, ethylene, and acetylene

Hydrogen sulfide oxidation without oxygen - oxidation products and pathways

International Nuclear Information System (INIS)

Fossing, H.

1992-01-01

Hydrogen sulfide oxidation was studied in anoxic marine sediments-both in undisturbed sediment cores and in sediment slurries. The turn over of hydrogen sulfide was followed using 35 S-radiolabeled hydrogen sulfide which was injected into the sediment. However, isotope exchange reactions between the reduced sulfur compounds, in particular between elemental sulfur and hydrogen sulfide, influenced on the specific radioactivity of these pools. It was, therefore, not possible to measure the turn over rates of the reduced sulfur pools by the radiotracer technique but merely to use the radioisotope to demonstrate some of the oxidation products. Thiosulfate was one important intermediate in the anoxic oxidation of hydrogen sulfide and was continuously turned over by reduction, oxidation and disproportionation. The author discusses the importance of isotope exchange and also presents the results from experiments in which both 35 S-radiolabeled elemental sulfur, radiolabeled hydrogen sulfide and radiolabeled thiosulfate were used to study the intermediates in the oxidative pathways of the sulfur cycle

A Single Enzyme Transforms a Carboxylic Acid into a Nitrile through an Amide Intermediate.

Science.gov (United States)

Nelp, Micah T; Bandarian, Vahe

2015-09-01

The biosynthesis of nitriles is known to occur through specialized pathways involving multiple enzymes; however, in bacterial and archeal biosynthesis of 7-deazapurines, a single enzyme, ToyM, catalyzes the conversion of the carboxylic acid containing 7-carboxy-7-deazaguanine (CDG) into its corresponding nitrile, 7-cyano-7-deazaguanine (preQ0 ). The mechanism of this unusual direct transformation was shown to proceed via the adenylation of CDG, which activates it to form the newly discovered amide intermediate 7-amido-7-deazaguanine (ADG). This is subsequently dehydrated to form the nitrile in a process that consumes a second equivalent of ATP. The authentic amide intermediate is shown to be chemically and kinetically competent. The ability of ToyM to activate two different substrates, an acid and an amide, accounts for this unprecedented one-enzyme catalysis of nitrile synthesis, and the differential rates of these two half reactions suggest that this catalytic ability is derived from an amide synthetase that gained a new function. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reaction pathways of photoexcited retinal in proteorhodopsin studied by pump-dump-probe spectroscopy.

Science.gov (United States)

Rupenyan, Alisa; van Stokkum, Ivo H M; Arents, Jos C; van Grondelle, Rienk; Hellingwerf, Klaas J; Groot, Marie Louise

2009-12-17

Proteorhodopsin (pR) is a membrane-embedded proton pump from the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization on the femtosecond to picosecond time scales. Here, we report a study on the photoisomerization dynamics of the retinal chromophore of pR, using dispersed ultrafast pump-dump-probe spectroscopy. The application of a pump pulse initiates the photocycle, and with an appropriately tuned dump pulse applied at a time delay after the dump, the molecules in the initial stages of the photochemical process can be de-excited and driven back to the ground state. In this way, we were able to resolve an intermediate on the electronic ground state that represents chromophores that are unsuccessful in isomerization. In particular, the fractions of molecules that undergo slow isomerization (20 ps) have a high probability to enter this state rather than the isomerized K-state. On the ground state reaction surface, return to the stable ground state conformation via a structural or vibrational relaxation occurs in 2-3 ps. Inclusion of this intermediate in the kinetic scheme led to more consistent spectra of the retinal-excited state, and to a more accurate estimation of the quantum yield of isomerization (Phi = 0.4 at pH 6).

Quantum Chemical Investigation on Photochemical Reactions of Nonanoic Acids at Air-Water Interface.

Science.gov (United States)

Xiao, Pin; Wang, Qian; Fang, Wei-Hai; Cui, Ganglong

2017-06-08

Photoinduced chemical reactions of organic compounds at the marine boundary layer have recently attracted significant experimental attention because this kind of photoreactions has been proposed to have substantial impact on local new particle formation and their photoproducts could be a source of secondary organic aerosols. In this work, we have employed first-principles density functional theory method combined with cluster models to systematically explore photochemical reaction pathways of nonanoic acids (NAs) to form volatile saturated and unsaturated C 9 and C 8 aldehydes at air-water interfaces. On the basis of the results, we have found that the formation of C 9 aldehydes is not initiated by intermolecular Norrish type II reaction between two NAs but by intramolecular T 1 C-O bond fission of NA generating acyl and hydroxyl radicals. Subsequently, saturated C 9 aldehydes are formed through hydrogenation reaction of acyl radical by another intact NA. Following two dehydrogenation reactions, unsaturated C 9 aldehydes are generated. In parallel, the pathway to C 8 aldehydes is initiated by T 1 C-C bond fission of NA, which generates octyl and carboxyl radicals; then, an octanol is formed through recombination reaction of octyl with hydroxyl radical. In the following, two dehydrogenation reactions result into an enol intermediate from which saturated C 8 aldehydes are produced via NA-assisted intermolecular hydrogen transfer. Finally, two dehydrogenation reactions generate unsaturated C 8 aldehydes. In these reactions, water and NA molecules are found to play important roles. They significantly reduce relevant reaction barriers. Our work has also explored oxygenation reactions of NA with molecular oxygen and radical-radical dimerization reactions.

Carbon monosulfide: a useful synthetic intermediate

International Nuclear Information System (INIS)

Kramer, M.P.

1986-01-01

The physical properties of carbon monosulfide, CS, are well documented. The molecule has been observed in interstellar space and is found to be a common intermediate in the thermal decomposition of carbon disulfide and other sulfur compounds. Interestingly enough, the chemistry of carbon monosulfide, a molecule that is isovalent with carbon monoxide, has received little attention. The explosive nature of the carbon monosulfide monomer, which hindered previous workers, was overcome by the development of special handling techniques. The ability to produce carbon monosulfide in gram quantities had lead to synthesis of novel compounds and to a more direct synthetic route for certain known compounds. Specifically, the following general reaction demonstrates the capabilities of carbon monosulfide on the synthetic scale. CS + RXY → RXC(S)Y;(X = N,S), (Y = H, Cl). Note: The initial product formed in the reaction can be an unstable intermediate

Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

Energy Technology Data Exchange (ETDEWEB)

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

2012-03-27

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

Studies on the nature of intermediates in enzyme mechanisms

International Nuclear Information System (INIS)

Clark, J.D.

1988-01-01

The reaction pathway followed by malate synthase has been studied by the double isotope fractionation method to determine whether the reaction is stepwise or concerted. A primary deuterium kinetic isotope effect ( D V/K) of 1.3 ± 0.1 has been found using [ 2 H 3 ]acetyl-CoA as substrate. The 13 C isotope effect at the aldehydic carbon of glyoxylate has also been measured. For this determination, the malate product was quantitatively transformed into a new sample of malate having the carbon of interest at C-4. This material was decarboxylated to produce the appropriate CO 2 for isotope ratio mass spectrometric analysis. If the essential Zn(II) ion of yeast aldolase interacts with the carbonyl groups of bound substrates, we can expect that these will be more reactive toward reduction by borohydrides than those free in solution. Tritiated sodium borohydride was therefore used to reduce the substrates of yeast aldolase in the presence and absence of enzyme, and the enantiomeric and diastereomeric ratios of the products were analyzed. Experiments were conducted in an effort to distinguish between endocyclic and exocyclic cleavage in the hydrolysis catalyzed by lysozyme. Tritiated sodium borohydride was used in an attempt to trap the putative oxocarbonium intermediate

Intermediates and Generic Convergence to Equilibria

DEFF Research Database (Denmark)

Marcondes de Freitas, Michael; Wiuf, Carsten; Feliu, Elisenda

2017-01-01

Known graphical conditions for the generic and global convergence to equilibria of the dynamical system arising from a reaction network are shown to be invariant under the so-called successive removal of intermediates, a systematic procedure to simplify the network, making the graphical conditions...

Dexter energy transfer pathways.

Science.gov (United States)

Skourtis, Spiros S; Liu, Chaoren; Antoniou, Panayiotis; Virshup, Aaron M; Beratan, David N

2016-07-19

Energy transfer with an associated spin change of the donor and acceptor, Dexter energy transfer, is critically important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Dexter transfer between chemically linked donors and acceptors is bridge mediated, presenting an enticing analogy with bridge-mediated electron and hole transfer. However, Dexter coupling pathways must convey both an electron and a hole from donor to acceptor, and this adds considerable richness to the mediation process. We dissect the bridge-mediated Dexter coupling mechanisms and formulate a theory for triplet energy transfer coupling pathways. Virtual donor-acceptor charge-transfer exciton intermediates dominate at shorter distances or higher tunneling energy gaps, whereas virtual intermediates with an electron and a hole both on the bridge (virtual bridge excitons) dominate for longer distances or lower energy gaps. The effects of virtual bridge excitons were neglected in earlier treatments. The two-particle pathway framework developed here shows how Dexter energy-transfer rates depend on donor, bridge, and acceptor energetics, as well as on orbital symmetry and quantum interference among pathways.

Freeze-quench (57)Fe-Mössbauer spectroscopy: trapping reactive intermediates.

Science.gov (United States)

Krebs, Carsten; Bollinger, J Martin

2009-01-01

(57)Fe-Mössbauer spectroscopy is a method that probes transitions between the nuclear ground state (I=1/2) and the first nuclear excited state (I=3/2). This technique provides detailed information about the chemical environment and electronic structure of iron. Therefore, it has played an important role in studies of the numerous iron-containing proteins and enzymes. In conjunction with the freeze-quench method, (57)Fe-Mössbauer spectroscopy allows for monitoring changes of the iron site(s) during a biochemical reaction. This approach is particularly powerful for detection and characterization of reactive intermediates. Comparison of experimentally determined Mössbauer parameters to those predicted by density functional theory for hypothetical model structures can then provide detailed insight into the structures of reactive intermediates. We have recently used this methodology to study the reactions of various mononuclear non-heme-iron enzymes by trapping and characterizing several Fe(IV)-oxo reaction intermediates. In this article, we summarize these findings and demonstrate the potential of the method. © Springer Science+Business Media B.V. 2009

Formation of trihalomethanes from the halogenation of 1,3-dihydroxybenzenes in dilute aqueous solution: synthesis of 2-13C-resorcinol and its reaction with chlorine and bromine

International Nuclear Information System (INIS)

Boyce, S.D.; Barefoot, A.C.; Britton, D.R.; Hornig, J.F.

1983-01-01

As part of this study, the reaction of bromine with resorcinol and structurally related substrates to produce bromoform was examined. Preliminary results suggest that the chlorination and bromination of dihydroxybenzenes proceeded by similar reaction pathways. This chapter describes the successful synthesis of 2- 13 C-1, 3-dihydroxybenzene. Treatment of the isotopically labelled substrate with chlorine and bromine in dilute aqueous solution has elucidated many important details of the sequence of reactions leading to the production of chloroform (CHCl 3 ) and bromoform (CHBr 3 ). The 13 C-enriched products and intermediates formed during these reactions were identified by gas chromatography/mass spectrometry

Bioelectrocatalytic dechlorination of trichloroacetic acid at gel-immobilized hemoglobin on multiwalled carbon nanotubes modified graphite electrode: Kinetic modeling and reaction pathways

International Nuclear Information System (INIS)

Liu, Qi; Yu, Jianming; Xu, Yinghua; Wang, Jiade; Ying, Le; Song, Xinxin; Zhou, Gendi; Chen, Jianmeng

2013-01-01

Highlights: ► The electrons transfer from enzyme in the electrode to COCs was the key step. ► The average current efficiency was influenced by pH and temperature of the systems. ► The most favourable degradation conditions for TCA were found to be pH 3 and 310 K. ► The activation energy of 26.2 kJ mol −1 was also calculated by the Arrhenius equation. ► Bioelectrocatalytic mechanism of TCA was verified by kinetic expressions. -- Abstract: In bioelectrochemically reductive dechlorination of chlorinated organic compounds (COCs), the electrons transfer from enzyme in the electrode to COCs was the key step, which determined the average current efficiency (CE) and was influenced by the pH and temperature of the systems. In this work, the effect of temperature (288–318 K) and pH (2–11) of the electrolyte on decholrination of trichloroacetic acid (TCA) was investigated in the sodium alginate/hemoglobin-multiwalled carbon nanotubes-graphite composite electrode (Hb/SA–MWCNT–GE). The results showed that the most favourable degradation conditions for TCA by Hb/SA–MWCNT–GE were found to be pH 3 and 310 K. By varying the pH of the systems, it was found that a proton accompanied with an electron transfer between the electrode and heme Fe(III)/Fe(II) of Hb during the reaction. Additionally, the activation energy of 26.2 kJ mol −1 was also calculated by the Arrhenius equation for the reaction. The total mass balance of the reactant and the products was in the range of 97–105% during the bioelectrochemically reductive reaction. The CE only decreased from 87% to 83% when the Hb/SA–MWCNT–GE was used 5 times. Based on the intermediates detected, a pathway was proposed for TCA degradation in which it underwent dechlorination process. The main degradation mechanism described by a parallel reaction rather than by a sequential reaction for dechlorination of TCA in Hb/SA–MWCNT–GE system was proposed. These data provided relevant information about the

An Alternative Reaction Pathway for Iridium Catalyzed Water Oxidation Driven by CAN

KAUST Repository

Bucci, Alberto; Menendez Rodriguez, Gabriel; Bellachioma, Gianfranco; Zuccaccia, Cristiano; Poater, Albert; Cavallo, Luigi; Macchioni, Alceo

2016-01-01

The generation of solar fuels by means of a photosynthetic apparatus strongly relies on the development of an efficient water oxidation catalyst (WOC). Cerium ammonium nitrate (CAN) is the most commonly used sacrificial oxidant to explore the potentiality of WOCs. It is usually assumed that CAN has the unique role to oxidatively energize WOCs, making them capable to offer a low energy reaction pathway to transform H2O to O2. Herein we show that CAN might have a much more relevant and direct role in WO, mainly related to the capture and liberation of O–O containing molecular moieties.

An Alternative Reaction Pathway for Iridium Catalyzed Water Oxidation Driven by CAN

KAUST Repository

Bucci, Alberto

2016-06-10

The generation of solar fuels by means of a photosynthetic apparatus strongly relies on the development of an efficient water oxidation catalyst (WOC). Cerium ammonium nitrate (CAN) is the most commonly used sacrificial oxidant to explore the potentiality of WOCs. It is usually assumed that CAN has the unique role to oxidatively energize WOCs, making them capable to offer a low energy reaction pathway to transform H2O to O2. Herein we show that CAN might have a much more relevant and direct role in WO, mainly related to the capture and liberation of O–O containing molecular moieties.

Determination of rate constants for the oxygen reduction reaction

Energy Technology Data Exchange (ETDEWEB)

Racz, A.; Walter, T.; Stimming, U. [Munich Technical Univ., Garching (Germany). Dept. of Physics

2008-07-01

The oxygen reduction reaction (ORR) in fuel cells is a complex and fundamental electrochemical reaction. However, greater insight is needed into this multi-electron reaction in order to develop efficient and innovative catalysts. The rotating ring disc electrode (RRDE) is a useful tool for studying reaction intermediates of the ORR and to better understand the reaction pathway. Carbon materials such as carbon nanofilaments-platelets (CNF-PL) have high electrical conductivity and may be considered for fuel cells. In particular Pt and RuSe{sub x}, deposited on CNF-PL materials could act as efficient catalysts in fuel cells. This study used the RRDE to evaluate the oxygen reduction kinetics of these catalysts in oxygen-saturated, diluted sulphuric acid at room temperature. Kinetic data and hydrogen peroxide formation were determined by depositing a thin-film of the catalyst on the Au disc. The values for the constants k1, k2 and k3 were obtained using diagnostic criteria and expressions to calculate the rate constants of the cathodic oxygen reduction reaction for RuSe on new carbon supports. A potential dependency of the constants k1 and k2 for RuSe{sub x}/CNF-PL was observed. The transition of the Tafel slopes for this catalyst was obtained. 4 refs., 1 fig.

Medium effects in direct reactions

International Nuclear Information System (INIS)

Karakoc, M; Bertulani, C

2013-01-01

We discuss medium corrections of the nucleon-nucleon (NN) cross sections and their influence on direct reactions at intermediate energies ≳50 MeV/nucleon. The results obtained with free NN cross sections are compared with those obtained with a geometrical treatment of Pauli-blocking and Dirac-Bruecker methods. We show that medium corrections may lead to sizable modifications for collisions at intermediate energies and that they are more pronounced in reactions involving weakly bound nuclei.

Search for ternary fragmentation in the reaction 856 MeV 98Mo + 51V: Kinematic probing of intermediate-mass-fragment emissions

International Nuclear Information System (INIS)

Vardaci, Emanuele; Kaplan, Morton; Parker, Winifred E.; Moses, David J.; Boger, J.T.; Gilfoyle, G.T.; McMahan, M.A.; Montoya, M.

2000-05-01

A new technique has been applied to coincidence measurements between fission fragments (FF) and intermediate mass fragments (IMF) emitted from the composite system 149 65 Tb at an excitation energy of 224 MeV. The method permits simultaneous observation of IMF emissions along and normal to the FF separation axes. For the integrated total of 0.10 +-0.02 IMF emitted per fission, we find no significant correlation with FF direction, suggesting that IMFs associated with fission reactions are predominantly emitted from the system prior to fission

The return of metabolism: biochemistry and physiology of the pentose phosphate pathway

Science.gov (United States)

Stincone, Anna; Prigione, Alessandro; Cramer, Thorsten; Wamelink, Mirjam M. C.; Campbell, Kate; Cheung, Eric; Olin-Sandoval, Viridiana; Grüning, Nana-Maria; Krüger, Antje; Alam, Mohammad Tauqeer; Keller, Markus A.; Breitenbach, Michael; Brindle, Kevin M.; Rabinowitz, Joshua D.; Ralser, Markus

2015-01-01

The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide and amino acid biosynthesis, to provide reducing molecules for anabolism, and to defeat oxidative stress. The PPP shares reactions with the Entner–Doudoroff pathway and Calvin cycle and divides into an oxidative and non-oxidative branch. The oxidative branch is highly active in most eukaryotes and converts glucose 6-phosphate into carbon dioxide, ribulose 5-phosphate and NADPH. The latter function is critical to maintain redox balance under stress situations, when cells proliferate rapidly, in ageing, and for the ‘Warburg effect’ of cancer cells. The non-oxidative branch instead is virtually ubiquitous, and metabolizes the glycolytic intermediates fructose 6-phosphate and glyceraldehyde 3-phosphate as well as sedoheptulose sugars, yielding ribose 5-phosphate for the synthesis of nucleic acids and sugar phosphate precursors for the synthesis of amino acids. Whereas the oxidative PPP is considered unidirectional, the non-oxidative branch can supply glycolysis with intermediates derived from ribose 5-phosphate and vice versa, depending on the biochemical demand. These functions require dynamic regulation of the PPP pathway that is achieved through hierarchical interactions between transcriptome, proteome and metabolome. Consequently, the biochemistry and regulation of this pathway, while still unresolved in many cases, are archetypal for the dynamics of the metabolic network of the cell. In this comprehensive article we review seminal work that led to the discovery and description of the pathway that date back now for 80 years, and address recent results about genetic and metabolic mechanisms that regulate its activity. These biochemical principles are discussed in the context of PPP deficiencies causing metabolic disease and the role of this pathway in biotechnology, bacterial and

The effects of reactants ratios, reaction temperatures and times on Maillard reaction products of the L-ascorbic acid/L-glutamic acid system

Directory of Open Access Journals (Sweden)

Yong-Yan ZHOU

2016-01-01

Full Text Available Abstract The transformation law of the Maillard reaction products with three different reactants ratios - equimolar reactants, excess L-glutamic acid and excess L-ascorbic acid reaction respectively, five different temperatures, and different time conditions for the L-ascorbic acid / L-glutamic acid system were investigated. Results showed that, the increase of the reaction time and temperature led to the increase of the browning products, uncoloured intermediate products, as well as aroma compounds. Compared with the equimolar reaction system, the excess L-ascorbic acid reaction system produced more browning products and uncoloured intermediate products, while the aroma compounds production remained the same. In the excess L-glutamic acid system, the uncoloured intermediate products increased slightly, the browning products remained the same, while the aroma compounds increased.

Atmospheric fates of Criegee intermediates in the ozonolysis of isoprene.

Science.gov (United States)

Nguyen, Tran B; Tyndall, Geoffrey S; Crounse, John D; Teng, Alexander P; Bates, Kelvin H; Schwantes, Rebecca H; Coggon, Matthew M; Zhang, Li; Feiner, Philip; Milller, David O; Skog, Kate M; Rivera-Rios, Jean C; Dorris, Matthew; Olson, Kevin F; Koss, Abigail; Wild, Robert J; Brown, Steven S; Goldstein, Allen H; de Gouw, Joost A; Brune, William H; Keutsch, Frank N; Seinfeld, John H; Wennberg, Paul O

2016-04-21

We use a large laboratory, modeling, and field dataset to investigate the isoprene + O3 reaction, with the goal of better understanding the fates of the C1 and C4 Criegee intermediates in the atmosphere. Although ozonolysis can produce several distinct Criegee intermediates, the C1 stabilized Criegee (CH2OO, 61 ± 9%) is the only one observed to react bimolecularly. We suggest that the C4 Criegees have a low stabilization fraction and propose pathways for their decomposition. Both prompt and non-prompt reactions are important in the production of OH (28% ± 5%) and formaldehyde (81% ± 16%). The yields of unimolecular products (OH, formaldehyde, methacrolein (42 ± 6%) and methyl vinyl ketone (18 ± 6%)) are fairly insensitive to water, i.e., changes in yields in response to water vapor (≤4% absolute) are within the error of the analysis. We propose a comprehensive reaction mechanism that can be incorporated into atmospheric models, which reproduces laboratory data over a wide range of relative humidities. The mechanism proposes that CH2OO + H2O (k(H2O)∼ 1 × 10(-15) cm(3) molec(-1) s(-1)) yields 73% hydroxymethyl hydroperoxide (HMHP), 6% formaldehyde + H2O2, and 21% formic acid + H2O; and CH2OO + (H2O)2 (k(H2O)2∼ 1 × 10(-12) cm(3) molec(-1) s(-1)) yields 40% HMHP, 6% formaldehyde + H2O2, and 54% formic acid + H2O. Competitive rate determinations (kSO2/k(H2O)n=1,2∼ 2.2 (±0.3) × 10(4)) and field observations suggest that water vapor is a sink for greater than 98% of CH2OO in a Southeastern US forest, even during pollution episodes ([SO2] ∼ 10 ppb). The importance of the CH2OO + (H2O)n reaction is demonstrated by high HMHP mixing ratios observed over the forest canopy. We find that CH2OO does not substantially affect the lifetime of SO2 or HCOOH in the Southeast US, e.g., CH2OO + SO2 reaction is a minor contribution (production by stabilized Criegees is likely unimportant in regions dominated by the reactivity of ozone with isoprene. In contrast

Phenomena and significance of intermediate spillover in electrocatalysis of oxygen and hydrogen electrode reactions

Directory of Open Access Journals (Sweden)

Jakšić Jelena M.

2012-01-01

conductivity and non-exchanged initial pure mono-bronze spillover and catalytic properties. The underpotential spillover double layer (DL charging and discharging properties of the primary oxide (M-OH, interrelated with the interactive self-catalytic effect of dipole-oriented water molecules, has also been proved and pointed out as the phenomenological appearance and aspect of the interactive spillover featuring intermediates. In fact, phenomenological aspects of spillover for the main reacting intermediate species in oxygen and hydrogen electrode reactions along with earned and withdrawn theoretical knowledge represent the basic concepts and aims of the present study.

Reaction pathways of biomass-derived oxygenates on noble metal surfaces

Science.gov (United States)

McManus, Jesse R.

As the global demand for energy continues to rise, the environmental concerns associated with increased fossil fuel consumption have motivated the use of biomass as an alternative, carbon-renewable energy feedstock. Controlling reactive chemistry of the sugars that comprise biomass through the use of catalysis becomes essential in effectively producing green fuels and value-added chemicals. Recent work on biomass conversion catalysts have demonstrated the efficacy of noble metal catalyst systems for the reforming of biomass to hydrogen fuel, and the hydrodeoxygenation of biomass-derived compounds to value-added chemicals. In particular, Pt and Pd surfaces have shown considerable promise as reforming catalysts in preliminary aqueous phase reforming studies. It becomes important to understand the mechanisms by which these molecules react on the catalyst surfaces in order to determine structure-activity relationships and bond scission energetics as to provide a framework for engineering more active and selective catalysts. Fundamental surface science techniques provide the tools to do this; however, work in this field has been so far limited to simple model molecules like ethanol and ethylene glycol. Herein, temperature programmed desorption and high resolution electron energy loss spectroscopy are utilized in an ultra-high vacuum surface science study of the biomass-derived sugar glucose on Pt and Pd single crystal catalysts. Overall, it was determined that the aldehyde function of a ring-open glucose molecule plays an integral part in the initial bonding and reforming reaction pathway, pointing to the use of aldoses glycolaldehyde and glyceraldehyde as the most appropriate model compounds for future studies. Furthermore, the addition of adatom Zn to a Pt(111) surface was found to significantly decrease the C-H and C-C bond scission activity in aldehyde containing compounds, resulting in a preferred deoxygenation pathway in opposition to the decarbonylation pathway

Intermediate energy nuclear physics (Task C) and charge exchange reactions (Task W). Technical progress report, October 1, 1985-October 1, 1986

International Nuclear Information System (INIS)

Kraushaar, J.J.

1986-10-01

This report describes the experimental work in intermediate energy research carried out over the past year at the University of Colorado. The experimental program is very broad in nature, ranging from investigations in pion-nucleus interactions, nucleon charge exchange, inelastic electron scattering, and nucleon transfer reactions. The experiments were largely carried out at the Los Alamos Meson Physics Facility, but important programs were conducted at the Tri-University Meson Facility at the University of British Columbia, the Indiana University Cyclotron Facility and Netherlands Institute for Nuclear Physics Research (NIKHEF-K)

Electrode Reaction Pathway in Oxide Anode for Solid Oxide Fuel Cells

Science.gov (United States)

Li, Wenyuan

the electrolyte to change 3PB kinetics. Compared to Ni, Co doping activates the bulk oxygen more significantly, promoting the reaction at 2PB. The active surface reaction zone is found to be enlarged by the electrolyte with high oxygen activity (SSZ vs. YSZ) when charge transfer is one of the RDS. Due to the larger exchange current for charge transfer in 3PB with SSZ electrolyte, the adsorption gradient zone is broadened, leading to enhanced surface reaction kinetics. The potential application of such finding is demonstrated on SSZ/YSZ/SSZ sandwich, showing largely improved electrode performance, opening a wide door for the utilization of electrolytes that are too expensive, fragile or instable to be used before. The bulk path way in 2PB reaction can be affected by overpotential in terms of local vacancy concentration, built-in electrical field and stability. It is proven that an uneven distribution of lattice oxygen is established under operation conditions with overpotential by both qualitative analysis and analytic solution. An electrostatic field force is present besides the concentration gradient in the anode lattice to control the motion of oxygen ions. Compared to the usual estimation based on chemical diffusion mechanism, the real deviation of ionic defects concentration under polarization from the equilibrium state near electrode/electrolyte interface is smaller with the built-in electrical field. The overpotential is demonstrated to be able to open up or shut down the bulk pathway depending on the ionic defects of electrodes. The analysis on the bulk pathway in terms of local charged species and various potentials provides new insight in anion diffusion and electrode stability.

Future possibilities with intermediate-energy neutron beams

International Nuclear Information System (INIS)

Brady, F.P.

1987-01-01

Future possibilities for using neutrons of intermediate energies (50 - 200 MeV) as a probe of the nucleus are discussed. Some of the recent thinking concerning a systematic approach for studying elastic and inelastic scattering of electrons and hadrons and the important role of medium- and intermediate-energy neutrons in such a programme is reviewed. The advantages of neutrons in this energy range over neutrons with lower energies and over intermediate-energy pions for determining nuclear-transition and ground state densities, and for distinguishing proton from neutron density (isovector sensitivity), are noted. The important role of (n,p) charge exchange reactions in nuclear excitation studies is also reviewed. Experimental methods for utilizing neutrons as probes in elastic, inelastic, and charge exchange studies at these energies are discussed

Oxidation of Tris (2-chloroethyl) phosphate in aqueous solution by UV-activated peroxymonosulfate: Kinetics, water matrix effects, degradation products and reaction pathways.

Science.gov (United States)

Xu, Xinxin; Chen, Jing; Qu, Ruijuan; Wang, Zunyao

2017-10-01

The feasibility of UV-activated peroxymonosulfate (PMS) technology for the degradation of Tris (2-chloroethyl) phosphate (TCEP) in an aqueous solution was investigated in this study. The conditions of [PMS] 0 : [TCEP] 0  = 20:1, T = 25 ± 2 °C and pH = 5.5 ± 0.5 cause a 94.6% removal of TCEP (1 mg L -1 ) after 30 min of Hg lamp irradiation. The effects of operating parameters (the oxidant doses, pH and presence of typical cations (Fe 3+ , Cu 2+ , Ni 2+ , NH 4 + ), anions (Cl - , HCO 3 - , NO 3 - , HPO 4 2- ) and humic acid (HA)) were evaluated. It was found that an increase of the PMS dose and the presence of Fe 3+ could accelerate the reaction, while the anions and HA inhibited the reaction. Meanwhile, TCEP removal in various water matrices was compared, and the order for TCEP removal was as follows: ultrapure water > tap water > synthetic water > secondary clarifier effluent > Jiuxiang river water. Twenty-two oxidation products were identified using an electrospray time-of-flight mass spectrometer, and the degradation pathways mainly involved radicals' addition and CO bond cleavage. Furthermore, ECOSAR analysis revealed that the intermediate products during the TCEP oxidation process were generally not harmful to three typical aquatic species. Hence, UV/PMS can be used as an efficient technology to treat TCEP-containing water and wastewaters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rate Constant Change of Photo Reaction of Bacteriorhodopsin Observed in Trimeric Molecular System.

Science.gov (United States)

Tsujiuchi, Yutaka; Masumoto, Hiroshi; Goto, Takashi

2016-04-01

To elucidate the time evolution of photo reaction of bacteriorhodopsin in glycerol mixed purple membrane at around 196 K under irradiation by red light, a kinetic model was constructed. The change of absorption with irradiation at times of 560 nm and 412 nm was analyzed for the purpose of determining reaction rates of photo reaction of bacteriorhodopsin and its product M intermediate. In this study it is shown that reaction rates of conversion from bacteriorhodopsin to the M intermediate can be explained by a set of linear differential equations. This model analysis concludes that bacteriorhodopsin in which constitutes a trimer unit with other two bacteriorhodopsin molecules changes into M intermediates in the 1.73 of reaction rate, in the initial step, and according to the number of M intermediate in a trimer unit, from three to one, the reaction rate of bacteriorhodopsin into M intermediates smaller as 1.73, 0.80, 0.19 which caused by influence of inter-molecular interaction between bacteriorhodopsin.

Probabilistic pathway construction.

Science.gov (United States)

Yousofshahi, Mona; Lee, Kyongbum; Hassoun, Soha

2011-07-01

Expression of novel synthesis pathways in host organisms amenable to genetic manipulations has emerged as an attractive metabolic engineering strategy to overproduce natural products, biofuels, biopolymers and other commercially useful metabolites. We present a pathway construction algorithm for identifying viable synthesis pathways compatible with balanced cell growth. Rather than exhaustive exploration, we investigate probabilistic selection of reactions to construct the pathways. Three different selection schemes are investigated for the selection of reactions: high metabolite connectivity, low connectivity and uniformly random. For all case studies, which involved a diverse set of target metabolites, the uniformly random selection scheme resulted in the highest average maximum yield. When compared to an exhaustive search enumerating all possible reaction routes, our probabilistic algorithm returned nearly identical distributions of yields, while requiring far less computing time (minutes vs. years). The pathways identified by our algorithm have previously been confirmed in the literature as viable, high-yield synthesis routes. Prospectively, our algorithm could facilitate the design of novel, non-native synthesis routes by efficiently exploring the diversity of biochemical transformations in nature. Copyright © 2011 Elsevier Inc. All rights reserved.

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

International Nuclear Information System (INIS)

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

2010-01-01

The YBCO thin film growth process from TFA precursors involves a complex reaction path which includes several oxide, fluoride and oxyfluoride intermediate phases, and the final microstructure and properties of the films are strongly influenced by the morphological and chemical evolution of these intermediate phases. In this work we present a study of the evolution of the intermediate phases involved in the TFA YBCO growth process under normal pressure conditions and we show that the oxygen partial pressure during pyrolysis of the TFA precursors is an important parameter. The Cu phase after the TFA pyrolysis can be either CuO, Cu 2 O or a mixture of both as the oxygen partial pressure is modified. The kinetics evolution of the intermediate phases has been determined for films pyrolysed in oxygen and nitrogen atmospheres and it is concluded that non-equilibrium phase transformations influence the reaction path towards epitaxial YBCO films and its microstructure. The intermediate phase evolution in these two series of films is summarized in kinetic phase diagrams.

Density functional computational studies on the glucose and glycine Maillard reaction: Formation of the Amadori rearrangement products

Science.gov (United States)

Jalbout, Abraham F.; Roy, Amlan K.; Shipar, Abul Haider; Ahmed, M. Samsuddin

Theoretical energy changes of various intermediates leading to the formation of the Amadori rearrangement products (ARPs) under different mechanistic assumptions have been calculated, by using open chain glucose (O-Glu)/closed chain glucose (A-Glu and B-Glu) and glycine (Gly) as a model for the Maillard reaction. Density functional theory (DFT) computations have been applied on the proposed mechanisms under different pH conditions. Thus, the possibility of the formation of different compounds and electronic energy changes for different steps in the proposed mechanisms has been evaluated. B-Glu has been found to be more efficient than A-Glu, and A-Glu has been found more efficient than O-Glu in the reaction. The reaction under basic condition is the most favorable for the formation of ARPs. Other reaction pathways have been computed and discussed in this work.0

The pentadehydro-Diels-Alder reaction.

Science.gov (United States)

Wang, Teng; Naredla, Rajasekhar Reddy; Thompson, Severin K; Hoye, Thomas R

2016-04-28

In the classic Diels-Alder [4 + 2] cycloaddition reaction, the overall degree of unsaturation (or oxidation state) of the 4π (diene) and 2π (dienophile) pairs of reactants dictates the oxidation state of the newly formed six-membered carbocycle. For example, in the classic Diels-Alder reaction, butadiene and ethylene combine to produce cyclohexene. More recent developments include variants in which the number of hydrogen atoms in the reactant pair and in the resulting product is reduced by, for example, four in the tetradehydro-Diels-Alder (TDDA) and by six in the hexadehydro-Diels-Alder (HDDA) reactions. Any oxidation state higher than tetradehydro (that is, lacking more than four hydrogens) leads to the production of a reactive intermediate that is more highly oxidized than benzene. This increases the power of the overall process substantially, because trapping of the reactive intermediate can be used to increase the structural complexity of the final product in a controllable and versatile manner. Here we report an unprecedented overall 4π + 2π cycloaddition reaction that generates a different, highly reactive intermediate known as an α,3-dehydrotoluene. This species is in the same oxidation state as a benzyne. Like benzynes, α,3-dehydrotoluenes can be captured by various trapping agents to produce structurally diverse products that are complementary to those arising from the HDDA process. We call this new cycloisomerization process a pentadehydro-Diels-Alder (PDDA) reaction-a nomenclature chosen for chemical taxonomic reasons rather than mechanistic ones. In addition to alkynes, nitriles (RC≡N), although non-participants in aza-HDDA reactions, readily function as the 2π component in PDDA cyclizations to produce, via trapping of the α,3-(5-aza)dehydrotoluene intermediates, pyridine-containing products.

Mechanisms of deterioration of intermediate moisture food systems

Science.gov (United States)

Labuza, T. P.

1972-01-01

A study of shelf stability in intermediate moisture foods was made. Major efforts were made to control lipid oxidation and nonenzymatic browning. In order to determine means of preventing these reactions, model systems were developed having the same water activity content relationship of intermediate moisture foods. Models were based on a cellulose-lipid and protein-lipid system with glycerol added as the humectant. Experiments with both systems indicate that lipid oxidation is promoted significantly in the intermediate moisture range. The effect appeared to be related to increased mobility of either reactants or catalysts, since when the amount of water in the system reached a level where capillary condensation occurred and thus free water was present, the rates of oxidation increased. With added glycerol, which is water soluble and thus increases the amount of mobile phase, the increase in oxidation rate occurs at a lower relative humidity. The rates of oxidation were maximized at 61% RH and decreased again at 75% RH probably due to dilution. No significant non-enzymatic browning occurred in the protein-lipid systems. Prevention of oxidation by the use of metal chelating agents was enhanced in the cellulose system, whereas, with protein present, the lipid soluble chain terminating antioxidants (such as BHA) worked equally as well. Preliminary studies of foods adjusted to the intermediate moisture range bear out the results of oxidation in model systems. It can be concluded that for most fat containing intermediate moisture foods, rancidity will be the reaction most limiting stability.

Hydronium-Induced Switching between CO2 Electroreduction Pathways.

Science.gov (United States)

Seifitokaldani, Ali; Gabardo, Christine M; Burdyny, Thomas; Dinh, Cao-Thang; Edwards, Jonathan P; Kibria, Md Golam; Bushuyev, Oleksandr S; Kelley, Shana O; Sinton, David; Sargent, Edward H

2018-03-21

Over a broad range of operating conditions, many CO 2 electroreduction catalysts can maintain selectivity toward certain reduction products, leading to materials and surfaces being categorized according to their products; here we ask, is product selectivity truly a property of the catalyst? Silver is among the best electrocatalysts for CO in aqueous electrolytes, where it reaches near-unity selectivity. We consider the hydrogenations of the oxygen and carbon atoms via the two proton-coupled-electron-transfer processes as chief determinants of product selectivity; and find using density functional theory (DFT) that the hydronium (H 3 O + ) intermediate plays a key role in the first oxygen hydrogenation step and lowers the activation energy barrier for CO formation. When this hydronium influence is removed, the activation energy barrier for oxygen hydrogenation increases significantly, and the barrier for carbon hydrogenation is reduced. These effects make the formate reaction pathway more favorable than CO. Experimentally, we then carry out CO 2 reduction in highly concentrated potassium hydroxide (KOH), limiting the hydronium concentration in the aqueous electrolyte. The product selectivity of a silver catalyst switches from entirely CO under neutral conditions to over 50% formate in the alkaline environment. The simulated and experimentally observed selectivity shift provides new insights into the role of hydronium on CO 2 electroreduction processes and the ability for electrolyte manipulation to directly influence transition state (TS) kinetics, altering favored CO 2 reaction pathways. We argue that selectivity should be considered less of an intrinsic catalyst property, and rather a combined product of the catalyst and reaction environment.

Breakup reactions at intermediate and high energy

International Nuclear Information System (INIS)

Shotter, A.C.; Bice, A.N.

1981-01-01

Having considered some general aspects of peripheral break-up reactions involving heavy ions for the incident energy range 10-2000 MeV/A, specific experiments carried out at Berkeley in 1980 in the energy range 10-20 MeV/A are discussed. These indicate that sequential break-up processes from non-sequential inelastic processes both play significant roles in the mechanism. (UK)

Possible reaction pathways of the lincomycin molecule according to the DFT calculation method

Directory of Open Access Journals (Sweden)

Eren Bahar

2017-01-01

Full Text Available Human-used antibiotics are eliminated from the body with little or no transformation at all. Traces of eliminated antibiotics enter the receiving environment directly since they cannot be treated in prevalent wastewater treatment facilities. Thus, wastewaters containing traces of antibiotics have to be treated accordingly. Lincomycin is subsequently isolated from Streptomyces lincolnensis. Lincomycin and its derivatives are antibiotics exhibiting biological activity against Gram-positive bacteria, and are natural antibiotics in the environment as pollutants. This study aims to predict the degradation mechanism of lincomycin molecule in the gaseous phase and aqueous media. Probable reaction path of lincomycin molecule with OH radicals was analyzed. Optimized geometry was calculated via Gauss View 5. Subsequently, the lowest energy status was determined through geometric optimization via Gaussian 09 program. Aiming to determine the intermediates in photocatalytic degradation mechanism of lincomycin, geometric optimization of the molecule was realized through DFT method. Activation energy for the probable reaction path was calculated, and their most stable state from the thermodynamic perspective determined for the gaseous phase and aqueous media. Impact of water solvent was investigated using the conductor-like screening solvation model (COSMO. The predicted mechanism was confirmed by comparison with experimental results on simple structures reported in literature.

A theoretical study of the reaction of O(3P) with an allyl radical C3H5

Science.gov (United States)

Park, Jong-Ho; Lee, Hohjai; Choi, Jong-Ho

2003-11-01

Ab initio calculations of the reaction of ground-state atomic oxygen [O(3P)] with an allyl radical (C3H5) have been carried out using the density functional method and the complete basis set model. On the calculated lowest doublet potential energy surface, the barrierless association of O(3P) to C3H5 forms three energy-rich addition intermediates, which are predicted to undergo subsequent isomerization and decomposition steps leading to various products: C3H4O+H, CH2O+C2H3, C2H4+CHO, C2H2O+CH3, C2H5+CO, C3H4+OH, and C2H4O+CH. The respective reaction mechanisms through the three addition intermediates are presented, and it has been found that the barrier height, reaction enthalpy, and the number of intermediates involved along the reaction coordinate are of extreme importance in understanding such reactive scattering processes. With the aid of Rice-Ramsperger-Kassel-Marcus calculations, the major reaction pathway is predicted to be the formation of acrolein (C3H4O)+H, which is consistent with the previous gas-phase bulk kinetic experiment performed by Gutman et al. [J. Phys. Chem. 94, 3652 (1990)]. For the minor C3H4+OH channel, which has been newly found in the recent crossed beam investigations, a second barrierless, direct H-atom abstraction from the central carbon of C3H5 is calculated to compete with the addition process due to the little C-H bond dissociation energy and the formation of a stable allene product. The dynamic and kinetic characteristics of the reaction mechanism are discussed on the basis of the comparison of prior statistical calculations to the nascent internal distributions of the observed OH product.

Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine

DEFF Research Database (Denmark)

Qin, Jiufu; Zhou, Yongjin J.; Krivoruchko, Anastasia

2015-01-01

intermediates can serve as platform cell factories for production of such products. Here we implement a modular pathway rewiring (MPR) strategy and demonstrate its use for pathway optimization resulting in high-level production of L-ornithine, an intermediate of L-arginine biosynthesis and a precursor...

Needs for experiment and theory in intermediate energy reactions

International Nuclear Information System (INIS)

Blann, M.

1991-01-01

We summarize several reasons intermediate energy data are needed in both basic and applied science. The status of the data base at energies up to 2 GeV is cursorily reviewed. Experimental excitation functions, single and double differential cross sections are compared with predictions of the nuclear model code ALICE. The strengths and weaknesses of the code to reproduce data are summarized. Opinions are given as to areas where data are too few or totally lacking, yet are needed for the verification of models and theories. (author). 25 refs, 22 figs

Reaction pathways for reduction of nitrate ions on platinum, rhodium, and platinum-rhodium alloy electrodes

International Nuclear Information System (INIS)

Cunha, M.C.P.M. da; De Souza, J.P.I.; Nart, F.C.

2000-01-01

The reduction of nitrate ions on platinum, rhodium, and platinum-rhodium alloy electrodes has been investigated using differential electrochemical mass spectrometry and in situ FTIR measurements. For 3 M HNO 3 concentration it has been found that nitrate starts the reduction with partial N-O bond dissociation and N-N bond formation generating NO and N 2 O. At potentials lower than 0.2 V the reaction proceeds forming dissolved NH 4 + . For potentials lower than 0 V the reduction continues via a multiple pathway reaction leading to the nonselective production of N 2 , NH 2 OH, and N 2 H 2 . On the alloyed electrodes, the production of NO and N 2 O has been observed in both cathodic and anodic scans, while on pure platinum and rhodium electrodes the reaction has been observed only during the cathodic scan. Contrasting with the pure platinum and rhodium alloys, where the N-O bond break starts forming NO and N 2 O, on the alloys HNO 2 has been observed as the first reaction step. For alloys with higher rhodium composition, like Pt 75 Rh 25 , no N 2 has been detected for potentials lower than 0 V

Carbon-supported cubic CoSe2 catalysts for oxygen reduction reaction in alkaline medium

International Nuclear Information System (INIS)

Feng Yongjun; Alonso-Vante, Nicolas

2012-01-01

Highlights: ► Cubic CoSe 2 a non-precious metal electrocatalyst for oxygen reduction in KOH. ► The catalyst shows four-electron transfer pathway in overall reaction. ► Catalyst has higher methanol tolerance than commercial Pt/C catalyst. - Abstract: A Carbon-supported CoSe 2 nanocatalyst has been developed as an alternative non-precious metal electrocatalyst for oxygen reduction reaction (ORR) in alkaline medium. The catalyst was prepared via a surfactant-free route and its electrocatalytic activity for the ORR has been investigated in detail in 0.1 M KOH electrolyte at 25 °C using rotating disk electrode (RDE) and rotating ring-disk electrode (RRDE) techniques. The prepared catalyst showed promising catalytic activity towards ORR in a four-electron transfer pathway and higher tolerance to methanol compared to commercial Pt/C catalyst in 0.1 M KOH. To some extent, the increase of CoSe 2 loading on the electrode favors a faster reduction of H 2 O 2 intermediate to H 2 O.

Covalent functionalization of graphene with reactive intermediates.

Science.gov (United States)

Park, Jaehyeung; Yan, Mingdi

2013-01-15

Graphene, a material made exclusively of sp(2) carbon atoms with its π 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

(p,n) reaction at intermediate energy

International Nuclear Information System (INIS)

Goodman, C.D.

1979-01-01

The use of the (p,n) reaction in exploring effective interactions is reviewed. Some recent data on self-conjugate nuclei taken at the Indiana University Cyclotron Facility (IUCF) are presented, and the differences between low- and high-energy data are emphasized. Experimental problems and techniques used are briefly described. It is concluded that forward-angle (p,n) spectra at energies greater than 100 MeV are dominated by Gamow-Teller (GT) transitions, while Fermi transitions (IAS transitions) dominate near 45 MeV. Prominent GT transitions are expected from a pion-exchange interaction, and it is expected that OPEP is the dominant component of the interaction in the energy range of 100 to 200 MeV. 27 figures, 2 tables

Studies of complex fragment emission in heavy ion reactions

International Nuclear Information System (INIS)

Charity, R.J.; Sobotka, L.G.

1993-01-01

The study of intermediate-energy heavy-ion nuclear reactions is reported. This work has two foci: the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities and the study of the relevant reaction mechanisms. Nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. The process leads to an understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. The program has the following objectives: to study energy, mass, and angular momentum deposition by studying incomplete fusion reactions; to gain confidence in the understanding of how highly excited systems decompose by studying all emissions from the highly excited systems; to push these kinds of studies into the intermediate energy domain (where intermediate mass fragment emission is not improbable) with excitation function studies; and to learn about the dynamics of the decays using particle-particle correlations. The last effort focuses on simple systems, where definitive statements are possible. These avenues of research share a common theme, large complex fragment production. It is this feature, more than any other, which distinguishes the intermediate energy domain

Studies of Silyl-Transfer Photochemical Reactions of N-[(Trimethylsilyl)alkyl]saccharins

Energy Technology Data Exchange (ETDEWEB)

Cho, Dae Won; Oh, Sun Wha; Park, Hea Jung; Yoon, Ung Chan [Pusan National University, Busan (Korea, Republic of); Kim, Dong Uk [Daegu National University of Education, Daegu (Korea, Republic of); Xue, Jin Ying [Harbin Normal University, Harbin (China); Mariano, Patrick S. [University of New Mexico, Albuquerque (United States)

2010-09-15

Photochemical studies of N-[(trimethylsilyl)alkyl]saccharins were carried out to investigate their photochemical behavior. Depending on the nature of the substrate and the solvent system employed, reactions of these substances can take place by either SET-promoted silyl migration from carbon to either the amide carbonyl or sulfonyl oxygen or by a N-S homolysis route. The results of the current studies show that an azomethine ylide, arising from a SET-promoted silyl migration pathway, is generated in photoreactions of N-[(trimethylsilyl)methyl]saccharin and this intermediate reacts to give various photoproducts depending on the conditions employed. In addition, irradiation of N-[(trimethylsily)ethyl]saccharin produces an excited state that reacts through two pathways, the relative importance is governed by solvent polarity and protic nature. Finally, photoirradiation of N-[(trimethylsilyl)propyl]saccharin in a highly polar solvent system comprised of 35% aqueous MeOH gives rise to formation of a tricyclic pyrrolizidine and saccharin that generated via competitive SET-promoted silyl transfer and γ-hydrogen abstraction pathways.

Studies of Silyl-Transfer Photochemical Reactions of N-[(Trimethylsilyl)alkyl]saccharins

International Nuclear Information System (INIS)

Cho, Dae Won; Oh, Sun Wha; Park, Hea Jung; Yoon, Ung Chan; Kim, Dong Uk; Xue, Jin Ying; Mariano, Patrick S.

2010-01-01

Photochemical studies of N-[(trimethylsilyl)alkyl]saccharins were carried out to investigate their photochemical behavior. Depending on the nature of the substrate and the solvent system employed, reactions of these substances can take place by either SET-promoted silyl migration from carbon to either the amide carbonyl or sulfonyl oxygen or by a N-S homolysis route. The results of the current studies show that an azomethine ylide, arising from a SET-promoted silyl migration pathway, is generated in photoreactions of N-[(trimethylsilyl)methyl]saccharin and this intermediate reacts to give various photoproducts depending on the conditions employed. In addition, irradiation of N-[(trimethylsily)ethyl]saccharin produces an excited state that reacts through two pathways, the relative importance is governed by solvent polarity and protic nature. Finally, photoirradiation of N-[(trimethylsilyl)propyl]saccharin in a highly polar solvent system comprised of 35% aqueous MeOH gives rise to formation of a tricyclic pyrrolizidine and saccharin that generated via competitive SET-promoted silyl transfer and γ-hydrogen abstraction pathways

An LL-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants.

Science.gov (United States)

Hudson, André O; Singh, Bijay K; Leustek, Thomas; Gilvarg, Charles

2006-01-01

Although lysine (Lys) biosynthesis in plants is known to occur by way of a pathway that utilizes diaminopimelic acid (DAP) as a central intermediate, the available evidence suggests that none of the known DAP-pathway variants found in nature occur in plants. A new Lys biosynthesis pathway has been identified in Arabidopsis (Arabidopsis thaliana) that utilizes a novel transaminase that specifically catalyzes the interconversion of tetrahydrodipicolinate and LL-diaminopimelate, a reaction requiring three enzymes in the DAP-pathway variant found in Escherichia coli. The LL-DAP aminotransferase encoded by locus At4g33680 was able to complement the dapD and dapE mutants of E. coli. This result, in conjunction with the kinetic properties and substrate specificity of the enzyme, indicated that LL-DAP aminotransferase functions in the Lys biosynthetic direction under in vivo conditions. Orthologs of At4g33680 were identified in all the cyanobacterial species whose genomes have been sequenced. The Synechocystis sp. ortholog encoded by locus sll0480 showed the same functional properties as At4g33680. These results demonstrate that the Lys biosynthesis pathway in plants and cyanobacteria is distinct from the pathways that have so far been defined in microorganisms.

Intermediate energy charge-exchange reactions induced by polarized 3He

International Nuclear Information System (INIS)

Kim, B.T.

1998-01-01

Spin polarization transfer is proven to be very useful in obtaining detailed information of the continuum nuclear responses. The data, taken for the (vector p,vector n) reactions, have enabled us to separate the response into the spin longitudinal and transverse components. These partial nuclear responses have been successfully used to make critical tests of nuclear structure models. In the present paper, we first summarize the results of the data and the theoretical analyses made so far. We then discuss information obtainable from the ( 3 vector He,vector t) reaction, emphasizing on the differences and similarities in comparison with the (vector p,vector n) reaction. The results of numerical calculations made for ( 3 vector He,vector t) reactions based on the microscopic distorted wave impulse approximation will also be reported. (orig.)

Nitrenes, carbenes, diradicals, and ylides. Interconversions of reactive intermediates.

Science.gov (United States)

Wentrup, Curt

2011-06-21

Rearrangements of aromatic and heteroaromatic nitrenes and carbenes can be initiated with either heat or light. The thermal reaction is typically induced by flash vacuum thermolysis, with isolation of the products at low temperatures. Photochemical experiments are conducted either under matrix isolation conditions or in solution at ambient temperature. These rearrangements are usually initiated by ring expansion of the nitrene or carbene to a seven-membered ring ketenimine, carbodiimide, or allene (that is, a cycloheptatetraene or an azacycloheptatetraene when a nitrogen is involved). Over the last few years, we have found that two types of ring opening take place as well. Type I is an ylidic ring opening that yields nitrile ylides or diazo compounds as transient intermediates. Type II ring opening produces either dienylnitrenes (for example, from 2-pyridylnitrenes) or 1,7-(1,5)-diradicals (such as those formed from 2-quinoxalinylnitrenes), depending on which of these species is better stabilized by resonance. In this Account, we describe our achievements in elucidating the nature of the ring-opened species and unraveling the connections between the various reactive intermediates. Both of these ring-opening reactions are found, at least in some cases, to dominate the subsequent chemistry. Examples include the formation of ring-opened ketenimines and carbodiimides, as well as the ring contraction reactions that form five-membered ring nitriles (such as 2- and 3-cyanopyrroles from pyridylnitrenes, N-cyanoimidazoles from 2-pyrazinyl and 4-pyrimidinylnitrenes, N-cyanopyrazoles from 2-pyrimidinylnitrenes and 3-pyridazinylnitrenes, and so forth). The mechanisms of formation of the open-chain and ring-contraction products were unknown at the onset of this study. In the course of our investigation, several reactions with three or more consecutive reactive intermediates have been unraveled, such as nitrene, seven-membered cyclic carbodiimide, and open-chain nitrile ylide

MCNP6 fragmentation of light nuclei at intermediate energies

Energy Technology Data Exchange (ETDEWEB)

Mashnik, Stepan G., E-mail: mashnik@lanl.gov [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Kerby, Leslie M. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); University of Idaho, Moscow, ID 83844 (United States)

2014-11-11

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

Development and implementation of a critical pathway for prevention of adverse reactions to contrast media for computed tomography

International Nuclear Information System (INIS)

Jang, Keun Jo; Kweon, Dae Cheol; Kim, Myeong Goo; Yoo, Beong Gyu

2007-01-01

The purpose of this study is to develop a critical pathway (CP) for the prevention of adverse reactions to contrast media for computed tomography. The CP was developed and implemented by a multidisciplinary group is Seoul National University Hospital. The CP was applied to CT patients. Patients who underwent CT scanning were included in the CP group from March in 2004. The satisfaction of the patients with CP was compared with non-CP groups. We also investigated the degree of satisfaction among the radiological technologists and nurses. The degree of patient satisfaction with the care process increased patient information (24%), prevention of adverse reactions to contrast media (19%), pre-cognitive effect of adverse reactions to contrast media (39%) and information degree of adverse reactions to contrast media (19%). This CP program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings

Development and implementation of a critical pathway for prevention of adverse reactions to contrast media for computed tomography

Energy Technology Data Exchange (ETDEWEB)

Jang, Keun Jo [Presbyterian Medical Center, Seoul (Korea, Republic of); Kweon, Dae Cheol; Kim, Myeong Goo [Seoul National University Hospital, Seoul (Korea, Republic of); Yoo, Beong Gyu [Wonkwang Health Science College, Iksan (Korea, Republic of)

2007-03-15

The purpose of this study is to develop a critical pathway (CP) for the prevention of adverse reactions to contrast media for computed tomography. The CP was developed and implemented by a multidisciplinary group is Seoul National University Hospital. The CP was applied to CT patients. Patients who underwent CT scanning were included in the CP group from March in 2004. The satisfaction of the patients with CP was compared with non-CP groups. We also investigated the degree of satisfaction among the radiological technologists and nurses. The degree of patient satisfaction with the care process increased patient information (24%), prevention of adverse reactions to contrast media (19%), pre-cognitive effect of adverse reactions to contrast media (39%) and information degree of adverse reactions to contrast media (19%). This CP program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings.

Dynamics of anion-molecule reactions at low energy

International Nuclear Information System (INIS)

Mikosch, J.

2007-11-01

Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S N 2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S N 2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S N 2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S N 2 mechanism involving CH 3 -rotation. (orig.)

Dynamics of anion-molecule reactions at low energy

Energy Technology Data Exchange (ETDEWEB)

Mikosch, J.

2007-11-15

Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S{sub N}2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S{sub N}2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S{sub N}2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S{sub N}2 mechanism involving CH{sub 3}-rotation. (orig.)

Catalytic Hydrotreatment of Fast Pyrolysis Oil: Model Studies on Reaction Pathways for the Carbohydrate Fraction

OpenAIRE

Wildschut, J.; Arentz, J.; Rasrendra, C. B.; Venderbosch, R. H.; Heeres, H. J.

2009-01-01

Fast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250-400 degrees C, 100-200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon-like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions during hydrotreatment is desirable to reduce the formation of by-products such as char and gaseous components. This paper deals with the catalytic hydrotreatment of representative model components for t...

Statistical properties of multistep enzyme-mediated reactions

OpenAIRE

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

2008-01-01

Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumu...

Gamow Teller strength from charge exchange reactions at intermediate energies

International Nuclear Information System (INIS)

Haeusser, O.

1989-07-01

Detailed studies of the spin-isospin structure of nuclear excitations are possible at TRIUMF's medium resolution spectrometer using the (n,p), ( p → , p →/ ) and (p,n) reactions. We discuss here results on isospin symmetry of inelastic nucleon scattering reactions populating isospin triads in A=6 and A=12 nuclei. The β + Gamow Teller strength function from (n,p) reactions on (sd) and (fp) shell targets is found to be substantially quenched compared to current nuclear structure models using the free-nucleon axial-vector coupling constant. (Author) 22 refs., 3 figs

ESL intermediate/advanced writing

CERN Document Server

Munoz Page, Mary Ellen; Jaskiewicz, Mary

2011-01-01

Master ESL (English as a Second Language) Writing with the study guide designed for non-native speakers of English. Skill-building lessons relevant to today's topics help ESL students write complete sentences, paragraphs, and even multi-paragraph essays. It's perfect for classroom use or self-guided writing preparation.DETAILS- Intermediate drills for improving skills with parallel structure, mood, correct shifting errors & dangling participles- Advanced essay drills focusing on narrative, descriptive, process, reaction, comparison and contrast- Superb preparation for students taking the TOEFL

Modeling reaction histories to study chemical pathways in condensed phase detonation

International Nuclear Information System (INIS)

Scott Stewart, D.; Hernández, Alberto; Lee, Kibaek

2016-01-01

The estimation of pressure and temperature histories, which are required to understand chemical pathways in condensed phase explosives during detonation, is discussed. We argue that estimates made from continuum models, calibrated by macroscopic experiments, are essential to inform modern, atomistic-based reactive chemistry simulations at detonation pressures and temperatures. We present easy to implement methods for general equation of state and arbitrarily complex chemical reaction schemes that can be used to compute reactive flow histories for the constant volume, the energy process, and the expansion process on the Rayleigh line of a steady Chapman-Jouguet detonation. A brief review of state-of-the-art of two-component reactive flow models is given that highlights the Ignition and Growth model of Lee and Tarver [Phys. Fluids 23, 2362 (1980)] and the Wide-Ranging Equation of State model of Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. We discuss evidence from experiments and reactive molecular dynamic simulations that motivate models that have several components, instead of the two that have traditionally been used to describe the results of macroscopic detonation experiments. We present simplified examples of a formulation for a hypothetical explosive that uses simple (ideal) equation of state forms and detailed comparisons. Then, we estimate pathways computed from two-component models of real explosive materials that have been calibrated with macroscopic experiments.

Discovery of competing anaerobic and aerobic pathways in umpolung amide synthesis allows for site-selective amide 18O-labeling

Science.gov (United States)

Shackleford, Jessica P.; Shen, Bo; Johnston, Jeffrey N.

2012-01-01

The mechanism of umpolung amide synthesis was probed by interrogating potential sources for the oxygen of the product amide carbonyl that emanates from the α-bromo nitroalkane substrate. Using a series of 18O-labeled substrates and reagents, evidence is gathered to advance two pathways from the putative tetrahedral intermediate. Under anaerobic conditions, a nitro-nitrite isomerization delivers the amide oxygen from nitro oxygen. The same homolytic nitro-carbon fragmentation can be diverted by capture of the carbon radical intermediate with oxygen gas (O2) to deliver the amide oxygen from O2. This understanding was used to develop a straightforward protocol for the preparation of 18O-labeled amides in peptides by simply performing the umpolung amide synthesis reaction under an atmosphere of . PMID:22184227

The hexadehydro-Diels-Alder reaction.

Science.gov (United States)

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

2012-10-11

Arynes (aromatic systems containing, formally, a carbon-carbon triple bond) are among the most versatile of all reactive intermediates in organic chemistry. They can be 'trapped' to give products that are used as pharmaceuticals, agrochemicals, dyes, polymers and other fine chemicals. Here we explore a strategy that unites the de novo generation of benzynes-through a hexadehydro-Diels-Alder reaction-with their in situ elaboration into structurally complex benzenoid products. In the hexadehydro-Diels-Alder reaction, a 1,3-diyne is engaged in a [4+2] cycloisomerization with a 'diynophile' to produce the highly reactive benzyne intermediate. The reaction conditions for this simple, thermal transformation are notable for being free of metals and reagents. The subsequent and highly efficient trapping reactions increase the power of the overall process. Finally, we provide examples of how this de novo benzyne generation approach allows new modes of intrinsic reactivity to be revealed.

Indirect Liquefaction of Biomass to Transportation Fuels Via Mixed Oxygenated Intermediates

Energy Technology Data Exchange (ETDEWEB)

Tan, Eric C.D.

2016-11-14

This paper presents a comparative techno-economic analysis of four emerging conversion pathways from biomass to gasoline-, jet-, and diesel-range hydrocarbons via indirect liquefaction with specific focus on pathways utilizing oxygenated intermediates. The processing steps include: biomass-to-syngas via indirect gasification, gas cleanup, conversion of syngas to alcohols/oxygenates followed by conversion of alcohols/oxygenates to hydrocarbon blendstocks via dehydration, oligomerization, and hydrogenation.

The mechanism for enhanced oxidation degradation of dioxin-like PCBs (PCB-77) in the atmosphere by the solvation effect.

Science.gov (United States)

Xin, Mei-Ling; Yang, Jia-Wen; Li, Yu

2017-07-11

The reaction pathways of PCB-77 in the atmosphere with ·OH, O 2 , NO x , and 1 O 2 were inferred based on density functional theory calculations with the 6-31G* basis set. The structures the reactants, transition states, intermediates, and products were optimized. The energy barriers and reaction heats were obtained to determine the energetically favorable reaction pathways. To study the solvation effect, the energy barriers and reaction rates for PCB-77 with different polar and nonpolar solvents (cyclohexane, benzene, carbon tetrachloride, chloroform, acetone, dichloromethane, ethanol, methanol, acetonitrile, dimethylsulfoxide, and water) were calculated. The results showed that ·OH preferentially added to the C5 atom of PCB-77, which has no Cl atom substituent, to generate the intermediate IM5. This intermediate subsequently reacted with O 2 via pathway A to generate IM5a, with an energy barrier of 7.27 kcal/mol and total reaction rate of 8.45 × 10 -8  cm 3 /molecule s. Pathway B involved direct dehydrogenation of IM5 to produce the OH-PCBs intermediate IM5b, with an energy barrier of 28.49 kcal/mol and total reaction rate of 1.15 × 10 -5  cm 3 /molecule s. The most likely degradation pathway of PCB-77 in the atmosphere is pathway A to produce IM5a. The solvation effect results showed that cyclohexane, carbon tetrachloride, and benzene could reduce the reaction energy barrier of pathway A. Among these solvents, the solvation effect of benzene was the largest, and could reduce the total reaction energy barrier by 25%. Cyclohexane, carbon tetrachloride, benzene, dichloromethane, acetone, and ethanol could increase the total reaction rate of pathway A. The increase in the reaction rate of pathway A with benzene was 8%. The effect of solvents on oxidative degradation of PCB-77 in the atmosphere is important. Graphical abstract The reaction pathways of PCB-77 in the atmosphere with •OH, O2, NOx, and 1O2 were inferred based on density functional theory

Chiral Nickel(II) Complex Catalyzed Enantioselective Doyle-Kirmse Reaction of α-Diazo Pyrazoleamides.

Science.gov (United States)

Lin, Xiaobin; Tang, Yu; Yang, Wei; Tan, Fei; Lin, Lili; Liu, Xiaohua; Feng, Xiaoming

2018-03-07

Although high enantioselectivity of [2,3]-sigmatropic rearrangement of sulfonium ylides (Doyle-Kirmse reaction) has proven surprisingly elusive using classic chiral Rh(II) and Cu(I) catalysts, in principle it is due to the difficulty in fine discrimination of the heterotopic lone pairs of sulfur and chirality inversion at sulfur of sulfonium ylides. Here, we show that the synergistic merger of new α-diazo pyrazoleamides and a chiral N, N'-dioxide-nickel(II) complex catalyst enables a highly enantioselective Doyle-Kirmse reaction. The pyrazoleamide substituent serves as both an activating and a directing group for the ready formation of a metal-carbene- and Lewis-acid-bonded ylide intermediate in the assistance of a dual-tasking nickel(II) complex. An alternative chiral Lewis-acid-bonded ylide pathway greatly improves the product enantiopurity even for the reaction of a symmetric diallylsulfane. The majority of transformations over a series of aryl- or vinyl-substituted α-diazo pyrazoleamindes and sulfides proceed rapidly (within 5-20 min in most cases) with excellent results (up to 99% yield and 96% ee), providing a breakthrough in enantioselective Doyle-Kirmse reaction.

The nuclear reaction matrix

International Nuclear Information System (INIS)

Krenciglowa, E.M.; Kung, C.L.; Kuo, T.T.S.; Osnes, E.; and Department of Physics, State University of New York at Stony Brook, Stony Brook, New York 11794)

1976-01-01

Different definitions of the reaction matrix G appropriate to the calculation of nuclear structure are reviewed and discussed. Qualitative physical arguments are presented in support of a two-step calculation of the G-matrix for finite nuclei. In the first step the high-energy excitations are included using orthogonalized plane-wave intermediate states, and in the second step the low-energy excitations are added in, using harmonic oscillator intermediate states. Accurate calculations of G-matrix elements for nuclear structure calculations in the Aapprox. =18 region are performed following this procedure and treating the Pauli exclusion operator Q 2 /sub p/ by the method of Tsai and Kuo. The treatment of Q 2 /sub p/, the effect of the intermediate-state spectrum and the energy dependence of the reaction matrix are investigated in detail. The present matrix elements are compared with various matrix elements given in the literature. In particular, close agreement is obtained with the matrix elements calculated by Kuo and Brown using approximate methods

Origin and pathways of Winter Intermediate Water in the Northwestern Mediterranean Sea using observations and numerical simulation

Science.gov (United States)

Juza, Mélanie; Renault, Lionel; Ruiz, Simon; Tintoré, Joaquin

2013-12-01

The study of water masses worldwide (their formation, spreading, mixing, and impact on general circulation) is essential for a better understanding of the ocean circulation and variability. In this paper, the formation and main pathways of Winter Intermediate Water (WIW) in the Northwestern Mediterranean Sea (NWMED) are investigated during the winter-spring 2011 using observations and numerical simulation. The main results show that the WIW, formed along the continental shelves of the Gulf of Lion and Balearic Sea, circulates southward following five preferential pathways depending on the WIW formation site location and the oceanic conditions. WIW joins the northeastern part of the Balearic Sea, or flows along the continental shelves until joining the Balearic Current (maximum of 0.33 Sv in early-April) or further south until the Ibiza Channel entrance. Two additional trajectories, contributing to water mass exchanges with the southern part of the Western Mediterranean Sea, bring the WIW through the Ibiza and Mallorca Channels (maxima of 0.26 Sv in late-March and 0.1 Sv in early-April, respectively). The circulation of WIW over the NWMED at 50-200 m depth, its mixing and spreading over the Western Mediterranean Sea (reaching the south of the Balearic Islands, the Algero-Provencal basin, the Ligurian and the Alboran Seas) suggest that the WIW may have an impact on the ocean circulation by eddy blocking effect, exchange of water masses between north and south subbasins of Western Mediterranean Sea through the Ibiza Channel or modification of the ocean stratification.

Theoretical investigation of the oxidation pathways of the Cl-initiated reaction of 2-methyl-3-buten-2-ol

Science.gov (United States)

Zhang, Weichao; Zhang, Dongju

2012-12-01

The mechanism and products of the reaction of 2-methyl-3-buten-2-ol (MBO232) with Cl atoms in the presence of O2 have been elucidated by performing high-level quantum chemistry calculations. The geometries of the reactants, intermediates, transition states, and products are optimized at the MP2(full)/6-311G(d, p) level, and their single-point energies are refined at the CCSD(T)/6-311 + G(d, p) level. The potential energy surface profiles have been constructed at the CCSD(T)/6-311 + G(d, p)//MP2(full)/6-311G(d, p) + 0.95 × ZPE level of theory, and the possible channels involved in the reaction are also discussed. The calculations indicate that the reaction predominantly proceeds via the addition of Cl atoms to the double bond rather than the direct abstraction of the H atoms in MBO232. The nascent adducts (CH3)2C(OH)CHCH2Cl (IM1) and (CH3)2C(OH)CHClCH2 (IM2) do not undergo subsequent isomerization and dissociation reactions, but rather react with O2. The theoretical results show that the major products are CH2ClCHO and CH3C(O)CH3 for the reaction of MBO232 + Cl in the presence of O2, which is in good agreement with the experimental finding.

Effects of Water Molecule on CO Oxidation by OH: Reaction Pathways, Kinetic Barriers, and Rate Constants.

Science.gov (United States)

Zhang, Linyao; Yang, Li; Zhao, Yijun; Zhang, Jiaxu; Feng, Dongdong; Sun, Shaozeng

2017-07-06

The water dilute oxy-fuel combustion is a clean combustion technology for near-zero emission power; and the presence of water molecule could have both kinetic and dynamic effects on combustion reactions. The reaction OH + CO → CO 2 + H, one of the most important elementary reactions, has been investigated by extensive electronic structure calculations. And the effects of a single water molecule on CO oxidation have been studied by considering the preformed OH(H 2 O) complex reacts with CO. The results show little change in the reaction pathways, but the additional water molecule actually increases the vibrationally adiabatic energy barriers (V a G ). Further thermal rate constant calculations in the temperature range of 200 to 2000 K demonstrate that the total low-pressure limit rate constant for the water assisted OH(H 2 O) + CO → CO 2 + H 2 O + H reaction is 1-2 orders lower than that of the water unassisted one, which is consistent with the change of V a G . Therefore, the hydrated radical OH(H 2 O) would actually slow down the oxidation of CO. Meanwhile, comparisons show that the M06-2X/aug-cc-pVDZ method gives a much better estimation in energy and thus is recommended to be employed for direct dynamics simulations.

Supercritical carbon dioxide versus toluene as reaction media in silica functionalisation: Synthesis and characterisation of bonded aminopropyl silica intermediate.

Science.gov (United States)

Ashu-Arrah, Benjamin A; Glennon, Jeremy D

2017-06-09

This research reports supercritical carbon dioxide versus toluene as reaction media in silica functionalisation for use in liquid chromatography. Bonded aminopropyl silica (APS) intermediates were prepared when porous silica particles (Exsil-pure, 3μm) were reacted with 3-aminopropyltriethoxysilane (3-APTES) or N,N-dimethylaminopropyltrimethoxysilane (DMAPTMS) using supercritical carbon dioxide (sc-CO 2 ) and toluene as reaction media. Covalent bonding to silica was confirmed using elemental microanalysis (CHN), thermogravimetric analysis (TGA), zeta potential (ξ), diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, scanning electron microscopy (SEM) and solid-state nuclear magnetic resonance (CP/MAS NMR) spectroscopy. The results demonstrate that under sc-CO 2 conditions of 100°C/414bar in a substantial reduced time of 3h, the surface coverage of APS (evaluated from%C obtained from elemental analysis) prepared with APTES (%C: 8.03, 5.26μmol/m -2 ) or DMAPTES (%C: 5.12, 4.58μmol/m 2 ) is somewhat higher when compared to organic based reactions under reflux in toluene at a temperature of 110°C in 24h with APTES (%C: 7.33, 4.71μmol/m 2 ) and DMAPTMS (%C: 4.93, 4.38μmol/m 2 ). Zeta potential measurements revealed a change in electrostatic surface charge from negative values for bare Exsil-pure silica to positive for functionalised APS materials indicating successful immobilization of the aminosilane onto the surface of silica. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface reaction modification: The effect of structured overlayers of sulfur on the kinetics and mechanism of the decomposition of formic acid on Pt(111)

Science.gov (United States)

Abbas, N.; Madix, R. J.

The reaction of formic acid (DCOOH) on Pt(111), Pt(111)-(2×2)S and Pt(111)-(√3×√3)R30°S surfaces was examined by temperature programmed reaction spectroscopy. On the clean surface formic acid decomposed to yield primarily carbon dioxide and the hydrogenic species (H 2, HD and D 2) at low coverages. Although the formation of water and carbon monoxide via a dehydration reaction was observed at these coverages, the yield of these products was small when compared to the other products of reaction. The evolution of CO 2 at low temperature was ascribed to the decomposition of the formate intermediate. In the presence of sulfur the amount of molecularly adsorbed formic acid decreased up to a factor of three on the (√3×√3)R30°S surface, and a decline in the reactivity of over an order of magnitude was also observed. The only products formed were the hydrogenic species and carbon dioxide. The absence of carbon monoxide indicated that the dehydration pathway was blocked by sulfur. In addition to the low temperature CO 2 peak a high temperature CO 2-producing path was also evident. It was inferred from both the stoichiometry and the coincident evolution of D 2 and CO 2 in the high temperature states that these products also evolved due to the decomposition of the formate intermediate. On increasing the sulfur coverage to one-third monolayer this intermediate was further stabilized, and a predominance of the decomposition via the high temperature path was observed. Stability of the formate intermediate was attributed to inhibition of the decomposition reaction by sulfur atoms. The activation energy for formate decomposition increased from 15 kcal/gmole on the clean surface to 24.3 kcal/gmol on the (√3×√3)R30°S overlayer.

Investigating the nature of palladium chain-walking in the enantioselective redox-relay Heck reaction of alkenyl alcohols.

Science.gov (United States)

Hilton, Margaret J; Xu, Li-Ping; Norrby, Per-Ola; Wu, Yun-Dong; Wiest, Olaf; Sigman, Matthew S

2014-12-19

The mechanism of the redox-relay Heck reaction was investigated using deuterium-labeled substrates. Results support a pathway through a low energy palladium-alkyl intermediate that immediately precedes product formation, ruling out a tautomerization mechanism. DFT calculations of the relevant transition structures at the M06/LAN2DZ+f/6-31+G* level of theory show that the former pathway is favored by 5.8 kcal/mol. Palladium chain-walking toward the alcohol, following successive β-hydride eliminations and migratory insertions, is also supported in this study. The stereochemistry of deuterium labels is determined, lending support that the catalyst remains bound to the substrate during the relay process and that both cis- and trans-alkenes form from β-hydride elimination.

Chemicals from Biomass: Combining Ring-Opening Tautomerization and Hydrogenation Reactions to Produce 1,5-Pentanediol from Furfural.

Science.gov (United States)

Brentzel, Zachary J; Barnett, Kevin J; Huang, Kefeng; Maravelias, Christos T; Dumesic, James A; Huber, George W

2017-04-10

A process for the synthesis of 1,5-pentanediol (1,5-PD) with 84 % yield from furfural is developed, utilizing dehydration/hydration, ring-opening tautomerization, and hydrogenation reactions. Although this process has more reaction steps than the traditional direct hydrogenolysis of tetrahydrofurfuryl alcohol (THFA), techno-economic analyses demonstrate that this process is the economically preferred route for the synthesis of biorenewable 1,5-PD. 2-Hydroxytetrahydropyran (2-HY-THP) is the key reaction pathway intermediate that allows for a decrease in the minimum selling price of 1,5-PD. The reactivity of 2-HY-THP is 80 times greater than that of THFA over a bimetallic hydrogenolysis catalyst. This enhanced reactivity is a result of the ring-opening tautomerization to 5-hydoxyvaleraldehyde and subsequent hydrogenation to 1,5-PD. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Elementary steps and reaction pathways in the aqueous phase alkylation of phenol with ethanol

Energy Technology Data Exchange (ETDEWEB)

Eckstein, Sebastian; Hintermeier, Peter H.; Olarte, Mariefel V.; Liu, Yue; Baráth, Eszter; Lercher, Johannes A.

2017-08-01

The hydronium ion normalized reaction rate in aqueous phase alkylation of phenol with ethanol on H-MFI zeolites increases with decreasing concentration of acid sites. Higher rates are caused by higher concentrations of phenol in the zeolite pores, as the concentration of hydronium ions generated by zeolite Brønsted acid sites decreases. Considering the different concentrations of reacting species it is shown that the intrinsic rate constant for alkylation is independent of the concentration of hydronium ions in the zeolite pores. Alkylation at the aromatic ring of phenol and of toluene as well as O-alkylation of phenol have the same activation energy, 104 ± 5 kJ/mol. This is energetic barrier to form the ethyl carbenium ion from ethanol associated to the hydronium ion. Thus, in both the reaction pathways the catalyst involves a carbenium ion, which forms a bond to a nucleophilic oxygen (ether formation) or carbon (alkylation).

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

Science.gov (United States)

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.

Exploring possible reaction pathways for the o-atom transfer reactions to unsaturated substrates catalyzed by a [Ni-NO2 ] ↔ [Ni-NO] redox couple using DFT methods.

Science.gov (United States)

Tsipis, Athanassios C

2017-07-15

The (nitro)(N-methyldithiocarbamato)(trimethylphospane)nickel(II), [Ni(NO 2 )(S 2 CNHMe)(PMe 3 )] complex catalyses efficiently the O-atom transfer reactions to CO and acetylene. Energetically feasible sequence of elementary steps involved in the catalytic cycle of the air oxidation of CO and acetylene are proposed promoted by the Ni(NO 2 )(S 2 CNHMe)(PMe 3 )] ↔ Ni(NO 2 )(S 2 CNHMe)(PMe 3 ) redox couple using DFT methods both in vacuum and dichloromethane solutions. The catalytic air oxidation of HC≡CH involves formation of a five-member metallacycle intermediate, via a [3 + 2] cyclo-addition reaction of HC≡CH to the Ni-N = O moiety of the Ni(NO 2 )(S 2 CNHMe)(PMe 3 )] complex, followed by a β H-atom migration toward the C α carbon atom of the coordinated acetylene and release of the oxidation product (ketene). The geometric and energetic reaction profile for the reversible [Ni( κN1-NO 2 )(S 2 CNHMe)(PMe 3 )] ⇌ [Ni( κO,O2-ONO)(S 2 CNHMe)(PMe 3 )] linkage isomerization has also been modeled by DFT calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Electron transfer reactions

CERN Document Server

Cannon, R D

2013-01-01

Electron Transfer Reactions deals with the mechanisms of electron transfer reactions between metal ions in solution, as well as the electron exchange between atoms or molecules in either the gaseous or solid state. The book is divided into three parts. Part 1 covers the electron transfer between atoms and molecules in the gas state. Part 2 tackles the reaction paths of oxidation states and binuclear intermediates, as well as the mechanisms of electron transfer. Part 3 discusses the theories and models of the electron transfer process; theories and experiments involving bridged electron transfe

[Intermediate energy nuclear physics

International Nuclear Information System (INIS)

1989-01-01

This report summarizes work in experimental Intermediate Energy Nuclear Physics carried out between October 1, 1988 and October 1, 1989 at the Nuclear Physics Laboratory of the University of Colorado, Boulder, under grant DE-FG02-86ER-40269 with the United States Department of Energy. The experimental program is very broadly based, including pion-nucleon studies at TRIUMF, inelastic pion scattering and charge exchange reactions at LAMPF, and nucleon charge exchange at LAMPF/WNR. In addition, a number of other topics related to accelerator physics are described in this report

Novel Fragmentation Pathways of Anionic Adducts of Steroids Formed by Electrospray Anion Attachment Involving Regioselective Attachment, Regiospecific Decompositions, Charge-Induced Pathways, and Ion-Dipole Complex Intermediates

Science.gov (United States)

Rannulu, Nalaka S.; Cole, Richard B.

2012-09-01

The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion]- adducts of these steroids revealed that fluoride adduct [M + F]- precursors first lose HF to produce [M - H]- and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d4-pregnenolone, are also discussed.

Nucleon induced reactions

International Nuclear Information System (INIS)

Gmuca, S.; Antalik, R.; Kristiak, J.

1988-01-01

The collection contains full texts of 37 contributions; all fall within the INIS Subject Scope. The topics treated include some unsolved problems of nuclear reactions and relevant problems of nuclear structure at low and intermediate energies. (Z.S.)

Influences of the molecular fuel structure on combustion reactions towards soot precursors in selected alkane and alkene flames.

Science.gov (United States)

Ruwe, Lena; Moshammer, Kai; Hansen, Nils; Kohse-Höinghaus, Katharina

2018-04-25

In this study, we experimentally investigate the high-temperature oxidation kinetics of n-pentane, 1-pentene and 2-methyl-2-butene (2M2B) in a combustion environment using flame-sampling molecular beam mass spectrometry. The selected C5 fuels are prototypes for linear and branched, saturated and unsaturated fuel components, featuring different C-C and C-H bond structures. It is shown that the formation tendency of species, such as polycyclic aromatic hydrocarbons (PAHs), yielded through mass growth reactions increases drastically in the sequence n-pentane fuel-dependent reaction sequences of the gas-phase combustion mechanism that provide explanations for the observed difference in the PAH formation tendency. First, we investigate the fuel-structure-dependent formation of small hydrocarbon species that are yielded as intermediate species during the fuel decomposition, because these species are at the origin of the subsequent mass growth reaction pathways. Second, we review typical PAH formation reactions inspecting repetitive growth sequences in dependence of the molecular fuel structure. Third, we discuss how differences in the intermediate species pool influence the formation reactions of key aromatic ring species that are important for the PAH growth process underlying soot formation. As a main result it was found that for the fuels featuring a C[double bond, length as m-dash]C double bond, the chemistry of their allylic fuel radicals and their decomposition products strongly influences the combination reactions to the initially formed aromatic ring species and as a consequence, the PAH formation tendency.

Comparative study of ion conducting pathways in borate glasses

International Nuclear Information System (INIS)

Hall, Andreas; Swenson, Jan; Adams, Stefan

2006-01-01

The conduction pathways in metal-halide doped silver, lithium, and sodium diborate glasses have been examined by bond valence analysis of reverse Monte Carlo (RMC) produced structural models of the glasses. Although all glass compositions have basically the same short-range structure of the boron-oxygen network, it is evident that the intermediate-range structure is strongly dependent on the type of mobile ion. The topography of the pathways and the coordination of the pathway sites differ distinctly between the three glass systems. The mobile silver ions in the AgI-doped glass tend to be mainly iodine-coordinated and travel in homogeneously distributed pathways located in salt-rich channels of the borate network. In the NaCl-doped glass, there is an inhomogeneous spatial distribution of pathways that reflects the inhomogeneous introduction of salt ions into the glass. However, since the salt clusters are not connected, no long-range conduction pathways are formed without including also oxygen-rich regions. The pathways in the LiCl-doped glass are slightly more evenly distributed compared to the NaCl-doped glass (but not as ordered as in the AgI-doped glass), and the regions of mainly oxygen-coordinated pathway sites are of higher importance for the long-range migration. In order to more accurately investigate how these differences in the intermediate-range order of the glasses affect the ionic conductivity, we have compared the realistic structure models to more or less randomized structures. An important conclusion from this comparison is that we find no evidence that a pronounced intermediate-range order in the atomic structure or in the network of conduction pathways, as in the AgI-doped glass, is beneficial for the dc conductivity

A genetic and pharmacological analysis of isoprenoid pathway by LC-MS/MS in fission yeast.

Directory of Open Access Journals (Sweden)

Tomonori Takami

Full Text Available Currently, statins are the only drugs acting on the mammalian isoprenoid pathway. The mammalian genes in this pathway are not easily amenable to genetic manipulation. Thus, it is difficult to study the effects of the inhibition of various enzymes on the intermediate and final products in the isoprenoid pathway. In fission yeast, antifungal compounds such as azoles and terbinafine are available as inhibitors of the pathway in addition to statins, and various isoprenoid pathway mutants are also available. Here in these mutants, treated with statins or antifungals, we quantified the final and intermediate products of the fission yeast isoprenoid pathway using liquid chromatography-mass spectrometry/mass spectrometry. In hmg1-1, a mutant of the gene encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR, ergosterol (a final sterol product, and squalene (an intermediate pathway product, were decreased to approximately 80% and 10%, respectively, compared with that of wild-type cells. Consistently in wild-type cells, pravastatin, an HMGR inhibitor decreased ergosterol and squalene, and the effect was more pronounced on squalene. In hmg1-1 mutant and in wild-type cells treated with pravastatin, the decrease in the levels of farnesyl pyrophosphate and geranylgeranyl pyrophosphate respectively was larger than that of ergosterol but was smaller than that of squalene. In Δerg6 or Δsts1 cells, mutants of the genes involved in the last step of the pathway, ergosterol was not detected, and the changes of intermediate product levels were distinct from that of hmg1-1 mutant. Notably, in wild-type cells miconazole and terbinafine only slightly decreased ergosterol level. Altogether, these studies suggest that the pleiotropic phenotypes caused by the hmg1-1 mutation and pravastatin might be due to decreased levels of isoprenoid pyrophosphates or other isoprenoid pathway intermediate products rather than due to a decreased ergosterol level.

Kinetics of formation of acrylamide and Schiff base intermediates from asparagine and glucose

DEFF Research Database (Denmark)

Hedegaard, Rikke Susanne Vingborg; Frandsen, Henrik; Skibsted, Leif H.

2008-01-01

From the concentration of glucose and asparagine as reactants and of acrylamide as product each determined by LC-MS during reaction in an acetonitrile/water (68:32) model system at pH 7.6 (0.04 M phosphate buffer) and from the relative concentration of the Schiff base intermediate, the decarboxyl......From the concentration of glucose and asparagine as reactants and of acrylamide as product each determined by LC-MS during reaction in an acetonitrile/water (68:32) model system at pH 7.6 (0.04 M phosphate buffer) and from the relative concentration of the Schiff base intermediate...

Nano-MnO2-mediated transformation of triclosan with humic molecules present: kinetics, products, and pathways.

Science.gov (United States)

Sun, Kai; Li, Shunyao; Waigi, Michael Gatheru; Huang, Qingguo

2018-05-01

It has been shown that manganese dioxide (MnO 2 ) can mediate transformation of phenolic contaminants to form phenoxyl radical intermediates, and subsequently, these intermediates intercouple to form oligomers via covalent binding. However, the reaction kinetics and transformation mechanisms of phenolic contaminants with humic molecules present in nano-MnO 2 -mediated systems were still unclear. In this study, it was proven that nano-MnO 2 were effective in transforming triclosan under acidic conditions (pH 3.5-5.0) during manganese reduction, and the apparent pseudo first-order kinetics rate constants (k = 0.0599-1.5314 h -1 ) increased as the pH decreased. In particular, the transformation of triclosan by nano-MnO 2 was enhanced in the presence of low-concentration humic acid (1-10 mg L -1 ). The variation in the absorption of humic molecules at 275 nm supported possible covalent binding between humic molecules and triclosan in the nano-MnO 2 -mediated systems. A total of four main intermediate products were identified by high-resolution mass spectrometry (HRMS), regardless of humic molecules present in the systems or not. These products correspond to a suite of radical intercoupling reactions (dimers and trimers), ether cleavage (2,4-dichlorophenol), and oxidation to quinone-like products, triggered by electron transfer from triclosan molecules to nano-MnO 2 . A possible reaction pathway in humic acid solutions, including homo-coupling, decomposition, oxidation, and cross-coupling, was proposed. Our findings provide valuable information regarding the environmental fate and transformation mechanism of triclosan by nano-MnO 2 in complex water matrices.

Trends in Catalytic Activity for SOFC Anode materials

DEFF Research Database (Denmark)

Rossmeisl, Jan; Bessler, W. G.

2008-01-01

that oxygen spillover, where adsorbed oxygen is a key intermediate, is the dominant reaction pathway under the conditions used in the experiments. In this way the activity is linked directly to the microscopic binding affinities of reaction intermediates, providing a new understanding of the anode reaction...

MCNP6 Simulation of Light and Medium Nuclei Fragmentation at Intermediate Energies

Energy Technology Data Exchange (ETDEWEB)

Mashnik, Stepan Georgievich [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kerby, Leslie Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of Idaho, Moscow, ID (United States)

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 sup>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.

Curation and Computational Design of Bioenergy-Related Metabolic Pathways

Energy Technology Data Exchange (ETDEWEB)

Karp, Peter D. [SRI International, Menlo Park, CA (United States)

2014-09-12

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manually curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds

Sterol partitioning by HMGR and DXR for routing intermediates toward withanolide biosynthesis.

Science.gov (United States)

Singh, Shefali; Pal, Shaifali; Shanker, Karuna; Chanotiya, Chandan Singh; Gupta, Madan Mohan; Dwivedi, Upendra Nath; Shasany, Ajit Kumar

2014-12-01

Withanolides biosynthesis in the plant Withania somnifera (L.) Dunal is hypothesized to be diverged from sterol pathway at the level of 24-methylene cholesterol. The conversion and translocation of intermediates for sterols and withanolides are yet to be characterized in this plant. To understand the influence of mevalonate (MVA) and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways on sterols and withanolides biosynthesis in planta, we overexpressed the WsHMGR2 and WsDXR2 in tobacco, analyzed the effect of transient suppression through RNAi, inhibited MVA and MEP pathways and fed the leaf tissue with different sterols. Overexpression of WsHMGR2 increased cycloartenol, sitosterol, stigmasterol and campesterol compared to WsDXR2 transgene lines. Increase in cholesterol was, however, marginally higher in WsDXR2 transgenic lines. This was further validated through transient suppression analysis, and pathway inhibition where cholesterol reduction was found higher due to WsDXR2 suppression and all other sterols were affected predominantly by WsHMGR2 suppression in leaf. The transcript abundance and enzyme analysis data also correlate with sterol accumulation. Cholesterol feeding did not increase the withanolide content compared to cycloartenol, sitosterol, stigmasterol and campesterol. Hence, a preferential translocation of carbon from MVA and MEP pathways was found differentiating the sterols types. Overall results suggested that MVA pathway was predominant in contributing intermediates for withanolides synthesis mainly through the campesterol/stigmasterol route in planta. © 2014 Scandinavian Plant Physiology Society.

Extracting reaction networks from databases-opening Pandora's box.

Science.gov (United States)

Fearnley, Liam G; Davis, Melissa J; Ragan, Mark A; Nielsen, Lars K

2014-11-01

Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge. © The Author 2013. Published by Oxford University Press.

Nucleon charge exchange reaction and antiproton elastic scattering at intermediate energies

International Nuclear Information System (INIS)

Kronenfeld, J.

1985-02-01

This work treats the medium energy nuclear (p,n) charge exchange reaction to analog states and the low energy elastic scattering of antiprotons and investigates the central aspects of a microscopic theory based on multiple-scattering series which are pertinent to these reactions. A two-step term of the Distorted Wave Impulse Approximation (DWIA) in treating the (p,n) reaction, was included. For the very absorptive p-bar interaction with nuclei we conjecture that a partial infinite summation, constituing a renormalization of the single scattering term of the optical potential series provides the dominant feature of this interaction. In this work the excitation of analog states is calculated and it was found that the (p,n) reaction is described fairly well by the DWIA. In the first part of the work the (p,n) reaction in the energy range 100-200 MeV was treated. The DWIA calculations were based on eikonalization. In the second part of the work the p-barA interaction with the selfconsistent scheme mentioned above, for scattering energies 30-120 MeV, was examined. (author)

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

International Nuclear Information System (INIS)

Wang Sufan; Smith, Sean C.

2006-01-01

The 'leading coordinate' approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information

DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

Science.gov (United States)

Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

2017-09-24

We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.

Photonucleon reactions in 40Ca at intermediate energies

International Nuclear Information System (INIS)

Adler, J.-O.; Bulow, B.; Jonsson, G.G.; Lindgren, K.

1976-01-01

The yields of the reactions 40 Ca(γ,n) 39 Ca* and 40 Ca(γ,p) 39 K* to the first three excited states have been measured for bremsstrahlung with end-point energies in the region 100-750 MeV. The C 2 S values for the first excited state were deduced from the pion photoproduction contribution to the measured yields. (Auth.)

Angular evolution of peripheral heavy ion reactions at intermediate energies

International Nuclear Information System (INIS)

Blumenfeld, Y.; Chomaz, P.; Frascaria, N.; Garron, J.P.; Jacmart, J.C; Roynette, J.C

1985-01-01

Energy spectra and angular distributions of projectile-like fragments have been measured in the vicinity of the grazing angle for the 40 Ar+ 40 Ca and 40 Ar+ 208 Pb reactions at 44MeV/nucleon. Measurements of the 40 Ar+ 40 Ca system at 27MeV/nucleon and 20 Ne+ 208 Pb reaction at 44MeV/nucleon at one angle have also been performed. For fragments with charge and mass close to the projectile numerous deviations from the standard fragmentation model have been observed including rapidly changing shapes of the angular distributions with the fragment mass. Moreover the isotopic distributions and mean fragment velocities are strongly dependent on detection angle. A surface transfer reaction component dominant at the grazing angle can be separated from a second component which cannot be entirely accounted for by a simple fragmentation mechanism

Experimental determination of primary and intermediate ions in a flame front

Energy Technology Data Exchange (ETDEWEB)

Fialkov, A.B.; Fialkov, B.S.

1988-10-01

A procedure is described for determining the primary and intermediate ions in the front of a flame rarefied using mass spectrometry. By using the method proposed here, primary CHO(+) and CHO2(+) ions as well as a series of short-lived intermediate ions have been identified. The possibility of using this method for obtaining quantitative data on the characteristic lifetimes of ions and rate constants of ion-molecular reactions in flames is demonstrated. 16 references.

Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

Science.gov (United States)

Zhang, Hong; Zuo, Ran; Zhang, Guoyi

2017-11-01

In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Energy Technology Data Exchange (ETDEWEB)

Xiang, Yong; Karaveg, Khanita; Moremen, Kelley W.

2016-11-17

Asn-linked glycosylation of newly synthesized polypeptides occurs in the endoplasmic reticulum of eukaryotic cells. Glycan structures are trimmed and remodeled as they transit the secretory pathway, and processing intermediates play various roles as ligands for folding chaperones and signals for quality control and intracellular transport. Key steps for the generation of these trimmed intermediates are catalyzed by glycoside hydrolase family 47 (GH47) α-mannosidases that selectively cleave α1,2-linked mannose residues. Despite the sequence and structural similarities among the GH47 enzymes, the molecular basis for residue-specific cleavage remains obscure. The present studies reveal enzyme–substrate complex structures for two related GH47 α-mannosidases and provide insights into how these enzymes recognize the same substrates differently and catalyze the complementary glycan trimming reactions necessary for glycan maturation.

Balanced activation of IspG and IspH to eliminate MEP intermediate accumulation and improve isoprenoids production in Escherichia coli.

Science.gov (United States)

Li, Qingyan; Fan, Feiyu; Gao, Xiang; Yang, Chen; Bi, Changhao; Tang, Jinlei; Liu, Tao; Zhang, Xueli

2017-11-01

The MEP pathway genes were modulated to investigate whether there were new rate-limiting steps and toxic intermediates in this pathway. Activating IspG led to significant decrease of cell growth and β-carotene production. It was found that ispG overexpression led to accumulation of intermediate HMBPP, which seriously interfered with synthesis machinery of nucleotide and protein in Escherichia coli. Activation of the downstream enzyme IspH could solve HMBPP accumulation problem and eliminate the negative effects of ispG overexpression. In addition, intermediate MECPP accumulated in the starting strain, while balanced activation of IspG and IspH could push the carbon flux away from MECPP and led to 73% and 77% increase of β-carotene and lycopene titer respectively. Our work for the first time identified HMBPP to be a cytotoxic intermediate in MEP pathway and demonstrated that balanced activation of IspG and IspH could eliminate accumulation of HMBPP and MECPP and improve isoprenoids production. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Absorption-Fluctuation Theorem for Nuclear Reactions: Brink-Axel, Incomplete Fusion and All That

International Nuclear Information System (INIS)

Hussein, M. S.

2008-01-01

We discuss the connection between absorption, averages and fluctuations in nuclear reactions. The fluctuations in the entrance channel result in the compound-nucleus Hauser-Feshbach cross section, and the fluctuations in the intermediate channels result in modifications of multistep reaction cross sections, while the fluctuations in the final channel result in hybrid cross sections that can be used to describe incomplete fusion reactions. We discuss the latter in detail and comment on the validity of the assumptions used in the development of the Surrogate method. We also discuss the theory of multistep reactions with regards to intermediate state fluctuations and the energy dependence and non-locality of the intermediate-channel optical potentials

Dynamics of light, intermediate, heavy and superheavy nuclear ...

Indian Academy of Sciences (India)

2014-05-01

May 1, 2014 ... Various features related to the dynamics of competing decay modes of nuclear systems are explored by addressing the experimental data of a number of reactions in light, intermediate, heavy and superheavy mass regions. The DCM, being a non-statistical description for the decay of a com- pound nucleus ...

Deeply inelastic collisions as a source of intermediate mass fragments at E/A = 27 MeV

International Nuclear Information System (INIS)

Borderie, B.; Montoya, M.; Rivet, M.F.; Jouan, D.; Cabot, C.; Fuchs, H.; Gardes, D.; Gauvin, H.; Jacquet, D.; Monnet, F.

1988-01-01

Intermediate-mass fragments detected in coincidence with heavy residues were measured in 40 Ar induced reactions on Ag at E/A = 27 MeV. From the observed characteristics, it is inferred that intermediate-mass fragments associated with the so-called intermediate-velocity source come mainly from deeply inelastic collisions occurring after or at the same time as preequilibrium particle emission. (orig.)

Crystalline state photoreactions direct observation of reaction processes and metastable intermediates

CERN Document Server

Ohashi, Yuji

2014-01-01

Offering some 300 references, this book focuses on chemical reactions in the crystalline state. The reactions span many fields in inorganic and organic chemistry, making this a useful resource for inorganic, organic and physical chemists and graduate students.

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

International Nuclear Information System (INIS)

Lin, Z. K.; Han, D. L.; Li, S. F.; Li, Y. Y.; Yuan, T.

2009-01-01

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

Mining the Human Phenome Using Allelic Scores That Index Biological Intermediates

DEFF Research Database (Denmark)

Evans, David M; Brion, Marie Jo A; Paternoster, Lavinia

2013-01-01

It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease...... aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we...

The MHD intermediate shock interaction with an intermediate wave: Are intermediate shocks physical?

International Nuclear Information System (INIS)

Wu, C.C.

1988-01-01

Contrary to the usual belief that MHD intermediate shocks are extraneous, the authors have recently shown by numerical solutions of dissipative MHD equations that intermediate shocks are admissible and can be formed through nonlinear steepening from a continuous wave. In this paper, he clarifies the differences between the conventional view and the results by studying the interaction of an MHD intermediate shock with an intermediate wave. The study reaffirms his results. In addition, the study shows that there exists a larger class of shocklike solutions in the time-dependent dissiaptive MHD equations than are given by the MHD Rankine-Hugoniot relations. it also suggests a mechanism for forming rotational discontinuities through the interaction of an intermediate shock with an intermediate wave. The results are of importance not only to the MHD shock theory but also to studies such as magnetic field reconnection models

A New Bioinspired Perchlorate Reduction Catalyst with Significantly Enhanced Stability via Rational Tuning of Rhenium Coordination Chemistry and Heterogeneous Reaction Pathway.

Science.gov (United States)

Liu, Jinyong; Han, Mengwei; Wu, Dimao; Chen, Xi; Choe, Jong Kwon; Werth, Charles J; Strathmann, Timothy J

2016-06-07

Rapid reduction of aqueous ClO4(-) to Cl(-) by H2 has been realized by a heterogeneous Re(hoz)2-Pd/C catalyst integrating Re(O)(hoz)2Cl complex (hoz = oxazolinyl-phenolato bidentate ligand) and Pd nanoparticles on carbon support, but ClOx(-) intermediates formed during reactions with concentrated ClO4(-) promote irreversible Re complex decomposition and catalyst deactivation. The original catalyst design mimics the microbial ClO4(-) reductase, which integrates Mo(MGD)2 complex (MGD = molybdopterin guanine dinucleotide) for oxygen atom transfer (OAT). Perchlorate-reducing microorganisms employ a separate enzyme, chlorite dismutase, to prevent accumulation of the destructive ClO2(-) intermediate. The structural intricacy of MGD ligand and the two-enzyme mechanism for microbial ClO4(-) reduction inspired us to improve catalyst stability by rationally tuning Re ligand structure and adding a ClOx(-) scavenger. Two new Re complexes, Re(O)(htz)2Cl and Re(O)(hoz)(htz)Cl (htz = thiazolinyl-phenolato bidentate ligand), significantly mitigate Re complex decomposition by slightly lowering the OAT activity when immobilized in Pd/C. Further stability enhancement is then obtained by switching the nanoparticles from Pd to Rh, which exhibits high reactivity with ClOx(-) intermediates and thus prevents their deactivating reaction with the Re complex. Compared to Re(hoz)2-Pd/C, the new Re(hoz)(htz)-Rh/C catalyst exhibits similar ClO4(-) reduction activity but superior stability, evidenced by a decrease of Re leaching from 37% to 0.25% and stability of surface Re speciation following the treatment of a concentrated "challenge" solution containing 1000 ppm of ClO4(-). This work demonstrates the pivotal roles of coordination chemistry control and tuning of individual catalyst components for achieving both high activity and stability in environmental catalyst applications.

Studies of heavy-ion reactions and transuranic nuclei

International Nuclear Information System (INIS)

Schroeder, W.U.

1993-08-01

This report contain papers on the following topics: The Cold-Fusion Saga; Decay Patterns of Dysprosium Nuclei Produced in 32 S + 118,124 Sn Fusion Reactions; Unexpected Features of Reactions Between Very Heavy Ions at Intermediate Bombarding Energies; Correlations Between Neutrons and Charged Products from the Dissipative Reaction 197 Au+ 208 Pb at E/A = 29 MeV; Dissipative Dynamics of Projectile-Like Fragment Production in the Reaction 209 Bi+ 136 Xe at E/A = 28.2 MeV; Dynamical Production of Intermediate-Mass Fragments in Peripheral 209 Bi+ 136 Xe Collisions at E lab /A = 28.2 MeV; The Rochester 960-Liter Neutron Multiplicity Meter; A Simple Pulse Processing Concept for a Low-Cost Pulse-Shape-Based Particle Identification; A One-Transistor Preamplifier for PMT Anode Signals; A Five-Channel Multistop TDC/Event Handler for the SuperBall Neutron Multiplicity Meter; Construction of the SuperBall -- a 16,000-Liter Neutron Detector for Calorimetric Studies of Intermediate-Energy Heavy-Ion Reactions; A Computer Code for Light Detection Efficiency Calculations for Photo-multipliers of a Neutron Detector; Evaluation of Gd-Loaded Liquid Scintillators for the SuperBall Neutron Calorimeter; and Measurement of the Interaction of Cosmic-Ray μ - with a Muon Telescope

DNA damage and radical reactions: Mechanistic aspects, formation in cells and repair studies

International Nuclear Information System (INIS)

Cadet, J.; Ravanat, J.L.; Carell, T.; Cellai, L.; Chatgilialoglu, Ch.; Gimisis, Th.; Miranda, M.; O'Neill, P.; Robert, M.

2008-01-01

Several examples of oxidative and reductive reactions of DNA components that lead to single and tandem modifications are discussed in this review. These include nucleophilic addition reactions of the one-electron oxidation-mediated guanine radical cation and the one-electron reduced intermediate of 8-bromo-purine 2'-de-oxy-ribo-nucleosides that give rise to either an oxidizing guanine radical or related 5',8-cyclo-purine nucleosides. In addition, mechanistic insights into the reductive pathways involved in the photolyase induced reversal of cyclo-buta-cli-pyrimidine and pyrimidine (6-4) pyrimidone photoproducts are provided. Evidence for the occurrence and validation in cellular DNA of (OH) · radical degradation pathways of guanine that have been established in model systems has been gained from the accurate measurement of degradation products. Relevant information on biochemical aspects of the repair of single and clustered oxidatively generated damage to DNA has been gained from detailed investigations that rely on the synthesis of suitable modified probes. Thus the preparation of stable carbocyclic derivatives of purine nucleoside containing defined sequence oligonucleotides has allowed detailed crystallographic studies of the recognition step of the base damage by enzymes implicated in the base excision repair (BER) pathway. Detailed insights are provided on the BER processing of non-double strand break bi-stranded clustered damage that may consist of base lesions, a single strand break or abasic sites and represent one of the main deleterious classes of radiation-induced DNA damage. (authors)

Intermediate species measurement during iso-butanol auto-ignition

KAUST Repository

Ji, Weiqi

2015-10-01

© 2015 The Combustion Institute.Published by Elsevier Inc. All rights reserved. This work presents the time histories of intermediate species during the auto-ignition of iso-butanol at high pressure and intermediate temperature conditions obtained using a rapid compression machine and recently developed fast sampling system. Iso-butanol ignition delays were acquired for iso-butanol/O2 mixture with an inert/O2 ratio of 7.26, equivalence ratio of 0.4, in the temperature range of 840-950 K and at pressure of 25 bar. Fast sampling and gas chromatography were used to acquire and quantify the intermediate species during the ignition delay of the same mixture at P = 25.3 bar and T = 905 K. The ignition delay times and quantitative measurements of the mole fraction time histories of methane, ethene, propene, iso-butene, iso-butyraldehyde, iso-butanol, and carbon monoxide were compared with predictions from the detailed mechanisms developed by Sarathy et al., Merchant et al., and Cai et al. It is shown that while the Sarathy mechanism well predicts the overall ignition delay time, it overpredicts ethene by a factor of 6-10, underpredicts iso-butene by a factor of 2, and overpredicts iso-butyraldehyde by a factor of 2. Reaction path and sensitivity analyses were carried out to identify the reactions responsible for the observed inadequacy. The rates of iso-butanol hydrogen atom abstraction by OH radical and the beta-scission reactions of hydroxybutyl radicals were updated based on recently published quantum calculation results. Significant improvements were achieved in predicting ignition delay at high pressures (25 and 30 bar) and the species concentrations of ethene and iso-butene. However, the updated mechanism still overpredicts iso-butyraldehyde concentrations. Also, the updated mechanism degrades the prediction in ignition delay at lower pressure (15 bar) compared to the original mechanism developed by Sarathy et al.

Intermediate species measurement during iso-butanol auto-ignition

KAUST Repository

Ji, Weiqi; Zhang, Peng; He, Tanjin; Wang, Zhi; Tao, Ling; He, Xin; Law, Chung K.

2015-01-01

© 2015 The Combustion Institute.Published by Elsevier Inc. All rights reserved. This work presents the time histories of intermediate species during the auto-ignition of iso-butanol at high pressure and intermediate temperature conditions obtained using a rapid compression machine and recently developed fast sampling system. Iso-butanol ignition delays were acquired for iso-butanol/O2 mixture with an inert/O2 ratio of 7.26, equivalence ratio of 0.4, in the temperature range of 840-950 K and at pressure of 25 bar. Fast sampling and gas chromatography were used to acquire and quantify the intermediate species during the ignition delay of the same mixture at P = 25.3 bar and T = 905 K. The ignition delay times and quantitative measurements of the mole fraction time histories of methane, ethene, propene, iso-butene, iso-butyraldehyde, iso-butanol, and carbon monoxide were compared with predictions from the detailed mechanisms developed by Sarathy et al., Merchant et al., and Cai et al. It is shown that while the Sarathy mechanism well predicts the overall ignition delay time, it overpredicts ethene by a factor of 6-10, underpredicts iso-butene by a factor of 2, and overpredicts iso-butyraldehyde by a factor of 2. Reaction path and sensitivity analyses were carried out to identify the reactions responsible for the observed inadequacy. The rates of iso-butanol hydrogen atom abstraction by OH radical and the beta-scission reactions of hydroxybutyl radicals were updated based on recently published quantum calculation results. Significant improvements were achieved in predicting ignition delay at high pressures (25 and 30 bar) and the species concentrations of ethene and iso-butene. However, the updated mechanism still overpredicts iso-butyraldehyde concentrations. Also, the updated mechanism degrades the prediction in ignition delay at lower pressure (15 bar) compared to the original mechanism developed by Sarathy et al.

Intermediate temperature heat release in an HCCI engine fueled by ethanol/n-heptane mixtures: An experimental and modeling study

KAUST Repository

Vuilleumier, David

2014-03-01

This study examines intermediate temperature heat release (ITHR) in homogeneous charge compression ignition (HCCI) engines using blends of ethanol and n-heptane. Experiments were performed over the range of 0-50% n-heptane liquid volume fractions, at equivalence ratios 0.4 and 0.5, and intake pressures from 1.4bar to 2.2bar. ITHR was induced in the mixtures containing predominantly ethanol through the addition of small amounts of n-heptane. After a critical threshold, additional n-heptane content yielded low temperature heat release (LTHR). A method for quantifying the amount of heat released during ITHR was developed by examining the second derivative of heat release, and this method was then used to identify trends in the engine data. The combustion process inside the engine was modeled using a single-zone HCCI model, and good qualitative agreement of pre-ignition pressure rise and heat release rate was found between experimental and modeling results using a detailed n-heptane/ethanol chemical kinetic model. The simulation results were used to identify the dominant reaction pathways contributing to ITHR, as well as to verify the chemical basis behind the quantification of the amount of ITHR in the experimental analysis. The dominant reaction pathways contributing to ITHR were found to be H-atom abstraction from n-heptane by OH and the addition of fuel radicals to O2. © 2013 The Combustion Institute.

Intermediate temperature heat release in an HCCI engine fueled by ethanol/n-heptane mixtures: An experimental and modeling study

KAUST Repository

Vuilleumier, David; Kozarac, Darko; Mehl, Marco; Saxena, Samveg; Pitz, William J.; Dibble, Robert W.; Chen, Jyhyuan; Sarathy, Mani

2014-01-01

This study examines intermediate temperature heat release (ITHR) in homogeneous charge compression ignition (HCCI) engines using blends of ethanol and n-heptane. Experiments were performed over the range of 0-50% n-heptane liquid volume fractions, at equivalence ratios 0.4 and 0.5, and intake pressures from 1.4bar to 2.2bar. ITHR was induced in the mixtures containing predominantly ethanol through the addition of small amounts of n-heptane. After a critical threshold, additional n-heptane content yielded low temperature heat release (LTHR). A method for quantifying the amount of heat released during ITHR was developed by examining the second derivative of heat release, and this method was then used to identify trends in the engine data. The combustion process inside the engine was modeled using a single-zone HCCI model, and good qualitative agreement of pre-ignition pressure rise and heat release rate was found between experimental and modeling results using a detailed n-heptane/ethanol chemical kinetic model. The simulation results were used to identify the dominant reaction pathways contributing to ITHR, as well as to verify the chemical basis behind the quantification of the amount of ITHR in the experimental analysis. The dominant reaction pathways contributing to ITHR were found to be H-atom abstraction from n-heptane by OH and the addition of fuel radicals to O2. © 2013 The Combustion Institute.

Kinetic intermediates en route to the final serpin-protease complex: studies of complexes of α1-protease inhibitor with trypsin.

Science.gov (United States)

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

2013-11-01

Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-Å translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, α1-protease inhibitor (α1PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled α1PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism.

Mechanism of action of clostridial glycine reductase: Isolation and characterization of a covalent acetyl enzyme intermediate

International Nuclear Information System (INIS)

Arkowitz, R.A.; Abeles, R.H.

1991-01-01

Clostridial glycine reductase consists of proteins A, B, and C and catalyzes the reaction glycine + P i + 2e - → acetyl phosphate + NH 4 + . Evidence was previously obtained that is consistent with the involvement of an acyl enzyme intermediate in this reaction. The authors now demonstrate that protein C catalyzes exchange of [ 32 P]P i into acetyl phosphate, providing additional support for an acetyl enzyme intermediate on protein C. Furthermore, they have isolated acetyl protein C and shown that it is qualitatively, catalytically competent. Acetyl protein C can be obtained through the forward reaction from protein C and Se-(carboxymethyl)selenocysteine-protein A, which is generated by the reaction of glycine with proteins A and B. Acetyl protein C can also be generated through the reverse reaction by the addition of acetyl phosphate to protein C. Both procedures lead to the same acetyl enzyme. The acetyl enzyme reacts with P i to give acetyl phosphate. When [ 14 C]acetyl protein C is denaturated with TCA and redissolved with urea, radioactivity remained associated with the protein. Treatment with KBH 4 removes all the radioactivity associated with protein C, resulting in the formation of [ 14 C]ethanol. They conclude that a thiol group on protein C is acetylated. Proteins A and C together catalyze the exchange of tritium atoms from [ 3 H]H 2 O into acetyl phosphate. This exchange reaction supports the proposal that an enol of the acetyl enzyme is an intermediate in the reaction sequence

Carbonylation as a key reaction in anaerobic acetone activation by Desulfococcus biacutus.

Science.gov (United States)

Gutiérrez Acosta, Olga B; Hardt, Norman; Schink, Bernhard

2013-10-01

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.

Photocatalytic oxidation of polycyclic aromatic hydrocarbons: Intermediates identification and toxicity testing

International Nuclear Information System (INIS)

Woo, O.T.; Chung, W.K.; Wong, K.H.; Chow, Alex T.; Wong, P.K.

2009-01-01

Polycyclic aromatic hydrocarbons (PAHs) are hydrophobic pollutants and their low water solubility limits their degradation in aqueous solution. The presence of water-miscible solvent such as acetone can increase the water solubility of PAHs, however acetone will also affect the degradation of PAH. In this study the effects of acetone on the photocatalytic degradation efficiency and pathways of 5 selected PAHs, namely naphthalene (2 rings), acenaphthylene (3 rings), phenanthrene (3 rings), anthracene (3 rings) and benzo[a]anthracene (4 rings) were investigated. The Microtox toxicity test was used to determine whether the PCO system can completely detoxify the parental PAHs and its intermediates. The addition of 16% acetone can greatly alter the degradation pathway of naphthalene and anthracene. Based on intermediates identified from degradation of the 5 PAHs, the location of parental PAHs attacked by reactive free radicals can be correlated with the localization energies of different positions of the compound. For toxicity analysis, irradiation by UV light was found to induce acute toxicity by generating intermediates/degradation products from PAHs and possibly acetone. Lastly, all PAHs (10 mg l -1 ) can be completely detoxified by titanium dioxide (100 mg l -1 ) within 24 h under UVA irradiation (3.9 mW cm -2 ).

Force, reaction time, and precision of Kung Fu strikes.

Science.gov (United States)

Neto, Osmar Pinto; Bolander, Richard; Pacheco, Marcos Tadeu Tavares; Bir, Cynthia

2009-08-01

The goal was to compare values of force, precision, and reaction time of several martial arts punches and palm strikes performed by advanced and intermediate Kung Fu practitioners, both men and women. 13 Kung Fu practitioners, 10 men and three women, participated. Only the men, three advanced and seven intermediate, were considered for comparisons between levels. Reaction time values were obtained using two high speed cameras that recorded each strike at 2500 Hz. Force of impact was measured by a load cell. For comparisons of groups, force data were normalized by participant's body mass and height. Precision of the strikes was determined by a high speed pressure sensor. The results show that palm strikes were stronger than punches. Women in the study presented, on average, lower values of reaction time and force but higher values of precision than men. Advanced participants presented higher forces than intermediate participants. Significant negative correlations between the values of force and precision and the values of force and reaction time were also found.

Pathway and Molecular Mechanisms for Malachite Green Biodegradation in Exiguobacterium sp. MG2

Science.gov (United States)

Wang, Ji’ai; Gao, Feng; Liu, Zhongzhong; Qiao, Min; Niu, Xuemei; Zhang, Ke-Qin; Huang, Xiaowei

2012-01-01

Malachite green (MG), N-methylated diaminotriphenylmethane, is one of the most common dyes in textile industry and has also been used as an effective antifungal agent. However, due to its negative impact on the environment and carcinogenic effects to mammalian cells, there is a significant interest in developing microbial agents to degrade this type of recalcitrant molecules. Here, an Exiguobacterium sp. MG2 was isolated from a river in Yunnan Province of China as one of the best malachite green degraders. This strain had a high decolorization capability even at the concentration of 2500 mg/l and maintained its stable activity within the pH range from 5.0 to 9.0. High-pressure liquid chromatography, liquid chromatography-mass spectrometry and gas chromatography–mass spectrometry were employed to detect the catabolic pathway of MG. Six intermediate products were identified and a potential biodegradation pathway was proposed. This pathway involves a series of reactions of N-demethylation, reduction, benzene ring-removal, and oxidation, which eventually converted N-methylated diaminotriphenylmethane into N, N-dimethylaniline that is the key precursor to MG. Furthermore, our molecular biology experiments suggested that both triphenylmethane reductase gene tmr and cytochrome P450 participated in MG degradation, consistent with their roles in the proposed pathway. Collectively, our investigation is the first report on a biodegradation pathway of triphenylmethane dye MG in bacteria. PMID:23251629

A study of the nucleus-nucleus total reaction cross section of stable systems at intermediate energies: An application to 12C

Science.gov (United States)

Hu, Liyuan; Song, Yushou; Hou, Yingwei; Liu, Huilan; Li, Hui

2018-07-01

A semi-microscopic analytical expression of the nucleus-nucleus total reaction cross section (σR) was proposed based on the strong absorption model. It is suitable for stable nuclei at intermediate energies. The matter density distributions of nuclei and the nucleon-nucleon total cross section were both considered. Particularly, the Fermi motion effect of the nucleons in a nucleus was also taken into account. The parametrization of σR was applied to the colliding systems including 12C. The experimental data at energies from 30 to 1000 MeV/nucleon were well reproduced, according to which an approach of deriving σR without adjustable parameters was developed. The necessity of considering the Fermi motion effect in the parametrization was discussed.

Stereoselectivity in catalytic reactions: CO oxidation on Pd(100) by rotationally aligned O2 molecules

Science.gov (United States)

Vattuone, L.; Gerbi, A.; Savio, L.; Cappelletti, D.; Pirani, F.; Rocca, M.

2010-05-01

We report on stereodynamical effects in heterogeneous catalytic reactions as measured by molecular beam-surface experiments. Specifically for CO oxidation on Pd(100) we find that the rotational alignment of the incoming O2 at low (Θ = 0.04 ML) and at intermediate (ΘCO = 0.17 ML) CO pre-coverage, causes a higher reactivity of molecules in high and in low helicity states, respectively (corresponding to helicoptering and cartwheeling motion of O2). In first approximation, at low CO pre-coverage the difference in reactivity is determined by the different location of the O atoms generated in the dissociation process by the different parent molecules, while at intermediate CO pre-coverage the reactivity is influenced also by the different ability of cartwheeling and helicoptering O2 to penetrate through the CO adlayer. In accord with this the total amount of CO2 produced is always largest for helicopters which generate supersurface O atoms at least in the low CO pre-coverage limit. A deeper inspection of the data indicates, however, that the dynamics is more complex, two different pathways being present for the reaction with O generated by helicopters and one for O generated by cartwheels. Moreover, cartwheels generated oxygen influences the reactivity of subsequently arriving helicopters.

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

Science.gov (United States)

Lu, Xiu Hui; Yu, Hai Bin; Wu, Wei Rong; Xu, Yue Hua

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second-order Møller-Plesset (MP2)/6-31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero-point energy (ZPE) and CCSD(T)/6-31G* single-point calculations. From the PES obtained with the CCSD(T)//MP2/6-31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four-membered ring intermediate, INT2, which is a barrier-free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four-membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier-free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier-free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol.

Oxidative demethylation of lanosterol in cholesterol biosynthesis: accumulation of sterol intermediates

International Nuclear Information System (INIS)

Shafiee, A.; Trzaskos, J.M.; Paik, Y.K.; Gaylor, J.L.

1986-01-01

With [ 3 H-24,25]-dihydrolanosterol as substrate, large-scale metabolic formation of intermediates of lanosterol demethylation was carried out to identify all compounds in the metabolic process. Utilizing knowledge of electron transport of lanosterol demethylation, we interrupted the demethylation reaction allowing accumulation and confirmation of the structure of the oxygenated intermediates lanost-8-en-3 beta,32-diol and 3 beta-hydroxylanost-8-en-32-al, as well as the demethylation product 4,4-dimethyl-cholesta-8,14-dien-3 beta-ol. Further metabolism of the delta 8.14-diene intermediate to a single product 4,4-dimethyl-cholest-8-en-3 beta-ol occurs under interruption conditions in the presence of 0.5 mM CN-1. With authentic compounds, each intermediate has been rigorously characterized by high performance liquid chromatography and gas-liquid chromatography plus mass spectral analysis of isolated and derivatized sterols. Intermediates that accumulated in greater abundance were further characterized by ultraviolet, 1 H-NMR, and infrared spectroscopy of the isolated sterols

Mining the human phenome using allelic scores that index biological intermediates

NARCIS (Netherlands)