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Sample records for 4alpha reaction mechanism

  1. Inorganic Reaction Mechanisms. Part I

    Science.gov (United States)

    Cooke, D. O.

    1976-01-01

    Provides a collection of data on the mechanistic aspects of inorganic chemical reactions. Wherever possible includes procedures for classroom demonstration or student project work. The material covered includes gas phase reactions, reactions in solution, mechanisms of electron transfer, the reaction between iron III and iodine, and hydrolysis. (GS)

  2. Inhibition of hepatocyte nuclear factor 1 and 4 alpha (HNF1α and HNF4α) as a mechanism of arsenic carcinogenesis.

    Science.gov (United States)

    Pastoret, Anna; Marcos, Ricard; Sampayo-Reyes, Adriana; Saucedo-Cardenas, Odila; Lozano-Garza, Gerardo H; Hernandez, Alba

    2013-06-01

    Inorganic arsenic (i-As) is a naturally occurring toxic metalloid affecting millions of people worldwide. It is known to be carcinogen, liver being a potential target, and related to the prevalence of diabetes in arseniasis-endemic areas. Hepatocyte nuclear factor 1 and 4 alpha (HNF1α and HNF4α) are key members of a transcriptional network essential for normal liver architecture. Changes in HNF1α and HNF4α expression are clearly associated with the development of liver malignancies and diabetes in humans. In this work, hepatic HepG2 cells and golden Syrian hamsters were exposed to sub-toxic, environmentally relevant doses of sodium arsenite (SA; up to 10 μM in vitro, 15 mg/L in vivo) in order to evaluate whether arsenic is able to compromise the expression of hepatocyte nuclear factors. Also, liver histopathological examination was carried out, and several markers of hepatocyte differentiation and glucose metabolism status were determined as a measure of i-As-induced effects. Results show a consistent down-regulation of HNF1α and HNF4α under a scenario of exposure where HepG2 cells (1) gained resistance to arsenic-induced toxicity/apoptosis, (2) attained loss of tissue-specific features (as shown by the observed down-regulation of ALDOB, PEPCK and CYP1A2, triggering of the epithelial-to-mesenchymal transition program and the hypersecretion of matrix metalloproteinase-2 and 9), (3) failed to maintain balanced expression of the "stemness" genes C-MYC, OCT3/4, LIN28 and NOTCH2 and (4) showed glucose metabolism impairment. We conclude that the i-As-induced down-regulation of HNF1α and HNF4α under chronic settings may play a central role in the features of disease and cancer observed both in vivo and in vitro.

  3. Analysis of kinetic reaction mechanisms

    CERN Document Server

    Turányi, Tamás

    2014-01-01

    Chemical processes in many fields of science and technology, including combustion, atmospheric chemistry, environmental modelling, process engineering, and systems biology, can be described by detailed reaction mechanisms consisting of numerous reaction steps. This book describes methods for the analysis of reaction mechanisms that are applicable in all these fields. Topics addressed include: how sensitivity and uncertainty analyses allow the calculation of the overall uncertainty of simulation results and the identification of the most important input parameters, the ways in which mechanisms can be reduced without losing important kinetic and dynamic detail, and the application of reduced models for more accurate engineering optimizations. This monograph is invaluable for researchers and engineers dealing with detailed reaction mechanisms, but is also useful for graduate students of related courses in chemistry, mechanical engineering, energy and environmental science and biology.

  4. [Mechanisms of cutaneous drug reactions].

    Science.gov (United States)

    Vaillant, L

    2000-06-15

    Two main mechanisms, pharmacologic and immunoallergic, are responsible for cutaneous reactions to drugs. Pharmacologic mechanisms can be predictable (overdosage, cumulative or delayed toxicity, adverse effects) or unpredictable (idiosyncratic, intolerance, or anaphylactic reaction). Immunoallergic mechanisms can be mediated by IgE (some types of urticaria and anaphylactic shock), due to circulating immune complexes (leukocytoclastic vasculitis, serum sickness-type reactions) or mediated by lymphocytes (exanthema, Lyell's syndrome, fixed pigmented erythema, photosensitization). The diagnostic work-up varies according to the causative mechanism. When the reaction is predictable, the responsible drug can be identified according to the data in the present bibliography. When the reaction is immunologic, only the chronologic sequence of events can identify the responsible drug. The risk of recurrence with an identical or related molecule also varies according to the causative mechanism. For urticaria, diagnosis and the risk of recurrence differ according to whether the cause is allergic (mediated by IgE or urticarial vasculitis) or is pharmacologic (urticaria due to aspirin or to conversion enzyme inhibitors).

  5. Inorganic Reaction Mechanisms Part II: Homogeneous Catalysis

    Science.gov (United States)

    Cooke, D. O.

    1976-01-01

    Suggests several mechanisms for catalysis by metal ion complexes. Discusses the principal factors of importance in these catalysis reactions and suggests reactions suitable for laboratory study. (MLH)

  6. Physical chemistry: The fingerprints of reaction mechanisms

    Science.gov (United States)

    Vallance, Claire

    2017-06-01

    Small changes to molecular structures can transform how reactions occur, but studying reaction mechanisms directly is difficult. An imaging technique that provides direct insights into competing mechanisms might improve matters.

  7. Mechanisms of severe transfusion reactions.

    Science.gov (United States)

    Kopko, P M; Holland, P V

    2001-06-01

    Serious adverse effects of transfusion may be immunologically or non-immunologically mediated. Currently, bacterial contamination of blood products, particularly platelets, is one of the most significant causes of transfusion-related morbidity and mortality. Septic transfusion reactions can present with clinical symptoms similar to immune-mediated hemolytic transfusion reactions and transfusion-related acute lung injury. Extremely high fever and/or gastrointestinal symptoms, in a transfusion recipient, may be indicative of sepsis. The diagnosis is based upon culturing the same organism from both the patient and the transfused blood component. Numerous organisms have been implicated as the cause of septic transfusion reactions. Due to different storage conditions, gram negative organisms are more often isolated from red blood cell components; gram positive organisms are more often isolated from platelets. Prevention of septic transfusion reactions is primarily dependent on an adequate donor history and meticulous preparation of the donor phlebotomy site. Visual inspection of blood components prior to transfusion is also vital to preventing these reactions. Several methods of detection of bacterial contamination and inactivation of pathogens are currently under active investigation.

  8. Organic Reaction Mechanisms at A-Level.

    Science.gov (United States)

    Norman, R. O. C.; Waddington, D. J.

    1979-01-01

    Advocates teaching of organic reaction mechanisms through the methods which are used in elucidating them. This also provides a useful way of illustrating the theories and methods of physical chemistry. Describes an approach to teaching three reaction mechanisms: substitution in alkanes; addition to alkenes; and ester hydrolysis. (Author/GA)

  9. Reaction mechanisms of DNA photolyase.

    Science.gov (United States)

    Brettel, Klaus; Byrdin, Martin

    2010-12-01

    DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH° occur in overall 1ns. Whereas the kinetics of FADH° was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH° to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.

  10. The mechanism of the modified Ullmann reaction

    OpenAIRE

    Sperotto, Elena; Klink, Gerard P.M. van; van Koten, Gerard; Vries, Johannes G. de

    2010-01-01

    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) made these reactions truly catalytic, with catalyst amounts as low as 1 mol% or even lower. Since these catalysts are homogeneous, it has opened up the possibility to investigate the mechanism of the...

  11. Heuristics-Guided Exploration of Reaction Mechanisms

    CERN Document Server

    Bergeler, Maike; Proppe, Jonny; Reiher, Markus

    2015-01-01

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

  12. Reaction mechanisms: Stripping down SN2

    Science.gov (United States)

    Orr-Ewing, Andrew J.

    2012-07-01

    The mechanism of the SN2 reaction is fundamental to understanding and controlling the stereochemistry of organic reactions, but surrounding solvent molecules may complicate the textbook picture. Micro-solvation studies have now explored the stereochemical consequences of the presence of one or two solvent molecules.

  13. organic reaction mechanism controversy: pedagogical implications ...

    African Journals Online (AJOL)

    Preferred Customer

    nature of reaction mechanism in organic chemistry as to whether it can be .... The graduate assistant, chemistry teacher and final year chemistry students were .... Rollnick (3), Sykes (10), and Bhattacharyya and Bodner (11) on these issues ...

  14. Reaction mechanism of -acylhydroxamate with cysteine proteases

    Indian Academy of Sciences (India)

    R Shankar; P Kolandaivel

    2007-09-01

    The gas-phase reaction mechanism of -acylhydroxamate with cysteine proteases has been investigated using ab initio and density functional theory. On the irreversible process, after breakdown of tetrahedral intermediate (INT1), small 1-2 anionotropic has been formed and rearranged to give stable by-products sulfenamide (P1) and thiocarbamate (P2) with considerable energy loss. While, on the reversible part of this reaction mechanism, intermediate (INT2) breaks down on oxidation, to form a stable product (P3). Topological and AIM analyses have been performed for hydrogen bonded complex in this reaction profile. Intrinsic reaction coordinates [IRC, minimum-energy path (MEP)] calculation connects the transition state between R-INT1, INT1-P1 and INT1-P2. The products P1, P2 and P3 are energetically more stable than the reactant and hence the reaction enthalpy is found to be exothermic.

  15. Heuristics-Guided Exploration of Reaction Mechanisms.

    Science.gov (United States)

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

    2015-12-08

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

  16. Characterizing the mechanism(s) of heavy element synthesis reactions

    Science.gov (United States)

    Loveland, Walter

    2016-12-01

    A review of the current state of our understanding of complete fusion reaction mechanisms is presented, from the perspective of an experimentalist. For complete fusion reactions, the overall uncertainties in predicting heavy element synthesis cross sections are examined in terms of the uncertainties associated with the calculations of capture cross sections, fusion probabilities and survival probabilities.

  17. The mechanism of the modified Ullmann reaction.

    Science.gov (United States)

    Sperotto, Elena; van Klink, Gerard P M; van Koten, Gerard; de Vries, Johannes G

    2010-11-21

    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) made these reactions truly catalytic, with catalyst amounts as low as 1 mol% or even lower. Since these catalysts are homogeneous, it has opened up the possibility to investigate the mechanism of these modified Ullmann reactions. Most authors agree that Cu(I) is the true catalyst even though Cu(0) and Cu(II) catalysts have also shown to be active. It should be noted however that Cu(I) is capable of reversible disproportionation into Cu(0) and Cu(II). In the first step, the nucleophile displaces the halide in the LnCu(I)X complex forming LnCu(I)ZR (Z = O, NR′, S). Quite a number of mechanisms have been proposed for the actual reaction of this complex with the aryl halide: 1. Oxidative addition of ArX forming a Cu(III) intermediate followed by reductive elimination; 2. Sigma bond metathesis; in this mechanism copper remains in the Cu(II) oxidation state; 3. Single electron transfer (SET) in which a radical anion of the aryl halide is formed (Cu(I)/Cu(II)); 4. Iodine atom transfer (IAT) to give the aryl radical (Cu(I)/Cu(II)); 5. π-complexation of the aryl halide with the Cu(I) complex, which is thought to enable the nucleophilic substitution reaction. Initially, the radical type mechanisms 3 and 4 where discounted based on the fact that radical clock-type experiments with ortho-allyl aryl halides failed to give the cyclised products. However, a recent DFT study by Houk, Buchwald and co-workers shows that the modified Ullmann reaction between aryl iodide and amines or primary alcohols proceeds either via an SET or an IAT mechanism. Van Koten has shown that stalled aminations can be rejuvenated by the addition of Cu(0), which serves to reduce the formed Cu(II) to Cu

  18. Mechanisms of inorganic and organometallic reactions

    CERN Document Server

    The purpose of this series is to provide a continuing critical review of the literature concerned with mechanistic aspects of inorganic and organo­ metallic reactions in solution, with coverage being complete in each volume. The papers discussed are selected on the basis of relevance to the elucidation of reaction mechanisms and many include results of a nonkinetic nature when useful mechanistic information can be deduced. The period of literature covered by this volume is July 1982 through December 1983, and in some instances papers not available for inclusion in the previous volume are also included. Numerical results are usually reported in the units used by the original authors, except where data from different papers are com­ pared and conversion to common units is necessary. As in previous volumes material included covers the major areas of redox processes, reactions of the nonmetallic elements, reaction of inert and labile metal complexes and the reactions of organometallic compounds. While m...

  19. HNF4alpha dysfunction as a molecular rational for cyclosporine induced hypertension.

    Directory of Open Access Journals (Sweden)

    Monika Niehof

    Full Text Available Induction of tolerance against grafted organs is achieved by the immunosuppressive agent cyclosporine, a prominent member of the calcineurin inhibitors. Unfortunately, its lifetime use is associated with hypertension and nephrotoxicity. Several mechanism for cyclosporine induced hypertension have been proposed, i.e. activation of the sympathetic nervous system, endothelin-mediated systemic vasoconstriction, impaired vasodilatation secondary to reduction in prostaglandin and nitric oxide, altered cytosolic calcium translocation, and activation of the renin-angiotensin system (RAS. In this regard the molecular basis for undue RAS activation and an increased signaling of the vasoactive oligopeptide angiotensin II (AngII remain elusive. Notably, angiotensinogen (AGT is the precursor of AngII and transcriptional regulation of AGT is controlled by the hepatic nuclear factor HNF4alpha. To better understand the molecular events associated with cyclosporine induced hypertension, we investigated the effect of cyclosporine on HNF4alpha expression and activity and searched for novel HNF4alpha target genes among members of the RAS cascade. Using bioinformatic algorithm and EMSA bandshift assays we identified angiotensin II receptor type 1 (AGTR1, angiotensin I converting enzyme (ACE, and angiotensin I converting enzyme 2 (ACE2 as genes targeted by HNF4alpha. Notably, cyclosporine represses HNF4alpha gene and protein expression and its DNA-binding activity at consensus sequences to AGT, AGTR1, ACE, and ACE2. Consequently, the gene expression of AGT, AGTR1, and ACE2 was significantly reduced as evidenced by quantitative real-time RT-PCR. While RAS is composed of a sophisticated interplay between multiple factors we propose a decrease of ACE2 to enforce AngII signaling via AGTR1 to ultimately result in vasoconstriction and hypertension. Taken collectively we demonstrate cyclosporine to repress HNF4alpha activity through calcineurin inhibitor mediated inhibition

  20. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

    Science.gov (United States)

    Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

    2016-06-01

    Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

  1. Mechanical gating of a mechanochemical reaction cascade

    Science.gov (United States)

    Wang, Junpeng; Kouznetsova, Tatiana B.; Boulatov, Roman; Craig, Stephen L.

    2016-11-01

    Covalent polymer mechanochemistry offers promising opportunities for the control and engineering of reactivity. To date, covalent mechanochemistry has largely been limited to individual reactions, but it also presents potential for intricate reaction systems and feedback loops. Here we report a molecular architecture, in which a cyclobutane mechanophore functions as a gate to regulate the activation of a second mechanophore, dichlorocyclopropane, resulting in a mechanochemical cascade reaction. Single-molecule force spectroscopy, pulsed ultrasonication experiments and DFT-level calculations support gating and indicate that extra force of >0.5 nN needs to be applied to a polymer of gated gDCC than of free gDCC for the mechanochemical isomerization gDCC to proceed at equal rate. The gating concept provides a mechanism by which to regulate stress-responsive behaviours, such as load-strengthening and mechanochromism, in future materials designs.

  2. Elucidating reaction mechanisms on quantum computers.

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

    2017-07-18

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  3. Analyzing Complex Reaction Mechanisms Using Path Sampling.

    Science.gov (United States)

    van Erp, Titus S; Moqadam, Mahmoud; Riccardi, Enrico; Lervik, Anders

    2016-11-08

    We introduce an approach to analyze collective variables (CVs) regarding their predictive power for a reaction. The method is based on already available path sampling data produced by, for instance, transition interface sampling or forward flux sampling, which are path sampling methods used for efficient computation of reaction rates. By a search in CV space, a measure of predictiveness can be optimized and, in addition, the number of CVs can be reduced using projection operations which keep this measure invariant. The approach allows testing hypotheses on the reaction mechanism but could, in principle, also be used to construct the phase-space committor surfaces without the need of additional trajectory sampling. The procedure is illustrated for a one-dimensional double-well potential, a theoretical model for an ion-transfer reaction in which the solvent structure can lower the barrier, and an ab initio molecular dynamics study of water auto-ionization. The analysis technique enhances the quantitative interpretation of path sampling data which can provide clues on how chemical reactions can be steered in desired directions.

  4. Reaction mechanisms in heavy ion fusion

    Directory of Open Access Journals (Sweden)

    Lubian J.

    2011-10-01

    Full Text Available We discuss the reaction mechanisms involved in heavy ion fusion. We begin with collisions of tightly bound systems, considering three energy regimes: energies above the Coulomb barrier, energies just below the barrier and deep sub-barrier energies. We show that channel coupling effects may influence the fusion process at above-barrier energies, increasing or reducing the cross section predicted by single barrier penetration model. Below the Coulomb barrier, it enhances the cross section, and this effect increases with the system’s size. It is argued that this behavior can be traced back to the increasing importance of Coulomb coupling with the charge of the collision partners. The sharp drop of the fusion cross section observed at deep sub-barrier energies is addressed and the theoretical approaches to this phenomenon are discussed. We then consider the reaction mechanisms involved in fusion reactions of weakly bound systems, paying particular attention to the calculations of complete and incomplete fusion available in the literature.

  5. New methods for quantum mechanical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Ward Hugh [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-12-01

    Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L2) representation of the outgoing wave scattering Green`s function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green`s function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC- can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC- geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H3O- system, providing information about the potential energy surface for the OH + H2 reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the

  6. Photochromic properties and reaction mechanism of naphthopyran

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The photochromic properties and reaction mechanism of title compounds have been examined with steady method on compounds 3-phenyl-3-[3-methylbenzothiophene-2-yl]-3H- naphtho[2,1-b]pyran (1) and 3-phenyl-3-[benzofuran-2-yl]-3H-naphtho[2,1-b]pyran (2) and nanosecond laser flash photolysis techniques on compound 3-phenyl-3-[1,2-dimethylindol-3-yl]- 3H-naphtho[2,1-b]pyran (3). The influence of oxygen on transient spectra and decay kinetics of compound 3 has been investigated. Both excited singlet state and triplet state are involved in the photochromic mechanism of compound 3. The influence of molecular structure on photochromic behavior has been studied also. Decay kinetics indicated that the lifetime of colored forms of 1 and 2 were several orders of magnitude longer than that of 3.

  7. Photochromic properties and reaction mechanism of naphthopyran

    Institute of Scientific and Technical Information of China (English)

    潘桂兰; 魏景强; 朱爱平; 明阳福; 樊美公; 姚思德

    2001-01-01

    The photochromic properties and reaction mechanism of title compounds have been examined with steady method on compounds 3-phenyl-3-[3-methylbenzothiophene-2-yl]-3H-naphtho[2,1-b]pyran (1) and 3-phenyl-3-[benzofuran-2-yl]-3H-naphtho[2,1-b]pyran (2) and nanosecond laser flash photolysis techniques on compound 3-phenyl-3-[1,2-dimethylindol-3-yl]-3H-naphtho[2,1-b]pyran (3). The influence of oxygen on transient spectra and decay kinetics of compound 3 has been investigated. Both excited singlet state and triplet state are involved in the photochromic mechanism of compound 3. The influence of molecular structure on photochromic behavior has been studied also. Decay kinetics indicated that the lifetime of colored forms of 1 and 2 were several orders of magnitude longer than that of 3.

  8. Angular correlation measurements for 4-{alpha} decaying states in {sup 16}O

    Energy Technology Data Exchange (ETDEWEB)

    Wuosmaa, A.H.; Back, B.B.; Betts, R.R. [and others

    1995-08-01

    Previous measurements of the {sup 12}C({sup 12}C,{sup 8}Be){sup 16}O{sup *}(4 {alpha}) reaction identified discrete levels in {sup 16}O which decay by breakup into 4 {alpha} particles through a number of different decay sequences, including {sup 16}O{sup *} {yields} {sup 8}Be + {sup 8}Be and {alpha} + {sup 12}C (O{sub 2}{sup +}). These states are observed in a range of excitation energies where resonances are observed in inelastic {alpha} + {sup 12}C scattering leading to the {sup 8}Be + {sup 8}Be and {alpha} + {sup 12}C final states. These resonances were associated with 4 {alpha}-particle chain configurations in {sup 16}O. Should the states populated in the {sup 12}C + {sup 12}C reaction possess this same extended structure, it would serve as an important piece of evidence supporting the idea that even more deformed structures are formed in the {sup 24}Mg compound system. In order to more firmly make this association, it is important to determine the spins of the states populated in the {sup 12}C + {sup 12}C reaction.

  9. Knockout Reaction Mechanism for 6He+%Knockout Reaction Mechanism for 6He+

    Institute of Scientific and Technical Information of China (English)

    吕林辉; 叶沿林; 曹中鑫; 肖军; 江栋兴; 郑涛; 华辉; 李智焕; 葛俞成; 李湘庆; 楼建玲; 李阔昂; 李奇特; 乔锐; 游海波; 陈瑞九

    2012-01-01

    A knockout reaction experiment was carried out by using the 6He beam at 82.5 MeV/nucleon impinging on CH2 and C targets. The a core fragments at forward angles were detected in coincidence with the recoiled protons at larger angles. From this exclusive measure- ment the valence nucleon knockout mechanism and the core knockout mechanism are separated. This study provides a basis for the exclusive spectroscopic investigation of the exotic nuclei.

  10. Computerized approaches to enhance understanding of organic reaction mechanisms: CAN reaction mechanisms and CPLEX prelaboratory methodology

    Science.gov (United States)

    Al-Shammari, Abdulrahman G. Alhamzani

    2008-10-01

    Two approaches to enhance the understanding of organic reaction mechanisms are described. First, a new method for teaching organic reaction mechanisms that can be used in a Computer-Assisted Instruction (CAI) environment is proposed and tested (Chapter 1). The method concentrates upon the important intermediate structures, which are assumed to be on the reaction coordinate, and which can be evaluated and graded by currently available computer techniques. At the same time, the "curved arrows" that show the electron flow in a reaction mechanism are neglected, since they cannot be evaluated and graded with currently available computer techniques. By allowing student practice for learning organic reaction mechanisms using the Curved Arrow Neglect (CAN) method within a "Practice Makes Perfect" CAI method, student performance in the drawing of traditional reaction mechanisms, in which students had to include the "curved arrows" on their written classroom exams, was significantly enhanced. Second, computerized prelaboratory experiments (CPLEX) for organic chemistry laboratory 1 & 2 courses have been created, used, and evaluated (Chapters 2 and 3). These computerized prelabs are unique because they combine both "dry lab" actions with detailed animations of the actual chemistry occurring at the molecular level. The "dry lab" serves to simulate the actual physical manipulations of equipment and chemicals that occur in the laboratory experiment through the use of drag-and-drop computer technology. At the same time, these physical actions are accompanied on a separate part of the computer screen by animations showing the chemistry at the molecular level that is occurring in the experiment. These CPLEX modules were made into Internet accessible modules. The students were allowed to access the CPLEX modules prior to performing the actual laboratory experiment. A detailed evaluation of students' perception of the modules was accomplished via survey methodology during the entire

  11. Detailed reduction of reaction mechanisms for flame modeling

    Science.gov (United States)

    Wang, Hai; Frenklach, Michael

    1991-01-01

    A method for reduction of detailed chemical reaction mechanisms, introduced earlier for ignition system, was extended to laminar premixed flames. The reduction is based on testing the reaction and reaction-enthalpy rates of the 'full' reaction mechanism using a zero-dimensional model with the flame temperature profile as a constraint. The technique is demonstrated with numerical tests performed on the mechanism of methane combustion.

  12. Carbonitriding reactions of diatomaceous earth: phase evolution and reaction mechanisms

    Directory of Open Access Journals (Sweden)

    BRANKO MATOVIC

    2006-06-01

    Full Text Available The possibility of using diatomaceous earth as Si precursor for low temperature synthesis of non-oxide powders by carbothermal reduction-nitridation was studied. It was found that carbonitriding reactions produce phases of the Si–Al–O–N system. Already at 1300 °C, nanosized, non-oxide powders were obtained. The comparatively low reaction temperatures is attributred to the nano-porous nature of the raw material. The evolution of crystalline phases proceeded via many intermediate stages. The powders were characterized by X-ray and SEM investigations. The results showed that diatomaceous earth can be a very effective source for obtaining non-oxide powders.

  13. The mechanism of the modified Ullmann reaction

    NARCIS (Netherlands)

    Sperotto, Elena; Klink, Gerard P.M. van; Koten, Gerard van; Vries, Johannes G. de

    2010-01-01

    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) ma

  14. A Reduced Reaction Mechanism For Isooctane Combustion

    Directory of Open Access Journals (Sweden)

    C.R.Berlin Selva Rex,

    2011-05-01

    Full Text Available A reduced chemical kinetic mechanism for the oxidation of iso-octane has been developed and a detailed study on the ignition of iso-octane has been conducted analytically using a kinetic scheme with 994 elementary reactions and 201 species. The activation energies of isooctane are higher than n-octane. Hence iso-octane is widelyused for combustion simulations. A program has been developed in MATLAB for the calculation and prediction of the concentration of 201 intermediate species and the ignition delay in the combustion of Iso-octane. The various initial conditions considered was in between the temperatures of 600K to 1250K with pressure ranging from 10atm to40atm at various equivalence ratios of 0.3 and 0.6. Nitrogen is considered as the diluent. The diluent percentage is assumed as 79% to make a comparison with atmospheric condition. The criteria for determination of ignition delay times are based on the OH concentrations to reach to a value of 1x10-9 moles/cc. The ignition delay times are obtained by varying initial conditions of the mixture in the combustion of Iso-octane. The results on ignition delays have been found to be agreeable with those available in the literature. Cantera (an object oriented software for reacting flows software is used in this study.

  15. Purification and characterization of a novel thermostable 4-alpha-glucanotransferase of Thermotoga maritima cloned in Escherichia coli.

    Science.gov (United States)

    Liebl, W; Feil, R; Gabelsberger, J; Kellermann, J; Schleifer, K H

    1992-07-01

    Maltodextrin glycosyltransferase (4-alpha-glucanotransferase) of the extremely thermophilic ancestral bacterium Thermotoga maritima has been purified from an Escherichia coli clone expressing the corresponding T. maritima MSB8 chromosomal gene. T. maritima 4-alpha-glucanotransferase, an approximately 53-kDa monomeric enzyme, is the most thermophilic glycosyltransferase described to date. It retained more than 90% of its maximum activity at temperatures from 55 degrees C up to 80 degrees C. The proposed action modus is the transfer of 1,4-alpha-glucanosyl chains, thus resulting in the disproportionation of 1,4-alpha-glucans. It converted soluble starch, amylopectin, and amylose, thereby changing the iodine staining properties of these substrates. The addition of low-molecular-mass malto-oligosaccharides, which act as glucanosyl acceptor molecules, enhanced the reaction and resulted in the formation of a series of linear maltohomologues from two to more than nine glucose units in size. Use of either of the malto-oligosaccharides maltotetraose, maltopentaose, maltohexaose, or maltoheptaose as sole substrate also yielded linear maltohomologues. On the other hand, maltose and maltotriose were not disproportionated by 4-alpha-glucanotransferase, although both were good acceptors for glucanosyl transfer. Glucose did not function as an acceptor in transfer reactions. Glucose also never appeared as a reaction product. The chain length of glucanosyl segments transferred ranged from two to probably far more than six glucose residues. Comparison of the N-terminal amino acid sequence of 4-alpha-glucanotransferase with other published protein sequences revealed significant similarity to sequences near the N-termini of various eucaryotic maltases and bacterial cyclodextrin glycosyltransferases, suggesting its relatedness on the molecular level with other starch- and maltodextrin-converting enzymes.

  16. MACiE: A Database of Enzyme Reaction Mechanisms

    Science.gov (United States)

    Holliday, Gemma L.; Bartlett, Gail J.; Almonacid, Daniel E.; O’Boyle, Noel M.; Murray-Rust, Peter; Thornton, Janet M.; Mitchell, John B. O.

    2009-01-01

    Summary MACiE (Mechanism, Annotation and Classification in Enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. PMID:16188925

  17. Acute exercise reduces hepatic glucose production through inhibition of the Foxo1/HNF-4alpha pathway in insulin resistant mice.

    Science.gov (United States)

    De Souza, Cláudio T; Frederico, Marisa J S; da Luz, Gabrielle; Cintra, Dennys E; Ropelle, Eduardo R; Pauli, José R; Velloso, Lício A

    2010-06-15

    and HNF-4alpha activities are important mechanisms involved in exercise-induced improvement of glucose homeostasis in insulin resistant states.

  18. Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

    Science.gov (United States)

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

    2016-10-11

    The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an SN1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

  19. Study of Reaction Mechanism in Tracer Munitions

    Science.gov (United States)

    1974-12-01

    Regression Rates (Furnished by Frankford Arsenal) 35 13 Calculated Heat Fluxes and Energy Partitions 43 4 I NOMENCLATURE B = preexponential factor... anhydride disproportionates in a fast step: N2 0 3 - 2 + NO (4) so that the resulting dioxide can react with more nitrite in another fast reaction: Sr

  20. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics.

    Science.gov (United States)

    Shemesh, Dorit; Nizkorodov, Sergey A; Gerber, R Benny

    2016-09-15

    Photochemistry of carbonyl compounds is of major importance in atmospheric and organic chemistry. The photochemistry of cyclohexanone is studied here using on-the-fly molecular dynamics simulations on a semiempirical multireference configuration interaction potential-energy surface to predict the distribution of photoproducts and time scales for their formation. Rich photochemistry is predicted to occur on a picosecond time scale following the photoexcitation of cyclohexanone to the first singlet excited state. The main findings include: (1) Reaction channels found experimentally are confirmed by the theoretical simulations, and a new reaction channel is predicted. (2) The majority (87%) of the reactive trajectories start with a ring opening via C-Cα bond cleavage, supporting observations of previous studies. (3) Mechanistic details, time scales, and yields are predicted for all reaction channels. These benchmark results shed light on the photochemistry of isolated carbonyl compounds in the atmosphere and can be extended in the future to photochemistry of more complex atmospherically relevant carbonyl compounds in both gaseous and condensed-phase environments.

  1. Reaction Mechanism Investigation Using Vibrational Mode Analysis for the Multichannel Reaction of CH3O + CO

    Institute of Scientific and Technical Information of China (English)

    ZHOU,Zheng-Yu(周正宇); CHENG,Xue-Li(程学礼); GUO,Li(郭丽)

    2002-01-01

    On the basis of the computed results got by the Gaussian 94 package at B3LYP/6-311 + +G * * level, the reaction mechanism of CH3O radical with CO has been investigated thoroughly via the vibrational model analysis. And the relationships among the reactants, eight transition states, four intermediates and various products involved this multichannel reaction are elucidated. The vibrational mode analysis shows that the reaction mechanism is reliable.

  2. A thermochemically derived global reaction mechanism for detonation application

    Science.gov (United States)

    Zhu, Y.; Yang, J.; Sun, M.

    2012-07-01

    A 4-species 4-step global reaction mechanism for detonation calculations is derived from detailed chemistry through thermochemical approach. Reaction species involved in the mechanism and their corresponding molecular weight and enthalpy data are derived from the real equilibrium properties. By substituting these global species into the results of constant volume explosion and examining the evolution process of these global species under varied conditions, reaction paths and corresponding rates are summarized and formulated. The proposed mechanism is first validated to the original chemistry through calculations of the CJ detonation wave, adiabatic constant volume explosion, and the steady reaction structure after a strong shock wave. Good agreement in both reaction scales and averaged thermodynamic properties has been achieved. Two sets of reaction rates based on different detailed chemistry are then examined and applied for numerical simulations of two-dimensional cellular detonations. Preliminary results and a brief comparison between the two mechanisms are presented. The proposed global mechanism is found to be economic in computation and also competent in description of the overall characteristics of detonation wave. Though only stoichiometric acetylene-oxygen mixture is investigated in this study, the method to derive such a global reaction mechanism possesses a certain generality for premixed reactions of most lean hydrocarbon mixtures.

  3. Mechanisms for control of biological electron transfer reactions.

    Science.gov (United States)

    Williamson, Heather R; Dow, Brian A; Davidson, Victor L

    2014-12-01

    Electron transfer (ET) through and between proteins is a fundamental biological process. The rates and mechanisms of these ET reactions are controlled by the proteins in which the redox centers that donate and accept electrons reside. The protein influences the magnitudes of the ET parameters, the electronic coupling and reorganization energy that are associated with the ET reaction. The protein can regulate the rates of the ET reaction by requiring reaction steps to optimize the system for ET, leading to kinetic mechanisms of gated or coupled ET. Amino acid residues in the segment of the protein through which long range ET occurs can also modulate the ET rate by serving as staging points for hopping mechanisms of ET. Specific examples are presented to illustrate these mechanisms by which proteins control rates of ET reactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Mapping of HNF4alpha target genes in intestinal epithelial cells

    DEFF Research Database (Denmark)

    Boyd, Mette; Bressendorff, Simon; Moller, Jette

    2009-01-01

    in the human intestinal epithelial cells in order to elucidate the role of HNF4alpha in the intestinal differentiation progress. METHODS: We have performed a ChIP-chip analysis of the human intestinal cell line Caco-2 in order to make a genome-wide identification of HNF4alpha binding to promoter regions......ABSTRACT: BACKGROUND: The role of HNF4alpha has been extensively studied in hepatocytes and pancreatic beta-cells, and HNF4alpha is also regarded as key regulator of intestinal epithelial cell differentiation as well. The aim of the present work is to identify novel HNF4alpha target genes......), and the tight junction protein cingulin (CGN) promoters verified that these genes are bound by HNF4alpha in Caco2 cells and for the Cdx-2 and trehalase promoters the HNF4alpha binding was verified in mouse small intestine epithelium. CONCLUSION: The HNF4alpha regulation of the Cdx-2 promoter unravels...

  5. Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino

    2016-06-27

    This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies.

  6. Multiple post-translational modifications in hepatocyte nuclear factor 4{alpha}

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Atsushi; Katsura, Shogo; Ito, Ryo; Hashiba, Waka; Sekine, Hiroki; Fujiki, Ryoji [Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Kato, Shigeaki, E-mail: uskato@mail.ecc.u-tokyo.ac.jp [Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)

    2011-07-15

    Highlights: {yields} We performed comprehensive PTM analysis for HNF4{alpha} protein. {yields} We identified 8 PTMs in HNF4{alpha} protein including newly identified PTMs. {yields} Among them, we found acetylation at lysine 458 was one of the prime PTMs for HNF4{alpha} function. {yields} Acetylation at lysine 458 was inhibitory for HNF4{alpha} transcription function. {yields} This modification fluctuated in response to extracellular condition. -- Abstract: To investigate the role of post-translational modifications (PTMs) in the hepatocyte nuclear factor 4{alpha} (HNF4{alpha})-mediated transcription, we took a comprehensive survey of PTMs in HNF4{alpha} protein by massspectrometry and identified totally 8 PTM sites including newly identified ubiquitilation and acetylation sites. To assess the impact of identified PTMs in HNF4{alpha}-function, we introduced point mutations at the identified PTM sites and, tested transcriptional activity of the HNF4{alpha}. Among the point-mutations, an acetylation site at lysine 458 was found significant in the HNF4{alpha}-mediated transcriptional control. An acetylation negative mutant at lysine 458 showed an increased transcriptional activity by about 2-fold, while an acetylation mimic mutant had a lowered transcriptional activation. Furthermore, this acetylation appeared to be fluctuated in response to extracellular nutrient conditions. Thus, by applying an comprehensive analysis of PTMs, multiple PTMs were newly identified in HNF4{alpha} and unexpected role of an HNF4{alpha} acetylation could be uncovered.

  7. Revision of outcome and mechanism of a new multicomponent reaction.

    Science.gov (United States)

    Carballares, Santiago; Espinosa, Juan F

    2005-06-09

    [reaction: see text] A recently reported multicomponent reaction (MCR) produces pyrido[1,2-a]pyrazines and not the previously described 1H-imidazol-4-yl-pyridines. This different structure is proposed on the basis of a new mechanism of formation and the spectroscopic data.

  8. Synthesis of 7-Ethyl-10-hydroxycamptothecin and Proposed Reaction Mechanism

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The improved 3-step preparation of a key antitumor agent, 7-ethyl-10-hydroxycamptothecin(SN-38), which consists of ethylation, oxidation and photo-chemical rearrangement, is described. The proposed reaction mechanism is also discussed.

  9. Mechanisms of shock-induced reactions in high explosives

    Science.gov (United States)

    Kay, Jeffrey J.

    2017-01-01

    Understanding the mechanisms by which shock waves initiate chemical reactions in explosives is key to understanding their unique and defining property: the ability to undergo rapid explosive decomposition in response to mechanical stimulus. Although shock-induced reactions in explosives have been studied experimentally and computationally for decades, the nature of even the first chemical reactions that occur in response to shock remain elusive. To predictively understand how explosives respond to shock, the detailed sequence of events that occurs - mechanical deformation, energy transfer, bond breakage, and first chemical reactions - must be understood at the quantum-mechanical level. This paper reviews recent work in this field and ongoing experimental and theoretical work at Sandia National Laboratories in this important area of explosive science.

  10. Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms.

    Science.gov (United States)

    Maeda, Satoshi; Morokuma, Keiji

    2011-08-09

    In these five decades, many useful tools have been developed for exploring quantum chemical potential energy surfaces. The success in theoretical studies of chemical reaction mechanisms has been greatly supported by these tools. However, systematic prediction of reaction mechanisms starting only from given reactants and catalysts is still very difficult. Toward this goal, we describe the artificial force induced reaction (AFIR) method for automatically finding reaction paths of type A + B → X (+ Y). By imposing an artificial force to given reactants and catalysts, the method can find the reactive sites very efficiently. Further pressing by the artificial force provides approximate transition states and product structures, which can be easily reoptimized to the corresponding true ones. This procedure can be executed very efficiently just by minimizing a single function called the AFIR function. All important reaction paths can be found by repeating this cycle starting from many initial orientations. We also discuss perspectives of automated reaction path search methods toward the above goal.

  11. Reaction Mechanism of the Multi-channel Decomposition Reactions of 1-Pentenyl Free Radicals

    Institute of Scientific and Technical Information of China (English)

    CHENG,Xue-Li; ZHAO,Yan-Yun; LI,Feng; LI,Li-Qing; TAO,Xiu-Jun

    2008-01-01

    The reactions of 1-pentenyl decomposition system have been studied extensively at the B3LYP/6-311++G** level with Gaussion 98 package. The potential energy surface with zero-point energy correction was drawn. All reaction channels were fully investigated with the vibrational mode analysis, frontier orbital analysis and electron population analysis to confirm the transition states and reveal the reaction mechanism.

  12. Electron flow in reaction mechanisms--revealed from first principles.

    Science.gov (United States)

    Knizia, Gerald; Klein, Johannes E M N

    2015-04-27

    The "curly arrow" of Robinson and Ingold is the primary tool for describing and rationalizing reaction mechanisms. Despite this approach's ubiquity and stellar success, its physical basis has never been clarified and a direct connection to quantum chemistry has never been found. Here we report that the bond rearrangements expressed by curly arrows can be directly observed in ab initio computations, as transformations of intrinsic bond orbitals (IBOs) along the reaction coordinate. Our results clarify that curly arrows are rooted in physical reality-a notion which has been challenged before-and show how quantum chemistry can directly establish reaction mechanisms in intuitive terms and unprecedented detail.

  13. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

    Science.gov (United States)

    Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

    2013-10-28

    Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

  14. Reaction mechanisms of ruthenium tetroxide mediated oxidations of organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Froehaug, Astrid Elisabeth

    1995-12-31

    This thesis reports a study of the mechanism of ruthenium tetroxide mediated oxidations of saturated hydrocarbons, ethers, alkenes and alcohols. Several methods were used. The RuO{sub 4}-mediated oxidations of adamantane and cis-decalin were studied in CCl{sub 4}-CH{sub 3}CN-H{sub 2}O and in acetone-water. The rate of reaction was found to be moderately influenced by the polarity of the solvent. Solvent properties other than the polarity were also found to influence the reaction rates. From the oxidations of adamantane and adamantane-1,3,5,7-d{sub 4} two primary kinetic deuterium isotope effects were found. These were comparable with the deuterium isotope effects found for the analogous oxidations of cis-decalin and cis-decalin-d{sub 18}. The results seem to exclude both a one step hydride abstraction reaction mechanism and a one step concerted mechanism, as well as a scheme where two such mechanisms compete. The observations may be explained by a two step reaction mechanism consisting of a pre-equilibrium with formation of a substrate-RuO{sub 4} complex followed by a concerted rate determining reaction. The RuO{sub 4}-mediated oxidation of ethers was of kinetic second order with a small enthalpy of activation and a large negative entropy of activation. Oxidation of cyclopropylmethyl methyl ether gave methyl cyclopropanecarboxylate, no rearranged products were observed. On RuO{sub 4} oxidations in CCl{sub 4} with NaIO{sub 4} as stoichiometric oxidant, no chlorinated products were observed. Several observations not in agreement with a hydride or a hydrogen abstraction mechanism may be explained by assuming that the reaction proceeds by either a concerted reaction or by a reversible oxidative addition of the ether to RuO{sub 4} followed by a slow concerted step. 228 refs., 9 figs., 27 tabs.

  15. Atherton–Todd reaction: mechanism, scope and applications

    Directory of Open Access Journals (Sweden)

    Stéphanie S. Le Corre

    2014-05-01

    Full Text Available Initially, the Atherton–Todd (AT reaction was applied for the synthesis of phosphoramidates by reacting dialkyl phosphite with a primary amine in the presence of carbon tetrachloride. These reaction conditions were subsequently modified with the aim to optimize them and the reaction was extended to different nucleophiles. The mechanism of this reaction led to controversial reports over the past years and is adequately discussed. We also present the scope of the AT reaction. Finally, we investigate the AT reaction by means of exemplary applications, which mainly concern three topics. First, we discuss the activation of a phenol group as a phosphate which allows for subsequent transformations such as cross coupling and reduction. Next, we examine the AT reaction applied to produce fire retardant compounds. In the last section, we investigate the use of the AT reaction for the production of compounds employed for biological applications. The selected examples to illustrate the applications of the Atherton–Todd reaction mainly cover the past 15 years.

  16. On the Reaction Mechanism of Br2 with OCS

    Institute of Scientific and Technical Information of China (English)

    Hai Tao YU; Hua ZHONG; Ming Xia LI; Hong Gang FU; Jia Zhong SUN

    2005-01-01

    The reaction mechanism of photochemical reaction between Br2 ( 1 ∑ ) and OCS ( 1 ∑ ) is predicted by means of theoretical methods. The calculated results indicate that the direct addition of Br2 to the CS bond of OCS molecule is more favorable in energy than the direct addition of Br2to the CO bond. Furthermore, the intermediate isomer syn-BrC(O)SBr is more stable thermodynamically and kinetically than anti-BrC(O)SBr. The original resultant anti-BrC(O)SBr formed in the most favorable reaction channel can easily isomerize into the final product syn-BrC(O)SBr with only 31.72 kJ/mol reaction barrier height. The suggested mechanism is in good agreement with previous experimental study.

  17. Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction.

    Science.gov (United States)

    Polyak, Iakov; Reetz, Manfred T; Thiel, Walter

    2012-02-08

    We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.

  18. Reaction mechanisms for on-surface synthesis of covalent nanostructures.

    Science.gov (United States)

    Björk, J

    2016-03-02

    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

  19. Cyclodextrin-Catalyzed Organic Synthesis: Reactions, Mechanisms, and Applications

    Directory of Open Access Journals (Sweden)

    Chang Cai Bai

    2017-09-01

    Full Text Available Cyclodextrins are well-known macrocyclic oligosaccharides that consist of α-(1,4 linked glucose units and have been widely used as artificial enzymes, chiral separators, chemical sensors, and drug excipients, owing to their hydrophobic and chiral interiors. Due to their remarkable inclusion capabilities with small organic molecules, more recent interests focus on organic reactions catalyzed by cyclodextrins. This contribution outlines the current progress in cyclodextrin-catalyzed organic reactions. Particular emphases are given to the organic reaction mechanisms and their applications. In the end, the future directions of research in this field are proposed.

  20. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, W.M.

    1985-01-01

    The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs.

  1. Detailed surface reaction mechanism in a three-way catalyst.

    Science.gov (United States)

    Chatterjee, D; Deutschmann, O; Warnatz, J

    2001-01-01

    Monolithic three-way catalysts are applied to reduce the emission of combustion engines. The design of such a catalytic converter is a complex process involving the optimization of different physical and chemical parameters (in the simplest case, e.g., length, cell densities or metal coverage of the catalyst). Numerical simulation can be used as an effective tool for the investigation of the catalytic properties of a catalytic converter and for the prediction of the performance of the catalyst. To attain this goal, a two-dimensional flow-field description is coupled with a detailed surface reaction model (gas-phase reactions can be neglected in three-way catalysts). This surface reaction mechanism (with C3H6 taken as representative of unburnt hydrocarbons) was developed using sub-mechanisms recently developed for hydrogen, carbon monoxide and methane oxidation, literature values for C3H6 oxidation, and estimates for the remaining unknown reactions. Results of the simulation of a monolithic single channel are used to validate the surface reaction mechanism. The performance of the catalyst was simulated under lean, nearly stoichiometric and rich conditions. For these characteristic conditions, the oxidation of propene and carbon monoxide and the reduction of NO on a typical Pt/Rh coated three-way catalyst were simulated as a function of temperature. The numerically predicted conversion data are compared with experimentally measured data. The simulation further reveals the coupling between chemical reactions and transport processes within the monolithic channel.

  2. Systematic development of reduced reaction mechanisms for dynamic modeling

    Science.gov (United States)

    Frenklach, M.; Kailasanath, K.; Oran, E. S.

    1986-01-01

    A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.

  3. A new comprehensive reaction mechanism for combustion of hydrocarbon fuels

    Energy Technology Data Exchange (ETDEWEB)

    Ranzi, E.; Sogaro, A.; Gaffuri, P.; Pennati, G. [Politecnico di Milano (Italy). Dipt. di Chimica Industriale e Ingegneria Chimica; Westbrook, C.K.; Pitz, W.J. [Lawrence Livermore National Lab., CA (United States)

    1993-12-03

    A chemical kinetic model has been developed which describes pyrolysis, ignition and oxidation of many small hydrocarbon fuels over a wide range of experimental conditions. Fuels include carbon monoxide and hydrogen, methane and other alkane species up to n-butane, ethylene, propene, acetylene, and oxygenated species such as methanol, acetaldehyde and ethanol. Formation of some larger intermediate and product species including benzene, butadiene, large olefins, and cyclopentadiene has been treated in a semi-empirical manner. The reaction mechanism has been tested for conditions that do not involve transport and diffusional processes, including plug flow and stirred reactors, batch reactors and shock tubes. The present kinetic model and its validation differ from previous reaction mechanisms in two ways. First, in addition to conventional combustion data, experiments more commonly associated with chemical engineering problems such as oxidative coupling, oxidative pyrolysis and steam cracking are used to test the reaction mechanism, making it even more general than previous models. In addition, H atom abstraction and some other reaction rates, even for the smaller C{sub 2}, C{sub 3} and C{sub 4} species, are treated using approximations that facilitate future extensions to larger fuels in a convenient manner. Construction of the reaction mechanism and comparisons with experimental data illustrate the generality of the model.

  4. Divergent reaction mechanisms in the aminofluorination of alkenes.

    Science.gov (United States)

    Kong, Wangqing; Merino, Estíbaliz; Nevado, Cristina

    2014-01-01

    The aminofluorination of alkenes has become an attractive platform for the synthesis of β-amino-fluorinated compounds, valuable building blocks in medicinal and agricultural chemistry. The novel methodologies disclosed in recent years have unraveled a broad array of reaction mechanisms, so that the interest in these transformations transcends the mere synthetic aspects. This review aims to summarize the most relevant findings in this area attending at the nature of the fluorine source, and thus the specific mechanism operating in each of these transformations, namely electrophilic, nucleophilic, radical, and late transition metal-catalyzed reactions.

  5. Thermal degradation reaction mechanism of xylose: A DFT study

    Science.gov (United States)

    Huang, Jinbao; He, Chao; Wu, Longqin; Tong, Hong

    2016-08-01

    The thermal degradation reaction mechanism of xylose as hemicellulose model compound was investigated by using density functional theory methods M062X with the 6-31++G(d,p) basis set. Eight possible pyrolytic reaction pathways were proposed and the standard kinetic and thermodynamic parameters in all reaction pathways were calculated at different temperatures. In reaction pathway (1), xylose is first transformed into acyclic containing-carbonyl isomer, and then the isomer further decomposes through four possible pyrolysis pathways (1-1)-(1-4). Pathways (2) and (3) depict an immediate ring-opening process through the simultaneous breaking of C-O and C-C bonds. Pathways (4)-(7) describe the pyrolysis processes of various anhydro-xyloses through a direct ring-opening process. Pathway (8) gives the evolutionary process of pyranones. The calculation results show that reaction pathways (1), (2) and (5) are the major reaction channels and reaction pathways (3), (4), and (6)-(8) are the competitive reaction channels in pyrolysis of xylose. The major products of xylose pyrolysis are low molecular products such as 2-furaldehyde, glycolaldehyde, acetaldehyde, methylglyoxal and acetone, and the main competitive products are formaldehyde, formic acid, acetic acid, CO2, CH4, acetol, pyranone, and so on.

  6. Reaction mechanism study of 7Li(7Li, 6He) reaction at above Coulomb barrier energies

    Indian Academy of Sciences (India)

    V V Parkar; V Jha; S Santra; B J Roy; K Ramachandran; A Shrivastava; K Mahata; A Chatterjee; S Kailas

    2009-02-01

    The elastic scattering and the 6He angular distributions were measured in 7Li + 7Li reaction at two energies, lab = 20 and 25 MeV. FRDWBA calculations have been performed to explain the measured 6He data. The calculations were very sensitive to the choice of the optical model potentials in entrance and exit channels. The one-step proton transfer was found to be the dominant reaction mechanism in 6He production.

  7. Reaction mechanism and reaction coordinates from the viewpoint of energy flow.

    Science.gov (United States)

    Li, Wenjin; Ma, Ao

    2016-03-21

    Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

  8. Physical Mechanism of Nuclear Reactions at Low Energies

    CERN Document Server

    Oleinik, V P; Arepjev, Yu.D

    2002-01-01

    The physical mechanism of nuclear reactions at low energies caused by spatial extension of electron is considered. Nuclear reactions of this type represent intra-electronic processes, more precisely, the processes occurring inside the area of basic localization of electron. Distinctive characteristics of these processes are defined by interaction of the own field produced by electrically charged matter of electron with free nuclei. Heavy nucleus, appearing inside the area of basic localization of electron, is inevitably deformed because of interaction of protons with the adjoining layers of electronic cloud, which may cause nuclear fission. If there occur "inside" electron two or greater number of light nuclei, an attractive force appears between the nuclei which may result in the fusion of nuclei. The intra-electronic mechanism of nuclear reactions is of a universal character. For its realization it is necessary to have merely a sufficiently intensive stream of free electrons, i.e. heavy electric current, an...

  9. Hydroxylation Reaction Mechanism for Nitrosodimethylamine by Oxygen Atom

    Institute of Scientific and Technical Information of China (English)

    LI Lan; LIN Xiao-yan; LI Zong-he

    2011-01-01

    The hydroxylation reaction mechanism of nitrosodimethylamine(NDMA)by oxygen atom was theoretically investigated at the B3LYP/6-31G** level.It has been found that the path of the oxydation of the C-H bond is easier than the path involving a Singlet/Triplet crossing.The study of the potential surface shows that both solvent effect at B3LYP/6-31G** level and different method at more credible MP2/6-311G** level in the gas phase have no effect on the hydroxylation reaction mechanism.The oxidation hydroxylation process of NDMA by O is exothermic reaction and easy to occur.

  10. Reaction Mechanisms of the Initial Oligomerization of Aluminophosphate.

    Science.gov (United States)

    Xiang, Yan; Xin, Liang; Deetz, Joshua D; Sun, Huai

    2016-05-12

    The mechanisms of aluminophosphate oligomerization were investigated using density functional theory with the SMD solvation model. Two aluminum species, Al(OH)4(-) and Al(H2O)6(3+), and four phosphorus species, H3PO4, H2PO4(-), HPO4(2-), and PO4(3-), were considered as the monomers for polycondensation reactions. It was found that the most favorable pathway to dimerization was a Lewis acid-base reaction: the aprotic oxygen of phosphoric acid (P═O) performs a nucleophilic attack on the central aluminum atom of Al(OH)4(-). Using this mechanism as a pattern, plausible dimerization mechanisms were investigated by varying the proticity and hydration of the phosphorus and aluminum monomers, respectively. The relative reaction rates of each mechanism were estimated under different pH conditions. The chain growth of aluminophosphates to trimers, tetramers, and pentamers and the cyclization of a linear tetramer were also investigated. For oligomerization reactions beyond dimer formation, it is found that cluster growth favors the addition of the phosphoric monomers rather than aluminum monomers.

  11. nonlinear kinetics and mechanism of nile blue reaction

    African Journals Online (AJOL)

    Prof. S.B. Jonnalagadda

    under varied oxidative and reducing media is pivotal in their applications as ... communication, we report the complex mechanism of the reaction between nile blue ... Both the instruments were interfaced for data storage and have ..... The authors acknowledge the financial support received from the University of Durban-.

  12. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

    Science.gov (United States)

    Liu, Haiyan; Lu, Zhenyu; Cisneros, G Andres; Yang, Weitao

    2004-07-08

    The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

  13. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    Energy Technology Data Exchange (ETDEWEB)

    Gorman, Brian P [Colorado School of Mines, Golden, CO (United States)

    2015-09-02

    Project Description: The general objective of the proposed research is to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, pCO2, and modest ranges in T and P. This will be accomplished by studying both reaction rates and solubility from changes in solution chemistry, and making nanoscale observations of calcite precipitate surface morphology and composition at the micro-to-nano-scale to provide an understanding of controlling reaction mechanisms and pathways. The specific objectives necessary to reach the general objective are: a) determination of how pCO2, Ca2+, ionic strength and “foreign” ions influence reaction rates; and b) investigate the influence of these parameters on apparent kinetic solubility from dissolution and precipitation reactions. This information will clearly be central to the construction of reliable reaction-transport models to predict reservoir and formation response to increased CO2 in saline waters. This program was initially collaborative with John Morse at Texas A&M, however his passing shortly after the beginning of this program resulted in abbreviated research time and effort. Summary of Results: Early studies using electron microscopy and spectroscopy indicated that carbonate precipitation from natural seawater (NSW) conditions onto aragonite substrates was mediated by a surface amorphous calcium carbonate layer. It was hypothesized that this ACC layer (observed after < 5days reaction time) was responsible for the abnormal reaction kinetics and also served as a metastable seed layer for growth of epitaxial aragonite. Further studies of the ACC formation mechanism indicated a strong dependence on the Mg concentration in solution. Subsequent studies at shorter times (10 hrs) on calcite substrates and in a wide range of supersaturation conditions did not indicate any ACC layer. Instead, an epitaxial layer by layer

  14. DFT study on mechanism of the classical Biginelli reaction

    Institute of Scientific and Technical Information of China (English)

    Jin Guang Ma; Ji Ming Zhang; Hai Hui Jiang; Wan Yong Ma; Jian Hua Zhou

    2008-01-01

    The condensation of benzaldehyde, urea, and ethyl acetoacetate according to the procedure described by Biginelli was investigated at the B3LYP/6-31G(d), B3LYP/6-31+G(d,p), and B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) levels to explore the reaction mechanism. According to the mechanism proposed by Kappe, structures of five intermediates were optimized and four transition states were found. The calculation results proved that the mechanism proposed by Kappe is right.

  15. Molecular-dynamics study of detonation. II. The reaction mechanism

    Science.gov (United States)

    Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.

    1996-01-01

    In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.

  16. Reaction mechanisms in the 6Li+ 52Cr system

    Directory of Open Access Journals (Sweden)

    Pandey Bhawna

    2015-01-01

    Full Text Available Reactions induced by the weakly bound 6Li projectile interacting with the intermediate mass target 52Cr are investigated. The choice of this particular reaction in our study is because it is proposed as a surrogate reaction [6Li(52Cr, d56Fe*] for the measurement of 55Fe(n,p reaction cross-section, which has been found to be very important in fusion reactor studies. All the conditions which have to be satisfied for using the surrogate method have been checked. The energy of 6Li beam is selected in a way so as to get equivalent neutron energy in the region of 9-14 MeV, which is of primary interest in fusion reactor application. In the present work, statistical model calculations PACE (Projection-Angular-Momentum-Coupled-Evaporation, ALICE and Continuum-Discretized–Coupled-Channel (CDCC: FRESCO have been used to provide information for the 6Li + 52Cr system and the respective contributions of different reaction mechanisms. The present theoretical work is an important step in the direction towards studying the cross-section of the 55Fe(n, p55Mn reaction by surrogate method.

  17. Theoretical study of reaction mechanism for NCO + HCNO

    Science.gov (United States)

    Zhang, Weichao; Du, Benni; Feng, Changjun

    2007-07-01

    A detailed quantum chemical study is performed on the mechanism of the NCO + HCNO reaction, which has never been studied by theory. The potential energy surface for this reaction is characterized at the B3LYP/6-311++G(d,p) level of theory, combined with high-level CBS-QB3 single point energy calculation. Four possible product channels have been investigated. From the calculations it can be seen that the formation of HCN + NO + CO is the dominant product channel, while the pathway to products of HCNN + CO 2 is expected to be minor one, and these conclusions are in good agreement with the experimental results.

  18. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD)

    KAUST Repository

    Quitterer, Felix

    2013-05-29

    The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Density Functional Study on the Reaction Mechanism for the Reaction of Ni+ with Ethane

    Institute of Scientific and Technical Information of China (English)

    ZHANG,Dong-Ju(张冬菊); LIU,Cheng-Bu(刘成卜); LIU,Yong-Jun(刘永军); HU,Hai-Quan(胡海泉)

    2002-01-01

    The mechanism of the reaction of Ni+ (2D) with ethane in the gas-phase was studied by using density functional theory. Both the B3LYP and BLYP functionals with standard all-electron basis sets are used to give the detailed information of the potential energy surface (PES) of [Ni, C2, H6 ] +. Tne mechanisms forming the products CH4 and H2 in the reaction of Ni+with ethane are proposed. The reductive eliminations of CH4and H2 are typical addition-elimination reactions. Each of the two reactions consists of two elementary steps: C-C or CH bond activations to form inserted species followed by isomerizations to form product-like intermediate. The rate determining steps for the elimination reatcions of forming CH4 and H2 are the isomerizations of the inserted species rather than C-C or C-H bond activations. The elimination reaction of forming H2 was found to be thermodynamically favored compared to that of CH4.

  20. Reactions of a stable dialkylsilylene and their mechanisms

    Indian Academy of Sciences (India)

    Mitsuo Kira

    2012-11-01

    Various reactions for a stable dialkylsilylene, 2,2,5,5-tetrakis(trimethylsilyl)silacyclopentane-1,1-diyl (1), are summarized and their mechanisms are discussed. Silylene 1 isomerizes to the corresponding silaethene via the 1,2-trimethylsilyl migration. Reduction of 1 with alkali metals affords the corresponding radical anion 1.− with a relatively small 29Si hfs constant (2.99 mT) and a large g-factor (g = 2.0077) compared with those for trivalent silyl radicals. Photo-excitation of 1 generates the corresponding singlet excited state (11*) with the lifetime of 80.5 ns. The excited state reacts with C=C double bond compounds including benzene, naphthalene, and ()- and ()-2-butenes. Although the thermal reactions of 1 with haloalkanes occur via radical mechanisms, the insertion into O-H, Si-H and Si-Cl bonds proceeds concertedly via the threemembered cyclic transition states. The reaction of 1 with H2SiCl2 gives the Si-Cl insertion product exclusively, while the quantitative insertion to Si-H bond occurs when Me2SiHCl is used as a substrate. The origin of the rather unusual Si-H/Si-Cl selectivity is elucidated using DFT calculations. Silylene 1 adds to C=C, C≡C, and C=O bonds to afford the corresponding silacycles as stable compounds. The importance of the carbonyl silaylides during the reactions of silylenes with aldehydes and ketones is emphasized.

  1. Automated exploration of the mechanism of elementary reactions

    Energy Technology Data Exchange (ETDEWEB)

    Najm, Habib N. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Zador, Judit [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2012-09-01

    Optimization of new transportation fuels and engine technologies requires the characterization of the combustion chemistry of a wide range of fuel classes. Theoretical studies of elementary reactions — the building blocks of complex reaction mechanisms — are essential to accurately predict important combustion processes such as autoignition of biofuels. The current bottleneck for these calculations is a user-intensive exploration of the underlying potential energy surface (PES), which relies on the “chemical intuition” of the scientist to propose initial guesses for the relevant chemical configurations. For newly emerging fuels, this approach cripples the rate of progress because of the system size and complexity. The KinBot program package aims to accelerate the detailed chemical kinetic description of combustion, and enables large-scale systematic studies on the sub-mechanism level.

  2. Chemical reactions modulated by mechanical stress: extended Bell theory.

    Science.gov (United States)

    Konda, Sai Sriharsha M; Brantley, Johnathan N; Bielawski, Christopher W; Makarov, Dmitrii E

    2011-10-28

    A number of recent studies have shown that mechanical stress can significantly lower or raise the activation barrier of a chemical reaction. Within a common approximation due to Bell [Science 200, 618 (1978)], this barrier is linearly dependent on the applied force. A simple extension of Bell's theory that includes higher order corrections in the force predicts that the force-induced change in the activation energy will be given by -FΔR - ΔχF(2)∕2. Here, ΔR is the change of the distance between the atoms, at which the force F is applied, from the reactant to the transition state, and Δχ is the corresponding change in the mechanical compliance of the molecule. Application of this formula to the electrocyclic ring-opening of cis and trans 1,2-dimethylbenzocyclobutene shows that this extension of Bell's theory essentially recovers the force dependence of the barrier, while the original Bell formula exhibits significant errors. Because the extended Bell theory avoids explicit inclusion of the mechanical stress or strain in electronic structure calculations, it allows a computationally efficient characterization of the effect of mechanical forces on chemical processes. That is, the mechanical susceptibility of any reaction pathway is described in terms of two parameters, ΔR and Δχ, both readily computable at zero force.

  3. Synthesis of new derivatives from 1,2{alpha},4{alpha},5-tetramethyl-8-oxabicyclo[3.2.1]oct-6-en-3-one; Sintese de novos herbicidas derivados do 1,2{alpha},4{alpha},5-tetrametil-8-oxabiciclo[3.2.1]oct-6-en-3-ona

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, Luiz Claudio de Almeida; Maltha, Celia Regina Alvares; Demuner, Antonio Jacinto; Filomeno, Claudinei Andrade [Vicosa Univ., MG (Brazil). Dept. de Quimica]. E-mail: crmaltha@ufv.br; Silva, Antonio Alberto da [Vicosa Univ., MG (Brazil). Dept. de Fitotecnia

    2004-04-01

    In this paper we report the synthesis of biologically active compounds through a [3+4] cycloaddition reaction to produce the main frame structure, followed by several conventional transformations. The 1,2{alpha},4{alpha},5-tetramethyl-8-oxabicyclo[3.2.1]oct-6-en-3-one (11) obtained from a [3+4] cycloaddition reaction was converted into 1,2{alpha},4{alpha},5-tetramethyl-6,7-exo-isopropylidenedioxi-8 -oxabicyclo[3.2.1]octan-3-one (13) in 46% yield. This was further converted into the alcohols 1,2{alpha},4{alpha},5-tetramethyl-6,7-exo-isopropylidenedioxi-8-oxabicyclo[3.2= .1]octan-3{alpha}-ol (14), 1,2{alpha},4{alpha},5-tetramethyl-6,7-exo-isopropylidenedioxi-8 -oxabicyclo[3.2.1]octan-3{beta}-ol (15), 1,2{alpha},4{alpha},5-tetramethyl-3-butyl-6,7-exo-isopropylidenedioxi-8-oxabic= yclo[3.2.1]octan-3 {alpha}-ol (17), 1,2{alpha},4{alpha},5-tetramethyl-3-hexyl-6,7-exo-isopropylidenedioxi-8-oxabic= yclo[3.2.1]octan-3 {alpha}-ol (18) and 1,2{alpha},4{alpha},5-tetramethyl-3-decyl-6,7-exo-isopropylidenedioxi-8-oxabic= yclo[3.2.1]octan-3 {alpha}-ol (19). Dehydration of 17, 18 and 19 with thionyl chloride in pyridine resulted in the alkenes 20, 21 and 22 in ca. 82% - 89% yields from starting alcohols. The herbicidal activity of the compounds synthesized was evaluated at a concentration of 100 {mu}g g{sup -1}. The most active compound was 21 causing 42,7% inhibition against Cucumis sativus L. (author)

  4. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

    2015-01-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

  5. Facilitating effects of berberine on rat pancreatic islets through modulating hepatic nuclear factor 4 alpha expression and glucokinase activity

    Institute of Scientific and Technical Information of China (English)

    Zhi-Quan Wang; Fu-Er Lu; San-Hua Leng; Xin-Sheng Fang; Guang Chen; Zeng-Si Wang; Li-Ping Dong; Zhong-Qing Yan

    2008-01-01

    AIM: To observe the effect of berberine on insulin secretion in rat pancreatic islets and to explore its possible molecular mechanism.METHODS: Primary rat islets were isolated from male Sprague-Dawley rats by collagenase digestion and treated with different concentrations (1, 3, 10 and 30 μmol/L) of berberine or 1 μmol/L Glibenclamide (GB) for 24 h. Glucose-stimulated insulin secretion (GSIS) assay was conducted and insulin was determined by radioimmunoassay. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (NTT) assay was performed to evaluate cytotoxicity. The mRNA level of hepatic nuclear factor 4 alpha (HNF4α) was determined by reverse transcription polymerase chain reaction (RT-PCR). Indirect immunofluorescence staining and Western blot analysis were employed to detect protein expression of HNF4α in the islets. Glucokinase (GK) activity was measured by spectrophotometric method.RESULTS: Berberine enhanced GSIS rather than basal insulin secretion dose-dependently in rat islets and showed no significant cytotoxicity on islet cells at the concentration of 10 μmol/L. Both mRNA and protein expressions of HNF4α were up-regulated by berberine in a dose-dependent manner, and GK activity was also increased accordingly. However, GB demonstrated no regulatory effects on HNF4α expression or GK activity.CONCLUSION: Berberine can enhance GSIS in rat islets, and probably exerts the insulinotropic effect via a pathway involving HNF4α and GK, which is distinct from sulphonylureas (SUs).

  6. Reaction route graphs. III. Non-minimal kinetic mechanisms.

    Science.gov (United States)

    Fishtik, Ilie; Callaghan, Caitlin A; Datta, Ravindra

    2005-02-24

    The concept of reaction route (RR) graphs introduced recently by us for kinetic mechanisms that produce minimal graphs is extended to the problem of non-minimal kinetic mechanisms for the case of a single overall reaction (OR). A RR graph is said to be minimal if all of the stoichiometric numbers in all direct RRs of the mechanism are equal to +/-1 and non-minimal if at least one stoichiometric number in a direct RR is non-unity, e.g., equal to +/-2. For a given mechanism, four unique topological characteristics of RR graphs are defined and enumerated, namely, direct full routes (FRs), empty routes (ERs), intermediate nodes (INs), and terminal nodes (TNs). These are further utilized to construct the RR graphs. One algorithm involves viewing each IN as a central node in a RR sub-graph. As a result, the construction and enumeration of RR graphs are reduced to the problem of balancing the peripheral nodes in the RR sub-graphs according to the list of FRs, ERs, INs, and TNs. An alternate method involves using an independent set of RRs to draw the RR graph while satisfying the INs and TNs. Three examples are presented to illustrate the application of non-minimal RR graph theory.

  7. Reaction Mechanisms of Magnesium Potassium Phosphate Cement and its Application

    Science.gov (United States)

    Qiao, Fei

    Magnesium potassium phosphate cement (MKPC) is a kind of cementitious binder in which the chemical bond is formed via a heterogeneous acid-base reaction between dead burned magnesia powder and potassium phosphate solution at room temperature. Small amount of boron compounds can be incorporated in the cement as a setting retarder. The final reaction product of MgO-KH2PO4-H 2O ternary system is identified as magnesium potassium phosphate hexahydrate, MgKPO4·6H2O. However, the mechanisms and procedures through which this crystalline product is formed and the conditions under which the crystallization process would be influenced are not yet clear. Understanding of the reaction mechanism of the system is helpful for developing new methodologies to control the rapid reaction process and furthermore, to adjust the phase assemblage of the binder, and to enhance the macroscopic properties. This study is mainly focused on the examination of the reaction mechanism of MKPC. In addition, the formulation optimization, microstructure characterization and field application in rapid repair are also systematically studied. The chemical reactions between magnesia and potassium dihydrogen phosphate are essentially an acid-base reaction with strong heat release, the pH and temperature variation throughout the reaction process could provide useful information to disclose the different stages in the reaction. However, it would be very difficult to conduct such tests on the cement paste due to the limited water content and fast setting. In the current research, the reaction mechanism of MKPC is investigated on the diluted MKPC system through monitoring the pH and temperature development, identification of the solid phase formed, and measurement of the ionic concentration of the solution. The reaction process can be explained as follows: when magnesia and potassium phosphate powder are mixed with water, phosphate is readily dissolved, which is instantly followed by the dissociation of

  8. Insight into the Mechanism of the Michael Reaction.

    Science.gov (United States)

    Giraldo, Carolina; Gómez, Sara; Weinhold, Frank; Restrepo, Albeiro

    2016-07-01

    The mechanism for the nucleophilic addition step of the Michael reaction between methanethiol as a model Michael donor and several α-substituted methyl acrylates (X=F, Cl, Me, H, CN, NO2 ) as model Michael acceptors is described in detail. We suggest a novel way to condense electrophilic Fukui functions at specific atoms in terms of the contributions from the atomic orbitals to the LUMO or, more generally, to the orbital controlling the reaction. This procedure correctly associates activation energies to local electrophilic Fukui indices for the cases treated in this work. The calculated reaction barriers strongly depend on the nature of the substituent. As a general rule, activation energies are governed by structural changes, although electronic factors are significant for electron-withdrawing groups. Nucleophilic addition to Michael receptors is best described as a highly nonsynchronous process, in which the geometry of the transition state comprises a nonplanar six-membered ring. Formation of the S⋅⋅⋅C bond, which defines the interaction between the reactants, progresses ahead of all other primitive processes in the early stages of the transformation. In view of our results, we postulate that highly complex chemical reactions, as is the case for the nucleophilic addition step studied herein, that involve cleavage/formation of a total of six bonds, lower their activation energies by favoring nonsynchronicity, that is, for these types of systems, primitive changes should advance at different rates.

  9. REACTION MECHANISM OF BENZOPHENONE-PHOTOINITIATED CROSSLINKING OF POLYETHYLENE

    Institute of Scientific and Technical Information of China (English)

    Bao-jun Qu

    2002-01-01

    The radical intermediates, the crosslink microstructures, and the reaction mechanism of benzophenone (BP)-photoinitiated crosslinking of low-density polyethylene (LDPE) and model compounds (MD) have been reviewed in detail.The spin-trapping electron spin resonance (ESR) spectra obtained from the LDPE/BP systems with spin-trap agents showthat two kinds of polymer radical intermediates are mainly formed: tertiary carbon and secondary carbon radicals. The spin-trapping ESR studies of MD/BP systems give further evidence that photocrosslinking reactions of PE predominantly takeplace at sites of tertiary carbon, secondary carbon, and especially allylic carbon when available. The high resolution 13C-NMR spectra obtained from LDPE and MD systems show that the crosslink microstructures have H- and Y-type links andthat their concentrations are of the same order. The fluorescence, ESR, 13C and 1H-NMR spectra from the PE and MDsystems demonstrate that the main photoreduction product of BP (PPB) is benzpinacol formed by the recombination of twodiphenylhydroxymethyl (K*) radical intermediates. Two new PPB products: an isomer of benzpinacol with quinoid structure,1-phenylhydroxymethylene-4-diphenylhydroxymethyl-2,5-cyclohexadiene and three kinds of a-alkyl-benzhydrols have beendetected and identified. These results provide new experimental evidence for elucidating the reaction mechanism in the BP-photoinitiated crosslinking of polyethylene.

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

    Science.gov (United States)

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

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

  11. BlenX-based compositional modeling of complex reaction mechanisms

    CERN Document Server

    Zámborszky, Judit; 10.4204/EPTCS.19.6

    2010-01-01

    Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model buildin...

  12. A discrete model to study reaction-diffusion-mechanics systems.

    Science.gov (United States)

    Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  13. A discrete model to study reaction-diffusion-mechanics systems.

    Directory of Open Access Journals (Sweden)

    Louis D Weise

    Full Text Available This article introduces a discrete reaction-diffusion-mechanics (dRDM model to study the effects of deformation on reaction-diffusion (RD processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material. Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  14. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    Energy Technology Data Exchange (ETDEWEB)

    Ziaul Huque

    2007-08-31

    This is the final technical report for the project titled 'Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks'. The aim of the project was to develop an efficient chemistry model for combustion simulations. The reduced chemistry model was developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) was used via a new network topology known as Non-linear Principal Components Analysis (NPCA). A commonly used Multilayer Perceptron Neural Network (MLP-NN) was modified to implement NPCA-NN. The training rate of NPCA-NN was improved with the GEneralized Regression Neural Network (GRNN) based on kernel smoothing techniques. Kernel smoothing provides a simple way of finding structure in data set without the imposition of a parametric model. The trajectory data of the reaction mechanism was generated based on the optimization techniques of genetic algorithm (GA). The NPCA-NN algorithm was then used for the reduction of Dimethyl Ether (DME) mechanism. DME is a recently discovered fuel made from natural gas, (and other feedstock such as coal, biomass, and urban wastes) which can be used in compression ignition engines as a substitute for diesel. An in-house two-dimensional Computational Fluid Dynamics (CFD) code was developed based on Meshfree technique and time marching solution algorithm. The project also provided valuable research experience to two graduate students.

  15. Roles of interfacial reaction on mechanical properties of solder interfaces

    Science.gov (United States)

    Liu, Pilin

    This study investigated roles of interfacial reaction in fracture and fatigue of solder interconnects. The interfacial reaction phases in the as-reflowed and after aging were examined by cross-sectional transmission electron microscopy (TEM) while interfacial mechanical properties were determined from a flexural peel fracture mechanics technique. Because of their widespread uses in microelectronic packaging, SnPb solder interfaces, and Bi-containing Pb-free solder interfaces were chosen as the subjects of this study. In the interfacial reaction study, we observed a complicated micro structural evolution during solid-state aging of electroless-Ni(P)/SnPb solder interconnects. In as-reflowed condition, the interfacial reaction produced Ni3Sn 4 and P-rich layers. Following overaging, the interfacial microstructure degenerated into a complex multilayer structure consisting of multiple layers of Ni-Sn compounds and transformed Ni-P phases. In SnPb solder interfacial system, fatigue study showed that the overaging of the high P electroless Ni-P/SnPb interconnects resulted in a sharp reduction in the fatigue resistance of the interface in the high crack growth rate regime. Fracture mechanism analysis indicated that the sharp drop in fatigue resistance was triggered by the brittle fracture of the Ni3Sn2 intermetallic phase developed at the overaged interface. The fatigue behavior was strongly dependent on P concentration in electroless Ni. Kirkendall voids were found in the interfacial region after aging, but they did not cause premature fracture of the solder interfaces. In Bi-containing solder interfacial system, we found that Bi segregated to the Cu-intermetallic interface during aging in SnBi/Cu interconnect. This caused serious embrittlement of Sn-Bi/Cu interface. Further aging induced numerous voids along the Cu3Sn/Cu interface. These interfacial voids were different from Kirkendall voids. Their formation was explained on basis of vacancy condensation at the

  16. Microstructure and Mechanical Properties of Reaction-Formed Joints in Reaction Bonded Silicon Carbide Ceramics

    Science.gov (United States)

    Singh, M.

    1998-01-01

    A reaction-bonded silicon carbide (RB-SiC) ceramic material (Carborundum's Cerastar RB-SIC) has been joined using a reaction forming approach. Microstructure and mechanical properties of three types of reaction-formed joints (350 micron, 50-55 micron, and 20-25 micron thick) have been evaluated. Thick (approximately 350 micron) joints consist mainly of silicon with a small amount of silicon carbide. The flexural strength of thick joints is about 44 plus or minus 2 MPa, and fracture always occurs at the joints. The microscopic examination of fracture surfaces of specimens with thick joints tested at room temperature revealed the failure mode to be typically brittle. Thin joints (<50-55 micron) consist of silicon carbide and silicon phases. The room and high temperature flexural strengths of thin (<50-55 micron) reaction-formed joints have been found to be at least equal to that of the bulk Cerastar RB-SIC materials because the flexure bars fracture away from the joint regions. In this case, the fracture origins appear to be inhomogeneities inside the parent material. This was always found to be the case for thin joints tested at temperatures up to 1350C in air. This observation suggests that the strength of Cerastar RB-SIC material containing a thin joint is not limited by the joint strength but by the strength of the bulk (parent) materials.

  17. Peptide Bond Synthesis by a Mechanism Involving an Enzymatic Reaction and a Subsequent Chemical Reaction.

    Science.gov (United States)

    Abe, Tomoko; Hashimoto, Yoshiteru; Zhuang, Ye; Ge, Yin; Kumano, Takuto; Kobayashi, Michihiko

    2016-01-22

    We recently reported that an amide bond is unexpectedly formed by an acyl-CoA synthetase (which catalyzes the formation of a carbon-sulfur bond) when a suitable acid and l-cysteine are used as substrates. DltA, which is homologous to the adenylation domain of nonribosomal peptide synthetase, belongs to the same superfamily of adenylate-forming enzymes, which includes many kinds of enzymes, including the acyl-CoA synthetases. Here, we demonstrate that DltA synthesizes not only N-(d-alanyl)-l-cysteine (a dipeptide) but also various oligopeptides. We propose that this enzyme catalyzes peptide synthesis by the following unprecedented mechanism: (i) the formation of S-acyl-l-cysteine as an intermediate via its "enzymatic activity" and (ii) subsequent "chemical" S → N acyl transfer in the intermediate, resulting in peptide formation. Step ii is identical to the corresponding reaction in native chemical ligation, a method of chemical peptide synthesis, whereas step i is not. To the best of our knowledge, our discovery of this peptide synthesis mechanism involving an enzymatic reaction and a subsequent chemical reaction is the first such one to be reported. This new process yields peptides without the use of a thioesterified fragment, which is required in native chemical ligation. Together with these findings, the same mechanism-dependent formation of N-acyl compounds by other members of the above-mentioned superfamily demonstrated that all members most likely form peptide/amide compounds by using this novel mechanism. Each member enzyme acts on a specific substrate; thus, not only the corresponding peptides but also new types of amide compounds can be formed.

  18. Reaction kinetics and mechanism of magnetic field effects in cryptochrome

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Schulten, Klaus

    2012-01-01

    Creatures as varied as mammals, fish, insects, reptiles, and birds have an intriguing sixth sense that allows them to orient themselves in the Earth's magnetic field. Despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically...... sensitive radical pair reactions occurring in the retina, the light-sensitive part of animal eyes. A photoreceptor, cryptochrome, has been suggested to endow birds with magnetoreceptive abilities as the protein has been shown to exhibit the biophysical properties required for an animal magnetoreceptor...

  19. Allenes and computational chemistry: from bonding situations to reaction mechanisms.

    Science.gov (United States)

    Soriano, Elena; Fernández, Israel

    2014-05-07

    The present review is focused on the application of computational/theoretical methods to the wide and rich chemistry of allenes. Special emphasis is made on the interplay and synergy between experimental and computational methodologies, rather than on recent developments in methods and algorithms. Therefore, this review covers the state-of-the-art applications of computational chemistry to understand and rationalize the bonding situation and vast reactivity of allenes. Thus, the contents of this review span from the most fundamental studies on the equilibrium structure and chirality of allenes to recent advances in the study of complex reaction mechanisms involving allene derivatives in organic and organometallic chemistry.

  20. Characterization of the proposed 4-{\\alpha} cluster state candidate in 16O

    CERN Document Server

    Li, K C W; Adsley, P; Papka, P; Smit, F D; Brümmer, J W; Diget, C Aa; Freer, M; Harakeh, M N; Kokalova, Tz; Nemulodi, F; Pellegri, L; Rebeiro, B; Swartz, J A; Triambak, S; van Zyl, J J; Wheldon, C

    2016-01-01

    The $\\mathrm{^{16}O}(\\alpha, \\alpha^{\\prime})$ reaction was studied at $\\theta_{lab} = 0^\\circ$ at an incident energy of $\\textrm{E}_{lab}$ = 200 MeV using the K600 magnetic spectrometer at iThemba LABS. Proton and $\\alpha$-decay from the natural parity states were observed in a large-acceptance silicon-strip detector array at backward angles. The coincident charged particle measurements were used to characterize the decay channels of the $0_{6}^{+}$ state in $\\mathrm{^{16}O}$ located at $E_{x} = 15.097(5)$ MeV. This state is identified by several theoretical cluster calculations to be a good candidate for the 4-$\\alpha$ cluster state. The results of this work suggest the presence of a previously unidentified resonance at $E_{x}\\approx15$ MeV that does not exhibit a $0^{+}$ character. This unresolved resonance may have contaminated previous observations of the $0_{6}^{+}$ state.

  1. The mechanism of copper-catalyzed azide-alkyne cycloaddition reaction: a quantum mechanical investigation.

    Science.gov (United States)

    Ozen, Cihan; Tüzün, Nurcan Ş

    2012-04-01

    In this study, the mechanism of CuAAC reaction and the structure of copper acetylides have been investigated with quantum mechanical methods, namely B3LYP/6-311+G(d,p). A series of possible copper-acetylide species which contain up to four copper atoms and solvent molecules as ligand has been evaluated and a four-copper containing copper-acetylide, M1A, was proposed more likely to form based on its thermodynamic stability. The reaction has been modeled with a representative simple alkyne and a simple azide to concentrate solely on the electronic effects of the mechanism. Later, the devised mechanism has been applied to a real system, namely to the reaction of 2-azido-1,1,1-trifluoroethane and ethynylbenzene in the presence of copper. The copper catalyst transforms the concerted uncatalyzed reaction to a stepwise process and lowers the activation barrier. The pre-reactive complexation of the negatively charged secondary nitrogen of azide and the positively charged copper of copper-acetylide brings the azide and the alkyne to a suitable geometry for cycloaddition to take place. The calculated activation barrier difference between the catalyzed and the uncatalyzed reactions is consistent with faster and the regioselective synthesis of triazole product. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. A New Formulation of the Lindemann Mechanism of Unimolecular Reactions

    Institute of Scientific and Technical Information of China (English)

    钱人元

    2003-01-01

    A new formulation of the Lindemann mechanism of unimolecular reactions in gaseous phase is presented, without the use of steady state hypothesis. It is hereby shown that the nature of applicability of steady state hypothesis in the regime of high reactant gas pressure is different from that in the regime of low gas pressure. In the former case it is an equilibrium approximation, while in the latter case it is a highly reactive intermediate approximation in no connection with a steady state. Furthermore for the latter case it is shown that in the classical formulation of Lindemann mecbRnism the use of steady state hypothesis is an ad hoc assumption. A highly reactive intermediate in the sense that its concentration is very small during the whole course of reaction is a necessary condition for the applicability of very reactive intermediate approximation. When the two distinctive nature of the applicability of steady state hypothesis is mlxed-up, wrong or useless conclusion may be arrived at. The only possible case of realizing a true steady state in a complex reaction is pointed out.

  3. Complete reaction mechanisms of mercury oxidation on halogenated activated carbon.

    Science.gov (United States)

    Rungnim, Chompoonut; Promarak, Vinich; Hannongbua, Supa; Kungwan, Nawee; Namuangruk, Supawadee

    2016-06-05

    The reaction mechanisms of mercury (Hg) adsorption and oxidation on halogenated activated carbon (AC) have been completely studied for the first time using density functional theory (DFT) method. Two different halogenated AC models, namely X-AC and X-AC-X (X=Cl, Br, I), were adopted. The results revealed that HgX is found to be stable-state on the AC edge since its further desorption from the AC as HgX, or further oxidation to HgX2, are energetically unfavorable. Remarkably, the halide type does not significantly affect the Hg adsorption energy but it strongly affects the activation energy barrier of HgX formation, which obviously increases in the order HgIBr-AC>Cl-AC. Thus, the study of the complete reaction mechanism is essential because the adsorption energy can not be used as a guideline for the rational material design in the halide impregnated AC systems. The activation energy is an important descriptor for the predictions of sorbent reactivity to the Hg oxidation process.

  4. 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.

  5. Mechanism of chimera formation during the Multiple Displacement Amplification reaction

    Directory of Open Access Journals (Sweden)

    Stockwell Timothy B

    2007-04-01

    Full Text Available Abstract Background Multiple Displacement Amplification (MDA is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.

  6. Development and validation of a reduced combined biodiesel–diesel reaction mechanism

    DEFF Research Database (Denmark)

    Ng, Hoon Kiat; Gan, Suyin; Ng, Jo-Han

    2013-01-01

    In this study, a compact combined biodiesel–diesel (CBD) reaction mechanism for diesel engine simulations is proposed through the combination of three component mechanisms using a chemical class-based approach. The proposed mechanism comprises the reaction mechanisms of methyl crotonate (MC...... and MB are methodologically reduced. The MC mechanism by Gail et al. with 301 species and 1516 reactions is reduced to 47 species and 210 reactions, while the MB mechanism by Brakora et al. with 41 species and 150 reactions is reduced to 33 species and 105 reactions. The mechanisms are reduced from...... a combination of methods, including peak molar concentration analysis, reaction flux analysis and the removal of individual species. In the second phase, the reduced MC and MB mechanisms are combined with the n-heptane mechanism by Pang et al. with 46 species and 112 reactions. Upon the combination...

  7. Structural Basis of Natural Promoter Recognition by a Unique Nuclear Receptor, HNF4[alpha

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Peng; Rha, Geun Bae; Melikishvili, Manana; Wu, Guangteng; Adkins, Brandon C.; Fried, Michael G.; Chi, Young-In (Kentucky)

    2010-11-09

    HNF4{alpha} (hepatocyte nuclear factor 4{alpha}) plays an essential role in the development and function of vertebrate organs, including hepatocytes and pancreatic {beta}-cells by regulating expression of multiple genes involved in organ development, nutrient transport, and diverse metabolic pathways. As such, HNF4{alpha} is a culprit gene product for a monogenic and dominantly inherited form of diabetes, known as maturity onset diabetes of the young (MODY). As a unique member of the nuclear receptor superfamily, HNF4{alpha} recognizes target genes containing two hexanucleotide direct repeat DNA-response elements separated by one base pair (DR1) by exclusively forming a cooperative homodimer. We describe here the 2.0 {angstrom} crystal structure of human HNF4{alpha} DNA binding domain in complex with a high affinity promoter element of another MODY gene, HNF1{alpha}, which reveals the molecular basis of unique target gene selection/recognition, DNA binding cooperativity, and dysfunction caused by diabetes-causing mutations. The predicted effects of MODY mutations have been tested by a set of biochemical and functional studies, which show that, in contrast to other MODY gene products, the subtle disruption of HNF4{alpha} molecular function can cause significant effects in afflicted MODY patients.

  8. Study on the Reaction Mechanism of Naphthalene with Oxalyl Chloride

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The reaction of naphthalene with oxalyl chloride in the presence of anhydrous AlCl3 was investigated. The homolog of dinaphthyl methanone can be obtained mainly from this reaction. Naphthalene conversion does not have evident correlation with the amount of AlCl3. The results show that the reaction proceeds via carbon cation electrophilic substitution reaction-free radical substitution reaction pathway.

  9. Optimized reaction mechanism rate rules for ignition of normal alkanes

    KAUST Repository

    Cai, Liming

    2016-08-11

    The increasing demand for cleaner combustion and reduced greenhouse gas emissions motivates research on the combustion of hydrocarbon fuels and their surrogates. Accurate detailed chemical kinetic models are an important prerequisite for high fidelity reacting flow simulations capable of improving combustor design and operation. The development of such models for many new fuel components and/or surrogate molecules is greatly facilitated by the application of reaction classes and rate rules. Accurate and versatile rate rules are desirable to improve the predictive accuracy of kinetic models. A major contribution in the literature is the recent work by Bugler et al. (2015), which has significantly improved rate rules and thermochemical parameters used in kinetic modeling of alkanes. In the present study, it is demonstrated that rate rules can be used and consistently optimized for a set of normal alkanes including n-heptane, n-octane, n-nonane, n-decane, and n-undecane, thereby improving the predictive accuracy for all the considered fuels. A Bayesian framework is applied in the calibration of the rate rules. The optimized rate rules are subsequently applied to generate a mechanism for n-dodecane, which was not part of the training set for the optimized rate rules. The developed mechanism shows accurate predictions compared with published well-validated mechanisms for a wide range of conditions.

  10. BlenX-based compositional modeling of complex reaction mechanisms

    Directory of Open Access Journals (Sweden)

    Judit Zámborszky

    2010-02-01

    Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.

  11. Mechanism of heterogeneous reaction of carbonyl sulfide on magnesium oxide.

    Science.gov (United States)

    Liu, Yongchun; He, Hong; Xu, Wenqing; Yu, Yunbo

    2007-05-24

    Heterogeneous reaction of carbonyl sulfide (OCS) on magnesium oxide (MgO) under ambient conditions was investigated by in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), quadrupole mass spectrometer (QMS), and density functional theory (DFT) calculations. It reveals that OCS can be catalytically hydrolyzed by surface hydroxyl on MgO to produce carbon dioxide (CO2) and hydrogen sulfide (H2S), and then H2S can be further catalytically oxidized by surface oxygen or gaseous oxygen on MgO to form sulfite (SO3(2-)) and sulfate (SO4(2-)). Hydrogen thiocarbonate (HSCO2-) was found to be the crucial intermediate. Surface hydrogen sulfide (HS), sulfur dioxide (SO2), and surface sulfite (SO3(2-)) were also found to be intermediates for the formation of sulfate. Furthermore, the surface hydroxyl contributes not only to the formation of HSCO2- but also to HSCO2- decomposition. On the basis of experimental results, the heterogeneous reaction mechanism of OCS on MgO was discussed.

  12. Reaction mechanisms and staggering in S+Ni collisions

    Energy Technology Data Exchange (ETDEWEB)

    D' Agostino, M., E-mail: dagostino@bo.infn.it [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Bruno, M. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Gulminelli, F. [LPC (IN2P3-CNRS/Ensicaen et Universite), F-14076 Caen cedex (France); Morelli, L. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Baiocco, G. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); LPC (IN2P3-CNRS/Ensicaen et Universite), F-14076 Caen cedex (France); Bardelli, L. [INFN, Firenze (Italy); INFN, Catania (Italy); Barlini, S. [INFN, Firenze (Italy); Cannata, F. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Casini, G. [INFN, Firenze (Italy); Geraci, E. [Dipartimento di Fisica dell' Universita, Catania (Italy); INFN, Catania (Italy); Gramegna, F.; Kravchuk, V.L. [INFN, Laboratori Nazionali di Legnaro (Italy); Marchi, T. [INFN, Laboratori Nazionali di Legnaro (Italy); Dipartimento di Fisica dell' Universita, Padova (Italy); Moroni, A. [INFN, Milano (Italy); Ordine, A. [INFN, Napoli (Italy); Raduta, Ad.R. [NIPNE, Bucharest-Magurele, POB-MG6 (Romania)

    2011-07-01

    The reactions {sup 32}S+{sup 58}Ni and {sup 32}S+{sup 64}Ni are studied at 14.5 A MeV. After a selection of the collision mechanism, we show that important even-odd effects are present in the isotopic fragment distributions when the excitation energy is small. Close to the multifragmentation threshold this staggering appears hidden by the rapid variation of the production yields with the fragment size. Once this effect is accounted for, the staggering appears to be a universal feature of fragment production, slightly enhanced when the emission source is neutron poor. A closer look at the behavior of the production yields as a function of the neutron excess N-Z, reveals that odd-even effects cannot be explained by pairing effects in the nuclear masses alone, but depend in a more complex way on the de-excitation chain.

  13. Mechanical reaction-diffusion model for bacterial population dynamics

    CERN Document Server

    Ngamsaad, Waipot

    2015-01-01

    The effect of mechanical interaction between cells on the spreading of bacterial population was investigated in one-dimensional space. A nonlinear reaction-diffusion equation has been formulated as a model for this dynamics. In this model, the bacterial cells are treated as the rod-like particles that interact, when contacting each other, through the hard-core repulsion. The repulsion introduces the exclusion process that causes the fast diffusion in bacterial population at high density. The propagation of the bacterial density as the traveling wave front in long time behavior has been analyzed. The analytical result reveals that the front speed is enhanced by the exclusion process---and its value depends on the packing fraction of cell. The numerical solutions of the model have been solved to confirm this prediction.

  14. Reaction mechanisms and staggering in S+Ni collisions

    Science.gov (United States)

    D'Agostino, M.; Bruno, M.; Gulminelli, F.; Morelli, L.; Baiocco, G.; Bardelli, L.; Barlini, S.; Cannata, F.; Casini, G.; Geraci, E.; Gramegna, F.; Kravchuk, V. L.; Marchi, T.; Moroni, A.; Ordine, A.; Raduta, Ad. R.

    2011-07-01

    The reactions S32+Ni58 and S32+Ni64 are studied at 14.5 A MeV. After a selection of the collision mechanism, we show that important even-odd effects are present in the isotopic fragment distributions when the excitation energy is small. Close to the multifragmentation threshold this staggering appears hidden by the rapid variation of the production yields with the fragment size. Once this effect is accounted for, the staggering appears to be a universal feature of fragment production, slightly enhanced when the emission source is neutron poor. A closer look at the behavior of the production yields as a function of the neutron excess N-Z, reveals that odd-even effects cannot be explained by pairing effects in the nuclear masses alone, but depend in a more complex way on the de-excitation chain.

  15. [Reaction mechanism of cefotaxime with human serum albumin].

    Science.gov (United States)

    Liu, Luo-sheng; Wang, Xing-po; Zhao, Quan-qin; Zhang, Yu-yi

    2006-06-01

    The reaction mechanism of cefotaxime with human serum albumin (HSA) and the affinity between cefotaxime and beta-lactamase were investigated by spectrometry and spectrofluorimetry. The interaction dissociation constants of human serum albumin and cefotaxime were determined from a double reciprocal Lineweaver-Burk plot. The binding distance and transfer efficiency between cefotaxime and HSA were also obtained according to the theory of Förster non-radiation energy transfer. The result suggested that the main binding force between cefotaxime and HSA is electrostatic force interaction. The high beta-lactamase stability of cefotaxime may be correlative with its molecular structure. The antibiotic activity and valence are connected with transfer efficiency and dissociation constant. The effect of cefotaxime on the conformation of HSA was also analyzed using synchronous fluorescence spectrometry.

  16. Low Energy Electrons as Probing Tool for Astrochemical Reaction Mechanisms

    Science.gov (United States)

    Hendrik Bredehöft, Jan; Swiderek, Petra; Hamann, Thorben

    The complexity of molecules found in space varies widely. On one end of the scale of molecular complexity is the hydrogen molecule H2 . Its formation from H atoms is if not understood than at least thoroughly investigated[1]. On the other side of said spectrum the precursors to biopolymers can be found, such as amino acids[2,3], sugars[4], lipids, cofactors[5], etc, and the kerogen-like organic polymer material in carbonaceous meteorites called "black stuff" [6]. These have also received broad attention in the last decades. Sitting in the middle between these two extremes are simple molecules that are observed by radio astronomy throughout the Universe. These are molecules like methane (CH4 ), methanol (CH3 OH), formaldehyde (CH2 O), hydrogen cyanide (HCN), and many many others. So far more than 40 such species have been identified.[7] They are often used in laboratory experiments to create larger complex molecules on the surface of simulated interstellar dust grains.[2,8] The mechanisms of formation of these observed starting materials for prebiotic chemistry is however not always clear. Also the exact mechanisms of formation of larger molecules in photochemical experiments are largely unclear. This is mostly due to the very complex chemistry going on which involves many different radicals and ions. The creation of radicals and ions can be studied in detail in laboratory simulations. They can be created in a setup mimicking interstellar grain chemistry using slow electrons. There is no free electron radiation in space. What can be found though is a lot of radiation of different sorts. There is electromagnetic radiation (UV light, X-Rays, rays, etc.) and there is particulate radiation as well in the form of high energy ions. This radiation can provide energy that drives chemical reactions in the ice mantles of interstellar dust grains. And while the multitude of different kinds of radiation might be a little confusing, they all have one thing in common: Upon

  17. On the mechanism of effective chemical reactions with turbulent mixing of reactants and finite rate of molecular reactions

    Science.gov (United States)

    Vorotilin, V. P.

    2017-01-01

    A generalization of the theory of chemical transformation processes under turbulent mixing of reactants and arbitrary values of the rate of molecular reactions is presented that was previously developed for the variant of an instantaneous reaction [13]. The use of the features of instantaneous reactions when considering the general case, namely, the introduction of the concept of effective reaction for the reactant volumes and writing a closing conservation equation for these volumes, became possible due to the partition of the whole amount of reactants into "active" and "passive" classes; the reactants of the first class are not mixed and react by the mechanism of instantaneous reactions, while the reactants of the second class approach each other only through molecular diffusion, and therefore their contribution to the reaction process can be neglected. The physical mechanism of reaction for the limit regime of an ideal mixing reactor (IMR) is revealed and described. Although formally the reaction rate in this regime depends on the concentration of passive fractions of the reactants, according to the theory presented, the true (hidden) mechanism of the reaction is associated only with the reaction of the active fractions of the reactants with vanishingly small concentration in the volume of the reactor. It is shown that the rate constant of fast chemical reactions can be evaluated when the mixing intensity of reactants is much less than that needed to reach the mixing conditions in an IMR.

  18. An efficient quantum mechanical method for radical pair recombination reactions

    Science.gov (United States)

    Lewis, Alan M.; Fay, Thomas P.; Manolopoulos, David E.

    2016-12-01

    The standard quantum mechanical expressions for the singlet and triplet survival probabilities and product yields of a radical pair recombination reaction involve a trace over the states in a combined electronic and nuclear spin Hilbert space. If this trace is evaluated deterministically, by performing a separate time-dependent wavepacket calculation for each initial state in the Hilbert space, the computational effort scales as O (Z2log ⁡Z ) , where Z is the total number of nuclear spin states. Here we show that the trace can also be evaluated stochastically, by exploiting the properties of spin coherent states. This results in a computational effort of O (M Z log ⁡Z ) , where M is the number of Monte Carlo samples needed for convergence. Example calculations on a strongly coupled radical pair with Z >106 show that the singlet yield can be converged to graphical accuracy using just M =200 samples, resulting in a speed up by a factor of >5000 over a standard deterministic calculation. We expect that this factor will greatly facilitate future quantum mechanical simulations of a wide variety of radical pairs of interest in chemistry and biology.

  19. Preparation by a Rheological Phase Reaction Method and Thermal Decomposition Reaction Mechanism of Nickelous Salicylate Tetrahydrate

    Institute of Scientific and Technical Information of China (English)

    Wang Jin-long; Yuan Liang-jie; Yang Yi-yong; Sun Ju-tang; Zhang Ke-li

    2003-01-01

    The single crystal nickel salicylate tetrahydrate was prepared with the rheological phase reaction method from nickelous hydroxide and salicylic acid. The crystal structure was determined. It is monoclinic, space group P21 /n, a =0.67874(3), b=0. 515 91(2), c=2. 313 30(9) nm, β=90.9286(17)°, V=0. 809 94(6) nm3, Z=2, ρcalcd =0. 065 0[I >2a(I)]. The thermal decomposition mechanism in an inert atmosphere was investigated via TG, DTG and DTA. The thermal decomposition products were characterized with IR and micro-powder X-ray diffraction method. A new coordination polymer (NiC6 H4O)n as an intermediate product and nanoscale metal nickel were obtained in the ranges of 364-429 ℃ and 429-680 ℃, respectively.

  20. Correction: Reaction mechanisms in ionic liquids: the kinetics and mechanism of the reaction of O,O-diethyl (2,4-dinitrophenyl) phosphate triester with secondary alicyclic amines.

    Science.gov (United States)

    Pavez, Paulina; Millán, Daniela; Morales, Javiera; Rojas, Mabel; Céspedes, Daniel; Santos, José G

    2016-01-28

    Correction for 'Reaction mechanisms in ionic liquids: the kinetics and mechanism of the reaction of O,O-diethyl (2,4-dinitrophenyl) phosphate triester with secondary alicyclic amines' by Paulina Pavez et al., Org. Biomol. Chem., 2016, DOI: 10.1039/c5ob02128f.

  1. First half-reaction mechanism of nitric oxide synthase: the role of proton and oxygen coupled electron transfer in the reaction by quantum mechanics/molecular mechanics.

    Science.gov (United States)

    Cho, Kyung-Bin; Carvajal, Maria Angels; Shaik, Sason

    2009-01-08

    The first half-reaction of nitric oxide synthase (NOS) is investigated by means of quantum mechanical/molecular mechanical (QM/MM) calculations. An energetically feasible arginine hydroxylation path was found only when the iron-oxy complex accepted one proton from an external source. The so formed species has not been considered in heme chemistry; it is described as Por(+*)Fe(III)-OOH and is characterized by the same molecular constituency as the more known ferric-hydroperoxide species, compound 0, but has a cation-radical porphyrin moiety. The reaction itself is found to involve proton coupled electron transfer (PCET) and oxygen coupled electron transfer (OCET) steps en route to the formation of compound I and the ultimate monooxygenation of arginine. The cofactor H(4)B turns out to be a key player in the mechanism acting alternatively as an electron donor (when neutral) and an electron sink (when in its radical-cation state) and, thereby, providing the electron transfer component in the various coupled proton and oxygen transfer steps (see Scheme 4 ). The various pieces of this mechanism account for many of the experimental observations, such as the following: (a) the origins of the second proton supplied to the heme, (b) the elusiveness of compound I, (c) the inactivity of peroxide-shunt pathways in NOS first half-reaction, (d) the inhibition of the H(4)B analogue 4-amino-H(4)B due to protonation at the N3 position, (e) the roles of Trp188 (iNOS numbering) and the crystal water at the active site (W115), and so on. Alternative mechanistic hypotheses are tested and excluded, and a new mechanism for the NOS second half-reaction is proposed.

  2. Reaction mechanisms in irradiated, precipitated, and mesoporous silica.

    Science.gov (United States)

    Dondi, D; Buttafava, A; Zeffiro, A; Bracco, S; Sozzani, P; Faucitano, A

    2013-04-25

    A matrix EPR spectroscopy study of the low temperature γ radiolysis of precipitated (Zeosil) and mesoporous high surface silica has afforded evidence of the formation of trapped H-atoms, H-atom centers, siloxy radicals ≡Si-O(•), anomalous silyl peroxy radicals ≡Si-OO(•) with reduced g tensor anisotropy, siloxy radical-cations (≡Si-O-Si≡)(+•), E' centers, and two species from Ge impurity. Coordination of peroxyl radicals with diamagnetic ≡Si(+) centers is proposed and tested by DFT computations in order to justify the observed g tensor. Coordination of H-atoms to ≡Si(+) centers is also proposed for the structure of the H-atom centers as an alternative model not requiring the intervention of Ge, Sn, or CO impurities. The DFT method has been employed to assess the electronic structure of siloxy radical-cations and its similarity with that of the carbon radical-cation analogues; the results have prompted a revision of the structures proposed in the literature for ST1 and ST2 centers. The comparison between the two types of silica has afforded evidence of different radiolysis mechanisms leading to a greater yield of trapped H-atoms and H-atom centers in zeosil silica, which is reckoned with the 4-fold greater concentration of silanol groups. Parallel radiolysis experiments carried out by using both types of silica with polybutadiene oligomers as adsorbate have afforded evidence of free valence and energy migration phenomena leading to irreversible linking of polybutadiene chains onto silica. Reaction mechanisms are proposed based on the detection of SiO2-bonded free radicals whose structure has been defined by EPR.

  3. Quantum Mechanics Rate Constant for the N+ND Reaction

    Institute of Scientific and Technical Information of China (English)

    Ai-jie Zhang; Guo-zhong He

    2011-01-01

    We present nonadiabatic quantum dynamical calculations on the two coupled potential energy surfaces (12A' and 22A') [J.Theor.Comput.Chem.8,849 (2009)] for the reaction.Initial state-resolved reaction probabilities and cross sections for the N+ND→N2+D reaction and N'+ND→N+N'D reaction for collision energies of 5 meV to 1.0 eV are determined,respectively.It is found that the N+ND→N2+D reaction is dominated in the N+ND reaction.In addition,we obtained the rate constants for the N+ND→N2+D reaction which demand further experimental investigations.

  4. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    Energy Technology Data Exchange (ETDEWEB)

    Nelson Butuk

    2005-12-01

    This is an annual technical report for the work done over the last year (period ending 9/30/2005) on the project titled ''Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks''. The aim of the project is to develop an efficient chemistry model for combustion simulations. The reduced chemistry model will be developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) will be used via a new network topology know as Non-linear Principal Components Analysis (NPCA). We report on the development of a novel procedure to speed up the training of NPCA. The same procedure termed L{sub 2}Boost can be used to increase the order of approximation of the Generalized Regression Neural Network (GRNN). It is pointed out that GRNN is a basic procedure for the emerging mesh free CFD. Also reported is an efficient simple approach of computing the derivatives of GRNN function approximation using complex variables or the Complex Step Method (CSM). The results presented demonstrate the significance of the methods developed and will be useful in many areas of applied science and engineering.

  5. Theoretical Study on the Mechanism of Sonogashira Coupling Reaction

    Institute of Scientific and Technical Information of China (English)

    CHEN Li-Ping; HONG San-Guo; HOU Hao-Qing

    2008-01-01

    The mechanism of palladium-catalyzed Sonogashira cross-coupling reaction has been studied theoretically by DFT (density functional theory) calculations. The model system studied consists of Pd(PH3)2 as the starting catalyst complex, phenyl bromide as the substrate and acetylene as the terminal alkyne, without regarding to the co-catalyst and base. Mechanistically and energetically plausible catalytic cycles for the cross-coupling have been identified. The DFT analysis shows that the catalytic cycle occurs in three stages: oxidative addition of phenyl bromide to the palladium center, alkynylation of palladium(II) intermediate, and reductive elimination to phenylacetylene. In the oxidative addition, the neutral and anionic pathways have been investigated, which could both give rise to cis-configured palladium(II) diphosphine intermediate. Starting from the palladium(II) diphosphine intermediate, the only identifiable pathway in alkynylation involves the dissociation of Br group and the formation of square-planar palladium(II) intermediate, in which the phenyl and alkynyl groups are oriented cis to each other. Due to the close proximity of phenyl and alkynyl groups, the reductive elimination of phenylacetylene proceeds smoothly.

  6. Structure and reaction mechanism of basil eugenol synthase.

    Directory of Open Access Journals (Sweden)

    Gordon V Louie

    Full Text Available Phenylpropenes, a large group of plant volatile compounds that serve in multiple roles in defense and pollinator attraction, contain a propenyl side chain. Eugenol synthase (EGS catalyzes the reductive displacement of acetate from the propenyl side chain of the substrate coniferyl acetate to produce the allyl-phenylpropene eugenol. We report here the structure determination of EGS from basil (Ocimum basilicum by protein x-ray crystallography. EGS is structurally related to the short-chain dehydrogenase/reductases (SDRs, and in particular, enzymes in the isoflavone-reductase-like subfamily. The structure of a ternary complex of EGS bound to the cofactor NADP(H and a mixed competitive inhibitor EMDF ((7S,8S-ethyl (7,8-methylene-dihydroferulate provides a detailed view of the binding interactions within the EGS active site and a starting point for mutagenic examination of the unusual reductive mechanism of EGS. The key interactions between EMDF and the EGS-holoenzyme include stacking of the phenyl ring of EMDF against the cofactor's nicotinamide ring and a water-mediated hydrogen-bonding interaction between the EMDF 4-hydroxy group and the side-chain amino moiety of a conserved lysine residue, Lys132. The C4 carbon of nicotinamide resides immediately adjacent to the site of hydride addition, the C7 carbon of cinnamyl acetate substrates. The inhibitor-bound EGS structure suggests a two-step reaction mechanism involving the formation of a quinone-methide prior to reduction. The formation of this intermediate is promoted by a hydrogen-bonding network that favors deprotonation of the substrate's 4-hydroxyl group and disfavors binding of the acetate moiety, akin to a push-pull catalytic mechanism. Notably, the catalytic involvement in EGS of the conserved Lys132 in preparing the phenolic substrate for quinone methide formation through the proton-relay network appears to be an adaptation of the analogous role in hydrogen bonding played by the equivalent

  7. Reaction of Np atom with H₂O in the gas phase: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-01

    The gas-phase reaction of an Np atom with H2O was investigated using density functional theory and ab initio molecular dynamics. The reaction mechanisms and the corresponding potential energy profiles for different possible spin states were analyzed. Three reaction channels were found in the mechanism study: the isomerization channel, the H2 elimination channel, and the H atom elimination channel. The latter two were observed in the dynamics simulation. It was found that the branching ratio of the title reaction depends on the initial kinetic energy along the transition vector. Product energy distributions for the reaction were evaluated by performing direct classical trajectory calculations on the lowest sextet potential energy surface. The results indicate that most of the available energy appears as the translational energy of the products. The overall results indicate that the H2 elimination channel with low kinetic energy is thermodynamically favored but competes with the H atom elimination channel with higher kinetic energy.

  8. Mechanisms in adverse reactions to food. The nose

    DEFF Research Database (Denmark)

    Høst, A

    1995-01-01

    Rhinitis is a common symptom in food allergic patients, but rhinitis is rarely the only symptom. Rhinitis due to adverse reactions to preservatives and colorants is very rare. In anaphylactic systemic reactions to foods the rhinitis symptoms are caused by inflammatory mediators transported...... by the circulation. In non-anaphylactic reactions, the nasal inflammation and symptoms are probably induced by interaction with food allergens transported to the nasal mucosa via the blood circulation....

  9. Preparation by a Rheological Phase Reaction Method and Thermal Decomposition Reaction Mechanism of Nickelous Salicylate Tetrahydrate

    Institute of Scientific and Technical Information of China (English)

    WangJin-long; YuanLiang-jie; YangYi-yong; SunJu-tang; ZhangKe-li

    2003-01-01

    The single crystal nickel salicylate tetrahydrate was prepared with the rheological phase reaction method from nickelous hydroxide and salicylic acid. The crystal structure was determinecL It is monoclinic, space group P21/n, α=0.678 74(3), b=0. 515 91(2), c=2. 313 30(9) nm, β=90.9286(17)°,V=0. 809 94(6) nm3, Z=2, ρcalod =1. 661 g· cm-3. Final R indices: R=0. 027 9 and ωR=0.065 0[Ⅰ>2σ(Ⅰ)]. The thermal decomposition mechanism in an inert atmosphere was investigated via TG, DTG and DTA. The thermal decomposition products were characterized with IR and micro-powder X-ray diffraction method. A new coordination polymer ( NiC6 H4 O)n as an intermediate product and nanoscale metal nickel were obtained in the ranges of 364-429℃ and 429-680℃, respectively.

  10. HNF4alpha and CDH1 are associated with ulcerative colitis in a Dutch cohort

    NARCIS (Netherlands)

    Sommeren, S. van; Visschedijk, M.C.; Festen, E.A.; Jong, D.J. de; Ponsioen, C.Y.; Wijmenga, C.; Weersma, R.K.

    2011-01-01

    BACKGROUND: Inflammatory bowel diseases (IBDs), consisting of ulcerative colitis (UC) and Crohn's disease (CD), are complex disorders with multiple genes contributing to disease pathogenesis. A recent genome-wide association scan identified three novel susceptibility loci for UC: HNF4alpha, CDH1, an

  11. HNF4 alpha and CDH1 Are Associated with Ulcerative Colitis in a Dutch Cohort

    NARCIS (Netherlands)

    van Sommeren, Suzanne; Visschedijk, Marijn C.; Festen, Eleonora A. M.; de Jong, Dirk J.; Ponsioen, Cyriel Y.; Wijmenga, Cisca; Weersma, Rinse K.

    2011-01-01

    Background: Inflammatory bowel diseases (IBDs), consisting of ulcerative colitis (UC) and Crohn's disease (CD), are complex disorders with multiple genes contributing to disease pathogenesis. A recent genome-wide association scan identified three novel susceptibility loci for UC: HNF4 alpha, CDH1, a

  12. A GH57 4-alpha-glucanotransferase of hyperthermophilic origin with potential for alkyl glycoside production

    NARCIS (Netherlands)

    Paul, Catherine J.; Leemhuis, Hans; Dobruchowska, Justyna M.; Grey, Carl; Onnby, Linda; van Leeuwen, Sander S.; Dijkhuizen, Lubbert; Karlsson, Eva Nordberg

    4-alpha-Glucanotransferase (GTase) enzymes (EC 2.4.1.25) modulate the size of alpha-glucans by cleaving and reforming alpha-1,4 glycosidic bonds in alpha-glucans, an essential process in starch and glycogen metabolism in plants and microorganisms. The glycoside hydrolase family 57 enzyme (GTase57)

  13. Monosaccharide templates for de novo designed 4-alpha-helix bundle proteins: template effects in carboproteins

    DEFF Research Database (Denmark)

    Brask, Jesper; Dideriksen, J.M.; Nielsen, John;

    2003-01-01

    De novo design and total chemical synthesis of proteins provide powerful approaches to critically test our understanding of protein folding, structure, and stability. The 4-alpha-helix bundle is a frequently studied structure in which four amphiphilic alpha-helical peptide strands form a hydropho......)) and melting points in chemical and thermal denaturation experiments....

  14. Crystallization and melt behaviour of isotactic poly((4-alpha,alpha-dimethyl-benzyl)phenyl methacrylate)

    NARCIS (Netherlands)

    vanEkenstein, GORA; Tan, YY

    1997-01-01

    The crystallization and melting behaviour of practically 100% isotactic poly((4-alpha,alpha-dimethylbenzyl) phenyl methacrylate) has been studied by d.s.c. and light microscopy. Crystallization from the melt seemed to be non-spherulitic. The maximum crystallization rate, which could only be

  15. A GH57 4-alpha-glucanotransferase of hyperthermophilic origin with potential for alkyl glycoside production

    NARCIS (Netherlands)

    Paul, Catherine J.; Leemhuis, Hans; Dobruchowska, Justyna M.; Grey, Carl; Onnby, Linda; van Leeuwen, Sander S.; Dijkhuizen, Lubbert; Karlsson, Eva Nordberg

    2015-01-01

    4-alpha-Glucanotransferase (GTase) enzymes (EC 2.4.1.25) modulate the size of alpha-glucans by cleaving and reforming alpha-1,4 glycosidic bonds in alpha-glucans, an essential process in starch and glycogen metabolism in plants and microorganisms. The glycoside hydrolase family 57 enzyme (GTase57) s

  16. Organic Reaction Mechanisms in the Sixth Form Part 2.

    Science.gov (United States)

    Simpson, Peter

    1989-01-01

    Presents the mechanistic ideas underlying reactions between nucleophiles and carbonyl compounds as well as some popular misconceptions. Relates reactions of carboxylic acid derivatives to those of aldehydes and ketones. Discusses leaving group ability and the ability of carbonyl oxygen to accept a negative charge. (Author/MVL)

  17. Mechanism of reaction synthesis of Li-B alloys

    Institute of Scientific and Technical Information of China (English)

    LIU; Zhijian; (刘志坚); QU; Xuanhui; (曲选辉); LI; Zhiyou; (李志友); HUANG; Baiyun; (黄伯云)

    2003-01-01

    A model for reaction synthesis of Li-B alloys has been presented. Results show that the first exothermal reaction can be divided into three stages. The first stage is an instantaneous reaction on the boundary between boron particles and lithium melting, in which the caloric released is inversely proportional to the particle size of the boron powder. The second stage is a reaction between the unreacted boron and the lithium that diffuses through the product LiB3 on the surface of the boron particle. This process can be described by Johnston model. The third stage is dissolution of the product LiB3 to Li liquid, which takes place at temperature up to 420℃. At the same time, the second exothermal reaction begins, which consists of nucleation and growth of the last Li-B compound. It can be divided into two substages, i.e. the nucleation pregnant stage and the exploded reaction stage. When the concentration of the particle nucleated is high enough, an exploding reaction takes place. The lower the temperature, the longer the time needed for the exploding reaction. By the model presented, the experimental phenomena in the synthesis are explained.

  18. Theoretical Study of Sodium-Water Surface Reaction Mechanism

    Science.gov (United States)

    Kikuchi, Shin; Kurihara, Akikazu; Ohshima, Hiroyuki; Hashimoto, Kenro

    Computational study of the sodium-water reaction at the gas (water) - liquid (sodium) interface has been carried out using the ab initio (first-principle) method. A possible reaction channel has been identified for the stepwise OH bond dissociations of a single water molecule. The energetics including the binding energy of a water molecule on the sodium surface, the activation energies of the bond cleavages, and the reaction energies, have been evaluated, and the rate constants of the first and second OH bond-breakings have been compared. It was found that the estimated rate constant of the former was much larger than the latter. The results are the basis for constructing the chemical reaction model used in a multi-dimensional sodium-water reaction code, SERAPHIM, being developed by Japan Atomic Energy Agency (JAEA) toward the safety assessment of the steam generator (SG) in a sodium-cooled fast reactor (SFR).

  19. Theoretical Study on Reaction Mechanism of Aluminum-Water System

    Institute of Scientific and Technical Information of China (English)

    Yun-lan Sun; Yan Tian; Shu-fen Li

    2008-01-01

    A theoretical study on the reaction of aluminum with water in the gas phase was performed using the hybrid density functional B3LYP and QCISD(T) methods with the 6-311+G(d,p) and the 6-311++G(d,p) basis sets. The results show that there are three possible reaction pathways that involve four isomers, seven transition structures, and two possible products for the reaction of aluminum with water. The two most favorable reaction pathways were found, whose intermediates and products agreed quite well with experimental results. The enthalpy and Gibbs free energy change of the reaction between AI and H2O at 298 and 2000 K were calculated. Some results are also in good agreement with the previous calculations or experimental results.

  20. New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.

    Directory of Open Access Journals (Sweden)

    Louis D Weise

    Full Text Available Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.

  1. Database of atomistic reaction mechanisms with application to kinetic Monte Carlo.

    Science.gov (United States)

    Terrell, Rye; Welborn, Matthew; Chill, Samuel T; Henkelman, Graeme

    2012-07-07

    Kinetic Monte Carlo is a method used to model the state-to-state kinetics of atomic systems when all reaction mechanisms and rates are known a priori. Adaptive versions of this algorithm use saddle searches from each visited state so that unexpected and complex reaction mechanisms can also be included. Here, we describe how calculated reaction mechanisms can be stored concisely in a kinetic database and subsequently reused to reduce the computational cost of such simulations. As all accessible reaction mechanisms available in a system are contained in the database, the cost of the adaptive algorithm is reduced towards that of standard kinetic Monte Carlo.

  2. Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism.

    Science.gov (United States)

    Demissie, Taye B; Garabato, Brady D; Ruud, Kenneth; Kozlowski, Pawel M

    2016-09-12

    The methylation of Hg(II) (SCH3 )2 by corrinoid-based methyl donors proceeds in a concerted manner through a single transition state by transfer of a methyl radical, in contrast to previously proposed reaction mechanisms. This reaction mechanism is a consequence of relativistic effects that lower the energies of the mercury 6p1/2 and 6p3/2 orbitals, making them energetically accessible for chemical bonding. In the absence of spin-orbit coupling, the predicted reaction mechanism is qualitatively different. This is the first example of relativity being decisive for the nature of an observed enzymatic reaction mechanism.

  3. Novel P2 promoter-derived HNF4{alpha} isoforms with different N-terminus generated by alternate exon insertion

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Jianmin, E-mail: jmhuang@partners.org [Pediatric Endocrine Unit, MassGeneral Hospital for Children and Harvard Medical School, Boston, Massachusetts, 02114-2696 (United States); Levitsky, Lynne L. [Pediatric Endocrine Unit, MassGeneral Hospital for Children and Harvard Medical School, Boston, Massachusetts, 02114-2696 (United States); Rhoads, David B., E-mail: rhoads@helix.mgh.harvard.edu [Pediatric Endocrine Unit, MassGeneral Hospital for Children and Harvard Medical School, Boston, Massachusetts, 02114-2696 (United States)

    2009-04-15

    Hepatocyte nuclear factor 4{alpha} (HNF4{alpha}) is a critical transcription factor for pancreas and liver development and functions in islet {beta} cells to maintain glucose homeostasis. Mutations in the human HNF4A gene lead to maturity onset diabetes of the young (MODY1) and polymorphisms are associated with increased risk for type 2 diabetes mellitus (T2DM). Expression of six HNF4{alpha} variants, three each from two developmentally regulated promoters, has been firmly established. We have now detected a new set of HNF4{alpha} variants designated HNF4{alpha}10-12 expressed from distal promoter P2. These variants, generated by inclusion of previously undetected exon 1E (human = 222 nt, rodent = 136 nt) following exon 1D have an altered N-terminus but identical remaining reading frame. HNF4{alpha}10-{alpha}12 are expressed in pancreatic islets (and liver) and exhibit transactivation potentials similar to the corresponding {alpha}7-{alpha}9 isoforms. DNA-binding analyses implied much higher protein levels of HNF4{alpha}10-{alpha}12 in liver than expected from the RT-PCR data. Our results provide evidence for a more complex expression pattern of HNF4{alpha} than previously appreciated. We recommend inclusion of exon 1E and nearby DNA sequences in screening for HNF4{alpha} mutations and polymorphisms in genetic analyses of MODY1 and T2DM.

  4. Mechanisms in adverse reactions to food. The sinuses

    DEFF Research Database (Denmark)

    Høst, A

    1995-01-01

    Food allergy is an extremely rare cause of chronic sinusitis. Mucosal inflammation in chronic sinusitis is rarely caused by allergic reactions to foods but rather viral infections in the upper respiratory tract.......Food allergy is an extremely rare cause of chronic sinusitis. Mucosal inflammation in chronic sinusitis is rarely caused by allergic reactions to foods but rather viral infections in the upper respiratory tract....

  5. Generation Mechanism of Deferoxamine Radical by Tyrosine-Tyrosinase Reaction.

    Science.gov (United States)

    Tada, Mika; Niwano, Yoshimi; Kohno, Masahiro

    2015-01-01

    Nitroxide radical formations of deferoxamine mesylate (DFX) that is used clinically to treat iron-overload patients was examined by a tyrosine-tyrosinase reaction system as models of the H-atom transfer or proton-coupled electron transfer. When DFX was exposed to the tyrosine-tyrosinase reaction, nine-line ESR spectrum (g = 2.0063, hfcc; aN = 0.78 mT, aH(2) = 0.63 mT) was detected, indicating that the oxidation of DFX leads to a nitroxide radical. The signal intensity of the DFX radical increased dependently on the concentrations of tyrosine and tyrosinase. The amounts of DMPO-OH spin adducts via the tyrosine-tyrosinase reaction declined with DFX. Furthermore, mass spectra of an extra removed from the tyrosine-tyrosinase reaction mixture showed that the enzyme reactions might not be degradations of DFX. Therefore, there might be two types of DFX reaction passways, which could be through an internal electron transfer from tyrosine and hydrogen absorptions by ·OH directly.

  6. The Kabachnik–Fields Reaction: Mechanism and Synthetic Use

    Directory of Open Access Journals (Sweden)

    György Keglevich

    2012-11-01

    Full Text Available The Kabachnik–Fields (phospha-Mannich reaction involving the condensation of primary or secondary amines, oxo compounds (aldehydes and ketones and >P(OH species, especially dialkyl phosphites, represents a good choice for the synthesis of α-aminophosphonates that are of significant importance due to their biological activity. In general, these three-component reactions may take place via an imine or an α-hydroxy-phosphonate intermediate. The monitoring of a few Kabachnik–Fields reactions by in situ Fourier transform IR spectroscopy has indicated the involvement of the imine intermediate that was also justified by theoretical calculations. The Kabachnik–Fields reaction was extended to >P(OH species, comprising cyclic phosphites, acyclic and cyclic H-phosphinates, as well as secondary phosphine oxides. On the other hand, heterocyclic amines were also used to prepare new α-amino phosphonic, phosphinic and phosphine oxide derivatives. In most cases, the synthesis under solvent-free microwave (MW conditions is the method of choice. It was proved that, in the cases studied by us, there was no need for the use of any catalyst. Moreover, it can be said that sophisticated and environmentally unfriendly catalysts suggested are completely unnecessary under MW conditions. Finally, the double Kabachnik–Fields reaction has made available bis(phosphonomethylamines, bis(phosphinoxidomethylamines and related species. The bis(phosphinoxidomethylamines serve as precursors for bisphosphines that furnish ring platinum complexes on reaction with dichlorodibenzonitriloplatinum.

  7. Hybrid Quantum Mechanical/Molecular Mechanics Study of the SN2 Reaction of CH3Cl+OH- in Water

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Hongyun; Wang, Dunyou; Valiev, Marat

    2011-11-03

    The SN2 mechanism for the reaction of CH3Cl + OH- in aqueous solution was investigated using combined quantum mechanical and molecular mechanics methodology. We analyzed structures of reactant, transition and product states along the reaction pathway. The free energy profile was calculated using the multi-layered representation with the DFT and CCSD(T) level of theory for the quantum-mechanical description of the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process. We find that solvation energy contribution raises the reaction barrier by ~18.9 kcal/mol and the reaction free energy by ~24.5 kcal/mol. The presence of the solvent also induces perturbations in the electronic structure of the solute leading to an increase of 3.5 kcal/mol for the reaction barrier and a decrease of 5.6 kcal/mol for the reaction free energy respectively. Combining the results of two previous calculation results on CHCl3 + OH- and CH2Cl2 + OH- reactions in water, we demonstrate that increase in the chlorination of the methyl group (from CH3Cl to CHCl3) is accompanied by the decrease in the free energy reaction barrier, with the CH3Cl + OH- having the largest barrier among the three reactions.

  8. Acceleration and Reaction Mechanism of the N-Nitrosation Reaction of Dimethylamine with Nitrite in Ice.

    Science.gov (United States)

    Kitada, Kodai; Suda, Yusuke; Takenaka, Norimichi

    2017-07-27

    Some reactions (e.g., oxidation of nitrite, denitrification of ammonium) are accelerated in freeze-concentrated solution (FCS) compared to those in aqueous solution. Ice is highly intolerant to impurities, and the ice excludes those that would accelerate reactions. Here we show the acceleration of the N-nitrosation reaction of dimethylamine (DMA) with nitrite to produce N-nitrosodimethylamine (NDMA) in FCS. NDMA is a carcinogenic compound, and this reaction is potentially accelerated in frozen fish/meat. The eaction rate of the N-nitrosation reaction becomes fastest at specific pH. This means that it is a third-order reaction. Theoretical pH values of the peak in the third-order reaction are higher than the experimental one. Freeze-concentration of acidic solution causes pH decrement; however, the freeze-concentration alone could not explain the difference of pH values. The theoretical value was obtained under the assumption that no solute took part in ice. However, solutes are incorporated in ice with a small distribution coefficient of solutes into ice. This small incorporation enhanced the decrement of pH values. Using the distribution coefficient of chloride and sodium ion and assuming those of nitrite and DMA to explain the enhancement, we succeeded in estimating the distribution coefficients of nitrite: 2 × 10(-3) and DMA: 3 × 10(-2).

  9. Identifying the n=2 reaction mechanism of FAD through voltammetric simulations

    Energy Technology Data Exchange (ETDEWEB)

    Cable, Morgan [Harriet L. Wilkes Honors College, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458 (United States); Smith, Eugene T. [Harriet L. Wilkes Honors College, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458 (United States)]. E-mail: esmith@fau.edu

    2005-04-29

    In a previous study [E.T. Smith, C.A. Davis, M.J. Barber, Anal. Biochem. 323 (2003) 114-121], cyclic voltammograms were simulated using DigiSim software for reaction mechanisms involving multiple electron transfer steps coupled to proton transfer. Specifically, the overall reaction mechanism of the form: FAD+2e{sup -}+2H{sup +}-bar FADH{sub 2} was used to simulate experimental reduction potentials as a function of pH. Experimental observations for free FAD were simulated based on selected reduction potentials and acid dissociation constants for three different reaction mechanisms. In this study, these three reaction mechanisms were examined further using simulations of concentration profiles to identify species that are present in significant concentrations during the electron transfer process. These concentration profiles can then be used as working curves to identify reaction mechanisms and equilibrium constants. For example, two of the three reaction mechanisms, both of which involve a redox reaction coupled to a single proton, indicate significant formation of the semiquinone species at the electrode surface at high pH and low potentials. Previous spectroscopic studies of flavoproteins with an n=2 reaction mechanism have been unable to detect the formation of a semiquinone under any experimental conditions. Thus, the most reasonable pathway for a proton-coupled n=2 reaction mechanism is likely to involve two protons.

  10. Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism.

    Science.gov (United States)

    Zhao, Zhiqiang; Zhang, Zhaojun; Liu, Shu; Zhang, Dong H

    2017-02-22

    Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.

  11. Assessment of existing H2/O2 chemical reaction mechanisms at reheat gas turbine conditions

    CERN Document Server

    Weydahl, Torleif; Seljeskog, Morten; Haugen, Nils Erland L

    2011-01-01

    This paper provides detailed comparisons of chemical reaction mechanisms of H2 applicable at high preheat temperatures and pressures relevant to gas turbine and particularly Alstom's reheat gas turbine conditions. It is shown that the available reaction mechanisms exhibit large differences in several important elementary reaction coefficients. The reaction mechanisms are assessed by comparing ignition delay and laminar flame speed results obtained from CHEMKIN with available data, however, the amount of data at these conditions is scarce and a recommended candidate among the mechanisms can presently not be selected. Generally, the results with the GRI-Mech and Leeds mechanisms deviate from the Davis, Li, O'Conaire, Konnov and San Diego mechanisms, but there are also significant deviations between the latter five mechanisms that altogether are better adapted to hydrogen. The differences in ignition delay times between the dedicated hydrogen mechanisms (O'Conaire, Li and Konnov) range from approximately a maxim...

  12. How NO{sub 2} affects the reaction mechanism of the SCR reaction

    Energy Technology Data Exchange (ETDEWEB)

    Koebel, M.; Madia, G.; Raimondo, F.; Wokaun, A.

    2003-03-01

    The rate of the selective catalytic reduction (SCR) of NO with N-containing reducing agents may be considerably enhanced by converting part of the NO into NO{sub 2}. The reaction using an equimolar mixture of NO and NO{sub 2} is known as 'fast SCR reaction' and the rate enhancement is most pronounced at low temperatures (T<300{sup o}C). In the present work the possible role of NO{sub 2} on catalysts based on TiO{sub 2}-WO{sub 3}-V{sub 2}O{sub 5} was investigated by in-situ Raman spectroscopy. The experiments suggest that the V{sup +4} species formed during the reduction of NO with ammonia are reoxidized faster by NO{sub 2} than by oxygen, resulting in an increased reaction rate of the fast SCR reaction. (author)

  13. Theoretical and Experimental Studies on the Reaction Mechanism of Cl2+I2=2ICl

    Institute of Scientific and Technical Information of China (English)

    YANG Guo-Ying; YUAN Li-Xia; SUN De-Sheng; WANG Zun-Yao; JIANG Tao

    2006-01-01

    The gas phase reaction mechanism of Cl2 + I2 = 2ICI has been theoretically investigated by DFT method at the B3LYP/3-21G* level. Transition states of three reaction channels were consequently given. The results indicate that in the title reaction the least activation energy of bi-molecular reaction was smaller than the dissociation energies of I2 and Cl2, and thus the reaction mechanism was the course of molecule-molecule interaction at low reaction rate. If other factors such as illumination were taken into account, I2 could dissociate into I atoms and then react with Cl2,or Cl2 dissociates into Cl atoms and reacts with I2. These were photochemical reactions with high reaction speed. The theoretical results were further validated with absorbance measurement at 516 nm.

  14. Catalytic effect and reaction mechanism of Ti doped in NaAlH4: A review

    Institute of Scientific and Technical Information of China (English)

    WANG Qiang; CHEN YunGui; WU ChaoLing; TAO MingDa

    2008-01-01

    Catalytic effect and hydrogen reaction mechanism of Ti doped in NaAlH4 were elaborated in this paper, and current viewpoints about Ti active species in hydrogen reaction were discussed, in a further step, the possibility and practicality of the hydrogen reaction mechanism of Ti-doped NaAlH4 were elucidated. They could be summarized as follows: while the current theory about the hydrogen reaction mecha-nism of Ti-doped NaAlH4 should be further improved and modified, the research on Ti-doped NaAlH4 would be a recommendable pattern for the catalyst research in other metal complex hydrides.

  15. Revisiting the mechanisms of low-temperature, base-catalysed ester interchange reactions

    Directory of Open Access Journals (Sweden)

    Dijkstra Albert J.

    2008-05-01

    Full Text Available Ester interchange reactions such as the interesterification of triglycerides and their transesterification with methanol (methanolysis to produce FAME (biodiesel nowadays invariably use a basic catalyst such as an alkali alcoholate or hydroxide. Whereas it was formerly assumed that the catalytically active intermediates in the interesterification reaction and the methanolysis reaction were the glycerolate anion and the methanolate anion respectively, it now looks far more likely that the enolate anion plays a major role whenever the concentration of free alcohol groups in the reaction medium is small in comparison with the concentration of fatty acid moieties. Which mechanism dominates in which reaction and which reaction stage will be explained and discussed.

  16. Alcali-silica reactions: Mechanisms for crack formations

    DEFF Research Database (Denmark)

    Goltermann, Per

    2006-01-01

    Alkali-silica reactions (ASR) are found all over the world and cause a large number of damage, which have lead to different sets of requirements in the different countries for the aggregates, the cements and the admixtures. One of the reasons for the damage and the different requirements is that ...

  17. Tris(Cyclopentadienyl)Uranium-t-Butyl: Synthesis, reactions, and mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Weydert, M.

    1993-04-01

    Compounds (RC{sub 5}H{sub 4}){sub 3}U(t-Bu) were prepared for R = H, Me, Et. Their decomposition products in aromatic solvents are consistent with a radical decomposition pathway induced by solvent-assisted U-C bond homolysis. NMR was used to study the reactions of (RC{sub 5}H{sub 4}){sub 3}UCl with t-BuLi (R = t-Bu, Me{sub 3}Si). Reactions of (MeC{sub 5}H{sub 4}){sub 3}U(t-Bu) with Lewis bases and fluorocarbons were studied. Analogous reaction chemistry between (RC{sub 5}H{sub 4}){sub 3}ThX systems and t-BuLi was also studied, and reactivity differences between U and Th are discussed. Synthesis of sterically crowded (RC{sub 5}H{sub 4}){sub 4}U compounds is next considered. Reaction of the trivalent (RC{sub 5}H{sub 4}){sub 3}U with (RC{sub 5}H{sub 4}){sub 2}Hg results in formation of (RC{sub 5}H{sub 4}){sub 4}U. Steric congestion, cyclopentadienyl ligand exchange, and electron transfer are discussed. (DLC)

  18. Tris(Cyclopentadienyl)Uranium-t-Butyl: Synthesis, reactions, and mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Weydert, M.

    1993-04-01

    Compounds (RC[sub 5]H[sub 4])[sub 3]U(t-Bu) were prepared for R = H, Me, Et. Their decomposition products in aromatic solvents are consistent with a radical decomposition pathway induced by solvent-assisted U-C bond homolysis. NMR was used to study the reactions of (RC[sub 5]H[sub 4])[sub 3]UCl with t-BuLi (R = t-Bu, Me[sub 3]Si). Reactions of (MeC[sub 5]H[sub 4])[sub 3]U(t-Bu) with Lewis bases and fluorocarbons were studied. Analogous reaction chemistry between (RC[sub 5]H[sub 4])[sub 3]ThX systems and t-BuLi was also studied, and reactivity differences between U and Th are discussed. Synthesis of sterically crowded (RC[sub 5]H[sub 4])[sub 4]U compounds is next considered. Reaction of the trivalent (RC[sub 5]H[sub 4])[sub 3]U with (RC[sub 5]H[sub 4])[sub 2]Hg results in formation of (RC[sub 5]H[sub 4])[sub 4]U. Steric congestion, cyclopentadienyl ligand exchange, and electron transfer are discussed. (DLC)

  19. Mechanisms in adverse reactions to food. The ear

    DEFF Research Database (Denmark)

    Høst, A

    1995-01-01

    Otitis media with effusion is rarely caused by allergy to food. Allergic inflammation in the nasal mucosa, mainly due to IgE-mediated reactions to foods, may cause eustachian tube dysfunction and subsequent otitis media with effusion. Inflammatory mediators from the nasal mucosa transported via t...

  20. Iron Contamination Mechanism and Reaction Performance Research on FCC Catalyst

    Directory of Open Access Journals (Sweden)

    Zhaoyong Liu

    2015-01-01

    Full Text Available FCC (Fluid Catalytic Cracking catalyst iron poisoning would not only influence units’ product slate; when the poisoning is serious, it could also jeopardize FCC catalysts’ fluidization in reaction-regeneration system and further cause bad influences on units’ stable operation. Under catalytic cracking reaction conditions, large amount of iron nanonodules is formed on the seriously iron contaminated catalyst due to exothermic reaction. These nodules intensify the attrition between catalyst particles and generate plenty of fines which severely influence units’ smooth running. A dense layer could be formed on the catalysts’ surface after iron contamination and the dense layer stops reactants to diffuse to inner structures of catalyst. This causes extremely negative effects on catalyst’s heavy oil conversion ability and could greatly cut down gasoline yield while increasing yields of dry gas, coke, and slurry largely. Research shows that catalyst’s reaction performance would be severely deteriorated when iron content in E-cat (equilibrium catalyst exceeds 8000 μg/g.

  1. E/Z-Thesinine-O-4'-alpha-rhamnoside, pyrrolizidine conjugates produced by grasses (Poaceae).

    Science.gov (United States)

    Koulman, Albert; Seeliger, Claudine; Edwards, Patrick J B; Fraser, Karl; Simpson, Wayne; Johnson, Linda; Cao, Mingshu; Rasmussen, Susanne; Lane, Geoffrey A

    2008-06-01

    Based on direct infusion mass spectrometry we identified a novel alkaloid as a major component of perennial ryegrass (Lolium perenne). Initial mass spectral data suggested it to be a pyrrolizidine conjugate. As this class of alkaloids has not been described before from grasses, we isolated it to elucidate its structure. The isolated alkaloid proved to be a mixture of two stereoisomers. The structures of the two compounds as determined by 1D and 2D NMR spectroscopy, were E-thesinine-O-4'-alpha-rhamnoside (1) and Z-thesinine-O-4'-alpha-rhamnoside (2). These identifications were supported by the characterisation by GC-MS and optical rotation of (+)-isoretronecanol as the necine base released on alkaline hydrolysis of these alkaloids. 1 and 2 together with the aglycone and a hexoside were also detected in tall fescue (Festuca arundinacea). This is the first report of pyrrolizidine alkaloids produced by grasses (Poaceae).

  2. Molecular genetics and phenotypic characteristics of MODY caused by hepatocyte nuclear factor 4alpha mutations in a large European collection.

    NARCIS (Netherlands)

    Pearson, E.R.; Pruhova, S.; Tack, C.J.J.; Johansen, A.; Castleden, H.A.; Lumb, P.J.; Wierzbicki, A.S.; Clark, P.M.; Lebl, J.; Pedersen, O.; Ellard, S.; Hansen, T.; Hattersley, A.T.

    2005-01-01

    AIMS/HYPOTHESIS: Heterozygous mutations in the gene of the transcription factor hepatocyte nuclear factor 4alpha (HNF-4alpha) are considered a rare cause of MODY with only 14 mutations reported to date. The description of the phenotype is limited to single families. We investigated the genetics and

  3. Unified connected theory of few-body reaction mechanisms in N-body scattering theory

    Science.gov (United States)

    Polyzou, W. N.; Redish, E. F.

    1978-01-01

    A unified treatment of different reaction mechanisms in nonrelativistic N-body scattering is presented. The theory is based on connected kernel integral equations that are expected to become compact for reasonable constraints on the potentials. The operators T/sub +-//sup ab/(A) are approximate transition operators that describe the scattering proceeding through an arbitrary reaction mechanism A. These operators are uniquely determined by a connected kernel equation and satisfy an optical theorem consistent with the choice of reaction mechanism. Connected kernel equations relating T/sub +-//sup ab/(A) to the full T/sub +-//sup ab/ allow correction of the approximate solutions for any ignored process to any order. This theory gives a unified treatment of all few-body reaction mechanisms with the same dynamic simplicity of a model calculation, but can include complicated reaction mechanisms involving overlapping configurations where it is difficult to formulate models.

  4. 1, 4-alpha-Glucan phosphorylase from Klebsiella pneumoniae purification, subunit structure and amino acid composition.

    Science.gov (United States)

    Linder, D; Kurz, G; Bender, H; Wallenfels, K

    1976-11-01

    1. A 1,4-alpha-glucan phosphorylase from Klebsiella pneumoniae has been purified about 80-fold with an over-all yield greater than 35%. The purified enzyme has been shown to be homogeneous by gel electrophoresis at different pH-values, by isoelectric focusing, by dodecylsulfate electrophoresis and by ultracentrifugation. 2. The molecular weight of the native enzyme has been determined to be 180 000 by ultra-centrifugation studies, in good agreement with the value of 189 000 estimated by gel permeation chromatography. 3. The enzyme dissociates in the presence of 0.1% dodecylsulfate or 5 M guanidine hydrochloride into polypeptide chains. The molecular weight of these polypeptide chains has been found to be 88 000 by dodecylsulfate polyacrylamide gel electrophoresis and 99 000 by sedimentation equilibrium studies, indicating that the native enzyme is composed of two polypeptide chains. 4. The enzyme contains pyridoxalphosphate with a stoichiometry of two moles per 180 000 g protein, confirming that the 1,4-alpha-glucan phosphorylase from Klebsiella pneumoniae is a dimeric enzyme. 5. The amino acid composition of the enzyme has been determined, and its correspondence to that of 1,4-alpha-glucan phosphorylases from other sources is discussed. 6. The pI of the enzyme has been shown to be 5.3 and its pH-optimum to be about pH 5.9. The enzyme is stable in the range from pH 5.9 to 10.5.

  5. Reaction between Chromium(III) and EDTA Ions: an Overlooked Mechanism of Case Study Reaction of Chemical Kinetics.

    Science.gov (United States)

    Cerar, Janez

    2015-01-01

    Widely cited and accepted explanation of reaction mechanism of the case study reaction of chemical kinetics between Cr(III) ions and ethylenediaminetetraacetic acid (EDTA) contradicts modern chromium(III) coordination chemistry data. Absorption UV and visible light spectra were recorded during the reaction between aqueous solution of Cr(NO(3))(3) and EDTA in order to obtain new information about this reaction. Analysis of the spectra showed that only very small fraction of intermediates may be present in solution during the course of the reaction. The reaction scheme was established and according to it calculations based on a simplified model were carried out. Literature data for constants were used if known, otherwise, adjusted values of their sound estimates were applied. Reasonable agreement of the model calculations with the experimental data was obtained for pH values 3.8 and 4.5 but the model failed to reproduce measured rate of reaction at pH 5.5, probably due to the use of the oversimplified model.

  6. Elucidation of Reaction Mechanisms Far from Thermodynamic Equilibrium.

    Science.gov (United States)

    Nagao, Raphael

    2016-04-01

    Far from equilibrium: This thesis provides a deep mechanistic analysis of the electrooxidation of methanol when the system is kept far from the thermodynamic equilibrium. Under an oscillatory regime, interesting characteristics between the elementary reaction steps were observed. We were able to elucidate the effect of the intrinsic drift in a potential time-series responsible for spontaneous transition of temporal patterns and the carbon dioxide decoupling from direct and indirect pathways.

  7. Chlorination of tramadol: Reaction kinetics, mechanism and genotoxicity evaluation.

    Science.gov (United States)

    Cheng, Hanyang; Song, Dean; Chang, Yangyang; Liu, Huijuan; Qu, Jiuhui

    2015-12-01

    Tramadol (TRA) is one of the most detected analgesics in environmental matrices, and it is of high significance to study the reactivity of TRA during chlorination considering its potential toxicity to the environment. The chlorine/TRA reaction is first order with respect to the TRA concentration, and a combination of first-order and second-order with respect to chlorine concentration. The pH dependence of the observed rate constants (kobs) showed that the TRA oxidation reactivity increased with increasing pH. kobs can be quantitatively described by considering all active species including Cl2, Cl2O and HOCl, and the individual rate constants of HOCl/TRA(0), HOCl/TRAH(+), Cl2/TRA and Cl2O/TRA reactions were calculated to be (2.61±0.29)×10(3)M(-1)s(-1), 14.73±4.17M(-1)s(-1), (3.93±0.34)×10(5)M(-1)s(-1) and (5.66±1.83)×10(6)M(-1)s(-1), respectively. Eleven degradation products were detected with UPLC-Q-TOF-MS, and the corresponding structures of eight products found under various pH conditions were proposed. The amine group was proposed to be the initial attack site under alkaline pH conditions, where reaction of the deprotonated amine group with HOCl is favorable. Under acidic and neutral pH conditions, however, two possible reaction pathways were proposed. One is an electrophilic substitution on the aromatic ring, and another is an electrophilic substitution on the nitrogen, leading to an N-chlorinated intermediate, which can be further oxidized. Finally, the SOS/umu test showed that the genotoxicity of TRA chlorination products increased with increasing dosage of chlorine, which was mostly attributed to the formation of some chlorine substitution products.

  8. Experimental and Guided Theoretical Investigation of Complex Reaction Mechanisms in a Prins Reaction of Glyoxylic Acid and Isobutene

    Science.gov (United States)

    Angelici, Gaetano; Nicolet, Stefan; Uda, Narasimha R.; Creus, Marc

    2014-01-01

    A laboratory experiment was designed for undergraduate students, in which the outcome of an easy single-step organic synthesis with well-defined conditions was not elucidated until the end of the exercise. In class, students predict and discuss the possible products using their knowledge of reaction mechanisms. In the laboratory, they learn how to…

  9. Kinetics and mechanism of the chlorine dioxide-trithionate reaction.

    Science.gov (United States)

    Cseko, György; Horváth, Attila K

    2012-03-22

    The trithionate-chlorine dioxide reaction has been studied spectrophotometrically in a slightly acidic medium at 25.0 ± 0.1 °C in acetate/acetic acid buffer monitoring the decay of chlorine dioxide at constant ionic strength (I = 0.5 M) adjusted by sodium perchlorate. We found that under our experimental conditions two limiting stoichiometries exist and the pH, the concentration of the reactants, and even the concentration of chloride ion affects the actual stoichiometry of the reaction that can be augmented by an appropriate linear combination of these limiting processes. It is also shown that although the formal kinetic order of trithionate is strictly one that of chlorine dioxide varies between 1 and 2, depending on the actual chlorine dioxide excess and the pH. Moreover, the otherwise sluggish chloride ion, which is also a product of the reaction, slightly accelerates the initial rate of chlorine dioxide consumption and may therefore act as an autocatalyst. In addition to that, overshoot-undershoot behavior is also observed in the [(·)ClO(2)]-time curves in the presence of chloride ion at chlorine dioxide excess. On the basis of the experiments, a 13-step kinetic model with 6 fitted kinetic parameter is proposed by nonlinear parameter estimation. © 2012 American Chemical Society

  10. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

    2015-01-01

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first

  11. Quantum Chemical Study on a New Mechanism of One-carbon Unit Transfer Reaction:The Water-assisted Mechanism

    Institute of Scientific and Technical Information of China (English)

    QIAO,Qing-An(乔青安); CAI,Zheng-Ting(蔡政亭); FENG,Da-Cheng(冯大诚)

    2004-01-01

    It is a theoretical study on the water-assisted mechanism of one-carbon unit transfer reaction, in which the energy barrier for each transition state lowered by about 80-100 kJ/mol when compared with the one in no-water-involved mechanism. The water-assisted path 4 is the favorite reaction way. Our results well explained the presumption from experiments.

  12. Kinetics and mechanism of the reaction between thiourea and iodate in unbuffered medium

    Institute of Scientific and Technical Information of China (English)

    WANG; Shun; LIN; Juanjuan; CHEN; Fan; HU; Maolin; HU; Xinge

    2004-01-01

    The reaction between iodate and thiourea has been studied in an unbuffered acidic medium. In excess iodate the reaction shows not only oligooscillations in pH, Pt potential and the concentration of iodide ion, [I-], but also an initial induction period which has the linear relation with initial pH. At the end of the induction period, [I-] decreases sharply and a yellow coloration (due to iodine) appears transiently. While in excess thiourea iodine is produced and finally consumed, leaving milky deposits (due to sulfur) at the end of the reaction. The induction period from the start of the reaction to the maximum of [I2] is also directly proportional to initial pH. A 14-step mechanism, including a H+-mediated preequalibrium, Dusman reaction, iodine-sulfur reactions and sulfur-sulfur reactions, is proposed. Computer simulations using this mechanism give good agreement with experiments.

  13. Eletromagnetic radiation and the mechanical reactions arising from it

    CERN Document Server

    Schott, G A

    1912-01-01

    Fundamental equations of the electron theory ; transformation of the potentials ; other types of solution ; physical interpretation of the solutions obtained ; illustrative examples ; remarks on the solutions obtained and on the methods of calculating the potentials in general ; periodic motions ; on the distant field due to a moving charge ; pseudo-periodic and aperiodic motions ; on the field near the orbit of a moving charge or group ; the mechanical forces acting on electric charges in motion ; the motion of groups of electric charges ; on the Doppler effect ; on the disturbed motion of a ring of electrons ; on the field close to a point charge in motion ; the mechanical force exterted by an electron on itself ; the mechanical explanation of the electron ; the mechanics of the Lorentz electron ; problems illustrative of the motion of the Lorentz electron.

  14. Program Helps To Determine Chemical-Reaction Mechanisms

    Science.gov (United States)

    Bittker, D. A.; Radhakrishnan, K.

    1995-01-01

    General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

  15. THE MECHANISM OF THE ABDERHALDEN REACTION : STUDIES ON IMMUNITY. I.

    Science.gov (United States)

    Bronfenbrenner, J

    1915-03-01

    1. The Abderhalden reaction is specific. 2. The properties of serum on which it depends develop in experimental animals simultaneously with antibodies during the process of immunization. 3. It is impossible to observe by direct methods the presence of digesting ferments in the blood of immune animals. 4. The Abderhalden test may be resolved into two phases. A dialyzable substance appears in the second phase and is the result of the autodigestion of serum. 5. The autodigestion of serum in the Abderhalden test is due to the removal of antitrypsin from the serum by the sensitized substratum.

  16. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics.

    Science.gov (United States)

    De Wispelaere, Kristof; Ensing, Bernd; Ghysels, An; Meijer, Evert Jan; Van Speybroeck, Veronique

    2015-06-22

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.

  17. Theoretical Studies of the Reaction Mechanisms of CH3S + NO2

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The potential energy surface for the CH3S + NO2 reaction has been studied using the ab initio G3 (MP2) method. A variety of possible complexes and saddle points along the minimum energy reaction paths have been characterized at UMP2 (full)/6-31G(d) level. The calculations reveal dominating reaction mechanisms of the title reaction: CH3S + NO2 firstly produce intermediate CH3SONO, then break up into CH3SO + NO. The results are valuable to understand the atmospheric sulfur compounds oxidation mechanism.

  18. Reaction mechanism and kinetics of the NCN +NO reaction: Comparison of theory and experiment

    Science.gov (United States)

    Huang, Chih-Liang; Tseng, Shiang Yang; Wang, Tzu Yi; Wang, Niann S.; Xu, Z. F.; Lin, M. C.

    2005-05-01

    The rate constants for the NCN +NO reaction have been measured by laser photolysis/laser-induced fluorescence technique in the temperature range of 254-353K in the presence of He (40-600Torr) and N2 (30-528Torr) buffer gases. The NCN radical was produced from the photodissociation of NCN3 at 193nm and monitored with a dye laser at 329.01nm. The reaction was found to be strongly positive-pressure dependent with negative-temperature dependence, as was reported previously. The experimental data could be reasonably accounted for by dual-channel Rice-Ramsperger-Kassel-Marcus calculations based on the predicted potential-energy surface using the modified Gaussian-2 method. The reaction is predicted to occur via weak intermediates, cis- and trans-NCNNO, in the A″2 state which crosses with the A'2 state containing more stable cis- and trans-NCNNO isomers. The high barriers for the fragmentation of these isomers and their trapping in the A'2 state by collisional stabilization give rise to the observed positive-pressure dependence and negative-temperature effect. The predicted energy barrier for the fragmentation of the cis-NCNNO (A'2) to CN +N2O also allows us to quantitatively account for the rate constant previously measured for the reverse process CN +N2O→NCN+NO.

  19. Solvothermal synthesis and reaction mechanism of CoO nanoparticles

    Institute of Scientific and Technical Information of China (English)

    YE; Yin; YUAN; Fang-li; HU; Peng; LI; Shao-hua; KE; Jia-jun

    2005-01-01

    Pure CoO nanoparticles have been synthesized using solvothermal method at 150℃ with Co(CH3COO)2 · 4H2O and anhydrous ethanol as reactants. SEM, TEM and XRD were employed to characterize the size, morphology and crystalline structure of the as-synthesized CoO nanoparti cles. It is revealed that the CoO nanoparticles are of octahedron configuration in face-centered cubic (FCC) structure with a lattice constant of 0. 426 nm and have an average particle size of about 50 nm. Typically, when the concentration of Co(CH3COO)2·4H2O in CH3CH2OH reduces from 0.24 mol/L to 0.08 mol/L, the size of CoO nanoparticles decreases from 500 nm to 50 nm. Based on the results of IR analysis of the finished reaction liquid and XRD of products, the reaction mech anism of the solvothermal system has been discussed.

  20. Nuclear and hadronic reaction mechanisms producing spin asymmetry

    Indian Academy of Sciences (India)

    Ken-Ichi Kubo

    2001-08-01

    We briefly review concept of the quark recombination (QRC) model and a general success of the model. To solve the existing problem, so called anomalous spin observables, in the high energy hyperon spin phenomena, we propose a mechanism; the primarily produced quarks, which are predominantly and quarks, act as the leading partons to form the hyperons. Extension of the quark recombination concept with this mechanism is successful in providing a good account of the anomalous spin observables. Another kind of anomaly, the non-zero analysing power and spin depolarization in the hyperon productions, are also discussed and well understood by the presently proposed mechanism. Recently, a further difficulty was observed in an exclusive K+ production and we will indicate a possible diagram for resolving it.

  1. Reaction kinetics and mechanism of magnetic field effects in cryptochrome

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Schulten, Klaus

    2012-01-01

    Creatures as varied as mammals, fish, insects, reptiles, and birds have an intriguing sixth sense that allows them to orient themselves in the Earth's magnetic field. Despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically...

  2. The Art of Writing Reasonable Organic Reaction Mechanisms, 2nd Edition (Robert B. Grossman)

    Science.gov (United States)

    Holman, R. W.

    2003-11-01

    The highest compliment a reviewer can give is to adopt the text that he reviews. The next advanced course I teach will use The Art of Writing Reasonable Reaction Mechanisms with the goal that students will be able to posit a plausible mechanism for any new reaction that they encounter. To those of you who have taught traditional physical organic chemistry out of the classic texts, I ask you to consider trying something, well… completely different. The Art of Writing Reasonable Reaction Mechanisms might just change the way you do things.

  3. Fasting induces basolateral uptake transporters of the SLC family in the liver via HNF4alpha and PGC1alpha.

    Science.gov (United States)

    Dietrich, Christoph G; Martin, Ina V; Porn, Anne C; Voigt, Sebastian; Gartung, Carsten; Trautwein, Christian; Geier, Andreas

    2007-09-01

    Fasting induces numerous adaptive changes in metabolism by several central signaling pathways, the most important represented by the HNF4alpha/PGC-1alpha-pathway. Because HNF4alpha has been identified as central regulator of basolateral bile acid transporters and a previous study reports increased basolateral bile acid uptake into the liver during fasting, we hypothesized that HNF4alpha is involved in fasting-induced bile acid uptake via upregulation of basolateral bile acid transporters. In rats, mRNA of Ntcp, Oatp1, and Oatp2 were significantly increased after 48 h of fasting. Protein expression as determined by Western blot showed significant increases for all three transporters 72 h after the onset of fasting. Whereas binding activity of HNF1alpha in electrophoretic mobility shift assays remained unchanged, HNF4alpha binding activity to the Ntcp promoter was increased significantly. In line with this result, we found significantly increased mRNA expression of HNF4alpha and PGC-1alpha. Functional studies in HepG2 cells revealed an increased endogenous NTCP mRNA expression upon cotransfection with either HNF4alpha, PGC-1alpha, or a combination of both. We conclude that upregulation of the basolateral bile acid transporters Ntcp, Oatp1, and Oatp2 in fasted rats is mediated via the HNF4alpha/PGC-1alpha pathway.

  4. Development of reduced-fat mayonnaise using 4alphaGTase-modified rice starch and xanthan gum.

    Science.gov (United States)

    Mun, Saehun; Kim, Young-Lim; Kang, Choon-Gil; Park, Kwan-Hwa; Shim, Jae-Yong; Kim, Yong-Ro

    2009-06-01

    In this study a disproportionating enzyme, 4-alpha-glucanotransferase (4alphaGTase), was used to modify the structural properties of rice starch to produce a suitable fat substitute in reduced-fat (RF) mayonnaise. The mayonnaise fat was partially substituted with the 4alphaGTase-treated starch paste at levels up to 50% in combination with xanthan gum and the physical and rheological properties of the modified RF mayonnaise samples were investigated. All mayonnaises prepared in this study exhibited shear thinning behavior and yield stress. Viscoelastic properties of mayonnaise were characterized using dynamic oscillatory shear test and it was observed that mayonnaises exhibited weak gel-like properties. The magnitude of elastic and loss moduli was also affected by 4alphaGTase-treated starch concentration and presence of xanthan gum. In relation to microstructure, RF mayonnaise prepared with 3.8 or 5.6 wt% of 4alphaGTase-treated starch and xanthan gum showed smaller droplets. The use of 5.6 wt% of 4alphaGTase-treated starch and 0.1 wt% of xanthan gum produced a RF mayonnaise with similar rheological properties and appearances as FF mayonnaise with gum. This study demonstrated a high feasibility for using 4alphaGTase-treated rice starch as a viable fat replacer in mayonnaise.

  5. Reaction kinetics, molecular action, and mechanisms of cellulolytic proteins.

    Science.gov (United States)

    Mosier, N S; Hall, P; Ladisch, C M; Ladisch, M R

    1999-01-01

    Cellulolytic proteins form a complex of enzymes that work together to depolymerize cellulose to the soluble products cellobiose and glucose. Fundamental studies on their molecular mechanisms have been facilitated by advances in molecular biology. These studies have shown homology between cellulases from different microorganisms, and common mechanisms between enzymes whose modes of action have sometimes been viewed as being different, as suggested by the distribution of soluble products. A more complete picture of the cellulolytic action of these proteins has emerged and combines the physical and chemical characteristics of solid cellulose substrates with the specialized structure and function of the cellulases that break it down. This chapter combines the fundamentals of cellulose structure with enzyme function in a manner that relates the cellulose binding and biochemical kinetics at the catalytic site of the proteins to the macroscopic behavior of cellulase enzyme systems.

  6. On the Reaction Mechanism of Acetaldehyde Decomposition on Mo(110)

    Energy Technology Data Exchange (ETDEWEB)

    Mei, Donghai; Karim, Ayman M.; Wang, Yong

    2012-02-16

    The strong Mo-O bond strength provides promising reactivity of Mo-based catalysts for the deoxygenation of biomass-derived oxygenates. Combining the novel dimer saddle point searching method with periodic spin-polarized density functional theory calculations, we investigated the reaction pathways of a acetaldehyde decomposition on the clean Mo(110) surface. Two reaction pathways were identified, a selective deoxygenation and a nonselective fragmentation pathways. We found that acetaldehyde preferentially adsorbs at the pseudo 3-fold hollow site in the η2(C,O) configuration on Mo(110). Among four possible bond (β-C-H, γ-C-H, C-O and C-C) cleavages, the initial decomposition of the adsorbed acetaldehyde produces either ethylidene via the C-O bond scission or acetyl via the β-C-H bond scission while the C-C and the γ-C-H bond cleavages of acetaldehyde leading to the formation of methyl (and formyl) and formylmethyl are unlikely. Further dehydrogenations of ethylidene into either ethylidyne or vinyl are competing and very facile with low activation barriers of 0.24 and 0.31 eV, respectively. Concurrently, the formed acetyl would deoxygenate into ethylidyne via the C-O cleavage rather than breaking the C-C or the C-H bonds. The selective deoxygenation of acetaldehyde forming ethylene is inhibited by relatively weaker hydrogenation capability of the Mo(110) surface. Instead, the nonselective pathway via vinyl and vinylidene dehydrogenations to ethynyl as the final hydrocarbon fragment is kinetically favorable. On the other hand, the strong interaction between ethylene and the Mo(110) surface also leads to ethylene decomposition instead of desorption into the gas phase. This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). This work was financially supported

  7. Oxygen Atom Exchange Mechanism in Reaction of OH Radical with AsO

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Oxygen atom exchange reaction mechanism in the reaction of OH radicals with AsO was investigated by means of the density functional theory (DFT) with 6-311++G(3df,3pd) and 6-311++G(d,p) basis sets. The calculated results suggest that the reaction between OH and AsO should make the oxygen atoms exchange rapidly because the barrier to isomerization is significantly less than the HO-AsO bond dissociation energy.

  8. Effect of compound nuclear reaction mechanism in 12C(6Li,d) reaction at sub-Coulomb energy

    Science.gov (United States)

    Mondal, Ashok; Adhikari, S.; Basu, C.

    2017-09-01

    The angular distribution of the 12C(6Li,d) reaction populating the 6.92 and 7.12 MeV states of 16O at sub-Coulomb energy (Ecm=3 MeV) are analysed in the framework of the Distorted Wave Born Approximation (DWBA). Recent results on excitation function measurements and backward angle angular distributions derive ANC for both the states on the basis of an alpha transfer mechanism. In the present work, we show that considering both forward and backward angle data in the analysis, the 7.12 MeV state at sub-Coulomb energy is populated from Compound nuclear process rather than transfer process. The 6.92 MeV state is however produced from direct reaction mechanism.

  9. Theoretical study on the reaction mechanism of CN radical with ketene

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The bimolecular single collision reaction potential energy surface of CN radical with ketene (CH2CO) was investigated by means of B3LYP and QCISD(T) methods. The calculated results indicate that there are three possible channels in the reaction. The first is an attack reaction by the carbon atom of CN at the carbon atom of the methylene of CH2CO to form the intermediate NCCH2CO followed by a rupture reaction of the C-C bond combined with -CO group to the products CH2CN+CO. The second is a direct addition reaction between CN and CH2CO to form the intermediate CH2C(O)CN followed by its isomerization into NCCH2CO via a CN-shift reaction, and subsequently, NCCH2CO dissociates into CH2CN+CO through a CO-loss reaction. The last is a direct hydrogen abstraction reaction of CH2CO by CN radical. Because of the existence of a 15.44 kJ/mol reaction barrier and higher energy of reaction products, the path can be ruled out as an important channel in the reaction kinetics. The present theoretical computation results, which give an available suggestion on the reaction mechanism, are in good agreement with previous experimental studies.

  10. Degradation of quinoline by wet oxidation - kinetic aspects and reaction mechanisms

    DEFF Research Database (Denmark)

    Thomsen, A.B.

    1998-01-01

    of succinic acid is suggested to be a result of a coupling reaction of the acetic acid radical A reaction mechanism is suggested for the degradation of quinoline: it involves hydroxyl radicals and the possible interaction with autoclave walls is discussed. (C) 1998 Elsevier Science Ltd. All rights reserved....

  11. The Reaction Mechanism and Rate Constants in the Radiolysis of Fe2+-Cu2+ Solutions

    DEFF Research Database (Denmark)

    Bjergbakke, Erling; Sehested, Knud; Rasmussen, O. Lang

    1976-01-01

    Pulse radiolysis and gamma radiolysis have been used to study the reaction mechanism in the radiolysis of aqueous solutions of Fe2+ and Cu2+. A reaction scheme has been developed and confirmed by computation of the corresponding complete set of differential equations. The rate constants for some...

  12. 1,4-alpha-Glucan phosphorylase form Klebsiella pneumoniae covalently couple on porous glass.

    Science.gov (United States)

    Wengenmayer, F; Linder, D; Wallenfels, K

    1977-09-01

    A simplified procedure for the preparation of 1,4-alpha-glucan phosphorylase from Klebsiella pneumoniae is described. An 80-fold purification is achieved in two steps with an overall yield of about 50%. The specific activity of the homogeneous enzyme protein is 17.7 units/mg. Compared with glycogen phosphorylase from rabbit muscle the enzyme from K. pneumoniae shows a markedly higher stability against deforming and chaotropic agents. The 1,4-alpha-glucan phosphorylase was covalently bound to porous glass particles by three different methods. Coupling with glutaraldehyde gave the highest specific activity, i.e., 5.6 units/mg of bound protein or 133 units/g of glass with maltodextrin as substrate. This corresponds to about 30% of the specific activity of the soluble enzyme. With substrates of higher molecular weight, such as glycogen or amylopectin, lower relative activity was observed. The immobilized enzyme preparations showed pH activity profiles which were slightly displaced to higher values and exhibited an increased temperature stability.

  13. Reaction Mechanism of Oxygen Atoms with Unsaturated Hydrocarbons by the Crossed-Molecular-Beams Method

    Science.gov (United States)

    Buss, R. J.; Baseman, R. J.; Guozhong, H.; Lee, Y. T.

    1982-04-01

    From a series of studies of the reaction of oxygen atoms with unsaturated hydrocarbons using the crossed molecular beam method, the dominant reaction mechanisms were found to be the simple substitution reactions with oxygen atoms replacing H, Cl, Br atom or alkyl groups. Complication due to secondary reaction was avoided by carrying out experiments under single collisions and observing primary products directly. Primary products were identified by measuring the angular and velocity distributions of products at all the mass numbers which could be detected by the mass spectrometer, and from comparison of these distributions, applying the requirement of energy and momentum conservation.

  14. Theoretical study on the reaction mechanism of (CH3)3CO+CO

    Institute of Scientific and Technical Information of China (English)

    ZHAO; Hongmei; SUN; Chengke; ZHANG; Rongchang; XI; Hongmi

    2005-01-01

    The reaction mechanism of (CH3)3CO with CO has been theoretically investigated using density-functional theory (DFT) calculations at B3LYP/6-31G* level. In order to get more reliable energy values the single-point energy is evaluated at CCSD (T)/6-31++G** level. The results show that the reaction is multi-channel and the reaction of (CH3)3CO radical with CO mostly produces (CH3)3C + CO2. The reaction could play a role in eliminating air pollution.

  15. Reaction Mechanism and Control of Selectivity in Catalysis by Oxides: Some Challenges and Open Questions

    Directory of Open Access Journals (Sweden)

    Siglinda Perathoner

    2001-11-01

    Full Text Available Some aspects of the reaction mechanisms in multistep selective (ammoxidation reactions over oxide surfaces are discussed evidencing some of the challenges for surface science and theory in describing these reactions, and for applied catalysis in order to have a more in deep identification of the key factors governing surface reactivity and which may be used to improve catalytic performances. In particular, the role of chemisorbed species in the modification of the surface reactivity and the presence of multiple pathways of reaction are evidenced by comparing the behavior of V-based catalysts in C3-C4 alkanes and alkene oxidation.

  16. Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.

    Science.gov (United States)

    Kel, Alexander E; Niehof, Monika; Matys, Volker; Zemlin, Rüdiger; Borlak, Jürgen

    2008-01-01

    We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4alpha binding sites and significantly improved an overall recognition of faithful HNF4alpha targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.

  17. Kinetic modeling of mechanisms of industrially important organic reactions in gas and liquid phase

    Energy Technology Data Exchange (ETDEWEB)

    Vahteristo, K.

    2010-07-01

    This dissertation is based on 5 articles which deal with reaction mechanisms of the following selected industrially important organic reactions: 1. dehydrocyclization of n-butylbenzene to produce naphthalene, 2. dehydrocyclization of 1-(p-tolyl)-2-methylbutane (MB) to produce 2,6-dimethylnaphthalene, 3. esterification of neopentyl glycol (NPG) with different carboxylic acids to produce monoesters, 4. skeletal isomerization of 1-pentene to produce 2-methyl-1-butene and 2-methyl-2-butene. The results of initial- and integral-rate experiments of n-butylbenzene dehydrocyclization over selfmade chromia/alumina catalyst were applied when investigating reaction 2. Reaction 2 was performed using commercial chromia/alumina of different acidity, platina on silica and vanadium/calcium/alumina as catalysts. On all catalysts used for the dehydrocyclization, major reactions were fragmentation of MB and 1-(p-tolyl)-2-methylbutenes (MBes), dehydrogenation of MB, double bond transfer, hydrogenation and 1,6-cyclization of MBes. Minor reactions were 1,5-cyclization of MBes and methyl group fragmentation of 1,6- cyclization products. Esterification reactions of NPG were performed using three different carboxylic acids: propionic, isobutyric and 2-ethylhexanoic acid. Commercial heterogeneous gellular (Dowex 50WX2), macroreticular (Amberlyst 15) type resins and homogeneous para-toluene sulfonic acid were used as catalysts. At first NPG reacted with carboxylic acids to form corresponding monoester and water. Then monoester esterified with carboxylic acid to form corresponding diester. In disproportionation reaction two monoester molecules formed NPG and corresponding diester. All these three reactions can attain equilibrium. Concerning esterification, water was removed from the reactor in order to prevent backward reaction. Skeletal isomerization experiments of 1-pentene were performed over HZSM-22 catalyst. Isomerization reactions of three different kind were detected: double bond, cis

  18. 2013 Gordon Research Conference, Inorganic reaction mechanisms, Galveston, TX, March 3-8 2013

    Energy Technology Data Exchange (ETDEWEB)

    Abu-Omar, Mahdi M. [Purdue Univ., West Lafayette, IN (United States)

    2012-12-08

    The 2013 Gordon Conference on Inorganic Reaction Mechanisms will present cutting-edge research on the molecular aspects of inorganic reactions involving elements from throughout the periodic table and state-of-the art techniques that are used in the elucidation of reaction mechanisms. The Conference will feature a wide range of topics, such as homogeneous and heterogeneous catalysis, metallobiochemistry, electron-transfer in energy reactions, polymerization, nitrogen fixation, green chemistry, oxidation, solar conversion, alkane functionalization, organotransition metal chemistry, and computational chemistry. The talks will cover themes of current interest including energy, materials, and bioinorganic chemistry. Sections cover: Electron-Transfer in Energy Reactions; Catalytic Polymerization and Oxidation Chemistry; Kinetics and Spectroscopy of Heterogeneous Catalysts; Metal-Organic Chemistry and its Application in Synthesis; Green Energy Conversion;Organometallic Chemistry and Activation of Small Molecules; Advances in Kinetics Modeling and Green Chemistry; Metals in Biology and Disease; Frontiers in Catalytic Bond Activation and Cleavage.

  19. Reduced chemical reaction mechanisms: experimental and HCCI modelling investigations of autoignition processes of iso-octane in internal combustion engines

    OpenAIRE

    Machrafi, Hatim; Lombaert, K.; Cavadias, S; Guibert, P.; Amouroux, J

    2005-01-01

    A semi-reduced (70 species, 210 reactions) and a skeletal (27 species, 29 reactions) chemical reaction mechanism for iso-octane are constructed from a semi-detailed iso-octane mechanism (84 species, 412 reactions) of the Chalmers University of Technology in Sweden. The construction of the reduced mechanisms is performed by using reduction methods such as the quasi-steady-state assumption and the partial equilibrium assumption. The obtained reduced iso-octane mechanisms show, at the mentioned ...

  20. Reaction mechanism for the thermal decomposition of BCl3/CH4/H2 gas mixtures.

    Science.gov (United States)

    Reinisch, Guillaume; Vignoles, Gérard L; Leyssale, Jean-Marc

    2011-10-27

    This paper presents an ab initio study of the B/C/Cl/H gas phase mechanism, featuring 10 addition-elimination reactions involving BH(i)Cl(j) (i + j ≤ 3) species and a first description of the chemical interaction between the carbon-containing and boron-containing subsystems through the three reactions BCl(3) + CH(4) ⇌ BCl(2)CH(3) + HCl, BHCl(2) + CH(4) ⇌ BCl(2)CH(3) + H(2), and BCl(2) + CH(4) ⇌ BHCl(2) + CH(3). A reaction mechanism is then proposed and used to perform some illustrative equilibrium and kinetic calculations in the context of chemical vapor deposition (CVD) of boron carbide. Our results show that the new addition-elimination reaction paths play a crucial role by lowering considerably the activation barrier with respect to previous theoretical evaluations; they also confirm that BCl(2)CH(3) is an important species in the mechanism.

  1. Multiple cathodic reaction mechanisms in seawater cathodic biofilms operating in sediment microbial fuel cells.

    Science.gov (United States)

    Babauta, Jerome T; Hsu, Lewis; Atci, Erhan; Kagan, Jeff; Chadwick, Bart; Beyenal, Haluk

    2014-10-01

    In this study, multiple reaction mechanisms in cathodes of sediment microbial fuel cells (SMFCs) were characterized by using cyclic voltammetry and microelectrode measurements of dissolved oxygen and pH. The cathodes were acclimated in SMFCs with sediment and seawater from San Diego Bay. Two limiting current regions were observed with onset potentials of approximately +400 mVAg/AgCl for limiting current I and -120 mVAg/AgCl for limiting current II. The appearance of two catalytic waves suggests that multiple cathodic reaction mechanisms influence cathodic performance. Microscale oxygen concentration measurements showed a zero surface concentration at the electrode surface for limiting current II but not for limiting current I, which allowed us to distinguish limiting current II as the conventional oxygen reduction reaction and limiting current I as a currently unidentified cathodic reaction mechanism. Microscale pH measurements further confirmed these results.

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

    Science.gov (United States)

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

    2016-11-01

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

  3. Reaction mechanisms in ionic liquids: the kinetics and mechanism of the reaction of O,O-diethyl (2,4-dinitrophenyl) phosphate triester with secondary alicyclic amines.

    Science.gov (United States)

    Pavez, Paulina; Millán, Daniela; Morales, Javiera; Rojas, Mabel; Céspedes, Daniel; Santos, José G

    2016-01-28

    The reactions of O,O-diethyl 2,4-dinitrophenyl phosphate triester (1) with secondary alicyclic (SA) amines in the ionic liquids [Bmim]BF4 and [Bmim]DCA were subjected to a kinetic study. Eyring plots were obtained for the title reactions in the above ionic liquids (ILs) and also in aqueous ethanol (44 wt% ethanol). Two different reaction pathways were observed in [Bmim]BF4: nucleophilic attack at the phosphoryl center, SN2(P), and at the C-1 aromatic carbon, SN(Ar), where the product distribution remained constant and independent of the amine nature. In contrast, in [Bmim]DCA only the SN2(P) pathway was found. From the kinetic analysis of the SN2(P) pathway in both ILs, curved upwards plots of kobsdvs. 1-formylpiperazine concentration were obtained. Based on the kinetic behavior, a change in the mechanism of the SN2(P) pathway is proposed for the aminolysis of 1, from a concerted process in aqueous ethanol to a stepwise mechanism, through a zwitterionic pentacoordinate intermediate, when [Bmim]BF4 and [Bmim]DCA are used as the solvents of the reaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Pierre O., E-mail: pierre.hubin@unamur.be [Laboratoire de Physico-Chimie Informatique (PCI), Unité de Chimie Physique Théorique et Structurale, University of Namur, 61 rue de Bruxelles, 5000 Namur (Belgium); Jacquemin, Denis [Laboratoire CEISAM – UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP92208, 44322 Nantes Cedex 3 (France); Institut Universitaire de France 103, Boulevard St Michel, 75005 Paris Cedex 5 (France); Leherte, Laurence; Vercauteren, Daniel P. [Laboratoire de Physico-Chimie Informatique (PCI), Unité de Chimie Physique Théorique et Structurale, University of Namur, 61 rue de Bruxelles, 5000 Namur (Belgium)

    2014-04-15

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

  5. Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.

    Science.gov (United States)

    Zinovjev, Kirill; Ruiz-Pernía, J Javier; Tuñón, Iñaki

    2013-08-13

    We present a combination of the string method and a path collective variable for the exploration of the free energy surface associated to a chemical reaction in condensed environments. The on-the-fly string method is employed to find the minimum free energy paths on a multidimensional free energy surface defined in terms of interatomic distances, which is a convenient selection to study bond forming/breaking processes. Once the paths have been determined, a reaction coordinate is defined as a measure of the advance of the system along these paths. This reaction coordinate can be then used to trace the reaction Potential of Mean Force from which the activation free energy can be obtained. This combination of methodologies has been here applied to the study, by means of Quantum Mechanics/Molecular Mechanics simulations, of the reaction catalyzed by guanidinoacetate methyltransferase. This enzyme catalyzes the methylation of guanidinoacetate by S-adenosyl-l-methionine, a reaction that involves a methyl transfer and a proton transfer and for which different reaction mechanisms have been proposed.

  6. An insight into the process and mechanism of a mechanically activated reaction for synthesizing AlH3 nano-composites.

    Science.gov (United States)

    Duan, Congwen; Hu, Lianxi; Sun, Yu; Zhou, Haiping; Yu, Huan

    2015-10-07

    The reaction pathway as well as the mechanism of the solid state reaction between MgH2 and AlCl3 has been a mystery so far. Based on SEM, TEM and NMR (Nuclear Magnetic Resonance) analyses, an amorphous intermediate (AlH6)n was preferentially formed and recrystallized as a γ phase at the final stage of the reaction. As a novel finding, this research provides a deep insight into the process and mechanism of this mechanically activated reaction.

  7. A multilayered representation, quantum mechanical and molecular mechanics study of the CH3 F + OH(-) reaction in water.

    Science.gov (United States)

    Chen, Jie; Xu, Yulong; Wang, Dunyou

    2014-03-05

    The bimolecular nucleophilic substitution (SN 2) reaction of CH3 F + OH(-) in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ∼21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol.

  8. DFT studies on cobalt-catalyzed cyclotrimerization reactions: the mechanism and origin of reaction improvement under microwave irradiation.

    Science.gov (United States)

    Rodriguez, Antonio M; Cebrián, Cristina; Prieto, Pilar; García, José Ignacio; de la Hoz, Antonio; Díaz-Ortiz, Ángel

    2012-05-14

    A DFT computational mechanistic study of the [2+2+2] cyclotrimerization of a diyne with benzonitrile, catalyzed by a cobalt complex, has been carried out. Three alternative catalytic cycles have been examined together with the precatalytic step (responsible for the induction period). The favored mechanism takes place by means of an intramolecular metal-assisted [4+2] cycloaddition. The beneficial role of microwave activation has been studied. It is concluded that microwave irradiation can decrease the catalytic induction period through thermal effects and can also increase the triplet lifetime and promote the reaction, thus improving the final yield.

  9. Multi-Level Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl(-) + CH3I Reaction in Water.

    Science.gov (United States)

    Liu, Peng; Li, Chen; Wang, Dunyou

    2017-09-25

    The Cl(-) + CH3I → CH3Cl + I(-) reaction in water was studied using combined multi-level quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculations with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 kcal/mol and 19.0 kcal/mol respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

  10. Revealing the reaction mechanisms of Li–O2 batteries using environmental transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Langli; Liu, Bin; Song, Shidong; Xu, Wu; Zhang, Ji-Guang; Wang, Chongmin

    2017-03-27

    The capacity, Coulombic efficiency, rate, and cyclability of a Li-O2 battery critically depend on the electrode reaction mechanism and the structure/morphology of the reaction product as well as their spatial and temporal evolution1-8, which are all further complicated by the choice of different electrolyte. For the case of aprotic cell, the discharge product, Li2O2, is formed through solution and surface mechanisms9,10, but little is known on the formation mechanism of the perplexing morphology of the reaction product11-15. For the case of Li-O2 battery using solid electrolyte, neither electrode reaction mechanism nor the nature of the reaction production is known. Herein, we reveal the full cycle reaction pathway for Li-O2 batteries and its correlation with the nature of the reaction product. Using an aberration-corrected environmental TEM under oxygen environment, we captured, for the first time, the morphology and phase evolution on the carbon nanotube (CNT) cathode of a working solid-state Li-O2 nano-battery16 and directly correlated these features with electrochemical reaction. We found that the oxygen reduction reaction on CNTs initially produces LiO2, which subsequently evolves to Li2O2 and O2 through disproportionation reaction. Surprisingly it is just the releasing of O2 that inflates the particles to a hollow structure with a Li2O outer surface layer and Li2O2 inner-shell, demonstrating that, in general, accommodation of the released O2 coupled with the Li+ ion diffusion and electron transport paths across both spatial and temporal scales critically governs the morphology of the discharging/charging product in Li-O2 system. We anticipate that the direct observation of Li-O2 reaction mechanisms and their correlation with the morphology of the reaction product set foundation for quantitative understanding/modeling of the electrochemical processes in the Li-O2 system, enabling rational design of both solid-state and aprotic Li-O2 batteries.

  11. Effect of nuclear-reaction mechanisms on the population of excited nuclear states and isomeric ratios

    Science.gov (United States)

    Skobelev, N. K.

    2016-07-01

    Experimental data on the cross sections for channels of fusion and transfer reactions induced by beams of radioactive halo nuclei and clustered and stable loosely bound nuclei were analyzed, and the results of this analysis were summarized. The interplay of the excitation of single-particle states in reaction-product nuclei and direct reaction channels was established for transfer reactions. Respective experiments were performed in stable (6Li) and radioactive (6He) beams of the DRIBs accelerator complex at the Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, and in deuteron and 3He beams of the U-120M cyclotron at the Nuclear Physics Institute, Academy Sciences of Czech Republic (Řež and Prague, Czech Republic). Data on subbarrier and near-barrier fusion reactions involving clustered and loosely bound light nuclei (6Li and 3He) can be described quite reliably within simple evaporation models with allowance for different reaction Q-values and couple channels. In reactions involving halo nuclei, their structure manifests itself most strongly in the region of energies below the Coulomb barrier. Neutron transfer occurs with a high probability in the interactions of all loosely bound nuclei with light and heavy stable nuclei at positive Q-values. The cross sections for such reactions and the respective isomeric ratios differ drastically for nucleon stripping and nucleon pickup mechanisms. This is due to the difference in the population probabilities for excited single-particle states.

  12. Mechanism and kinetics of the NOCO reaction on Rh

    Science.gov (United States)

    Zhdanov, V. P.; Kasemo, B.

    During the past 15 years, the NOCO reaction on Rh has attracted considerable attention of the researchers working in academic and applied surface science. The practical importance of this reaction is connected with its relevance for environmental chemistry. From the point of view of academic studies, the NOCO reaction on Rh is of interest because it represents one of the simplest examples from the class of catalytic reactions occurring via decomposition of adsorbed species. At present, the detailed kinetic data for this reaction are available both for single-crystal and supported Rh, at ultrahigh vacuum (UHV) conditions and also at realistic pressures. For this reason, the NOCO reaction on Rh has become one of the major testing platforms for a microscopic, surface-science based approach to heterogeneous catalysis. The present review shows how far the progress in this field has come. In particular, the review describes in detail the evolution of the ideas for the mechanism of the reaction and also presents the data for the elementary reaction steps, obtained primarily on Rh(1 1 1) at UHV conditions. Then, the possibility of using these data for simulation of the reaction kinetics at moderate pressures, P NO ⋍ P CO ⋍ 0.01 bar, is discussed. The technological aspects of application of Rh in the automotive exhaust systems are surveyed as well, but only briefly.

  13. Formation of degradation compounds from lignocellulosic biomass in the biorefinery: sugar reaction mechanisms

    DEFF Research Database (Denmark)

    Rasmussen, Helena; Sørensen, Hanne R.; Meyer, Anne S.

    2014-01-01

    , several aldehydes and ketones and many different organic acids and aromatic compounds may be generated during hydrothermal treatment of lignocellulosic biomass. The reaction mechanisms are of interest because the very same compounds that are possible inhibitors for biomass processing enzymes......The degradation compounds formed during pretreatment when lignocellulosic biomass is processed to ethanol or other biorefinery products include furans, phenolics, organic acids, as well as mono- and oligomeric pentoses and hexoses. Depending on the reaction conditions glucose can be converted to 5...... and microorganisms may be valuable biobased chemicals. Hence a new potential for industrial scale synthesis of chemicals has emerged. A better understanding of the reaction mechanisms and the impact of the reaction conditions on the product formation is thus a prerequisite for designing better biomass processing...

  14. Reaction mechanisms and rate constants of waste degradation in landfill bioreactor systems with enzymatic-enhancement.

    Science.gov (United States)

    Jayasinghe, P A; Hettiaratchi, J P A; Mehrotra, A K; Kumar, S

    2014-06-01

    Augmenting leachate before recirculation with peroxidase enzymes is a novel method to increase the available carbon, and therefore the food supply to microorganisms at the declining phase of the anaerobic landfill bioreactor operation. In order to optimize the enzyme-catalyzed leachate recirculation process, it is necessary to identify the reaction mechanisms and determine rate constants. This paper presents a kinetic model developed to ascertain the reaction mechanisms and determine the rate constants for enzyme catalyzed anaerobic waste degradation. The maximum rate of reaction (Vmax) for MnP enzyme-catalyzed reactors was 0.076 g(TOC)/g(DS).day. The catalytic turnover number (k(cat)) of the MnP enzyme-catalyzed was 506.7 per day while the rate constant (k) of the un-catalyzed reaction was 0.012 per day.

  15. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions.

    Science.gov (United States)

    Cheng, Gui-Juan; Zhang, Xinhao; Chung, Lung Wa; Xu, Liping; Wu, Yun-Dong

    2015-02-11

    Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

  16. Understanding reaction mechanisms in organic chemistry from catastrophe theory applied to the electron localization function topology.

    Science.gov (United States)

    Polo, Victor; Andres, Juan; Berski, Slawomir; Domingo, Luis R; Silvi, Bernard

    2008-08-07

    Thom's catastrophe theory applied to the evolution of the topology of the electron localization function (ELF) gradient field constitutes a way to rationalize the reorganization of electron pairing and a powerful tool for the unambiguous determination of the molecular mechanisms of a given chemical reaction. The identification of the turning points connecting the ELF structural stability domains along the reaction pathway allows a rigorous characterization of the sequence of electron pair rearrangements taking place during a chemical transformation, such as multiple bond forming/breaking processes, ring closure processes, creation/annihilation of lone pairs, transformations of C-C multiple bonds into single ones. The reaction mechanism of some relevant organic reactions: Diels-Alder, 1,3-dipolar cycloaddition and Cope rearrangement are reviewed to illustrate the potential of the present approach.

  17. Theoretical study on the reaction mechanism of (CH3)3CO(.) radical with NO

    Institute of Scientific and Technical Information of China (English)

    ZHAO Hongmei; LIU Kun; SUN Chengke; LI Zonghe

    2004-01-01

    The reaction mechanism of (CH3)3CO(.) radical with NO is theoretically investigated at the B3LYP/6-31G* level. The results show that the reaction is multi-channel in the single state and triplet state. The potential energy surfaces of reaction paths in the single state are lower than that in the triple state. The balance reaction: (CH3)3CONO←→ (CH3)3CO(.)+NO, whose potential energy surface is the lowest in all the reaction paths, makes the probability of measuring (CH3)3CO(.) radical increase. So NO may be considered as a stabilizing reagent for the (CH3)3CO(.)radical.

  18. Prediction of Tetraoxygen Reaction Mechanism with Sulfur Atom on the Singlet Potential Energy Surface

    Directory of Open Access Journals (Sweden)

    Ashraf Khademzadeh

    2014-01-01

    Full Text Available The mechanism of S+O4 (D2h reaction has been investigated at the B3LYP/6-311+G(3df and CCSD levels on the singlet potential energy surface. One stable complex has been found for the S+O4 (D2h reaction, IN1, on the singlet potential energy surface. For the title reaction, we obtained four kinds of products at the B3LYP level, which have enough thermodynamic stability. The results reveal that the product P3 is spontaneous and exothermic with −188.042 and −179.147 kcal/mol in Gibbs free energy and enthalpy of reaction, respectively. Because P1 adduct is produced after passing two low energy level transition states, kinetically, it is the most favorable adduct in the 1S+1O4 (D2h atmospheric reactions.

  19. Mechanism for the gas-phase reaction between OH and 3-methylfuran: A theoretical study

    Science.gov (United States)

    Zhang, Weichao; Du, Benni; Mu, Lailong; Feng, Changjun

    The mechanism for the OH + 3-methylfuran reaction has been studied via ab initio calculations to investigate various reaction pathways on the doublet potential energy surface. Optimizations of the reactants, products, intermediates, and transition structures are conducted using the MP2 level of theory with the 6-311G(d,p) basis set. The single-point electronic energy of each optimized geometry is refined with G3MP2 and G3MP2B3 calculations. The theoretical study suggests that the OH + 3-methylfuran reaction is dominated by the formation of HC(O)CH dbond C(CH3)CHOH (P7) and CH(OH)CH dbond C(CH3)C(O)H (P9), formed from two low-lying adducts, IM1 and IM2. The direct hydrogen abstraction pathways and the SN2 reaction may play a minor or negligible role in the overall reaction of OH with 3-methylfuran.

  20. Unraveling the reaction mechanisms governing methanol-to-olefins catalysis by theory and experiment.

    Science.gov (United States)

    Hemelsoet, Karen; Van der Mynsbrugge, Jeroen; De Wispelaere, Kristof; Waroquier, Michel; Van Speybroeck, Veronique

    2013-06-03

    The conversion of methanol to olefins (MTO) over a heterogeneous nanoporous catalyst material is a highly complex process involving a cascade of elementary reactions. The elucidation of the reaction mechanisms leading to either the desired production of ethene and/or propene or undesired deactivation has challenged researchers for many decades. Clearly, catalyst choice, in particular topology and acidity, as well as the specific process conditions determine the overall MTO activity and selectivity; however, the subtle balances between these factors remain not fully understood. In this review, an overview of proposed reaction mechanisms for the MTO process is given, focusing on the archetypal MTO catalysts, H-ZSM-5 and H-SAPO-34. The presence of organic species, that is, the so-called hydrocarbon pool, in the inorganic framework forms the starting point for the majority of the mechanistic routes. The combination of theory and experiment enables a detailed description of reaction mechanisms and corresponding reaction intermediates. The identification of such intermediates occurs by different spectroscopic techniques, for which theory and experiment also complement each other. Depending on the catalyst topology, reaction mechanisms proposed thus far involve aromatic or aliphatic intermediates. Ab initio simulations taking into account the zeolitic environment can nowadays be used to obtain reliable reaction barriers and chemical kinetics of individual reactions. As a result, computational chemistry and by extension computational spectroscopy have matured to the level at which reliable theoretical data can be obtained, supplying information that is very hard to acquire experimentally. Special emphasis is given to theoretical developments that open new perspectives and possibilities that aid to unravel a process as complex as methanol conversion over an acidic porous material.

  1. Structural snapshots of the SCR reaction mechanism on Cu-SSZ-13.

    Science.gov (United States)

    Günter, Tobias; Carvalho, Hudson W P; Doronkin, Dmitry E; Sheppard, Thomas; Glatzel, Pieter; Atkins, Andrew J; Rudolph, Julian; Jacob, Christoph R; Casapu, Maria; Grunwaldt, Jan-Dierk

    2015-06-04

    The structure of copper sites in Cu-SSZ-13 during NH3-SCR was unravelled by a combination of novel operando X-ray spectroscopic techniques. Strong adsorption of NH3 on Cu, its reaction with weakly adsorbed NO from the gas phase, and slow re-oxidation of Cu(I) were proven. Thereby the SCR reaction mechanism is significantly different to that observed for Fe-ZSM-5.

  2. Memorable experiences with sad music-reasons, reactions and mechanisms of three types of experiences.

    OpenAIRE

    Tuomas Eerola; Henna-Riikka Peltola

    2016-01-01

    Reactions to memorable experiences of sad music were studied by means of a survey administered to a convenience (N = 1577), representative (N = 445), and quota sample (N = 414). The survey explored the reasons, mechanisms, and emotions of such experiences. Memorable experiences linked with sad music typically occurred in relation to extremely familiar music, caused intense and pleasurable experiences, which were accompanied by physiological reactions and positive mood changes in about a third...

  3. Hepatocyte nuclear factor 4 alpha is a key factor related to depression and physiological homeostasis in the mouse brain.

    Directory of Open Access Journals (Sweden)

    Kyosuke Yamanishi

    Full Text Available Major depressive disorder (MDD is a common psychiatric disorder that involves marked disabilities in global functioning, anorexia, and severe medical comorbidities. MDD is associated with not only psychological and sociocultural problems, but also pervasive physical dysfunctions such as metabolic, neurobiological and immunological abnormalities. Nevertheless, the mechanisms underlying the interactions between these factors have yet to be determined in detail. The aim of the present study was to identify the molecular mechanisms responsible for the interactions between MDD and dysregulation of physiological homeostasis, including immunological function as well as lipid metabolism, coagulation, and hormonal activity in the brain. We generated depression-like behavior in mice using chronic mild stress (CMS as a model of depression. We compared the gene expression profiles in the prefrontal cortex (PFC of CMS and control mice using microarrays. We subsequently categorized genes using two web-based bioinformatics applications: Ingenuity Pathway Analysis and The Database for Annotation, Visualization, and Integrated Discovery. We then confirmed significant group-differences by analyzing mRNA and protein expression levels not only in the PFC, but also in the thalamus and hippocampus. These web tools revealed that hepatocyte nuclear factor 4 alpha (Hnf4a may exert direct effects on various genes specifically associated with amine synthesis, such as genes involved in serotonin metabolism and related immunological functions. Moreover, these genes may influence lipid metabolism, coagulation, and hormonal activity. We also confirmed the significant effects of Hnf4a on both mRNA and protein expression levels in the brain. These results suggest that Hnf4a may have a critical influence on physiological homeostasis under depressive states, and may be associated with the mechanisms responsible for the interactions between MDD and the dysregulation of

  4. Numerical prediction of oblique detonation wave structures using detailed and reduced reaction mechanisms

    Science.gov (United States)

    Thaker, A. A.; Chelliah, H. K.

    1997-12-01

    Modelling of the structure and the limiting flow turning angles of an oblique detonation wave, established by a two-dimensional wedge, requires the implementation of detailed chemical kinetic models involving a large number of chemical species. In this paper, a method of reducing the computational effort involved in simulating such high-speed reacting flows by implementing a systematically reduced reaction mechanism is presented. For a hydrogen - air mixture, starting with an elementary mechanism having eight species in 12 reactions, three alternate four-step reduced reaction mechanisms are developed by introducing the steady-state approximation for the reaction intermediates HO2, O and OH, respectively. Additional reduction of the computational effort is achieved by introducing simplifications to the thermochemical data evaluations. The influence of the numerical grid used in predicting the induction process behind the shock is also investigated. Comparisons of the induction zone predicted by two-dimensional oblique detonation wave calculations with that of a static reactor model (with initial conditions of the gas mixture specified by those behind the nonreactive oblique shock wave) are also presented. The reasonably good agreement between the three four-step reduced mechanism predictions and the starting mechanism predictions indicates that further reduction to a two-step mechanism is feasible for the physical flow time scales (corresponding to inflow Mach numbers of 8 - 10) considered here, and needs to be pursued in the future.

  5. Experimental investigations of mechanical and reaction responses for drop-weight impacted energetic particles

    Science.gov (United States)

    Bao, Xiao-Wei; Wu, Yan-Qing; Wang, Ming-Yang; Huang, Feng-Lei

    2017-02-01

    Low-velocity drop-weight impact experiments on individual and multiple Cyclotetramethylene tetranitramine (HMX) energetic particles were performed using a modified drop-weight machine equipped with high-speed photography components. Multiple particles experienced more severe burning reactions than an individual particle. Comparisons between impacted salt and HMX particle show that jetting in HMX is mainly due to the motion of fragmented particles driven by gaseous reaction products. Velocity of jetting, flame propagation, and area expansion were measured via image processing, making it possible to quantify the chemical reaction or mechanical deformation violence at different stages.

  6. Synthesis in solid state, structural regularity and reaction mechanism for [VS4-Cun] clusters

    Institute of Scientific and Technical Information of China (English)

    余秀芬; 郑发鲲; 黄锦顺

    1996-01-01

    The reaction system (NH4)3VS4/CuCl/PPh3/Et4NBr afforded a series of [VS4-Cun] dusters with various core configurations in the solid state at low heating temperature. The structural regularity of [VS4-Cun] dusters and the influence of the CuCl:(NH4)3VS4 ratio as well as that of reaction temperature and time on the formation of duster core have been summarized. The reaction mechanism of forming V-Cu-S clusters has also been explored.

  7. Ab Initio MO Studies on the Reaction Mechanism for Carbonyl Insertion Catalyzed by Carbonyl Cobalt Complex

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Ab initio method, under the effective core potential(ECP) approximation at HF/LANL2DZ level, has been employed to study the reaction mechanism of the carbonyl insertion of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3. The two reaction paths have been discussed. The calculated potential energy barriers for the carbonyl migration and the ethyl group migration are 105.0 kJ/mol and 39.17 kJ/mol, respectively. The results indicate that the reaction path via ethyl migration is more energetically favorable than that via carbonyl insertion.

  8. Understanding organometallic reaction mechanisms and catalysis experimental and computational tools computational and experimental tools

    CERN Document Server

    Ananikov, Valentin P

    2014-01-01

    Exploring and highlighting the new horizons in the studies of reaction mechanisms that open joint application of experimental studies and theoretical calculations is the goal of this book. The latest insights and developments in the mechanistic studies of organometallic reactions and catalytic processes are presented and reviewed. The book adopts a unique approach, exemplifying how to use experiments, spectroscopy measurements, and computational methods to reveal reaction pathways and molecular structures of catalysts, rather than concentrating solely on one discipline. The result is a deeper

  9. Catalytic conversion reactions in nanoporous systems with concentration-dependent selectivity: Statistical mechanical modeling

    Science.gov (United States)

    García, Andrés; Wang, Jing; Windus, Theresa L.; Sadow, Aaron D.; Evans, James W.

    2016-05-01

    Statistical mechanical modeling is developed to describe a catalytic conversion reaction A →Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Furthermore, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A .

  10. Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

    Science.gov (United States)

    Sankar, Punnaivanam; Aghila, Gnanasekaran

    2007-01-01

    The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

  11. Theoretical Study on the Mechanism of the Gas-phase Reaction of Sc+ with Propargyl Alcohol

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yi-Ping; CHEN Hong-Yan; CHENG Wei-Xian; FENG Yu; YANG Li-Jun

    2008-01-01

    In order to elucidate the reaction mechanisms of reaction Sc+ with propargyl alcohol(PPA),the triplet potential energy surface for the reactions has been theoretically investigated using a DFT method.The geometries for the reactants,intermediates,transition states and products were completely optimized at B3LYP/DZVP level.The single point energy of each stationary point was calculated at MP4/(6-311+G** for C,H,O and Lanl2dz for Sc+)level.All the transition states were verified by the vibrational analysis and the internal reaction coordinate(IRC)calculations.The present results show that the reaction takes an insertion-elimination mechanism both along the O-H and C-O bond activation branches,but the C-O bond activation is much more favorable in energy than the O-H bond activation.All theoretical results not only support the existing conclusions inferred from early experiment,but also complement the pathway and mechanism for this reaction.

  12. Explaining reaction mechanisms using the dual descriptor: a complementary tool to the molecular electrostatic potential.

    Science.gov (United States)

    Martínez-Araya, Jorge Ignacio

    2013-07-01

    The intrinsic reactivity of cyanide when interacting with a silver cation was rationalized using the dual descriptor (DD) as a complement to the molecular electrostatic potential (MEP) in order to predict interactions at the local level. It was found that DD accurately explains covalent interactions that cannot be explained by MEP, which focuses on essentially ionic interactions. This allowed the rationalization of the reaction mechanism that yields silver cyanide in the gas phase. Other similar reaction mechanisms involving a silver cation interacting with water, ammonia, and thiosulfate were also explained by the combination of MEP and DD. This analysis provides another example of the usefulness of DD as a tool for gaining a deeper understanding of any reaction mechanism that is mainly governed by covalent interactions.

  13. Chemical reaction of hexagonal boron nitride and graphite nanoclusters in mechanical milling systems

    Energy Technology Data Exchange (ETDEWEB)

    Muramatsu, Y.; Grush, M.; Callcott, T.A. [Univ. of Tennessee, Knoxville, TN (United States)] [and others

    1997-04-01

    Synthesis of boron-carbon-nitride (BCN) hybrid alloys has been attempted extensively by many researchers because the BCN alloys are considered an extremely hard material called {open_quotes}super diamond,{close_quotes} and the industrial application for wear-resistant materials is promising. A mechanical alloying (MA) method of hexagonal boron nitride (h-BN) with graphite has recently been studied to explore the industrial synthesis of the BCN alloys. To develop the MA method for the BCN alloy synthesis, it is necessary to confirm the chemical reaction processes in the mechanical milling systems and to identify the reaction products. Therefore, the authors have attempted to confirm the chemical reaction process of the h-BN and graphite in mechanical milling systems using x-ray absorption near edge structure (XANES) methods.

  14. Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study.

    Science.gov (United States)

    Xu, Yulong; Zhang, Jingxue; Wang, Dunyou

    2015-06-28

    The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

  15. Microalloying of transition metal silicides by mechanical activation and field-activated reaction

    Energy Technology Data Exchange (ETDEWEB)

    Munir, Zuhair A. (Davis, CA); Woolman, Joseph N. (Davis, CA); Petrovic, John J. (Los Alamos, NM)

    2003-09-02

    Alloys of transition metal suicides that contain one or more alloying elements are fabricated by a two-stage process involving mechanical activation as the first stage and densification and field-activated reaction as the second stage. Mechanical activation, preferably performed by high-energy planetary milling, results in the incorporation of atoms of the alloying element(s) into the crystal lattice of the transition metal, while the densification and field-activated reaction, preferably performed by spark plasma sintering, result in the formation of the alloyed transition metal silicide. Among the many advantages of the process are its ability to accommodate materials that are incompatible in other alloying methods.

  16. Kinetic calculations and mechanism definition for reactions in an ammonium perchlorate flame

    Energy Technology Data Exchange (ETDEWEB)

    Ermolin, N.E.; Fomin, V.M.; Korobeinichev, O.P.; Tereshchenko, A.G.

    1982-09-01

    This article reports on detailed calculations on the reaction kinetics in APC flames on the basis of a wide set of possible reactions and experimental data on the initial composition of the gas mixture (gasification products from APC). The purpose is to select the most important reactions in this system by comparing the calculations on the kinetics with experimental data on the concentration profiles in APC flames. Discusses kinetic equations; rate constants as the reaction mechanism; results from kinetic calculations; and identification of major stages. A laminar flame such as that provided by ammonium perchlorate is described in general form by a system of differential equations that incorporate the transport of heat and matter in the presence of chemical reactions. APC is a system consisting of 4 elements (N,H,Cl and O). Points out that the scheme enables one to determine which reactions are responsible for producing the final products. Suggests that in the future one will be able to analyze experimental data on the reaction-rate profiles for stable components in order to determine either the atom and radical concentrations or the rate constants of the reactions involving them.

  17. Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid

    Institute of Scientific and Technical Information of China (English)

    于海涛; 付宏刚; 等

    2003-01-01

    The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311++G(3df,2p)//UMP2(full)/6-311+G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.

  18. New Perspectives for Studies of Reaction Mechanisms at Low-Medium Energies

    Science.gov (United States)

    Gramegna, F.; Mastinu, P. F.; Vannucci, L.; Boscolo Marchi, E.; Cherubini, R.; Moroni, A.; Bracco, A.; Camera, F.; Million, B.; Wieland, O.; Benzoni, G.; Leoni, S.; Airoldi, A.; Sacchi, R.; Galbusera, E.; Giussani, A.; Ottolenghi, A.; Gadioli, E.; Ballarini, F.; Maj, A.; Brekiesz, M.; Kmiecik, M.; Barlini, S.; Lanchais, A.; Bruno, M.; D'Agostino, M.; Geraci, E.; Vannini, G.; Ordine, A.; Casini, G.; Nannini, A.; Chiari, M.; Abbondanno, U.; Milazzo, P. M.; Margagliotti, G. V.; Bonasera, A.

    2003-04-01

    Many open questions regarding the study of reaction mechanisms with heavy ions have still to be solved, even in the energetic range between 5 and 20 MeV/u, which is covered by the accelerating system Tandem XTU--Linac ALPI of the Laboratori Nazionali of Legnaro. Using complex apparatuses like GARFIELD, coupled with different ancillary detectors, it is possible to perform exclusive measurements, which should be capable of giving new important information, in order to better understand both nuclear structure problems, like for example the study of the mechanisms underlying the Giant Dipole Resonance Damping, and reaction mechanisms phenomena, like the characterization of those mechanisms which are responsible for the many-fragment emission. Preliminary results and future plans to be performed with the GARFIELD facility have been described.

  19. New Perpspectives for Studies of Reaction Mechanisms at Low Medium Energies

    Science.gov (United States)

    Gramegna, F.; Mastinu, P. F.; Vannucci, L.; Marchi, E. Boscolo; Cherubini, R.; Moroni, A.; Bracco, A.; Camera, F.; Million, B.; Wieland, O.; Benzoni, G.; Leoni, S.; Airoldi, A.; Sacchi, R.; Galbusera, E.; Giussani, A.; Ottolenghi, A.; Gadioli, E.; Ballarini, F.; Maj, A.; Brekiesz, M.; Kmiecik, M.; Barlini, S.; Lanchais, A.; Bruno, M.; D'Agostino, M.; Geraci, E.; Vannini, G.; Ordine, A.; Casini, G.; Nannini, A.; Chiari, M.; Abbondanno, U.; Milazzo, P. M.; Margagliotti, G. V.; Bonasera, A.

    2003-07-01

    In the energetic range between 5 and 20 MeV/n, which is covered by the accelerating system Tandem XTU - Linac ALPI of the Laboratori Nazionali of Legnaro, many open questions regarding the study of reaction mechanisms with heavy ions have still to be solved. Using complex apparatuses like GARFIELD coupled with different ancillary detectors, it is possible to perform exclusive measurements, which are necessary to get new important information. This will bring to a better understanding both on nuclear structure problems, like for example the study of the mechanisms underlying the Giant Dipole Resonance Damping, and on reaction mechanisms phenomena, like the characterization of those mechanisms, which are responsible for the many-fragment emission. Preliminary results and plans to be performed with the GARFIELD facility have been described.

  20. Revealing a double-inversion mechanism for the F⁻+CH₃Cl SN2 reaction.

    Science.gov (United States)

    Szabó, István; Czakó, Gábor

    2015-01-19

    Stereo-specific reaction mechanisms play a fundamental role in chemistry. The back-side attack inversion and front-side attack retention pathways of the bimolecular nucleophilic substitution (SN2) reactions are the textbook examples for stereo-specific chemical processes. Here, we report an accurate global analytic potential energy surface (PES) for the F(-)+CH₃Cl SN2 reaction, which describes both the back-side and front-side attack substitution pathways as well as the proton-abstraction channel. Moreover, reaction dynamics simulations on this surface reveal a novel double-inversion mechanism, in which an abstraction-induced inversion via a FH···CH₂Cl(-) transition state is followed by a second inversion via the usual [F···CH₃···Cl](-) saddle point, thereby opening a lower energy reaction path for retention than the front-side attack. Quasi-classical trajectory computations for the F(-)+CH₃Cl(ν1=0, 1) reactions show that the front-side attack is a fast direct, whereas the double inversion is a slow indirect process.

  1. Formation of degradation compounds from lignocellulosic biomass in the biorefinery: sugar reaction mechanisms.

    Science.gov (United States)

    Rasmussen, Helena; Sørensen, Hanne R; Meyer, Anne S

    2014-02-19

    The degradation compounds formed during pretreatment when lignocellulosic biomass is processed to ethanol or other biorefinery products include furans, phenolics, organic acids, as well as mono- and oligomeric pentoses and hexoses. Depending on the reaction conditions glucose can be converted to 5-(hydroxymethyl)-2-furaldehyde (HMF) and/or levulinic acid, formic acid and different phenolics at elevated temperatures. Correspondingly, xylose can follow different reaction mechanisms resulting in the formation of furan-2-carbaldehyde (furfural) and/or various C-1 and C-4 compounds. At least four routes for the formation of HMF from glucose and three routes for furfural formation from xylose are possible. In addition, new findings show that biomass monosaccharides themselves can react further to form pseudo-lignin and humins as well as a wide array of other compounds when exposed to high temperatures. Hence, several aldehydes and ketones and many different organic acids and aromatic compounds may be generated during hydrothermal treatment of lignocellulosic biomass. The reaction mechanisms are of interest because the very same compounds that are possible inhibitors for biomass processing enzymes and microorganisms may be valuable biobased chemicals. Hence a new potential for industrial scale synthesis of chemicals has emerged. A better understanding of the reaction mechanisms and the impact of the reaction conditions on the product formation is thus a prerequisite for designing better biomass processing strategies and forms an important basis for the development of new biorefinery products from lignocellulosic biomass as well.

  2. Reduction of hydrogen peroxide by glutathione peroxidase mimics: reaction mechanism and energetics.

    Science.gov (United States)

    Heverly-Coulson, Gavin S; Boyd, Russell J

    2010-02-04

    The reaction mechanism for the reduction of hydrogen peroxide by N,N-dimethylbenzylamine diselenide, its selenol analogue, and the charged analogues of the diselenide and selenol are elucidated using reliable electronic structure techniques. It is found that the reaction using the diselenide has a large Gibbs energy barrier of 173.5 kJ/mol. The cationic diselenide, with both amines protonated, shows a lower barrier of 103.5 kJ/mol. Both diselenide species show significant Se-Se bond lengthening upon oxidation. An unusual two-step mechanism is found for the selenol with barriers of 136.3 and 141.9 kJ/mol, respectively, showing that it is unlikely that the selenol is the active form. The zwitterion, selenolate, and protonated amine analogues of the selenol show one-step reactions with energy barriers of 82.7, 92.7, and 102.3 kJ/mol, respectively. The zwitterion of the selenol shows the most favorable reaction energies, which is in good agreement with proposed mechanisms for this reaction.

  3. The three transglycosylation reactions catalyzed by cyclodextrin glycosyltransferase from Bacillus circulans (strain 251) proceed via different kinetic mechanisms

    NARCIS (Netherlands)

    Veen, Bart A. van der; Alebeek, Gert-Jan W.M. van; Uitdehaag, Joost C.M.; Dijkstra, Bauke W.; Dijkhuizen, Lubbert

    2000-01-01

    Cyclodextrin glycosyltransferase (CGTase) catalyzes three transglycosylation reactions via a double displacement mechanism involving a covalent enzyme-intermediate complex (substituted-enzyme intermediate). Characterization of the three transglycosylation reactions, however, revealed that they diffe

  4. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

    Science.gov (United States)

    Faheem, Muhammad; Heyden, Andreas

    2014-08-12

    We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

  5. A DFT Study Toward the Reaction Mechanisms of TNT With Hydroxyl Radicals for Advanced Oxidation Processes.

    Science.gov (United States)

    He, Xi; Zeng, Qun; Zhou, Yang; Zeng, Qingxuan; Wei, Xianfeng; Zhang, Chaoyang

    2016-05-26

    The degradation pathway of environmental contaminant 2,4,6-trinitrotoluene (TNT) was investigated computationally at the SMD(Pauling)/M06-2X/6-311+G(d,p) level of theory. The dominant decomposition pathway of TNT → 4,6-dinitro-o-cresol → 4,6-dinitro-2-hydroxybenzylalcohol → 4,6-dinitro-2-hydroxybenzaldehyde was provided, and the corresponding predicted products and their distributions are in a good agreement with available experimental data on TNT degradation by Fenton reaction. It was shown that the mechanism of addition-elimination is crucial for this stage of the reaction. The reaction of H atom abstraction is a minor competing pathway. The details on transition states, intermediate radicals, and free energy surfaces for all proposed reactions are given and make up for a lack of experimental knowledge.

  6. Reaction mechanism of 3-chlorophenol with OH, H in aqueous solution

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The reaction mechanism of 3-chlorophenol with OH, H inaqueous solution was studied by transient technology. The3-chlorophenol aqueous solutions have been saturated with air or N2previously. Under alkaline condition, the reaction of OH radicalwith 3-chlorophenol produces 3-chlorinated phenoxyl radical, withthe absorption peaks at 400 nm and 417 nm. Under neutral condition,the reaction of OH radical with 3-chlorophenol produces OH-adductwith the maximal absorption at about 340 nm. And in acid solution,the reaction of H with 3-chlorophenol produces H-adduct with themaximal absorption at about 320 nm. 3-chlorophenol is compared with4- and 2-chlorophenols from the free radical pathways. The resultsshow that the positions of chlorine on the aromatic ring stronglyinfluence the dehalogenation and degradation process.

  7. Theoretical Study of Reaction Mechanism of 1-Propenyl Radical with NO

    Institute of Scientific and Technical Information of China (English)

    Xue-li Cheng; Yan-yun Zhao; Feng Li; Ren-tao Wu

    2008-01-01

    The reaction system of 1-propenyl radical with NO is an ideal model for studying the intermolecu- lax and intramolecular reactions of complex organic free radicals containing C=C double bonds. On the basis of the full optimization of all species with the Gaussian 98 package at the B3LYP/6- 311++G** level, the reaction mechanism was elucidated extensively using the vibrational mode analy- sis. There are seven reaction pathways and five sets of small molecule end products: CH2O+CH3CN, CH2CHCN+H2O, CH3CHO+HCN, CH3CHO+HNC, and CH3CCH+HNO. The channel of C3H5·+NO→IM1→TS1→IM2→TS2→IM3→TS3→CH3CHO+HCN is thermodynamically most favorable.

  8. Reaction mechanism of 3-chlorophenol with OH, H in aqueous solution.

    Science.gov (United States)

    Zhu, Jie; Chen, Ye-Fei; Dong, Wen-Bo; Pan, Xun-Xi; Hou, Hui-Qi

    2003-01-01

    The reaction mechanism of 3-chlorophenol with OH, H in aqueous solution was studied by transient technology. The 3-chlorophenol aqueous solutions have been saturated with air or N2 previously. Under alkaline condition, the reaction of OH radical with 3-chlorophenol produces 3-chlorinated phenoxyl radical, with the absorption peaks at 400 nm and 417 nm. Under neutral condition, the reaction of OH radical with 3-chlorophenol produces OH-adduct with the maximal absorption at about 340 nm. And in acid solution, the reaction of H with 3-chlorophenol produces H-adduct with the maximal absorption at about 320 nm. 3-chlorophenol is compared with 4-and 2-chlorophenols from the free radical pathways. The results show that the positions of chlorine on the aromatic ring strongly influence the dehalogenation and degradation process.

  9. Reaction Mechanism of Thiophene on Vanadium Oxides under FCC Operating Conditions

    Institute of Scientific and Technical Information of China (English)

    Wang Peng; Zheng Aiguo; Tian Huiping; Long Jun

    2004-01-01

    The reaction mechanism of thiophene on vanadium oxides under FCC operating conditions had been preliminary studied using in-situ FT-IR analysis of thiophene and atmospheric pressure continuous fixed-bed reaction, followed by characterization via pyridine adsorption-temperature programmed desorption method, and FT-IR and XPS spectra. The research had discovered that, under 500C thiophene could undergo the redox reaction with V2O5, while being converted into CO, CO2 as well as SO2 with its conversion rate reaching 41.2%. At the same time the oxidation number of vanadium decreased. The existence of a few Bronsted acid centers on V2O5 could lead to an increase of H2S yield among the products derived from the reaction with thiophene.

  10. Reaction mechanism of dimethyl ether carbonylation to methyl acetate over mordenite

    DEFF Research Database (Denmark)

    Rasmussen, Dominik Bjørn; Christensen, Jakob Munkholt; Temel, B.

    2017-01-01

    The reaction mechanism of dimethyl ether carbonylation to methyl acetate over mordenite was studied theoretically with periodic density functional theory calculations including dispersion forces and experimentally in a fixed bed flow reactor at pressures between 10 and 100 bar, dimethyl ether...... concentrations in CO between 0.2 and 2.0%, and at a temperature of 438 K. The theoretical study showed that the reaction of CO with surface methyl groups, the rate-limiting step, is faster in the eight-membered side pockets than in the twelve-membered main channel of the zeolite; the subsequent reaction...... of dimethyl ether with surface acetyl to form methyl acetate was demonstrated to occur with low energy barriers in both the side pockets and in the main channel. The present analysis has thus identified a path, where the entire reaction occurs favourably on a single site within the side pocket, in good...

  11. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

    2016-11-03

    The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

  12. Hybrid direct carbon fuel cells and their reaction mechanisms - a review

    DEFF Research Database (Denmark)

    Deleebeeck, Lisa; Kammer Hansen, Kent

    2014-01-01

    with carbon capture and storage (CCS) due to the high purity of CO2 emitted in the exhaust gas. Direct carbon (or coal) fuel cells (DCFCs) are directly fed with solid carbon to the anode chamber. The fuel cell converts the carbon at the anode and the oxygen at the cathode into electricity, heat and reaction...... is discussed on the fuel cell stack and system levels. The range of DCFC types can be roughly broken down into four fuel cell types: aqueous hydroxide, molten hydroxide, molten carbonate and solid oxide fuel cells. Emphasis is placed on the electrochemical reactions occurring at the anode and the proposed...... mechanism(s) of these reactions for molten carbonate, solid oxide and hybrid direct carbon fuel cells. Additionally, the criteria of choosing the ‘best’ DCFC technology is explored, including system design (continuous supply of solid fuel), performance (power density, efficiency), environmental burden...

  13. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Gray, S.K. [Argonne National Laboratory, IL (United States)

    1993-12-01

    A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.

  14. Kinetics and Mechanism of the Exothermic First-stage Decomposition Reaction of Dinitroglycoluril

    Institute of Scientific and Technical Information of China (English)

    ZHAO,Feng-Qi(赵凤起); HU,Rong-Zu(胡荣祖); CHEN,Pei(陈沛); LUO,Yang(罗阳); GAO,Sheng-Li(高胜利); SONG,Ji-Rong(宋纪蓉); SHI,Qi-Zhen(史启祯)

    2004-01-01

    Under linear temperature increase condition, the thermal behavior, mechanism and kinetic parameters of the exothermic decomposition reaction of the title compound have been studied by means of DSC and IR. The initial stage of the mechanism was proposed. The empirical kinetic model function in differential form, apparent activation energy and pre-exponential constant of the exothermic decomposition reaction are α 0.526, 207.0 kJ·mol-1 and 1018.49 s-1, respectively. The critical temperature of thermal explosion of the compound is 252.87 ℃. The values of △S≠, △H≠ and △G≠ of the reaction are 128.4 J·mol-1·K-1, 218.9 kJ·mol-1 and 152.7 kJ·mol-1, respectively.

  15. Asymmetric hydrogenation with highly active IndolPhos-Rh catalysts: kinetics and reaction mechanism

    NARCIS (Netherlands)

    Wassenaar, J.; Kuil, M.; Lutz, M.; Spek, A.L.; Reek, J.N.H.

    2010-01-01

    The mechanism of the IndolPhos-Rh-catalyzed asymmetric hydrogenation of prochiral olefins has been investigated by means of X-ray crystal structure determination, kinetic measurements, high-pressure NMR spectroscopy, and DFT calculations. The mechanistic study indicates that the reaction follows an

  16. The oxygen reduction reaction mechanism on Pt(111) from density functional theory calculations

    DEFF Research Database (Denmark)

    Tripkovic, Vladimir; Skulason, Egill; Siahrostami, Samira;

    2010-01-01

    We study the oxygen reduction reaction (ORR) mechanism on a Pt(1 1 1) surface using density functional theory calculations We find that at low overpotentials the surface is covered with a half dissociated water layer We estimate the barrier for proton transfer to this surface and the barrier for ...

  17. Kinetic versus Static Visuals for Facilitating College Students' Understanding of Organic Reaction Mechanisms in Chemistry

    Science.gov (United States)

    Aldahmash, Abdulwali H.; Abraham, Michael R.

    2009-01-01

    Using animated computer-generated graphics to assist instruction has recently attracted the attention of educators and educational researchers. The specific focus of this study is to compare the influence of animated visuals with static visuals on college students' understanding of organic reaction mechanisms in chemistry. This study also focuses…

  18. Effect of CO2-induced reactions on the mechanical behaviour of fractured wellbore cement

    NARCIS (Netherlands)

    Wolterbeek, T.K.T.; Hangx, S.J.T.; Spiers, C.J.

    2016-01-01

    Geomechanical damage, such as fracturing of wellbore cement, can severely impact well integrity in CO2 storage fields. Chemical reactions between the cement and CO2-bearing fluids may subsequently alter the cement’s mechanical properties, either enhancing or inhibiting damage accumulation during ong

  19. Asymmetric hydrogenation with highly active IndolPhos-Rh catalysts: kinetics and reaction mechanism

    NARCIS (Netherlands)

    Wassenaar, J.; Kuil, M.; Lutz, M.; Spek, A.L.; Reek, J.N.H.

    2010-01-01

    The mechanism of the Indol- Phos–Rh-catalyzed asymmetric hydrogenation of prochiral olefins has been investigated by means of X-ray crystal structure determination, kinetic measurements, high-pressure NMR spectroscopy, and DFT calculations. The mechanistic study indicates that the reaction follows a

  20. Asymmetric hydrogenation with highly active IndolPhos-Rh catalysts: kinetics and reaction mechanism

    NARCIS (Netherlands)

    Wassenaar, J.; Kuil, M.; Lutz, M.; Spek, A.L.; Reek, J.N.H.

    2010-01-01

    The mechanism of the IndolPhos-Rh-catalyzed asymmetric hydrogenation of prochiral olefins has been investigated by means of X-ray crystal structure determination, kinetic measurements, high-pressure NMR spectroscopy, and DFT calculations. The mechanistic study indicates that the reaction follows an

  1. Mechanism and kinetics of the electrocatalytic reaction responsible for the high cost of hydrogen fuel cells.

    Science.gov (United States)

    Cheng, Tao; Goddard, William A; An, Qi; Xiao, Hai; Merinov, Boris; Morozov, Sergey

    2017-01-25

    The sluggish oxygen reduction reaction (ORR) is a major impediment to the economic use of hydrogen fuel cells in transportation. In this work, we report the full ORR reaction mechanism for Pt(111) based on Quantum Mechanics (QM) based Reactive metadynamics (RμD) simulations including explicit water to obtain free energy reaction barriers at 298 K. The lowest energy pathway for 4 e(-) water formation is: first, *OOH formation; second, *OOH reduction to H2O and O*; third, O* hydrolysis using surface water to produce two *OH and finally *OH hydration to water. Water formation is the rate-determining step (RDS) for potentials above 0.87 Volt, the normal operating range. Considering the Eley-Rideal (ER) mechanism involving protons from the solvent, we predict the free energy reaction barrier at 298 K for water formation to be 0.25 eV for an external potential below U = 0.87 V and 0.41 eV at U = 1.23 V, in good agreement with experimental values of 0.22 eV and 0.44 eV, respectively. With the mechanism now fully understood, we can use this now validated methodology to examine the changes upon alloying and surface modifications to increase the rate by reducing the barrier for water formation.

  2. Revealing the reaction mechanisms of Li-O2 batteries using environmental transmission electron microscopy

    Science.gov (United States)

    Luo, Langli; Liu, Bin; Song, Shidong; Xu, Wu; Zhang, Ji-Guang; Wang, Chongmin

    2017-07-01

    The performances of a Li-O2 battery depend on a complex interplay between the reaction mechanism at the cathode, the chemical structure and the morphology of the reaction products, and their spatial and temporal evolution; all parameters that, in turn, are dependent on the choice of the electrolyte. In an aprotic cell, for example, the discharge product, Li2O2, forms through a combination of solution and surface chemistries that results in the formation of a baffling toroidal morphology. In a solid electrolyte, neither the reaction mechanism at the cathode nor the nature of the reaction product is known. Here we report the full-cycle reaction pathway for Li-O2 batteries and show how this correlates with the morphology of the reaction products. Using aberration-corrected environmental transmission electron microscopy (TEM) under an oxygen environment, we image the product morphology evolution on a carbon nanotube (CNT) cathode of a working solid-state Li-O2 nanobattery and correlate these features with the electrochemical reaction at the electrode. We find that the oxygen-reduction reaction (ORR) on CNTs initially produces LiO2, which subsequently disproportionates into Li2O2 and O2. The release of O2 creates a hollow nanostructure with Li2O outer-shell and Li2O2 inner-shell surfaces. Our findings show that, in general, the way the released O2 is accommodated is linked to lithium-ion diffusion and electron-transport paths across both spatial and temporal scales; in turn, this interplay governs the morphology of the discharging/charging products in Li-O2 cells.

  3. Reaction mechanism and influence factors analysis for calcium sulfide generation in the process of phosphogypsum decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Liping, E-mail: lpma2522@hotmail.com [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China); Niu, Xuekui; Hou, Juan; Zheng, Shaocong; Xu, Wenjuan [Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650093 (China)

    2011-11-10

    Highlights: Black-Right-Pointing-Pointer Reusing phosphogypsum is to decompose and recycle Ca and sulfur. Black-Right-Pointing-Pointer FactSage6.1 software was used to simulate the decomposition reactions. Black-Right-Pointing-Pointer Experiments had been taken with high sulfur concentration coal as reducing agent. Black-Right-Pointing-Pointer The reaction mechanism of CaS generation had been analysis, 1100 Degree-Sign C could be the best temperature for PG decomposition. - Abstract: FactSage6.1 software simulation and experiments had been used to analysis the reaction mechanism and influence factors for CaS generation during the process of phosphogypsum decomposition. Thermodynamic calculation showed that the reaction for CaS generation was very complex and CaS was generated mainly through solid-solid reaction and gas-solid reaction. The proper CO and CO{sub 2} have benefit for improving the decomposition effects of phosphogypsum and reducing the generation of CaS at 1100 Degree-Sign C. Using high sulfur concentration coal as reducer, the proper reaction conditions to control the generation of CaS were: the coal particle size was between 60 mesh and 100 mesh, reaction temperature was above 1100 Degree-Sign C and the heating rate was 5 Degree-Sign C/min. Experimental and theoretical calculation indicated that the concentration of CaS was only ten percents in the solid product at 1100 Degree-Sign C, which is favorable for the further cement producing using solid production.

  4. Theoretical Study on the Reaction Mechanism of F2+2HBr=2HF+Br2

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The gas phase reaction mechanism of F2 + 2HBr = 2HF + Br2 has been investigated by (U)MP2 at 6-311G** level, and a series of four-center and three-center transition states have been obtained. The reaction mechanism was achieved by comparing the activation energy of seven reaction paths, i.e. the dissociation energy of F2 is less than the activation energy of the bimolecular elementary reaction F2 + HBr → HF + BrF. Thus it is theoretically proved that the title reaction occurs more easily inthe free radical reaction with three medium steps.

  5. Automated Prediction of Catalytic Mechanism and Rate Law Using Graph-Based Reaction Path Sampling.

    Science.gov (United States)

    Habershon, Scott

    2016-04-12

    In a recent article [ J. Chem. Phys. 2015 , 143 , 094106 ], we introduced a novel graph-based sampling scheme which can be used to generate chemical reaction paths in many-atom systems in an efficient and highly automated manner. The main goal of this work is to demonstrate how this approach, when combined with direct kinetic modeling, can be used to determine the mechanism and phenomenological rate law of a complex catalytic cycle, namely cobalt-catalyzed hydroformylation of ethene. Our graph-based sampling scheme generates 31 unique chemical products and 32 unique chemical reaction pathways; these sampled structures and reaction paths enable automated construction of a kinetic network model of the catalytic system when combined with density functional theory (DFT) calculations of free energies and resultant transition-state theory rate constants. Direct simulations of this kinetic network across a range of initial reactant concentrations enables determination of both the reaction mechanism and the associated rate law in an automated fashion, without the need for either presupposing a mechanism or making steady-state approximations in kinetic analysis. Most importantly, we find that the reaction mechanism which emerges from these simulations is exactly that originally proposed by Heck and Breslow; furthermore, the simulated rate law is also consistent with previous experimental and computational studies, exhibiting a complex dependence on carbon monoxide pressure. While the inherent errors of using DFT simulations to model chemical reactivity limit the quantitative accuracy of our calculated rates, this work confirms that our automated simulation strategy enables direct analysis of catalytic mechanisms from first principles.

  6. The transcriptional activity of hepatocyte nuclear factor 4 alpha is inhibited via phosphorylation by ERK1/2

    Science.gov (United States)

    Bacquet, Caroline; Kiss, Judit; Sipeki, Szabolcs; Martin, Ludovic; Buday, László; Bálint, Bálint L.; Arányi, Tamás

    2017-01-01

    Hepatocyte nuclear factor 4 alpha (HNF4α) nuclear receptor is a master regulator of hepatocyte development, nutrient transport and metabolism. HNF4α is regulated both at the transcriptional and post-transcriptional levels by different mechanisms. Several kinases (PKA, PKC, AMPK) were shown to phosphorylate and decrease the activity of HNF4α. Activation of the ERK1/2 signalling pathway, inducing proliferation and survival, inhibits the expression of HNF4α. However, based on our previous results we hypothesized that HNF4α is also regulated at the post-transcriptional level by ERK1/2. Here we show that ERK1/2 is capable of directly phosphorylating HNF4α in vitro at several phosphorylation sites including residues previously shown to be targeted by other kinases, as well. Furthermore, we also demonstrate that phosphorylation of HNF4α leads to a reduced trans-activational capacity of the nuclear receptor in luciferase reporter gene assay. We confirm the functional relevance of these findings by demonstrating with ChIP-qPCR experiments that 30-minute activation of ERK1/2 leads to reduced chromatin binding of HNF4α. Accordingly, we have observed decreasing but not disappearing binding of HNF4α to the target genes. In addition, 24-hour activation of the pathway further decreased HNF4α chromatin binding to specific loci in ChIP-qPCR experiments, which confirms the previous reports on the decreased expression of the HNF4a gene due to ERK1/2 activation. Our data suggest that the ERK1/2 pathway plays an important role in the regulation of HNF4α-dependent hepatic gene expression. PMID:28196117

  7. Theoretical study of the dark-oxidation reaction mechanisms for organic polymers

    Science.gov (United States)

    Wang, Guixiu; Zhu, Rongxiu; Zhang, Dongju; Liu, Chengbu

    2006-08-01

    To model the dark-oxidation mechanism of organic polymers, the reactions of the corresponding model compounds, including cumene, methyl 2-methylbutyrate, methyl methacrylate and methylacrylic acid, with triplet O 2 molecule, have been studied by performing density functional theory calculations at the UB3LYP/6-31G(d) level. The calculated results show that these model compounds can be oxygenated by O 2 via an H-abstract mechanism. The structures of initial contact charge transfer complexes, transition states, intermediates of cage-like pairs of radicals, and final hydro-peroxides involved in the reactions have been shown in details. The present results are expected to provide a general guidance for understanding the dark-oxidation mechanism of organic polymers.

  8. Quantitative interpretation to the chain mechanism of free radical reactions in cyclohexane pyrolysis

    Institute of Scientific and Technical Information of China (English)

    Yingxian Zhao; Bo Shen; Feng Wei

    2011-01-01

    Pyrolysis of cyclohexane was conducted with a plug flow tube reactor in the temperature range of 873-973 K.Based on the experimental data,the mechanism and kinetic model of cyclohexane pyrolysis reaction were proposed.The kinetic analysis shows that overall conversion of cyclohexane is a first order reaction,of which the rate constant increased from 0.0086 to 0.0225 to 0.0623 s- 1 with the increase of temperature from 873 to 923 to 973 K,and the apparent activation energy was determined to be 155.0+1.0 kJ.mo1-1.The mechanism suggests that the cyclohexane is consumed by four processes:the homolysis of C-C bond (Path Ⅰ),the homolysis of C-H bond (Path Ⅱ) in reaction chain initiation,the H-abstraction of various radicals from the feed molecules in reaction chain propagation (Path Ⅲ),and the process associated with coke formation (Path Ⅳ).The reaction path probability (RPP) ratio of Xpath Ⅰ ∶ Xpath Ⅱ∶ XPath Ⅲ ∶ XPath Ⅳ was 0.5420 ∶ 0.0045 ∶ 0.3897 ∶ 0.0638 at 873 K,and 0.4336 ∶ 0.0061 ∶ 0.4885 ∶ 0.0718 at 973 K,respectively.

  9. Pulse radiolysis study on the mechanisms of reactions of CCl3OO· radical with quercetin, rutin and epigallocatechin gallate

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The mechanisms of reactions between CCl3OO· radical and quercetin, rutin and epigallocatechin gallate (EGCG) have been studied using pulse radiolytic technique. It is suggested that the electron transfer reaction is the main reaction between CCl3OO· radical and rutin, EGCG, but there are two main pathways for the reaction of CCl3OO· radical with quercetin, one is the electron transfer reaction, the other is addition reaction. The reaction rate constants were determined. It is proved that quercetin and rutin are better CCl3OO· radical scavengers than EGCG.

  10. Reaction mechanisms of aqueous monoethanolamine with carbon dioxide: a combined quantum chemical and molecular dynamics study.

    Science.gov (United States)

    Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya

    2015-01-14

    Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.

  11. Centripetal Acceleration Reaction: An Effective and Robust Mechanism for Flapping Flight in Insects.

    Directory of Open Access Journals (Sweden)

    Chao Zhang

    Full Text Available Despite intense study by physicists and biologists, we do not fully understand the unsteady aerodynamics that relate insect wing morphology and kinematics to lift generation. Here, we formulate a force partitioning method (FPM and implement it within a computational fluid dynamic model to provide an unambiguous and physically insightful division of aerodynamic force into components associated with wing kinematics, vorticity, and viscosity. Application of the FPM to hawkmoth and fruit fly flight shows that the leading-edge vortex is the dominant mechanism for lift generation for both these insects and contributes between 72-85% of the net lift. However, there is another, previously unidentified mechanism, the centripetal acceleration reaction, which generates up to 17% of the net lift. The centripetal acceleration reaction is similar to the classical inviscid added-mass in that it depends only on the kinematics (i.e. accelerations of the body, but is different in that it requires the satisfaction of the no-slip condition, and a combination of tangential motion and rotation of the wing surface. Furthermore, the classical added-mass force is identically zero for cyclic motion but this is not true of the centripetal acceleration reaction. Furthermore, unlike the lift due to vorticity, centripetal acceleration reaction lift is insensitive to Reynolds number and to environmental flow perturbations, making it an important contributor to insect flight stability and miniaturization. This force mechanism also has broad implications for flow-induced deformation and vibration, underwater locomotion and flows involving bubbles and droplets.

  12. Numerical comparison of hydrogen-air reaction mechanisms for unsteady shockinduced combustion applications

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, P. Pradeep; Kim, Kui Soon; Oh, Se Jong; Choi, Jeong Yeol [Pusan National University, Busan (Korea, Republic of)

    2015-03-15

    An unsteady shock-induced combustion (SIC) is characterized by the regularly oscillating combustion phenomenon behind the shock wave supported by the blunt projectile flying around the speed of Chapman-Jouguet detonation wave. The SIC is the coupling phenomenon between the hypersonic flow and the chemical kinetics, but the effects of chemical kinetics have been rarely reported. We compared hydrogen-air reaction mechanisms for the shock-induced combustion to demonstrate the importance of considering the reaction mechanisms for such complex flows. Seven hydrogen-air reaction mechanisms were considered, those available publically and used in other researches. As a first step in the comparison of the hydrogen combustion, ignition delay time of hydrogen-oxygen mixtures was compared at various initial conditions. Laminar premixed flame speed was also compared with available experimental data and at high pressure conditions. In addition, half-reaction length of ZND (Zeldovich-Neumann-Doering) detonation structure accounts for the length scale in SIC phenomena. Oscillation frequency of the SIC is compared by running the time-accurate 3rd-order Navier-Stokes CFD code fully coupled with the detailed chemistry by using four levels of grid resolutions.

  13. Chemical nature and reaction mechanisms of the molybdenum cofactor of xanthine oxidoreductase.

    Science.gov (United States)

    Okamoto, Ken; Kusano, Teruo; Nishino, Takeshi

    2013-01-01

    Xanthine oxidoreductase (XOR), a complex flavoprotein, catalyzes the metabolic reactions leading from hypoxanthine to xanthine and from xanthine to urate, and both reactions take place at the molybdenum cofactor. The enzyme is a target of drugs for therapy of gout or hyperuricemia. We review the chemical nature and reaction mechanisms of the molybdenum cofactor of XOR, focusing on molybdenum-dependent reactions of actual or potential medical importance, including nitric oxide (NO) synthesis. It is now generally accepted that XOR transfers the water-exchangeable -OH ligand of the molybdenum atom to the substrate. The hydroxyl group at OH-Mo(IV) can be replaced by urate, oxipurinol and FYX-051 derivatives and the structures of these complexes have been determined by xray crystallography under anaerobic conditions. Although formation of NO from nitrite or formation of xanthine from urate by XOR ischemically feasible, it is not yet clear whether these reactions have any physiological significance since the reactions are catalyzed at a slow rate even under anaerobic conditions.

  14. ARTICLES: Theoretical Study on Mechanism of Cycloadditional Reaction Between Dichloro-Germylidene and Formaldehyde

    Science.gov (United States)

    Lu, Xiu-hui; Li, Yong-qing; Xu, Yue-hua; Han, Jun-feng; Shi, Le-yi

    2010-06-01

    Mechanism of the cycloadditional reaction between singlet dichloro-germylidene and formaldehyde has been investigated with MP2/6-31G* method, including geometry optimization, vibrational analysis and energies for the involved stationary points on the potential energy surface. Prom the potential energy profile, we predict that the cycloaddition reaction between singlet dichloro-germylidene and formaldehyde has two competitive dominant reaction pathways, going with the formation of two side products (INT3 and INT4), simultaneously. Both of the two competitive reactions consist of two steps, two reactants firstly form a three-membered ring intermediate INT1 and a twisted four-membered ring intermediate INT2, respectively, both of which are barrier-free exothermic reactions of 41.5 and 72.3 kJ/mol; then INT1 isomerizes to a four-membered ring product P1 via transition state TS1, and INT2 isomerizes to a chlorine-transfer product P2 via transition state TS2, with the barriers of 2.9 and 0.3 kJ/mol, respectively. Simultaneously, P1 and INT2 further react with formaldehyde to form INT3 and INT4, respectively, which are also barrier-free exothermic reaction of 74.9 and 88.1 kJ/mol.

  15. Modeling cardiac mechano-electrical feedback using reaction-diffusion-mechanics systems

    Science.gov (United States)

    Keldermann, R. H.; Nash, M. P.; Panfilov, A. V.

    2009-06-01

    In many practically important cases, wave propagation described by the reaction-diffusion equation initiates deformation of the medium. Mathematically, such processes are described by coupled reaction-diffusion-mechanics (RDM) systems. RDM systems were recently used to study the effects of deformation on wave propagation in cardiac tissue, so called mechano-electrical feedback (MEF). In this article, we review the results of some of these studies, in particular those relating to the effects of deformation on pacemaker activity and spiral wave dynamics in the heart. We also provide brief descriptions of the numerical methods used, and the underlying cardiac physiology.

  16. Theoretical Studies on the Reaction Mechanism of 1-Chloroethane with Hydroxyl Radical

    Institute of Scientific and Technical Information of China (English)

    WANG Bing-Xing; WANG Li

    2007-01-01

    The reaction mechanism of 1-chloroethane with hydroxyl radical has been investigated by using density functional theory (DFT) B3LYP/6-31G (d, p) method. All bond dissociation enthalpies were computed at the same theoretical level. It was found that hydrogen abstraction pathway is the most favorable. There are two hydrogen abstraction pathways with activation barriers of 0.630 and 4.988 kJ/mol, respectively, while chlorine abstraction pathway was not found. It was observed that activation energies have a more reasonable correlation with the reaction enthalpy changes (ΔHr) than with bond dissociation enthalpies (BDE).

  17. Alkali-Silica Reaction Inhibited by LiOH and Its Mechanism

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A high alkali reactive aggregate-zeolitization perlite was used to test the long-term effectiveness of LiOH in inhibiting alkali-silica reaction.In this paper,the rigorous conditions were designed that the mortar bars had been cured at 80℃ for 3 years after autoclaved 24 hours at 150℃.Under this condition,LiOH was able to inhibit the alkali-silica reaction long-term effectiveness.Not only the relationship between the molar ratio of n(Li)/(Na) and the alkali contents in systems was established, but also the governing mechanism of such effects was also studied by SEM.

  18. Reaction mechanism in high Nb containing TiAl alloy by elemental powder metallurgy

    Institute of Scientific and Technical Information of China (English)

    WANG Yan-hang; LIN Jun-pin; HE Yue-hui; WANG Yan-li; LIN Zhi; CHEN Guo-liang

    2006-01-01

    High Nb containing TiAl alloy was fabricated in argon atmosphere by reactive hot pressing process. Reaction mechanism was investigated by means of microstructural analyses and thermodynamic calculations. The results show that it is feasible to prepare high Nb containing TiAl alloy with fine lamellar colonies by reactive hot pressing process. The reaction between Ti and Al powders is dominant in Ti-Al-Nb system. Nb powders dissolve into the Ti-Al matrix by diffusion. Pore nests are formed in situ after Nb powders diffusion. The hot pressing atmosphere is optimized by thermodynamic calculations. Vacuum or argon protective atmosphere should be adopted.

  19. A theoretical study on the mechanism of the reaction between azacyclopropenylidene and oxirane

    Directory of Open Access Journals (Sweden)

    Jing Ying

    2015-01-01

    Full Text Available The reaction mechanism between azacyclopropenylidene and oxirane has been systematically investigated employing the second-order Møller-Plesset perturbation theory (MP2 method to better understand the azacyclopropenylidene reactivity with three-membered ring compound oxirane. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Energies of all the species are also further corrected by CCSD(T/6-311+G* single-point calculations. Our calculational results show that there are two possible reaction pathways. From the kinetic viewpoint, the first pathway is primary. From the viewpoint of thermodynamics, the second is dominating.

  20. Ab initio MO study of reaction mechanism for carbonyl migration of Co complex

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Ab initio method under the effective core potential (ECP) approximation is employed to study the reaction mechanism of carbonyl migration of the cycle of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3 at Hartree-Fock (HF) level. The structures of the reactant, transition state and product for the reaction are determined. The energy of each stationary point is corrected at MP2/LAN2DZ//LANL2DZ+ZPE (zero-point energy) level. The calculated activation barrier is 28.89 kJ/mol.

  1. Mechanisms of capture- and recombination-enhanced defect reactions in semiconductors

    Science.gov (United States)

    Shinozuka, Yuzo

    2001-12-01

    Proposed mechanisms on defect reactions in semiconductors (defect creation, annihilation, multiplication, reconstruction, impurity diffusion, etc.) are reexamined with particular attention to the instability of the lattice and the transient lattice vibration induced by successive carrier captures. (1) Thermal activation process to overcome the potential barrier Un: it which depends on the electronic state n the reaction rate is given by p 0 exp(-U n/k BT) . (2) Instability mechanism: the lattice relaxation after an electronic transition at a defect promptly induces the reaction coordinate QR. (3) Phonon kick mechanism (single capture): if the relaxation mode Q1 partially includes QR, an electronic transition to the state n enhances the defect reaction during the lattice relaxation time τ∼2 π⧸Δ ω where Δ ω is the width of the frequency distribution of related phonons. (4) Phonon kick mechanism (recombination): if N pairs of electron and hole are captured within a short period τ∼2 π/Δ ω and the central frequency ωR of QR is not so different from ω0 of Q1, the band gap energy Eg is transformed by a series of coherent carrier captures into the lattice vibration energy. The defect reaction rate is given by ( ω0/2 π)exp(- Eiact/ kBT) because only the first capture ( i=e,h) is to be activated. On the other hand, if ωR is much different from ω0, the rate is ( ω0/2 π)exp(- U0*/ kBT) with U0-( Eiact+ Eith) because the N phonon-kicks are out of phase.

  2. Mechanism of electron transfer reaction of ternary dipicolinatochromium(III) complex involving oxalate as secondary ligand

    Indian Academy of Sciences (India)

    Hassan Amroun Ewais; Iqbal Mohamed Ibrhium Ismail

    2013-09-01

    Mechanism of electron transfer reaction of ternary Mechanism of the oxidation of [CrIII(DPA)(OX)(H2O)]− (DPA = dipicolinate and OX = oxalate) by periodate in aqueous acidic medium has been studied spectrophotometrically over the pH range of 4.45-5.57 at different temperatures. The reaction is first order with respect to both [IO$^{−}_{4}$] and the complex concentration, and it obeys the following rate law: $$d[{\\text Cr}^{\\text{VI}}]/dt = k_6K_4K_6[{\\text IO}^−_4][{\\text{Cr}}^{\\text{III}}]_{\\text{T}}/\\{([H^+] + K_4) + (K_5[H+] + K_6K_4)[{\\text{IO}}^{−}_{4}]\\}.$$ The rate of the reaction increases with increasing pH due to the deprotonation equilibria of the complex. The experimental rate law is consistent with a mechanism in which the deprotonated form [CrIII(DPA)(OX)(OH)]2− is more reactive than the conjugated acid. It is proposed that electron transfer proceeds through an inner-sphere mechanism via coordination of IO$^{−}_{4}$ to chromium(III). Thermodynamic activation parameters were calculated using the transition state theory equation.dipicolinatochromium(III) complex involving oxalate as secondary ligand

  3. A reaction mechanism for gasoline surrogate fuels for large polycyclic aromatic hydrocarbons

    KAUST Repository

    Raj, Abhijeet

    2012-02-01

    This work aims to develop a reaction mechanism for gasoline surrogate fuels (n-heptane, iso-octane and toluene) with an emphasis on the formation of large polycyclic aromatic hydrocarbons (PAHs). Starting from an existing base mechanism for gasoline surrogate fuels with the largest chemical species being pyrene (C 16H 10), this new mechanism is generated by adding PAH sub-mechanisms to account for the formation and growth of PAHs up to coronene (C 24H 12). The density functional theory (DFT) and the transition state theory (TST) have been adopted to evaluate the rate constants for several PAH reactions. The mechanism is validated in the premixed laminar flames of n-heptane, iso-octane, benzene and ethylene. The characteristics of PAH formation in the counterflow diffusion flames of iso-octane/toluene and n-heptane/toluene mixtures have also been tested for both the soot formation and soot formation/oxidation flame conditions. The predictions of the concentrations of large PAHs in the premixed flames having available experimental data are significantly improved with the new mechanism as compared to the base mechanism. The major pathways for the formation of large PAHs are identified. The test of the counterflow diffusion flames successfully predicts the PAH behavior exhibiting a synergistic effect observed experimentally for the mixture fuels, irrespective of the type of flame (soot formation flame or soot formation/oxidation flame). The reactions that lead to this synergistic effect in PAH formation are identified through the rate-of-production analysis. © 2011 The Combustion Institute.

  4. [P16(INK4alpha)/Ki-67 immunocytochemical dual staining for detection of cervical lesions associated to papillomavirus infection].

    Science.gov (United States)

    Toro de Méndez, Morelva; Ferrández Izquierdo, Antonio; Llombart-Bosch, Antonio

    2014-09-01

    We aimed to explore the expression pattern of p16(INK4alpha)/Ki-67 immunocytochemical dual-staining and to establish the potential clinical utility for early detection of cervical lesions. Liquid-based cytologies of cervical specimens of cervical cancer screening were processed for p16(INK4alpha)/Ki-67 immunocytochemical dual-staining using the CINtec Plus Kit. HPV testing was performed with the INNO-LiPA HPV genotyping Extra Reverse Hybridization Line Probe Assay kit. One hundred and fifteen cervical cytologies were analyzed with the following results: 11(9.6%) were negative for intraepithelial lesions or malignancy (NILM); 32 (27.8%) presented atypical squamous cells of undetermined significance (ASC-US); 62 (53.9%) exhibited low grade squamous intraepithelial lesions (LSIL) and 10 (8.7%) showed high grade squamous intraepithelial lesions (HSIL). No cases of cervical cancer were detected. The overall prevalence of DNA HPV detection was 81.7% (94/115). The following specific HPV genotypes were identified in 42 (45.0%) cases: HPV16 (26.2%), HPV51 (21.4%), HPV52 (14.3%) and HPV66 (7.1%). Viral sequences of an unknown single HPV were detected in 23.8% of the cases. A total of 42/115 (36.5%) were p16(IVK4alpha)/Ki-67 dual-staining-positive, being more frequent in HSIL (70.0%), decreasing in LSIL (44.0%), detected in a minority of ASC-US (25.0%) and negative in NILM cases (p p16(INK4alpha)/Ki-67 dual-staining, including 6/32 (18.8%) ASC-US, 26/62 (42.0%) LSIL and 8/10 (80.0%) HSIL, which represent a strong association between positivity for HPV, p16(INK4alpha)/Ki-67 staining and severe cytological abnormalities (p cervical lesions.

  5. Mechanisms and Kinetics of Radical Reaction of O(1D,3P) + HCN System

    Institute of Scientific and Technical Information of China (English)

    HUANG Yu-Cheng; DU Jin-Yan; JU Xue-Hai; YE Shi-Yong; ZHOU Tao

    2008-01-01

    The reaction of HCN with O(1D, 3P) radical has been investigated by density functional theory (DFT) and ab initio methods. The stationary points on the reaction paths(reactants, intermediates and products) were optimized at the (U)B3LYP/aug-cc-pVTZ level.Single-point calculations were performed at the (U)QCISD(T)/aug-cc-pVTZ level for the optimized structures and all the total energies were corrected by zero-point energy. It is shown that there exist three competing mechanisms of oxygen attacking nitrogen O→N, oxygen attacking carbon O→C and oxygen attacking hydrogen O→H. The rate constants were obtained via Eyring transition-state theory in the temperature range of 600~2000 K. The linear relationship between lnk and 1/T was presented. The results show that path 1 is the main reaction channel and the product of NCO + H is predominant.

  6. Reaction mechanism for methanol oxidation on Au(1 1 1): A density functional theory study

    Science.gov (United States)

    Liu, Shuping; Jin, Peng; Zhang, Donghui; Hao, Ce; Yang, Xueming

    2013-01-01

    The microscopic reaction mechanism for methanol oxidation on Au(1 1 1) surface has been thoroughly investigated by means of density functional theory (DFT) computations. The adsorption geometries and energies were obtained for all the adsorbates, including the reactants, the products, and various possible intermediates on the metal. According to different oxygen conditions, we propose two possible reaction pathways for methanol oxidation on Au(1 1 1): (1) HCHO esterification: the intermediate formaldehyde and methoxy couple to yield methyl formate at low oxygen coverage or without the presence of oxygen atoms; (2) HCHO oxidation: the formaldehyde is oxidized to form formate at high oxygen coverage, which further dissociates to give CO2. Our study emphasizes the critical role of oxygen coverage during the methanol oxidation reaction, and can perfectly explain the difference in product distributions observed in previous experiments.

  7. Elastic scattering and reaction mechanisms of the halo nucleus $^{11}$Be around the Coulomb barrier

    CERN Document Server

    Di Pietro, A; Fisichella, M; Borge, M J G; Randisi, G; Milin, M; Figuera, P; Gomez-Camacho, J; Raabe, R; Amorini, F; Fraile, L M; Rizzo, F; Zadro, M; Torresi, D; Wenander, F; Pellegriti, M G; Papa, M; Jeppesen, H; Santonocito, D; Scuderi, V; Acosta, L; Perez-Bernal, F; Tengblad, O; Lattuada, M; Musumarra, A; Scalia, G; Maira Vidal, A; Voulot, D

    2010-01-01

    Collisions induced by $^{9}$Be, $^{10}$Be, $^{11}$Be on a $^{64}$Zn target at the same c. m. energy were studied. For the first time, strong effects of the $^{11}$Be halo structure on elastic-scattering and reaction mechanisms at energies near the Coulomb barrier are evidenced experimentally. The elastic-scattering cross section of the $^{11}$Be halo nucleus shows unusual behavior in the Coulomb-nuclear interference peak angular region. The extracted total-reaction cross section for the $^{11}$Be collision is more than double the ones measured in the collisions induced by $^{9}$Be, $^{10}$Be. It is shown that such a strong enhancement of the total-reaction cross section with $^{11}$Be is due to transfer and breakup processes.

  8. Theoretical Study on the Mechanism of the Cycloaddition Reaction between Alkylidene Carbene and Ethylene

    Institute of Scientific and Technical Information of China (English)

    LU,Xiu-Hui(卢秀慧); ZHAI,Li-Min(翟利民); WU,Wei-Rong(武卫荣)

    2004-01-01

    The mechanism of cycloaddition reaction between singlet alkylidene carbene and ethylene has been investigated with second-order Moller-Plesset perturbation theory (MP2). By using 6-31G* basis , geometry optimization, vibrational analysis and energetics have been calculated for the involved stationary points on the potential energy surface. The results show that the title reaction has two major competition channels. An energy-rich intermediate (INT) is firstly formed between alkylidene carbene and ethylene through a barrier-free exothermic reaction of 63.62 kJ/mol, and the intermediate then isomerizes to a three-membered ring product (P1) and a four-memberd ring product (P2) via transition state TS1 and TS2, in which energy barriers are 47.00 and 51.02 kJ/mol, respectively. P1 is the main product.

  9. Synthesis, phase and reaction mechanism of nonlinear optical material MnTeMoO{sub 6}

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Chengguo; Shao, Juxiang; Yang, Junsheng; Wan, Mingjie [Yibin University, Key Laboratory of Computational Physics of Sichuan Province, Yibin (China); Yibin University, School of Physics and Electronic Engineering, Yibin (China); Luo, Huafeng [Yibin University, College of Chemistry and Chemical Engineering, Yibin (China); Huang, Xingyong [Yibin University, School of Physics and Electronic Engineering, Yibin (China); Wang, Fanhou [Yibin University, Key Laboratory of Computational Physics of Sichuan Province, Yibin (China)

    2016-09-15

    Pure polycrystalline MnTeMoO{sub 6} is highly desirable to crystal growth. Polycrystalline MnTeMoO{sub 6} has been synthesized by solid-state reaction techniques. The optimized preparation process, phase purity and reaction mechanism of polycrystalline MnTeMoO{sub 6} were investigated. The reaction will be paused if the atoms cannot pass through the grain boundary and restarted after ground intimately. A new method combined with X-ray diffraction and microscopic observation is employed to determine the phase purity of polycrystalline MnTeMoO{sub 6}. Pure polycrystalline MnTeMoO{sub 6} with gray color and single crystalline phase can be obtained after the reactant was calcined at 500 C for 20 h three times and can be used to crystal growth. This method for determining the phase purity of powder sample can be used in the synthesis of other polycrystalline powders. (orig.)

  10. Quantum Chemical Study on the Reaction Mechanism of OBrO Radical with OH Radical

    Institute of Scientific and Technical Information of China (English)

    ZhAO,Min(赵岷); ZHAO,Yan-Ling(赵艳玲); LIU,Peng-Jun(刘朋军); CHANG,Ying-Fei(常鹰飞); PAN,Xiu-Mei(潘秀梅); SU,Zhong-Min(苏忠民); WANG,Rong-Shun(王荣顺)

    2004-01-01

    The reaction mechanism of OBrO with OH has been studied using the B3LYP/6-31 l+G(d,p) and the high-level electron-correlation CCSD(T)/6-311 +G(d,p) at single-point. The results show that the title reaction could probably proceed by four possible schemes, generating HOBr+O2, HBr+O3, BrO+HO2 and HOBrO2 products, respectively. The main channel is the one to yield HOBr+ O2. The whole reaction involves the formation of three-membered, four-membered and five-membered rings, followed by the complicated processes of association,H-shift, Br-shift and dissociation. All routes are exothermic.

  11. Competing E2 and SN2 Mechanisms for the F(-) + CH3CH2I Reaction.

    Science.gov (United States)

    Yang, Li; Zhang, Jiaxu; Xie, Jing; Ma, Xinyou; Zhang, Linyao; Zhao, Chenyang; Hase, William L

    2017-02-09

    Anti-E2, syn-E2, inv-, and ret-SN2 reaction channels for the gas-phase reaction of F(-) + CH3CH2I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-SN2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-SN2 shows the least feasibility to occur at room temperature. Negative activation energies (-16.9, -16.0, and -4.9 kcal/mol, respectively) for inv-SN2, anti-E2, and syn-E2 indicate that inv-SN2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F(-) + CH3CH2Y (Y = F, Cl, Br, and I) leads to monotonically decreasing barriers, which relates to the gradually looser TS structures following the order F > Cl > Br > I. The reactivity of each channel nearly holds unchanged except for the perturbation between anti-E2 and inv-SN2. RRKM calculation reveals that the reaction of the fluorine ion with ethyl iodide occurs predominately via anti-E2 elimination, and the inv-SN2 pathway is suppressed, although it is energetically favored. This phenomenon indicates that, in evaluating the competition between E2 and SN2 processes, the kinetic or dynamical factors may play a significant role. By comparison with benchmark CCSD(T) energies, MP2, CAM-B3LYP, and M06 methods are recommended to perform dynamics simulations of the title reaction.

  12. Fundamental reaction mechanism and free energy profile for (-)-cocaine hydrolysis catalyzed by cocaine esterase.

    Science.gov (United States)

    Liu, Junjun; Hamza, Adel; Zhan, Chang-Guo

    2009-08-26

    The fundamental reaction mechanism of cocaine esterase (CocE)-catalyzed hydrolysis of (-)-cocaine and the corresponding free energy profile have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations. On the basis of the QM/MM-FE results, the entire hydrolysis reaction consists of four reaction steps, including the nucleophilic attack on the carbonyl carbon of (-)-cocaine benzoyl ester by the hydroxyl group of Ser117, dissociation of (-)-cocaine benzoyl ester, nucleophilic attack on the carbonyl carbon of (-)-cocaine benzoyl ester by water, and finally dissociation between the (-)-cocaine benzoyl group and Ser117 of CocE. The third reaction step involving the nucleophilic attack of a water molecule was found to be rate-determining, which is remarkably different from (-)-cocaine hydrolysis catalyzed by wild-type butyrylcholinesterase (BChE; where the formation of the prereactive BChE-(-)-cocaine complex is rate-determining) or its mutants containing Tyr332Gly or Tyr332Ala mutation (where the first chemical reaction step is rate-determining). Besides, the role of Asp259 in the catalytic triad of CocE does not follow the general concept of the "charge-relay system" for all serine esterases. The free energy barrier calculated for the rate-determining step of CocE-catalyzed hydrolysis of (-)-cocaine is 17.9 kcal/mol, which is in good agreement with the experimentally derived activation free energy of 16.2 kcal/mol. In the present study, where many sodium ions are present, the effects of counterions are found to be significant in determining the free energy barrier. The finding of the significant effects of counterions on the free energy barrier may also be valuable in guiding future mechanistic studies on other charged enzymes.

  13. Dehydriding reaction kinetic mechanism of MgH2-Nb2O5 by Chou model

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Chou model was used to investigate the dehydriding reaction kinetic mechanism of MgH2-Nb2O5 hydrogen storage materials at 573 K.A new conception,"characteristic absorption/desorption time(yc)"was introduced to characterize the reaction rate.The fitting results show that for the hydrogen desorbing mechanism.the surface penetration iS the rate.controlling step.The mechanism remains the same even when the original particle size of Nb2O5 is before ball milling(BM)or when the BM time changes.And tc indicates that the desorption rate of MgH2-Nb2O5 will be faster than that of MgH2-Nb2O5 by BM.The dehydriding reaction rate of MgH2-Nb2O5(micro particle)BMed for 50 h is 4.76 times faster than that of the MgH2-Nb2O5(micro particle)BMed for 0.25 h,while the dehydriding reaction rate of MgH2-Nb2O5(nano particle)BMed for 50 h is only 1.1 8 times as that of the MgH2-Nb2O5 (nano particle)BMed for 0.25 h.The dehydriding reaction rate of the BMed MgH2-Nb2O5(nano particle)is 1-9 times faster than that of the BMed MgH2-Nb2O5(micro particle).

  14. An experimental and theoretical study of reaction mechanisms between nitriles and hydroxylamine.

    Science.gov (United States)

    Vörös, Attila; Mucsi, Zoltán; Baán, Zoltán; Timári, Géza; Hermecz, István; Mizsey, Péter; Finta, Zoltán

    2014-10-28

    The industrially relevant reaction between nitriles and hydroxylamine yielding amidoximes was studied in different molecular solvents and in ionic liquids. In industry, this procedure is carried out on the ton scale in alcohol solutions and the above transformation produces a significant amount of unexpected amide by-product, depending on the nature of the nitrile, which can cause further analytical and purification issues. Although there were earlier attempts to propose mechanisms for this transformation, the real reaction pathway is still under discussion. A new detailed reaction mechanistic explanation, based on theoretical and experimental proof, is given to augment the former mechanisms, which allowed us to find a more efficient, side-product free procedure. Interpreting the theoretical results obtained, it was shown that the application of specific imidazolium, phosphonium and quaternary ammonium based ionic liquids could decrease simultaneously the reaction time while eliminating the amide side-product, leading to the targeted product selectively. This robust and economic procedure now affords a fast, selective amide free synthesis of amidoximes.

  15. Eclogite-melt/peridotite reaction: Experimental constrains on the destruction mechanism of the North China Craton

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    To study the mechanism of melt-peridotite reaction pertinent to the destruction of the North China Craton (NCC) lithosphere, a series of experiments were performed at a pressure of 2.0 GPa and temperatures from 1250 to 1400°C using Bixiling eclogite and Damaping peridotite as starting materials. The experimental results show that the reaction between eclogite melt and peridotite causes dissolution of olivine and orthopyroxene and precipitation of clinopyroxene in the melt. The experimental run products, characterized by a lherzolite/pyroxenite/garnet-pyroxenite sequence, are consistent with the mantle xenoliths in the Neogene Hannuoba basalt of the NCC found by Liu et al. (2005). It suggests that the mafic lower continental crust was probably recycled into the mantle during the Mesozoic Era. In the experiments conducted at 1300 and 1350°C, the resulting melts have a high Mg# andesite signature, indicating that the melt-peridotite reaction may have played a major role in the generation of high Mg# andesite. Our experimental results support the hypothesis that melts derived from foundered eclogite in the asthenosphere will consume the lithospheric peridotites. Therefore, melt-peridotite reaction is an important mechanism for the destruction/thinning of the lithosphere.

  16. Prediction of Mechanism and Thermochemical Properties of O3 + H2S Atmospheric Reaction

    Directory of Open Access Journals (Sweden)

    Morteza Vahedpour

    2013-01-01

    Full Text Available Ozone and hydrogen sulfide reaction mechanism including a complex was studied at the B3LYP/6-311++G(3df,3pd and CCSD/6-311++G(3df,3pd//B3LYP/6-311++G(3df,3pd levels of computation. The interaction between sulfur atom of hydrogen sulfide and terminal oxygen atom of ozone produces a stable H2S-O3 complex with no barrier. With the decomposition of this complex, four possible product channels have been found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the suggested mechanism. Thermodynamic data at T = 298.15 K and the atmospheric pressure have been calculated. The results show that the production of H2O + SO2 is the main reaction channel with ΔG° = −645.84 kJ/mol. Rate constants of H2S + O3 reaction show two product channels, SO2 + H2O and HSO + HOO, which compete with each other based on the temperature.

  17. Transition path sampling with quantum/classical mechanics for reaction rates.

    Science.gov (United States)

    Gräter, Frauke; Li, Wenjin

    2015-01-01

    Predicting rates of biochemical reactions through molecular simulations poses a particular challenge for two reasons. First, the process involves bond formation and/or cleavage and thus requires a quantum mechanical (QM) treatment of the reaction center, which can be combined with a more efficient molecular mechanical (MM) description for the remainder of the system, resulting in a QM/MM approach. Second, reaction time scales are typically many orders of magnitude larger than the (sub-)nanosecond scale accessible by QM/MM simulations. Transition path sampling (TPS) allows to efficiently sample the space of dynamic trajectories from the reactant to the product state without an additional biasing potential. We outline here the application of TPS and QM/MM to calculate rates for biochemical reactions, by means of a simple toy system. In a step-by-step protocol, we specifically refer to our implementation within the MD suite Gromacs, which we have made available to the research community, and include practical advice on the choice of parameters.

  18. Mechanism and kinetics for the reaction of O(3P) with DMSO: A theoretical study

    Science.gov (United States)

    Mandal, Debasish; Bagchi, Sabyasachi; Das, Abhijit K.

    2012-11-01

    Mechanism and kinetics for the reaction of DMSO with O(3P) have been investigated by M06-2X/MG3S, CBS-QB3 and G4MP2 methods. Four possible reaction pathways are identified. Among them, the O(3P) addition to S-atom followed by CH3 elimination is almost exclusive. Four pre-reactive complexes have been located. AIM theory is used to determine the nature of interactions in these complexes. Considering the formation of pre-reactive complex, the rate constant for major pathway is calculated using transition state theory applied to a two-step mechanism. Enthalpies of formation at 298.15 K (ΔfH°298.15) have been calculated using the composite CBS-QB3, G4MP2 and G3B3 methods.

  19. Chemical reaction mechanisms in solution from brute force computational Arrhenius plots.

    Science.gov (United States)

    Kazemi, Masoud; Åqvist, Johan

    2015-06-01

    Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.

  20. Studies on Mechanism of Hoesch Reaction with Mass Spectrometry and Its Improvement

    Institute of Scientific and Technical Information of China (English)

    LI,Shao-Bai; ZHENG,Hong-Yan

    2004-01-01

    @@ It has been about ninety years since Hoesch reaction was first discovered in 1915. To our knowledge, although several authors[1,2] have studied the mechanism of Hoesch reaction, it has not been explained clearly. Here we represent an investigation on the mechanism with isotopic mass spectrometry. The effects of isotopes on mass spectra were illustrated obviously. FAB spectrum contained intermediate molecular ions at m/z 336 (M+, 19.3), 338 (M+, 18.2), 340 (M+, 12.3),etc and the peak 364 had already arose. This isotopic cluster demonstrated the positive ion 4 (M+, 336) was in existence (isotopes of Zn: 64, 66, 67, 68, 70). A possible intermediate molecular structure of the signal at m/z 364 could be assigned to 3 (M+, 364). Ions peaks of a possible intermediate negative ions suggested the structure 7.

  1. A coupled mechanical and chemical damage model for concrete affected by alkali–silica reaction

    Energy Technology Data Exchange (ETDEWEB)

    Pignatelli, Rossella, E-mail: rossellapignatelli@gmail.com [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Lombardi Ingegneria S.r.l., Via Giotto 36, 20145 Milano (Italy); Comi, Claudia, E-mail: comi@stru.polimi.it [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Monteiro, Paulo J.M., E-mail: monteiro@ce.berkeley.edu [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)

    2013-11-15

    To model the complex degradation phenomena occurring in concrete affected by alkali–silica reaction (ASR), we formulate a poro-mechanical model with two isotropic internal variables: the chemical and the mechanical damage. The chemical damage, related to the evolution of the reaction, is caused by the pressure generated by the expanding ASR gel on the solid concrete skeleton. The mechanical damage describes the strength and stiffness degradation induced by the external loads. As suggested by experimental results, degradation due to ASR is considered to be localized around reactive sites. The effect of the degree of saturation and of the temperature on the reaction development is also modeled. The chemical damage evolution is calibrated using the value of the gel pressure estimated by applying the electrical diffuse double-layer theory to experimental values of the surface charge density in ASR gel specimens reported in the literature. The chemo-damage model is first validated by simulating expansion tests on reactive specimens and beams; the coupled chemo-mechanical damage model is then employed to simulate compression and flexure tests results also taken from the literature. -- Highlights: •Concrete degradation due to ASR in variable environmental conditions is modeled. •Two isotropic internal variables – chemical and mechanical damage – are introduced. •The value of the swelling pressure is estimated by the diffuse double layer theory. •A simplified scheme is proposed to relate macro- and microscopic properties. •The chemo-mechanical damage model is validated by simulating tests in literature.

  2. Modeling of the Reaction Mechanism of Enzymatic Radical C–C Coupling by Benzylsuccinate Synthase

    Directory of Open Access Journals (Sweden)

    Maciej Szaleniec

    2016-04-01

    Full Text Available Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C–C coupling catalyzed by benzylsuccinate synthase (BSS. BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i What mechanistic details of the BSS reaction yield the most probable molecular model? (ii What is the molecular basis of enantiospecificity of BSS? (iii Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R-benzylsuccinate as a product and a kinetic isotope effect (KIE ranging between 2 and 4? The quantum mechanics (QM modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C–H activation and not C–C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R orientation and reverse preference of benzyl radical attack on fumarate in pro(S pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5 is still higher than the experimentally observed values (4.0 which suggests that both C–H activation and radical quenching may jointly be involved in the kinetic control of the reaction.

  3. Drift mechanism of mass transfer on heterogeneous reaction in crystalline silicon substrate

    Energy Technology Data Exchange (ETDEWEB)

    Kukushkin, S.A. [Institute of Problems of Mechanical Engineering, Russian Academy of Science, St Petersburg, 199178 (Russian Federation); St. Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101 (Russian Federation); Osipov, A.V., E-mail: Andrey.V.Osipov@gmail.com [Institute of Problems of Mechanical Engineering, Russian Academy of Science, St Petersburg, 199178 (Russian Federation); St. Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101 (Russian Federation)

    2017-05-01

    This work aims to study the pressure dependence of the thickness of the epitaxial silicon carbide film growing from crystalline silicon due to the heterogeneous reaction with gaseous carbon monoxide. It turned out that this dependence exhibits the clear maximum. On further pressure increasing the film thickness decreases. The theoretical model has been developed which explains such a character of the dependence by the fact that the gaseous silicon monoxide reaction product inhibits the drift of the gaseous reagent through the channels of a crystal lattice, thus decreasing their hydraulic diameter. In the proposed hydraulic model, the dependences of the film thickness both on the gas pressure and time have been calculated. It was shown that not only the qualitative but also quantitative correspondence between theoretical and experimental results takes place. As one would expect, due to the Einstein relation, at short growth times the drift model coincides with the diffusion one. Consequences of this drift mechanism of epitaxial film growing are discussed. - Graphical abstract: This work aims to study the pressure dependence of the thickness of the epitaxial silicon carbide film growing from crystalline silicon due to the heterogeneous reaction with gaseous carbon monoxide. It turned out that this dependence exhibits the clear maximum. On further pressure increasing the film thickness decreases. The theoretical model has been developed which explains such a character of the dependence by the fact that the gaseous silicon monoxide reaction product inhibits the drift of the gaseous reagent through the channels of a crystal lattice, thus decreasing their hydraulic diameter. - Highlights: • It is established that the greater pressure, the smaller is the reaction rate. • The reaction product prevents penetration of the reagent into a reaction zone. • For description the hydraulic model of crystal lattice channels is developed. • Theoretical results for polytropic

  4. Mechanism and kinetics of the reaction NO3 + C2H4.

    Science.gov (United States)

    Nguyen, Thanh Lam; Park, Jaehee; Lee, Kyungjun; Song, Kihyung; Barker, John R

    2011-05-19

    The reaction of NO(3) radical with C(2)H(4) was characterized using the B3LYP, MP2, B97-1, CCSD(T), and CBS-QB3 methods in combination with various basis sets, followed by statistical kinetic analyses and direct dynamics trajectory calculations to predict product distributions and thermal rate constants. The results show that the first step of the reaction is electrophilic addition of an O atom from NO(3) to an olefinic C atom from C(2)H(4) to form an open-chain adduct. A concerted addition reaction mechanism forming a five-membered ring intermediate was investigated, but is not supported by the highly accurate CCSD(T) level of theory. Master-equation calculations for tropospheric conditions predict that the collisionally stabilized NO(3)-C(2)H(4) free-radical adduct constitutes 80-90% of the reaction yield and the remaining products consist mostly of NO(2) and oxirane; the other products are produced in very minor yields. By empirically reducing the barrier height for the initial addition step by 1 kcal mol(-1) from that predicted at the CBS-QB3 level of theory and treating the torsional modes explicitly as one-dimensional hindered internal rotations (instead of harmonic oscillators), the computed thermal rate constants (including quantum tunneling) can be brought into very good agreement with the experimental data for the overall reaction rate constant.

  5. Insights into the mechanism and catalysis of the native chemical ligation reaction.

    Science.gov (United States)

    Johnson, Erik C B; Kent, Stephen B H

    2006-05-24

    Native chemical ligation of unprotected peptide segments involves reaction between a peptide-alpha-thioester and a cysteine-peptide, to yield a product with a native amide bond at the ligation site. Peptide-alpha-thioalkyl esters are commonly used because of their ease of preparation. These thioalkyl esters are rather unreactive so the ligation reaction is catalyzed by in situ transthioesterification with thiol additives. The most common thiol catalysts used to date have been either a mixture of thiophenol/benzyl mercaptan, or the alkanethiol MESNA. Despite the use of these thiol catalysts, ligation reactions typically take 24-48 h. To gain insight into the mechanism of native chemical ligaton and in order to find a better catalyst, we investigated the use of a number of thiol compounds. Substituted thiophenols with pK(a) > 6 were found to best combine the ability to exchange rapidly and completely with thioalkyl esters, and to then act as effective leaving groups in reaction of the peptide-thioester with the thiol side chain of a cysteine-peptide. A highly effective and practical catalyst was (4-carboxylmethyl)thiophenol ('MPAA'), a nonmalodorous, water-soluble thiol. Use of MPAA gave an order of magnitude faster reaction in model studies of native chemical ligation and in the synthesis of a small protein, turkey ovomucoid third domain (OMTKY3). MPAA should find broad use in native chemical ligation and in the total synthesis of proteins.

  6. Sonochemical degradation of diclofenac: byproduct assessment, reaction mechanisms and environmental considerations.

    Science.gov (United States)

    Ziylan, Asu; Dogan, Sifa; Agopcan, Sesil; Kidak, Rana; Aviyente, Viktorya; Ince, Nilsun H

    2014-05-01

    The study covers a thorough assessment of the overall degradation of diclofenac-Na (DCF) by high-frequency ultrasound, focusing particularly on identification, interpretation, and characterization of the oxidation byproducts and their reaction mechanisms. It was found that sonication of 5 mg L(-1) DCF at near neutral pH rendered complete conversion of the compound, 45 % carbon, 30 % chlorine, and 25 % nitrogen mineralization. Density functional theory (DFT) calculations confirmed the experimentally detected major byproduct 2,6-dichloroaniline, the formation of which was explained by OH• addition to the ipso-position of the amino group. The stability of UV absorption at around 276-280 nm throughout reaction was in agreement with the detected byproduct structures, i.e., the presence of amino/amine groups and phenolic, aniline, benzene, and quinine-type derivatives, which all absorbed at around the same band. Microtox toxicity of the reactor aliquots at early reaction showed that initially the reaction products, specifically 1-(2,6-dichlorophenyl)-2-indoline-one, were very toxic; subsequently toxicity exhibited a fluctuating pattern, and a steady declination towards the "non-toxic" level was observed only after 90 min. Oxygen uptake analysis also revealed the formation of harmful products at early reaction, but the reactor was totally biodegradable upon 1-h sonication.

  7. Quantum chemistry investigation on the reaction mechanism of the elemental mercury, chlorine, bromine and ozone system.

    Science.gov (United States)

    Gao, Zhengyang; Lv, Shaokun; Yang, Weijie; Yang, Pengfei; Ji, Shuo; Meng, Xinxin

    2015-06-01

    Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) for other species. Molecular energies were calculated at QCISD (T) level with zero point energy. Activation energies were calculated along with pre-exponential factors . The reaction rate constants within 298-1800 K were calculated according to transition state theory (TST). The influences of O3 on the reaction of Hg(0) with halogen are discussed. Hg(0) can be oxidized to Hg(1+) by halogen and O3, and halogen and O3 can be arranged in decreasing order as: Br2 > BrO > O3 > Br > Cl, BrCl > HBr > HCl, Br2 > Cl2 according to reaction rate constants. When O3 is presented, Br2, HBr, BrCl, Cl2 and HCl react with O3 and are initially converted to BrO and ClO. O3 is unfavorable for oxidation of Hg(0) by Br2. The mixture of HBr and O3 has better oxidizing Hg(0) performance than HBr and O3. Cl is less effective than Br for oxidation of Hg(0).

  8. 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.

  9. New Insights into Reaction Mechanisms of Ethanol Steam Reforming on Co-ZrO2

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Junming; Karim, Ayman M.; Mei, Donghai; Engelhard, Mark H.; Bao, Xinhe; Wang, Yong

    2015-01-01

    The reaction pathway of ethanol steam reforming on Co-ZrO2 has been identified and the active sites associated with each step are proposed. Ethanol is converted to acetaldehyde and then to acetone, followed by acetone steam reforming. More than 90% carbon was found to follow this reaction pathway. N2-Sorption, X-ray Diffraction (XRD), Temperature Programmed Reduction (TPR), in situ X-ray Photoelectron Spectroscopy (XPS), Transmission Electron Microscopy, as well as theoretical Density Functional Theory (DFT) calculations have been employed to identify the structure and functionality of the catalysts, which was further used to correlate their performance in ESR. It was found that metallic cobalt is mainly responsible for the acetone steam reforming reactions; while, CoO and basic sites on the support play a key role in converting ethanol to acetone via dehydrogenation and condensation/ketonization reaction pathways. The current work provides fundamental understanding of the ethanol steam reforming reaction mechanisms on Co-ZrO2 catalysts and sheds light on the rational design of selective and durable ethanol steam reforming catalysts.

  10. Investigation of organometallic reaction mechanisms with one and two dimensional vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cahoon, James Francis [Univ. of California, Berkeley, CA (United States)

    2008-12-01

    One and two dimensional time-resolved vibrational spectroscopy has been used to investigate the elementary reactions of several prototypical organometallic complexes in room temperature solution. The electron transfer and ligand substitution reactions of photogenerated 17-electron organometallic radicals CpW(CO)3 and CpFe(CO)2 have been examined with one dimensional spectroscopy on the picosecond through microsecond time-scales, revealing the importance of caging effects and odd-electron intermediates in these reactions. Similarly, an investigation of the photophysics of the simple Fischer carbene complex Cr(CO)5[CMe(OMe)] showed that this class of molecule undergoes an unusual molecular rearrangement on the picosecond time-scale, briefly forming a metal-ketene complex. Although time-resolved spectroscopy has long been used for these types of photoinitiated reactions, the advent of two dimensional vibrational spectroscopy (2D-IR) opens the possibility to examine the ultrafast dynamics of molecules under thermal equilibrium conditions. Using this method, the picosecond fluxional rearrangements of the model metal carbonyl Fe(CO)5 have been examined, revealing the mechanism, time-scale, and transition state of the fluxional reaction. The success of this experiment demonstrates that 2D-IR is a powerful technique to examine the thermally-driven, ultrafast rearrangements of organometallic molecules in solution.

  11. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Jorge, Nelly Lidia [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain); Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Romero, Jorge Marcelo [Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Grand, Andre [INAC, SCIB, Laboratoire ' Lesions des Acides Nucleiques' , UMR CEA-UJF E3, CEA-Grenoble, 17 Rue des Martyrs, 38054 Grenoble cedex 9 (France); Hernandez-Laguna, Alfonso, E-mail: ahlaguna@ugr.es [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain)

    2012-01-17

    Highlights: Black-Right-Pointing-Pointer Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. Black-Right-Pointing-Pointer Gas chromatography and computational potential energy surfaces were performed. Black-Right-Pointing-Pointer A mechanism in steps looked like the most probable mechanism. Black-Right-Pointing-Pointer A spin-orbit coupling appeared at the singlet and triple diradical open structures. Black-Right-Pointing-Pointer A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463-503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 {+-} 0.8 kcal/mol and 5.2 Multiplication-Sign 10{sup 13} s{sup -1}, respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G{sup Asterisk-Operator Asterisk-Operator} level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin-orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  12. Mechanism for the Reaction of a Tungsten-Germylyne Complex with , -Unsaturated Ketones: A DFT Study

    Indian Academy of Sciences (India)

    Meng Li; Qiaoqiao Yang; Ran Fang

    2015-08-01

    In this report we present results of theoretical analysis for the reaction mechanism involving a tungsten-germylyne complex with , -unsaturated ketones. Three different substituents, namely H, Me and CF3 in -position of the unsaturated ketones have been selected to account for a variety of experimental observations. The computed results for different unsaturated ketones are in good agreement with experimental evidence and suggest that the formation of the final product can be achieved through steric as well as electronic effects.

  13. Mechanical stimulation of the foot sole in a supine position for ground reaction force simulation

    OpenAIRE

    2014-01-01

    Background:\\ud To promote early rehabilitation of walking, gait training can start even when patients are on bed rest. Supine stepping in the early phase after injury is proposed to maximise the beneficial effects of gait restoration. In this training paradigm, mechanical loading on the sole of the foot is required to mimic the ground reaction forces that occur during overground walking. A pneumatic shoe platform was developed to produce adjustable forces on the heel and the forefoot with an ...

  14. Doorway states in nuclear reactions as a manifestation of the "super-radiant" mechanism

    CERN Document Server

    Auerbach, N

    2007-01-01

    A mechanism is considered for generating doorway states and intermediate structure in low-energy nuclear reactions as a result of collectivization of widths of unstable intrinsic states coupled to common decay channels. At the limit of strong continuum coupling, the segregation of broad (''super-radiating") and narrow (''trapped") states occurs revealing the separation of direct and compound processes. We discuss the conditions for the appearance of intermediate structure in this process and doorways related to certain decay channels.

  15. The Reaction Mechanism with Free Energy Barriers at Constant Potentials for the Oxygen Evolution Reaction at the IrO2 (110) Surface.

    Science.gov (United States)

    Ping, Yuan; Nielsen, Robert J; Goddard, William A

    2017-01-11

    How to efficiently oxidize H2O to O2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OER at the IrO2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. This allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.

  16. Mechanism and Kinetics Analysis of NO/SO2/N2/O2 Dissociation Reactions in Non-Thermal Plasma

    Institute of Scientific and Technical Information of China (English)

    WANG Xinliang; LI Tingting; WEI Dongxiang; WEI Yanli; GU Fan

    2008-01-01

    The kinetics mechanism of the dissociation reactions in a NO/SO2/N2/O2 system was investigated in consideration of energetic electrons' impacts on a non-thermal plasma. A model was derived from the Boltzmann equation and molecule collision theory to predict the dissociation reaction rate coefficients. Upon comparison with available literature, the model was confirmed to be acceptably accurate in general. Several reaction rate coefficients of the NO/SO2/N2/O2 dissociation system were derived according to the Arrhenius formula. The activation energies of each plasma reaction were calculated by quantum chemistry methods. The relation between the dissociation reaction rate coefficient and electron temperature was established to describe the importance of each reaction and to predict relevant processes of gaseous chemical reactions. The sensitivity of the mechanism of NO/SO2/N2/O2 dissociation reaction in a non-thermal plasma was also analysed.

  17. DFT studies on the SCR reaction mechanism of nitrogen monoxide with propylene catalyzed by copper oxide

    Institute of Scientific and Technical Information of China (English)

    TIAN Ying; XU Jing; ZHAO Jing-xiang

    2007-01-01

    The SCR reaction mechanism of NO with C3H6catalyzed by CuO was studied by the method of Density Functional Theory (DFT) at the B3LYP/LanL2DZ levels. The optimized geometries of the stationary points on the potential surface were obtained and the transition state was confirmed by IRC and vibration analysis. The activation energy was calculated being 34. 26 kJ/mol. It was shown that propylene reacted firstly with Cu forming intermediate, and then nitrogen monoxide immediately reacted with the intermediate to be reduced. It was proved to be a direct interaction mechanism.

  18. Diffusive coupling can discriminate between similar reaction mechanisms in an allosteric enzyme system

    Directory of Open Access Journals (Sweden)

    Nicola Ernesto M

    2010-11-01

    Full Text Available Abstract Background A central question for the understanding of biological reaction networks is how a particular dynamic behavior, such as bistability or oscillations, is realized at the molecular level. So far this question has been mainly addressed in well-mixed reaction systems which are conveniently described by ordinary differential equations. However, much less is known about how molecular details of a reaction mechanism can affect the dynamics in diffusively coupled systems because the resulting partial differential equations are much more difficult to analyze. Results Motivated by recent experiments we compare two closely related mechanisms for the product activation of allosteric enzymes with respect to their ability to induce different types of reaction-diffusion waves and stationary Turing patterns. The analysis is facilitated by mapping each model to an associated complex Ginzburg-Landau equation. We show that a sequential activation mechanism, as implemented in the model of Monod, Wyman and Changeux (MWC, can generate inward rotating spiral waves which were recently observed as glycolytic activity waves in yeast extracts. In contrast, in the limiting case of a simple Hill activation, the formation of inward propagating waves is suppressed by a Turing instability. The occurrence of this unusual wave dynamics is not related to the magnitude of the enzyme cooperativity (as it is true for the occurrence of oscillations, but to the sensitivity with respect to changes of the activator concentration. Also, the MWC mechanism generates wave patterns that are more stable against long wave length perturbations. Conclusions This analysis demonstrates that amplitude equations, which describe the spatio-temporal dynamics near an instability, represent a valuable tool to investigate the molecular effects of reaction mechanisms on pattern formation in spatially extended systems. Using this approach we have shown that the occurrence of inward

  19. Competitive inhibition reaction mechanisms for the two-step model of protein aggregation.

    Science.gov (United States)

    Whidden, Mark; Ho, Allison; Ivanova, Magdalena I; Schnell, Santiago

    2014-01-01

    We propose three new reaction mechanisms for competitive inhibition of protein aggregation for the two-step model of protein aggregation. The first mechanism is characterized by the inhibition of native protein, the second is characterized by the inhibition of aggregation-prone protein and the third mechanism is characterized by the mixed inhibition of native and aggregation-prone proteins. Rate equations are derived for these mechanisms, and a method is described for plotting kinetic results to distinguish these three types of inhibitors. The derived rate equations provide a simple way of estimating the inhibition constant of native or aggregation-prone protein inhibitors in protein aggregation. The new approach is used to estimate the inhibition constants of different peptide inhibitors of insulin aggregation.

  20. Comparison of automatically generated reaction mechanism for oxidation of simple hydrocarbons in IC engine

    Directory of Open Access Journals (Sweden)

    Muhammad Mansha

    2011-10-01

    Full Text Available In this work, a detailed kinetic reaction mechanism, consisting of 208 reactions and 79 species, has been developed todescribe the oxidation of simple hydrocarbon fuel (natural gas in IC engine. The performance of the proposed mechanismis tested using simulation, tool CHEMKIN 4.1.1, and experimental measurements. The simulation results of the proposedreaction scheme were compared with those of reference mechanisms (GRI v3.0 and Konnov 0.5 version as well as experimentaldata. Based upon simulation results, it can be concluded that the proposed mechanism shows good concordanceswith GR I3.0 mechanism especially in the prediction of temperature, pressure, and major product species (H2O, CO2 profilesat stoichiometric conditions (= 1.0. Although, there are some discrepancies among each predicted profile, the proposeddetailed mechanism is good to describe the oxidation of natural gas in IC engine. The experimental data also showed favorableresults for prediction of major product species (CO2, H2O & CO at various engine operating speeds in idle mode.

  1. Drift and breakup of spiral waves in reaction-diffusion-mechanics systems.

    Science.gov (United States)

    Panfilov, A V; Keldermann, R H; Nash, M P

    2007-05-08

    Rotating spiral waves organize excitation in various biological, physical, and chemical systems. They underpin a variety of important phenomena, such as cardiac arrhythmias, morphogenesis processes, and spatial patterns in chemical reactions. Important insights into spiral wave dynamics have been obtained from theoretical studies of the reaction-diffusion (RD) partial differential equations. However, most of these studies have ignored the fact that spiral wave rotation is often accompanied by substantial deformations of the medium. Here, we show that joint consideration of the RD equations with the equations of continuum mechanics for tissue deformations (RD-mechanics systems), yield important effects on spiral wave dynamics. We show that deformation can induce the breakup of spiral waves into complex spatiotemporal patterns. We also show that mechanics leads to spiral wave drift throughout the medium approaching dynamical attractors, which are determined by the parameters of the model and the size of the medium. We study mechanisms of these effects and discuss their applicability to the theory of cardiac arrhythmias. Overall, we demonstrate the importance of RD-mechanics systems for mathematics applied to life sciences.

  2. Palladium-atom catalyzed formic acid decomposition and the switch of reaction mechanism with temperature.

    Science.gov (United States)

    He, Nan; Li, Zhen Hua

    2016-04-21

    Formic acid decomposition (FAD) reaction has been an innovative way for hydrogen energy. Noble metal catalysts, especially palladium-containing nanoparticles, supported or unsupported, perform well in this reaction. Herein, we considered the simplest model, wherein one Pd atom is used as the FAD catalyst. With high-level theoretical calculations of CCSD(T)/CBS quality, we investigated all possible FAD pathways. The results show that FAD catalyzed by one Pd atom follows a different mechanism compared with that catalyzed by surfaces or larger clusters. At the initial stage of the reaction, FAD follows a dehydration route and is quickly poisoned by CO due to the formation of very stable PdCO. PdCO then becomes the actual catalyst for FAD at temperatures approximately below 1050 K. Beyond 1050 K, there is a switch of catalyst from PdCO to Pd atom. The results also show that dehydration is always favoured over dehydrogenation on either the Pd-atom or PdCO catalyst. On the Pd-atom catalyst, neither dehydrogenation nor dehydration follows the formate mechanism. In contrast, on the PdCO catalyst, dehydrogenation follows the formate mechanism, whereas dehydration does not. We also systematically investigated the performance of 24 density functional theory methods. We found that the performance of the double hybrid mPW2PLYP functional is the best, followed by the B3LYP, B3PW91, N12SX, M11, and B2PLYP functionals.

  3. Theoretical study on the initial reaction mechanisms of ansa-metallocene zirconium precursor on hydroxylated Si(1 0 0) surface.

    Science.gov (United States)

    Zhou, Guangfen; Ren, Jie; Zhang, Shaowen

    2016-05-01

    The initial reaction mechanisms for depositing ZrO2 thin films using ansa-metallocene zirconium (Cp2CMe2)ZrMe2 precursor were studied by density functional theory (DFT) calculations. The (Cp2CMe2)ZrMe2 precursor could be absorbed on the hydroxylated Si(1 0 0) surface via physisorption. Possible reaction pathways of (Cp2CMe2)ZrMe2 were proposed. For each reaction, the activation energies and reaction energies were compared, and stationary points along the reaction pathways were shown. In addition, the influence of dispersion effects on the reactions was evaluated by non-local dispersion corrected DFT calculations.

  4. Analysis of Vibration Mode for H2+F→HF+H Reaction Mechanism: Density functional Theory Calculation

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Three density functional theory methods (DFT) have been used to investigate the H2+F?HF+H reaction comparing with the Hartree-Fock method and Moller-Plesset (MP2) perturbation theory method. Through the analysis of the vibrational mode and vibrational frequency in the reaction process, the reaction mechanism has been discussed. The activation energy, the reorganization energy and rate constant of the ET reaction are calculated at semi-quantitative level.

  5. Experimental study of the knockout reaction mechanism using O14 at 60 MeV/nucleon

    Science.gov (United States)

    Sun, Y. L.; Lee, J.; Ye, Y. L.; Obertelli, A.; Li, Z. H.; Aoi, N.; Ong, H. J.; Ayyad, Y.; Bertulani, C. A.; Chen, J.; Corsi, A.; Cappuzzello, F.; Cavallaro, M.; Furono, T.; Ge, Y. C.; Hashimoto, T.; Ideguchi, E.; Kawabata, T.; Lou, J. L.; Li, Q. T.; Lorusso, G.; Lu, F.; Liu, H. N.; Nishimura, S.; Suzuki, H.; Tanaka, J.; Tanaka, M.; Tran, D. T.; Tsang, M. B.; Wu, J.; Xu, Z. Y.; Yamamoto, T.

    2016-04-01

    Background: For the deeply bound one-nucleon removal at intermediate energies using a Be9 or C12 target, a strong reduction of cross section was observed relative to the prediction of eikonal theoretical model. The large disagreement has not been explained and the systematic trend is inconsistent with results from transfer reactions. The recently observed asymmetric parallel momentum distribution of the knockout residue indicates the significant dissipative core-target interaction in the knockout reaction with a composite target, implying new reaction mechanisms beyond the eikonal reaction descriptions. Purpose: To investigate the reaction mechanism for deeply bound nucleon removal at intermediate energies. Method: Neutron removal from O14 using a C12 target at 60 MeV/nucleon was performed. Nucleon knockout cross sections were measured. The unbound excited states of O13 were reconstructed by using the invariant mass method with the residues and the associated decay protons measured in coincidence. The measured cross sections are compared with an intra-nuclear cascade (INC) prediction. Results: The measured cross section of (O14C11,) is 60(9) mb, which is 3.5 times larger than that of (O14O13,) channel. This 2 p n -removal cross section is consistent with INC prediction, which is 66 mb with the main contribution being non-direct reaction processes. On the other hand, the upper limit of the cross section for one-neutron removal from O14 followed by proton evaporation is 4.6(20) mb, integrated up to 6 MeV above the proton separation energy of O13 . The calculated total cross section for such reaction processes by the INC model is 2.5 mb, which is within the measured upper limit. Conclusions: The data provide the first constraint on the role of core excitation and evaporation processes in deeply bound nucleon removal from asymmetric nuclei. The experiment results suggest that non-direct reaction processes, which are not considered in the eikonal model, play an

  6. Methanol synthesis on ZnO(0001{sup ¯}). IV. Reaction mechanisms and electronic structure

    Energy Technology Data Exchange (ETDEWEB)

    Frenzel, Johannes, E-mail: johannes.frenzel@theochem.rub.de; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany)

    2014-09-28

    Methanol synthesis from CO and H{sub 2} over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(0001{sup ¯}) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving “near-surface” molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H{sub 2} stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are

  7. Methanol synthesis on ZnO(0001¯). IV. Reaction mechanisms and electronic structure.

    Science.gov (United States)

    Frenzel, Johannes; Marx, Dominik

    2014-09-28

    Methanol synthesis from CO and H2 over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(0001¯) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving "near-surface" molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H2 stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are discussed based on extensive

  8. Methanol synthesis on ZnO(000overline{1}). IV. Reaction mechanisms and electronic structure

    Science.gov (United States)

    Frenzel, Johannes; Marx, Dominik

    2014-09-01

    Methanol synthesis from CO and H2 over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(000overline{1}) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving "near-surface" molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H2 stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are discussed based on

  9. Rotational effects in complex-forming bimolecular substitution reactions: A quantum-mechanical approach

    Science.gov (United States)

    Hennig, Carsten; Schmatz, Stefan

    2009-12-01

    The quantum dynamics of the complex-forming SN2 reaction Cl-+CH3Br→ClCH3+Br- is studied with emphasis on rotational effects. The pseudotriatomic system Cl-Me-Br is treated with a corresponding three-dimensional (3D) potential energy surface as a function of the two scattering coordinates and the enclosed angle where the geometry of the methyl group Me is optimized at each point. The 3D space is divided into three different parts, the interaction region, an intermediate region, and the asymptotic region. In line with simple classical-mechanical arguments and previous classical trajectory calculations, initial rotational motion of CH3Br seemingly decreases the reaction probability. However, the dynamical inclusion of the rotational degree of freedom and the presence of the many rovibrational product states overall lead to a large increase in reactivity compared to our previous collinear study on this reaction. If the reactant is rotationally excited, the higher vibrational product states are depleted in favor of lower-lying levels. Starting the reaction with rotationless reactants may end up in significant rotational excitation in the product molecules (translation-to-rotation energy transfer). On the other hand, initial rotational energy in rotationally highly excited reactants is to a large amount converted into translational and vibrational energy. The average amount of rotational energy in the products shows a twofold vibrational excitation-independent saturation (i.e., memorylessness), with respect to both initial rotational excitation and translational energy. Since only about one-half of all reactant states end in rotationless products, the reaction probability should be increased by a factor of 2; the actually larger reactivity points to other dynamical effects that play an important role in the reaction.

  10. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, W.M.

    1983-11-01

    The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the ..cap alpha..,..cap alpha..'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included.

  11. DFT Investigation on the Mechanism of Pd(0) Catalyzed Sonogashira Coupling Reaction

    Institute of Scientific and Technical Information of China (English)

    CHEN Li-Ping; CHEN Hui-Ping

    2011-01-01

    Based on DFT calculations, the catalytic mechanism of palladium(0) atom, commonly considered as the catalytic center for Sonogashira cross-coupling reactions, has been analyzed in this study. In the cross-coupling reaction of iodobenzene with phenylacetylene without co-catalysts and bases involved, mechanistically plausible catalytic cycles have been computationally identified. These catalytic cycles typically occur in three stages: 1) oxidative addition of an iodobenzene to the Pd(0) atom, 2) reaction of the product of oxidative addition with phenylacetylene to generate an intermediate with the Csp bound to palladium, and 3) reductive elimination to couple the phenyl group with the phenylethynyl group and to regenerate the Pd(0) atom. The calculations show that the first stage gives rise to a two-coordinate palladium (Ⅱ) intermediate (ArPdI). Starting from this intermediate, the second oxidative stage, in which the C–H bond of acetylene adds to Pd(Ⅱ) without co-catalyst involved, is called alkynylation instead of transmetalation and proceeds in two steps. Stage 3 of reductive elimination of diphenylacetylene is energetically favorable. The results demonstrate that stage 2 requires the highest activation energy in the whole catalysis cycle and is the most difficult to happen, where co-catalysts help to carry out Sonogashira coupling reaction smoothly.

  12. Product lambda-doublet ratios as an imprint of chemical reaction mechanism

    Science.gov (United States)

    Jambrina, P. G.; Zanchet, A.; Aldegunde, J.; Brouard, M.; Aoiz, F. J.

    2016-11-01

    In the last decade, the development of theoretical methods has allowed chemists to reproduce and explain almost all of the experimental data associated with elementary atom plus diatom collisions. However, there are still a few examples where theory cannot account yet for experimental results. This is the case for the preferential population of one of the Λ-doublet states produced by chemical reactions. In particular, recent measurements of the OD(2Π) product of the O(3P)+D2 reaction have shown a clear preference for the Π(A') Λ-doublet states, in apparent contradiction with ab initio calculations, which predict a larger reactivity on the A'' potential energy surface. Here we present a method to calculate the Λ-doublet ratio when concurrent potential energy surfaces participate in the reaction. It accounts for the experimental Λ-doublet populations via explicit consideration of the stereodynamics of the process. Furthermore, our results demonstrate that the propensity of the Π(A') state is a consequence of the different mechanisms of the reaction on the two concurrent potential energy surfaces

  13. Calcium-Magnesium-Aluminosilicate (CMAS) Reactions and Degradation Mechanisms of Advanced Environmental Barrier Coatings

    Science.gov (United States)

    Ahlborg, Nadia L.; Zhu, Dongming

    2013-01-01

    The thermochemical reactions between calcium-magnesium-aluminosilicate- (CMAS-) based road sand and several advanced turbine engine environmental barrier coating (EBC) materials were studied. The phase stability, reaction kinetics and degradation mechanisms of rare earth (RE)-silicates Yb2SiO5, Y2Si2O7, and RE-oxide doped HfO2 and ZrO2 under the CMAS infiltration condition at 1500 C were investigated, and the microstructure and phase characteristics of CMAS-EBC specimens were examined using Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD). Experimental results showed that the CMAS dissolved RE-silicates to form crystalline, highly non-stoichiometric apatite phases, and in particular attacking the silicate grain boundaries. Cross-section images show that the CMAS reacted with specimens and deeply penetrated into the EBC grain boundaries and formed extensive low-melting eutectic phases, causing grain boundary recession with increasing testing time in the silicate materials. The preliminary results also showed that CMAS reactions also formed low melting grain boundary phases in the higher concentration RE-oxide doped HfO2 systems. The effect of the test temperature on CMAS reactions of the EBC materials will also be discussed. The faster diffusion exhibited by apatite and RE-doped oxide phases and the formation of extensive grain boundary low-melting phases may limit the CMAS resistance of some of the environmental barrier coatings at high temperatures.

  14. Iron-catalyzed photochemical transformation of benzoic acid in atmospheric liquids: Product identification and reaction mechanisms

    Science.gov (United States)

    Deng, Yiwei; Zhang, Kai; Chen, Hao; Wu, Taixing; Krzyaniak, Metthew; Wellons, Amina; Bolla, Dawn; Douglas, Kenneth; Zuo, Yuegang

    This study investigated iron-catalyzed photochemical oxidation of benzoic acid (BA), one of the major photodegradation products of petroleum hydrocarbons, under sunlight or monochromatic light irradiation in a wavelength range of 254-419 nm. The photochemical degradation of BA in the absence of iron (III) occurred at irradiation wavelengths below 300 nm. The photochemical transformation of BA in the presence Fe(III) was observed at both 254, 350, 419 nm and under solar irradiation. The half-life for the photodegradation of BA (100 μM) was 160±20 min in the presence of 20 μM Fe(III) at pH 3.20 on sunny August days at noon time. The degradation rate increased with increasing concentration of Fe(III). The reaction products were separated and identified using capillary electrophoresis (CE), gas chromatography/mass spectrometry (GC/MS) and UV-Visible spectrophotometry. The major reaction products were 2-hydroxybenzoic, 3-hydroxybenzoic and 4-hydroxybenzoic acids. Hydrogen peroxide (H 2O 2) and Fe(II) species were also formed during the photochemical reactions. The proposed reaction mechanisms include the photoexcitation of Fe(III) hydroxide complexes to form Fe(II) ions and hydroxyl radicals (OH rad ) that attack ortho, meta and para positions of BA to form corresponding monohydroxybenzoic acids and H 2O 2. The monohydroxybenzoic acids formed further react with hydroxyl and surperoxide radicals (HO 2- rad /O 2- rad ) to yield dihydroxybenzoic acids in atmospheric water droplets.

  15. Reaction Mechanism for m-Xylene Oxidation in the Claus Process by Sulfur Dioxide.

    Science.gov (United States)

    Sinha, Sourab; Raj, Abhijeet; Al Shoaibi, Ahmed S; Chung, Suk Ho

    2015-09-24

    In the Claus process, the presence of aromatic contaminants such benzene, toluene, and xylenes (BTX), in the H2S feed stream has a detrimental effect on catalytic reactors, where BTX form soot particles and clog and deactivate the catalysts. Among BTX, xylenes are proven to be most damaging contaminant for catalysts. BTX oxidation in the Claus furnace, before they enter catalyst beds, provides a solution to this problem. A reaction kinetics study on m-xylene oxidation by SO2, an oxidant present in Claus furnace, is presented. The density functional theory is used to study the formation of m-xylene radicals (3-methylbenzyl, 2,6-dimethylphenyl, 2,4-dimethylphenyl, and 3,5-dimethylphenyl) through H-abstraction and their oxidation by SO2. The mechanism begins with SO2 addition on the radicals through an O-atom rather than the S-atom with the release of 180.0-183.1 kJ/mol of reaction energies. This exothermic reaction involves energy barriers in the range 3.9-5.2 kJ/mol for several m-xylene radicals. Thereafter, O-S bond scission takes place to release SO, and the O-atom remaining on aromatics leads to CO formation. Among four m-xylene radicals, the resonantly stabilized 3-methylbenzyl exhibited the lowest SO2 addition and SO elimination rates. The reaction rate constants are provided to facilitate Claus process simulations to find conditions suitable for BTX oxidation.

  16. Study on the mechanism of coal liquefaction reaction and a new process concept

    Institute of Scientific and Technical Information of China (English)

    SHI Shi-dong; LI Wen-bo; WANG Yong; GUO Zhi; LI Ke-jian

    2008-01-01

    The coal hydrogenation reaction process is simply considered as three steps. In the first step, the smaller molecules associated with coal structure units are released as some gases and water in the condition of solvent and heating. In this step, some weaker bonds of the coal structure units are ruptured to form free radicals. The radicals are stabi-lized by hydrogen atoms from donor solvent and/or H2. In the second step, chain reaction occurs quickly. In the process of chain reaction, the covalent bonds of coal structure units are attacked by the radicals to form some asphaltenes. In the third step, asphaltenes are hydrogenated form more liquids and some gases. In coal liquefaction, the second step of coal hydrogenation reaction should be controlled to avoid integration of radicals, and the third step of coal hydrogenation should be accelerated to increase the coal conversion and the oil yield. A new concept of coal liquefaction process named as China direct coal lique-faction (CDCL) process is presented based on the mechanism study of coal liquefaction.

  17. Gravitropisms and reaction woods of forest trees - evolution, functions and mechanisms.

    Science.gov (United States)

    Groover, Andrew

    2016-08-01

    Contents 790 I. 790 II. 792 III. 795 IV. 797 V. 798 VI. 800 VII. 800 800 References 800 SUMMARY: The woody stems of trees perceive gravity to determine their orientation, and can produce reaction woods to reinforce or change their position. Together, graviperception and reaction woods play fundamental roles in tree architecture, posture control, and reorientation of stems displaced by wind or other environmental forces. Angiosperms and gymnosperms have evolved strikingly different types of reaction wood. Tension wood of angiosperms creates strong tensile force to pull stems upward, while compression wood of gymnosperms creates compressive force to push stems upward. In this review, the general features and evolution of tension wood and compression wood are presented, along with descriptions of how gravitropisms and reaction woods contribute to the survival and morphology of trees. An overview is presented of the molecular and genetic mechanisms underlying graviperception, initial graviresponse and the regulation of tension wood development in the model angiosperm, Populus. Critical research questions and new approaches are discussed.

  18. Theoretical Research on the Mechanism of the Dimerization Reactions of Alkyl Ketene

    Directory of Open Access Journals (Sweden)

    Zhiguo Zhang

    2013-01-01

    Full Text Available A quantum chemical method was employed to investigate the mechanism of dimerization reactions of alkyl ketene. All the geometric configurations of the stationary points on the reactions path were optimized with Gaussian03 employing density functional theory at the B3LYP/6-311G++(d, p level by energy gradient technique. The transition states were also investigated through synchronous transit method, and its reasonability was confirmed by using frequency analysis and intrinsic reaction coordinate analysis. The results can be summed up as follows: according to the frontier orbital theory, the dimerization reaction (3 to generate four-membered carbon cyclic product P3 is forbidden. Two different dimerization processes of alkyl ketene are all concerted but nonsynchronous, taking place through twisted four-membered cyclic transition states. The activation energies were calculated to be 34.54 and 61.73 kJ/mol, respectively for the two ketene dimerization processes. Calculation results satisfactorily explained the experimental facts.

  19. Variation near the hepatocyte nuclear factor (HNF)-4alpha gene associates with type 2 diabetes in the Danish population

    DEFF Research Database (Denmark)

    Hansen, S K; Rose, C S; Glümer, C

    2005-01-01

    The hepatocyte nuclear factor (HNF)-4alpha is an orphan nuclear receptor, which plays crucial roles in regulating hepatic gluconeogenesis and insulin secretion. The gene encoding HNF-4alpha (HNF4A) is located on chromosome 20q12-q13 in a region that in several studies has shown linkage with type 2...... diabetes. Recently, two independent studies identified single nucleotide polymorphisms (SNPs) in a 90-kb region spanning HNF4A, which showed strong association with type 2 diabetes in the Finnish and Ashkenazi Jewish populations. In an attempt to replicate and extend these findings, we selected four SNPs...... in the same HNF4A region, which in the Finnish and Ashkenazi Jewish populations were associated with type 2 diabetes, and examined their relationships with type 2 diabetes and prediabetic phenotypes in the Danish Caucasian population....

  20. Memorable Experiences with Sad Music-Reasons, Reactions and Mechanisms of Three Types of Experiences.

    Directory of Open Access Journals (Sweden)

    Tuomas Eerola

    Full Text Available Reactions to memorable experiences of sad music were studied by means of a survey administered to a convenience (N = 1577, representative (N = 445, and quota sample (N = 414. The survey explored the reasons, mechanisms, and emotions of such experiences. Memorable experiences linked with sad music typically occurred in relation to extremely familiar music, caused intense and pleasurable experiences, which were accompanied by physiological reactions and positive mood changes in about a third of the participants. A consistent structure of reasons and emotions for these experiences was identified through exploratory and confirmatory factor analyses across the samples. Three types of sadness experiences were established, one that was genuinely negative (Grief-Stricken Sorrow and two that were positive (Comforting Sorrow and Sweet Sorrow. Each type of emotion exhibited certain individual differences and had distinct profiles in terms of the underlying reasons, mechanisms, and elicited reactions. The prevalence of these broad types of emotional experiences suggested that positive experiences are the most frequent, but negative experiences were not uncommon in any of the samples. The findings have implications for measuring emotions induced by music and fiction in general, and call attention to the non-pleasurable aspects of these experiences.

  1. Memorable Experiences with Sad Music-Reasons, Reactions and Mechanisms of Three Types of Experiences.

    Science.gov (United States)

    Eerola, Tuomas; Peltola, Henna-Riikka

    2016-01-01

    Reactions to memorable experiences of sad music were studied by means of a survey administered to a convenience (N = 1577), representative (N = 445), and quota sample (N = 414). The survey explored the reasons, mechanisms, and emotions of such experiences. Memorable experiences linked with sad music typically occurred in relation to extremely familiar music, caused intense and pleasurable experiences, which were accompanied by physiological reactions and positive mood changes in about a third of the participants. A consistent structure of reasons and emotions for these experiences was identified through exploratory and confirmatory factor analyses across the samples. Three types of sadness experiences were established, one that was genuinely negative (Grief-Stricken Sorrow) and two that were positive (Comforting Sorrow and Sweet Sorrow). Each type of emotion exhibited certain individual differences and had distinct profiles in terms of the underlying reasons, mechanisms, and elicited reactions. The prevalence of these broad types of emotional experiences suggested that positive experiences are the most frequent, but negative experiences were not uncommon in any of the samples. The findings have implications for measuring emotions induced by music and fiction in general, and call attention to the non-pleasurable aspects of these experiences.

  2. [Influencing factor and mechanism analysis of adverse drug reaction in traditional Chinese medicine injection].

    Science.gov (United States)

    Wei, Xu; Xie, Yan-Ming

    2012-09-01

    Adverse drug reaction (ADR) is the key contents in traditional Chinese medicine (TCM) injection safety research. However, influencing factors of ADR is not clearly, mechanism research is relatively rare, which are to be found in the literature to date. Qualified drugs and normal usage and dosage are the premise condition of ADR judgment. Age, sex, basic diseases, allergic constitution or drug allergy history are common factors. Kinds of solvent, drug concentration, storage time after liquid drug preparation, dripping speed, incompatibility of TCM injection and clinical commonly used medicine are the major ADR research factors. Adverse events mechanism should be synthetically judged by pre-clinical research, clinical manifestation, drug epidemiological trials results. In order to judge and study ADR correctly, It should be acquainted with TCM injection adverse events or ADR influencing factors,improve injection specification, and pay attention to the ADR mechanism, promote post-marketed reevaluation of safety in TCM injection.

  3. Theoretical study on the gas-phase reaction mechanism between palladium monoxide and methane.

    Science.gov (United States)

    Yang, Hua-Qing; Hu, Chang-Wei; Gao, Chao; Yang, Meng-Yao; Li, Fang-Ming; Li, Cai-Qin; Li, Xiang-Yuan

    2011-12-01

    The gas-phase reaction mechanism between palladium monoxide and methane has been theoretically investigated on the singlet and triplet state potential energy surfaces (PESs) at the CCSD(T)/AVTZ//B3LYP/6-311+G(2d, 2p), SDD level. The major reaction channel leads to the products PdCH(2) + H(2)O, whereas the minor channel results in the products Pd + CH(3)OH, CH(2)OPd + H(2), and PdOH + CH(3). The minimum energy reaction pathway for the formation of main products (PdCH(2) + H(2)O), involving one spin inversion, prefers to start at the triplet state PES and afterward proceed along the singlet state PES, where both CH(3)PdOH and CH(3)Pd(O)H are the critical intermediates. Furthermore, the rate-determining step is RS-CH(3) PdOH → RS-2-TS1cb → RS-CH(2)Pd(H)OH with the rate constant of k = 1.48 × 10(12) exp(-93,930/RT). For the first C-H bond cleavage, both the activation strain ΔE(≠)(strain) and the stabilizing interaction ΔE(≠)(int) affect the activation energy ΔE(≠), with ΔE(≠)(int) in favor of the direct oxidative insertion. On the other hand, in the PdCH(2) + H(2) O reaction, the main products are Pd + CH(3)OH, and CH(3)PdOH is the energetically preferred intermediate. In the CH(2)OPd + H(2) reaction, the main products are Pd + CH(3)OH with the energetically preferred intermediate H(2)PdOCH(2). In the Pd + CH(3)OH reaction, the main products are CH(2)OPd + H(2), and H(2)PdOCH(2) is the energetically predominant intermediate. The intermediates, PdCH(2), H(2) PdCO, and t-HPdCHO are energetically preferred in the PdC + H(2), PdCO + H(2), and H(2)Pd + CO reactions, respectively. Besides, PdO toward methane activation exhibits higher reaction efficiency than the atom Pd and its first-row congener NiO.

  4. Reaction Mechanisms and HCCI Combustion Processes of Mixtures of n-Heptane and the Butanols

    Directory of Open Access Journals (Sweden)

    Hu eWang

    2015-03-01

    Full Text Available A reduced primary reference fuel (PRF-Alcohol-Di-tert-butyl Peroxide (DTBP mechanism with 108 species and 435 reactions, including sub-mechanisms of PRF, methanol, ethanol, DTBP and the four butanol isomers, is proposed for homogeneous charge compression ignition (HCCI engine combustion simulations of butanol isomers/n-heptane mixtures. HCCI experiments fuelled with butanol isomer/n-heptane mixtures on two different engines are conducted for the validation of proposed mechanism. The mechanism has been validated against shock tube ignition delays, laminar flame speeds, species profiles in premixed flames and engine HCCI combustion data, and good agreements with experimental results are demonstrated under various validation conditions. It is found that although the reactivity of neat tert-butanol is the lowest, mixtures of tert-butanol/n-heptane exhibit the highest reactivity among the butanol isomer/n-heptane mixtures if the n-heptane blending ratio exceeds 20% (mole. Kinetic analysis shows that the highest C-H bond energy in the tert-butanol molecule is partially responsible for this phenomenon. It is also found that the reaction tC4H9OH+CH3O2 =tC4H9O+CH3O2H plays important role and eventually produces the OH radical to promote the ignition and combustion. The proposed mechanism is able to capture HCCI combustion processes of the butanol/n-heptane mixtures under different operating conditions. In addition, the trend that tert-butanol /n-heptane has the highest reactivity is also captured in HCCI combustion simulations. The results indicate that the current mechanism can be used for HCCI engine predictions of PRF and alcohol fuels.

  5. Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F(-) + CH3I reaction in aqueous solution.

    Science.gov (United States)

    Liu, Peng; Zhang, Jingxue; Wang, Dunyou

    2017-06-07

    A double-inversion mechanism of the F(-) + CH3I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol(-1) at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol(-1) calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol(-1), which agrees very well with the experimental value at 25.2 kcal mol(-1) in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.

  6. Quantum interference between H + D2 quasiclassical reaction mechanisms.

    Science.gov (United States)

    Jambrina, Pablo G; Herráez-Aguilar, Diego; Aoiz, F Javier; Sneha, Mahima; Jankunas, Justinas; Zare, Richard N

    2015-08-01

    Interferences are genuine quantum phenomena that appear whenever two seemingly distinct classical trajectories lead to the same outcome. They are common in elastic scattering but are seldom observable in chemical reactions. Here we report experimental measurements of the state-to-state angular distribution for the H + D2 reaction using the 'photoloc' technique. For products in low rotational and vibrational states, a characteristic oscillation pattern governs backward scattering. The comparison between the experiments, rigorous quantum calculations and classical trajectories on an accurate potential energy surface allows us to trace the origin of that structure to the quantum interference between different quasiclassical mechanisms, a phenomenon analogous to that observed in the double-slit experiment.

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

    Science.gov (United States)

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

    2015-09-28

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

  8. Theoretical Study on Reaction Mechanism of Tautomerization of Indazole and 3-halogeno-indazole

    Science.gov (United States)

    Yu, Hai-yan; Li, Bao-zong; Guo, Yong-min

    2006-06-01

    The molecular structures of indazole and 3-halogeno-indazole tautomers were calculated by the B3LYP method at the 6-311G** level, both in the gaseous and aqueous phases, with full geometry optimization. The geometry and electronic structure of the tautomers of indazole, 3-halogeno-indazole and their transition states were obtained. The Onsager solvate theory model was employed for the aqueous solution calculations. The results of the calculation indicated that the N1-H form of the studied molecule is more stable than that of the N2-H form. The influences of the different 3-halogeno and solvent effects on the geometry, energy, charge and activation energy were discussed. The reaction mechanism of the tautomerization of indazole and 3-halogeno-indazole was also studied and a three-membered cyclic transition state of the tautomer reaction has been obtained.

  9. Reaction mechanism studies on isoquinoline with hydroxyl radical in aqueous solutions

    Institute of Scientific and Technical Information of China (English)

    ZHU Dazhang; WANG Shilong; SUN Xiaoyu; NI Yarning; YAO Side

    2007-01-01

    The reaction mechanism between isoquinoline and .OH radical in aqueous dilute solutions under different conditions was studied by pulse radiolysis. The main chara-cteristic peaks in these transient absorption spectra were attributed and the growth-decay trends of several transient species were investigated. Under neutral or alkaline condi-tions, the reaction of-OH radical and isoquinoline produces OH-adducts with respective rate constants of 3.4 × 109 and 6.6× 109 mol-1.dm3·s-1 while under acidic conditions, the isoquinoline was firstly protonated and then -OH added to the benzene ring and produced protonated isoquinoline OH-adducts with a rate constant of 3.9× 109 mol-1.dm3·s-1.With a better understanding on radiolysis ofisoquinoline, this study is of help for its degradation and for environmental protection.

  10. Theoretic study of the reaction mechanism between (Me)3CO·radical and trans-3-hexene

    Institute of Scientific and Technical Information of China (English)

    SHI GuoSheng; DING YiHong

    2008-01-01

    The reaction mechanism between (Me)3CO· radical and trans-3-hexene in benzene was studied for the first time at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d)+ZPVE level. Two distinct elementary channels were identified as: (1) abstraction-addition; (2) addition-addition-elimination. Analysis of the potential energy surface demonstrates that for the title reaction, channels (1) and (2) have the major and minor contribution, respectively. Our calculated results can well explain the recently observed product dis-tribution by Coseri et al. (J. Org. Chem. 2005, 70, 4629). However, we found that the addition-abstraction channel proposed by Coseri et al. Is kinetically infeasible.

  11. Mechanism and kinetics in reactions of caffeic acid with radicals by pulse radiolysis and calculation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab

    2000-03-01

    The interaction of caffeic acid with e{sub aq}{sup -}, (CH{sub 3}){sub 2}(OH) CCH{sub 2}{sup {center_dot}}, CO{sub 2}{sup {center_dot}}{sup -}, H{sup {center_dot}}, {center_dot}OH and N{sub 3}{sup {center_dot}} radicals were studied by {gamma}-, pulse radiolysis and molecular orbital calculation. UV-visible spectra of electron/{center_dot}OH adducts, semi-quinone radicals of caffeic ions, and the stable products from the reactions were derived. The rate constants were determined. The attacked sites and the most favorable structures of the transient radicals were predicted. Reaction mechanisms were proposed. (author)

  12. Microstructure and Mechanical Properties of Reaction-Formed Silicon Carbide (RFSC) Ceramics

    Science.gov (United States)

    Singh, M.; Behrendt, D. R.

    1994-01-01

    The microstructure and mechanical properties of reaction-formed silicon carbide (RFSC) ceramics fabricated by silicon infiltration of porous carbon preforms are discussed. The morphological characterization of the carbon preforms indicates a very narrow pore size distribution. Measurements of the preform density by physical methods and by mercury porosimetry agree very well and indicate that virtually all of the porosity in the preforms is open to infiltrating liquids. The average room temperature flexural strength of the RFSC material with approximately 8 at.% free silicon is 369 +/- 28 MPa (53.5 +/- 4 ksi). The Weibull strength distribution data give a characteristic strength value of 381 MPa (55 ksi) and a Weibull modulus of 14.3. The residual silicon content is lower and the strengths are superior to those of most commercially available reaction-bonded silicon carbide materials.

  13. From Sound to Significance: Exploring the Mechanisms Underlying Emotional Reactions to Music.

    Science.gov (United States)

    Juslin, Patrik N; Barradas, Gonçalo; Eerola, Tuomas

    2015-01-01

    A common approach to studying emotional reactions to music is to attempt to obtain direct links between musical surface features such as tempo and a listener's responses. However, such an analysis ultimately fails to explain why emotions are aroused in the listener. In this article we explore an alternative approach, which aims to account for musical emotions in terms of a set of psychological mechanisms that are activated by different types of information in a musical event. This approach was tested in 4 experiments that manipulated 4 mechanisms (brain stem reflex, contagion, episodic memory, musical expectancy) by selecting existing musical pieces that featured information relevant for each mechanism. The excerpts were played to 60 listeners, who were asked to rate their felt emotions on 15 scales. Skin conductance levels and facial expressions were measured, and listeners reported subjective impressions of relevance to specific mechanisms. Results indicated that the target mechanism conditions evoked emotions largely as predicted by a multimechanism framework and that mostly similar effects occurred across the experiments that included different pieces of music. We conclude that a satisfactory account of musical emotions requires consideration of how musical features and responses are mediated by a range of underlying mechanisms.

  14. Monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 enzymes.

    Science.gov (United States)

    Hrycay, Eugene G; Bandiera, Stelvio M

    2015-01-01

    This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex.

  15. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-06

    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  16. Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis.

    Science.gov (United States)

    Renger, Gernot; Kühn, Philipp

    2007-06-01

    This mini review is an attempt to briefly summarize our current knowledge on light driven oxidative water splitting in photosynthesis. The reaction leading to molecular oxygen and four protons via photosynthesis comprises thermodynamic and kinetic constraints that require a balanced fine tuning of the reaction coordinates. The mode of coupling between electron (ET) and proton transfer (PT) reactions is shown to be of key mechanistic relevance for the redox turnover of Y(Z) and the reactions within the WOC. The WOC is characterized by peculiar energetics of its oxidation steps in the WOC. In all oxygen evolving photosynthetic organisms the redox state S(1) is thermodynamically most stable and therefore this general feature is assumed to be of physiological relevance. Available information on the Gibbs energy differences between the individual redox states S(i+1) and S(i) and on the activation energies of their oxidative transitions are used to construct a general reaction coordinate of oxidative water splitting in photosystem II (PS II). Finally, an attempt is presented to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and the active role of the protein environment in tuning the local proton activity that depends on time and redox state S(i). The O-O linkage is assumed to take place within a multistate equilibrium at the redox level of S(3), comprising both redox isomerism and proton tautomerism. It is proposed that one state, S(3)(P), attains an electronic configuration and nuclear geometry that corresponds with a hydrogen bonded peroxide which acts as the entatic state for the generation of complexed molecular oxygen through S(3)(P) oxidation by Y(Z)(ox).

  17. Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme.

    Directory of Open Access Journals (Sweden)

    Collin Joseph

    Full Text Available The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae. The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient [Formula: see text] for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory.

  18. Reaction mechanism of cobalt-substituted homoprotocatechuate 2,3-dioxygenase: a QM/MM study.

    Science.gov (United States)

    Cao, Lili; Dong, Geng; Lai, Wenzhen

    2015-04-01

    The reaction mechanisms of cobalt-substituted homoprotocatechuate 2,3-dioxygenase (Co-HPCD) with electron-rich substrate homoprotocatechuate (HPCA) and electron-poor substrate 4-nitrocatechol (4NC) were investigated by quantum mechanical/molecular mechanical (QM/MM) calculations. Our results demonstrated that the Co-O2 adducts has doublet ground state with a Co(III)-O2(•-) character when 4NC was used as the substrate, in good agreement with the EPR spectroscopic experiment. The reactive oxygen species is the doublet Co(III)-O2(•-) for Co-HPCD/4NC and the quartet SQ(•↑)-Co(II)-O2(•-↓) species for Co-HPCD/HPCA, indicating that the substrate plays important roles in the dioxygen activation by Co-HPCD. B3LYP was found to overestimate the rate-limiting barriers in Co-HPCD. TPSSh predicts barriers of 21.5 versus 12.0 kcal/mol for Co-HPCD/4NC versus Co-HPCD/HPCA, which is consistent with the fact that the rate of the reaction is decreased when the substrate was changed from HPCA to 4NC.

  19. Substrate Oxidation by Indoleamine 2,3-Dioxygenase: EVIDENCE FOR A COMMON REACTION MECHANISM.

    Science.gov (United States)

    Booth, Elizabeth S; Basran, Jaswir; Lee, Michael; Handa, Sandeep; Raven, Emma L

    2015-12-25

    The kynurenine pathway is the major route of L-tryptophan (L-Trp) catabolism in biology, leading ultimately to the formation of NAD(+). The initial and rate-limiting step of the kynurenine pathway involves oxidation of L-Trp to N-formylkynurenine. This is an O2-dependent process and catalyzed by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase. More than 60 years after these dioxygenase enzymes were first isolated (Kotake, Y., and Masayama, I. (1936) Z. Physiol. Chem. 243, 237-244), the mechanism of the reaction is not established. We examined the mechanism of substrate oxidation for a series of substituted tryptophan analogues by indoleamine 2,3-dioxygenase. We observed formation of a transient intermediate, assigned as a Compound II (ferryl) species, during oxidation of L-Trp, 1-methyl-L-Trp, and a number of other substrate analogues. The data are consistent with a common reaction mechanism for indoleamine 2,3-dioxygenase-catalyzed oxidation of tryptophan and other tryptophan analogues.

  20. A New Method for Describing the Mechanism of a Chemical Reaction Based on the Unified Reaction Valley Approach.

    Science.gov (United States)

    Zou, Wenli; Sexton, Thomas; Kraka, Elfi; Freindorf, Marek; Cremer, Dieter

    2016-02-09

    The unified reaction valley approach (URVA) used for a detailed mechanistic analysis of chemical reactions is improved in three different ways: (i) Direction and curvature of path are analyzed in terms of internal coordinate components that no longer depend on local vibrational modes. In this way, the path analysis is no longer sensitive to path instabilities associated with the occurrences of imaginary frequencies. (ii) The use of third order terms of the energy for a local description of the reaction valley allows an extension of the URVA analysis into the pre- and postchemical regions of the reaction path, which are typically characterized by flat energy regions. (iii) Configurational and conformational processes of the reaction complex are made transparent even in cases where these imply energy changes far less than a kcal/mol by exploiting the topology of the potential energy surface. As examples, the rhodium-catalyzed methanol carbonization, the Diels-Alder reaction between 1,3-butadiene and ethene, and the rearrangement of HCN to CNH are discussed.

  1. Theoretical Study on the Reaction Mechanism between Dichlorocarbene and Armchair Single-walled Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    LI Rui-Fang; SHANG Zhen-Feng; XU Xiu-Fang; WANG Gui-Chang

    2006-01-01

    The reaction mechanism between CCl2 and armchair single-walled carbon nanotubes (ASWCNTs) (3,3) and (4,4) has been studied by semiempirical AM1 and ab initio methods. The activation barriers of CCl2 adding to ASWCNT (3,3) and (4,4) are computed and compared. The lower barrier of CCl2 forms cycloaddition isomer on (3,3) maybe because the strain energy of (3,3) is larger than that of (4,4). Our theoretical results are consistent with the experimental results.

  2. Mechanism of reaction of phenol with toluene on a zeolite catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Kozhevnikov, S.A.; Sibarov, D.A.; Proskuryakov, V.A.

    1988-04-10

    The high-molecular-weight products formed from phenol and toluene on zeolite-containing catalyst were isolated and studied. By independent synthesis, and by PMR, /sup 13/C NMR, IR, and TLC methods it was shown that these products are hydroxy- and dihydroxydiphenyl-methane type compounds. The role of hydroxy- and dihydroxydiphenylmethanes as intermediates in cresol formation from phenol and toluene and their high coking activity were proved. A probable mechanism of cresol formation was proposed with the participation of hydroxy- and dihydroxydiphenylmethanes in the reaction of phenol with toluene on zeolites.

  3. Further study on mechanism of production of light complex particles in nucleon-induced reactions

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Dexian; Mao, Lihua; Wang, Ning; Liu, Min; Ou, Li, E-mail: only.ouli@gmail.com

    2015-01-15

    The Improved Quantum Molecular Dynamics model incorporated with the statistical decay model is used to investigate the intermediate energy nucleon-induced reactions. In our last work, by introducing a phenomenological mechanism called surface coalescence and emission into ImQMD model, the description on the light complex particle emission has been great improved. In this work, taking account of different specific binding energies and separation energies for various light complex particles, the phase space parameters in surface coalescence model are readjusted. By using the new phase space parameters set with better physical fundament, the double differential cross sections of light complex particles are found to be in better agreement with experimental data.

  4. Reduction of Large Detailed Chemical Kinetic Mechanisms for Autoignition Using Joint Analyses of Reaction Rates and Sensitivities

    Energy Technology Data Exchange (ETDEWEB)

    Saylam, A; Ribaucour, M; Pitz, W J; Minetti, R

    2006-11-29

    A new technique of reduction of detailed mechanisms for autoignition, which is based on two analysis methods is described. An analysis of reaction rates is coupled to an analysis of reaction sensitivity for the detection of redundant reactions. Thresholds associated with the two analyses have a great influence on the size and efficiency of the reduced mechanism. Rules of selection of the thresholds are defined. The reduction technique has been successfully applied to detailed autoignition mechanisms of two reference hydrocarbons: n-heptane and iso-octane. The efficiency of the technique and the ability of the reduced mechanisms to reproduce well the results generated by the full mechanism are discussed. A speedup of calculations by a factor of 5.9 for n-heptane mechanism and by a factor of 16.7 for iso-octane mechanism is obtained without losing accuracy of the prediction of autoignition delay times and concentrations of intermediate species.

  5. Unraveling the Concerted Reaction Mechanism of the Noncatalyzed Mukaiyama Reaction between C,O,O-Tris(trimethylsilyl)ketene Acetal and Aldehydes Using Density Functional Theory.

    Science.gov (United States)

    Hadj Mohamed, Slim; Trabelsi, Mahmoud; Champagne, Benoît

    2016-07-21

    The uncatalyzed Mukaiyama aldol reaction between C,O,O-tris(trimethylsilyl)ketene acetal and aldehydes bearing alkyl, vinyl, and aromatic substituents has been studied theoretically using density functional theory with the M06-2X exchange-correlation functional. These DFT calculations mostly demonstrate that (i) the syn product is both kinetically and thermodynamically favored, (ii) the diastereoselectivity of the uncatalyzed reaction is larger than observed for the reaction catalyzed by HgI2 and it is inverted with respect to the latter, (iii) solvents with larger dielectric constants increase the activation barrier but reduce the diastereoselectivity, (iv) the concerted reaction is preferred over the stepwise reaction, and (v) the OSiMe3 group in geminal lowers the activation barrier and increases the energy of reaction. Analyzing the concerted mechanism unravels four types of cyclic transition states, two pro-anti and two pro-syn. Then, the relative energy of the most stable transition state of each type as well as of the corresponding anti and syn products shows that the syn reaction path is located at lower Gibbs enthalpy than the anti reaction path for all substituents.

  6. First-principles modeling of catalysts: novel algorithms and reaction mechanisms

    Science.gov (United States)

    Richard, Bryan Goldsmith

    A molecular level understanding of a reaction mechanism and the computation of rates requires knowledge of the stable structures and the corresponding transition states that connect them. Temperature, pressure, and environment effects must be included to bridge the 'materials gap' so one can reasonably compare ab initio (first-principles, i.e., having no empirical parameters) predictions with experimental measurements. In this thesis, a few critical problems pertaining to ab initio modeling of catalytic systems are addressed; namely, 1) the issue of building representative models of isolated metal atoms grafted on amorphous supports, 2) modeling inorganic catalytic reactions in non-ideal solutions where the solvent participates in the reaction mechanism, and 3) bridging the materials gap using ab initio thermodynamics to predict the stability of supported nanoparticles under experimental reaction conditions. In Chapter I, a background on first-principles modeling of heterogeneous and homogenous catalysts is provided. Subsequently, to address the problem of modeling catalysis by isolated metal atoms on amorphous supports, we present in Chapter II a sequential-quadratic programming algorithm that systematically predicts the structure and reactivity of isolated active sites on insulating amorphous supports. Modeling solution phase reactions is also a considerable challenge for first-principles modeling, yet when done correctly it can yield critical kinetic and mechanistic insight that can guide experimental investigations. In Chapter III, we examine the formation of peroxorhenium complexes by activation of H2O2, which is key in selective oxidation reactions catalyzed by CH3ReO3 (methyltrioxorhenium, MTO). New experiments and density functional theory (DFT) calculations were conducted to better understand the activation of H2O2 by MTO and to provide a strong experimental foundation for benchmarking computational studies involving MTO and its derivatives. It was found

  7. Quantum mechanical/molecular mechanical study on the enantioselectivity of the enzymatic Baeyer-Villiger reaction of 4-hydroxycyclohexanone.

    Science.gov (United States)

    Polyak, Iakov; Reetz, Manfred T; Thiel, Walter

    2013-05-02

    We report a combined quantum mechanical/molecular mechanical (QM/MM) study of the effect of mutations of the Phe434 residue in the active site of cyclohexanone monooxygenase (CHMO) on its enantioselectivity toward 4-hydroxycyclohexanone. In terms of our previously established model of the enzymatic Baeyer-Villiger reaction, enantioselectivity is governed by the preference toward the equatorial ((S)-selectivity) or axial ((R)-selectivity) conformation of the substituent at the C4 carbon atom of the cyclohexanone ring in the Criegee intermediate and the subsequent rate-limiting transition state for migration (TS2). We assess the enantiopreference by locating all relevant TS2 structures at the QM/MM level. In the wild-type enzyme we find that the axial conformation is energetically slightly more stable, thus leading to a small excess of (R)-product. In the Phe434Ser mutant, there is a hydrogen bond between the serine side chain and the equatorial substrate hydroxyl group that is retained during the whole reaction, and hence there is pronounced reverse (S)-enantioselectivity. Another mutant, Phe434Ile, is shown to preserve and enhance the (R)-selectivity. All these findings are in accordance with experiment. The QM/MM calculations allow us to explain the effect of point mutations on CHMO enantioselectivity for the first time at the molecular level by an analysis of the specific interactions between substrate and active-site environment in the TS2 structures that satisfy the basic stereoelectronic requirement of anti-periplanarity for the migrating σ-bond.

  8. Theoretical Study on the Reaction Mechanism of SiCl4 with H in the Gas Phase

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The reaction mechanism of SiCl4 with H2 has been studied theoretically using Gaussian 98 program at B3LYP/6-311G* level. Three different reaction paths (a, b, c) in the gas phase were obtained. The geometries, vibrational frequencies and energies of every stagnation point in the reaction channel were calculated and the mechanisms have been confirmed. The results show that path a has an activation energy of 79.12 kcal/mol, which was considered as the main reaction path. Comparably, paths b and c have the energy barriers of 125.07 and 136.25 kcal/mol, res- pectively. The reaction rate constant was calculated by TST method over a wide temperature range of 900~1600 K, which further confirmed that path a was the main reaction channel.

  9. Dissipative structure of mechanically stimulated reaction; Kikaiteki reiki hanno ni okeru san`itsu kozo

    Energy Technology Data Exchange (ETDEWEB)

    Hida, M. [Okayama Univ., Okayama (Japan). Faculty of Engineering

    1994-12-20

    Recently various studies have been conducted concerning the state changes of materials obtained through mechanical alloying (MA) or mechano-chemical (MC) processing. What is noticeable is the quasi-steady state of almost all the materials obtained through various processes including MA and MC, and that the super cooling, supersaturating and high residue distortion realized under unbalanced conditions have not been clarified. In other words, the tracing capability to the external binding conditions is low. In this report, the appearance of the high temperature phase and high pressure phase obtained through MA or MC processing, the forming of amorphous, the mesomerism of the amorphous materials, the interesting phenomena generated by combination between the mechanical disturbance and chemical reactions were discussed with concrete examples, and a steady dissipative organization theory was approached from the viewpoint of dissipative structure development which is equal to the forming process of the quasi-steady phase. 34 refs., 2 figs.

  10. Reaction mechanisms in the {sup 6}Li + {sup 59}Co system

    Energy Technology Data Exchange (ETDEWEB)

    Souza, F.A. [Instituto de Fisica - Universidade de Sao Paulo, Departamento de Fisica Nuclear, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)], E-mail: fsouza@dfn.if.usp.br; Beck, C. [Institut Pluridisciplinaire Hubert Curien, UMR 7178, CNRS-IN2P3 et Universite Louis Pasteur, Boite Postale 28, F-67037 Strasbourg, Cedex 2 (France); Carlin, N. [Instituto de Fisica - Universidade de Sao Paulo, Departamento de Fisica Nuclear, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil); Keeley, N. [CEA-Saclay DSM/IRFU/SPhN, F-91191 Gif sur Yvette Cedex (France); Neto, R. Liguori; Moura, M.M. de; Munhoz, M.G.; Del Santo, M.G.; Suaide, A.A.P.; Szanto, E.M.; Szanto de Toledo, A. [Instituto de Fisica - Universidade de Sao Paulo, Departamento de Fisica Nuclear, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)

    2009-04-15

    The reactions induced by the weakly bound {sup 6}Li projectile interacting with the intermediate mass target {sup 59}Co were investigated. Light charged particles singles and {alpha}-d coincidence measurements were performed at the near barrier energies E{sub lab}=17.4, 21.5, 25.5 and 29.6 MeV. The main contributions of the different competing mechanisms are discussed. A statistical model analysis, Continuum-Discretized Coupled-Channels (CDCC) calculations and two-body kinematics were used as tools to provide information to disentangle the main components of these mechanisms. A significant contribution of the direct breakup was observed through the difference between the experimental sequential breakup cross section and the CDCC prediction for the non-capture breakup cross section.

  11. Automatic analysis and reduction of reaction mechanisms for complex fuel combustion

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Daniel

    2001-05-01

    This work concentrates on automatic procedures for simplifying chemical models for realistic fuels using skeletal mechanism construction and Quasi Steady-State Approximation (QSSA) applied to detailed reaction mechanisms. To automate the selection of species for removal or approximation, different indices for species ranking have thus been proposed. Reaction flow rates are combined with sensitivity information for targeting a certain quantity, and used to determine a level of redundancy for automatic skeletal mechanism construction by exclusion of redundant species. For QSSA reduction, a measure of species lifetime can be used for species ranking as-is, weighted by concentrations or molecular transport timescales, and/or combined with species sensitivity. Maximum values of the indices are accumulated over ranges of parameters, (e.g. fuel-air ratio and octane number), and species with low accumulated index values are selected for removal or steady-state approximation. In the case of QSSA, a model with a certain degree of reduction is automatically implemented as FORTRAN code by setting a certain index limit. The code calculates source terms of explicitly handled species from reaction rates and the steady-state concentrations by internal iteration. Homogeneous-reactor and one-dimensional laminar-flame models were used as test cases. A staged combustor fuelled by ethylene with monomethylamine addition is modelled by two homogeneous reactors in sequence, i.e. a PSR (Perfectly Stirred Reactor) followed by a PFR (Plug Flow Reactor). A modified PFR model was applied for simulation of a Homogeneous Charge Compression Ignition (HCCI) engine fuelled with four-component natural gas, whereas a two-zone model was required for a knocking Spark Ignition (SI) engine powered by Primary Reference Fuel (PRF). Finally, a laminar one-dimensional model was used to simulate premixed flames burning methane and an aeroturbine kerosene surrogate consisting of n-decane and toluene. In

  12. A detailed look at the reaction mechanisms of substituted carbenes with water.

    Science.gov (United States)

    Gómez, Sara; Guerra, Doris; López, José G; Toro-Labbé, Alejandro; Restrepo, Albeiro

    2013-03-07

    Two competitive reaction mechanisms for the gas-phase chemical transformation of singlet chlorocarbene into chloromethanol in the presence of one and two water molecules are examined in detail. An analysis of bond orders and bond order derivatives as well as of properties of bond critical points in the electron densities along the intrinsic reaction coordinates (IRCs for intermediates → transition state (TS) → products) suggests that, from the perspective of bond breaking/formation, both reactions should be considered to be highly nonsynchronous, concerted processes. Both transition states are early, resembling the intermediates, yielding rate constants whose magnitudes are mostly influenced by structural changes and to a lesser degree by bond breaking/formation. For the case of one water molecule, most of the energy in the reactants region of the IRC is used for structural changes, while the transition state region encompasses the majority of electron activity, except for the formation of the C-O bond, which extends well into the products region. In the case of two water molecules, very little electron flux and comparatively less work required for structural changes is noticed in the reactants region, leading to an earlier transition state and therefore to a smaller activation energy and to a larger rate constant. This, together with evidence gathered from other sources, allows us to provide plausible explanations for the observed difference in rate constants.

  13. Mechanism and electronic effects in nitrogen ylide-promoted asymmetric aziridination reaction.

    Science.gov (United States)

    Rajeev, Ramanan; Sunoj, Raghavan B

    2011-04-07

    The mechanism and stereoselectivity of the aziridination reaction between guanidinium ylide and a series of para-substituted benzaldehydes have been studied by using density functional theory methods. The mechanistic details and analyses of the key elementary steps involved in (a) the addition of nitrogen ylide to benzaldehydes and (b) subsequent fragmentation of the resulting oxaspirocyclic intermediate are presented. The relative energies of important transition states and intermediates are found to be useful toward rationalizing reported diastereoselective product formation. The relative energies of the key transition states could be rationalized on the basis of the differences in steric, electrostatic, and other stabilizing weak interactions. The deformation analysis of the transition state geometries exhibited good correlation with the predicted activation barriers. The changes in cis/trans diastereoselectivity preferences upon changes in the electron donating/withdrawing abilities of the para substituents on benzaldehyde are identified as arising due to vital differences in the preferred pathways. The large value of reaction constant (ρ > 4.8) estimated from the slope of good linear Hammett plots indicated high sensitivity to the electronic nature of substituents on benzaldehyde. The formation of trans-aziridine in the case of strong electron donating groups and cis-aziridines with weakly electron donating/withdrawing group has been explained by the likely changes in the mechanistic course of the reaction. In general, the predicted trends are found to be in good agreement with the earlier experimental reports.

  14. Effect of atmospheric oxidative plasma treatments on polypropylenic fibers surface: Characterization and reaction mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Nisticò, Roberto, E-mail: roberto.nistico@unito.it [University of Torino, Department of Chemistry and NIS Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); Magnacca, Giuliana [University of Torino, Department of Chemistry and NIS Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); Faga, Maria Giulia; Gautier, Giovanna [CNR-IMAMOTER, Strada delle Cacce 73, 10135 Torino (Italy); D’Angelo, Domenico; Ciancio, Emanuele [Clean-NT Lab, Environment Park S.p.A., Via Livorno 60, 10144 Torino (Italy); Lamberti, Roberta; Martorana, Selanna [Herniamesh S.r.l., Via F.lli Meliga 1/C, 10034 Chivasso (Italy)

    2013-08-15

    Atmospheric pressure plasma-dielectric barrier discharge (APP-DBD, open chamber configuration) was used to functionalize polypropylene (PP) fibers surface in order to generate oxidized-reactive groups such as hydroperoxides, alcohols and carbonyl species (i.e. ketones and others). Such a species increased the surface polarity, without causing material degradation. Three different types of plasma mixture (He, He/O{sub 2}, He/O{sub 2}/H{sub 2}O) under three different values of applied power (750, 1050, 1400 W) were investigated. The formed plasma species (O{sub 2}{sup +}, O single atom and OH radical) and their distribution were monitored via optical emission spectrometry (OES) measurements, and the plasma effects on PP surface species formation were followed by X-ray photoemission spectroscopy (XPS). Results allowed to better understand the reaction pathways between plasma phase and PP fibers. In fact, two reaction mechanisms were proposed, the first one concerning the plasma phase reactions and the second one involving material surface modifications.

  15. Triplet state dissolved organic matter in aquatic photochemistry: reaction mechanisms, substrate scope, and photophysical properties.

    Science.gov (United States)

    McNeill, Kristopher; Canonica, Silvio

    2016-11-09

    Excited triplet states of chromophoric dissolved organic matter ((3)CDOM*) play a major role among the reactive intermediates produced upon absorption of sunlight by surface waters. After more than two decades of research on the aquatic photochemistry of (3)CDOM*, the need for improving the knowledge about the photophysical and photochemical properties of these elusive reactive species remains considerable. This critical review examines the efforts to date to characterize (3)CDOM*. Information on (3)CDOM* relies mainly on the use of probe compounds because of the difficulties associated with directly observing (3)CDOM* using transient spectroscopic methods. Singlet molecular oxygen ((1)O2), which is a product of the reaction between (3)CDOM* and dissolved oxygen, is probably the simplest indicator that can be used to estimate steady-state concentrations of (3)CDOM*. There are two major modes of reaction of (3)CDOM* with substrates, namely triplet energy transfer or oxidation (via electron transfer, proton-coupled electron transfer or related mechanisms). Organic molecules, including several environmental contaminants, that are susceptible to degradation by these two different reaction modes are reviewed. It is proposed that through the use of appropriate sets of probe compounds and model photosensitizers an improved estimation of the distribution of triplet energies and one-electron reduction potentials of (3)CDOM* can be achieved.

  16. Kinetics and mechanism of the reaction of sodium azide with hypochlorite in aqueous solution.

    Science.gov (United States)

    Betterton, Eric A; Lowry, Joe; Ingamells, Robin; Venner, Brad

    2010-10-15

    Production of toxic sodium azide (NaN(3)) surged worldwide over the past two decades to meet the demand for automobile air bag inflator propellant. Industrial activity and the return of millions of inflators to automobile recycling facilities are leading to increasing release of NaN(3) to the environment so there is considerable interest in learning more about its environmental fate. Water soluble NaN(3) could conceivably be found in drinking water supplies so here we describe the kinetics and mechanism of the reaction of azide with hypochlorite, which is often used in water treatment plants. The reaction stoichiometry is: HOCl + 2N(3)(-) = 3N(2) + Cl(-) + OH(-), and proceeds by a key intermediate chlorine azide, ClN(3), which subsequently decomposes by reaction with a second azide molecule in the rate determining step: ClN(3) + N(3)(-) --> 3N(2) + Cl(-) (k = 0.52+/-0.04 M(-1) s(-1), 25 degrees C, mu = 0.1 M). We estimate that the half-life of azide would be approximately 15 s at the point of chlorination in a water treatment plant and approximately 24 days at some point downstream where only residual chlorine remains. Hypochlorite is not recommended for treatment of concentrated azide waste due to formation of the toxic chlorine azide intermediate under acidic conditions and the slow kinetics under basic conditions.

  17. A Theoretical Investigation on the Reaction Mechanism of the C9H+ 12·Side-chain Decomposition

    Institute of Scientific and Technical Information of China (English)

    CHENG,Xueli; ZHAO,Yanyun; LI,Feng; ZHANG,Dongsheng

    2009-01-01

    n-Phenylpropane cation C9H+·12 serves as a prototype to investigate the reaction mechanisms of alkylbenzene cations.The decomposition reactions of C9H+·12 system have been studied extensively at the B3LYP/6-311 + + G**level with Gaussian 98 program package.All reaction channels were fully investigated with the vibrational mode analysis to confirm the transition states and with electron population analysis to discuss the electron redistribution,and to elucidate the reaction mechanism.The reaction mechanism shows that there is a non-barrier channel of C9H+·12→C7H+7+C2H·5,which is thermodynamically most favorable.

  18. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations.

    Science.gov (United States)

    Ardèvol, Albert; Rovira, Carme

    2015-06-24

    Carbohydrate-active enzymes such as glycoside hydrolases (GHs) and glycosyltransferases (GTs) are of growing importance as drug targets. The development of efficient competitive inhibitors and chaperones to treat diseases related to these enzymes requires a detailed knowledge of their mechanisms of action. In recent years, sophisticated first-principles modeling approaches have significantly advanced in our understanding of the catalytic mechanisms of GHs and GTs, not only the molecular details of chemical reactions but also the significant implications that just the conformational dynamics of a sugar ring can have on these mechanisms. Here we provide an overview of the progress that has been made in the past decade, combining molecular dynamics simulations with density functional theory to solve these sweet mysteries of nature.

  19. 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.

  20. Detailed Chemical Kinetic Reaction Mechanisms for Primary Reference Fuels for Diesel Cetane Number and Spark-Ignition Octane Number

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C K; Pitz, W J; Mehl, M; Curran, H J

    2010-03-03

    For the first time, a detailed chemical kinetic reaction mechanism is developed for primary reference fuel mixtures of n-hexadecane and 2,2,4,4,6,8,8-heptamethyl nonane for diesel cetane ratings. The mechanisms are constructed using existing rules for reaction pathways and rate expressions developed previously for the primary reference fuels for gasoline octane ratings, n-heptane and iso-octane. These reaction mechanisms are validated by comparisons between computed and experimental results for shock tube ignition and for oxidation under jet-stirred reactor conditions. The combined kinetic reaction mechanism contains the submechanisms for the primary reference fuels for diesel cetane ratings and submechanisms for the primary reference fuels for gasoline octane ratings, all in one integrated large kinetic reaction mechanism. Representative applications of this mechanism to two test problems are presented, one describing fuel/air autoignition variations with changes in fuel cetane numbers, and the other describing fuel combustion in a jet-stirred reactor environment with the fuel varying from pure 2,2,4,4,6,8,8-heptamethyl nonane (Cetane number of 15) to pure n-hexadecane (Cetane number of 100). The final reaction mechanism for the primary reference fuels for diesel fuel and gasoline is available on the web.

  1. A new, double-inversion mechanism of the F(-) + CH3Cl SN2 reaction in aqueous solution.

    Science.gov (United States)

    Liu, Peng; Wang, Dunyou; Xu, Yulong

    2016-11-23

    Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F(-) + CH3Cl SN2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.

  2. Kinetics and reaction mechanism of yeast alcohol dehydrogenase with long-chain primary alcohols.

    Science.gov (United States)

    Schöpp, W; Aurich, H

    1976-01-01

    Kinetic studies of yeast alcohol dehydrogenase with NAD+ and ethanol, hexanol or decanol as substrates invariably result in non-linear Lineweaver-Burk plots if the alcohol is the variable substrate. The kinetic coefficients determined from secondary plots are consistent with an 'equilibrium random-order' mechanism for extremely low alcohol concentrations and for all alcohols, the transformation of the ternary complexes being the rate-limiting step of the reaction. This mechanism also applies to long-chain substrates at high concentrations, whereas the rate of the ethanol-NAD+ reaction at high ethanol concentrations is determined by the dissociation of the enzyme-NADH complex. The dissociation constants for the enzyme-NAD+ complex and for the enzyme-alcohol complexes obtained from the kinetic quotients satisfactorily correspond to the dissociation constants obtained by use of other techniques. It is suggested that the non-linear curves may be attributed to a structural change in the enzyme itself, caused by the alcohol. PMID:183740

  3. Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction.

    Science.gov (United States)

    Teramoto, Takamasa; Fujikawa, Yukari; Kawaguchi, Yoshirou; Kurogi, Katsuhisa; Soejima, Masayuki; Adachi, Rumi; Nakanishi, Yuichi; Mishiro-Sato, Emi; Liu, Ming-Cheh; Sakakibara, Yoichi; Suiko, Masahito; Kimura, Makoto; Kakuta, Yoshimitsu

    2013-01-01

    Post-translational protein modification by tyrosine sulfation has an important role in extracellular protein-protein interactions. The protein tyrosine sulfation reaction is catalysed by the Golgi enzyme called the tyrosylprotein sulfotransferase. To date, no crystal structure is available for tyrosylprotein sulfotransferase. Detailed mechanism of protein tyrosine sulfation reaction has thus remained unclear. Here we present the first crystal structure of the human tyrosylprotein sulfotransferase isoform 2 complexed with a substrate peptide (C4P5Y3) derived from complement C4 and 3'-phosphoadenosine-5'-phosphate at 1.9 Å resolution. Structural and complementary mutational analyses revealed the molecular basis for catalysis being an SN2-like in-line displacement mechanism. Tyrosylprotein sulfotransferase isoform 2 appeared to recognize the C4 peptide in a deep cleft by using a short parallel β-sheet type interaction, and the bound C4P5Y3 forms an L-shaped structure. Surprisingly, the mode of substrate peptide recognition observed in the tyrosylprotein sulfotransferase isoform 2 structure resembles that observed for the receptor type tyrosine kinases.

  4. TDDFT Study on Different Sensing Mechanisms of Similar Cyanide Sensors Based on Michael Addition Reaction

    Institute of Scientific and Technical Information of China (English)

    Guang-yue Li; Ping Song; Guo-zhong He

    2011-01-01

    The solvents and substituents of two similar fluorescent sensors for cyanide, 7-diethylamino-3-formylcoumarin (sensor a) and 7-diethylamino-3-(2-nitrovinyl)coumarin (sensor b), are proposed to account for their distinct sensing mechanisms and experimental phenomena.The time-dependent density functional theory has been applied to investigate the ground states and the first singlet excited electronic states of the sensor as well as their possible Michael reaction products with cyanide, with a view to monitoring their geometries and photophysical properties. The theoretical study indicates that the protic water solvent could lead to final Michael addition product of sensor a in the ground state, while the aprotic acetonitrile solvent could lead to carbanion as the final product of sensor b. Furthermore,the Michael reaction product of sensor a has been proved to have a torsion structure in its first singlet excited state. Correspondingly, sensor b also has a torsion structure around the nitrovinyl moiety in its first singlet excited state, while not in its carbanion structure. This could explain the observed strong fluorescence for sensor a and the quenching fluorescencefor the sensor b upon the addition of the cyanide anions in the relevant sensing mechanisms.

  5. Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase.

    Science.gov (United States)

    Kim, Hun; Choi, Jongkeun; Kim, Truc; Lokanath, Neratur K; Ha, Sung Chul; Suh, Se Won; Hwang, Hye-Yeon; Kim, Kyeong Kyu

    2010-04-01

    UDP-glucose pyrophosphorylases (UGPase; EC 2.7.7.9) catalyze the conversion of UTP and glucose-1-phosphate to UDP-glucose and pyrophosphate and vice versa. Prokaryotic UGPases are distinct from their eukaryotic counterparts and are considered appropriate targets for the development of novel antibacterial agents since their product, UDP-glucose, is indispensable for the biosynthesis of virulence factors such as lipopolysaccharides and capsular polysaccharides. In this study, the crystal structures of UGPase from Helicobacter pylori (HpUGPase) were determined in apo- and UDP-glucose/Mg(2+)-bound forms at 2.9 A and 2.3 A resolutions, respectively. HpUGPase is a homotetramer and its active site is located in a deep pocket of each subunit. Magnesium ion is coordinated by Asp130, two oxygen atoms of phosphoryl groups, and three water molecules with octahedral geometry. Isothermal titration calorimetry analyses demonstrated that Mg(2+) ion plays a key role in the enzymatic activity of UGPase by enhancing the binding of UGPase to UTP or UDP-glucose, suggesting that this reaction is catalyzed by an ordered sequential Bi Bi mechanism. Furthermore, the crystal structure explains the specificity for uracil bases. The current structural study combined with functional analyses provides essential information for understanding the reaction mechanism of bacterial UGPases, as well as a platform for the development of novel antibacterial agents.

  6. Electronically excited states and photochemical reaction mechanisms of β-glucose.

    Science.gov (United States)

    Tuna, Deniz; Sobolewski, Andrzej L; Domcke, Wolfgang

    2014-01-07

    Carbohydrates are important molecular components of living matter. While spectroscopic and computational studies have been performed on carbohydrates in the electronic ground state, the lack of a chromophore complicates the elucidation of the excited-state properties and the photochemistry of this class of compounds. Herein, we report on the first computational investigation of the singlet photochemistry of β-glucose. It is shown that low-lying singlet excited states are of nσ* nature. Our computations of the singlet vertical excitation energies predict absorption from 6.0 eV onward. Owing to a dense manifold of weakly-absorbing states, a sizable and broad absorption in the ultraviolet-C range arises. We have explored two types of photochemical reaction mechanisms: hydrogen-detachment processes for each of the five O-H groups and a C-O ring-opening process. Both types of reactions are driven by repulsive nσ* states that are readily accessible from the Franck-Condon region and lead to conical intersections in a barrierless fashion. We have optimized the geometries of the conical intersections involved in these photochemical processes and found that these intersections are located around 5.0 eV for the O-H hydrogen-detachment reactions and around 4.0 eV for the C-O ring-opening reaction. The energies of all conical intersections are well below the computed absorption edge. The calculations were performed using linear-response methods for the computation of the vertical excitation energies and multiconfigurational methods for the optimization of conical intersections and the computation of energy profiles.

  7. Mechanism of the heterogeneous reaction of carbonyl sulfide with typical components of atmospheric aerosol

    Institute of Scientific and Technical Information of China (English)

    WU Hongbo; WANG Xiao; CHEN Jianmin; YU Hongkun; XUE Huaxin; PAN Xunxi; HOU Huiqi

    2004-01-01

    The homogeneous reactions of earbonyl sulfide (COS) with OH and oxygen radicals have been studied thoroughly. However, the heterogeneous chemical processes involving COS and atmospheric particles are still not well understood. The reactivity of COS with atmospheric mineral oxides such as A12O3, CaO, SiO2, Fe2O3 and MnO2 has been explored. The gaseous and solid products of the reaction were identified by in situ Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy respectively.The mechanism and kinetics of the heterogeneous reaction are also discussed in detail. The results showed that COS can be catalytically oxidized on the surfaces of different atmospheric mineral oxides with the products of CO2, S and SO42-.The reactivity of the oxides with COS differs widely. A12O3 exhibits excellent reactivity, and Fe2O3 is inferior to it. CaO shows weak reactivity, while SiO2 and MnO2 nearly have no activity for the oxidation of COS. The absorbed oxygen and hydroxyls on the surfaces of the oxides are the main active sites in the conversion of COS. When O2 in the experimental system was much excessive, the catalytic oxidation on the surface of AI2O3 is a pseudo first order reaction with respect to COS. The acidity of A12O3 influences the reactivity significantly. The rate constants of the catalytic oxidation of COS on the surface of basic, neutral and acidic A12O3 are respectively 1.51xl0-4, 9.81x10-s and 3.06x10-6 s-1.

  8. Reaction Mechanism for m- Xylene Oxidation in the Claus Process by Sulfur Dioxide

    KAUST Repository

    Sinha, Sourab

    2015-09-24

    In the Claus process, the presence of aromatic contaminants such benzene, toluene, and xylenes (BTX), in the H2S feed stream has a detrimental effect on catalytic reactors, where BTX form soot particles and clog and deactivate the catalysts. Among BTX, xylenes are proven to be most damaging contaminant for catalysts. BTX oxidation in the Claus furnace, before they enter catalyst beds, provides a solution to this problem. A reaction kinetics study on m-xylene oxidation by SO2, an oxidant present in Claus furnace, is presented. The density functional theory is used to study the formation of m-xylene radicals (3-methylbenzyl, 2,6-dimethylphenyl, 2,4-dimethylphenyl, and 3,5-dimethylphenyl) through H-abstraction and their oxidation by SO2. The mechanism begins with SO2 addition on the radicals through an O-atom rather than the S-atom with the release of 180.0-183.1 kJ/mol of reaction energies. This exothermic reaction involves energy barriers in the range 3.9-5.2 kJ/mol for several m-xylene radicals. Thereafter, O-S bond scission takes place to release SO, and the O-atom remaining on aromatics leads to CO formation. Among four m-xylene radicals, the resonantly stabilized 3-methylbenzyl exhibited the lowest SO2 addition and SO elimination rates. The reaction rate constants are provided to facilitate Claus process simulations to find conditions suitable for BTX oxidation. © 2015 American Chemical Society.

  9. Pathophysiological mechanisms of local (pulmonary inflammatory reaction at the traumatic disease of the spinal cord

    Directory of Open Access Journals (Sweden)

    Uljanov V.Yu.

    2015-06-01

    Full Text Available Objective: to study pathophysiological mechanisms of local (pulmonary inflammatory reaction in the sharp and early periods of a traumatic disease of a spinal cord on the basis of an assessment of dynamic changes of cellular structure of a bronchial secret, an alveolar epithelium and a microbic landscape of a tracheobronchial tree at patients with the complicated damages of cervical department of a backbone. Materials and methods. Methods of cytologic, immunofermental and bacteriological researches at 40 patients with the complicated damages of cervical department of a backbone to dynamics studied the contents the neutrofil of leukocytes and alveolar macrophages in a bronchial secret, a mutsin antigene 3GE5 and surfaktant protein D in serum of blood, character of microbic flora of a tracheobronchial tree and its some biological properties. Results. Activation of local (pulmonary inflammatory reaction in the sharp and early periods of a traumatic disease of a spinal cord is characterized by increase of the contents the neutrofil of leukocytes in a bronchial secret for the 7-14th days, lymphocyts — for the 1-14th days increase in the maintenance of a mutsin antigene 3GE5 for the 14th days and SP-D —for the 1-14th days, allocation from respiratory substrata of opportunistic microorganisms in clinically significant concentration; knocking over — increase of quantity of alveolar macrophages, decrease in the maintenance of a mutsin antigene 3GE5 and SP-D for the 21-30th days and sanitation of a locus of an infection in a tracheobronchial tree. Conclusion. The pathophysiological mechanisms defining changes of cellular structure of a bronchial secret, an alveolar epithelium and a microbic landscape of a tracheobronchial tree in the sharp and early periods of a traumatic disease of a spinal cord play an important role in development of organ (pulmonary inflammatory reaction.

  10. Ablation characteristics and reaction mechanism of insulation materials under slag deposition condition

    Science.gov (United States)

    Guan, Yiwen; Li, Jiang; Liu, Yang

    2017-07-01

    Current understanding of the physical and chemical processes involved in the ablation of insulation materials by highly aluminized solid propellants is limited. The study on the heat transfer and ablation principle of ethylene propylene diene monomer (EPDM) materials under slag deposition condition is essential for future design or modification of large solid rocket motors (SRMs) for launch application. In this paper, the alumina liquid flow pattern and the deposition principle in full-scale SRM engines are discussed. The interaction mechanism between the alumina droplets and the wall are analyzed. Then, an experimental method was developed to simulate the insulation material ablation under slag deposition condition. Experimental study was conducted based on a laboratory-scale device. Meanwhile, from the analysis of the cross-sectional morphology and chemical composition of the charring layer after ablation, the reaction mechanism of the charring layer under deposition condition was discussed, and the main reaction equation was derived. The numerical simulation and experimental results show the following. (i) The alumina droplet flow in the deposition section of the laboratory-scale device is similar to that of a full-scale SRM. (ii) The charring layer of the EPDM insulator displays a porous tight/loose structure under high-temperature slag deposition condition. (iii) A seven-step carbothermal reduction in the alumina is derived and established under high-pressure and high-temperature environment in the SRM combustion chamber. (iv) The analysis using thermodynamic software indicates that the reaction of the alumina and charring layer initially forms Al4C3 during the operation. Then, Al element and Al2OC compound are subsequently produced with the reduction in the release of gas CO as well with continuous environmental heating.

  11. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order.

    Science.gov (United States)

    Wongnate, Thanyaporn; Ragsdale, Stephen W

    2015-04-10

    Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.

  12. On Cosmic-Ray-Driven Electron Reaction Mechanism for Ozone Hole and Chlorofluorocarbon Mechanism for Global Climate Change

    CERN Document Server

    Lu, Qing-Bin

    2012-01-01

    Numerous laboratory measurements have provided a sound physical basis for the cosmic-ray driven electron-induced reaction (CRE) mechanism of halogen-containing molecules for the ozone hole. And observed spatial and time correlations between polar ozone loss or stratospheric cooling and cosmic rays have shown strong evidence of the CRE mechanism [Q.-B. Lu, Phys. Rep. 487, 141-167(2010)]. Chlorofluorocarbons (CFCs) were also long-known greenhouse gases but were thought to play only a minor role in climate change. However, recent observations have shown evidence of the saturation in greenhouse effect of non-CFC gases. A new evaluation has shown that halocarbons alone (mainly CFCs) could account for the rise of 0.5~0.6 deg C in global surface temperature since 1950, leading to the striking conclusion that not CO2 but CFCs were the major culprit for global warming in the late half of the 20th century [Q.-B. Lu, J. Cosmology 8, 1846-1862(2010)]. Surprizingly, a recent paper [J.-W. Grooss and R. Muller, Atmos. Envir...

  13. Mechanisms before Reactions: A Mechanistic Approach to the Organic Chemistry Curriculum Based on Patterns of Electron Flow

    Science.gov (United States)

    Flynn, Alison B.; Ogilvie, William W.

    2015-01-01

    A significant redesign of the introductory organic chemistry curriculum at the authors' institution is described. There are two aspects that differ greatly from a typical functional group approach. First, organic reaction mechanisms and the electron-pushing formalism are taught before students have learned a single reaction. The conservation of…

  14. Mechanisms before Reactions: A Mechanistic Approach to the Organic Chemistry Curriculum Based on Patterns of Electron Flow

    Science.gov (United States)

    Flynn, Alison B.; Ogilvie, William W.

    2015-01-01

    A significant redesign of the introductory organic chemistry curriculum at the authors' institution is described. There are two aspects that differ greatly from a typical functional group approach. First, organic reaction mechanisms and the electron-pushing formalism are taught before students have learned a single reaction. The conservation of…

  15. A novel mechanism for the oxidation reaction of VO2+ on a graphite electrode in acidic solutions

    Science.gov (United States)

    Wang, Wenjun; Fan, Xinzhuang; Liu, Jianguo; Yan, Chuanwei; Zeng, Chaoliu

    2014-09-01

    With the consideration of optimizing the performance of the all-vanadium redox flow battery (VRB), the oxidation reaction mechanism of VO2+ on a rotating graphite disk electrode has been investigated by potentiodynamic polarization in sulfuric acid solutions with various pH and vanadium concentrations. Furthermore, the reaction orders of VO2+ and H+ for the oxidation reaction of VO2+ have been calculated from the polarization results and compared with the theoretical results according to the possible reaction mechanisms available in the literature. However, a new oxidation reaction mechanism has been proposed to describe the oxidation of VO2+ at last, and the theoretic reaction orders of VO2+ and H+ based on the new mechanism are consistent with the experimental results when the electrochemical reaction is the rate-limited process. Moreover, a corresponding kinetic equation has been established for the oxidation reaction of VO2+ on a spectroscopically pure graphite electrode, and can be well used to predict the polarization behavior in V (IV) acidic solutions.

  16. EFFECT OF FLUORINE AND CHLORINE IONS ON THE REACTION SINTERING OF MECHANICALLY ACTIVATED ZIRCON-ALUMINA MIXTURE

    Directory of Open Access Journals (Sweden)

    R. Zamani Foroshani

    2015-09-01

    Full Text Available The aim of this work was to study the effect of fluorine and chlorine ions on the formation of mullite during the reaction sintering of mechanically activated zircon-alumina powder mixture. The results showed that mechanical activation of zirconalumina powder mixture for 20 h led to grain refinement and partial amorphization. In the presence of fluorine and chlorine ions, complete formation of mullite in the mechanically activated sample occurred after 2 h of reaction sintering at 1300oC and 1400oC, respectively. In the sample lacking fluorine and chlorine ions, mullitization was not completed even after 2 h of reaction sintering at 1400oC. It was concluded that presence of fluorine and chlorine ions enhance the dissociation of zircon and formation of mullite during the reaction sintering of mechanically activated zircon-alumina mixture.

  17. NO-CO-O2 Reaction on a Metal Catalytic Surface using Eley-Rideal Mechanism

    Institute of Scientific and Technical Information of China (English)

    Waqar Ahmad

    2008-01-01

    Interactions among the reacting species NO, CO and O2 on metal catalytic surfaces are studied by means of Monte Carlo simulation using the Eley-Rideal (ER) mechanism. The study of this three-component system is important for understanding of the reaction kinetics by varying the relative ratios of the reactants. It is found that contrary to the conventional Langmuir-Hinshelwood (LH) thermal mechanism in which two irreversible phase transitions are obtained between active states and poisoned states, a single phase transition is observed when the ER mechanism is combined with the LH mechanism. The phase diagrams of the surface coverage and the steady state production of CO2, N2 and N2O are evaluated as a function of the partial pressures of the reactants in the gas phase. The continuous production of CO2 starts as soon as the CO pressure is switched on and the second order phase transition at the first critical point is eliminated, which is in agreement with the experimental findings.

  18. Cell mechanics and stress: from molecular details to the 'universal cell reaction' and hormesis.

    Science.gov (United States)

    Agutter, Paul S

    2007-04-01

    The 'universal cell reaction' (UCR), a coordinated biphasic response to external (noxious and other) stimuli observed in all living cells, was described by Nasonov and his colleagues in the mid-20th century. This work has received no attention from cell biologists in the West, but the UCR merits serious consideration. Although it is non-specific, it is likely to be underpinned by precise mechanisms and, if these mechanisms were characterized and their relationship to the UCR elucidated, then our understanding of the integration of cellular function could be improved. As a step towards identifying such mechanisms, I review some recent advances in understanding cell mechanics and the stress response and I suggest potentially testable hypotheses. There is a particular need for time-course studies of cellular responses to different stimulus doses or intensities. I also suggest a correspondence with hormesis; re-investigation of the UCR using modern biophysical and molecular-biological techniques might throw light on this much-discussed phenomenon.

  19. Reaction Mechanism Investigation Using Vibrational Mode Anal—ysis for the Multichannel Reacition of CH3O+CO

    Institute of Scientific and Technical Information of China (English)

    周正宇; 程学礼; 等

    2002-01-01

    On the basis of the computed results got by the Gaussian 94 package at B3LYP/6-311++G** level,the reaction mechanism of CH3O radical with CO has been investiagted thoroughly via the vibrational model analysis ,And the relationships among the reactants,eight transition states,four intermediates and various products involved this multichannel reation are eluci-dated,The vibrational mode anaysis shows that the reaction mechanism is relialbe.

  20. Loss of hepatocyte-nuclear-factor-4alpha affects colonic ion transport and causes chronic inflammation resembling inflammatory bowel disease in mice.

    Directory of Open Access Journals (Sweden)

    Mathieu Darsigny

    Full Text Available BACKGROUND: Hnf4alpha, an epithelial specific transcriptional regulator, is decreased in inflammatory bowel disease and protects against chemically-induced colitis in mice. However, the precise role of this factor in maintaining normal inflammatory homeostasis of the intestine remains unclear. The aim of this study was to evaluate the sole role of epithelial Hnf4alpha in the maintenance of gut inflammatory homeostasis in mice. METHODOLOGY/PRINCIPAL FINDINGS: We show here that specific epithelial deletion of Hnf4alpha in mice causes spontaneous chronic intestinal inflammation leading to focal areas of crypt dropout, increased cytokines and chemokines secretion, immune cell infiltrates and crypt hyperplasia. A gene profiling analysis in diseased Hnf4alpha null colon confirms profound genetic changes in cell death and proliferative behaviour related to cancer. Among the genes involved in the immune protection through epithelial barrier function, we identify the ion transporter claudin-15 to be down-modulated early in the colon of Hnf4alpha mutants. This coincides with a significant decrease of mucosal ion transport but not of barrier permeability in young animals prior to the manifestation of the disease. We confirm that claudin-15 is a direct Hnf4alpha gene target in the intestinal epithelial context and is down-modulated in mouse experimental colitis and inflammatory bowel disease. CONCLUSION: Our results highlight the critical role of Hnf4alpha to maintain intestinal inflammatory homeostasis during mouse adult life and uncover a novel function for Hnf4alpha in the regulation of claudin-15 expression. This establishes Hnf4alpha as a mediator of ion epithelial transport, an important process for the maintenance of gut inflammatory homeostasis.

  1. Shrinkage Cracking: A mechanism for self-sustaining carbon mineralization reactions in olivine rocks

    Science.gov (United States)

    Zhu, W.; Fusseis, F.; Lisabeth, H. P.; Xing, T.; Xiao, X.; De Andrade, V. J. D.; Karato, S. I.

    2015-12-01

    The hydration and carbonation of olivine results in an up to ~44% increase in solid molar volume, which may choke off of fluid supply and passivate reactive surfaces, thus preventing further carbonation reactions. The carbonation of olivine has ben studied extensively in the laboratory. To date, observations from these experimental studies indicate that carbonation reaction rates generally decrease with time and the extent of carbonation is limited in olivine rocks. Field studies, however, show that 100% hydration and carbonation occur naturally in ultramafic rocks. The disagreement between the laboratory results under controlled conditions and the field observations underlines the lack of understanding of the mechanisms responsible for the self-sustaining carbonation interaction in nature. We developed a state-of-the-art pressurized hydrothermal cell that is transparent to X-rays to characterize the real-time evolution of pore geometry during fluid-rock interaction using in-situ synchrotron-based X-ray microtomography. Through a time series of high-resolution 3-dimensional images, we document the microstructural evolution of a porous olivine aggregate reacting with a sodium bicarbonate solution at elevated pressure and temperature conditions. We observed porosity increases, near constant rate of crystal growth, and pervasive reaction-induced fractures. Based on the nanometer scale tomography data, we propose that shrinkage cracking is the mechanism responsible for producing new reactive surface and keep the carbonation reaction self-sustaining in our experiment. Shrinkage cracks are commonly observed in drying mud ponds, cooling lava flows and ice wedge fields. Stretching of a contracting surface bonded to a substrate of nearly constant dimensions leads to a stress buildup in the surface layer. When the stress exceeds the tensile strength, polygonal cracks develop in the surface layer. In our experiments, the stretching mismatch between the surface and interior of

  2. Structure and mechanism of styrene monooxygenase reductase: new insight into the FAD-transfer reaction.

    Science.gov (United States)

    Morrison, Eliot; Kantz, Auric; Gassner, George T; Sazinsky, Matthew H

    2013-09-03

    The two-component flavoprotein styrene monooxygenase (SMO) from Pseudomonas putida S12 catalyzes the NADH- and FAD-dependent epoxidation of styrene to styrene oxide. In this study, we investigate the mechanism of flavin reduction and transfer from the reductase (SMOB) to the epoxidase (NSMOA) component and report our findings in light of the 2.2 Å crystal structure of SMOB. Upon rapidly mixing with NADH, SMOB forms an NADH → FADox charge-transfer intermediate and catalyzes a hydride-transfer reaction from NADH to FAD, with a rate constant of 49.1 ± 1.4 s(-1), in a step that is coupled to the rapid dissociation of NAD(+). Electrochemical and equilibrium-binding studies indicate that NSMOA binds FADhq ∼13-times more tightly than SMOB, which supports a vectoral transfer of FADhq from the reductase to the epoxidase. After binding to NSMOA, FADhq rapidly reacts with molecular oxygen to form a stable C(4a)-hydroperoxide intermediate. The half-life of apoSMOB generated in the FAD-transfer reaction is increased ∼21-fold, supporting a protein-protein interaction between apoSMOB and the peroxide intermediate of NSMOA. The mechanisms of FAD dissociation and transport from SMOB to NSMOA were probed by monitoring the competitive reduction of cytochrome c in the presence and absence of pyridine nucleotides. On the basis of these studies, we propose a model in which reduced FAD binds to SMOB in equilibrium between an unreactive, sequestered state (S state) and more reactive, transfer state (T state). The dissociation of NAD(+) after the hydride-transfer reaction transiently populates the T state, promoting the transfer of FADhq to NSMOA. The binding of pyridine nucleotides to SMOB-FADhq shifts the FADhq-binding equilibrium from the T state to the S state. Additionally, the 2.2 Å crystal structure of SMOB-FADox reported in this work is discussed in light of the pyridine nucleotide-gated flavin-transfer and electron-transfer reactions.

  3. PCDD/F Formation mechanism: effect of surface composition on chlorination and condensation reactions

    Energy Technology Data Exchange (ETDEWEB)

    Sidhu, S.; Nath, P.

    2002-07-01

    The post-combustion zone immediately following the incineration (flame) zone is a potential pollutant formation zone as it contains excess O{sub 2} (3-9%), sufficient residence time (from sub seconds to minutes) and catalytically active fly ash particles. This is an ideal reaction environment for the C{sub 1} and C{sub 2} compounds exiting the flame zone to undergo condensation and chlorination reactions. Heterogeneous reactions of short-chain aliphatic and chlorinated aliphatic combustion products in both high-temperature and low-temperature post-combustion zones can be important in the formation of larger organic pollutants (e. g. polychlorinated biphenyls, polychlorianted dibenzo-p-dioxins/dibenzofurans, chlorohenols, chlorobenzenes, etc). Fly ash formed in the combustion process provides the active surface for chlorination/condensation reactions in the post-combustion zone. The presence of several metals in flay ashes give rise to the question whether there is one specific metal or a complex of metals that is responsoble for the chlorination. Although fly ash contains many metallic species, most researchers investigations the PCDD/F formation mechanisms have used copper as the catalytic surface in their pollutant formation studies because copper is a known commercial oxychloriantion catalyst. The specific catalytic effects of various copper compounds in the formation of PCDD/F from aliphatica and aromatic compounds have been examined by us and a number of other investigators. In limited studies, iron compounds have also been used as PCDD/F formation catalysts, although these iron studies have produced contradictory results. Review of commercially important polymerization reactions shows that at varying temperatures and pressures, c and C{sub 4} olefinic polymerization reactions may be catalyzed by HCI-activated Al{sub 2}O{sub 3} SiO{sub 2} (aromatization also observed), aluminosilicates (1% Al{sub 2}O{sub 3} in SiO{sub 2}), and Fe oxides on aluminosilicates

  4. Preparation of Polystryenylphosphonous Acid of Low Polymerization Degree and Influence of Initiators upon the Free Radical Reaction Mechanism

    Institute of Scientific and Technical Information of China (English)

    XiangKaiFU; YanSUI; 等

    2002-01-01

    The polystyrenylphosphonous acid (PSPA) of low polymerization degress was prepared with one step reaction. The reaction mechanism was changed with different initiators. For the reaction with AIBN or BPO as the initiator, therer are 2 or 3 serives of radical reaction chains and 5 or 9 series of polystyrenyl products. The main products are PSPA without or with the fragment of the initiator H[CH(C6H5)-CH2]n-PO2H2 and C6H5CO2-[CH2CH(C6H5)]n-PO2H2 respectively.

  5. Preparation of Polystyrenylphosphonous Acid of Low Polymerization Degree and Influence of Initiators upon the Free Radical Reaction Mechanism

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The polystyrenylphosphonous acid (PSPA) of low polymerization degree was prepared with one step reaction. The reaction mechanism was changed with different initiators. For the reaction with AIBN or BPO as the initiator, there are 2 or 3 series of radical reaction chains and 5 or 9 series of polystyrenyl products. The main products are PSPA without or with the fragment of the initiator H[CH(C6H5)-CH2]n-PO2H2 and C6H5CO2-[CH2CH (C6H5)]n-PO2H2 respectively.

  6. SnCl2/Cu-Mediated Carbonyl Allylation Reaction in Water:Scope,Selectivity and Mechanism

    Institute of Scientific and Technical Information of China (English)

    TAN,Xiang-Hui(谭翔晖); HOU,Yong-Quan(侯永泉); LIU,Lei(刘磊); GUO,Qing-Xiang(郭庆祥)

    2004-01-01

    Copper was found to be able to promote the SnC12-mediated carbonyl allylation reactions in water,giving the corresponding homoallylic alcohol products in very high yields.Detailed studies showed that the reaction could be applied to a variety of carbonyl compounds including those with hydroxyl,amino and nitro groups.It was also found that this reaction showed good regioselectivities for some substrates.Furthermore,carefully controled experiments and in situ NMR measurements provided important insights into the mechanism of the newly developed reaction.

  7. Rational approach to polymer-supported catalysts: synergy between catalytic reaction mechanism and polymer design.

    Science.gov (United States)

    Madhavan, Nandita; Jones, Christopher W; Weck, Marcus

    2008-09-01

    Supported catalysis is emerging as a cornerstone of transition metal catalysis, as environmental awareness necessitates "green" methodologies and transition metal resources become scarcer and more expensive. Although these supported systems are quite useful, especially in their capacity for transition metal catalyst recycling and recovery, higher activity and selectivity have been elusive compared with nonsupported catalysts. This Account describes recent developments in polymer-supported metal-salen complexes, which often surpass nonsupported analogues in catalytic activity and selectivity, demonstrating the effectiveness of a systematic, logical approach to designing supported catalysts from a detailed understanding of the catalytic reaction mechanism. Over the past few decades, a large number of transition metal complex catalysts have been supported on a variety of materials ranging from polymers to mesoporous silica. In particular, soluble polymer supports are advantageous because of the development of controlled and living polymerization methods that are tolerant to a wide variety of functional groups, including controlled radical polymerizations and ring-opening metathesis polymerization. These methods allow for tuning the density and structure of the catalyst sites along the polymer chain, thereby enabling the development of structure-property relationships between a catalyst and its polymer support. The fine-tuning of the catalyst-support interface, in combination with a detailed understanding of catalytic reaction mechanisms, not only permits the generation of reusable and recyclable polymer-supported catalysts but also facilitates the design and realization of supported catalysts that are significantly more active and selective than their nonsupported counterparts. These superior supported catalysts are accessible through the optimization of four basic variables in their design: (i) polymer backbone rigidity, (ii) the nature of the linker, (iii) catalyst

  8. Structures and reaction mechanisms of the two related enzymes, PurN and PurU.

    Science.gov (United States)

    Sampei, Gen-ichi; Kanagawa, Mayumi; Baba, Seiki; Shimasaki, Toshiaki; Taka, Hiroyuki; Mitsui, Shohei; Fujiwara, Shinji; Yanagida, Yuki; Kusano, Mayumi; Suzuki, Sakiko; Terao, Kayoko; Kawai, Hiroya; Fukai, Yoko; Nakagawa, Noriko; Ebihara, Akio; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kawai, Gota

    2013-12-01

    The crystal structures of glycinamide ribonucleotide transformylases (PurNs) from Aquifex aeolicus (Aa), Geobacillus kaustophilus (Gk) and Symbiobacterium toebii (St), and of formyltetrahydrofolate hydrolase (PurU) from Thermus thermophilus (Tt) were determined. The monomer structures of the determined PurN and PurU were very similar to the known structure of PurN, but oligomeric states were different; AaPurN and StPurN formed dimers, GkPurN formed monomer and PurU formed tetramer in the crystals. PurU had a regulatory ACT domain in its N-terminal side. So far several structures of PurUs have been determined, yet, the mechanisms of the catalysis and the regulation of PurU have not been elucidated. We, therefore, modelled ligand-bound structures of PurN and PurU, and performed molecular dynamics simulations to elucidate the reaction mechanisms. The evolutionary relationship of the two enzymes is discussed based on the comparisons of the structures and the catalytic mechanisms.

  9. Synthesis Mechanism and Strengthening Effects of Laminated NiAl by Reaction Annealing

    Science.gov (United States)

    Du, Yan; Fan, Guohua; Wang, Qingwei; Geng, Lin

    2017-01-01

    N iA l with a laminated microstructure has been fabricated by reaction annealing of Ni-Al system at 1473 K (1200 °C). The laminated NiAl shows heterogeneity of chemical gradient and bimodal grain size distribution. The objective of this study is to investigate the synthesis mechanism and the strengthening effect of this laminated NiAl, therefore to promote further application of NiAl as a high-temperature structural material. Heat treatments at 1473 K (1200 °C) and subsequent characterization were utilized to study the synthesis mechanism. It shows that in original Al regions NiAl nuclei precipitate from Al(Ni) liquid phase and form fine-grained NiAl layers, whereas in original Ni regions NiAl nuclei precipitate from Ni(Al) saturated solution through diffusion and form coarse-grained NiAl layers. Moreover, heterogeneity of chemical gradient is generated through diffusion during annealing. The mechanical properties of laminated NiAl have also been studied via nanoindentation method. It shows that both chemical gradient and bimodal grain size distribution could strengthen the laminated NiAl.

  10. High Electrocatalytic Response of a Mechanically Enhanced NbC Nanocomposite Electrode Towards Hydrogen Evolution Reaction

    KAUST Repository

    Coy, Emerson

    2017-08-22

    Resistant and efficient electrocatalysts for hydrogen evolution reaction (HER) are desired to replace scarce and commercially expensive platinum electrodes. Thin film electrodes of metal-carbides are a promising alternative due to their reduced price and similar catalytic properties. However, most of the studied structures to date neglect long lasting chemical and structural stability, focusing only on electrochemical efficiency. Herein we report on a new approach to easily deposit and control the micro/nanostructure of thin film electrodes based on niobium carbide (NbC) and their electrocatalytic response. We will show that, by improving the mechanical properties of the NbC electrodes, microstructure and mechanical resilience can be obtained whilst maintaining high electro catalytic response. We also address the influence of other parameters such as conductivity and chemical composition on the overall performance of the thin film electrodes. Finally, we show that nanocomposite NbC electrodes are promising candidates towards HER , and furthermore, that the methodology presented here is suitable to produce other transition metal carbides (TM-C) with improved catalytic and mechanical properties.

  11. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    Science.gov (United States)

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

    2016-05-17

    solving complex problems and proposing new detailed reaction mechanisms that rationalize the experimental findings. For each of the considered reactions, a consistent mechanism is presented, the experimentally observed selectivities are reproduced, and their sources are identified. Reproducing selectivities requires high accuracy in computing relative transition state energies. As demonstrated by the results summarized in this Account, this accuracy is possible with the use of the presented methodology, benefiting of course from a large extent of cancellation of systematic errors. It is argued that as the employed models become larger, the number of rotamers and isomers that have to be considered for every stationary point increases and a careful assessment of their energies is therefore necessary in order to ensure that the lowest energy conformation is located. This issue constitutes a bottleneck of the investigation in some cases and is particularly important when analyzing selectivities, since small energy differences need to be reproduced.

  12. Three autocatalysts and self-inhibition in a single reaction: a detailed mechanism of the chlorite-tetrathionate reaction.

    Science.gov (United States)

    Horváth, Attila K; Nagypál, István; Epstein, Irving R

    2006-11-27

    The chlorite-tetrathionate reaction has been studied spectrophotometrically in the pH range of 4.65-5.35 at T = 25.0 +/- 0.2 degrees C with an ionic strength of 0.5 M, adjusted with sodium acetate as a buffer component. The reaction is unique in that it demonstrates autocatalysis with respect to the hydrogen and chloride ion products and the key intermediate, HOCl. The thermodynamically most-favorable stoichiometry, 2S(4)O(6)2- + 7ClO2- + 6H2O --> 8SO(4)2- + 7Cl- + 12H+, is not found. Under our experimental conditions, chlorine dioxide, the chlorate ion, or both are detected in appreciable amounts among the products. Initial rate studies reveal that the formation of chlorine dioxide varies in an unusual way, with the chlorite ion acting as a self-inhibitor. The reaction is supercatalytic (i.e., second order with respect to autocatalyst H+). The autocatalytic behavior with respect to Cl- comes from chloride catalysis of the chlorite-hypochlorous acid and hypochlorous acid-tetrathionate subsystems. A detailed kinetic study and a model that explains this unusual kinetic behavior are presented.

  13. Implications of sterically constrained n-butane oxidation reactions on the reaction mechanism and selectivity to 1-butanol

    Science.gov (United States)

    Dix, Sean T.; Gómez-Gualdrón, Diego A.; Getman, Rachel B.

    2016-11-01

    Density functional theory (DFT) is used to analyze the reaction network in n-butane oxidation to 1-butanol over a Ag/Pd alloy catalyst under steric constraints, and the implications on the ability to produce 1-butanol selectively using MOF-encapsulated catalysts are discussed. MOFs are porous crystalline solids comprised of metal nodes linked by organic molecules. Recently, they have been successfully grown around metal nanoparticle catalysts. The resulting porous networks have been shown to promote regioselective chemistry, i.e., hydrogenation of trans-1,3-hexadiene to 3-hexene, presumably by forcing the linear alkene to stand "upright" on the catalyst surface and allowing only the terminal C-H bonds to be activated. In this work, we extend this concept to alkane oxidation. Our goal is to determine if a MOF-encapsulated catalyst could be used to selectively produce 1-butanol. Reaction energies and activation barriers are presented for more than 40 reactions in the pathway for n-butane oxidation. We find that C-H bond activation proceeds through an oxygen-assisted pathway and that butanal and 1-butanol are some of the possible products.

  14. Reaction of benzophenone triplet with aliphatic amines. What a potent neurotoxin can tell us about the reaction mechanism.

    Science.gov (United States)

    Grimm, Michelle L; Allen, William J; Finn, Meghan; Castagnoli, Neal; Tanko, James M

    2011-02-15

    A photochemical model study of benzophenone triplet ((3)BP) with the MAO-B substrate 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine [MPTP (1)] and two of it's derivatives, 1-cyclopropyl-4-phenyl-1,2,3,6-tetrahydropyridine (2) and (±)-[trans-2-phenylcyclopropyl-4-phenyl-1,2,3,6-tetrahydropyridine (3) were performed. Literature precedent and calculations reported herein suggest that the barrier to ring opening for aminyl radical cations derived from N-cyclopropyl derivatives of tertiary amines (such as MPTP) will be low. The LFP results reported herein demonstrate that pathways for the reaction of (3)BP with 1, 2, and 3 are very similar. In each instance, disappearance of (3)BP is accompanied solely by appearance of bands corresponding to the diphenylhydroxylmethyl radical and neutral radical derived from MPTP and it's two derivatives 2 and 3. These results suggest that the reaction between benzophenone triplet and tertiary aliphatic amines proceed via a simple hydrogen atom transfer reaction. Additionally these model examinations provide evidence that oxidations of N-cyclopropyl derivatives of MPTP catalyzed by MAO-B may not be consistent with a pure SET pathway.

  15. Kinetic Study on Nucleophilic Substitution Reactions of Aryl Diphenylphosphinates with Butane-2,3-dione Monoximate and Aryloxide Anions: Reaction Mechanism and Origin of the α-Effect

    Energy Technology Data Exchange (ETDEWEB)

    Um, Ik-Hwan; Han, Jeong-Yoon [Ewha Womans University, Seoul (Korea, Republic of)

    2016-08-15

    A kinetic study is reported for nucleophilic substitution reactions of X-substituted-phenyl diphenylphosphinates (3a-3f) with butane-2,3-dione monoximate (Ox{sup -}) and a series of Y-substituted-phenoxide (Y-PhO{sup -}) ions in 50 mol % H{sub 2}O/50 mol % DMSO at 25.0 ± 0.1 .deg. C. The reactions of 3a-3f with Ox{sup -} and 4-chlorophenoxide (4-ClPhO{sup -}) result in linear Brønsted-type plots with β{sub lg} = -0.70 and -0.64, respectively, a typical β{sub lg} value for reactions reported previously to proceed through a concerted mechanism. The Brønsted-type plots for the reactions of 4-chloro-2-nitrophenyl diphenylphosphinate (3a), 4-nitrophenyl diphenylphosphinate (3b), and 4-acetylphenyl diphenylphosphinate (3d) with Y-PhO{sup -} are also linear with β{sub nuc} = 0.15-0.35. The current reactions have been concluded to proceed through a concerted mechanism in which the bond formation is much less advanced than the bond rupture in the TS on the basis of the β{sub lg} and β{sub nuc} values. The α-effect observe d in this study is very small (i.e., the k{sub Ox}{sup -}/k{sub p-ClPhO{sup -}} ratio = 16.4 - 43.5) and is independent of the leaving-group basicity. It has been concluded that the α-effect shown by Ox{sup -} in the current reactions is mainly due to desolvation of Ox{sup -} in the reaction medium (ground-state contribution) rather than stabilization of the transition-state (TS contribution) on the basis of the kinetic results.

  16. Global reaction mechanism for the auto-ignition of full boiling range gasoline and kerosene fuels

    Science.gov (United States)

    Vandersickel, A.; Wright, Y. M.; Boulouchos, K.

    2013-12-01

    Compact reaction schemes capable of predicting auto-ignition are a prerequisite for the development of strategies to control and optimise homogeneous charge compression ignition (HCCI) engines. In particular for full boiling range fuels exhibiting two stage ignition a tremendous demand exists in the engine development community. The present paper therefore meticulously assesses a previous 7-step reaction scheme developed to predict auto-ignition for four hydrocarbon blends and proposes an important extension of the model constant optimisation procedure, allowing for the model to capture not only ignition delays, but also the evolutions of representative intermediates and heat release rates for a variety of full boiling range fuels. Additionally, an extensive validation of the later evolutions by means of various detailed n-heptane reaction mechanisms from literature has been presented; both for perfectly homogeneous, as well as non-premixed/stratified HCCI conditions. Finally, the models potential to simulate the auto-ignition of various full boiling range fuels is demonstrated by means of experimental shock tube data for six strongly differing fuels, containing e.g. up to 46.7% cyclo-alkanes, 20% napthalenes or complex branched aromatics such as methyl- or ethyl-napthalene. The good predictive capability observed for each of the validation cases as well as the successful parameterisation for each of the six fuels, indicate that the model could, in principle, be applied to any hydrocarbon fuel, providing suitable adjustments to the model parameters are carried out. Combined with the optimisation strategy presented, the model therefore constitutes a major step towards the inclusion of real fuel kinetics into full scale HCCI engine simulations.

  17. An automatic modeling system of the reaction mechanisms for chemical vapor deposition processes using real-coded genetic algorithms.

    Science.gov (United States)

    Takahashi, Takahiro; Nakai, Hiroyuki; Kinpara, Hiroki; Ema, Yoshinori

    2011-09-01

    The identification of appropriate reaction models is very helpful for developing chemical vapor deposition (CVD) processes. In this study, we have developed an automatic system to model reaction mechanisms in the CVD processes by analyzing the experimental results, which are cross-sectional shapes of the deposited films on substrates with micrometer- or nanometer-sized trenches. We designed the inference engine to model the reaction mechanism in the system by the use of real-coded genetic algorithms (RCGAs). We studied the dependence of the system performance on two methods using simple genetic algorithms (SGAs) and the RCGAs; the one involves the conventional GA operators and the other involves the blend crossover operator (BLX-alpha). Although we demonstrated that the systems using both the methods could successfully model the reaction mechanisms, the RCGAs showed the better performance with respect to the accuracy and the calculation cost for identifying the models.

  18. Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations.

    Science.gov (United States)

    Shi, Qicun; Meroueh, Samy O; Fisher, Jed F; Mobashery, Shahriar

    2008-07-23

    Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2

  19. Theoretical Study of the Scattering Resonance State, Reaction Mechanism and Partial Potential Energy Surface of the F+CH4→HF +CH3 Reaction

    Institute of Scientific and Technical Information of China (English)

    Qiang WANG; Zheng Ting CAI; Da Cheng FENG

    2006-01-01

    The partial potential energy surface was constructed by ab initio method [QCISD(T)/6-311++G(2df,2pd)]for F+CH4→HF+CH3 reaction system. It not only explained the reaction mechanism brought forward by Diego Troya by means of quasiclassical trajectory (QCT) but also successfully validated Kopin Liu's experimental phenomena about the existence of the reactive resonance. The lifetime of the scattering resonance state was about 0.07 ps. All these were in agreement with the experiments.

  20. Kinetics and Mechanism of Deoxygenation Reactions over Proton-Form and Molybdenum-Modified Zeolite Catalysts

    Science.gov (United States)

    Bedard, Jeremy William

    The depletion of fossil fuel resources and the environmental consequences of their use have dictated the development of new sources of energy that are both sustainable and economical. Biomass has emerged as a renewable carbon feedstock that can be used to produce chemicals and fuels traditionally obtained from petroleum. The oxygen content of biomass prohibits its use without modification because oxygenated hydrocarbons are non-volatile and have lower energy content. Chemical processes that eliminate oxygen and keep the carbon backbone intact are required for the development of biomass as a viable chemical feedstock. This dissertation reports on the kinetic and mechanistic studies conducted on high and low temperature catalytic processes for deoxygenation of biomass precursors to produce high-value chemicals and fuels. Low temperature, steady state reaction studies of acetic acid and ethanol were used to identify co-adsorbed acetic acid/ethanol dimers as surface intermediates within specific elementary steps involved in the esterification of acetic acid with ethanol on zeolites. A reaction mechanism involving two dominating surface species, an inactive ethanol dimeric species adsorbed on Bronsted sites inhibiting ester formation and a co-adsorbed complex of acetic acid and ethanol on the active site reacting to produce ethyl acetate, is shown to describe the reaction rate as a function of temperature (323 -- 383 K), acetic acid (0.5 -- 6.0 kPa), and ethanol (5.0 -- 13.0 kPa) partial pressure on proton-form BEA, FER, MFI, and MOR zeolites. Measured differences in rates as a function of zeolite structure and the rigorous interpretation of these differences in terms of esterification rate and equilibrium constants is presented to show that the intrinsic rate constant for the activation of the co-adsorbed complex increases in the order FER carbon dioxide with methane (CH3COOH/CH4 = 0.04-0.10, HCOOH/CH 4 = 0.01-0.03, CO2/CH4 = 0.01-0.03) on Mo/H-ZSM-5 formulations at

  1. Kinetics and mechanisms of reactions between H2O2 and copper and copper oxides.

    Science.gov (United States)

    Björkbacka, Åsa; Yang, Miao; Gasparrini, Claudia; Leygraf, Christofer; Jonsson, Mats

    2015-09-28

    One of the main challenges for the nuclear power industry today is the disposal of spent nuclear fuel. One of the most developed methods for its long term storage is the Swedish KBS-3 concept where the spent fuel is sealed inside copper canisters and placed 500 meters down in the bedrock. Gamma radiation will penetrate the canisters and be absorbed by groundwater thereby creating oxidative radiolysis products such as hydrogen peroxide (H2O2) and hydroxyl radicals (HO˙). Both H2O2 and HO˙ are able to initiate corrosion of the copper canisters. In this work the kinetics and mechanism of reactions between the stable radiolysis product, H2O2, and copper and copper oxides were studied. Also the dissolution of copper into solution after reaction with H2O2 was monitored by ICP-OES. The experiments show that both H2O2 and HO˙ are present in the systems with copper and copper oxides. Nevertheless, these species do not appear to influence the dissolution of copper to the same extent as observed in recent studies in irradiated systems. This strongly suggests that aqueous radiolysis can only account for a very minor part of the observed radiation induced corrosion of copper.

  2. Atmospheric chemistry of benzyl alcohol: kinetics and mechanism of reaction with OH radicals.

    Science.gov (United States)

    Bernard, François; Magneron, Isabelle; Eyglunent, Grégory; Daële, Véronique; Wallington, Timothy J; Hurley, Michael D; Mellouki, Abdelwahid

    2013-04-02

    The atmospheric oxidation of benzyl alcohol has been investigated using smog chambers at ICARE, FORD, and EUPHORE. The rate coefficient for reaction with OH radicals was measured and an upper limit for the reaction with ozone was established; kOH = (2.8 ± 0.4) × 10(-11) at 297 ± 3 K (averaged value including results from Harrison and Wells) and kO(3) FTIR spectroscopy, HPLC-UV/FID, and GC-PID and quantified in a yield of (24 ± 5) %. Ring retaining products originating from OH-addition to the aromatic ring such as o-hydroxybenzylalcohol and o-dihydroxybenzene as well as ring-cleavage products such as glyoxal were also identified and quantified with molar yields of (22 ± 2)%, (10 ± 3)%, and (2.7 ± 0.7)%, respectively. Formaldehyde was observed with a molar yield of (27 ± 10)%. The results are discussed with respect to previous studies and the atmospheric oxidation mechanism of benzyl alcohol.

  3. Studies on adsorption, reaction mechanisms and kinetics for photocatalytic degradation of CHD, a pharmaceutical waste.

    Science.gov (United States)

    Sarkar, Santanu; Bhattacharjee, Chiranjib; Curcio, Stefano

    2015-11-01

    The photocatalytic degradation of chlorhexidine digluconate (CHD), a disinfectant and topical antiseptic and adsorption of CHD catalyst surface in dark condition has been studied. Moreover, the value of kinetic parameters has been measured and the effect of adsorption on photocatalysis has been investigated here. Substantial removal was observed during the photocatalysis process, whereas 40% removal was possible through the adsorption route on TiO2 surface. The parametric variation has shown that alkaline pH, ambient temperature, low initial substrate concentration, high TiO2 loading were favourable, though at a certain concentration of TiO2 loading, photocatalytic degradation efficiency was found to be maximum. The adsorption study has shown good confirmation with Langmuir isotherm and during the reaction at initial stage, it followed pseudo-first-order reaction, after that Langmuir Hinshelwood model was found to be appropriate in describing the system. The present study also confirmed that there is a significant effect of adsorption on photocatalytic degradation. The possible mechanism for adsorption and photocatalysis has been shown here and process controlling step has been identified. The influences of pH and temperature have been explained with the help of surface charge distribution of reacting particles and thermodynamic point of view respectively.

  4. Effects of alpha-amylase reaction mechanisms on analysis of resistant-starch contents.

    Science.gov (United States)

    Moore, Samuel A; Ai, Yongfeng; Chang, Fengdan; Jane, Jay-lin

    2015-01-22

    This study aimed to understand differences in the resistant starch (RS) contents of native and modified starches obtained using two standard methods of RS content analysis: AOAC Method 991.43 and 2002.02. The largest differences were observed in native potato starch, cross-linked wheat distarch phosphate, and high-amylose corn starch stearic-acid complex (RS5) between using AOAC Method 991.43 with Bacillus licheniformis α-amylase (BL) and AOAC Method 2002.02 with porcine pancreatic α-amylase (PPA). To determine possible reasons for these differences, we hydrolyzed raw-starch granules with BL and PPA with equal activity at pH 6.9 and 37°C for up to 84 h and observed the starch granules displayed distinct morphological differences after the hydrolysis. Starches hydrolyzed by BL showed erosion on the surface of the granules; those hydrolyzed by PPA showed pitting on granule surfaces. These results suggested that enzyme reaction mechanisms, including the sizes of the binding sites and the reaction patterns of the two enzymes, contributed to the differences in the RS contents obtained using different methods of RS analysis.

  5. Surface reaction mechanisms during ozone and oxygen plasma assisted atomic layer deposition of aluminum oxide.

    Science.gov (United States)

    Rai, Vikrant R; Vandalon, Vincent; Agarwal, Sumit

    2010-09-07

    We have elucidated the reaction mechanism and the role of the reactive intermediates in the atomic layer deposition (ALD) of aluminum oxide from trimethyl aluminum in conjunction with O(3) and an O(2) plasma. In situ attenuated total reflection Fourier transform infrared spectroscopy data show that both -OH groups and carbonates are formed on the surface during the oxidation cycle. These carbonates, once formed on the surface, are stable to prolonged O(3) exposure in the same cycle. However, in the case of plasma-assisted ALD, the carbonates decompose upon prolonged O(2) plasma exposure via a series reaction kinetics of the type, A (CH(3)) --> B (carbonates) --> C (Al(2)O(3)). The ratio of -OH groups to carbonates on the surface strongly depends on the oxidizing agent, and also the duration of the oxidation cycle in plasma-assisted ALD. However, in both O(3) and O(2) plasma cycles, carbonates are a small fraction of the total number of reactive sites compared to the hydroxyl groups.

  6. Reaction Mechanism and Distribution Behavior of Arsenic in the Bottom Blown Copper Smelting Process

    Directory of Open Access Journals (Sweden)

    Qinmeng Wang

    2017-08-01

    Full Text Available The control of arsenic, a toxic and carcinogenic element, is an important issue for all copper smelters. In this work, the reaction mechanism and distribution behavior of arsenic in the bottom blown copper smelting process (SKS process were investigated and compared to the flash smelting process. There are obvious differences of arsenic distribution in the SKS process and flash process, resulting from the differences of oxygen potentials, volatilizations, smelting temperatures, reaction intensities, and mass transfer processes. Under stable production conditions, the distributions of arsenic among matte, slag, and gas phases are 6%, 12%, and 82%, respectively. Less arsenic is reported in the gas phase with the flash process than with the SKS process. The main arsenic species in gas phase are AsS (g, AsO (g, and As2 (g. Arsenic exists in the slag predominantly as As2O3 (l, and in matte as As (l. High matte grade is harmful to the elimination of arsenic to gas. The changing of Fe/SiO2 has slight effects on the distributions of arsenic. In order to enhance the removal of arsenic from the SKS smelting system to the gas phase, low oxygen concentration, low ratios of oxygen/ore, and low matte grade should be chosen. In the SKS smelting process, no dust is recycled, and almost all dust is collected and further treated to eliminate arsenic and recover valuable metals by other process streams.

  7. Thermochemical reaction mechanism of lead oxide with poly(vinyl chloride) in waste thermal treatment.

    Science.gov (United States)

    Wang, Si-Jia; Zhang, Hua; Shao, Li-Ming; Liu, Shu-Meng; He, Pin-Jing

    2014-12-01

    Poly(vinyl chloride) (PVC) as a widely used plastic that can promote the volatilization of heavy metals during the thermal treatment of solid waste, thus leading to environmental problems of heavy metal contamination. In this study, thermogravimetric analysis (TGA) coupled with differential scanning calorimeter, TGA coupled with Fourier transform infrared spectroscopy and lab-scale tube furnace experiments were carried out with standard PVC and PbO to explicate the thermochemical reaction mechanism of PVC with semi-volatile lead. The results showed that PVC lost weight from 225 to 230°C under both air and nitrogen with an endothermic peak, and HCl and benzene release were also detected. When PbO was present, HCl that decomposed from PVC instantly reacted with PbO via an exothermal gas-solid reaction. The product was solid-state PbCl2 at 501°C, PbCl2 melted, volatilized and transferred into flue gas or condensed into fly ash. Almost all PbCl2 volatilized above 900°C, while PbO just started to volatilize slowly at this temperature. Therefore, the chlorination effect of PVC on lead was apt to lower-temperature and rapid. Without oxygen, Pb2O was generated due to the deoxidizing by carbon, with oxygen, the amount of residual Pb in the bottom ash was significantly decreased.

  8. Density functional theory investigations on sulfur ylide promoted cyclopropanation reactions: insights on mechanism and diastereoselection issues.

    Science.gov (United States)

    Janardanan, Deepa; Sunoj, Raghavan B

    2007-01-19

    The mechanism and diastereoselectivity of synthetically useful sulfur ylide promoted cyclopropanation reactions have been studied using the density functional theory method. Addition of different substituted ylides (Me2S+CH-R) to enone ((E)-pent-3-en-2-one, MeHC=CH-COMe) has been investigated. The nature of the substituent on the ylidic carbon brings about subtle changes in the reaction profile. The stabilized (R=COMe) and semistabilized (R=Ph) ylides follow a cisoid addition mode, leading to 1,2-trans and 1,2-cis cyclopropanes, respectively, via syn and anti betaine intermediates. The simplest and highly reactive model ylide (R=H) prefers a transoid addition mode. Diastereoselectivity is controlled by the barrier for cisoid-transoid rotation in the case of stabilized ylides, whereas the initial electrophilic addition is found to be the diastereoselectivity-determining step for semistabilized ylides. High selectivity toward trans cyclopropanes with stabilized ylides are predicted on the basis of the relative activation energies of diastereomeric torsional transition states. The energy differences between these transition states could be rationalized with the help of weak intramolecular as well as other stereoelectronic interactions.

  9. Temperature perturbations evolution as a possible mechanism of exothermal reaction kernels formation in shock tubes

    Science.gov (United States)

    Drakon, A. V.; Kiverin, A. D.; Yakovenko, I. S.

    2016-11-01

    The basic question raised in the paper concerns the origins of exothermal reaction kernels and the mechanisms of detonation onset behind the reflected shock wave in shock-tube experiments. Using the conventional experimental technique, it is obtained that in the certain diapason of conditions behind the reflected shocks a so-called “mild ignition” arises which is characterized by the detonation formation from the kernel distant from the end-wall. The results of 2-D and 3-D simulations of the flow evolution behind the incident and reflected shocks allow formulation of the following scenario of ignition kernels formation. Initial stage during and after the diaphragm rupture is characterized by a set of non-steady gasdynamical processes. As a result, the flow behind the incident shock occurs to be saturated with temperature perturbations. Further evolution of these perturbations provides generating of the shear stresses in the flow accompanied with intensification of velocity and temperature perturbations. After reflection the shock wave interacts with the formed kernels of higher temperature and more pronounced kernels arise on the background of reactivity profile determined by moving reflected shock. Exothermal reaction starts inside such kernels and propagates into the ambient medium as a spontaneous ignition wave with minimum initial speed equal to the reflected shock wave speed.

  10. Structure-Based Mechanism for Early PLP-Mediated Steps of Rabbit Cytosolic Serine Hydroxymethyltransferase Reaction

    Directory of Open Access Journals (Sweden)

    Martino L. Di Salvo

    2013-01-01

    Full Text Available Serine hydroxymethyltransferase catalyzes the reversible interconversion of L-serine and glycine with transfer of one-carbon groups to and from tetrahydrofolate. Active site residue Thr254 is known to be involved in the transaldimination reaction, a crucial step in the catalytic mechanism of all pyridoxal 5′-phosphate- (PLP- dependent enzymes, which determines binding of substrates and release of products. In order to better understand the role of Thr254, we have expressed, characterized, and determined the crystal structures of rabbit cytosolic serine hydroxymethyltransferase T254A and T254C mutant forms, in the absence and presence of substrates. These mutants accumulate a kinetically stable gem-diamine intermediate, and their crystal structures show differences in the active site with respect to wild type. The kinetic and crystallographic data acquired with mutant enzymes permit us to infer that conversion of gem-diamine to external aldimine is significantly slowed because intermediates are trapped into an anomalous position by a misorientation of the PLP ring, and a new energy barrier hampers the transaldimination reaction. This barrier likely arises from the loss of the stabilizing hydrogen bond between the hydroxymethyl group of Thr254 and the ε-amino group of active site Lys257, which stabilizes the external aldimine intermediate in wild type SHMTs.

  11. [Regional graft vs host reaction to H-Y antigen (immunological mechanisms)].

    Science.gov (United States)

    Volkova, L V; Verbitskiĭ, M Sh; Sapin, M R; Aminova, G G; Rusina, A K

    1987-08-01

    Structural changes in the regional popliteal lymph nodes have been studied in C57Bl/6 male mice at the peak of the reaction "graft-versus-host" to H-Y antigen. Morphological and morphometrical investigations have been carried out in three groups of males (10 animals in each group). The first group includes intact animals (the first control group). To the males of the second group (the second control group) lymphoid cells are inoculated from intact C57Bl/6 females. To the males of the third group (experimental group) lymphoid cells are inoculated from H-Y antigen immunized C57Bl/6 females (anti-H-Y effector lymphocytes). The popliteal lymph nodes of the male mice from the third group twice increase in their size comparing to those in the control (the first and the second groups). Miotic activity increases in them 4.5 times, amount of cellular blast forms in medullary cords--4 times and 10 times--in the light zone of the cortical substance. Ratio of macrophages and eosinophils in structural components of the lymph nodes studied changes; this is, evidently, connected with massive destructive progresses, that take place in the lymph nodes of the animals from the third group. The results of the morphological investigations are in agreement with the hypothesis suggested, explaining the mechanism of development of the regional reaction "graft-versus-host" to H-Y antigen, basing on idiotype-antiidiotype interaction (the idiotypic network in the immune system).

  12. Nanostructured Materials for Heterogeneous Electrocatalytic CO2 Reduction and Related Reaction Mechanisms.

    Science.gov (United States)

    Gong, Jinlong; Zhang, Lei; Zhao, Zhi-Jian

    2017-02-06

    The gradually increased concentration of carbon dioxide (CO2) in the atmosphere has been recognized as the primary culprit for the raise of the global mean temperature, thus resulting in the aggravated desert formation and extinction of species. In recent years, development of the routes for highly efficient conversion of CO2 has received numerous attentions. Among them, the reduction of CO2 with electric power is an important transformation route with high application prospect, due to its high environmental compatibility and good combination with other renewable energy sources such as solar and wind energy. This review describes recent progress on the design and synthesis of solid state catalysts (i.e., heterogeneous catalysts) and their emerging catalytic performances in the CO2 reduction. The significance for catalytic conversion of CO2 and the advantages of CO2 electroreduction will be presented in the introduction section, followed by the general parameters for CO2 electroreduction and the summary of reaction apparatus. We also discuss various types of solid catalysts according to CO2 conversion mechanisms. Furthermore, we summarize the crucial factors (particle size, surface structure, composition and etc.) determining the performance for electroreduction. These studies in improvement of solid state catalysts for CO2 reduction offer numerous experiences for developing potential industrialized CO2 electroreduction catalysts in the future. Additionally, the abundant experience for controllable synthesis of solid state catalysts could effectively guide the rational design of catalysts for other electrocatalytic reactions.

  13. Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

    Institute of Scientific and Technical Information of China (English)

    侯若冰; 陈志达; 义祥辉; 卞江; 徐光宪

    2000-01-01

    Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR+ are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,

  14. Understanding the charge/discharge mechanisms and passivation reactions in Na-O2 batteries

    Science.gov (United States)

    Landa-Medrano, Imanol; Frith, James T.; Ruiz de Larramendi, Idoia; Lozano, Iñigo; Ortiz-Vitoriano, Nagore; Garcia-Araez, Nuria; Rojo, Teófilo

    2017-03-01

    Sodium-oxygen batteries are becoming of increasing interest in the research community as they are able to overcome some of the difficulties associated with lithium-oxygen batteries. The interpretation of the processes governing the discharge and charge of these batteries, however, has been under debate since their early development. In this work we combine different electrochemical methods to build up a model of the discharge product formation and decomposition. We initially analyze the formation and decomposition of the discharge products by means of electrochemical impedance spectroscopy. After that, and for the first time, oxygen electrode processes in Na-O2 cells are analyzed by means of electrochemical quartz crystal microbalance experiments. Based on the combination of these two techniques it is possible to evidence the stabilization of the discharge products in the electrolyte prior to their precipitation. The deposition of passivating products that cannot be stripped off during charge is also demonstrated. Cyclic voltammetry experiments at different potential limits further confirm these passivation reactions. In conclusion, this work provides an accurate picture of the mechanism of the Na-O2 cell reactions by combining different electrochemical techniques.

  15. Anode reaction mechanism and crossover in direct dimethyl ether fuel cell

    Science.gov (United States)

    Mizutani, Itsuko; Liu, Yan; Mitsushima, Shigenori; Ota, Ken-ichiro; Kamiya, Nobuyuki

    The anode reaction mechanism and the crossover of a direct dimethyl ether fuel cell (DDMEFC) have been investigated. This was done by considering the anode products of the half-cell and DDMEFC experiments. It was found that the CO 2 current efficiency of the DDMEFC was almost 1 at 30-80 °C and that this value was higher than that of a DMFC. The main by-products of the DDMEFC were methyl formate and methanol whose amounts are negligibly small compared to CO 2. With respect to crossover, the influence of DME on the oxygen reduction reaction (ORR) was examined with a half-cell, and the amount of crossover of DME was measured while operating an actually constructed DDMEFC. From these experiments, it was found that DME does not influence the ORR as much as methanol under similar conditions. Furthermore, the amount of crossover of DME decreased with an increase in temperature and current density and it was one-half that of methanol on open circuit and at 80 °C. The CO 2 current efficiency of the DDMEFC is higher than that of a DMFC, and the influence of crossover in the DDMEFC is less than that in the DMFC. Since the temperature dependence of the reactivity of DME is larger than that of methanol, the higher output is expected for the DDMEFC at the elevated temperature. Therefore, the DDMEFC has a promising potential as a portable power source in the future.

  16. Studies on the Reaction Mechanism of CPP and the Factors Affecting the Yields of Ethylene and Propylene

    Institute of Scientific and Technical Information of China (English)

    HouDianguo; WangXieqing; 等

    2002-01-01

    The reaction mechanisms of Catalytic Pyrolysis Process and the ethylene and propylene forma-tion reaction are analyzed,and ethylene and propylene are produced through both the free radical reac-tion and carbenium ion reaction.The factors affecting the yields of ethylene and propylene are discussed.The results showed that greater yields of ethylene and propylene can be obtained on ZSM-5 catalysts rather than USY and REY catalysts,and the modified ZSM-5 could improve the ethylene yield.A higher temperature is favorable for enhancement of the free radical reaction as opposed to carbenium ion reaction,and change in temperature can adjust the ratio of ethylene and propylene production.A higher steam amount could produce more ethylene and propylene and less coke,and lowering the catalyst/oil ratio is favorable for producing ethylene.

  17. Studies on the Reaction Mechanism of CPP and the Factors Affecting the Yields of Ethylene and Propylene

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The reaction mechanisms of Catalytic Pyrolysis Process and the ethylene and propylene forma-tion reaction are analyzed, and ethylene and propylene are produced through both the free radical reac-tion and carbenium ion reaction. The factors affecting the yields of ethylene and propylene are discussed.The results showed that greater yields of ethylene and propylene can be obtained on ZSM-5 catalystsrather than USY and REY catalysts, and the modified ZSM-5 could improve the ethylene yield. A highertemperature is favorable for enhancement of the free radical reaction as opposed to carbenium ion reaction,and change in temperature can adjust the ratio of ethylene and propylene production. A higher steamamount could produce more ethylene and propylene and less coke, and lowering the catalyst/oil ratio isfavorable for producing ethylene.

  18. Studies on the Reaction Mechanism of CPP and the Factors Affecting the Yields of Ethylene and Propylene

    Institute of Scientific and Technical Information of China (English)

    Hou Dianguo; Wang Xieqing; Xie Chaogang; Shi Zhicheng

    2002-01-01

    The reaction mechanisms of Catalytic Pyrolysis Process and theethylene and propylene forma-tion reaction are analyzed, and ethylene and propylene are produced through both the free radical reac-tion and carbenium ion reaction. The factors affecting the yields of ethylene and propylene are discussed.The results showed that greater yields of ethylene and propylene can be obtained on ZSM-5 catalystsrather than USY and REY catalysts, and the modified ZSM-5 could improve the ethylene yield. A highertemperature is favorable for enhancement of the free radical reaction as opposed to carbenium ion reaction,and change in temperature can adjust the ratio of ethylene and propylene production. A higher steamamount could produce more ethylene and propylene and less coke, and lowering the catalyst/oil ratio isfavorable for producing ethylene.

  19. NATO Advanced Research Workshop on the Mechanisms of Reactions of Organometallic Compounds with Surfaces

    CERN Document Server

    Williams, J

    1989-01-01

    A NATO Advanced Research Workshop on the "Mechanisms of Reactions of Organometallic Compounds with Surfaces" was held in St. Andrews, Scotland in June 1988. Many of the leading international researchers in this area were present at the workshop and all made oral presentations of their results. In addition, significant amounts of time were set aside for Round Table discussions, in which smaller groups considered the current status of mechanistic knowledge, identified areas of dispute or disagreement, and proposed experiments that need to be carried out to resolve such disputes so as to advance our understanding of this important research area. All the papers presented at the workshop are collected in this volume, together with summaries of the conclusions reached at the Round Table discussions. The workshop could not have taken place without financial support from NATO, and donations were also received from Associated Octel, Ltd., STC Ltd., and Epichem Ltd., for which the organisers are very grateful. The orga...

  20. Reaction mechanisms in the organometallic vapor phase epitaxial growth of GaAs

    Science.gov (United States)

    Larsen, C. A.; Buchan, N. I.; Stringfellow, G. B.

    1988-01-01

    The decomposition mechanisms of AsH3, trimethylgallium (TMGa), and mixtures of the two have been studied in an atmospheric-pressure flow system with the use of D2 to label the reaction products which are analyzed in a time-of-flight mass spectrometer. AsH3 decomposes entirely heterogeneously to give H2. TMGa decomposes by a series of gas-phase steps, involving methyl radicals and D atoms to produce CH3D, CH4, C2H6, and HD. TMGa decomposition is accelerated by the presence of AsH3. When the two are mixed, as in the organometallic vapor phase epitaxial growth of GaAs, both compounds decompose in concert to produce only CH4. A likely model is that of a Lewis acid-base adduct that forms and subsequently eliminates CH4.

  1. Structrue and Characteristics of Mesoporous Silica Synthesized in Acid Medium and Its Reaction Mechanism

    Institute of Scientific and Technical Information of China (English)

    LEI Jia-heng; ZHAO Jun; CHEN Yong-xi; GUO Li-ping; LIU Dan

    2004-01-01

    Structrue and pore characteristics of the mesoporous silica synthesized in acid medium were studied by means of XRD, HRTEM, BET, FT-IR, DSC-TGA, and the reaction mechanism was also investigated deeply. The results show that mesopores in the sample possess hexagonal arrays obviously, whereas the structure of silica matrix is amorphous. The results also show that the acting mode of silica and CTMA+ inside the mesopores was chemical bonding force. The structure of mesoporous silica was mainly dependent on the aggregational condition of micelle of CTMA+ as well as their liquid-crystallized status. In addition, condensation and dehydration of silicate radicals were accompanied in the process of calcination, which resulted in the mesoporous structure ordered in local range and the pore sizes largening.

  2. Mechanism of arylboronic acid-catalyzed amidation reaction between carboxylic acids and amines.

    Science.gov (United States)

    Wang, Chen; Yu, Hai-Zhu; Fu, Yao; Guo, Qing-Xiang

    2013-04-07

    Arylboronic acids were found to be efficient catalysts for the amidation reactions between carboxylic acids and amines. Theoretical calculations have been carried out to investigate the mechanism of this catalytic process. It is found that the formation of the acyloxyboronic acid intermediates from the carboxylic acid and the arylboronic acid is kinetically facile but thermodynamically unfavorable. Removal of water (as experimentally accomplished by using molecular sieves) is therefore essential for overall transformation. Subsequently C-N bond formation between the acyloxyboronic acid intermediates and the amine occurs readily to generate the desired amide product. The cleavage of the C-O bond of the tetracoordinate acyl boronate intermediates is the rate-determining step in this process. Our analysis indicates that the mono(acyloxy)boronic acid is the key intermediate. The high catalytic activity of ortho-iodophenylboronic acid is attributed to the steric effect as well as the orbital interaction between the iodine atom and the boron atom.

  3. A New Reforming Reaction Mechanism of Carbon Dioxide with Methane on Nano Scale Nickel catalyst

    Directory of Open Access Journals (Sweden)

    Long Wei

    2016-01-01

    Full Text Available The reforming mechanism of CO2-CH4 on Nano scale Ni metal catalyst was investigated using the B3LYP density functional method and MP2/Lanl2dz method. It was found that the reaction include thirteen steps and the activation energy of each step was 44.7175, 200.4707, 171.0781, 307.2596, 124.5252, 330.7904, 593.9056, 177.5526, 226.6793, 277.789 2, 394.5525,399.5340 and 105.4115 kJ·mol−1. The rate determining step was the fourth step. The enthalpy value of each step was 31.6136, 106.7138, −104.2589, 79.9641, 93.5573,174.6 121, 259.6409, −141.9192, −439.9338, −265.4756, −208.3245, 131.6561 and −86.1765 kJ·mol−1.

  4. Alkene cleavage catalysed by heme and nonheme enzymes: reaction mechanisms and biocatalytic applications.

    Science.gov (United States)

    Mutti, Francesco G

    2012-01-01

    The oxidative cleavage of alkenes is classically performed by chemical methods, although they display several drawbacks. Ozonolysis requires harsh conditions (-78°C, for a safe process) and reducing reagents in a molar amount, whereas the use of poisonous heavy metals such as Cr, Os, or Ru as catalysts is additionally plagued by low yield and selectivity. Conversely, heme and nonheme enzymes can catalyse the oxidative alkene cleavage at ambient temperature and atmospheric pressure in an aqueous buffer, showing excellent chemo- and regioselectivities in certain cases. This paper focuses on the alkene cleavage catalysed by iron cofactor-dependent enzymes encompassing the reaction mechanisms (in case where it is known) and the application of these enzymes in biocatalysis.

  5. Point-source idealization in classical field theories. II. Mechanical energy losses from electromagnetic radiation reaction

    Science.gov (United States)

    Kates, Ronald E.; Rosenblum, Arnold

    1982-05-01

    This paper compares the mechanical energy losses due to electromagnetic radiation reaction on a two-particle, slow-motion system, as calculated from (1) the method of matched asymptotic expansions and (2) the Lorentz-Dirac equation, which assumes point sources. The matching derivation of the preceding paper avoided the assumption of a δ-function source by using Reissner-Nordström matching zones. Despite the differing mathematical assumptions of the two methods, their results are in agreement with each other and with the electromagnetic-field energy losses calculated by the evaluation of flux integrals. Our purpose is eventually to analyze Rosenblum's use of point sources as a possible cause of disagreement between the analogous calculations of gravitational radiation on a slow-motion system of two bodies. We begin with the simpler electromagnetic problem.

  6. The mechanism of bursting phenomena in Belousov-Zhabotinsky(BZ) chemical reaction with multiple time scales

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The dynamics of a typical Belousov-Zhabotinsky(BZ)reaction with multiple time scales is investigated in this paper.Different forms of periodic bursting phenomena,and specially,three types of chaotic bursters with different structures can be obtained,which are in common with the behaviors observed in experiments.The bifurcations connecting the quiescent state and the repetitive spikes are presented to account for the occurrence of the NKoscillations as well as the different forms of chaotic bursters.The mechanism of the period-adding bifurcation sequences is explored to reveal why the length of the periods in the sequences does not change continuously with the continuous variation of the parameters.

  7. Study on reaction mechanism of low temperature preparation of nanocrystalline LaCoO3-λ

    Institute of Scientific and Technical Information of China (English)

    SHEN Haiyun; YANG Qiuhua; LI Ning

    2008-01-01

    Perovskite-type oxide nanocrystalline LaCoO3-λ was prepared using the citrate method.The structure and morphology of the sam-pies were characterized by powder X-ray diffraction (XRD) and transmission electron microscopy (TEM).The intermediate products were analyzed by thermal gravimetric and differential thermal analysis (TG-DTA) technology.The results showed that nanocrystaUine LaCoO3-λwith a granula of 30-50 nm had a cubic perovskite structure.The reaction mechanism of low temperature preparation was suggested as fol-lows:the metal complex was first formed by the combination of metal ion and citric acid;and then it decomposed into an aconitie acid com-plex, followed by an oxycarbonate,and finally a perovskite-type oxide.

  8. Mechanism of electron transfer reaction for xanthene dye-sensitized formation of methyl viologen radical

    Energy Technology Data Exchange (ETDEWEB)

    Usui, Y.; Misawa, H.; Sakuragi, H.; Tokumaru, K.

    1987-05-01

    Sensitized reduction of methyl viologen, MV/sup 2 +/, occurs efficiently through electron transfer from triplet xanthene dyes to MV/sup 2 +/ followed by electron transfer to the resulting semioxidized dyes from a reductant like triethanolamine. Unreactive ion pair complexes between these dyes and MV/sup 2 +/ are formed (formation constant: 1.2 x 10/sup 3/ M/sup -1/ for Eosine Y and MV/sup 2 +/ in 50% aqueous ethanol solution). The quantum yield for the reduced methyl viologen radical depends on the concentrations of MV/sup 2 +/ and the amine and on the ionic strength of solution. The efficiency of the electron transfer from triplet dyes to MV/sup 2 +/ is increased by addition of alcohol, and solvent effects on the reaction mechanism are discussed. 38 references, 5 figures, 2 tables.

  9. Further study on mechanism of production of light complex particles in nucleon-induced reactions

    CERN Document Server

    Wei, Dexian; Wang, Ning; Liu, Min; Ou, Li

    2015-01-01

    The Improved Quantum Molecular Dynamics (ImQMD) model incorporated with the statistical decay model is used to investigate the intermediate energy nucleon-induced reactions. In our last work, the description on light complex particle emission has been great improved with a phenomenological mechanism called surface coalescence and emission introduced into ImQMD model. In this work, taking account of different specific binding energies and separation energies for various light complex particles, the phase space parameters in surface coalescence model are readjusted. By using the new phase space parameters set with better physical fundament, the double differential cross sections of emitted light complex particles are found to be in better agreement with experimental data.

  10. A reaction-diffusion-based coding rate control mechanism for camera sensor networks.

    Science.gov (United States)

    Yamamoto, Hiroshi; Hyodo, Katsuya; Wakamiya, Naoki; Murata, Masayuki

    2010-01-01

    A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal.

  11. Implicit coupling of turbulent diffusion with chemical reaction mechanisms for prognostic atmospheric dispersion models

    Energy Technology Data Exchange (ETDEWEB)

    Berlowitz, D.R.

    1996-11-01

    In the last few decades the negative impact by humans on the thin atmospheric layer enveloping the earth, the basis for life on this planet, has increased steadily. In order to halt, or at least slow down this development, the knowledge and study of these anthropogenic influence has to be increased and possible remedies have to be suggested. An important tool for these studies are computer models. With their help the atmospheric system can be approximated and the various processes, which have led to the current situation can be quantified. They also serve as an instrument to assess short or medium term strategies to reduce this human impact. However, to assure efficiency as well as accuracy, a careful analysis of the numerous processes involved in the dispersion of pollutants in the atmosphere is called for. This should help to concentrate on the essentials and also prevent excessive usage of sometimes scarce computing resources. The basis of the presented work is the EUMAC Zooming Model (ETM), and particularly the component calculating the dispersion of pollutants in the atmosphere, the model MARS. The model has two main parts: an explicit solver, where the advection and the horizontal diffusion of pollutants are calculated, and an implicit solution mechanism, allowing the joint computation of the change of concentration due to chemical reactions, coupled with the respective influence of the vertical diffusion of the species. The aim of this thesis is to determine particularly the influence of the horizontal components of the turbulent diffusion on the existing implicit solver of the model. Suggestions for a more comprehensive inclusion of the full three dimensional diffusion operator in the implicit solver are made. This is achieved by an appropriate operator splitting. A selection of numerical approaches to tighten the coupling of the diffusion processes with the calculation of the applied chemical reaction mechanisms are examined. (author) figs., tabs., refs.

  12. Mechanism of coupling drug transport reactions located in two different membranes

    Directory of Open Access Journals (Sweden)

    Helen I. Zgurskaya

    2015-02-01

    Full Text Available Gram- negative bacteria utilize a diverse array of multidrug transporters to pump toxic compounds out of cells. Some transporters together with periplasmic membrane fusion proteins (MFPs and outer membrane channels assemble trans-envelope complexes that expel multiple antibiotics across outer membranes of Gram-negative bacteria and into the external medium. Others further potentiate this efflux by pumping drugs across the inner membrane into the periplasm. Together these transporters create a powerful network of efflux that protect bacteria against a broad range of antimicrobial agents. This review is focused on the mechanism of coupling transport reactions located in two different membranes of Gram-negative bacteria. Using a combination of biochemical, genetic and biophysical approaches we have reconstructed the sequence of events leading to the assembly of trans-envelope drug efflux complexes and characterized the roles of periplasmic and outer membrane proteins in this process. Our recent data suggest a critical step in the activation of intermembrane efflux pumps, which is controlled by MFPs. We propose that the reaction cycles of transporters are tightly coupled to the assembly of the trans-envelope complexes. Transporters and MFPs exist in the inner membrane as dormant complexes. The activation of complexes is triggered by MFP binding to the outer membrane channel, which leads to a conformational change in the membrane proximal domain of MFP needed for stimulation of transporters. The activated MFP-transporter complex engages the outer membrane channel to expel substrates across the outer membrane. The recruitment of the channel is likely triggered by binding of effectors (substrates to MFP or MFP-transporter complexes. This model together with recent structural and functional advances in the field of drug efflux provides a fairly detailed understanding of the mechanism of drug efflux across the two membranes.

  13. Probing the reaction mechanism of IspH protein by x-ray structure analysis

    KAUST Repository

    Gräwert, Tobias

    2009-12-28

    Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovereddeoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl- 2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PPi reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of Lewis-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the β-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP).

  14. Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods.

    Science.gov (United States)

    Maeda, Satoshi; Ohno, Koichi; Morokuma, Keiji

    2013-03-21

    Global reaction route mapping (GRRM), a fully-automated search for all important reaction pathways relevant to a given purpose, on the basis of quantum chemical calculations enables systematic elucidation of complex chemical reaction mechanisms. However, GRRM had previously been limited to very simple systems. This is mainly because such calculations are highly demanding even in small systems when a brute-force sampling is considered. Hence, we have developed two independent but complementary methods: anharmonic downward distortion following (ADDF) and artificial force induced reaction (AFIR) methods. ADDF can follow reaction pathways starting from local minima on the potential energy surface (PES) toward transition structures (TSs) and dissociation channels. AFIR can find pathways starting from two or more reactants toward TSs for their associative reactions. In other words, ADDF searches for A → X type isomerization and A → X + Y type dissociation pathways, whereas AFIR finds A + B → X (+ Y) type associative pathways. Both follow special paths called the ADDF path and the AFIR path, and these tend to pass through near TSs of corresponding reaction pathways, giving approximate TSs. Such approximate TSs can easily be re-optimized to corresponding true TSs by standard geometry optimizations. On the basis of these two methods, we have proposed practical strategies of GRRM. The GRRM strategies have been applied to a variety of chemical systems ranging from thermal- and photochemical-reactions in small systems to organometallic- and enzyme-catalysis, on the basis of quantum chemical calculations. In this perspective, we present an overview of the GRRM strategies and some results of applications. Their practical usage for systematic prediction is also discussed.

  15. Isospin transport and reaction mechanism in nuclear reactions in the range 20–40 MeV/n

    Energy Technology Data Exchange (ETDEWEB)

    Barlini, S., E-mail: barlini@fi.infn.it; Piantelli, S.; Casini, G.; Olmi, A.; Bini, M.; Pasquali, G.; Poggi, G.; Stefanini, A. A.; Valdré, S.; Pastore, G. [Dipartimento di Fisica ed Astronomia dell’Università and INFN Sezione di Firenze, Firenze (Italy); Bougault, R.; Lopez, O.; Le Neindre, N.; Parlog, M.; Vient, E. [LPC, IN2P3-CNRS, ENSICAEN et Université de Caen, F-14050 Caen-Cedex (France); Bonnet, E.; Chibhi, A.; Frankland, J. D. [GANIL, CEA/DSM-CNRS/IN2P3, B.P.5027, F-14076 Caen cedex (France); Borderie, B.; Rivet, M. F. [Institut de Physique Nucléaire, CNRS/IN2P3, Université Paris-Sud 11, F-91406 Orsay cedex (France); and others

    2015-10-15

    In recent years, many efforts have been devoted to the investigation of the isospin degree of freedom in nuclear reactions. Comparing systems involving partners with different N/Z, it has been possible to investigate the isospin transport process and its influence on the final products population. This can be then related to the symmetry energy term of the nuclear EOS. From the experimental point of view, this task requires detectors able to measure both charge and mass of the emitted products, in the widest possible range of energy and size of the fragments. With this objective, the FAZIA and GARFIELD+RCo apparatus have been used with success in some recent experiments.

  16. Isospin transport and reaction mechanism in nuclear reactions in the range 20-40 MeV/n

    Science.gov (United States)

    Barlini, S.; Piantelli, S.; Casini, G.; Olmi, A.; Bini, M.; Pasquali, G.; Poggi, G.; Stefanini, A. A.; Bougault, R.; Bonnet, E.; Borderie, B.; Chibhi, A.; Frankland, J. D.; Gruyer, D.; Lopez, O.; Le Neindre, N.; Parlog, M.; Rivet, M. F.; Vient, E.; Rosato, E.; Vigilante, M.; Bruno, M.; Marchi, T.; Morelli, L.; Cinausero, M.; Degerlier, M.; Gramegna, F.; Kozik, T.; Twarog, T.; Fabris, D.; Valdré, S.; Pastore, G.

    2015-10-01

    In recent years, many efforts have been devoted to the investigation of the isospin degree of freedom in nuclear reactions. Comparing systems involving partners with different N/Z, it has been possible to investigate the isospin transport process and its influence on the final products population. This can be then related to the symmetry energy term of the nuclear EOS. From the experimental point of view, this task requires detectors able to measure both charge and mass of the emitted products, in the widest possible range of energy and size of the fragments. With this objective, the FAZIA and GARFIELD+RCo apparatus have been used with success in some recent experiments.

  17. Conversion Reaction Mechanisms in Lithium Ion Batteries: Study of the Binary Metal Fluoride Electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Feng; Robert, Rosa; Chernova, Natasha A.; Pereira, Nathalie; Omenya, Fredrick; Badway, Fadwa; Hua, Xiao; Ruotolo, Michael; Zhang, Ruigang; Wu, Lijun; Volkov, Vyacheslav; Su, Dong; Key, Baris; Whittingham, M. Stanley; Grey, Clare P.; Amatucci, Glenn G.; Zhu, Yimei; Graetz, Jason (Binghamton); (Rutgers); (BNL); (Cambridge); (SBU)

    2015-10-15

    Materials that undergo a conversion reaction with lithium (e.g., metal fluorides MF{sub 2}: M = Fe, Cu, ...) often accommodate more than one Li atom per transition-metal cation, and are promising candidates for high-capacity cathodes for lithium ion batteries. However, little is known about the mechanisms involved in the conversion process, the origins of the large polarization during electrochemical cycling, and why some materials are reversible (e.g., FeF{sub 2}) while others are not (e.g., CuF{sub 2}). In this study, we investigated the conversion reaction of binary metal fluorides, FeF{sub 2} and CuF{sub 2}, using a series of local and bulk probes to better understand the mechanisms underlying their contrasting electrochemical behavior. X-ray pair-distribution-function and magnetization measurements were used to determine changes in short-range ordering, particle size and microstructure, while high-resolution transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS) were used to measure the atomic-level structure of individual particles and map the phase distribution in the initial and fully lithiated electrodes. Both FeF{sub 2} and CuF{sub 2} react with lithium via a direct conversion process with no intercalation step, but there are differences in the conversion process and final phase distribution. During the reaction of Li{sup +} with FeF{sub 2}, small metallic iron nanoparticles (<5 nm in diameter) nucleate in close proximity to the converted LiF phase, as a result of the low diffusivity of iron. The iron nanoparticles are interconnected and form a bicontinuous network, which provides a pathway for local electron transport through the insulating LiF phase. In addition, the massive interface formed between nanoscale solid phases provides a pathway for ionic transport during the conversion process. These results offer the first experimental evidence explaining the origins of the high lithium reversibility in FeF{sub 2}. In contrast

  18. A Detailed Chemical Kinetic Reaction Mechanism for Oxidation of Four Small Alkyl Esters in Laminar Premixed Flames

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C K; Pitz, W J; Westmoreland, P R; Dryer, F L; Chaos, M; Osswald, P; Kohse-Hoinghaus, K; Cool, T A; Wang, J; Yang, B; Hansen, N; Kasper, T

    2008-02-08

    A detailed chemical kinetic reaction mechanism has been developed for a group of four small alkyl ester fuels, consisting of methyl formate, methyl acetate, ethyl formate and ethyl acetate. This mechanism is validated by comparisons between computed results and recently measured intermediate species mole fractions in fuel-rich, low pressure, premixed laminar flames. The model development employs a principle of similarity of functional groups in constraining the H atom abstraction and unimolecular decomposition reactions in each of these fuels. As a result, the reaction mechanism and formalism for mechanism development are suitable for extension to larger oxygenated hydrocarbon fuels, together with an improved kinetic understanding of the structure and chemical kinetics of alkyl ester fuels that can be extended to biodiesel fuels. Variations in concentrations of intermediate species levels in these flames are traced to differences in the molecular structure of the fuel molecules.

  19. Magnetic isotope effect and theory of atomic orbital hybridization to predict a mechanism of chemical exchange reactions.

    Science.gov (United States)

    Epov, Vladimir N

    2011-08-07

    A novel approach is suggested to investigate the mechanisms of chemical complexation reactions based on the results of Fujii with co-workers; they have experimentally observed that several metals and metalloids demonstrate mass-independent isotope fractionation during the reactions with the DC18C6 crown ether using solvent-solvent extraction. In this manuscript, the isotope fractionation caused by the magnetic isotope effect is used to understand the mechanisms of chemical exchange reactions. Due to the rule that reactions are allowed for certain electron spin states, and forbidden for others, magnetic isotopes show chemical anomalies during these reactions. Mass-independent fractionation is suggested to take place due to the hyperfine interaction of the nuclear spin with the electron spin of the intermediate product. Moreover, the sign of the mass-independent fractionation is found to be dependent on the element and its species, which is also explained by the magnetic isotope effect. For example, highly negative mass-independent isotope fractionation of magnetic isotopes was observed for reactions of DC18C6 with SnCl(2) species and with several Ru(III) chloro-species, and highly positive for reactions of this ether with TeCl(6)(2-), and with several Cd(II) and Pd(II) species. The atomic radius of an element is also a critical parameter for the reaction with crown ether, particularly the element ions with [Kr]4d(n)5s(m) electron shell fits the best with the DC18C6 crown ring. It is demonstrated that the magnetic isotope effect in combination with the theory of orbital hybridization can help to understand the mechanism of complexation reactions. The suggested approach is also applied to explain previously published mass-independent fractionation of Hg isotopes in other types of chemical exchange reactions.

  20. Kinetics and mechanism of the chain reaction between N-phenyl-1,4-benzoquinone monoimine and thiophenol

    Science.gov (United States)

    Varlamov, V. T.; Gadomsky, S. Ya.

    2017-05-01

    The kinetics of the reaction between N-phenyl-1,4-benzoquinone monoimine (quinone monoimine) and thiophenol is studied in chlorobenzene at 343 K. The reaction has the same mechanism proposed earlier for a similar reaction involving N,N'-diphenyl-1,4-benzoquinone diimine (quinone diimine). This mechanism has two paths: chain and nonchain. An important difference between the kinetics of the two reactions is the apparent reversible nature of the chain reaction in the quinone monoimine + thiophenol system. This nature reveals itself when the concentrations of thiophenol are comparable to or slightly higher than the concentrations of quinone imine. In light of this, kinetic research is conducted under conditions where the concentrations of thiophenol are significantly higher than those of quinone monoimine, allowing us to simplify the kinetic features and obtain interpretable data. The rate constants of the reaction's elementary steps are estimated and found to be three to five times lower for the reaction involving quinone monoamine than for the one involving quinone diimine. Both reactions have relatively short chains whose lengths do not exceed several tens of units.

  1. Effects of support acidity on the reaction mechanisms of selective catalytic reduction of NO by CH4 in excess oxygen

    Institute of Scientific and Technical Information of China (English)

    Shicheng XU; Junhua LI; Dong YANG; Jiming HAO

    2009-01-01

    The reaction mechanisms of selective catalytic reduction (SCR) of nitric oxide (NO) by methane (CH4)over solid superacid-based catalysts were proposed and testified by DRIFTS studies on transient reaction as well as by kinetic models. Catalysts derived from different supports would lead to different reaction pathways, and the acidity of solid superacid played an important role in determining the reaction mechanisms and the catalytic activities. Higher ratios of Bronsted acid sites to Lewis acid sites would lead to stronger oxidation of methane and then could facilitate the step of methane activation. Strong Bronsted acid sites would not necessarily lead to better catalytic performance, however, since the active surface NOy species and the corresponding reaction routes were determined by the overall acidity strength of the support.The reaction routes where NO2 moiety was engaged as an important intermediate involved moderate oxidation of methane, the rate of which could determine the overall activity. The reaction involving NO moiety was likely to be determined by the step of reduction of NO. Therefore, to enhance the SCR activity of solid superacid catalysts,reactions between appropriate couples of active NOy species and activated hydrocarbon intermediates should be realized by modification of the support acidity.

  2. Influence of additives on microstructures, mechanical properties and shock-induced reaction characteristics of Al/Ni composites

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Wei; Zhang, Xianfeng, E-mail: lynx@mail.njust.edu.cn; Wu, Yang; He, Yong; Wang, Chuanting; Guo, Lei

    2015-11-05

    Granular composites containing aluminum (Al) and nickel (Ni) are typical structural energetic materials, which possess ideal combination of both mechanical properties and energy release capability. The influence of two additives, namely Teflon (PTFE) and copper (Cu), on mechanical properties and shock-induced chemical reaction (SICR) characteristics of Al/Ni material system has been investigated. Three composites, namely Al/Ni, Al/Ni/PTFE and Al/Ni/Cu with same volumetric ratio of Al powder to Ni powder, were processed by means of static pressing. Scanning electron microscopy was used to study the microstructure of the mentioned three composites. Quasi static compression tests were also conducted to determine the mechanical properties and fracture behavior of the mentioned three composites. It was shown that the additives affected both compressive strength and fracture mode of the three composites. Impact initiation experiments on the mentioned three composites were performed to determine their shock-induced chemical reaction characteristics by considering pressure histories measured in the test chamber. The experimental results showed that the additives had significant effects on critical initiation velocity, reaction rate, reaction efficiency and post-reaction behavior. - Highlights: • .Al/Ni, Al/Ni/PTFE and Al/Ni/Cu were processed by means of static pressing. • .Microstructures, mechanical properties and shock-induced reactions were studied. • .Microstructures affect both compressive strength and fracture mode. • .Impact velocity is an important factor in shock-induced chemical characteristics. • .Each additive has significant effects on energy release behavior.

  3. Dataset for Modelling Reaction Mechanisms Using Density Functional Theory: Mechanism of ortho-Hydroxylation by High-Valent Iron-Oxo Species

    Directory of Open Access Journals (Sweden)

    Azaj Ansari

    2014-01-01

    Full Text Available Modelling reaction mechanisms using density functional theory is one of the popular routes to underpin the course of a chemical reaction. Although numerous publications have come out in this area, the pitfall of modelling such reactions and explicitly publishing the entire data set (structures, energies, coordinates, spin densities, etc. which lead to the conclusions are scarce. Here we have attempted to set a trend wherein all the computed data to underpin the reaction mechanism of ortho-hydroxylation of aromatic compounds by high-valent iron-oxo complexes (FeIII–OOH, FeIV=O, and FeV=O are collected. Since the structure, energetics and other details of the calculations can be employed in future to probe/understand the reactivity pattern of such species, establishing the data set is justified. Here by analysing the presented results we also discuss in brief the presented results.

  4. New insights into atrazine degradation by cobalt catalyzed peroxymonosulfate oxidation: kinetics, reaction products and transformation mechanisms.

    Science.gov (United States)

    Ji, Yuefei; Dong, Changxun; Kong, Deyang; Lu, Junhe

    2015-03-21

    The widespread occurrence of atrazine in waters poses potential risk to ecosystem and human health. In this study, we investigated the underlying mechanisms and transformation pathways of atrazine degradation by cobalt catalyzed peroxymonosulfate (Co(II)/PMS). Co(II)/PMS was found to be more efficient for ATZ elimination in aqueous solution than Fe(II)/PMS process. ATZ oxidation by Co(II)/PMS followed pseudo-first-order kinetics, and the reaction rate constant (k(obs)) increased appreciably with increasing Co(II) concentration. Increasing initial PMS concentration favored the decomposition of ATZ, however, no linear relationship between k(obs) and PMS concentration was observed. Higher efficiency of ATZ oxidation was observed around neutral pH, implying the possibility of applying Co(II)/PMS process under environmental realistic conditions. Natural organic matter (NOM), chloride (Cl(-)) and bicarbonate (HCO3(-)) showed detrimental effects on ATZ degradation, particularly at higher concentrations. Eleven products were identified by applying solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC/MS) techniques. Major transformation pathways of ATZ included dealkylation, dechlorination-hydroxylation, and alkyl chain oxidation. Detailed mechanisms responsible for these transformation pathways were discussed. Our results reveal that Co(II)/PMS process might be an efficient technique for remediation of groundwater contaminated by ATZ and structurally related s-triazine herbicides.

  5. [The reactions of hypersensitivity: the mechanisms of development, clinical manifestations, principles of diagnostic (a lecture)].

    Science.gov (United States)

    Tukavkina, S Yu; Kharseyeva, G G

    2014-05-01

    The article considers the principles of modern classification of hypersensitivity, pathogenic mechanisms of formation of its various types resulting in development of typical clinical symptoms and syndromes. The knowledge and comprehension of these issues is important for physicians of different specializations since it permits to properly make out and formulate diagnosis and timely send patient for examination and treatment to such specialist as allergist-immunologist. The particular attention was paid to description of pathogenesis of diseases and syndromes underlaid by IgE-mediated type of hypersensitivity since their share is highest and clinical manifestations frequently require emergency medical care. The diagnostic of allergic diseases is to be implemented sequentially (step-by-step) and include common clinical and special (specific) methods. In case of choosing of extent of specialized allergological examination the diagnostic significance of techniques and their safety is to be taken into account concerning condition of patient. The diagnosis is objectively formulated only by complex of examination results. It is worth to remember about possibility of development of syndromes similar to IgE-mediated allergy by their clinical manifestations but belonging to non-allergic type of hypersensitivity. It is important to know main causes, mechanisms and ways of formation of such reactions previously named as anaphylactoid ones.

  6. Surface damage of metallic implants due to mechanical loading and chemical reactions

    Science.gov (United States)

    Ryu, Jaejoong

    indicate that surface roughness undergoes continuous evolution during alternating contact loading and exposure to etchant. Surface roughness evolution is governed by the residual stress induced due to contact loading. Two different stress-assisted dissolution driven instabilities in roughness evolution have been identified. In order to investigate stressed surface damage by electrochemical reaction during active contact loading, in the first stage, surface failure due to sliding contact was investigated as a function of different residual stress states from compressive to tensile. Residual stress is usually developed during manufacturing process or former mechanical interactions playing an important role on service life of the surface. The wear mechanism of fatigue contact in the presence of residual stresses was explored by analytical model of fatigue crack growth by utilizing modified delamination wear theory with surface layer spalling model. Fatigue stress intensity factors (DeltaKI) loaded by contact stress and combined residual stress implied that buckling of subsurface crack with compressive residual stress opens crack-tip and consequently increase wear rate during sliding contact. As for the experimental verification of the modified delamination model, cyclic sliding contact experiment on metallic implant materials in ambient was conducted by utilizing atomic force microscope (AFM) and four-point-bending set up by which well characterized pre-stress was established on rectangular specimen. In addition, complex mechanism of corrosion on the damaged surface illustrated strong stress-dependent effects on wear rate in repassivating environment and dissolution rates in reactive environment.

  7. Studies of reaction mechanism in {sup 12}C + {sup 12}C system at intermediate energy of 28.7 MeV/N

    Energy Technology Data Exchange (ETDEWEB)

    Magiera, A. [Inst. of Physics, Jagiellonian Univ., Cracow (Poland)

    1996-12-31

    The reaction mechanism in {sup 12}C + {sup 12}C system at intermediate energy of about 30 MeV/nucleon was studied. The contribution of various reaction mechanisms (inelastic scattering, transfer reactions, compound nucleus reactions, sequential decay following inelastic excitation and transfer) to the total reaction cross section were found. The analysis of inclusive and coincidence spectra shows that sequential fragmentation processes dominate. 100 refs, 45 figs, 1 tab

  8. Reaction mechanism and thermal stability study on cathode materials for rechargeable lithium ion batteries

    Science.gov (United States)

    Fang, Jin

    Olivine-type lithium iron phosphate has been a very promising cathode material since it was proposed by Padhi in 1997, low-cost, environmental friendly and stable structure ensure the commercialization of LiFePO 4. In LiFePO4, during charge and discharge process, Li ions are transferred between two phases, Li-poor LialphaFePO 4 and Li-rich Li1-betaFePO4, which implies a significant energy barrier for the new phase nucleation and interface growth, contrary to the fast reaction kinetics experimentally observed. The understanding of the lithiation and delithiation mechanism of this material has spurred a lot of research interests. Many theory models have been proposed to explain the reaction mechanism of LiFePO4, among them, the single phase model claims that the reaction goes through a metastable single phase, and the over potential required to form this single phase is about 30mV, so we studied the driving force to transport lithium ions between Lialpha FePO4 and Li1-betaFePO4 phases and compared the particle sizes effect. Experiment results shows that, the nano-sized (30nm) LiFePO4 has wider solid solution range, lower solid solution formation temperature and faster kinetics than normal LiFePO4 (150nm). Also a 20mV over potential was observed in both samples, either after relaxing the FePO4/LiFePO4 system to equilibrium or transport lithium from one side to the other side, the experiment result is corresponding to theoretical calculation; indicates the reaction might go through single-phase reaction mechanism. The energy and power density of lithium ion battery largely depend on cathode materials. Mn substituted LiFePO4 has a higher voltage than LiFePO4, which results a higher theoretical energy density. Safety issue is one of the most important criterions for batteries, since cathode materials need to maintain stable structure during hundreds of charge and discharge cycles and ranges of application conditions. We have reported that iron-rich compound o-Fe1-yMnyPO4

  9. Effect of Precursor Mechanism on CO-NO Catalytic Reaction on Body-Centred Cubic Structure: Monte Carlo Simulation

    Institute of Scientific and Technical Information of China (English)

    A. U. Qaisrani; M. Khalid; M. K.Khan

    2005-01-01

    @@ The CO-NO catalytic reaction on body-centred cubic (bcc) lattice is studied by Monte Carlo simulation. The simple Langmuir-Hinshelwood (LH) mechanism yields a steady reactive window, which is separated by continuous and discontinuous irreversible phase transitions. The effect of precursor mechanism on the phase diagram of the system is also studied. According to this mechanism, the precursor motion of CO molecules is considered only on the surface of bcc lattice. Some interesting observations are reported.

  10. Reaction mechanisms in 24.3 MeV/nucleon {sup 238}U induced reactions through a comprehensive study of fission

    Energy Technology Data Exchange (ETDEWEB)

    Chbihi, A.; Galin; Guerreau, D.; Lewitowicz, M.; Morjean, M.; Pouthas, J. [Grand Accelerateur National d`Ions Lourds (GANIL), 14 - Caen (France); Piasecki, E.; Kordyasz, A.; Iwanicki, J.; Jastrzebski, J.; Pienkowski, L. [Warsaw Univ. (Poland); Crema, E. [Sao Paulo Univ., SP (Brazil). Inst. de Fisica; Czarnacki, W.; Kisielinski, M.; Tucholski, A. [Soltan Inst. for Nuclear Studies, Otwock-Swierk (Poland); Gatty, B.; Jacquet, D. [Paris-11 Univ., 91 - Orsay (France). Inst. de Physique Nucleaire; Jahnke, U. [Hahn-Meitner-Institut Berlin GmbH (Germany); Muchorowska, M.

    1994-12-31

    Nuclear reaction mechanisms for system characterized by very different asymmetries (U+C, Si, Ni, Au) have been investigated at 24.3 MeV/nucleon, using as observables both the fission products and the neutron multiplicity. It is clearly observed that the fusion process-whatever its completeness- can only occur with rather light target nuclei, indicating the persistence of potential energy effects much above the interaction barrier. (authors). 22 refs., 1 fig.

  11. Reaction site and mechanism in the UV or visible light induced TiO2 photodegradation of Orange G

    Institute of Scientific and Technical Information of China (English)

    YANG Shi-ying; LOU Li-ping; WU Xiao-na; CHEN Ying-xu

    2006-01-01

    For TiO2 heterogeneous reaction, the reaction site and the detailed mechanism are interesting and controversy topics. In this paper, effects of surface fluorination of TiO2 on the photocatalytic degradation of an azo dye, Orange G(OG) under UV or visible light irradiation were investigated, and the possible reaction site and mechanism were elucidated. The adsorption of OG on TiO2 was nearly inhibited by fluoride but its UV light induced photodegradation rate was greatly increased by a factor of about 2.7, which was due to the more generated free hydroxyl radicals. It supported the views that fluoride could desorb the oxidant species from surface and that the reaction sites could move to the bulk solution. In TiO2/Vis system, the observed inhibition effects of fluorination could be interpreted by the competitive adsorption, which provided additional evidences that the visible light sensitized photodegradation of dye pollutants on the catalyst surface.

  12. Final Report: Dominant Mechanisms of Uranium-Phosphate Reactions in Subsurface Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Catalano, Jeffrey G. [Washington Univ., St. Louis, MO (United States); Giammar, Daniel E. [Washington Univ., St. Louis, MO (United States); Wang, Zheming [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-08

    Phosphate addition is an in situ remediation approach that may enhance the sequestration of uranium without requiring sustained reducing conditions. However, the geochemical factors that determine the dominant immobilization mechanisms upon phosphate addition are insufficiently understood to design efficient remediation strategies or accurately predict U(VI) transport. The overall objective of our project is to determine the dominant mechanisms of U(VI)-phosphate reactions in subsurface environments. Our research approach seeks to determine the U(VI)-phosphate solid that form in the presence of different groundwater cations, characterize the effects of phosphate on U(VI) adsorption and precipitation on smectite and iron oxide minerals, examples of two major reactive mineral phases in contaminated sediments, and investigate how phosphate affects U(VI) speciation and fate during water flow through sediments from contaminated sites. The research activities conducted for this project have generated a series of major findings. U(VI) phosphate solids from the autunite mineral family are the sole phases to form during precipitation, with uranyl orthophosphate not occurring despite its predicted greater stability. Calcium phosphates may take up substantial quantities of U(VI) through three different removal processes (adsorption, coprecipitation, and precipitation) but the dominance of each process varies with the pathway of reaction. Phosphate co-adsorbs with U(VI) onto smectite mineral surfaces, forming a mixed uranium-phosphate surface complex over a wide range of conditions. However, this molecular-scale association of uranium and phosphate has not effect on the overall extent of uptake. In contrast, phosphate enhanced U(VI) adsorption to iron oxide minerals at acidic pH conditions but suppresses such adsorption at neutral and alkaline pH, despite forming mixed uranium-phosphate surface complexes during adsorption. Nucleation barriers exist that inhibit U(VI) phosphate

  13. Theoretical investigation of the mechanism of tritiated methane dehydrogenation reaction using nickel-based catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Liang; Li, Jiamao; Deng, Bing; Yang, Yong; Wang, Heyi [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900 (China); Li, Weiyi [School of Physics and Chemistry, Xihua University, Chengdu 610065 (China); Li, Shuo, E-mail: lishuo@cqut.edu.cn [School of Chemical Engineering, Chongqing University of Technology, Chongqing 400054 (China); Tan, Zhaoyi, E-mail: tanzhaoyi@caep.cn [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900 (China)

    2015-06-15

    Graphical abstract: - Highlights: • Four-step dehydrogenation of CT{sub 4} catalyzed by Ni to form Ni–C by releasing T{sub 2}. • The process of Ni + CT{sub 4} → NiCT{sub 2} + T{sub 2} is more achievable than that of NiCT{sub 2} → NiC + T{sub 2}. • TNiCT → T{sub 2}NiC step is the RDS with the rate constant of k = 2.8 × 10{sup 13} exp(−313,136/RT). • The hydrogen isotope effect value of k{sub H}/k{sub T} is 2.94, and k{sub D}/k{sub T} is 1.39. • CH{sub 4} and CD{sub 4} dehydrogenations are likely to occur, accompanied by the CT{sub 4} cracking. - Abstract: The mechanism of tritiated methane dehydrogenation reaction catalyzed by nickel-based catalyst was investigated in detail by density functional theory (DFT) at the B3LYP/[6-311++G(d, p), SDD] level. The computational results indicated that the dehydrogenation of tritiated methane is endothermic. The decomposition of tritiated methane catalyzed by Ni to form Ni-based carbon (Ni–C) after a four-step dehydrogenation companied with releasing tritium. After the first and second dehydrogenation steps, Ni + CT{sub 4} formed NiCT{sub 2}. After the third and fourth dehydrogenation steps, NiCT{sub 2} formed NiC. The first and second steps of dehydrogenation occurred on both the singlet and triplet states, and the lowest energy route is Ni + CT{sub 4} → {sup 1}COM → {sup 1}TS1 → {sup 3}IM1 → {sup 3}TS2 → {sup 3}IM2. The third and fourth steps of dehydrogenation occurred on both the singlet and quintet states, and the minimum energy reaction pathway appeared to be IM3 → {sup 1}TS4 → {sup 5}IM4 → {sup 5}TS5 → {sup 5}IM5 → {sup 5}pro + T{sub 2}. The fourth step of dehydrogenation TNiCT → T{sub 2}NiC was the rate-determining step of the entire reaction with the rate constant of k{sub 2} = 2.8 × 10{sup 13} exp(−313,136/RT) (in cm{sup 3} mol{sup −1} s{sup −1}), and its activation energy barrier was calculated to be 51.8 kcal/mol. The Ni-catalyzed CH{sub 4} and CD{sub 4} cracking

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

    Science.gov (United States)

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

    2015-01-23

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

  15. Establishment of the C(2)H(5)+O(2) reaction mechanism: a combustion archetype.

    Science.gov (United States)

    Wilke, Jeremiah J; Allen, Wesley D; Schaefer, Henry F

    2008-02-21

    The celebrated C(2)H(5)+O(2) reaction is an archetype for hydrocarbon combustion, and the critical step in the process is the concerted elimination of HO(2) from the ethylperoxy intermediate (C(2)H(5)O(2)). Master equation kinetic models fitted to measured reaction rates place the concerted elimination barrier 3.0 kcal mol(-1) below the C(2)H(5)+O(2) reactants, whereas the best previous electronic structure computations yield a barrier more than 2.0 kcal mol(-1) higher. We resolve this discrepancy here by means of the most rigorous computations to date, using focal point methods to converge on the ab initio limit. Explicit computations were executed with basis sets as large as cc-pV5Z and correlation treatments as extensive as coupled cluster through full triples with a perturbative inclusion of quadruple excitations [CCSDT(Q)]. The final predicted barrier is -3.0 kcal mol(-1), bringing the concerted elimination mechanism into precise agreement with experiment. This work demonstrates that higher correlation treatments such as CCSDT(Q) are not only feasible on systems of chemical interest but are necessary to supply accuracy beyond 0.5 kcal mol(-1), which is not obtained with the "gold standard" CCSD(T) method. Finally, we compute the enthalpy of formation of C(2)H(5)O(2) to be Delta(f)H degrees (298 K)=-5.3+/-0.5 kcal mol(-1) and Delta(f)H degrees (0 K)=-1.5+/-0.5 kcal mol(-1).

  16. Establishment of the C2H5+O2 reaction mechanism: A combustion archetype

    Science.gov (United States)

    Wilke, Jeremiah J.; Allen, Wesley D.; Schaefer, Henry F.

    2008-02-01

    The celebrated C2H5+O2 reaction is an archetype for hydrocarbon combustion, and the critical step in the process is the concerted elimination of HO2 from the ethylperoxy intermediate (C2H5O2). Master equation kinetic models fitted to measured reaction rates place the concerted elimination barrier 3.0kcalmol-1 below the C2H5+O2 reactants, whereas the best previous electronic structure computations yield a barrier more than 2.0kcalmol-1 higher. We resolve this discrepancy here by means of the most rigorous computations to date, using focal point methods to converge on the ab initio limit. Explicit computations were executed with basis sets as large as cc-pV5Z and correlation treatments as extensive as coupled cluster through full triples with a perturbative inclusion of quadruple excitations [CCSDT(Q)]. The final predicted barrier is -3.0kcalmol-1, bringing the concerted elimination mechanism into precise agreement with experiment. This work demonstrates that higher correlation treatments such as CCSDT(Q) are not only feasible on systems of chemical interest but are necessary to supply accuracy beyond 0.5kcalmol-1, which is not obtained with the "gold standard" CCSD(T) method. Finally, we compute the enthalpy of formation of C2H5O2 to be ΔfH °(298K)=-5.3±0.5kcalmol-1 and ΔfH°(0K)=-1.5±0.5kcalmol-1.

  17. Structure and Reaction Mechanism of Phosphoethanolamine Methyltransferase from the Malaria Parasite Plasmodium falciparum

    Science.gov (United States)

    Lee, Soon Goo; Kim, Youngchang; Alpert, Tara D.; Nagata, Akina; Jez, Joseph M.

    2012-01-01

    In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to phosphocholine for membrane biogenesis. This pathway is also found in plant and nematodes, but PMT from these organisms use multiple methyltransferase domains for the S-adenosylmethionine (AdoMet) reactions. Because PfPMT is essential for normal growth and survival of Plasmodium and is not found in humans, it is an antiparasitic target. Here we describe the 1.55 Å resolution crystal structure of PfPMT in complex with AdoMet by single-wavelength anomalous dispersion phasing. In addition, 1.19–1.52 Å resolution structures of PfPMT with pEA (substrate), phosphocholine (product), sinefungin (inhibitor), and both pEA and S-adenosylhomocysteine bound were determined. These structures suggest that domain rearrangements occur upon ligand binding and provide insight on active site architecture defining the AdoMet and phosphobase binding sites. Functional characterization of 27 site-directed mutants identifies critical active site residues and suggests that Tyr-19 and His-132 form a catalytic dyad. Kinetic analysis, isothermal titration calorimetry, and protein crystallography of the Y19F and H132A mutants suggest a reaction mechanism for the PMT. Not only are Tyr-19 and His-132 required for phosphobase methylation, but they also form a “catalytic” latch that locks ligands in the active site and orders the site for catalysis. This study provides the first insight on this antiparasitic target enzyme essential for survival of the malaria parasite; however, further studies of the multidomain PMT from plants and nematodes are needed to understand the evolutionary division of metabolic function in the phosphobase pathway of these organisms. PMID:22117061

  18. The mechanisms of sudden-onset type adverse reactions to oseltamivir.

    Science.gov (United States)

    Hama, R; Bennett, C L

    2017-02-01

    Oseltamivir is contraindicated for people aged 10-19 in principle in Japan, due to concern about abnormal behaviours. Sudden death is another concern. This review examines growing evidence of their association and discusses underlying mechanisms of these sudden-onset type reactions to oseltamivir. First, the importance of animal models and the concept of human equivalent dose (HED) is summarized. Second, the specific condition for oseltamivir use, influenza infection, is reviewed. Third, findings from toxicity studies conducted prior to and after the marketing of oseltamivir are reported on to provide context on the observation of a possible causal association. Fourth, similarity and consistency of toxicity in humans with that in other animals is described. Finally, coherence of toxicokinetic and molecular level of evidence (channels, receptors and enzymes), including differences from the toxicity of other neuraminidase inhibitors, is reviewed. It is concluded that unchanged oseltamivir has various effects on the central nervous system (CNS) that may be related to clinical findings including hypothermia, abnormal behaviours including with fatal outcome, and sudden death. Among receptors and enzymes related to CNS action, it is known that oseltamivir inhibits nicotinic acetylcholine receptors, which are closely related to hypothermia, as well as human monoamine oxidase-A (MAO-A), which is closely related to abnormal or excitatory behaviours. Receptors such as GABAA , GABAB and NMDA and their related receptors/channels including Na(+) and Ca(2+) channels are thought to be other candidates for investigation related to respiratory suppression followed by sudden death and psychotic reactions (both acute and chronic), respectively.

  19. Elucidation of inorganic reaction mechanisms in ionic liquids: the important role of solvent donor and acceptor properties.

    Science.gov (United States)

    Schmeisser, Matthias; van Eldik, Rudi

    2014-11-14

    In this article, we focus on the important role of solvent donor and acceptor properties of ionic liquids in the elucidation of inorganic reaction mechanisms. For this purpose, mechanistic and structural studies on typical inorganic reactions, performed in ionic liquids, have been conducted. The presented systems range from simple complex-formation and ligand-substitution reactions to the activation of small molecules by catalytically active complexes. The data obtained for the reactions in ionic liquids are compared with those for the same reactions carried out in conventional solvents, and are discussed with respect to the donor and acceptor properties of the applied ionic liquids. The intention of this perspective is to gain more insight into the role of ILs as solvents and their interaction with metal ions and complexes in solution.

  20. Asymmetric Horner-Wadsworth-Emmons Reactions with meso-Dialdehydes: Scope, Mechanism, and Synthetic Applications

    DEFF Research Database (Denmark)

    Rein, Tobias; Vares, Lauri; Kawasaki, Ikuo

    1999-01-01

    Asymmetric Homer-Wadsworth-Emmons reactions between chiral phosphonate reagents and various meso-dialdehydes have been investigated. A mechanistic model useful for rationalizing the experimentally observed stereoselectivities is presented. Furthermore; strategies for applying these reactions to t...

  1. Density Functional Study on the Mechanism of Collision Reaction among Protons,N2 and Water Vapor

    Institute of Scientific and Technical Information of China (English)

    SUN,Hao(孙昊); PAN,Xiu-Mei(潘秀梅); ZHAO,Min(赵岷); LIU,Peng-Jun(刘朋军); SU,Zhong-Min(苏忠民); WANG,Rong-Shun(王荣顺)

    2004-01-01

    The mechanism of collision reaction among protons, N2 and water vapor was theoretically studied using Density Functional Theory. The geometries of reactants, transition states, intermediates and products were optimized at the B3LYP/6-311 + G** level by the BERNY gradient analysis method. Transition states and intermediates have been identified by vibrational frequency analysis. The relationship among reactants, intermediates, transition states and products was affirmed by IRC calculation. The variations of energy and geometry along the IRC-determined reaction paths were described. The possible reaction pathways were represented and the optimal one was decided from the viewpoint of energy.

  2. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

    Directory of Open Access Journals (Sweden)

    Daniel E Almonacid

    2010-03-01

    Full Text Available Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3 show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1 catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56% suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to

  3. Breaking down the reactivity of λ(3)-iodanes: the impact of structure and bonding on competing reaction mechanisms.

    Science.gov (United States)

    Pinto de Magalhães, Halua; Lüthi, Hans Peter; Togni, Antonio

    2014-09-05

    The functionalization of arenes via diaryliodonium salts has gained considerable attention in synthesis, as these compounds react under mild conditions. Mechanistic studies have shown that the formation of corresponding λ(3)-iodane intermediates takes a key role, as they determine the course and selectivity of the reaction. Bridged diaryliodonium salts, featuring a heterocyclic moiety involving the iodine atom, were shown to exhibit a distinctly different reactivity, leading to different products. These products are not just the result of reductive elimination reactions but may also arise via radical mechanisms. Our quantum chemical calculations reveal that the λ(3)-iodane intermediate is also the "gateway" for reactions that are observed only for strained bridged systems. At the same time, we find a remarkable affinity of the hypervalent region to planarity for all reaction mechanisms. This also explains the correlation between the size of the bridge connecting the aryl groups and the reaction products observed. Furthermore, the energetics of these competing reactions are examined by analysis of the mechanisms. Finally, using model compounds, some of the basic features governing the reactivity of λ(3)-iodanes are discussed.

  4. The Role of Various Stressors in the Trigger Mechanism of Raynaud's Disease (Hemorheological and Vascular Reactions

    Directory of Open Access Journals (Sweden)

    Mantskava M.M.

    2014-05-01

    Full Text Available The emergence and spread of stress reactions are provided by the blood circulation system. In its turn, the adequacy of blood circulation depends on the hemorheological and vascular mechanisms. The changeability of their properties appears to be the basis of the increasing of stress stages. From the viewpoint of biophysical reactions, any change and movement occur with the expenditure and accumulation of energy. Higher level of adaptation energy waste and secondary level take place, when a small stressor entails a small expenditure. There is a maximum possible rate of adaptive energy consumption and at this maximum the organism cannot cope with any additional stimulus. At the same time adaptive and stress diseases develop. Let’s consider the duration and manifestation of Raynaud's disease from the perspective of adaptation diseases and diseases of the third grade, which appears to be the cause of the double stress effect - cold and emotional- physical and psychic. Total of 97 patients with Raynaud's disease were examined. For a new vision of the problem it was necessary to find out how the streessors of various nature impact the hemoreheological status and vascular resistance. For this purpose all the patients were examined for a resistance index of resistive arteries of the hand and the indices of erythrocyte aggregation and deformability. The patients were divided into four subgroups. The first subgroup – the patients after chilblain, the second subgroup – the patients with psychic strerssor, the third subgroup – the patients with prolonged chronic stress, and the fourth subgroup – the patients without the differentiation of the stressors. According to the obtained results, it is obvious that at cold and emotional stress (I and II subgroups the hemorheological and vascular parameters are changed. However, this change (hemorheological and vascular is more pronounced at chronic emotional stress (III subgroup as compared both to the

  5. HF(v′ = 3) forward scattering in the F + H2 reaction: Shape resonance and slow-down mechanism

    Science.gov (United States)

    Wang, Xingan; Dong, Wenrui; Qiu, Minghui; Ren, Zefeng; Che, Li; Dai, Dongxu; Wang, Xiuyan; Yang, Xueming; Sun, Zhigang; Fu, Bina; Lee, Soo-Y.; Xu, Xin; Zhang, Dong H.

    2008-01-01

    Crossed molecular beam experiments and accurate quantum dynamics calculations have been carried out to address the long standing and intriguing issue of the forward scattering observed in the F + H2 → HF(v′ = 3) + H reaction. Our study reveals that forward scattering in the reaction channel is not caused by Feshbach or dynamical resonances as in the F + H2 → HF(v′ = 2) + H reaction. It is caused predominantly by the slow-down mechanism over the centrifugal barrier in the exit channel, with some small contribution from the shape resonance mechanism in a very small collision energy regime slightly above the HF(v′ = 3) threshold. Our analysis also shows that forward scattering caused by dynamical resonances can very likely be accompanied by forward scattering in a different product vibrational state caused by a slow-down mechanism. PMID:18434547

  6. An investigation on the formation mechanism of nano ZrB{sub 2} powder by a magnesiothermic reaction

    Energy Technology Data Exchange (ETDEWEB)

    Jalaly, M., E-mail: maisam_jalaly@iust.ac.ir [School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Narmak, Tehran 16846-13114 (Iran, Islamic Republic of); Bafghi, M.Sh.; Tamizifar, M. [School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Narmak, Tehran 16846-13114 (Iran, Islamic Republic of); Gotor, F.J. [Instituto de Ciencia de Materiales de Sevilla (CSIC-US), Americo Vespucio 49, 41092 Sevilla (Spain)

    2014-03-05

    Highlights: • Synthesis of zirconium diboride by magnesiothermic reduction. • Using high energy ball milling to perform mechanochemical reactions. • Study of mechanism of ZrB{sub 2} synthesis by studying subreactions and thermal analysis. -- Abstract: Nanocrystalline zirconium diboride (ZrB{sub 2}) powder was produced by mechanochemistry from the magnesiothermic reduction in the Mg/ZrO{sub 2}/B{sub 2}O{sub 3} system. The use of high-energy milling conditions was essential to induce a mechanically induced self-sustaining reaction (MSR) and significantly reduce the milling time required for complete conversion. Under these conditions, it was found that the ignition time for ZrB{sub 2} formation was only about a few minutes. In this study, the mechanism for the formation of ZrB{sub 2} in this system was determined by studying the relevant sub-reactions, the effect of stoichiometry, and the thermal behavior of the system.

  7. Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease

    Science.gov (United States)

    Martínez-González, José Ángel; Rodríguez, Alex; Puyuelo, María Pilar; González, Miguel; Martínez, Rodrigo

    2015-01-01

    The main reactions of the hepatitis C virus NS3/NS4A serine protease are studied using the second-order Møller-Plesset ab initio method and rather large basis sets to correct the previously reported AM1/CHARMM22 potential energy surfaces. The reaction efficiencies measured for the different substrates are explained in terms of the tetrahedral intermediate formation step (the rate-limiting process). The energies of the barrier and the corresponding intermediate are so close that the possibility of a concerted mechanism is open (especially for the NS5A/5B substrate). This is in contrast to the suggested general reaction mechanism of serine proteases, where a two-step mechanism is postulated.

  8. Structural and mechanical characterization of detonation coatings formed by reaction products of titanium with components of the spraying atmosphere

    Science.gov (United States)

    Ulianitsky, Vladimir Yu.; Dudina, Dina V.; Panin, Sergey V.; Vlasov, Ilya V.; Batraev, Igor S.; Bokhonov, Boris B.

    2016-11-01

    Structural characterization of detonation deposits formed by reaction products of titanium with the components of the spraying atmosphere showed that ceramic-based coatings of unique microstructures—consisting of alternating layers of different compositions—can be formed. For the first time, mechanical characteristics of the coatings formed by reaction-accompanied detonation spraying of titanium were evaluated. It was found that high-yield transformation of titanium into oxides and nitrides during spraying can result in the formation of coatings with high fracture resistance and interface fracture toughness. The hardness of the coatings measured along the cross-section of the specimens was higher than that on the surface of the coatings, which indicated mechanical anisotropy of the deposited material. In terms of mechanical properties, coatings formed by the reaction products appear to be more attractive than those specially treated to preserve metallic titanium.

  9. Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

    Science.gov (United States)

    Davison, James M.; Lickwar, Colin R.; Song, Lingyun; Breton, Ghislain; Crawford, Gregory E.; Rawls, John F.

    2017-01-01

    Microbiota influence diverse aspects of intestinal physiology and disease in part by controlling tissue-specific transcription of host genes. However, host genomic mechanisms mediating microbial control of intestinal gene expression are poorly understood. Hepatocyte nuclear factor 4 (HNF4) is the most ancient family of nuclear receptor transcription factors with important roles in human metabolic and inflammatory bowel diseases, but a role in host response to microbes is unknown. Using an unbiased screening strategy, we found that zebrafish Hnf4a specifically binds and activates a microbiota-suppressed intestinal epithelial transcriptional enhancer. Genetic analysis revealed that zebrafish hnf4a activates nearly half of the genes that are suppressed by microbiota, suggesting microbiota negatively regulate Hnf4a. In support, analysis of genomic architecture in mouse intestinal epithelial cells disclosed that microbiota colonization leads to activation or inactivation of hundreds of enhancers along with drastic genome-wide reduction of HNF4A and HNF4G occupancy. Interspecies meta-analysis suggested interactions between HNF4A and microbiota promote gene expression patterns associated with human inflammatory bowel diseases. These results indicate a critical and conserved role for HNF4A in maintaining intestinal homeostasis in response to microbiota. PMID:28385711

  10. A case study of the mechanism of alcohol-mediated Morita Baylis-Hillman reactions. The importance of experimental observations.

    Science.gov (United States)

    Plata, R Erik; Singleton, Daniel A

    2015-03-25

    The mechanism of the Morita Baylis-Hillman reaction has been heavily studied in the literature, and a long series of computational studies have defined complete theoretical energy profiles in these reactions. We employ here a combination of mechanistic probes, including the observation of intermediates, the independent generation and partitioning of intermediates, thermodynamic and kinetic measurements on the main reaction and side reactions, isotopic incorporation from solvent, and kinetic isotope effects, to define the mechanism and an experimental mechanistic free-energy profile for a prototypical Morita Baylis-Hillman reaction in methanol. The results are then used to critically evaluate the ability of computations to predict the mechanism. The most notable prediction of the many computational studies, that of a proton-shuttle pathway, is refuted in favor of a simple but computationally intractable acid-base mechanism. Computational predictions vary vastly, and it is not clear that any significant accurate information that was not already apparent from experiment could have been garnered from computations. With care, entropy calculations are only a minor contributor to the larger computational error, while literature entropy-correction processes lead to absurd free-energy predictions. The computations aid in interpreting observations but fail utterly as a replacement for experiment.

  11. Chlorination of N-methylacetamide and amide-containing pharmaceuticals. Quantum-chemical study of the reaction mechanism.

    Science.gov (United States)

    Šakić, Davor; Šonjić, Pavica; Tandarić, Tana; Vrček, Valerije

    2014-03-27

    Chlorination of amides is of utmost importance in biochemistry and environmental chemistry. Despite the huge body of data, the mechanism of reaction between amides and hypochlorous acid in aqueous environment remains unclear. In this work, the three different reaction pathways for chlorination of N-methylacetamide by HOCl have been considered: the one-step N-chlorination of the amide, the chlorination via O-chlorinated intermediate, and the N-chlorination of the iminol intermediate. The high-level quantum chemical G3B3 composite procedure, double-hybrid B2-PLYPD, B2K-PLYP methods, and global hybrid M06-2X and BMK methods have been employed. The calculated energy barriers have been compared to the experimental value of ΔG(#)298 ≈ 87 kJ/mol, which corresponds to reaction rate constant k(r) ≈ 0.0036 M(-1) s(-1). Only the mechanism in which the iminol form of N-methylacetamide reacts with HOCl is consistent (ΔG(#)298 = 87.3 kJ/mol at G3B3 level) with experimental results. The analogous reaction mechanism has been calculated as the most favorable pathway in the chlorination of small-sized amides and amide-containing pharmaceuticals: carbamazepine, acetaminophen, and phenytoin. We conclude that the formation of the iminol intermediate followed by its reaction with HOCl is the general mechanism of N-chlorination for a vast array of amides.

  12. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

    Science.gov (United States)

    Kuechler, Erich R.; York, Darrin M.

    2014-02-01

    The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

  13. Mechanism of sperm capacitation and the acrosome reaction: role of protein kinases

    Institute of Scientific and Technical Information of China (English)

    Debby Ickowicz; Maya Finkelstein; Haim Breitbart

    2012-01-01

    Mammalian sperm must undergo a series of biochemical and physiological modifications,collectively called capacitation,in the female reproductive tract prior to the acrosome reaction (AR).The mechanisms of these modifications are not well characterized though protein kinases were shown to be involved in the regulation of intracellular Ca2+ during both capacitation and the AR.In the present review,we summarize some of the signaling events that are involved in capacitation.During the capacitation process,phosphatidyl-inositol-3-kinase (P13K) is phosphorylated/activated via a protein kinase A (PKA)-dependent cascade,and downregulated by protein kinase C α (PKCα).PKCα is active at the beginning of capacitation,resulting in P13K inactivation.During capacitation,PKCα as well as PP1γ2 is degraded by a PKA-dependent mechanism,allowing the activation of P13K.The activation of PKA during capacitation depends mainly on cyclic adenosine monophosphate (cAMP) produced by the bicarbonate-dependent soluble adenylyl cyclase.This activation of PKA leads to an increase in actin polymerization,an essential process for the development of hyperactivated motility,which is necessary for successful fertilization.Actin polymerization is mediated by PIP2 in two ways:first,P(I)P2 acts as a cofactor for phospholipase D (PLD) activation,and second,as a molecule that binds and inhibits actin-severing proteins such as gelsolin.Tyrosine phosphorylation of gelsolin during capacitation by Src family kinase (SFK) is also important for its inactivation.Prior to the AR,gelsolin is released from P(I)P2 and undergoes dephosphorylation/activation,resulting in fast F-actin depolymerization,leading to the AR.

  14. THE MECHANISM OF CURE REACTION OF 4,4'-DIAMINODIPHENYL METHANE WITH TETRAGLYCIDYL 4,4'-DIAMINODIPHENYL METHANE EPOXY

    Institute of Scientific and Technical Information of China (English)

    WANG Wei; WU Xuanzheng; QI Zongneng

    1992-01-01

    The cure reaction of tetraglycidyl 4,4'-diaminodiphenyl methane (TGDDM) epoxy resin with 4,4'-diaminodiphenyl methane (DDM) has been studied by using DSC. nstead of one exothermic peak, two exothermic peaks, indicative of a complex reaction mechanism, are shown in the DSC curve of TGDDM-DDM mixtures in nonisothermal cure experiments when the content of DDM is lower than stoichiometric ratio. The result of the kinetic analysis of the cure reaction shows that the activation energy of the lower temperature exotherm peak is about 56 kJ/mol and that of the higher temperature exotherm peak is about 136 kJ/mol. The lower temperature cure reaction peak can be attributed to the primary amine-epoxide and secondary amine-epoxide reactions, and the higher temperature cure reaction peak can be attributed to the epoxide-hydroxy reaction under catalysis of tertiary amine in the TGDDM epoxy resin. Because the network density of the cured epoxy resin is determined by these two reactions, the content of DDM has little effect on the glass transition temperature of cured epoxy resin.

  15. Kinetics and Mechanisms of the Acid-base Reaction Between NH3 and HCOOH in Interstellar Ice Analogs

    Science.gov (United States)

    Bergner, Jennifer B.; Öberg, Karin I.; Rajappan, Mahesh; Fayolle, Edith C.

    2016-10-01

    Interstellar complex organic molecules are commonly observed during star formation, and are proposed to form through radical chemistry in icy grain mantles. Reactions between ions and neutral molecules in ices may provide an alternative cold channel to complexity, as ion-neutral reactions are thought to have low or even no-energy barriers. Here we present a study of the kinetics and mechanisms of a potential ion-generating, acid-base reaction between NH3 and HCOOH to form the salt NH{}4+HCOO-. We observe salt growth at temperatures as low as 15 K, indicating that this reaction is feasible in cold environments. The kinetics of salt growth are best fit by a two-step model involving a slow “pre-reaction” step followed by a fast reaction step. The reaction energy barrier is determined to be 70 ± 30 K with a pre-exponential factor 1.4 ± 0.4 × 10-3 s-1. The pre-reaction rate varies under different experimental conditions and likely represents a combination of diffusion and orientation of reactant molecules. For a diffusion-limited case, the pre-reaction barrier is 770 ± 110 K with a pre-exponential factor of ˜7.6 × 10-3 s-1. Acid-base chemistry of common ice constituents is thus a potential cold pathway to generating ions in interstellar ices.

  16. Kinetics and mechanisms of the acid-base reaction between NH$_3$ and HCOOH in interstellar ice analogs

    CERN Document Server

    Bergner, Jennifer B; Rajappan, Mahesh; Fayolle, Edith C

    2016-01-01

    Interstellar complex organic molecules (COMs) are commonly observed during star formation, and are proposed to form through radical chemistry in icy grain mantles. Reactions between ions and neutral molecules in ices may provide an alternative cold channel to complexity, as ion-neutral reactions are thought to have low or even no energy barriers. Here we present a study of a the kinetics and mechanisms of a potential ion-generating acid-base reaction between NH$_{3}$ and HCOOH to form the salt NH$_{4}^{+}$HCOO$^{-}$. We observe salt growth at temperatures as low as 15K, indicating that this reaction is feasible in cold environments. The kinetics of salt growth are best fit by a two-step model involving a slow "pre-reaction" step followed by a fast reaction step. The reaction energy barrier is determined to be 70 $\\pm$ 30K with a pre-exponential factor 1.4 $\\pm$ 0.4 x 10$^{-3}$ s$^{-1}$. The pre-reaction rate varies under different experimental conditions and likely represents a combination of diffusion and or...

  17. Ageing mechanisms in chickpea seeds: Relationship of sugar hydrolysis and lipid peroxidation with Amadori and Millard reactions

    Directory of Open Access Journals (Sweden)

    mahdi shaaban

    2017-05-01

    Full Text Available This experiment was performed in order to study on ageing mechanisms of chickpea seeds (Cicer arietinum L. in natural storage and accelerated ageing conditions in seed laboratory of Gorgan Agricultural Science and Natural Resources, Gorgan, Iran at 2015. Experiment was in completely randomized design arrangement with four replications. Treatments were 2 and 4 years natural storage and 1-5 days of accelerated ageing with control treatment. The results showed that with increasing of natural storage and accelerated ageing duration, germination percentage was decreased. Increasing of ageing duration decreased soluble sugars, non-reducing sugars and soluble proteins but lipid peroxidation, reducing sugars, protein carbonylation and Amadori and Millard reaction were increased. In natural storage condition lipid peroxidation was more than sugar hydrolysis but in accelerated ageing condition sugar hydrolysis was more than lipid peroxidation. These results show that the main reason of Amadori and Millard reaction in chickpea seeds in natural storage condition is lipid peroxidation and in accelerated ageing condition is sugar hydrolysis. Also, the results showed that Amadori reaction in natural storage condition was more than Amadori reaction and in accelerated ageing condition Millard reaction was more than Amadori reaction. The results of the present study showed that sever Millard reaction after Amadori reaction induced higher damage on seed and results to more decrease of seed viability and reduce of seed germination percentage in accelerated ageing than natural storage.

  18. Conservation laws and path-independent integrals in mechanical-diffusion-electrochemical reaction coupling system

    Science.gov (United States)

    Yu, Pengfei; Wang, Hailong; Chen, Jianyong; Shen, Shengping

    2017-07-01

    In this study, the conservation laws οf dissipative mechanical-diffusion-electrochemical reaction system are systematically obtained based on Noether's theorem. According to linear, irreversible thermodynamics, dissipative phenomena can be described by an irreversible force and an irreversible flow. Additionally, the Lagrange function, L and the generalized Hamilton least-action principle are proposed to be used to obtain the conservation integrals. A group of these integrals, including the J-, M-, and L-integrals, can be then obtained using the classical Noether approach for dissipative processes. The relation between the J-integral and the energy release rate is illustrated. The path-independence of the J-integral is then proven. The J-integral, derived based on Noether's theorem, is a line integral, contrary to the propositions of existing published works that describe it both as a line and an area integral. Herein, we prove that the outcomes are identical, and identify the physical meaning of the area integral, a concept that was not explained previously. To show that the J-integral can dominate the distribution of the corresponding field quantities, an example of a partial, stress-diffusion coupling process is disscussed.

  19. Fluid Shearing for Accelerated Chemical Reactions - Fluid Mechanics in the VFD

    Science.gov (United States)

    Leivadarou, Evgenia; Dalziel, Stuart; G. K. Batchelor Laboratory, Department of Applied Mathematics; Theoretical Physics Team

    2016-11-01

    The Vortex Fluidic Device (VFD) is a rapidly rotating tube that can operate under continuous flow with a jet feeding liquid reactants to the tube's hemispherical base. It is a new 'green' approach to the organic synthesis with many industrial applications in cosmetics, protein folding and pharmaceutical production. The rate of reaction in the VFD is enhanced when the collision rate is increased. The aim of the project is to explain the fluid mechanics and optimize the performance of the device. One contribution to the increased yield is believed to be the high levels of shear stress. We attempt to enhance the shear stress by achieving high velocity gradients in the boundary layers. Another factor is the uncontrolled vibrations due to imperfections in the bearings and therefore it is important to assess their influence in the initial spreading. The surface area of the film should be maximized with respect to the rotation rate, geometry and orientation of the tube, flow rate, wettability and contact line dynamics. Experiments are presented for a flat disk and a curved bowl, establishing the optimum height of release, rotation rate and tube orientation. Vibrations were imposed to investigate the changes in the film formation. We discuss the implications of our results in the VFD.

  20. Wherefore Art Thou Copper? Structures and Reaction Mechanisms of Organocuprate Clusters in Organic Chemistry.

    Science.gov (United States)

    Nakamura; Mori

    2000-11-03

    Organocopper reagents provide the most general synthetic tools in organic chemistry for nucleophilic delivery of hard carbanions to electrophilic carbon centers. A number of structural and mechanistic studies have been reported and have led to a wide variety of mechanistic proposals, some of which might even be contradictory to others. With the recent advent of physical and theoretical methodologies, the accumulated knowledge on organocopper chemistry is being put together into a few major mechanistic principles. This review will summarize first the general structural features of organocopper compounds and the previous mechanistic arguments, and then describe the most recent mechanistic pictures obtained through high-level quantum mechanical calculations for three typical organocuprate reactions, carbocupration, conjugate addition, and S(N)2 alkylation. The unified view on the nucleophilic reactivities of metal organocuprate clusters thus obtained has indicated that organocuprate chemistry represents an intricate example of molecular recognition and supramolecular chemistry, which chemists have long exploited without knowing it. Reasoning about the uniqueness of the copper atom among neighboring metal elements in the periodic table will be presented.