Sample records for reaction mechanism causing

  1. Reaction mechanism of the acidic hydrolysis of highly twisted amides: Rate acceleration caused by the twist of the amide bond.

    Mujika, Jon I; Formoso, Elena; Mercero, Jose M; Lopez, Xabier


    We present an ab initio study of the acid hydrolysis of a highly twisted amide and a planar amide analogue. The aim of these studies is to investigate the effect that the twist of the amide bond has on the reaction barriers and mechanism of acid hydrolysis. Concerted and stepwise mechanisms were investigated using density functional theory and polarizable continuum model calculations. Remarkable differences were observed between the mechanism of twisted and planar amide, due mainly to the preference for N-protonation of the former and O-protonation of the latter. In addition, we were also able to determine that the hydrolytic mechanism of the twisted amide will be pH dependent. Thus, there is a preference for a stepwise mechanism with formation of an intermediate in the acid hydrolysis, whereas the neutral hydrolysis undergoes a concerted-type mechanism. There is a nice agreement between the characterized intermediate and available X-ray data and a good agreement with the kinetically estimated rate acceleration of hydrolysis with respect to analogous undistorted amide compounds. This work, along with previous ab initio calculations, describes a complex and rich chemistry for the hydrolysis of highly twisted amides as a function of pH. The theoretical data provided will allow for a better understanding of the available kinetic data of the rate acceleration of amides upon twisting and the relation of the observed rate acceleration with intrinsic differential reactivity upon loss of amide bond resonance.

  2. [Mechanisms of cutaneous drug reactions].

    Vaillant, L


    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).

  3. Urticarial Reaction Caused by Ethanol

    Yukinobu Nakagawa


    Discussion: Only acetic acid, a metabolite of alcohol, induced a positive prick test in the patient with alcohol-induced urticaria. This result was not observed in normal volunteers. An oral challenge test with diluted-alcohol or Shochu showed a positive wheal reaction in a dose dependent-manner which suggests that urticaria seen in this patient might be induced by alcohol-intolerance. However possible allergic reaction to acetaldehyde could not be excluded.

  4. Inorganic Reaction Mechanisms. Part I

    Cooke, D. O.


    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)

  5. Analysis of kinetic reaction mechanisms

    Turányi, Tamás


    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.

  6. Heuristics-Guided Exploration of Reaction Mechanisms

    Bergeler, Maike; Proppe, Jonny; Reiher, Markus


    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...

  7. Mechanisms of severe transfusion reactions.

    Kopko, P M; Holland, P V


    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. Heuristics-Guided Exploration of Reaction Mechanisms.

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


    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.

  9. Inorganic Reaction Mechanisms Part II: Homogeneous Catalysis

    Cooke, D. O.


    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)

  10. Physical chemistry: The fingerprints of reaction mechanisms

    Vallance, Claire


    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.

  11. Water Pollution (Causes, Mechanisms, Solution).

    Strandberg, Carl

    Written for the general public, this book illustrates the causes, status, problem areas, and prediction and control of water pollution. Water pollution is one of the most pressing issues of our time and the author communicates the complexities of this problem to the reader in common language. The purpose of the introductory chapter is to show what…

  12. Water Pollution (Causes, Mechanisms, Solution).

    Strandberg, Carl

    Written for the general public, this book illustrates the causes, status, problem areas, and prediction and control of water pollution. Water pollution is one of the most pressing issues of our time and the author communicates the complexities of this problem to the reader in common language. The purpose of the introductory chapter is to show what…

  13. Organic Reaction Mechanisms at A-Level.

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


    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)

  14. Reaction mechanisms of DNA photolyase.

    Brettel, Klaus; Byrdin, Martin


    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.

  15. The mechanism of the modified Ullmann reaction

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


    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...

  16. Reaction mechanisms: Stripping down SN2

    Orr-Ewing, Andrew J.


    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.

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

    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 ...

  18. Reaction mechanism of -acylhydroxamate with cysteine proteases

    R Shankar; P Kolandaivel


    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.

  19. Reaction time of drivers who caused road traffic accidents

    Đurić Predrag


    Full Text Available Introduction. Human factor is the single cause of road traffic injuries in 57%, and together with other factors in more than 90% of all road traffic accidents. Human factor includes many aspects, where reaction time is very important. Material and methods. Thirty healthy drivers 28-40 y.o. with 50-500 km passed per week, having caused at least one road traffic accident in the last ten years were selected, provided they were not under the influence of alcohol and drugs during traffic accident. The same number of control were selected. Both cases and controls were tested to reaction time. Results. We found statistically significant difference between car drivers who caused car accidents and those who did not in both simple and choice reaction times. Discussion. Car drivers who caused road traffic accidents have longer reaction time (both simple and choice reaction time, but as the tasks were more complex, that difference was less visible. Since drivers involved in this study had introductory phase before measuring their reaction times, they faced with unpleasant sound when they made mistake, which forced them to be aware not to make a mistake in further tasks, so they showed longer reaction times. Conclusion. Measuring of reaction time seems to be important, and as we have showed they are different in drivers who have caused road traffic accidents and those who have do not.

  20. Anaphylaxis and severe systemic reactions caused by skin contact with persulfates in hair-bleaching products.

    Hoekstra, Margriet; van der Heide, Sicco; Coenraads, Pieter Jan; Schuttelaar, Marie Louise Anna


    Persulfates have been reported to cause both delayed-type and immediate skin reactions. They may also cause immediate reactions of the mucous membranes of the bronchial system through inhalation, leading to asthma and rhinitis. Anaphylactic reactions caused by contact with persulfates are rare. The mechanism of immediate reactions caused by persulfates is unclear. To report 2 cases with systemic reactions after skin contact with persulfates, and to propose a test protocol for diagnosing immediate reactions caused by persulfates. Prick tests with serial dilutions of ammonium and potassium persulfate were performed. Patch tests were also performed with the two agents. Persulfate-specific IgE was detected with two different IgE immunoblotting techniques. Prick tests were positive with ammonium and potassium persufate, but no specific IgE was detected in the serum. Patch tests showed early positive reactions to both persulfates in 1 patient. Prick tests and patch tests can be valuable in the testing of patients with a suspicion of an immediate-type reaction caused by persulfates. The mechanism of these reactions remains unclear. © 2012 John Wiley & Sons A/S.

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

    Loveland, Walter


    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.

  2. The mechanism of the modified Ullmann reaction.

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


    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

  3. Mechanisms of inorganic and organometallic reactions

    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...

  4. Physical Mechanism of Nuclear Reactions at Low Energies

    Oleinik, V P; Arepjev, Yu.D


    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...

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

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


    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.

  6. Mechanical gating of a mechanochemical reaction cascade

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


    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.

  7. Elucidating reaction mechanisms on quantum computers.

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


    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.

  8. Analyzing Complex Reaction Mechanisms Using Path Sampling.

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


    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.

  9. Reaction mechanisms in heavy ion fusion

    Lubian J.


    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.

  10. New methods for quantum mechanical reaction dynamics

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


    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

  11. Photochromic properties and reaction mechanism of naphthopyran


    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.

  12. Photochromic properties and reaction mechanism of naphthopyran

    潘桂兰; 魏景强; 朱爱平; 明阳福; 樊美公; 姚思德


    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.

  13. Skin reactions caused by bone-anchored hearing aid (BAHA) implantation

    Gen-di Yin; Xiangli Zeng; Peng Li


    Objective: To report a case of intractable skin reactions caused by bone-anchored hearing aid (BAHA) implantation to improve our under-standing and treatment of BAHA implantation-caused skin reactions. Methods:We reported a case of severe skin reactions caused by BAHA implantation. Related literature were also reviewed. Results:We found grade IV skin reactions, including hyperplasia around the implant, which led to the removal of the BAHA implant 10 months after implantation. The findings indicated poor skin hygiene, allergy to titanium and inadequate surgicals skills as the possible causes of the skin reaction. Conclusion: Skin adverse reactions, usually rare in BAHA implantation patients, may cause implant removal and implantation failure. We suggest to further investigate the mechanisms underlying titanium allergy. Copyright © 2016, PLA General Hospital Department of Otolaryngology Head and Neck Surgery. Production and hosting by Elsevier (Singapore) Pte Ltd. This is an open access article under the CC BY-NC-ND license (

  14. Parkinsonism caused by adverse drug reactions: a case series

    Agaba Emmanuel I


    Full Text Available Abstract Introduction Parkinsonism puts a high direct cost burden on both patient and caregiver. Several reports of drug-induced parkinsonism have been published, but to the best of our knowledge, there has not been any report of quinine or halothane inducing parkinsonism. Case presentation We describe two cases of parkinsonism possibly caused by adverse drug reaction to quinine in a 29-year-old black Nigerian woman and to halothane in a 36-year-old black Hausa (Nigerian man who received it as general anaesthesia for appendicectomy in our teaching hospital. Conclusion These are two unusual cases of parkinsonism caused by adverse drug reactions to high-dose quinine and to halothane as general anaesthesia. We consider that these two cases are important in bringing this potential side-effect to the attention of both pharmacologists and primary care physicians as these are two of the most commonly used medications in our clinics. We conclude that parkinsonism should be included among the adverse drug reactions to high-dose quinine and halothane general anaesthetic.

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

    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


    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.

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

    Al-Shammari, Abdulrahman G. Alhamzani


    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

  17. Detailed reduction of reaction mechanisms for flame modeling

    Wang, Hai; Frenklach, Michael


    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.

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



    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.

  19. The mechanism of the modified Ullmann reaction

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


    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

  20. A Reduced Reaction Mechanism For Isooctane Combustion

    C.R.Berlin Selva Rex,


    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.

  1. MACiE: A Database of Enzyme Reaction Mechanisms

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


    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

  2. Mechanisms in adverse reactions to food. The sinuses

    Høst, A


    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....

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

    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

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

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori


    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.

  5. Anaphylaxis and severe systemic reactions caused by skin contact with persulfates in hair-bleaching products

    Hoekstra, Margriet; van der Heide, Sicco; Coenraads, Pieter Jan; Schuttelaar, Marielouise


    BACKGROUND: Persulfates have been reported to cause both delayed-type and immediate skin reactions. They may also cause immediate reactions of the mucous membranes of the bronchial system through inhalation, leading to asthma and rhinitis. Anaphylactic reactions caused by contact with persulfates ar

  6. Anaphylaxis and severe systemic reactions caused by skin contact with persulfates in hair-bleaching products

    Hoekstra, Margriet; van der Heide, Sicco; Coenraads, Pieter Jan; Schuttelaar, Marielouise

    BACKGROUND: Persulfates have been reported to cause both delayed-type and immediate skin reactions. They may also cause immediate reactions of the mucous membranes of the bronchial system through inhalation, leading to asthma and rhinitis. Anaphylactic reactions caused by contact with persulfates

  7. Study of Reaction Mechanism in Tracer Munitions


    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

  8. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics.

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


    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.

  9. The Cause and Mechanism of Cardiac Electrical Instability. Defibrillation Mechanism

    Rustam G. Habchabov


    Full Text Available The reason for the ominous arrhythmias pathway, causing sudden somatic death from cardiovascular diseases is still not clear, cardiological examinations of this phenomenon are conducted throughout the world. Laceration of connective insulating tissue membrane of heart pathway with ectopic nodes oxidation may cause ominous arrhythmias; nobody has considered this cause as a cardiac electrical instability before. Defibrillator electric discharges cannot penetrate into myocardium due to the connective insulating tissue membrane, nobody has considered nervous system, transmitting electricity.

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

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


    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.

  11. A thermochemically derived global reaction mechanism for detonation application

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


    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.

  12. Mechanisms for control of biological electron transfer reactions.

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


    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.

  13. Mechanical reaction-diffusion model for bacterial population dynamics

    Ngamsaad, Waipot


    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. Mechanisms in adverse reactions to food. The nose

    Høst, A


    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....

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

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


    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.

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

    Carballares, Santiago; Espinosa, Juan F


    [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.

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


    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.

  18. Mechanisms of shock-induced reactions in high explosives

    Kay, Jeffrey J.


    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.

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

    Maeda, Satoshi; Morokuma, Keiji


    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.

  20. Phototoxic and contact toxic reactions of the exocarp of sweet oranges: a common cause of cheilitis?

    Volden, G; Krokan, H; Kavli, G; Midelfart, K


    Irritant skin reactions were produced within 1 h after application of the exocarp of sweet oranges or alcoholic extracts therefrom. Such reactions faded within 48 h. The exocarp, or extracts thereof, induced phototoxic reactions which were strongest at 72 h after exposure. The phototoxic reactions were only induced in natural blondes and only with some oranges. The in vivo phototoxic reactions were confirmed in vitro, causing a slight but clear photo-inhibition of Candida albicans. Only some oranges inhibited growth.

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

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


    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.

  2. Mechanisms in adverse reactions to food. The ear

    Høst, A


    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...

  3. Real causes of apparent abnormal results in heavy ion reactions

    Mandaglio G.


    Full Text Available We study the effect of the static characteristics of nuclei and dynamics of the nucleus-nucleus interaction in the capture stage of reaction, in the competition between quasifission and complete fusion processes, as well as the angular momentum dependence of the competition between fission and evaporation processes along the de-excitation cascade of the compound nucleus. The results calculated for the mass-asymmetric and less mass-asymmetric reactions in the entrance channel are analyzed in order to investigate the role of the dynamical effects on the yields of the evaporation residue nuclei. We also discuss about uncertainties at the extraction of such relevant physical quantities as Γn/Γtot ratio or also excitation functions from the experimental results due to the not always realistic assumptions in the treatment and analysis of the detected events. This procedure can lead to large ambiguity when the complete fusion process is strongly hindered or when the fast fission contribution is large. We emphasize that a refined multiparameter model of the reaction dynamics as well as a more detailed and checked data analysis are strongly needed in heavy-ion collisions.

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

    Knizia, Gerald; Klein, Johannes E M N


    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.

  5. Suicide by cop: causes, reactions, and practical intervention strategies.

    Miller, Laurence


    Due to a combination of interpersonal manipulativeness, personal identification, and lack of heroic status, most police officers find suicide by cop (SBC) calls to be among the most disturbing shooting incidents. This article describes the dynamics of SBC and some of the factors that may contribute to it. Operational strategies and psychological techniques for de-escalating and resolving a SBC crisis are discussed. Finally, psychological reactions by officers to a SBC and psychotherapeutic strategies for dealing with the aftermath are described. Especially important is the recommendation that officers use intervention "failures" as tools for learning, so that purposeless remorse can be turned into enhanced life-saving skills for the next incident.

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

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


    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.

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

    Froehaug, Astrid Elisabeth


    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.

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

    Stéphanie S. Le Corre


    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.

  9. On the Reaction Mechanism of Br2 with OCS

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


    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.

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

    Tuomas Eerola; Henna-Riikka Peltola


    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...

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

    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

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

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


    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.

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

    Björk, J


    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.

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

    Chang Cai Bai


    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.

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

    Garrison, W.M.


    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.

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

    Chatterjee, D; Deutschmann, O; Warnatz, J


    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.

  17. Systematic development of reduced reaction mechanisms for dynamic modeling

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


    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.

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

    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)


    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.

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

    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.

  20. Divergent reaction mechanisms in the aminofluorination of alkenes.

    Kong, Wangqing; Merino, Estíbaliz; Nevado, Cristina


    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.

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

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


    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.

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

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


    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.

  3. Alcali-silica reactions: Mechanisms for crack formations

    Goltermann, Per


    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 ...

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

    Li, Wenjin; Ma, Ao


    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.

  5. Adverse drug reaction and toxicity caused by commonly used antimicrobials in canine practice

    K. Arunvikram


    Full Text Available An adverse drug reaction (ADR is a serious concern for practicing veterinarians and other health professionals, and refers to an unintended, undesired and unexpected response to a drug that negatively affects the patient's health. It may be iatrogenic or genetically induced, and may result in death of the affected animal. The ADRs are often complicated and unexpected due to myriad clinical symptoms and multiple mechanisms of drug-host interaction. Toxicity due to commonly used drugs is not uncommon when they are used injudiciously or for a prolonged period. Licosamides, exclusively prescribed against anaerobic pyoderma, often ends with diarrhoea and vomiting in canines. Treatment with Penicillin and β-lactam antibiotics induces onset of pemphigious vulgare, drug allergy or hypersensitivity. Chloroamphenicol and aminoglycosides causes Gray's baby syndrome and ototoxicity in puppies, respectively. Aminoglycosides are very often associated with nephrotoxicity, ototoxicity and neuromuscular blockage. Injudicious use of fluroquinones induces the onset of arthropathy in pups at the weight bearing joints. The most effective therapeutic measure in managing ADR is to treat the causative mediators, followed by supportive and symptomatic treatment. So, in this prospective review, we attempt to bring forth the commonly occurring adverse drug reactions, their classification, underlying mechanism, epidemiology, treatment and management as gleaned from the literature available till date and the different clinical cases observed by the authors.

  6. Hydroxylation Reaction Mechanism for Nitrosodimethylamine by Oxygen Atom

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


    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.

  7. Reaction Mechanisms of the Initial Oligomerization of Aluminophosphate.

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


    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.

  8. nonlinear kinetics and mechanism of nile blue reaction

    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-.

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

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


    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.

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

    Kitada, Kodai; Suda, Yusuke; Takenaka, Norimichi


    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).

  11. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

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


    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

  12. Voltage hysteresis of lithium ion batteries caused by mechanical stress.

    Lu, Bo; Song, Yicheng; Zhang, Qinglin; Pan, Jie; Cheng, Yang-Tse; Zhang, Junqian


    The crucial role of mechanical stress in voltage hysteresis of lithium ion batteries in charge-discharge cycles is investigated theoretically and experimentally. A modified Butler-Volmer equation of electrochemical kinetics is proposed to account for the influence of mechanical stresses on electrochemical reactions in lithium ion battery electrodes. It is found that the compressive stress in the surface layer of active materials impedes lithium intercalation, and therefore, an extra electrical overpotential is needed to overcome the reaction barrier induced by the stress. The theoretical formulation has produced a linear dependence of the height of voltage hysteresis on the hydrostatic stress difference between lithiation and delithiation, under both open-circuit conditions and galvanostatic operation. Predictions of the electrical overpotential from theoretical equations agree well with the experimental data for thin film silicon electrodes.

  13. DFT study on mechanism of the classical Biginelli reaction

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


    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.

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

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


    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.

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

    Pandey Bhawna


    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.

  16. Theoretical study of reaction mechanism for NCO + HCNO

    Zhang, Weichao; Du, Benni; Feng, Changjun


    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.

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

    Quitterer, Felix


    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.

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

    Zhaoyong Liu


    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.

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

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


    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. EFL Foreign Teacher Stress in Korea: Causes and Coping Mechanisms

    Brundage, Gregory C.


    Survey study of 53 foreign EFL teachers in Jeonju City, South Korea looks at causes of teacher stress and coping mechanisms between the years of 2004 and 2006. Results show foreign EFL teachers report moderate levels of stress and attribute stresses in roughly equal measures to student misbehavior and school director/administrative sources. Survey…

  1. Reactions of a stable dialkylsilylene and their mechanisms

    Mitsuo Kira


    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.

  2. Automated exploration of the mechanism of elementary reactions

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


    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.

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

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


    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.

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

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


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

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


    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.

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

    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

  7. Insight into the Mechanism of the Michael Reaction.

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


    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.


    Bao-jun Qu


    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.

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

    Kraka, Elfi; Cremer, Dieter


    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

  10. BlenX-based compositional modeling of complex reaction mechanisms

    Zámborszky, Judit; 10.4204/EPTCS.19.6


    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...

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

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


    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.

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

    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.

  13. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    Ziaul Huque


    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.

  14. HF(v′ = 3) forward scattering in the F + H2 reaction: Shape resonance and slow-down mechanism

    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.


    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

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

    Singh, M.


    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.

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

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


    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.

  17. Immunological reactions caused by helminthes and diagnosis of parasites using different methods



    Full Text Available Helminthes are one of the causer agents of the type I reactions of hypersensitivity. In this article will review the findings of recent human studies of the association between helminth parasite infections and allergy and discuss their potential relevance to public health. The parasitic worms are an important risk factor for anaphylaxy reaction, but this could be explained by an enhanced ability of atopics to produce IgE. The human immune response to helminth infections is associated with elevated levels of IgE, tissue eosinophilia and mastocytosis. The involvement of immunologic mechanisms in the pathogenesis which are caused by worms in the gastro-intestinal tract are associated with anaphylaxy response. For this study, faeces were collected primary in children aged 1-15 years old, because the worms are most frequent in these ages. Through the coproscopic method were analyzed as biological materials, the feces of 300 children for the presence of protozoa’s eggs, helminthes larva, trophosoids, cists, etc. We have taken the photo of the positive cases. The analysis have been done in the Parasitological Laboratory of the Institute of Public Health, Tirana through the method of concentration with floatation in sulphat zinc; the permanent color as Ziehln-Neelsen stain, Giemsa stain, Blu-metilen, etc. We have used the color methods and blood striche to diagnose the eosiniphilia presence. To determine the IgE are used the EIA kits. The level of the eosinophyle and IgE in the blood is performed in 152 individes who had been positive cases by helminths.

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

    Solov'yov, Ilia; Schulten, Klaus


    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.

    Soriano, Elena; Fernández, Israel


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

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


    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.

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

    Ozen, Cihan; Tüzün, Nurcan Ş


    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



    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.

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


    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. [Carbamylation of proteins--mechanism, causes and consequences].

    Pieniążek, Anna; Gwoździński, Krzysztof


    Carbamylation (carbamoylation) is a post-translational modification resulting from the nonenzymatic reaction between isocyanic acid and free functional groups of proteins, in particular with the free amino groups. This reaction alters structural and functional properties of proteins and results in faster aging of proteins. Urea present in the body can be transformed into cyanate and its more reactive form, isocyanic acid. High concentration of urea is associated with some diseases, especially with chronic renal failure and atherosclerosis. In human tissues, urea and cyanate are in equilibrium in aqueous solutions. Surprisingly, concentration of isocyanate in the body is much lower than it would appear from the kinetic parameters of urea decomposition. The low concentration of isocyanic acid results from its high reactivity and short half-life. In this review we describe the biochemical mechanism of carbamylation of proteins and free amino acids. We summarize the literature data for carbamylation of hemoglobin, lipoproteins, albumin, membrane proteins and erythropoietin in chronic renal failure. In summary, the carbamylation of proteins may have a negative impact on their biological activity and may contribute to the deterioration of patients with chronic renal failure.

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

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


    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.

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

    Stockwell Timothy B


    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.

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

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


    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...

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


    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. Successful desensitization protocol for hypersensitivity reaction probably caused by dabrafenib in a patient with metastatic melanoma.

    Bar-Sela, Gil; Abu-Amna, Mahmoud; Hadad, Salim; Haim, Nissim; Shahar, Eduardo


    Vemurafenib and dabrafenib are both orally bioavailable small molecule agents that block mitogen activated protein kinase signalling in patients with melanoma and BRAF(V600E) mutation. Generalized hypersensitivity reactions to vemurafenib or dabrafenib have not been described. Continuing vemurafenib or dabrafenib therapy despite hypersensitivity reaction is especially important in patients with melanoma and BRAF(V600E) mutation, in whom this mutation plays a critical role in tumour growth. Desensitization protocols to overcome hypersensitivity reactions by gradual reintroduction of small amounts of the offending drug up to full therapeutic doses are available for many anti-cancer agents, including vemurafenib but, to the best of our knowledge, have not been reported for dabrafenib. We describe a patient with metastatic melanoma who developed Type I hypersensitivity reaction to vemurafenib and to subsequent treatment with dabrafenib, and who was successfully treated by drug desensitization which allowed safe prolonged continuation of dabrafenib. The development of hypersensitivity reactions for both dabrafenib and vemurafinib in the current case could be because these drugs have a similar chemical structure and cause a cross-reactivity. However, hypersensitivity reaction to a non-medicinal ingredient shared by the two drugs is also possible. Oral desensitization appears to be an option for patients with hypersensitivity Type I to dabrafenib. This approach may permit clinicians to safely administer dabrafenib to patients who experience hypersensitivity reactions to this life-prolonging medication. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email:

  10. The perturbed magnetic fields caused by mechanical stress

    QIN Fei; YAN Dong-mei


    In the framework of the linearized magnetoelastic theory,the perturbed magnetic fields caused by mechanical stress and deformation were investigated theoretically.Governing equations and boundary conditions to determine the perturbed fields were derived.The effect of mechanical deformation on the magnetic fields was taken into account by coupling structural displacement into the perturbed magnetic field continuous conditions on the boundary of the structure.As an example,the perturbed field of a half-plane magnetized structure caused by a point force was calculated by the Fourier transform method.The results show that the calculated magnetic intensity component normal to the boundary of the structure reaches its maximum at the point force acted while the component tangent to the boundary inverses its direction sharply.The magnetic induction of the perturbed field is proportional to the applied force.Magnitude analysis proved that since the applied magnetic field has a relative weak intensity such as the Earth's magnetic field, influence of the magnetic field on deformation of the structure can be neglected.

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

    Cai, Liming


    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.


    Jelena TADIKJ


    Full Text Available Stuttering is a disorder that represents multifunctional problem. It probably exists since the beginning of mankind. Its’ frequency and severity are influenced by different factors. Among the most significant ones are the complexity of statement, speaking speed, and speakers’ emotional reaction to the whole speech situation and other co-speakers. Goal: To present the results of two-weeks intensive group stationary treatment of adults who stutter, especially stuttering severity and level of subjective distress caused by co-speakers’ reactions in the beginning and at the end of the treatment. Subjects: A group of 25 adults who stutter. Methodology: At the beginning and at the end of the group stationary treatment speech status was taken, consisting of counting, enumerating, repeating the sentences, reading a 100-word tale, retelling the read text, and conversation on a free subject. In the same time, subjective distress caused by 13 different co-speakers reactions was estimated. Results show that very positive results are achieved in the reduction of speech disfluences, as well as moderate reduction of subjective distress caused by co-speakers’ reactions. In the paper the results are shown in more details, and, subsequently, implications for further research and treatment.

  13. BlenX-based compositional modeling of complex reaction mechanisms

    Judit Zámborszky


    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.

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

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


    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.

  15. Reaction mechanisms and staggering in S+Ni collisions

    D' Agostino, M., E-mail: [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)


    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.

  16. Reaction mechanisms and staggering in S+Ni collisions

    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.


    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.

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

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


    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.

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

    Vorotilin, V. P.


    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.

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

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


    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.

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

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


    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.

  1. 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.

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


    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.

  2. Cutaneous reactions to heparin therapy: when are they caused by heparin allergy?

    Giuliana Zisa


    Full Text Available Introduction: Little is known about the incidence and causes of heparin-induced skin lesions. The most commonly reported causes are delayed-type hypersensitivity reactions. We describe 3 patients who were referred to our staff between March and October 2009 for suspected heparin allergies. All were scheduled to undergo major surgery (cardiovascular or orthopedic. Materials and methods: All 3 patients reported the development of itchy, erythematous rashes a few days after the subcutaneous administration of heparin (nadroparin calcium in cases 1 and 2, unspecified in case 3. Each of them underwent a diagnostic work-up for heparin allergy, which included prick and intradermal tests with commonly used heparins and patch testing with undiluted heparins and disinfectants. Results: Patch tests with disinfectants were negative in all 3 cases. In case 2, all allergological tests were negative. In cases 1 and 3, delayed positivity emerged for nadroparin calcium and at least one other heparin tested. Intravenous and/or subcutaneous provocation testing was done with an alternative heparin which produced negative results in skin tests (heparin sodium in case 1, pentasaccharide fondaparinux in case 3. In both cases the alternative drug was tolerated. After our evaluation, all 3 patients underwent surgery with no heparin-related complications. Discussion: The presenting clinical features in these 3 cases provided no information on which reactions were likely to be allergic: all 3 patients presented with similar local delayed reaction. The allergic reactions were identified only after cutaneous testing.

  3. Sedation for pediatric radiological procedures: analysis of potential causes of sedation failure and paradoxical reactions

    Karian, V.E.; Burrows, P.E.; Connor, L. [Dept. of Radiology, Children' s Hospital, Boston, MA (United States); Zurakowski, D. [Dept. of Biostatistics, Children' s Hospital, Boston, MA (United States); Mason, K.P. [Dept. of Anesthesiology, Children' s Hospital, Boston, MA (United States)


    Background. Sedation for diagnostic imaging and interventional radiologic procedures in pediatrics has greatly increased over the past decade. With appropriate patient selection and monitoring, serious adverse effects are infrequent, but failure to sedate and paradoxical reactions do occur. Objective. The purpose of this study was to determine, among patients undergoing sedation for radiologic procedures, the incidence of sedation failure and paradoxical reaction to pentobarbital and to identify potentially correctable causes. Materials and methods. Records of 1665 patients who were sedated in the radiology department from 1 November 1997 to 1 July 1998 were reviewed. Patients failing sedation or experiencing paradoxical reaction were compared with respect to sex, age group, diagnosis, scan type, time of day, NPO status, use of IV contrast and type of sedation agent using the Fisher exact test, Pearson chi-square, analysis of variance (ANOVA), the Student t-test, and logistic regression. Results. Data analysis revealed a sedation failure rate of 1 % and paradoxical reaction rate of 1.2 %. Stepwise multiple logistic regression revealed that the only significant independent multivariate predictor of failure was the need for the administration of a combination of pentobarbital, fentanyl, and midazolam IV. Conclusion. The low rate of sedation failure and paradoxical reactions to pentobarbital was near optimal and probably cannot be improved with the currently available sedatives. (orig.)

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

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


    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.

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


    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.

  6. Directed networks' different link formation mechanisms causing degree distribution distinction

    Behfar, Stefan Kambiz; Turkina, Ekaterina; Cohendet, Patrick; Burger-Helmchen, Thierry


    Within undirected networks, scientists have shown much interest in presenting power-law features. For instance, Barabási and Albert (1999) claimed that a common property of many large networks is that vertex connectivity follows scale-free power-law distribution, and in another study Barabási et al. (2002) showed power law evolution in the social network of scientific collaboration. At the same time, Jiang et al. (2011) discussed deviation from power-law distribution; others indicated that size effect (Bagrow et al., 2008), information filtering mechanism (Mossa et al., 2002), and birth and death process (Shi et al., 2005) could account for this deviation. Within directed networks, many authors have considered that outlinks follow a similar mechanism of creation as inlinks' (Faloutsos et al., 1999; Krapivsky et al., 2001; Tanimoto, 2009) with link creation rate being the linear function of node degree, resulting in a power-law shape for both indegree and outdegree distribution. Some other authors have made an assumption that directed networks, such as scientific collaboration or citation, behave as undirected, resulting in a power-law degree distribution accordingly (Barabási et al., 2002). At the same time, we claim (1) Outlinks feature different degree distributions than inlinks; where different link formation mechanisms cause the distribution distinctions, (2) in/outdegree distribution distinction holds for different levels of system decomposition; therefore this distribution distinction is a property of directed networks. First, we emphasize in/outlink formation mechanisms as causal factors for distinction between indegree and outdegree distributions (where this distinction has already been noticed in Barker et al. (2010) and Baxter et al. (2006)) within a sample network of OSS projects as well as Java software corpus as a network. Second, we analyze whether this distribution distinction holds for different levels of system decomposition: open

  7. 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.

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


    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.

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

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


    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.

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

    Ai-jie Zhang; Guo-zhong He


    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.

  10. Identifying the causes of differences in ozone production from the CB05 and CBMIV chemical mechanisms

    R. D. Saylor


    Full Text Available An investigation was conducted to identify the mechanistic differences between two versions of the carbon bond gas-phase chemical mechanism (CB05 and CBMIV which consistently lead to larger ground-level ozone concentrations being produced in the CB05 version of the National Air Quality Forecasting Capability (NAQFC modeling system even though the two parallel forecast systems utilize the same meteorology and base emissions and similar initial and boundary conditions. Box models of each of the mechanisms as they are implemented in the NAQFC were created and a set of 12 sensitivity simulations was designed. The sensitivity simulations independently probed the conceptual mechanistic differences between CB05 and CBMIV and were exercised over a 45-scenario simulation suite designed to emulate the wide range of chemical regimes encountered in a continental-scale atmospheric chemistry model. Results of the sensitivity simulations indicate that two sets of reactions that were included in the CB05 mechanism, but which were absent from the CBMIV mechanism, are the primary causes of the greater ozone production in the CB05 version of the NAQFC. One set of reactions recycles the higher organic peroxide species of CB05 (ROOH, resulting in additional photochemically reactive products that act to produce additional ozone in some chemical regimes. The other set of reactions recycles reactive nitrogen from less reactive forms back to NO2, increasing the effective NOx concentration of the system. In particular, the organic nitrate species (NTR, which was a terminal product for reactive nitrogen in the CBMIV mechanism, acts as a reservoir species in CB05 to redistribute NOx from major source areas to potentially NOx-sensitive areas where additional ozone may be produced in areas remote from direct NOx sources.

  11. Identifying the causes of differences in ozone production from the CB05 and CBMIV chemical mechanisms

    R. D. Saylor


    Full Text Available An investigation was conducted to identify the mechanistic differences between two versions of the carbon bond gas-phase chemical mechanism (CB05 and CBMIV which consistently lead to larger ground-level ozone concentrations being produced in the CB05 version of the National Air Quality Forecasting Capability (NAQFC modeling system even though the two parallel forecast systems utilize the same meteorology and base emissions and similar initial and boundary conditions. Box models of each of the mechanisms as they are implemented in the NAQFC were created and a set of 12 sensitivity simulations was designed. The sensitivity simulations independently probed the conceptual mechanistic differences between CB05 and CBMIV and were exercised over a 45-scenario simulation suite designed to emulate the wide range of chemical regimes encountered in a continental-scale atmospheric chemistry model. Results of the sensitivity simulations indicate that two sets of reactions that were included in the CB05 mechanism, but which were absent from the CBMIV mechanism, are the primary causes of the greater ozone production in the CB05 version of the NAQFC. One set of reactions recycles the higher organic peroxide species of CB05 (ROOH, resulting in additional photochemically reactive products that act to produce additional ozone in some chemical regimes. The other set of reactions recycles reactive nitrogen from less reactive forms back to NO2, increasing the effective NOx concentration of the system. In particular, the organic nitrate species (NTR, which was a terminal product for reactive nitrogen in the CBMIV mechanism, acts as a reservoir species in CB05 to redistribute NOx from major source areas to potentially NOx-sensitive areas where additional ozone may be produced in areas remote from direct NOx sources.

  12. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    Nelson Butuk


    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.

  13. Theoretical Study on the Mechanism of Sonogashira Coupling Reaction

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


    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.

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

    Pignatelli, Rossella, E-mail: [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: [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Monteiro, Paulo J.M., E-mail: [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)


    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.

  15. Structure and reaction mechanism of basil eugenol synthase.

    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

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

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


    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.

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

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


    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.

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

    Simpson, Peter


    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)

  19. Mechanism of reaction synthesis of Li-B alloys

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


    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.

  20. The mechanism by which fish antifreeze proteins cause thermal hysteresis.

    Kristiansen, Erlend; Zachariassen, Karl Erik


    Antifreeze proteins are characterised by their ability to prevent ice from growing upon cooling below the bulk melting point. This displacement of the freezing temperature of ice is limited and at a sufficiently low temperature a rapid ice growth takes place. The separation of the melting and freezing temperature is usually referred to as thermal hysteresis, and the temperature of ice growth is referred to as the hysteresis freezing point. The hysteresis is supposed to be the result of an adsorption of antifreeze proteins to the crystal surface. This causes the ice to grow as convex surface regions between adjacent adsorbed antifreeze proteins, thus lowering the temperature at which the crystal can visibly expand. The model requires that the antifreeze proteins are irreversibly adsorbed onto the ice surface within the hysteresis gap. This presupposition is apparently in conflict with several characteristic features of the phenomenon; the absence of superheating of ice in the presence of antifreeze proteins, the dependence of the hysteresis activity on the concentration of antifreeze proteins and the different capacities of different types of antifreeze proteins to cause thermal hysteresis at equimolar concentrations. In addition, there are structural obstacles that apparently would preclude irreversible adsorption of the antifreeze proteins to the ice surface; the bond strength necessary for irreversible adsorption and the absence of a clearly defined surface to which the antifreeze proteins may adsorb. This article deals with these apparent conflicts between the prevailing theory and the empirical observations. We first review the mechanism of thermal hysteresis with some modifications: we explain the hysteresis as a result of vapour pressure equilibrium between the ice surface and the ambient fluid fraction within the hysteresis gap due to a pressure build-up within the convex growth zones, and the ice growth as the result of an ice surface nucleation event at

  1. Theoretical Study of Sodium-Water Surface Reaction Mechanism

    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).

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

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


    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.

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

    Ahlborg, Nadia L.; Zhu, Dongming


    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.

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

    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.

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

    Eerola, Tuomas; Peltola, Henna-Riikka


    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.

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

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


    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.

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

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


    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.

  8. Current advances in ant venom proteins causing hypersensitivity reactions in the Asia-Pacific region.

    Srisong, Hathairat; Daduang, Sakda; Lopata, Andreas L


    The main insects causing allergy reactions to stinging insect in humans are Apidae (bees), Vespidae (wasps, yellow jackets and hornets) and Formicidae (ants). Their venom stings are composed of various biologically active peptides and protein components, some of which can cause toxicity or anaphylaxis in humans. The protein venom demonstrate some common allergenic activity such as for fire ants and vespids, which have two common allergens that are phospholipase A1 (enzymatic activity) and antigen 5 with unknown biological activity. The common allergens seem to share some degree of immunological cross-reactivity, particularly when the sequence homology is above 70%. Therefore immunotherapeutic approaches targeting more than one specific species are of interest. Recent widespread increases of various ant species in many countries have resulted in higher number of reported about serious allergic reactions to stings. Most insect-allergy related cases have been reported for species from Solenopsis, Myrmecia and Pachycondyla genera, and their stings can often result in human fatalities. In addition, stinging ants can have serious health effects on livestock, agricultural damage adversely affecting the biodiversity of the region. This review discusses the impact of important ant species on human health in the Asia-Pacific region along with the molecular immunological aspects of the identified venoms and current status of diagnostics and therapeutics. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

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

    Tada, Mika; Niwano, Yoshimi; Kohno, Masahiro


    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.

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

    György Keglevich


    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.

  11. Robot Vibrations Caused by Torque Ripples in Power Transmission Mechanisms

    小島, 宏行; 田口, 和哉; 辻, 浩明


    When an industrial robot with a power transmission mechanism such as a harmonic drive gear is operated, vibrations resulting from the torque ripple of the power transmission mechanism are frequently generated. However, few studies on robot vibration characteristics owing to torque ripples have been reported. In this paper, the vibrations of a horizontal two-link robot are investigated with consideration given to the torque ripple and the nonlinearity of the power transmission mechanism. In th...

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

    Yin, Hongyun; Wang, Dunyou; Valiev, Marat


    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.

  13. MECHANISMS IN ENDOCRINOLOGY: Novel genetic causes of short stature.

    Wit, Jan M; Oostdijk, Wilma; Losekoot, Monique; van Duyvenvoorde, Hermine A; Ruivenkamp, Claudia A L; Kant, Sarina G


    The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFκB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. Heterozygous NPR2 or SHOX defects may be found in ∼3% of short children, and also rasopathies (e.g., Noonan syndrome) can be found in children without clear syndromic appearance. Numerous other syndromes associated with short stature are caused by genetic defects in fundamental cellular processes, chromosomal abnormalities, CNVs, and imprinting disorders.

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

    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:


    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.

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

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


    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.

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

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


    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...

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

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


    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)

  18. Magnetic isotope effect and theory of atomic orbital hybridization to predict a mechanism of chemical exchange reactions.

    Epov, Vladimir N


    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.

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

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


    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.

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

    WANG Qiang; CHEN YunGui; WU ChaoLing; TAO MingDa


    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.

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

    Dijkstra Albert J.


    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.

  2. The Mechanisms of the Ecdysone Pulses that Cause Metamorphosis

    Møller, Morten Erik

    Maturation in both mammals and insects is caused by pulses of steroid hormones released from glands in response to a brain-derived signal. The timing of this developmental transition is secured by the integration of many developmental cues, such as size, external environment and nutritional...... condition, with hardwired genetic programs. In holometabolous insects, pulses of the steroid hormone ecdysone cause the transition between the larval stages and the initiation of the metamorphosis, which transforms the juvenile larva to a sexually mature adult. Ecdysone is produced in the prothoracic gland...

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

    Weydert, M.


    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)

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

    Weydert, M.


    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)

  5. Effect of atmospheric oxidative plasma treatments on polypropylenic fibers surface: Characterization and reaction mechanisms

    Nisticò, Roberto, E-mail: [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)


    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.

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

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


    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.

  7. Kinetics and reaction mechanism of yeast alcohol dehydrogenase with long-chain primary alcohols.

    Schöpp, W; Aurich, H


    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

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

    Cerar, Janez


    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.

  9. The Mechanisms of the Ecdysone Pulses that Cause Metamorphosis

    Møller, Morten Erik

    Maturation in both mammals and insects is caused by pulses of steroid hormones released from glands in response to a brain-derived signal. The timing of this developmental transition is secured by the integration of many developmental cues, such as size, external environment and nutritional...... condition, with hardwired genetic programs. In holometabolous insects, pulses of the steroid hormone ecdysone cause the transition between the larval stages and the initiation of the metamorphosis, which transforms the juvenile larva to a sexually mature adult. Ecdysone is produced in the prothoracic gland...... elucidated, many questions of how the system is regulated remain unknown. The first part of the thesis focuses on a genome-wide in-vivo RNAi screen, where 90 % of the protein coding genes in Drosophila were knocked down tissue-specifically in the cells of the PG. 15.2% of the genes led to developmental...

  10. Elucidation of Reaction Mechanisms Far from Thermodynamic Equilibrium.

    Nagao, Raphael


    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.

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

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


    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.

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

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


    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…

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

    Cseko, György; Horváth, Attila K


    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

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

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


    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


    Ai-ying Liu; Ming-jun Jiang; Yue-ping Yin; Jiang-fang Sun


    Objective To establish a multiplex polymerase chain reaction (M-PCR) assay for simultaneous detection of pathogens causing genital ulcer disease (GUD).Methods Based on the gene-specific region of the following pathogens: Chlamydia trachomatis ompl/ompb, herpes simplex virus (HSV) DNA polymerase, Treponema pallidum tpp47, Haemophilus ducreyi 16s rRNA, four sets of primers were designed and an M-PCR assay was developed to detect four pathogens in one test. The assay was evaluated with diagnostic result of golden standard for each pathogen.Results Of the 51 clinical samples, M-PCR showed slightly higher positive rate (47.1%) of HSV than cell culture (23.6%).Meanwhile, the positive rate of T. p allidum detected by M-PCR and dark-field microscopy was 19.6% ( 10/51) and 15.7% (8/51),respectively. Only one sample was positive for H. ducreyiand no sample was positive for C. trachomatis detected by both M-PCR assay and culture.Conclusion This primary study indicated that M-PCR assay can simultaneously and rapidly detect the four etiologic pathogens causing GUD.

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

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


    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.

  17. Altered cupular mechanics: a cause of peripheral vestibular disorders?

    Helling, Kai; Watanabe, Nobuhiro; Jijiwa, Hiroyasu; Mizuno, Yoshio; Watanabe, Satoru; Scherer, Hans


    It has taken many decades to arrive at today's concept of cupula mechanics in the stimulation of endolymphatic flows on the hair cells in the ampullae of the semicircular canal. While Steinhausen assumed free swing-door movement of the cupula in the 1930s, Hillman was the first to demonstrate firm cupula attachment to the ampulla wall as a physiological necessity in the 1970s. In contrast to the present clinical concepts of acute peripheral vestibular functional disorders (circulatory disturbances, viral or bacterial infection, altered electrolytes in the endolymph), this study examines the extent to which an impaired attachment mechanism can trigger peripheral vestibular disorders. For this purpose, we used a pigeon model (n = 8), in which mechanical detachment of the cupula from the ampulla wall was achieved by means of a targeted pressure increase in the ampulla of the lateral semicircular canal. In two additional animals the labyrinth was completely destroyed on one side in order to directly compare partial and complete vestibular disorders. In this way partial damage to the lateral semicircular canal ampulla presents a clinical picture whose symptoms are very similar to those of an idiopathic vestibular disorder in humans. Their intensity and course of compensation differ markedly from the symptoms of complete vestibular destruction. Subsequent histological examination revealed that the hair cells remained intact during the experimental detachment of the cupula. Our results thus show that only altered cupula mechanics seem to trigger the clinical picture of a peripheral vestibular disorder. This may result in completely new approaches to differential diagnosis and the therapy of vestibular neuronitis.

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

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


    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.

  19. Eletromagnetic radiation and the mechanical reactions arising from it

    Schott, G A


    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.

  20. Adult Scheuermann’s disease as cause of mechanic dorsalgia

    F.P. Cantatore


    Full Text Available Scheuermann’s disease (SD or vertebral osteochondrosis is the most frequent cause of non postural kyphosis and one of more frequent cause of adolescent’s dorsalgia. The criteria for the diagnosis are: more than 5° of wedging of at least three adjacent vertebrae at the apex of the kyphosis; a toracic kyphosis of more than 45° of Cobb’s degree; Schmorl’s nodes and endplates irregularities. In addition to classic SD, there are radiological alterations that remain asintomatic for a long time to reveal in adult age: in that case it speaks of adult Scheuermann’s disease (ASD. We considered the diagnosis of patients came from April 2006 to April 2007 on Day Hospital in our Clinic. ASD was diagnosed, besides, in 10 of these patients. 7 patients had previous diagnosis such as: dorsal Spondiloarthrosis (4 subjects; Osteoporosis with vertebral fractures (3 subjects. All these diagnosis was not confirmed by us. In case of chronic dorsalgia of adult, ASD is rarely considered as differential diagnosis. Besides, the vertebral dorsalgia, even in absence of red flags as fever, astenia, ipersedimetry, functional loss and aching spinal processes to tapping, could hide a serious scene that lead us to be careful in the differential diagnosis, because of similar radiological pictures of the MSA to other pathology as spondylodiscitis, primitive or metastasic spinal tumors, and brittleness vertebral fractures

  1. Point-source idealization in classical field theories. II. Mechanical energy losses from electromagnetic radiation reaction

    Kates, Ronald E.; Rosenblum, Arnold


    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.

  2. Program Helps To Determine Chemical-Reaction Mechanisms

    Bittker, D. A.; Radhakrishnan, K.


    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.


    Bronfenbrenner, J


    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.

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

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


    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.

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


    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.

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

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


    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.

  7. Solvothermal synthesis and reaction mechanism of CoO nanoparticles

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


    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.

  8. Nuclear and hadronic reaction mechanisms producing spin asymmetry

    Ken-Ichi Kubo


    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.

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

    Solov'yov, Ilia; Schulten, Klaus


    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...

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

    Holman, R. W.


    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.

  11. Automatic analysis and reduction of reaction mechanisms for complex fuel combustion

    Nilsson, Daniel


    general, detailed calculations of temperature, pressure, concentration and flame velocity show excellent agreement with measurements. Skeletal mechanisms for PRF were constructed for the SI engine case, reproducing autoignition well on removal of reactions pertaining to 15% of the species. QSSA reduction was tested on the staged combustor and the engines, using pure and weighted lifetime indices. Monitoring NO concentrations in the staged combustor and ignition timing in the engines, good reproduction is possible while approximating about 70% of the species. However, some species have to be manually retained for accuracy and numerical stability. For improved ranking, sensitivity was added to the index applied to the premixed flames, in addition to necessary molecular transport information. The maximum atomic mass fraction occupied by a certain molecular species was also constrained to limit the mass and energy deficiency caused by QSSA. For methane, the laminar flame velocities as well as concentration profiles are well predicted by the most strongly reduced mechanism with five global reaction steps. For the kerosene surrogate mechanism, QSSA involving 50% of the species was successfully attempted.

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

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


    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.

  13. Genital infection caused by Entamoeba histolytica confirmed by polymerase chain reaction analyses.

    Asano, Hiroshi; Kaneuchi, Masanori; Furuta, Itsuko; Yamaya, Yukie; Hatanaka, Kanako C; Takeda, Mahito; Matsuno, Yoshihiro; Sakuragi, Noriaki


    Entamoeba histolytica is estimated to infect approximately 1% of the global population. In Japan, the prevalence of amebic dysentery has been increasing, with more than 800 patients newly diagnosed annually. However, genital infection with E. histolytica is uncommon even in endemic areas. We present a case of vaginitis caused by E. histolytica. A 50-year-old Japanese woman without history of overseas travel presented to a nearby clinic with increased vaginal discharge. She had hemorrhagic erosion at the uterine cervix with yellowish vaginal discharge, and was referred to our hospital for exclusion of malignancy. Cervical cytology revealed periodic acid-Schiff-positive protozoa not aggregating around squamous cells, and thus amebic vaginitis was suspected. We performed polymerase chain reaction (PCR) analyses and identified E. histolytica. The vaginitis was treated with metronidazole, and the disappearance of amebic protozoa was confirmed by cytology and PCR. Therefore, it may be important to obtain early diagnosis by cervical cytology and PCR.

  14. The influence of the "cage effect" on the mechanism of reversible bimolecular multistage chemical reactions in solutions.

    Doktorov, Alexander B


    Manifestations of the "cage effect" at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a "cage complex." Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the "cage effect" leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

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

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


    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

  16. Mitigation Effect of Proanthocyanidin on Secondary Heart Injury in Rats Caused by Mechanical Trauma

    Ma, Shuo; Chen, Chong; Cao, Tingting; Bi, Yue; Zhou, Jicheng; Li, Xintao; Yu, Deqin; Li, Shuzhuang


    Multiple organ dysfunctional syndrome secondary to mechanical trauma (MT) has attracted considerable research attention. The heart is one of the most important organs of the body, and secondary cardiac insufficiency caused by MT seriously affects the quality of life. This study aims to investigate whether proanthocyanidin can alleviate myocardial injury and improve heart function in the process of MT leading to secondary cardiac insufficiency. Noble-Collip drum wasused to prepare MT model in rats. And myocardial apoptosis index was calculated after TUNEL staining. Ventricular intubation was employed to detect heart function. Changes in myocardial ultrastructure were observed using an electron microscope. ELISA was used to detect the content of TNF-α and reactive oxygen species generated from monocytes and cardiomyocytes. The changes in Ca2+ concentration in cardiomyocyte were observed by confocal microscope. Compared with trauma group, the administration group had a decreased apoptosis index of cardiomyocytes, and increased ±dp/dtmax. Meanwhile, proanthocyanidin can inhibit monocytes’ TNF-α production, and reduce plasma TNF-α concentration. Moreover, proanthocyanidin can attenuate the excessive oxidative stress reaction of cardiomyocyte, and inhibit calcium overload in cardiomyocytes. In conclusion, proanthocyanidin can effectively ease myocardial damage and improve cardiac function, through anti-inflammatory and antioxidant effects in secondary cardiac insufficiency caused by MT. PMID:28294148

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


    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.

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

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


    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.

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


    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.

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

    Thomsen, A.B.


    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....

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

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


    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...

  2. Kinetics and Mechanism of Deoxygenation Reactions over Proton-Form and Molybdenum-Modified Zeolite Catalysts

    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

  3. Type 2 lepra reaction as a cause of pyrexia of unknown origin.

    Vinod, K V; Chandramohan, R; Dutta, T K; Rajesh, N G; Basu, Debdatta


    Leprosy, a commonly encountered disease, can rarely present as a reactional state de novo with fever as the main presenting feature. Here we describe an uncommon presentation of leprosy [with type 2 lepra reaction] as pyrexia of unknown origin with prominent rheumatologic manifestations [acute polyarthritis], renal involvement and generalized lymphadenopathy with rare presentation of type 2 lepra reaction without the classic skin lesions of erythema nodosum leprosum, occurring in a treatment naive patient without prior history of leprosy.

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

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


    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.

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

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


    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.

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

    Siglinda Perathoner


    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.

  7. Mechanism of melanosomes action in antioxidant reactions following optic irradiation

    Lapina, Victoria A.; Dontsov, Alexander E.; Sakina, Natalia L.; Ostrovsky, Michail A.


    Hyphema is often associated with traumatic eye injuries. Its blood is subjected to considerable changes in aqueous humor and causes toxic effect on eye tissues. The metabolism disturbances in eye tissues unfavorably affecting their cell structures play a significant role in the development of pathologic conditions in cases of intraocular hemorrhages. This is to be attributed to the correlation of lipid peroxidation (LP) processes and antioxidant system (AOS) activity of both the cellular membrane and its environment necessary for maintaining cell homeostasis as a whole. The aim of the present work is an experimental study of LP processes of aqueous humor (AH) in total traumatic hyphema (TTH) after magnet-laser stimulation different doses (3 and 6 minutes). TTH and aqueous humor collection were made on the eyes on rabbit (Schinchilla) according to Krasnov A.M. under the local anaesthesia (dicaine 0.25%). The study of biochemical aqueous indices was carried out on healthy eyes and after development of hyphema on day 1, 3, 5, 7, 10, 14, 30, and 45. The animals were divided into three groups: in the first group the biochemical indices were defined in the aqueous humor in TTH; in the second and the third groups the similar investigation was carried out after magnet- laser radiation with 3 and 6 minutes exposition. The malonic dialdehyde (MDA) was defined according to Ishihara, Shiff's bases -- and their concentration was determined on the total amount of lipids (reagent kit of 'Lachema'). He-Ne laser (with power density of 0.05 mVt) was used, streaming impulsed magnet field voltage being 10 mTl. The magnet head of a magnet radiator was fixed 0.5 cm from the eye; laser beam being sent to the central hole of the magnet head. The duration of exposure was 3 minutes in the second group and 6 minutes in the third group, daily for 10 days. Significant increase of LP product concentration level with two clear ascending peaks was seen on the third and tenth days in the first

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

    Vahteristo, K.


    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

  9. 2013 Gordon Research Conference, Inorganic reaction mechanisms, Galveston, TX, March 3-8 2013

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


    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.

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

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


    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 ...

  11. [The reactions of hypersensitivity: the mechanisms of development, clinical manifestations, principles of diagnostic (a lecture)].

    Tukavkina, S Yu; Kharseyeva, G G


    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.

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

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


    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.

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

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


    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.

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

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


    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.

  15. 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.

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


    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.

  16. Determining the mechanical strength of CO2-induced reaction zones in wellbore cement: is it worth it?

    Hangx, Suzanne; Marcelis, Fons; van der Linden, Arjan; Liteanu, Emilia


    CO2 injection, either for long-term CO2 storage (CCS) or Enhanced Oil Recovery (EOR), strongly hinges on maintaining storage integrity. Injection and legacy wells penetrating the caprock pose one of the most likely points of leakage. In order to be able to predict the long-term integrity of such wellbores, it's important to understand their chemical, hydrological and mechanical behaviour, and how it may change due to CO2 exposure. Generally, in response to CO2/brine/cement interactions, a number of different reaction zones are observed, each with their own chemical, and hence mechanical, signature. To aid mechanical modelling efforts, assessing the risk of cement failure caused by stress and temperature changes, knowledge is required of the strength of each of these zones. We performed experiments on Class G Portland cement to investigate the chemical-mechanical coupling due to CO2-exposure. Batch reaction experiments, in the presence of CO2-rich brine, were performed under typical storage conditions (T = 65° C, PCO2 = 8 MPa) for various periods of time (1, 2, 3, 4, 5 and 6 months). After exposure, mechanical tests were performed on the observed reaction zones, using the so-called core scratching technique, to evaluate the unconfined compressive strength (UCS) as a function of exposure time. Chemical analyses (CT-imaging, SEM microscopy, EDX chemical analysis) showed the formation of three reaction zones, similarly to what has been observed in other studies. Measurements of the mechanical strength of these different zones showed highly variable results. Such variations have also been observed in other studies, using different measurement techniques. The large variability in strength measurements is most likely an inherent result of the heterogenic nature of cement, which affects the extent and location of reaction throughout the sample. This begs the question: is it worth studying the mechanical strength of reaction-induced zones in cement? Or will it suffice to

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

    Hubin, Pierre O., E-mail: [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)


    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.

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

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


    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.

  19. Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium-oxygen batteries

    Mahne, Nika; Schafzahl, Bettina; Leypold, Christian; Leypold, Mario; Grumm, Sandra; Leitgeb, Anita; Strohmeier, Gernot A.; Wilkening, Martin; Fontaine, Olivier; Kramer, Denis; Slugovc, Christian; Borisov, Sergey M.; Freunberger, Stefan A.


    Non-aqueous metal-oxygen batteries depend critically on the reversible formation/decomposition of metal oxides on cycling. Irreversible parasitic reactions cause poor rechargeability, efficiency, and cycle life, and have predominantly been ascribed to the reactivity of reduced oxygen species with cell components. These species, however, cannot fully explain the side reactions. Here we show that singlet oxygen forms at the cathode of a lithium-oxygen cell during discharge and from the onset of charge, and accounts for the majority of parasitic reaction products. The amount increases during discharge, early stages of charge, and charging at higher voltages, and is enhanced by the presence of trace water. Superoxide and peroxide appear to be involved in singlet oxygen generation. Singlet oxygen traps and quenchers can reduce parasitic reactions effectively. Awareness of the highly reactive singlet oxygen in non-aqueous metal-oxygen batteries gives a rationale for future research towards achieving highly reversible cell operation.

  20. Streptococcus pyogenes streptolysin O as a cause of false-positive CAMP reactions.

    Tapsall, J W; Phillips, E A


    The synergistic hemolysis of sheep erythrocytes in the CAMP reaction by the sequential action of staphylococcal beta-lysin and the CAMP factor of group B streptococci is the only known function of this extracellular product of group B streptococci. The reaction forms the basis of the CAMP test used to identify group B streptococci because the CAMP factor is believed to be restricted to this group of organisms. However, on occasion other streptococci, notably group A streptococci, may produce ...

  1. Power as the Cause of Motion and a New Foundation of Classical Mechanics

    Harokopos E.


    Full Text Available Laws of motion are derived based on power rather than on force. I show how power extends the law of inertia to include curvilinear motion and I also show that the law of action-reaction can be expressed in terms of the mutual time rate of change of kinetic energies instead of mutual forces. I then compare the laws of motion based on power to Newton’s Laws of Motion and I investigate the relation of power to Leibniz’s notion of vis viva. I also discuss briefly how the metaphysics of power as the cause of motion can be grounded in a modern version of occasionalism for the purpose of establishing an alternative foundation of mechanics. The laws of motion derived in this paper along with the metaphysical foundation proposed come in defense of the hypotheses that time emerges as an ordered progression of now and that gravitation is the effect of energy transfer between an unobservable substance and all matter in the Universe.

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

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


    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.

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

    Chen, Jie; Xu, Yulong; Wang, Dunyou


    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.

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

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


    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.

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

    Liu, Peng; Li, Chen; Wang, Dunyou


    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.

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

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


    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.

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

    Skobelev, N. K.


    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.

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

    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.

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

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


    , 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...

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

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


    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.

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

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


    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.

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

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


    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.

  13. Foreign body reaction after PLC reconstruction caused by a broken PLLA screw.

    Kim, Tae-Kwon; Jeong, Tae-Wan; Lee, Dae-Hee


    Foreign body reactions may occur in patients who receive bioabsorbable implants during orthopedic surgery for fractures and ligament repair. The authors describe a 34-year-old man who presented with a palpable tender mass on the lateral aspect of the left knee of 1 month's duration. He underwent posterior cruciate ligament and posterolateral corner reconstruction 3 years earlier. Physical examination showed a 1×1-cm soft, nontender mass without localized warmth on the lateral epicondyle of the distal femur. Magnetic resonance imaging showed a broken screw fragment surrounded by a cyst-like mass. Under general anesthesia, the surgeon excised the screw fragment and the fibrotic mass, enclosing it in the subcutaneous tissue at the lateral epicondyle, the site at which a poly-L-lactic acid bioabsorbable screw had been inserted to fix the graft for posterolateral corner reconstruction. Histologic evaluation showed a foreign body reaction to the degraded screw particles. To the authors' knowledge, this report is the first description of a patient presenting with a delayed foreign body reaction to a broken poly-L-lactic acid bioabsorbable screw at the lateral femoral epicondyle after posterolateral corner reconstruction. Because delayed foreign body reactions can occur at any site of poly-L-lactic acid bioabsorbable screw insertion, care should be taken to avoid screw protrusion during ligament reconstruction because it can lead to screw breakage and delayed foreign body reaction.

  14. Granulomatous tattoo reaction and erythema nodosum in a young woman: common cause or coincidence?

    Wollina, Uwe; Gruner, Monika; Schönlebe, Jaqueline


    Tattooing has become quite popular in Western countries. With the increasing prevalence, there is also an increased risk of adverse effects. We describe a 17-year-old female patient with a black and red-colored tattoo, who developed immediately after red tattooing general malaise with fever, nausea, and vomiting. A bullous reaction was temporarily seen within the red part of her tattoo. The reaction later shifted to a subacute dermatitis with bacterial superinfection. Two months later, she felt ill again. She developed painful tender nodules on the anterior aspect of both lower legs identified as erythema nodosum without sarcoidosis. Is this is a unique case of adverse reaction to tattoo pigments with a type I and a type IV reaction, or is this a coincidence? The treatment was initiated with systemic and topical corticosteroids and topical antibiotics combined with compression bandages for the legs. After 3 weeks of treatment, the erythema nodosum completely resolved and did not reappear during a 1-year follow-up. The treatment of the local reactions, however, was unsatisfactory without complete response. There is an indispensable need for regulation of tattoo pigments and tattooing to improve consumer safety.

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

    ZHAO Hongmei; LIU Kun; SUN Chengke; LI Zonghe


    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.

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

    Ashraf Khademzadeh


    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.

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

    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.

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

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


    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.

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

    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


    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.

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

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


    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.

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

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


    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.

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

    余秀芬; 郑发鲲; 黄锦顺


    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.

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


    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.

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

    Ananikov, Valentin P


    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

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

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


    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 .

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

    Sankar, Punnaivanam; Aghila, Gnanasekaran


    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.

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

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


    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.

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

    Martínez-Araya, Jorge Ignacio


    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.

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

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


    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.

  10. Chronic tattoo reactions cause reduced quality of life equaling cumbersome skin diseases

    Carlsen, Katrina Hutton; Serup, Jørgen


    Tattoos are often associated with mild complaints, but some people develop complications that may require medical treatment, and the burden of these events has hitherto been neglected. To understand the dimensions and the psychological symptomatology of adverse events both the sensory and affective...... applied to patients with chronic tattoo reactions, tattoo complaints and impact on quality of life that were comparable to patients presenting cumbersome dermatological disease such as psoriasis, eczema and pruritus, which often show widespread effects to the skin, were uncovered. In conclusion, chronic...... tattoo reactions should be ranked as a cumbersome dermatological disease and, accordingly, given priority attention and qualified treatment by the public health care system....

  11. Bacterial infection as a likely cause of adverse reactions to polyacrylamide hydrogel fillers in cosmetic surgery

    Christensen, Lise; Breiting, Vibeke; Bjarnsholt, Thomas


    Background. The etiology of long-lasting adverse reactions to gel fillers used in cosmetic surgery is not known. Bacterial infection and immunological reaction to the product have been suggested. Methods. We performed a case-control study, with 77 biopsies and 30 cytology specimens originating from...... in the presence of polyacrylamide filler in cosmetic surgery, possibly due to a biofilm mode of growth. Adequate skin preparation and use of sterile technique in these procedures are mandatory, but antibiotic prophylaxis prior to injection of nondegradable gels like polyacrylamide should be explored as well....

  12. Construction accidents: identification of the main associations between causes, mechanisms and stages of the construction process.

    Carrillo-Castrillo, Jesús A; Trillo-Cabello, Antonio F; Rubio-Romero, Juan C


    To identify the most frequent causes of accidents in the construction sector in order to help safety practitioners in the task of prioritizing preventive actions depending on the stage of construction. Official accident investigation reports are analysed. A causation pattern is identified with the proportion of causes in each of the different possible groups of causes. Significant associations of the types of causes with accident mechanisms and construction stages have been identified. Significant differences have been found in accident causation depending on the mechanism of the accident and the construction stage ongoing. These results should be used to prioritize preventive actions to combat the most likely causes for each accident mechanism and construction stage.

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

    Xu, Yulong; Zhang, Jingxue; Wang, Dunyou


    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.

  14. Frequency, severity and causes of unexpected allergic reactions to food: A systematic literature review

    Versluis, A.; Knulst, A.C.; Kruizinga, A.G.; Michelsen, A.; Houben, G.F.; Baumert, J.L.; Os-Medendorp, H. van


    Summary: Food allergic patients have to deal with an avoidance diet. Confusing labelling terms or precautionary labels can result in misinterpretation and risk-taking behaviour. Even those patients that strictly adhere to their diet experience (sometimes severe) unexpected allergic reactions to

  15. Corynebacterium renale as a cause of reactions to the complement fixation test for Johne's disease

    Gilmour, N.J.L.; Goudswaard, J.

    Complement fixation (C.F.) tests and fluorescent antibody (F.A.) tests were carried out on sera from rabbits inoculated with Corynebacterium renale and Mycobacterium johnei, and on sera from cattle with C. renale pyelonephritis and with Johne's disease. Cross-reactions were a feature of the C.F.

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

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


    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.

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

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


    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.

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

    于海涛; 付宏刚; 等


    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.

  19. Screening a diverse soybean germplasm collection for reaction to purple seed stain caused by Cercospora kikuchii

    Purple seed stain (PSS), caused by Cercospora kikuchii, is a prevalent soybean disease that causes latent seed infection, seed decay, purple seed discoloration, and overall quality deterioration. The objective of this research was to screen soybean accessions from the USDA germplasm collection for r...

  20. A review of adaptive mechanisms in cell responses towards oxidative stress caused by dental resin monomers.

    Krifka, Stephanie; Spagnuolo, Gianrico; Schmalz, Gottfried; Schweikl, Helmut


    Dental composite resins are biomaterials commonly used to aesthetically restore the structure and function of teeth impaired by caries, erosion, or fracture. Residual monomers released from resin restorations as a result of incomplete polymerization processes interact with living oral tissues. Monomers like triethylene glycol dimethacrylate (TEGDMA) or 2-hydroxylethyl methacrylate (HEMA) are cytotoxic via apoptosis, induce genotoxic effects, and delay the cell cycle. Monomers also influence the response of cells of the innate immune system, inhibit specific odontoblast cell functions, or delay the odontogenic differentiation and mineralization processes in pulp-derived cells including stem cells. These observations indicate that resin monomers act as environmental stressors which inevitably disturb regulatory cellular networks through interference with signal transduction pathways. We hypothesize that an understanding of the cellular mechanisms underlying these phenomena will provide a better estimation of the consequences associated with dental therapy using composite materials, and lead to innovative therapeutic strategies and improved materials being used at tissue interfaces within the oral cavity. Current findings strongly suggest that monomers enhance the formation of reactive oxygen species (ROS), which is most likely the cause of biological reactions activated by dental composites and resin monomers. The aim of the present review manuscript is to discuss adaptive cell responses to oxidative stress caused by monomers. The particular significance of a tightly controlled network of non-enzymatic as well as enzymatic antioxidants for the regulation of cellular redox homeostasis and antioxidant defense in monomer-exposed cells will be addressed. The expression of ROS-metabolizing antioxidant enzymes like superoxide dismutase (SOD1), glutathione peroxidase (GPx1/2), and catalase in cells exposed to monomers will be discussed with particular emphasis on the role

  1. Oxidation and nitration of tyrosine by ozone and nitrogen dioxide: reaction mechanisms and biological and atmospheric implications.

    Sandhiya, L; Kolandaivel, P; Senthilkumar, K


    The nitration of tyrosine by atmospheric oxidants, O3 and NO2, is an important cause for the spread of allergenic diseases. In the present study, the mechanism and pathways for the reaction of tyrosine with the atmospheric oxidants O3 and NO2 are studied using DFT-M06-2X, B3LYP, and B3LYP-D methods with the 6-311+G(d,p) basis set. The energy barrier for the initial oxidation reactions is also calculated at the CCSD(T)/6-31+G(d,p) level of theory. The reaction is studied in gas, aqueous, and lipid media. The initial oxidation of tyrosine by O3 proceeds by H atom abstraction and addition reactions and leads to the formation of six different intermediates. The subsequent nitration reaction is studied for all the intermediates, and the results show that the nitration affects both the side chain and the aromatic ring of tyrosine. The rate constant of the favorable oxidation and nitration reaction is calculated using variational transition state theory over the temperature range of 278-350 K. The spectral properties of the oxidation and nitration products are calculated at the TD-M06-2X/6-311+G(d,p) level of theory. The fate of the tyrosine radical intermediate is studied by its reaction with glutathione antioxidant. This study provides an enhanced understanding of the oxidation and nitration of tyrosine by O3 and NO2 in the context of improving the air quality and reducing the allergic diseases.

  2. Synergistic Degradation of a Hyperuricemia-Causing Metabolite Using One-Pot Enzyme-Nanozyme Cascade Reactions

    Jung, Secheon; Kwon, Inchan


    Multi-enzyme cascade reactions are frequently found in living organisms, in particular when an intermediate should be eliminated. Recently, enzyme-mimic nanomaterials (nanozymes) received much attention for various applications, because they are usually more stable and cost-effective than enzymes. However, enzyme-nanozyme cascade reations have not been yet extensively exploited. Therefore, in this study, we investigated one-pot enzyme-nanozyme cascade reactions using urate oxidase (UOX) and catalase-mimic gold nanoparticle nanozyme (AuNP) with the ultimate goal of treatment of hyperuricemia. UOX degrades hyperuricemia-causing uric acid, but also generates hydrogen peroxide raising several health concerns. We successfully demonstrated that one-pot UOX-AuNP cascade systems degrade uric acid more than five times faster than UOX alone, by eliminating potentially cytotoxic hydrogen peroxide, similar to enzyme-enzyme reactions. PMID:28287162

  3. The Role of Various Stressors in the Trigger Mechanism of Raynaud's Disease (Hemorheological and Vascular Reactions

    Mantskava M.M.


    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

  4. Slow Pain Generation Model Caused by Mechanical Stimulus Based on the Laminated Structure of Skin

    Matsunaga, Nobutomo; Akayama, Seiko; Kawaji, Shigeyasu

    For design of the autonomous robot, action learning ability based on the subjective feeling pain is an important issue. In our previous researches, artificial superficial pain model caused by impact had been studied and the transmission mechanism focused on the input-output relations was proposed. However, the generation mechanism of the pain has not been considered yet. In this paper, the pain model of slow pain considering the skin dynamics is proposed. It is clarified from the FEM simulations that the strain energy density (SED) caused around the layer is related to the subjective pain level. From the experimental pain caused by quasi-static motion, the proposed pain model is evaluated.

  5. Chronic tattoo reactions cause reduced quality of life equaling cumbersome skin diseases.

    Carlsen, Katrina Hutton; Serup, Jørgen


    Tattoos are often associated with mild complaints, but some people develop complications that may require medical treatment, and the burden of these events has hitherto been neglected. To understand the dimensions and the psychological symptomatology of adverse events both the sensory and affective impacts, including the effect on quality of life, should be studied. Itch severity and influence on quality of life can be measured objectively. The Itch Severity Scale and Dermatology Life Quality Index scoring systems have been applied to different dermatological diseases. When ISS and DLQI scores were applied to patients with chronic tattoo reactions, tattoo complaints and impact on quality of life that were comparable to patients presenting cumbersome dermatological disease such as psoriasis, eczema and pruritus, which often show widespread effects to the skin, were uncovered. In conclusion, chronic tattoo reactions should be ranked as a cumbersome dermatological disease and, accordingly, given priority attention and qualified treatment by the public health care system. © 2015 S. Karger AG, Basel.

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

    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.


    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.

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

    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.


    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.

  8. Oscillatory reaction cross sections caused by normal mode sampling in quasiclassical trajectory calculations

    Nagy, Tibor; Vikár, Anna; Lendvay, György, E-mail: [Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2., H-1117 Budapest (Hungary)


    The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH{sub 4} + H → CH{sub 3} + H{sub 2} and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C–H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C–H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling.

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

    Szabó, István; Czakó, Gábor


    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.

  10. Ammonium deficiency caused by heterogeneous reactions during a super Asian dust episode

    Hsu, Shih-Chieh; Lee, Celine Siu Lan; Huh, Chih-An; Shaheen, Robina; Lin, Fei-Jan; Liu, Shaw Chen; Liang, Mao-Chang; Tao, Jun


    Mineral dust particles exert profound impacts on air quality, visibility, and ocean biogeochemistry. Interactions between dust particles and other anthropogenic pollutants modify not only the size spectrum and morphology but also physicochemical properties of dust particles, thereby affecting their radiative properties and ability to act as cloud condensation nuclei and in turn their impact on climate. Here we report field observations on the surface chemical transformations in a super Asian dust plume captured in coastal areas of China and the adjacent marginal seas. The dust plume showed enhanced concentrations of sulfate, nitrate, and calcium along with a decrease in ammonium. The percentages of total Ca in water-soluble form increased from an intrinsic value of ~5% to 25-40% at four stations along the path of the dust plume. From these increases, we estimated the extent to which carbonate was modified by heterogeneous reactions and calculated that the enhanced sulfate and nitrate could account for 40-60% of the observed concentrations. Our observation suggests that the formation of ammonium sulfate via the H2SO4-NH3-H2O ternary system was impeded by heterogeneous reactions in the marine boundary layer when dust loads exceeded a certain threshold. A conceptual model is proposed to elucidate the heterogeneous reactions during the super Asian dust event and their impacts on atmospheric chemistry.

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

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


    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.

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

    Heverly-Coulson, Gavin S; Boyd, Russell J


    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.

  13. Episodic edema in type 2 lepra reaction can be caused by transient lymphatic obstruction in the lymph node.

    Stanley, J N; Pearson, J M; Ridley, D B


    Fourteen patients with lepromatous leprosy developed attacks of edema of the hands and/or feet associated with attacks of type 2 lepra reaction (erythema nodosum leprosum). The regional lymph nodes were enlarged and often tender when edema was present. Lymph node biopsies in five cases showed compression of the subcapsular sinus against the thickened fibrotic capsule of the inflamed node. It is suggested that this obstructs the inflow of lymph into the regional nodes, thereby causing the edema.

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

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


    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

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

    Faheem, Muhammad; Heyden, Andreas


    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.

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

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


    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.

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


    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.

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

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


    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.

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

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


    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.

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

    Wang Peng; Zheng Aiguo; Tian Huiping; Long Jun


    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.

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

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


    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...

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

    Deleebeeck, Lisa; Kammer Hansen, Kent


    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...

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

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


    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.

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

    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)


    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.

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

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


    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

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

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


    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 ...

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

    Aldahmash, Abdulwali H.; Abraham, Michael R.


    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…

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

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


    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

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

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


    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

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

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


    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

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

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


    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.

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

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


    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.

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

    Ma, Liping, E-mail: [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)


    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.

  14. Dermatologic surgery emergencies: Complications caused by systemic reactions, high-energy systems, and trauma.

    Minkis, Kira; Whittington, Adam; Alam, Murad


    While the overall incidence of emergencies in dermatologic surgery is low, emergent situations can occasionally pose a risk to patients undergoing such procedures. The clinical importance of several types of emergences related to systemic reactions, high energy systems, and trauma are reviewed, and relevant epidemiology, clinical manifestations, diagnosis, work-up, management, and prevention are discussed. Early detection of surgical emergencies can mitigate any associated adverse outcomes, thereby allowing the outstanding record of safety of dermatologic surgery to continue. Copyright © 2016 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

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


    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.

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

    Habershon, Scott


    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.

  17. A DFT study on the mechanism of palladium-catalyzed divergent reactions of 1,6-enyne carbonates

    Xing Hui Zhang; Zhi Yuan Geng; Teng Niu; Ke Tai Wang


    The reaction mechanisms of palladium-catalyzed divergent reactions of 1,6-enyne carbonates have been investigated using DFT calculations at the B3LYP/6-31G(d,p) (LanL2DZ for Pd) level. Solvent effects on these reactions have been considered by the polarizable continuum model (PCM) for the solvent (DMF). The formation of vinylidenepyridines and vinylidenepyrrolidines were generated through 5-exo-dig cyclization or 6-endo-dig cyclization. Our calculation results suggested the following: (i) The first step of the whole cycle is the rate-determining step, which causes allenic palladium intermediate through two plausible pathways. This intermediate provides the corresponding products and releases the palladium catalyst by a subsequent hydrogen transfer and elimination process. (ii) For the catalyst CH3OPdH, the reaction could occur through two possible pathways, but 5-exo-dig cyclization is favoured over 6-endo-dig cyclization. However, when the hydrogen atom is substituted with a phenyl group, the energy barriers for 5-exo-dig cyclization or 6-endo-dig cyclization become relatively high, 18.0–28.5 kcal/mol. The computational results provide good explanation for the experimental observations.

  18. The Effect of Mechanical Vibration Stimulation of Perception Subthreshold on the Muscle Force and Muscle Reaction Time of Lower Leg

    Huigyun Kim


    Full Text Available The objective of this study is to investigate the effect of mechanical vibration stimulation on the muscle force and muscle reaction time of lower leg according to perception threshold and vibration frequency. A vibration stimulation with perception threshold intensity was applied on the Achilles tendon and tibialis anterior tendon. EMG measurement and analysis system were used to analyze the change of muscle force and muscle reaction time according to perception threshold and vibration frequency. A root-mean-square (RMS value was extracted using analysis software and Maximum Voluntary Contraction (MVC and Premotor Time (PMT were analyzed. The measurement results showed that perception threshold was different from application sites of vibration frequency. Also, the muscle force and muscle reaction time showed difference according to the presence of vibration, frequency, and intensity. This result means that the vibration stimulation causes the change on the muscle force and muscle reaction time and affects the muscles of lower leg by the characteristics of vibration stimulation.

  19. Do early childhood immunizations influence the development of atopy and do they cause allergic reactions?

    Grüber, C; Nilsson, L; Björkstén, B


    Concerns about allergic side-effects of vaccines and about a possible promotion of allergic diseases contribute to incomplete vaccination rates in childhood. This article reviews the current understanding of these issues. There is evidence that pertussis and diphtheria/tetanus antigens elicit immunoglobulin E (IgE) antibody formation as part of the immune response. In murine models, pertussis toxin is an effective adjuvant for IgE formation against simultaneously administered antigens. In children, however, sensitization to unrelated antigens or development of allergic diseases do not seem to be augmented. In contrast, bacille Calmette-Guérin (BCG) and measles vaccination have been proposed as suppressors of allergy because of their T helper 1 (Th1)-fostering properties. In the murine system, BCG inhibits allergic sensitization and airway hyper-reactivity. Some epidemiological studies in humans suggest an inhibitory effect of tuberculosis on allergy. BCG vaccination in children, however, has no or merely a marginal suppressive effect on atopy. Other vaccine components such as egg proteins, gelatin, and antibiotics are a potential hazard to children with severe clinical reactions to these allergens. These rare children should be vaccinated under special precautions. In conclusion, vaccination programs do not explain the increasing prevalence of allergic diseases, but individual children may uncommonly develop an allergic reaction to a vaccine. The risks of not vaccinating children, however, far outweigh the risk for allergy. Therefore, childhood vaccination remains an essential part of child health programs and should not be withheld, even from children predisposed for allergy.

  20. Mechanical analysis of congestive heart failure caused by bundle branch block based on an electromechanical canine heart model

    Dou Jianhong; Xia Ling; Zhang Yu; Shou Guofa [Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027 (China); Wei Qing; Liu Feng; Crozier, Stuart [School of Information Technology and Electrical Engineering, University of Queensland, St Lucia, Brisbane, Queensland 4072 (Australia)], E-mail:


    Asynchronous electrical activation, induced by bundle branch block (BBB), can cause reduced ventricular function. However, the effects of BBB on the mechanical function of heart are difficult to assess experimentally. Many heart models have been developed to investigate cardiac properties during BBB but have mainly focused on the electrophysiological properties. To date, the mechanical function of BBB has not been well investigated. Based on a three-dimensional electromechanical canine heart model, the mechanical properties of complete left and right bundle branch block (LBBB and RBBB) were simulated. The anatomical model as well as the fiber orientations of a dog heart was reconstructed from magnetic resonance imaging (MRI) and diffusion tensor MRI (DT-MRI). Using the solutions of reaction-diffusion equations and with a strategy of parallel computation, the asynchronous excitation propagation and intraventricular conduction in BBB was simulated. The mechanics of myocardial tissues were computed with time-, sarcomere length-dependent uniaxial active stress initiated at the time of depolarization. The quantification of mechanical intra- and interventricular asynchrony of BBB was then investigated using the finite-element method with an eight-node isoparametric element. The simulation results show that (1) there exists inter- and intraventricular systolic dyssynchrony during BBB; (2) RBBB may have more mechanical synchrony and better systolic function of the left ventricle (LV) than LBBB; (3) the ventricles always move toward the early-activated ventricle; and (4) the septum experiences higher stress than left and right ventricular free walls in BBB. The simulation results validate clinical and experimental recordings of heart deformation and provide regional quantitative estimates of ventricular wall strain and stress. The present work suggests that an electromechanical heart model, incorporating real geometry and fiber orientations, may be helpful for better

  1. Mechanical analysis of congestive heart failure caused by bundle branch block based on an electromechanical canine heart model

    Dou, Jianhong; Xia, Ling; Zhang, Yu; Shou, Guofa; Wei, Qing; Liu, Feng; Crozier, Stuart


    Asynchronous electrical activation, induced by bundle branch block (BBB), can cause reduced ventricular function. However, the effects of BBB on the mechanical function of heart are difficult to assess experimentally. Many heart models have been developed to investigate cardiac properties during BBB but have mainly focused on the electrophysiological properties. To date, the mechanical function of BBB has not been well investigated. Based on a three-dimensional electromechanical canine heart model, the mechanical properties of complete left and right bundle branch block (LBBB and RBBB) were simulated. The anatomical model as well as the fiber orientations of a dog heart was reconstructed from magnetic resonance imaging (MRI) and diffusion tensor MRI (DT-MRI). Using the solutions of reaction-diffusion equations and with a strategy of parallel computation, the asynchronous excitation propagation and intraventricular conduction in BBB was simulated. The mechanics of myocardial tissues were computed with time-, sarcomere length-dependent uniaxial active stress initiated at the time of depolarization. The quantification of mechanical intra- and interventricular asynchrony of BBB was then investigated using the finite-element method with an eight-node isoparametric element. The simulation results show that (1) there exists inter- and intraventricular systolic dyssynchrony during BBB; (2) RBBB may have more mechanical synchrony and better systolic function of the left ventricle (LV) than LBBB; (3) the ventricles always move toward the early-activated ventricle; and (4) the septum experiences higher stress than left and right ventricular free walls in BBB. The simulation results validate clinical and experimental recordings of heart deformation and provide regional quantitative estimates of ventricular wall strain and stress. The present work suggests that an electromechanical heart model, incorporating real geometry and fiber orientations, may be helpful for better

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

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


    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.

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

    Yingxian Zhao; Bo Shen; Feng Wei


    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.

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


    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.

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

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


    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.

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

    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.

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

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


    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.

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

    Okamoto, Ken; Kusano, Teruo; Nishino, Takeshi


    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.

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

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


    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.

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

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


    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.

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

    WANG Bing-Xing; WANG Li


    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).

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


    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.

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

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


    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.

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

    Jing Ying


    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.

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


    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.

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

    Shinozuka, Yuzo


    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.

  17. Oxygenation mechanism of ions in dynamic reaction cell ICP-MS.

    Narukawa, Tomohiro; Chiba, Koichi


    A dynamic reaction cell (DRC) is one of the most effective tools for eliminating spectral interferences caused by polyatomic molecules in inductively coupled plasma mass spectrometry (ICP-MS). Oxygen gas (O2), by producing oxygenated ions, is very effective in reducing some specific spectral interferences. In this study, the oxygenation of elemental ions (M(+)) in the DRC was investigated experimentally, and a new explanation for oxygenation based on the enthalpy changes in the oxygenating reactions is proposed. The enthalpy changes of each M(+) were calculated and the possibility of each reaction occurring was evaluated. The calculations were in good agreement with experimental observations. Theoretical and experimental results supported the hypothesis that the enthalpy changes (ΔH) of M(+)+ O2 → MO(+) + O and M(+) + O → MO(+) and the thermodynamic stability of M(+)-O are key factors controlling oxygenation of M(+) in the DRC.

  18. Phenanthrene causes ocular developmental toxicity in zebrafish embryos and the possible mechanisms involved

    Huang, Lixing [State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005 (China); Wang, Chonggang [State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005 (China); State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen (China); Zhang, Youyu; Wu, Meifang [State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005 (China); Zuo, Zhenghong, E-mail: [State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005 (China); State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen (China)


    Highlights: • Phe exposure caused obvious morphological changes in the retina. • Phe exposure caused apoptosis and reduction of cell proliferation in the retina. • Phe causes ocular toxicity might be via the AhR/Zeb1/Mitf/Pax6 signaling pathway. • AhR is a repressor of Zeb1. -- Abstract: Recent studies show that polycyclic aromatic hydrocarbons (PAHs) may be a candidate cause of developmental defects of the retina, but the mechanism is still unclear. We evaluated the mechanism(s) underlying PAH-induced retinal development defects due to exposure to environmental concentrations of Phenanthrene (Phe) in zebrafish. We found that exposure to environmental concentrations of Phe caused obvious morphological changes, developmental retardation, apoptosis, and reduction of cell proliferation in the retina. Our results indicated that Phe could cause visual system developmental defects. Phe exposure up-regulated aryl hydrocarbon receptor (AhR) and microphthalmia-associated transcription factor (Mtif) expression, and down-regulated zinc finger E-box binding homeobox 1 (Zeb1) and paired box 6 (Pax6). Moreover, we demonstrated that AhR was a repressor of Zeb1. We propose that Phe's ocular toxicity is mediated by up-regulating AhR, which then down-regulates Zeb1, in turn inducing Mitf expression while inhibiting Pax6 expression.

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

    Hassan Amroun Ewais; Iqbal Mohamed Ibrhium Ismail


    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

  20. Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths.

    Lodola, Alessio; Sirirak, Jitnapa; Fey, Natalie; Rivara, Silvia; Mor, Marco; Mulholland, Adrian J


    The effects of structural fluctuations, due to protein dynamics, on enzyme activity are at the heart of current debates on enzyme catalysis. There is evidence that fatty acid amide hydrolase (FAAH) is an enzyme for which reaction proceeds via a high-energy, reactive conformation, distinct from the predominant enzyme-substrate complex (Lodola et al. Biophys. J. 2007, 92, L20-22). Identifying the structural causes of differences in reactivity between conformations in such complex systems is not trivial. Here, we show that multivariate analysis of key structural parameters can identify structural determinants of barrier height by analysis of multiple reaction paths. We apply a well-tested quantum mechanics/molecular mechanics (QM/MM) method to the first step of the acylation reaction between FAAH and oleamide substrate for 36 different starting structures. Geometrical parameters (consisting of the key bond distances that change during the reaction) were collected and used for principal component analysis (PCA), partial least-squares (PLS) regression analysis, and multiple linear regression (MLR) analysis. PCA indicates that different "families" of enzyme-substrate conformations arise from QM/MM molecular dynamics simulation and that rarely sampled, catalytically significant conformational states can be identified. PLS and MLR analyses allowed the construction of linear regression models, correlating the calculated activation barriers with simple geometrical descriptors. These analyses reveal the presence of two fully independent geometrical effects, explaining 78% of the variation in the activation barrier, which are directly correlated with transition-state stabilization (playing a major role in catalysis) and substrate binding. These results highlight the power of statistical approaches of this type in identifying crucial structural features that contribute to enzyme reactivity.

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

    Raj, Abhijeet


    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.

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

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


    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.

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

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


    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.

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

    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


    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.

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

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


    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.

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

    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)


    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.)

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

    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)


    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.

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

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


    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.

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

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


    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.

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


    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).

  11. “Eastern Turn” of Russian Foreign Policy: Causes, Risks, and the Reaction of the West

    Temchenko-Zavyalova Anastasia O.


    Full Text Available The author analyzes the evolution of foreign policy of new Russia, identifies trends and patterns of transition to various courses, prerequisites of the “eastern turn”, and characterizes the specificity of this direction in the contemporary realia. The author proposes a number of clarifying concepts within the analysis of the foreign policies of Russia. The foreign policy of Russia for the last decades underwent a number of the changes connected with its orientation to various groups of the countries. However, in connection with the events which took place in 2014, the Russian foreign policy carried out the “eastern turn” that entailed certain consequences and prospects by estimates of experts. The relevance of the research consists in the opportunity to estimate realities of a foreign policy of Russia, to analyse the reasons of its acceptance, possible risks and reaction of the western partners who changed in their turn a course concerning Russia. Scientific novelty of the present work consists in the systematization of the issue on the evolution of a foreign policy of Russia and the analysis of current trends taking into account the “eastern turn”. Besides, scientific definition of “eastern turn of the Russian foreign policy” and its consequence in the conditions of development of modern Russia is worked out. The author considers the main actions and the directions which formed the basis of the updated foreign policy of Russia from 2009 to 2013. The author made the conclusions concerning the analysis of modern Russia’s foreign policy and its turn to the east.

  12. Reaction wood – a key cause of variation in cell wall recalcitrance in willow

    Brereton Nicholas JB


    Full Text Available Abstract Background The recalcitrance of lignocellulosic cell wall biomass to deconstruction varies greatly in angiosperms, yet the source of this variation remains unclear. Here, in eight genotypes of short rotation coppice willow (Salix sp. variability of the reaction wood (RW response and the impact of this variation on cell wall recalcitrance to enzymatic saccharification was considered. Results A pot trial was designed to test if the ‘RW response’ varies between willow genotypes and contributes to the differences observed in cell wall recalcitrance to enzymatic saccharification in field-grown trees. Biomass composition was measured via wet chemistry and used with glucose release yields from enzymatic saccharification to determine cell wall recalcitrance. The levels of glucose release found for pot-grown control trees showed no significant correlation with glucose release from mature field-grown trees. However, when a RW phenotype was induced in pot-grown trees, glucose release was strongly correlated with that for mature field-grown trees. Field studies revealed a 5-fold increase in glucose release from a genotype grown at a site exposed to high wind speeds (a potentially high RW inducing environment when compared with the same genotype grown at a more sheltered site. Conclusions Our findings provide evidence for a new concept concerning variation in the recalcitrance to enzymatic hydrolysis of the stem biomass of different, field-grown willow genotypes (and potentially other angiosperms. Specifically, that genotypic differences in the ability to produce a response to RW inducing conditions (a ‘RW response’ indicate that this RW response is a primary determinant of the variation observed in cell wall glucan accessibility. The identification of the importance of this RW response trait in willows, is likely to be valuable in selective breeding strategies in willow (and other angiosperm biofuel crops and, with further work to dissect

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

    Morteza Vahedpour


    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.

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

    Gräter, Frauke; Li, Wenjin


    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.

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

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


    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.

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

    Kazemi, Masoud; Åqvist, Johan


    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.

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

    LI,Shao-Bai; ZHENG,Hong-Yan


    @@ 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.

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

    Maciej Szaleniec


    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.

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

    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: [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)


    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

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

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


    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.

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

    Johnson, Erik C B; Kent, Stephen B H


    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.

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

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


    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.

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

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


    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).

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

    Raj, Abhijeet


    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.

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

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


    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.

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

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


    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.

  7. Nicotine-induced upregulation of native neuronal nicotinic receptors is caused by multiple mechanisms.

    Govind, Anitha P; Walsh, Heather; Green, William N


    Nicotine causes changes in brain nicotinic acetylcholine receptors (nAChRs) during smoking that initiate addiction. Nicotine-induced upregulation is the long-lasting increase in nAChR radioligand binding sites in brain resulting from exposure. The mechanisms causing upregulation are not established. Many different mechanisms have been reported with the assumption that there is a single underlying cause. Using live rat cortical neurons, we examined for the first time how exposure and withdrawal of nicotine shape the kinetics of native α4β2-containing nAChR upregulation in real time. Upregulation kinetics demonstrates that at least two different mechanisms underlie this phenomenon. First, a transient upregulation occurs that rapidly reverses, faster than nAChR degradation, and corresponds to nAChR conformational changes as assayed by conformational-dependent, subunit-specific antibodies. Second, a long-lasting process occurs correlating with increases in nAChR numbers caused by decreased proteasomal subunit degradation. Previous radioligand binding measurements to brain tissue have measured the second process and largely missed the first. We conclude that nicotine-induced upregulation is composed of multiple processes occurring at different rates with different underlying causes.

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

    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: [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain)


    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.

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

    Meng Li; Qiaoqiao Yang; Ran Fang


    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.

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


    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 ...

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

    Auerbach, N


    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.

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

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


    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.

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

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


    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.

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

    TIAN Ying; XU Jing; ZHAO Jing-xiang


    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.

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

    Nicola Ernesto M


    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

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

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


    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.

  17. Reclassifying Anaphylaxis to Neuromuscular Blocking Agents Based on the Presumed Patho-Mechanism: IgE-Mediated, Pharmacological Adverse Reaction or “Innate Hypersensitivity”?

    David Spoerl


    Full Text Available Approximately 60% of perioperative anaphylactic reactions are thought to be immunoglobulin IgE mediated, whereas 40% are thought to be non-IgE mediated hypersensitivity reactions (both considered non-dose-related type B adverse drug reactions. In both cases, symptoms are elicited by mast cell degranulation. Also, pharmacological reactions to drugs (type A, dose-related may sometimes mimic symptoms triggered by mast cell degranulation. In case of hypotension, bronchospasm, or urticarial rash due to mast cell degranulation, identification of the responsible mechanism is complicated. However, determination of the type of the underlying adverse drug reaction is of paramount interest for the decision of whether the culprit drug may be re-administered. Neuromuscular blocking agents (NMBA are among the most frequent cause of perioperative anaphylaxis. Recently, it has been shown that NMBA may activate mast cells independently from IgE antibodies via the human Mas-related G-protein-coupled receptor member X2 (MRGPRX2. In light of this new insight into the patho-mechanism of pseudo-allergic adverse drug reactions, in which as drug-receptor interaction results in anaphylaxis like symptoms, we critically reviewed the literature on NMBA-induced perioperative anaphylaxis. We challenge the dogma that NMBA mainly cause IgE-mediated anaphylaxis via an IgE-mediated mechanism, which is based on studies that consider positive skin test to be specific for IgE-mediated hypersensitivity. Finally, we discuss the question whether MRGPRX2 mediated pseudo-allergic reactions should be re-classified as type A adverse reactions.

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

    Muhammad Mansha


    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.

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

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


    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.

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

    He, Nan; Li, Zhen Hua


    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.

  1. Analysis of in vivo penetration of textile dyes causing allergic reactions

    Lademann, J.; Patzelt, A.; Worm, M.; Richter, H.; Sterry, W.; Meinke, M.


    Contact allergies to textile dyes are common and can cause severe eczema. In the present study, we investigated the penetration of a fluorescent textile dye, dissolved from a black pullover, into the skin of one volunteer during perspiration and nonperspiration. Previously, wearing this pullover had induced a severe contact dermatitis in an 82-year old woman, who was not aware of her sensitization to textile dyes. The investigations were carried out by in vivo laser scanning microscopy. It could be demonstrated that the dye was eluted from the textile material by sweat. Afterwards, the dye penetrated into the stratum corneum and into the hair follicles. Inside the hair follicles, the fluorescent signal was still detectable after 24 h, whereas it was not verifiable anymore in the stratum corneum, Laser scanning microscopy represents an efficient tool for in vivo investigation of the penetration and storage of topically applied substances and allergens into the human skin and reveals useful hints for the development and optimization of protection strategies.

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

    Zhou, Guangfen; Ren, Jie; Zhang, Shaowen


    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.

  3. Drug Resistance Mechanisms in Bacteria Causing Sexually Transmitted Diseases and Associated with Vaginosis.

    Shaskolskiy, Boris; Dementieva, Ekaterina; Leinsoo, Arvo; Runina, Anastassia; Vorobyev, Denis; Plakhova, Xenia; Kubanov, Alexey; Deryabin, Dmitrii; Gryadunov, Dmitry


    Here, we review sexually transmitted diseases (STDs) caused by pathogenic bacteria and vaginal infections which result from an overgrowth of opportunistic bacterial microflora. First, we describe the STDs, the corresponding pathogens and the antimicrobials used for their treatment. In addition to the well-known diseases caused by single pathogens (i.e., syphilis, gonococcal infections, and chlamydiosis), we consider polymicrobial reproductive tract infections (especially those that are difficult to effectively clinically manage). Then, we summarize the biochemical mechanisms that lead to antimicrobial resistance and the most recent data on the emergence of drug resistance in STD pathogens and bacteria associated with vaginosis. A large amount of research performed in the last 10-15 years has shed light on the enormous diversity of mechanisms of resistance developed by bacteria. A detailed understanding of the mechanisms of antimicrobials action and the emergence of resistance is necessary to modify existing drugs and to develop new ones directed against new targets.

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


    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

    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.


    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. Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study.

    Tachikawa, Hiroto


    Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

  7. Supercritical water oxidation of Quinazoline: Effects of conversion parameters and reaction mechanism.

    Gong, Yanmeng; Guo, Yang; Wang, Shuzhong; Song, Wenhan


    The supercritical water oxidation reaction of quinazoline and a set of related reaction products were investigated in batch reactors by varying the temperature (T, 400-600 °C), time (t, 0-400 s), water density (ρ, 70.79-166.28  kg m(-3)) and oxidation coefficient (OC, 0-4.0). The TOC removal efficiency (CRE) increased significantly as the OC increased, whereas this effect was very limited at high OC (>2.0). Lack of oxygen resulted in low CRE and TN removal efficiency (NRE), also cause coke-formation, and giving high yield of NH3 and nitrogenous organic intermediates. Prolonging reaction time did not provide an appreciable improvement on CRE but remarkably increased NRE at temperature higher than 500 °C. Pyrimidines and pyridines as the nitrogenous intermediates were largely found in GC-MS spectrum. Polymerization among benzene, phenyl radical and benzyl radical played important roles in the formation of PAHs, such as naphthalene, biphenyl, phenanthrene. These collective results showed how the yield of intermediate products responded to changes in the process variables, which permitted the development of a potential reaction network for supercritical water oxidation of quinazoline.

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

    Frenzel, Johannes, E-mail:; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany)


    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

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

    Frenzel, Johannes; Marx, Dominik


    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

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

    Frenzel, Johannes; Marx, Dominik


    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

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

    Hennig, Carsten; Schmatz, Stefan


    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.

  12. Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction.

    Lammerding, Jan; Schulze, P Christian; Takahashi, Tomosaburo; Kozlov, Serguei; Sullivan, Teresa; Kamm, Roger D; Stewart, Colin L; Lee, Richard T


    Mutations in the lamin A/C gene (LMNA) cause a variety of human diseases including Emery-Dreifuss muscular dystrophy, dilated cardiomyopathy, and Hutchinson-Gilford progeria syndrome. The tissue-specific effects of lamin mutations are unclear, in part because the function of lamin A/C is incompletely defined, but the many muscle-specific phenotypes suggest that defective lamin A/C could increase cellular mechanical sensitivity. To investigate the role of lamin A/C in mechanotransduction, we subjected lamin A/C-deficient mouse embryo fibroblasts to mechanical strain and measured nuclear mechanical properties and strain-induced signaling. We found that Lmna-/- cells have increased nuclear deformation, defective mechanotransduction, and impaired viability under mechanical strain. NF-kappaB-regulated transcription in response to mechanical or cytokine stimulation was attenuated in Lmna-/- cells despite increased transcription factor binding. Lamin A/C deficiency is thus associated with both defective nuclear mechanics and impaired mechanically activated gene transcription. These findings suggest that the tissue-specific effects of lamin A/C mutations observed in the laminopathies may arise from varying degrees of impaired nuclear mechanics and transcriptional activation.

  13. Body fatness as a cause of cancer: epidemiologic clues to biologic mechanisms.

    Byers, Tim; Sedjo, Rebecca L


    Carrying excess body fat is a leading cause of cancer. Epidemiologic evidence gives strong clues about the mechanisms that link excess adiposity to risk for several cancer sites. For postmenopausal breast cancer and endometrial cancer, the hyper-estrogenic state that is induced by excess body fatness is the likely cause. For esophageal cancer and gallbladder cancer, chronic local inflammation induced by acid reflux and gallstones is the likely cause, and for liver cancer, local inflammation induced by hepatic fatty infiltration is the likely cause. However, for several other cancers known to be associated with excess adiposity, including cancers of the colon, pancreas, ovary, kidney, and prostate, specific causes are not known. Possible candidates include elevated systemic or local tissue inflammation induced by adiposity and effects of the elevated levels of leptin, insulin, IGFs, and depressed immune function that are seen with excess adiposity. There is growing evidence that intentional weight loss not only reduces circulating levels of cancer-associated factors but that it also reduces cancer incidence and recurrence. Better research is needed to understand the mechanisms that link excess body fat to cancer risk as well as to understand the amount of weight loss needed for substantial cancer risk reduction. Finally, as we develop better understanding of the mediators of the effects of excess body fatness on cancer risk, we should identify pharmacologic interventions that target those mediators so that they can be used to complement weight loss in order to reduce cancer risk. © 2015 Society for Endocrinology.

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

    Garrison, W.M.


    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.

  15. Communication: Enhanced oxygen reduction reaction and its underlying mechanism in Pd-Ir-Co trimetallic alloys

    Ham, Hyung Chul; Manogaran, Dhivya; Lee, Kang Hee; Kwon, Kyungjung; Jin, Seon-ah; You, Dae Jong; Pak, Chanho; Hwang, Gyeong S.


    Based on a combined density functional theory and experimental study, we present that the electrochemical activity of Pd3Co alloy catalysts toward oxygen reduction reaction (ORR) can be enhanced by adding a small amount of Ir. While Ir tends to favorably exist in the subsurface layers, the underlying Ir atoms are found to cause a substantial modification in the surface electronic structure. As a consequence, we find that the activation barriers of O/OH hydrogenation reactions are noticeably lowered, which would be mainly responsible for the enhanced ORR activity. Furthermore, our study suggests that the presence of Ir in the near-surface region can suppress Co out-diffusion from the Pd3Co substrate, thereby improving the durability of Pd-Ir-Co catalysts. We also discuss the relative roles played by Ir and Co in enhancing the ORR activity relative to monometallic Pd catalysts.

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

    CHEN Li-Ping; CHEN Hui-Ping


    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.

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

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


    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

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

    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.

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

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


    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.

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

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


    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.

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

    Groover, Andrew


    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.

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

    Zhiguo Zhang


    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.

  3. Horseback Riding Improves the Ability to Cause the Appropriate Action (Go Reaction) and the Appropriate Self-control (No-Go Reaction) in Children.

    Ohtani, Nobuyo; Kitagawa, Kenji; Mikami, Kinuyo; Kitawaki, Kasumi; Akiyama, Junko; Fuchikami, Maho; Uchiyama, Hidehiko; Ohta, Mitsuaki


    There are many obvious health benefits to riding, including developing a strong core and legs, but there are also many less obvious benefits, such as increased confidence and introspection. Few studies have addressed the effects of horseback riding on children and the mechanisms underlying how riding affects humans. We examined the effects of horseback riding on the ability to distinguish Go/No-go tasks and solve arithmetic problems in children. The subjects were 34 boys and 72 girls, aged 10-12 years old, which were divided into three groups (horse riding, walking, and resting). They were healthy typical children, who performed the Go/No-go tasks and solved the arithmetic problems. The heart rate and heart rate variability of the children, and the three-dimensional acceleration of the children while walking horses, were examined. Riding on a half-breed horse or a pony improved the ability to perform Go/No-go tasks and solve arithmetic problems, possibly through sympathetic activity. Some horses, like the Kiso, might provide a healing effect to children through parasympathetic activity. Statistically significant differences in the three-dimensional acceleration and the autonomic activities were observed among the three horses. The acceleration in the Kiso horse group during walking in hand was significantly different from those involving the other two horses, indicating that the vibrations produced by these horses might modify the autonomic activities. The most important beneficial factor of horseback riding for children and for human health appears to be associated with the horse's vibrations, which may differ among horses. Riding some horses may improve the ability of children to respond with an appropriate action depending on the situation (Go reaction) or use self-control appropriately (No-go reaction), possibly through the activation of the sympathetic nervous system.

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

    Wei, Xu; Xie, Yan-Ming


    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.

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

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


    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.

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

    Hu eWang


    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.

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

    Liu, Peng; Zhang, Jingxue; Wang, Dunyou


    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.

  8. Mechanisms by which nutritional disorders cause reduced bone mass in adults.

    Miller, Karen K


    Nutritional disorders that cause bone loss in adults include disordered eating behaviors (female athlete triad and anorexia nervosa), gastrointestinal diseases (celiac sprue, inflammatory bowel disease, and other malabsorption syndromes), alcoholism, and hypervitaminosis A. These disorders exert their effects on bone through a number of mechanisms, including estrogen deficiency. Deficiencies of anabolic hormones may also be important, including insulin-like growth factor I (IGF-I), a nutritionally regulated bone trophic factor. In addition, low weight itself is a risk factor for bone loss and decreased bone formation. Reduced calcium and vitamin D availability, with resultant secondary hyperparathyroidism, is another important mechanism of bone loss in nutritional disorders. This review discusses nutritional causes of reduced bone mass in adults and how nutritional disorders exert deleterious effects on the skeleton.

  9. Age-related differences in mechanism, cause, and location of trauma deaths

    Meisler, Rikke; Thomsen, Annemarie Bondegaard; Theilade, Peter


    BACKGROUND: Trauma death has traditionally been described as primarily occurring in young men exposed to penetrating trauma or road traffic accidents. The epidemiology of trauma fatalities in Europe may change as a result of the increasing proportion of elderly patients. The goal of this study...... was to describe age-related differences in trauma type, mechanism, cause and location of death in a well-defined European region. METHODS: We prospectively registered all trauma patients and severe burn patients in eastern Denmark over 12 consecutive months. We analyzed all trauma fatalities in our region...... regarding the trauma type, mechanism, cause and location of death. RESULTS: A total of 2923 patients were registered, of which 292 (9.9%) died within 30 days. Mortality increased with age, with a mortality of 46.1% in patients older than 80 years old. Blunt trauma was the most frequent trauma type at all...

  10. Quantum interference between H + D2 quasiclassical reaction mechanisms.

    Jambrina, Pablo G; Herráez-Aguilar, Diego; Aoiz, F Javier; Sneha, Mahima; Jankunas, Justinas; Zare, Richard N


    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.

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

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


    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.

  12. Theoretical Study on Reaction Mechanism of Tautomerization of Indazole and 3-halogeno-indazole

    Yu, Hai-yan; Li, Bao-zong; Guo, Yong-min


    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.

  13. Reaction mechanism studies on isoquinoline with hydroxyl radical in aqueous solutions

    ZHU Dazhang; WANG Shilong; SUN Xiaoyu; NI Yarning; YAO Side


    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.

  14. Theoretic study of the reaction mechanism between (Me)3CO·radical and trans-3-hexene

    SHI GuoSheng; DING YiHong


    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.

  15. Mechanism and kinetics in reactions of caffeic acid with radicals by pulse radiolysis and calculation

    Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab


    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)

  16. Microstructure and Mechanical Properties of Reaction-Formed Silicon Carbide (RFSC) Ceramics

    Singh, M.; Behrendt, D. R.


    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.

  17. From Sound to Significance: Exploring the Mechanisms Underlying Emotional Reactions to Music.

    Juslin, Patrik N; Barradas, Gonçalo; Eerola, Tuomas


    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.

  18. Monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 enzymes.

    Hrycay, Eugene G; Bandiera, Stelvio M


    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.

  19. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

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


    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.

  20. Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis.

    Renger, Gernot; Kühn, Philipp


    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).

  1. Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme.

    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.

  2. Reaction mechanism of cobalt-substituted homoprotocatechuate 2,3-dioxygenase: a QM/MM study.

    Cao, Lili; Dong, Geng; Lai, Wenzhen


    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.

  3. Substrate Oxidation by Indoleamine 2,3-Dioxygenase: EVIDENCE FOR A COMMON REACTION MECHANISM.

    Booth, Elizabeth S; Basran, Jaswir; Lee, Michael; Handa, Sandeep; Raven, Emma L


    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.

  4. Molecular beam studies of unimolecular reactions: Cl, F + C/sub 2/H/sub 3/Br. [Angular and velocity distributions, mechanism

    Buss, R.J.; Coggiola, M.J.; Lee, Y.T.


    Several methods currently used to study unimolecular decomposition in molecular beams are discussed. Experimental product angular and velocity distributions obtained for the reaction of F, Cl with C/sub 2/H/sub 3/Br are presented. The mechanism by which conservation of angular momemtum can cause coupling of the product angular and velocity distributions in dissociation of long-lived complexes is introduced. 14 references.

  5. A variety of microstructures in Mg/Cu super-laminate composites caused by competitive reactions during hydrogenation

    Tanaka, K.; Shibata, K.; Nishida, Y.; Kurumatani, K.; Kondo, R.; Kikuchi, S.; Takeshita, H. T.


    A variety of microstructures in Mg/Cu super-laminate composites (SLCs) caused by competitive reactions during hydrogenation has been shown experimentally. Two types of MgCu2 structures, three-dimensional (3-D) network and layer, were observed after initial hydrogenation of Mg/Cu SLCs under the conditions of 573K, 86.4ks in H2 of 3-3MPa. It was proposed that Mg/Cu SLCs could be hydrogenated by two kinds of processes. The one is alloying Mg with Cu to form Mg2Cu followed by hydrogenation of Mg2Cu, leading to the formation of 3-D network of MgCu2. The other is hydrogenation of Mg followed by the reaction of MgH2 to Cu, leading to the formation of layer MgCu2. SEM observations revealed that there existed Mg2Cu nano-crystals at the interface between Mg and Cu in as-rolled Mg/Cu SLCs, and layer MgCu2 at the interface between MgH2 and Cu in pellets of MgH2 powder and Cu powder heated under the conditions of 673K, 86.4ks in H2 of 8.0 MPa. The existence of Mg2Cu nano-crystals enables alloying Mg with Cu at low temperatures (<473K).

  6. Mechanical overloading causes mitochondrial superoxide and SOD2 imbalance in chondrocytes resulting in cartilage degeneration.

    Koike, Masato; Nojiri, Hidetoshi; Ozawa, Yusuke; Watanabe, Kenji; Muramatsu, Yuta; Kaneko, Haruka; Morikawa, Daichi; Kobayashi, Keiji; Saita, Yoshitomo; Sasho, Takahisa; Shirasawa, Takuji; Yokote, Koutaro; Kaneko, Kazuo; Shimizu, Takahiko


    Mechanical stress and aging are major risk factors of cartilage degeneration. Human studies have previously reported that oxidative damage increased, while SOD2 protein was reciprocally downregulated in osteoarthritic degenerated cartilage. However, it remains unclear whether mitochondrial superoxide imbalance in chondrocytes causes cartilage degeneration. We herein demonstrate that mechanical loading promoted mitochondrial superoxide generation and selective Sod2 downregulation in chondrocytes in vivo and that mitochondrial superoxide inducer also downregulated Sod2 expression in chondrocytes in vitro. A genetically manipulated model revealed that Sod2 deficiency in chondrocytes also resulted in mitochondrial superoxide overproduction and dysfunction, thus leading to cartilage degeneration. Intra-articular injection of a permeable antioxidant effectively suppressed the mechanical loading-induced mitochondrial superoxide generation and cartilage degeneration in mice. Our findings demonstrate that mitochondrial superoxide plays a pivotal role in the development and progression of osteoarthritis, and the mitochondrial superoxide balance may therefore be a promising target for the treatment of cartilage degeneration.

  7. A New Method for Describing the Mechanism of a Chemical Reaction Based on the Unified Reaction Valley Approach.

    Zou, Wenli; Sexton, Thomas; Kraka, Elfi; Freindorf, Marek; Cremer, Dieter


    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.

  8. Theoretical Study on the Reaction Mechanism between Dichlorocarbene and Armchair Single-walled Carbon Nanotubes

    LI Rui-Fang; SHANG Zhen-Feng; XU Xiu-Fang; WANG Gui-Chang


    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.

  9. Mechanism of reaction of phenol with toluene on a zeolite catalyst

    Kozhevnikov, S.A.; Sibarov, D.A.; Proskuryakov, V.A.


    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.

  10. Further study on mechanism of production of light complex particles in nucleon-induced reactions

    Wei, Dexian; Mao, Lihua; Wang, Ning; Liu, Min; Ou, Li, E-mail:


    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.

  11. Reduction of Large Detailed Chemical Kinetic Mechanisms for Autoignition Using Joint Analyses of Reaction Rates and Sensitivities

    Saylam, A; Ribaucour, M; Pitz, W J; Minetti, R


    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.

  12. Unraveling the Concerted Reaction Mechanism of the Noncatalyzed Mukaiyama Reaction between C,O,O-Tris(trimethylsilyl)ketene Acetal and Aldehydes Using Density Functional Theory.

    Hadj Mohamed, Slim; Trabelsi, Mahmoud; Champagne, Benoît


    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.

  13. First-principles modeling of catalysts: novel algorithms and reaction mechanisms

    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

  14. Quantum mechanical/molecular mechanical study on the enantioselectivity of the enzymatic Baeyer-Villiger reaction of 4-hydroxycyclohexanone.

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


    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.

  15. [Can cross-allergic reactions to food antigens be the cause of recurrent pancreatitis in children with food allergies?].

    Subbotina, O A; Geppe, N A; Primak, E A; Surikova, O A; Orekhova, V P


    Drug and food allergy in 80% of cases are the cause of duodenal inflammation disrupting the function of the pancreatic ducts. However, in some cases, elimination diet in patients with food allergy does not provide a sufficient effect. The article shows the effect of cross-allergic reactions on recurrent pancreatitis in 28 children with food allergy (mean age 11.7 +/- 2.9 years). As an additional diagnostic criterion the coefficient of degranulation of mast cell in the intestinal mucosa (the ratio of degranulated forms to granulated) was determined, through which the effect of cross-allergic reactions (between food antigens and drugs of animal origin) on the duration and frequency of exacerbations of chronic pancreatitis in children with food sensitization has been shown. The exception of enzyme preparations for children with sensitization to pork and exception of eubiotics prepared using sucrose-gelatin-milk medium for children with sensitization to cow's milk and beef led to feel better in a shorter time (2-3 days) and to reduce the frequency of relapses. Catamnesis observation for 3 years showed that the incidence of recurrent exacerbations of the disease in 11 children with excepted cross-allergic reactions in the first year of follow-up was 9.1%, in the second year--9.1% and in the third year--0%, while in control group (17 children) the frequency of exacerbations was respectively 23.5; 35.3; 35.3%. In patients of the main group there was a slight overall increase of mast cells in the intestinal mucosa from 211.7 to 230.2 mm2 (p > 0.05) with decreasing of degranulated forms from 163.6 to 138.71 mm2 (p > 0.05) and significant increase of granulated forms from 47.41 to 91.51 mm2 (p food antigens or cross-allergic reactions can be diagnosed with an additional diagnostic criterion--the coefficient of mast cell degranulation, whose exponents greater than 1.5 indicate evidence of antigenic exposure to the mucosa of the duodenum and allergic inflammation.

  16. Theoretical Study on the Reaction Mechanism of SiCl4 with H in the Gas Phase


    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.

  17. Dissipative structure of mechanically stimulated reaction; Kikaiteki reiki hanno ni okeru san`itsu kozo

    Hida, M. [Okayama Univ., Okayama (Japan). Faculty of Engineering


    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.

  18. Reaction mechanisms in the {sup 6}Li + {sup 59}Co system

    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:; 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)


    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.

  19. A detailed look at the reaction mechanisms of substituted carbenes with water.

    Gómez, Sara; Guerra, Doris; López, José G; Toro-Labbé, Alejandro; Restrepo, Albeiro


    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.

  20. Mechanism and electronic effects in nitrogen ylide-promoted asymmetric aziridination reaction.

    Rajeev, Ramanan; Sunoj, Raghavan B


    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.

  1. Triplet state dissolved organic matter in aquatic photochemistry: reaction mechanisms, substrate scope, and photophysical properties.

    McNeill, Kristopher; Canonica, Silvio


    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.

  2. Kinetics and mechanism of the reaction of sodium azide with hypochlorite in aqueous solution.

    Betterton, Eric A; Lowry, Joe; Ingamells, Robin; Venner, Brad


    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.

  3. A Theoretical Investigation on the Reaction Mechanism of the C9H+ 12·Side-chain Decomposition

    CHENG,Xueli; ZHAO,Yanyun; LI,Feng; ZHANG,Dongsheng


    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.

  4. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations.

    Ardèvol, Albert; Rovira, Carme


    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.

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

    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: [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)


    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.

  6. Interstitial lung disease caused by TS-1: a case of long-term drug retention as a fatal adverse reaction.

    Park, Joong-Min; Hwang, In Gyu; Suh, Suk-Won; Chi, Kyong-Choun


    TS-1 is an oral anti-cancer agent for gastric cancer with a high response rate and low toxicity. We report a case of long-term drug retention of TS-1 causing interstitial lung disease (ILD) as a fatal adverse reaction. A 65-year-old woman underwent a total gastrectomy with pathologic confirmation of gastric adenocarcinoma. She received 6 cycles of TS-1 and low-dose cisplatin for post-operative adjuvant chemotherapy followed by single-agent maintenance therapy with TS-1. After 8 months, the patient complained of a productive cough with sputum and mild dyspnea. A pulmonary evaluation revealed diffuse ILD in the lung fields, bilaterally. In spite of discontinuing chemotherapy and the administration of corticosteroids, the pulmonary symptoms did not improve, and the patient died of pulmonary failure. TS-1-induced ILD can be caused by long-term drug retention that alters the lung parenchyma irreversibly, the outcome of which can be life-threatening. Pulmonary evaluation for early detection of disease is recommended.

  7. Detailed Chemical Kinetic Reaction Mechanisms for Primary Reference Fuels for Diesel Cetane Number and Spark-Ignition Octane Number

    Westbrook, C K; Pitz, W J; Mehl, M; Curran, H J


    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.

  8. A new, double-inversion mechanism of the F(-) + CH3Cl SN2 reaction in aqueous solution.

    Liu, Peng; Wang, Dunyou; Xu, Yulong


    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.

  9. Developing a highly reliable cae analysis model of the mechanisms that cause bolt loosening in automobiles

    Ken Hashimoto


    Full Text Available In this study, we developed a highly reliable CAE analysis model of the mechanisms that cause loosening of bolt fasteners, which has been a bottleneck in automobile development and design, using a technical element model for highly accurate CAE that we had previously developed, and verified its validity. Specifically, drawing on knowledge gained from our clarification of the mechanisms that cause loosening of bolt fasteners using actual machine tests, we conducted an accelerated bench test consisting of a threedimensional vibration load test of the loosening of bolt fasteners used in mounts and rear suspension arms, where interviews with personnel at an automaker indicated loosening was most pronounced, and reproduced actual machine tests with CAE analysis based on a technical element model for highly accurate CAE analysis. Based on these results, we were able to reproduce dynamic behavior in which larger screw pitches (lead angles lead to greater non-uniformity of surface pressure, particularly around the nut seating surface, causing loosening to occur in areas with the lowest surface pressure. Furthermore, we implemented highly accurate CAE analysis with no error (gap compared to actual machine tests.

  10. Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction.

    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


    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.

  11. TDDFT Study on Different Sensing Mechanisms of Similar Cyanide Sensors Based on Michael Addition Reaction

    Guang-yue Li; Ping Song; Guo-zhong He


    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.

  12. Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase.

    Kim, Hun; Choi, Jongkeun; Kim, Truc; Lokanath, Neratur K; Ha, Sung Chul; Suh, Se Won; Hwang, Hye-Yeon; Kim, Kyeong Kyu


    UDP-glucose pyrophosphorylases (UGPase; EC 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.

  13. Electronically excited states and photochemical reaction mechanisms of β-glucose.

    Tuna, Deniz; Sobolewski, Andrzej L; Domcke, Wolfgang


    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.

  14. Mechanism of the heterogeneous reaction of carbonyl sulfide with typical components of atmospheric aerosol

    WU Hongbo; WANG Xiao; CHEN Jianmin; YU Hongkun; XUE Huaxin; PAN Xunxi; HOU Huiqi


    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.

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

    Sinha, Sourab


    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.

  16. Pathophysiological mechanisms of local (pulmonary inflammatory reaction at the traumatic disease of the spinal cord

    Uljanov V.Yu.


    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.

  17. Ablation characteristics and reaction mechanism of insulation materials under slag deposition condition

    Guan, Yiwen; Li, Jiang; Liu, Yang


    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.

  18. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order.

    Wongnate, Thanyaporn; Ragsdale, Stephen W


    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.

  19. On Cosmic-Ray-Driven Electron Reaction Mechanism for Ozone Hole and Chlorofluorocarbon Mechanism for Global Climate Change

    Lu, Qing-Bin


    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...

  20. Delayed allergic dermatitis presenting as a keloid-like reaction caused by sting from an Indo-Pacific Portuguese man-o'-war (Physalia utriculus).

    Guevara, B E K; Dayrit, J F; Haddad, V


    Cnidarian envenomations are common occurrences in the tropics that can affect holidaymakers. The cutaneous reactions are classified as immediate or delayed types. Delayed allergic reactions are persistently recurring dermatitis, which can occur within 1-4 weeks from the initial sting, and may last for several months. Hypertrophic scar-like or keloid-like reactions are rare, and are believed to be a type IV hypersensitivity reaction to sequestered antigens from stinging filaments. We report an unusual case of delayed allergic dermatitis with keloid-like presentation caused by Physalia utriculus.

  1. Mechanisms before Reactions: A Mechanistic Approach to the Organic Chemistry Curriculum Based on Patterns of Electron Flow

    Flynn, Alison B.; Ogilvie, William W.


    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…

  2. Mechanisms before Reactions: A Mechanistic Approach to the Organic Chemistry Curriculum Based on Patterns of Electron Flow

    Flynn, Alison B.; Ogilvie, William W.


    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…

  3. A novel mechanism for the oxidation reaction of VO2+ on a graphite electrode in acidic solutions

    Wang, Wenjun; Fan, Xinzhuang; Liu, Jianguo; Yan, Chuanwei; Zeng, Chaoliu


    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.


    R. Zamani Foroshani


    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.

  5. NO-CO-O2 Reaction on a Metal Catalytic Surface using Eley-Rideal Mechanism

    Waqar Ahmad


    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.

  6. Cell mechanics and stress: from molecular details to the 'universal cell reaction' and hormesis.

    Agutter, Paul S


    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.

  7. Fracture mechanism of TiAl intermetallics caused by hydride and atomic hydrogen

    高克玮; 王燕斌; 林志; 乔利杰; 褚武扬


    Hydrogen embrittlement (HE) of TiAl intermetallics was studied at room temperature. The results showed that there were two forms of HE in TiAl intermetallics, i.e. hydride HE and atomic HE. Most of hydrogen in TiAl intermetallics was transformed into hydrides at room temperature. The hydride exists as (TiAl)Hx for a low hydrogen concentration while it exists in several forms for a higher hydrogen concentration. Stress intensity factor KIC decreased with increase in hydride concentration. KIC decreased further when TiAl intermetallics were charged cathodically with hydrogen in 1 mol/L H2SO4 solution. Stress intensity factor during hydrogen charging KIH was about 50% KIC. 20% of the decrease was caused by hydrides while 30% was caused by atomic hydrogen. Mechanism of HE caused hydrides was the same as any other second phase in nature. Delayed fracture caused by atomic hydrogen resulted from hydrogen induced local plastic deformation.

  8. Candida Infections, Causes, Targets, and Resistance Mechanisms: Traditional and Alternative Antifungal Agents

    Claudia Spampinato


    Full Text Available The genus Candida includes about 200 different species, but only a few species are human opportunistic pathogens and cause infections when the host becomes debilitated or immunocompromised. Candida infections can be superficial or invasive. Superficial infections often affect the skin or mucous membranes and can be treated successfully with topical antifungal drugs. However, invasive fungal infections are often life-threatening, probably due to inefficient diagnostic methods and inappropriate initial antifungal therapies. Here, we briefly review our current knowledge of pathogenic species of the genus Candida and yeast infection causes and then focus on current antifungal drugs and resistance mechanisms. An overview of new therapeutic alternatives for the treatment of Candida infections is also provided.

  9. Reaction Mechanism Investigation Using Vibrational Mode Anal—ysis for the Multichannel Reacition of CH3O+CO

    周正宇; 程学礼; 等


    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.

  10. Systematization of the Mechanism by Which Plasma Irradiation Causes Cell Growth and Tumor Cell Death

    Shimizu, Nobuyuki


    New methods and technologies have improved minimally invasive surgical treatment and saved numerous patients. Recently, plasma irradiation has been demonstrated that might be useful in medical field and the plasma irradiation device is expected to become practically applicable. Mild plasma coagulator showed some advantages such as hemostasis and adhesion reduction in experimental animal model, but the mechanism of plasma irradiation remains unclear. Our study group aim to clarify the mechanism of plasma irradiation effects, mainly focusing on oxidative stress using cultured cell lines and small animal model. First, a study using cultured cell lines showed that the culture medium that was activated by plasma irradiation (we called this kind of medium as ``PAM'' -plasma activated medium-) induced tumor cell death. Although this effect was mainly found to be due to hydrogen peroxide, the remaining portion was considered as the specific effect of the plasma irradiation and we are now studying focusing on this effect. Second, we established a mouse intra-peritoneal adhesion model and checked biological reaction that occurred in the adhesion part. Histopathological study showed inflammatory cells infiltration into adhesion part and the expression of PTX3 that might involve tissue repair around adhesion part. We also confirmed that cytokines IL-6 and IL-10 might be useful as a marker of adhesion formation in this model. Applying ``PAM'' or mild plasma irradiation in this model, we examine the effects of plasma on inflamed cells. The samples in these experiments would be applied to targeted proteomics analysis, and we aim to demonstrate the systematization of the cell's reaction by plasma irradiation.

  11. Mechanisms of cadmium-caused eye hypoplasia and hypopigmentation in zebrafish embryos

    Zhang, Ting, E-mail:; Zhou, Xin-Ying, E-mail:; Ma, Xu-Fa, E-mail:; Liu, Jing-Xia, E-mail:


    Highlights: Using high-throughput in situ hybridization screening, we found that genes labeling the neural crest and its derivative pigment cells were sensitive to cadmium toxicity during zebrafish organogenesis, which might contribute to the molecular mechanisms underlying the phenotype defects of head and eye hypoplasia and hypopigmentation in cadmium-exposed embryos. Based on neural crest markers, we identified the doses and times of cadmium exposure that cause damage to the zebrafish organogenesis, and we also found that compounds BIO or RA could neutralize the toxic effects of cadmium. - Abstract: Cadmium-caused head and eye hypoplasia and hypopigmentation has been recognized for a long time, but knowledge of the underlying mechanisms is limited. In this study, we found that high mortality occurred in exposed embryos after 24 hpf, when cadmium (Cd) dosage was above 17.8 μM. Using high-throughput in situ hybridization screening, we found that genes labelling the neural crest and its derivative pigment cells exhibited obviously reduced expression in Cd-exposed embryos from 24 hpf, 2 days earlier than head and eye hypoplasia and hypopigmentation occurred. Moreover, based on expression of crestin, a neural crest marker, we found that embryos before the gastrula stage were more sensitive to cadmium toxicity and that damage caused by Cd on embryogenesis was dosage dependent. In addition, by phenotype observation and detection of neural crest and pigment cell markers, we found that BIO and retinoic acid (RA) could neutralize the toxic effects of Cd on zebrafish embryogenesis. In this study, we first determined that Cd blocked the formation of the neural crest and inhibited specification of pigment cells, which might contribute to the molecular mechanisms underlying the phenotype defects of head and eye hypoplasia and hypopigmentation in Cd-exposed embryos. Moreover, we found that compounds BIO or RA could neutralize the toxic effects of Cd.

  12. Discussion on Mechanism of Breech-Blow Caused by Propellant Charge


    From the view point of launch safety caused by fracture of propellant charge, this paper points out that the safety criterion of pressure wave is inadequate to evaluate the launch safety of propellant charge based on the initial negative differential pressure and sensitivity tests. Generally, the maximum barrel pressure does not depend upon the intensity of pressure wave correspondingly. The pressure wave intensity can not describe the fracture degree of propellant charge in chamber and reflect the mechanical environment of propellant charge fracturing exactly and wholly. The evaluation criterion for launch safety of propellant charge should be built on the basis of depicting the fracture degree of propellant bed.

  13. The Role of Multiplex Polymerase Chain Reaction in Detecting Etiological Causes of Bacterial Prostatitis Associated Benign Prostatic Hyperplasia

    Bramastha Rosadi


    Full Text Available Background: Benign Prostatic Hyperplasia (BPH has been correlated with chronic prostatitis according recent study. Chronic pelvic pain is the chief complain of BPH followed by prostatitis. The gold standard of the etiological diagnosis is urine culture, but the negativity rate is still high. Multiplex polymerase chain reaction (PCR as a diagnostic tool in search of etiological causes could identify microorganism on DNA level. This research aims to find out the role of multiplex polymerase chain reaction as diagnostic tools on prostatitis patients. Material and Method: A total of 12 samples collected during the TURP procedure in Sanglah General Hospital Denpasar – Bali from February until May 2015. All of the samples has been diagnosed prostatitis clinically and perform urine culture test. The prostate specimen taken was sent to the Pathological anatomy for histopathology diagnostic and underwent multiplex PCR for etiologic diagnostic. Result: 12 samples have been declared as prostatitis based on histopathology examination, and then were analyzed using multiplex PCR. 10 samples were positive (6 were E. coli, 2 were C. trachomatis, the rest were N. gonorrhea and P. aeruginosa. The urine culture revealed 9 positive, within the result 6 were E. coli, and the others were P. aeruginosa, M. morganii and A. haemolyticus. Conclusion: In prostatitis patient, the etiological diagnostic was important. Multiplex PCR as diagnostic tools could detect the microorganism on a negative urine culture. The combination of the urine culture test and multiplex PCR revealed a better result on etiologic diagnosis which leads to a better management of the disease. 

  14. Shrinkage Cracking: A mechanism for self-sustaining carbon mineralization reactions in olivine rocks

    Zhu, W.; Fusseis, F.; Lisabeth, H. P.; Xing, T.; Xiao, X.; De Andrade, V. J. D.; Karato, S. I.


    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

  15. Structure and mechanism of styrene monooxygenase reductase: new insight into the FAD-transfer reaction.

    Morrison, Eliot; Kantz, Auric; Gassner, George T; Sazinsky, Matthew H


    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.

  16. PCDD/F Formation mechanism: effect of surface composition on chlorination and condensation reactions

    Sidhu, S.; Nath, P.


    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

  17. Preparation of Polystryenylphosphonous Acid of Low Polymerization Degree and Influence of Initiators upon the Free Radical Reaction Mechanism

    XiangKaiFU; YanSUI; 等


    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.

  18. Preparation of Polystyrenylphosphonous Acid of Low Polymerization Degree and Influence of Initiators upon the Free Radical Reaction Mechanism


    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.

  19. SnCl2/Cu-Mediated Carbonyl Allylation Reaction in Water:Scope,Selectivity and Mechanism

    TAN,Xiang-Hui(谭翔晖); HOU,Yong-Quan(侯永泉); LIU,Lei(刘磊); GUO,Qing-Xiang(郭庆祥)


    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.

  20. Rational approach to polymer-supported catalysts: synergy between catalytic reaction mechanism and polymer design.

    Madhavan, Nandita; Jones, Christopher W; Weck, Marcus


    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

  1. Structures and reaction mechanisms of the two related enzymes, PurN and PurU.

    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


    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.

  2. Synthesis Mechanism and Strengthening Effects of Laminated NiAl by Reaction Annealing

    Du, Yan; Fan, Guohua; Wang, Qingwei; Geng, Lin


    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.

  3. High Electrocatalytic Response of a Mechanically Enhanced NbC Nanocomposite Electrode Towards Hydrogen Evolution Reaction

    Coy, Emerson


    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.

  4. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi


    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.

  5. Three autocatalysts and self-inhibition in a single reaction: a detailed mechanism of the chlorite-tetrathionate reaction.

    Horváth, Attila K; Nagypál, István; Epstein, Irving R


    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.

  6. Implications of sterically constrained n-butane oxidation reactions on the reaction mechanism and selectivity to 1-butanol

    Dix, Sean T.; Gómez-Gualdrón, Diego A.; Getman, Rachel B.


    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.

  7. Reaction of benzophenone triplet with aliphatic amines. What a potent neurotoxin can tell us about the reaction mechanism.

    Grimm, Michelle L; Allen, William J; Finn, Meghan; Castagnoli, Neal; Tanko, James M


    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.

  8. Thermal degradation of aqueous 2-aminoethylethanolamine in CO2 capture; identification of degradation products, reaction mechanisms and computational studies.

    Saeed, Idris Mohamed; Lee, Vannajan Sanghiran; Mazari, Shaukat Ali; Si Ali, B; Basirun, Wan Jeffrey; Asghar, Anam; Ghalib, Lubna; Jan, Badrul Mohamed


    Amine degradation is the main significant problems in amine-based post-combustion CO2 capture, causes foaming, increase in viscosity, corrosion, fouling as well as environmental issues. Therefore it is very important to develop the most efficient solvent with high thermal and chemical stability. This study investigated thermal degradation of aqueous 30% 2-aminoethylethanolamine (AEEA) using 316 stainless steel cylinders in the presence and absence of CO2 for 4 weeks. The degradation products were identified by gas chromatography mass spectrometry (GC/MS) and liquid chromatography-time-of-flight-mass spectrometry (LC-QTOF/MS). The results showed AEEA is stable in the absence of CO2, while in the presence of CO2 AEEA showed to be very unstable and numbers of degradation products were identified. 1-(2-Hydroxyethyl)-2-imidazolidinone (HEIA) was the most abundance degradation product. A possible mechanism for the thermal degradation of AEEA has been developed to explain the formation of degradation products. In addition, the reaction energy of formation of the most abundance degradation product HEIA was calculated using quantum mechanical calculation.

  9. 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

    Um, Ik-Hwan; Han, Jeong-Yoon [Ewha Womans University, Seoul (Korea, Republic of)


    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.

  10. Global reaction mechanism for the auto-ignition of full boiling range gasoline and kerosene fuels

    Vandersickel, A.; Wright, Y. M.; Boulouchos, K.


    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.

  11. An automatic modeling system of the reaction mechanisms for chemical vapor deposition processes using real-coded genetic algorithms.

    Takahashi, Takahiro; Nakai, Hiroyuki; Kinpara, Hiroki; Ema, Yoshinori


    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.

  12. 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.

    Shi, Qicun; Meroueh, Samy O; Fisher, Jed F; Mobashery, Shahriar


    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

  13. Theoretical Study of the Scattering Resonance State, Reaction Mechanism and Partial Potential Energy Surface of the F+CH4→HF +CH3 Reaction

    Qiang WANG; Zheng Ting CAI; Da Cheng FENG


    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.

  14. Kinetics and mechanisms of reactions between H2O2 and copper and copper oxides.

    Björkbacka, Åsa; Yang, Miao; Gasparrini, Claudia; Leygraf, Christofer; Jonsson, Mats


    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.

  15. Atmospheric chemistry of benzyl alcohol: kinetics and mechanism of reaction with OH radicals.

    Bernard, François; Magneron, Isabelle; Eyglunent, Grégory; Daële, Véronique; Wallington, Timothy J; Hurley, Michael D; Mellouki, Abdelwahid


    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.

  16. Studies on adsorption, reaction mechanisms and kinetics for photocatalytic degradation of CHD, a pharmaceutical waste.

    Sarkar, Santanu; Bhattacharjee, Chiranjib; Curcio, Stefano


    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.

  17. Effects of alpha-amylase reaction mechanisms on analysis of resistant-starch contents.

    Moore, Samuel A; Ai, Yongfeng; Chang, Fengdan; Jane, Jay-lin


    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.

  18. Surface reaction mechanisms during ozone and oxygen plasma assisted atomic layer deposition of aluminum oxide.

    Rai, Vikrant R; Vandalon, Vincent; Agarwal, Sumit


    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.

  19. Reaction Mechanism and Distribution Behavior of Arsenic in the Bottom Blown Copper Smelting Process

    Qinmeng Wang


    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.

  20. Thermochemical reaction mechanism of lead oxide with poly(vinyl chloride) in waste thermal treatment.

    Wang, Si-Jia; Zhang, Hua; Shao, Li-Ming; Liu, Shu-Meng; He, Pin-Jing


    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.