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Sample records for additional reaction pathways

  1. The Aldol Addition and Condensation: The Effect of Conditions on Reaction Pathway

    ERIC Educational Resources Information Center

    Crouch, R. David; Richardson, Amie; Howard, Jessica L.; Harker, Rebecca L.; Barker, Kathryn H.

    2007-01-01

    The reaction of a ketone and an aldehyde in aqueous Na[subscript 2]CO[subscript 2] is described. This experiment is performed in the absence of strong bases or organic solvents and offers the opportunity for students to observe the critical role that reaction temperature and base strength have in determining the product of the base-mediated…

  2. Investigation of the O+allyl addition/elimination reaction pathways from the OCH(2)CHCH(2) radical intermediate.

    PubMed

    Fitzpatrick, Benjamin L; Lau, Kai-Chung; Butler, Laurie J; Lee, Shih-Huang; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH(2)CHCH(2), a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH(2)CHCH(2) radicals; these undergo a facile ring opening to the OCH(2)CHCH(2) radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcalmol. To elucidate the product channels resulting from the OCH(2)CHCH(2) radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C(3)H(4)O (acrolein)+H, C(2)H(4)+HCO (formyl radical), and H(2)CO (formaldehyde)+C(2)H(3). A small signal from C(2)H(2)O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at me=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C(2)H(5)+CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to

  3. Combustion kinetics and reaction pathways

    SciTech Connect

    Klemm, R.B.; Sutherland, J.W.

    1993-12-01

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

  4. Pressure-dependent competition among reaction pathways from first- and second-O2 additions in the low-temperature oxidation of tetrahydrofuran

    DOE PAGES

    Antonov, Ivan O.; Zador, Judit; Rotavera, Brandon; Papajak, Ewa; Osborn, David L.; Taatjes, Craig A.; Sheps, Leonid

    2016-07-21

    Here, we report a combined experimental and quantum chemistry study of the initial reactions in low-temperature oxidation of tetrahydrofuran (THF). Using synchrotron-based time-resolved VUV photoionization mass spectrometry, we probe numerous transient intermediates and products at P = 10–2000 Torr and T = 400–700 K. A key reaction sequence, revealed by our experiments, is the conversion of THF-yl peroxy to hydroperoxy-THF-yl radicals (QOOH), followed by a second O2 addition and subsequent decomposition to dihydrofuranyl hydroperoxide + HO2 or to γ-butyrolactone hydroperoxide + OH. The competition between these two pathways affects the degree of radical chain-branching and is likely of central importancemore » in modeling the autoignition of THF. We interpret our data with the aid of quantum chemical calculations of the THF-yl + O2 and QOOH + O2 potential energy surfaces. On the basis of our results, we propose a simplified THF oxidation mechanism below 700 K, which involves the competition among unimolecular decomposition and oxidation pathways of QOOH.« less

  5. Pressure-Dependent Competition among Reaction Pathways from First- and Second-O2 Additions in the Low-Temperature Oxidation of Tetrahydrofuran.

    PubMed

    Antonov, Ivan O; Zádor, Judit; Rotavera, Brandon; Papajak, Ewa; Osborn, David L; Taatjes, Craig A; Sheps, Leonid

    2016-08-25

    We report a combined experimental and quantum chemistry study of the initial reactions in low-temperature oxidation of tetrahydrofuran (THF). Using synchrotron-based time-resolved VUV photoionization mass spectrometry, we probe numerous transient intermediates and products at P = 10-2000 Torr and T = 400-700 K. A key reaction sequence, revealed by our experiments, is the conversion of THF-yl peroxy to hydroperoxy-THF-yl radicals (QOOH), followed by a second O2 addition and subsequent decomposition to dihydrofuranyl hydroperoxide + HO2 or to γ-butyrolactone hydroperoxide + OH. The competition between these two pathways affects the degree of radical chain-branching and is likely of central importance in modeling the autoignition of THF. We interpret our data with the aid of quantum chemical calculations of the THF-yl + O2 and QOOH + O2 potential energy surfaces. On the basis of our results, we propose a simplified THF oxidation mechanism below 700 K, which involves the competition among unimolecular decomposition and oxidation pathways of QOOH. PMID:27441526

  6. Adverse reactions to food additives.

    PubMed

    Simon, R A

    1986-01-01

    There are thousands of agents that are intentionally added to the food that we consume. These include preservatives, stabilizers, conditioners, thickeners, colorings, flavorings, sweeteners, antioxidants, etc. etc. Yet only a surprisingly small number have been associated with hypersensitivity reactions. Amongst all the additives, FD&C dyes have been most frequently associated with adverse reactions. Tartrazine is the most notorious of them all; however, critical review of the medical literature and current Scripps Clinic studies would indicate that tartrazine has been confirmed to be at best only occasionally associated with flares of urticaria or asthma. There is no convincing evidence in the literature of reactivity to the other azo or nonazo dyes. This can also be said of BHA/BHT, nitrites/nitrates and sorbates. Parabens have been shown to elicit IgE mediated hypersensitivity reactions when used as pharmaceutical preservatives; however, as with the other additives noted above, ingested parabens have only occasionally been associated with adverse reactions. MSG, the cause of the 'Chinese restaurant syndrome' has only been linked to asthma in one report. Sulfiting agents used primarily as food fresheners and to control microbial growth in fermented beverages have been established as the cause of any where from mild to severe and even fatal reactions in at least 5% of the asthmatic population. Other reactions reported to follow sulfite ingestion include anaphylaxis, gastro intestinal complaints and dermatological eruptions. The prevalence of these non asthmatic reactions is unknown. The mechanism of sulfite sensitive asthma is also unknown but most likely involves hyperreactivity to inhale SO2 in the great majority of cases; however, there are reports of IgE mediated reactions and other sulfite sensitive asthmatics have been found with low levels of sulfite oxidase; necessary to oxidize endogenous sulfite to sulfate.

  7. Fundamental reaction pathways during coprocessing

    SciTech Connect

    Stock, L.M.; Gatsis, J.G.

    1992-12-01

    The objective of this research was to investigate the fundamental reaction pathways in coal petroleum residuum coprocessing. Once the reaction pathways are defined, further efforts can be directed at improving those aspects of the chemistry of coprocessing that are responsible for the desired results such as high oil yields, low dihydrogen consumption, and mild reaction conditions. We decided to carry out this investigation by looking at four basic aspects of coprocessing: (1) the effect of fossil fuel materials on promoting reactions essential to coprocessing such as hydrogen atom transfer, carbon-carbon bond scission, and hydrodemethylation; (2) the effect of varied mild conditions on the coprocessing reactions; (3) determination of dihydrogen uptake and utilization under severe conditions as a function of the coal or petroleum residuum employed; and (4) the effect of varied dihydrogen pressure, temperature, and residence time on the uptake and utilization of dihydrogen and on the distribution of the coprocessed products. Accomplishments are described.

  8. Electrophilic addition and cyclization reactions of allenes.

    PubMed

    Ma, Shengming

    2009-10-20

    Modern organic synthesis depends on the development of highly selective methods for the efficient construction of potentially useful target molecules. A primary goal in our laboratory is the discovery of new reactions that convert readily available starting materials to complex products with complete control of regio- and stereoselectivity. Allenes are one underused moiety in organic synthesis, because these groups are often thought to be highly reactive. However, many compounds containing the allene group, including natural products and pharmaceuticals, are fairly stable. The chemistry of allenes has been shown to have significant potential in organic synthesis. Electrophilic additions to allenes have often been considered to be synthetically less attractive due to the lack of efficient control of the regio- and stereoselectivity. However, this Account describes electrophilic reactions of allenes with defined regio- and stereoselectivity developed in our laboratory. Many substituted allenes are readily available from propargylic alcohols. Our work has involved an exploration of the reactions of these allenes with many different electrophiles: the E- or Z-halo- or seleno-hydroxylations of allenyl sulfoxides, sulfones, phosphine oxides, carboxylates, sulfides or selenides, butenolides, and arenes, and the halo- or selenolactonization reactions of allenoic acids and allenoates. These reactions have produced a host of new compounds such as stereodefined allylic alcohols, ethers, amides, thiiranes, and lactones. In all these reactions, water acts as a reactant and plays an important role in determining the reaction pathway and the stereoselectivity. The differing electronic properties of the two C=C bonds in these allenes determine the regioselectivity of these reactions. Through mechanistic studies of chirality transfer, isolation and reactivity of cyclic intermediates, (18)O-labeling, and substituent effects, we discovered that the E-stereoselectivity of some

  9. Multicomponent reactions of phosphines, enynedioates and benzylidene malononitriles generated highly substituted cyclopentenes through an unexpected phosphine α-addition-δ-evolvement of an anion pathway.

    PubMed

    Chuang, Shih-Ching; Sung, Shih-Ping; Deng, Jie-Cheng; Chiou, Mong-Feng; Hsu, Day-Shin

    2016-02-21

    Multicomponent reactions of phosphines, enynedioates and benzylidene malononitriles provide highly substituted syn-selective cyclopentenes appending the phosphorus ylide moiety in good yield with a diastereoselectivity of up to 100% through resonance-derived 1,5-dipolar species as the key intermediates, via the nucleophilic α(δ')-attack of phosphines toward enynedioates followed by addition to benzylidene malononitriles and 5-exo-dig cyclization. Through computational analyses, the overall reactions for the formation of syn- and anti-diastereomers are both exothermic with 65.6 and 66.3 kcal mol(-1) at the B3LYP-D3/6-31G(d) level of theory and were found to be kinetically controlled, which favours the formation of syn-diastereomers.

  10. Multistage reaction pathways in detonating high explosives

    SciTech Connect

    Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya

    2014-11-17

    Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N{sub 2} and H{sub 2}O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N{sub 2} and H{sub 2}O productions.

  11. Investigation of the O+allyl addition/elimination reaction pathways from the OCH{sub 2}CHCH{sub 2} radical intermediate

    SciTech Connect

    FitzPatrick, Benjamin L.; Lau, K.-C.; Butler, Laurie J.; Lee, S.-H.; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH{sub 2}CHCH{sub 2}, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH{sub 2}CHCH{sub 2} radicals; these undergo a facile ring opening to the OCH{sub 2}CHCH{sub 2} radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH{sub 2}CHCH{sub 2} radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C{sub 3}H{sub 4}O (acrolein)+H, C{sub 2}H{sub 4}+HCO (formyl radical), and H{sub 2}CO (formaldehyde)+C{sub 2}H{sub 3}. A small signal from C{sub 2}H{sub 2}O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C{sub 2}H{sub 5}+CO, does not contribute significantly to the product branching. The higher internal energy onset of the

  12. Roaming dynamics in radical addition-elimination reactions.

    PubMed

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

    2014-06-06

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

  13. Asthma and anaphylactoid reactions to food additives.

    PubMed Central

    Tarlo, S. M.; Sussman, G. L.

    1993-01-01

    Presumed allergic reactions to hidden food additives are both controversial and important. Clinical manifestations include asthma, urticaria, angioedema, and anaphylactic-anaphylactoid events. Most adverse reactions are caused by just a few additives, such as sulfites and monosodium glutamate. Diagnosis is suspected from the history and confirmed by specific challenge. The treatment is specific avoidance. PMID:8499792

  14. Radical addition-initiated domino reactions of conjugated oxime ethers.

    PubMed

    Ueda, Masafumi

    2014-01-01

    The application of conjugated oxime ethers to the synthesis of complex chemical scaffolds using domino radical reactions has been described in detail. The triethylborane-mediated hydroxysulfenylation reaction allows for the regioselective construction of a carbon-sulfur bond and a carbon-oxygen bond in a single operation for the formation of β-hydroxy sulfides. This reaction proceeds via a radical pathway involving regioselective thiyl addition and the subsequent trapping of the resulting α-imino radical with O₂, where the imino group enhances the stability of the intermediate radical. Hydroxyalkylation reactions that occur via a carbon radical addition reaction followed by the hydroxylation of the resulting N-borylenamine with O₂ have also been developed. We investigated sequential radical addition aldol-type reactions in detail to explore the novel domino reactions that occur via the generation of N-borylenamine. The radical reaction of a conjugated oxime ether with triethylborane in the presence of an aldehyde affords γ-butyrolactone via sequential processes including ethyl radical addition, the generation of N-borylenamine, an aldol-type reaction with an aldehyde, and a lactonization reaction. A novel domino reaction has also been developed involving the [3,3]-sigmatropic rearrangement of N-boryl-N-phenoxyenamine. The triethylborane-mediated domino reactions of O-phenyl-conjugated oxime ethers afforded the corresponding benzofuro[2,3-b]pyrrol-2-ones via a radical addition/[3,3]-sigmatropic rearrangement/cyclization/lactamization cascade.

  15. Divergent pathways in the reaction of Fischer carbenes and palladium.

    PubMed

    López-Alberca, María P; Mancheño, María J; Fernandez, Israel; Gómez-Gallego, Mar; Sierra, Miguel A; Torres, Rosario

    2007-04-26

    [reaction: see text] The Pd-catalyzed reaction of beta-arylaminochromium(0) carbene complexes produces by transmetalation the first isolated and X-ray structurally characterized bis-Pd(II) carbene complex, as well as other alternative reaction pathways, such as the oxidative addition-transmetalation sequence, not seen before in this chemistry.

  16. Allergic and immunologic reactions to food additives.

    PubMed

    Gultekin, Fatih; Doguc, Duygu Kumbul

    2013-08-01

    For centuries, food additives have been used for flavouring, colouring and extension of the useful shelf life of food, as well as the promotion of food safety. During the last 20 years, the studies implicating the additives contained in foods and medicine as a causative factor of allergic reactions have been proliferated considerably. In this review, we aimed to overview all of the food additives which were approved to consume in EU and find out how common and serious allergic reactions come into existence following the consuming of food additives.

  17. Exploring Transition Metal Catalyzed Reactions via AB Initio Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2011-06-01

    The study and prediction of chemical reactivity is one of the most influential contributions of quantum chemistry. A central concept in the theoretical treatment of chemical reactions is the reaction pathway, which can be quite difficult to integrate accurately and efficiently. This talk will outline our developments in the integration of these pathways on ab initio potential energy surfaces. We will also describe results from recent studies on the kinetics of transition metal catalyzed reactions, including the importance of vibrational coupling to the reaction coordinate and the role of this coupling in catalytic rate enhancement.

  18. Conjugate addition-enantioselective protonation reactions.

    PubMed

    Phelan, James P; Ellman, Jonathan A

    2016-01-01

    The addition of nucleophiles to electron-deficient alkenes represents one of the more general and commonly used strategies for the convergent assembly of more complex structures from simple precursors. In this review the addition of diverse protic and organometallic nucleophiles to electron-deficient alkenes followed by enantioselective protonation is summarized. Reactions are first categorized by the type of electron-deficient alkene and then are further classified according to whether catalysis is achieved with chiral Lewis acids, organocatalysts, or transition metals.

  19. Adverse reactions to the sulphite additives

    PubMed Central

    Misso, Neil LA

    2012-01-01

    Sulphites are widely used as preservative and antioxidant additives in the food and pharmaceutical industries. Exposure to sulphites has been reported to induce a range of adverse clinical effects in sensitive individuals, ranging from dermatitis, urticaria, flushing, hypotension, abdominal pain and diarrhoea to life-threatening anaphylactic and asthmatic reactions. Exposure to the sulphites arises mainly from the consumption of foods and drinks that contain these additives; however exposure may also occur through the use of pharmaceutical products, as well as in occupational settings. Most studies report a prevalence of sulphite sensitivity of 3 to 10% among asthmatic subjects who ingest these additives. However, the severity of these reactions varies, and steroid-dependent asthmatics, those with marked airway hyperresponsiveness, and children with chronic asthma, appear to be at greater risk. Although a number of potential mechanisms have been proposed, the precise mechanisms underlying sulphite sensitivity remain unclear. PMID:24834193

  20. Conjugate addition-enantioselective protonation reactions.

    PubMed

    Phelan, James P; Ellman, Jonathan A

    2016-01-01

    The addition of nucleophiles to electron-deficient alkenes represents one of the more general and commonly used strategies for the convergent assembly of more complex structures from simple precursors. In this review the addition of diverse protic and organometallic nucleophiles to electron-deficient alkenes followed by enantioselective protonation is summarized. Reactions are first categorized by the type of electron-deficient alkene and then are further classified according to whether catalysis is achieved with chiral Lewis acids, organocatalysts, or transition metals. PMID:27559372

  1. Serpentinization reaction pathways: implications for modeling approach

    SciTech Connect

    Janecky, D.R.

    1986-01-01

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

  2. Unraveling reaction pathways and specifying reaction kinetics for complex systems.

    PubMed

    Vinu, R; Broadbelt, Linda J

    2012-01-01

    Many natural and industrial processes involve a complex set of competing reactions that include several different species. Detailed kinetic modeling of such systems can shed light on the important pathways involved in various transformations and therefore can be used to optimize the process conditions for the desired product composition and properties. This review focuses on elucidating the various components involved in modeling the kinetics of pyrolysis and oxidation of polymers. The elementary free radical steps that constitute the chain reaction mechanism of gas-phase/nonpolar liquid-phase processes are outlined. Specification of the rate coefficients of the various reaction families, which is central to the theme of kinetics, is described. Construction of the reaction network on the basis of the types of end groups and reactive moieties in a polymer chain is discussed. Modeling frameworks based on the method of moments and kinetic Monte Carlo are evaluated using illustrations. Finally, the prospects and challenges in modeling biomass conversion are addressed.

  3. Minimum Energy Pathways for Chemical Reactions

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  4. A chain reaction approach to modelling gene pathways

    PubMed Central

    Cheng, Gary C.; Chen, Dung-Tsa; Chen, James J.; Soong, Seng-jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-01-01

    the nutrient-containing diets regulate gene expression in the estrogen synthesis pathway during puberty; (II) global tests to assess an overall association of this particular pathway with time factor by utilizing generalized linear models to analyze microarray data; and (III) a chain reaction model to simulate the pathway. This is a novel application because we are able to translate the gene pathway into the chemical reactions in which each reaction channel describes gene-gene relationship in the pathway. In the chain reaction model, the implicit scheme is employed to efficiently solve the differential equations. Data analysis results show the proposed model is capable of predicting gene expression changes and demonstrating the effect of nutrient-containing diets on gene expression changes in the pathway. One of the objectives of this study is to explore and develop a numerical approach for simulating the gene expression change so that it can be applied and calibrated when the data of more time slices are available, and thus can be used to interpolate the expression change at a desired time point without conducting expensive experiments for a large amount of time points. Hence, we are not claiming this is either essential or the most efficient way for simulating this problem, rather a mathematical/numerical approach that can model the expression change of a large set of genes of a complex pathway. In addition, we understand the limitation of this experiment and realize that it is still far from being a complete model of predicting nutrient-gene interactions. The reason is that in the present model, the reaction rates were estimated based on available data at two time points; hence, the gene expression change is dependent upon the reaction rates and a linear function of the gene expressions. More data sets containing gene expression at various time slices are needed in order to improve the present model so that a non-linear variation of gene expression changes at

  5. Unraveling reaction pathways and specifying reaction kinetics for complex systems.

    PubMed

    Vinu, R; Broadbelt, Linda J

    2012-01-01

    Many natural and industrial processes involve a complex set of competing reactions that include several different species. Detailed kinetic modeling of such systems can shed light on the important pathways involved in various transformations and therefore can be used to optimize the process conditions for the desired product composition and properties. This review focuses on elucidating the various components involved in modeling the kinetics of pyrolysis and oxidation of polymers. The elementary free radical steps that constitute the chain reaction mechanism of gas-phase/nonpolar liquid-phase processes are outlined. Specification of the rate coefficients of the various reaction families, which is central to the theme of kinetics, is described. Construction of the reaction network on the basis of the types of end groups and reactive moieties in a polymer chain is discussed. Modeling frameworks based on the method of moments and kinetic Monte Carlo are evaluated using illustrations. Finally, the prospects and challenges in modeling biomass conversion are addressed. PMID:22468596

  6. Method for promoting Michael addition reactions

    DOEpatents

    Shah, Pankaj V.; Vietti, David E.; Whitman, David William

    2010-09-21

    Homogeneously dispersed solid reaction promoters having an average particle size from 0.01 .mu.m to 500 .mu.m are disclosed for preparing curable mixtures of at least one Michael donor and at least one Michael acceptor. The resulting curable mixtures are useful as coatings, adhesives, sealants and elastomers.

  7. Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes generated furans appending reactive phosphorus ylides through cumulated trienoates as key intermediates: a phosphine α-addition-δ-evolvement of an anion pathway.

    PubMed

    Deng, Jie-Cheng; Chuang, Shih-Ching

    2014-11-01

    Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes have been demonstrated, providing trisubstituted furans appending reactive phosphorus ylides, through cumulated trienoates as key intermediates. The proposed trienoate intermediates, 1,5-dipolar species formed via nucleophilic α-attack of phosphines toward diynedioates (α-addition-δ-evolvement of an anion, abbreviated αAδE), undergo addition to aryl aldehydes followed by 5-endo-dig cyclization, proton transfer, and resonance to give trisubstituted furans. Furthermore, the phosphorus ylides are oxidized to α-keto ester furans and utilized as Wittig reagents.

  8. Classification of the Electrophilic Addition Reactions of Olefins and Acetylenes

    ERIC Educational Resources Information Center

    Wilson, Michael A.

    1975-01-01

    Divides addition reactions into molecular, stepwise, or termolecular, depending on whether the reaction is synchronous or multistep; and further into nucleophilic, electrophilic, or concerted, depending on how the electrons are transferred in the initiation step. (MLH)

  9. Techniques used to study the DNA polymerase reaction pathway

    PubMed Central

    Joyce, Catherine M.

    2009-01-01

    Summary A minimal reaction pathway for DNA polymerases was established over 20 years ago using chemical quench methods. Since that time there has been considerable interest in noncovalent steps in the reaction pathway, conformational changes involving the polymerase or its DNA substrate that may play a role in substrate specificity. Fluorescence-based assays have been devised in order to study these conformational transitions and the results obtained have added new detail to the reaction pathway. PMID:19665596

  10. Thiol-addition reactions and their applications in thiol recognition.

    PubMed

    Yin, Caixia; Huo, Fangjun; Zhang, Jingjing; Martínez-Máñez, Ramón; Yang, Yutao; Lv, Haigang; Li, Sidian

    2013-07-21

    Because of the biological importance of thiols, the development of probes for thiols has been an active research area in recent years. In this review, we summarize the results of recent exciting reports regarding thiol-addition reactions and their applications in thiol recognition. The examples reported can be classified into four reaction types including 1,1, 1,2, 1,3, 1,4 addition reactions, according to their addition mechanisms, based on different Michael acceptors. In all cases, the reactions are coupled to color and/or emission changes, although some examples dealing with electrochemical recognition have also been included. The use of thiol-addition reactions is a very simple and straightforward procedure for the preparation of thiol-sensing probes.

  11. Chromium-Catalyzed Asymmetric Dearomatization Addition Reactions of Halomethyl Heteroarenes.

    PubMed

    Tian, Qingshan; Bai, Jing; Chen, Bin; Zhang, Guozhu

    2016-04-15

    The first asymmetric dearomatization addition reaction of halomethyl arenes including benzofuran and benzothiophene was enabled by chromium catalysis. A variety of aldehydes served as suitable electrophiles under mild reaction conditions. Molecular complexities are quickly increased in a highly diastereo- and enantioselective manner.

  12. Deuterium separation by infrared-induced addition reaction

    DOEpatents

    Marling, John B.

    1977-01-01

    A method for deuterium enrichment by the infrared-induced addition reaction of a deuterium halide with an unsaturated aliphatic compound. A gaseous mixture of a hydrogen halide feedstock and an unsaturated aliphatic compound, particularly an olefin, is irradiated to selectively vibrationally excite the deuterium halide contained therein. The excited deuterium halide preferentially reacts with the unsaturated aliphatic compound to produce a deuterated addition product which is removed from the reaction mixture.

  13. Copper-Catalyzed Divergent Addition Reactions of Enoldiazoacetamides with Nitrones.

    PubMed

    Cheng, Qing-Qing; Yedoyan, Julietta; Arman, Hadi; Doyle, Michael P

    2016-01-13

    Catalyst-controlled divergent addition reactions of enoldiazoacetamides with nitrones have been developed. By using copper(I) tetrafluoroborate/bisoxazoline complex as the catalyst, a [3+3]-cycloaddition reaction was achieved with excellent yield and enantioselectivity under exceptionally mild conditions, which represents the first highly enantioselective base-metal-catalyzed vinylcarbene transformation. When the catalyst was changed to copper(I) triflate, Mannich addition products were formed in high yields with near exclusivity under otherwise identical conditions.

  14. Copper-Catalyzed Divergent Addition Reactions of Enoldiazoacetamides with Nitrones.

    PubMed

    Cheng, Qing-Qing; Yedoyan, Julietta; Arman, Hadi; Doyle, Michael P

    2016-01-13

    Catalyst-controlled divergent addition reactions of enoldiazoacetamides with nitrones have been developed. By using copper(I) tetrafluoroborate/bisoxazoline complex as the catalyst, a [3+3]-cycloaddition reaction was achieved with excellent yield and enantioselectivity under exceptionally mild conditions, which represents the first highly enantioselective base-metal-catalyzed vinylcarbene transformation. When the catalyst was changed to copper(I) triflate, Mannich addition products were formed in high yields with near exclusivity under otherwise identical conditions. PMID:26699516

  15. Continuous In Vitro Evolution of a Ribozyme that Catalyzes Three Successive Nucleotidyl Addition Reactions

    NASA Technical Reports Server (NTRS)

    McGinness, Kathleen E.; Wright, Martin C.; Joyce, Gerald F.

    2002-01-01

    Variants of the class I ligase ribozyme, which catalyzes joining of the 3' end of a template bound oligonucleotide to its own 5' end, have been made to evolve in a continuous manner by a simple serial transfer procedure that can be carried out indefinitely. This process was expanded to allow the evolution of ribozymes that catalyze three successive nucleotidyl addition reactions, two template-directed mononucleotide additions followed by RNA ligation. During the development of this behavior, a population of ribozymes was maintained against an overall dilution of more than 10(exp 406). The resulting ribozymes were capable of catalyzing the three-step reaction pathway, with nucleotide addition occurring in either a 5' yieldig 3' or a 3' yielding 5' direction. This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution.

  16. Stereoselective synthesis of indolines via organocatalytic thioester enolate addition reactions.

    PubMed

    Kolarovic, Andrej; Käslin, Alexander; Wennemers, Helma

    2014-08-15

    A straightforward stereoselective synthesis route to indolin-3-yl acetates has been developed using organocatalytic addition reactions of monothiomalonates to ortho-bromo nitrostyrenes as the key step. The addition products of this highly stereoselective one-pot addition-deprotection-decarboxylation sequence were easily further converted to the target indolin-3-yl acetates, via an intramolecular Buchwald-Hartwig coupling reaction. The route provided indolin-3-yl acetates bearing tertiary and exocyclic quarternary stereogenic centers in excellent stereoselectivities and overall yields of 34-83%.

  17. Catalytic Asymmetric 1,4-Addition Reactions of Simple Alkylnitriles.

    PubMed

    Yamashita, Yasuhiro; Sato, Io; Suzuki, Hirotsugu; Kobayashi, Shū

    2015-10-01

    The development of catalytic asymmetric carbon-carbon bond-forming reactions of alkylnitriles that do not have an activating group at the α-position, under proton-transfer conditions, is a challenging research topic. Here, we report catalytic asymmetric direct-type 1,4-addition reactions of alkylnitriles with α,β-unsaturated amides by using a catalytic amount of potassium hexamethyldisilazide (KHMDS) with a chiral macro crown ether. The desired reactions proceeded in high yields with good diastereo- and enantioselectivities. To our knowledge, this is the first example of catalytic asymmetric direct-type 1,4-addition reaction of alkylnitriles without any activating group at the α-position.

  18. Hydrogen addition reactions of aliphatic hydrocarbons in comets

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hitomi; Watanabe, N.; Watanabe, Y.; Fukushima, T.; Kawakita, H.

    2013-10-01

    Comets are thought as remnants of early solar nebula. Their chemical compositions are precious clue to chemical and physical evolution of the proto-planetary disk. Some hydrocarbons such as C2H6, C2H2 and CH4 in comets have been observed by using near-infrared spectroscopy. Although the compositions of C2H6 were about 1% relative to the water in normal comets, there are few reports on the detection of C2H6 in ISM. Some formation mechanisms of C2H6 in ISM have been proposed, and there are two leading hypotheses; one is the dimerizations of CH3 and another is the hydrogen addition reactions of C2H2 on cold icy grains. To evaluate these formation mechanisms for cometary C2H6 quantitatively, it is important to search the C2H4 in comets, which is the intermediate product of the hydrogen addition reactions toward C2H6. However, it is very difficult to detect the C2H4 in comets in NIR (3 microns) regions because of observing circumstances. The hydrogen addition reactions of C2H2 at low temperature conditions are not well characterized both theoretically and experimentally. For example, there are no reports on the reaction rate coefficients of those reaction system. To determine the production rates of those hydrogen addition reactions, we performed the laboratory experiments of the hydrogenation of C2H2 and C2H4. We used four types of the initial composition of the ices: pure C2H4, pure C2H2, C2H2 on amorphous solid water (ASW) and C2H4 on ASW at three different temperatures of 10, 20, and 30K. We found 1) reactions are more efficient when there are ASW in the initial compositions of the ice; 2) hydrogenation of C2H4 occur more rapid than that of C2H2.

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

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

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

  20. Mineral catalyzed hydrothermal reactions as precursors to extant anabolic pathways

    NASA Astrophysics Data System (ADS)

    Cody, G. D.

    Investigations into hydrothermal reactions under conditions of moderate hydrostatic pressure and in the presence of transition metal sulfides reveal reaction pathways the bear remarkable similarity with extant anabolic reactions. First, it is seen that most common transition metal sulfides are capable of promoting all of the key reactions at the core of Acetyl Co-A synthesis. These include CO reduction to methyl groups and carbonyl insertion to form transferable acetyl groups. The synthesis of alpha-keto acids are also promoted, presumably by double carbonylation. A pathway starting with CO2 and H2 has been identified leading to the synthesis of citric acid. Citric acid provides a crucial abiotic, anabolic, branch point to the prebiotic synthesis of various amino acids, as well. As the pyrimidines, orotic acid and uracil. In many cases the abiotic reaction pathways differ slightly from extant anabolic pathways by shunting past particularly reactive intermediates, e.g. oxaloacetic acid. These reactions have the capacity to provide the prebiotic world with many, but not all, of the molecular constituents to aid the emergence of an RNA world.

  1. Evaluation of reactions to food additives: the aspartame experience.

    PubMed

    Bradstock, M K; Serdula, M K; Marks, J S; Barnard, R J; Crane, N T; Remington, P L; Trowbridge, F L

    1986-03-01

    Despite the widespread use of chemical food additives, few criteria exist to evaluate consumer reports of adverse reactions. We analyzed 231 consumer complaints associated with the food additive aspartame. We developed a methodologic approach to evaluate all complaints by adapting general criteria used to investigate adverse reactions to medications. Complaints were ranked according to the effects of cessation and rechallenge. Using this method, we found no clear symptom complex that suggests a widespread public health hazard associated with aspartame use; however, we identified some case reports in which the symptoms may be attributable to aspartame in commonly-consumed amounts. The systematic application of pre-defined review criteria, such as those described here, to monitor consumer complaints related to food additives will help identify products that warrant more focused clinical studies.

  2. Thermochemical Kinetics for Multireference Systems: Addition Reactions of Ozone

    SciTech Connect

    Zhao, Yan; Tishchenko, Oksana; Gour, Jeffrey R.; Li, Wei; Lutz, Jesse; Piecuch, Piotr; Truhlar, Donald G.

    2009-05-14

    The 1,3-dipolar cycloadditions of ozone to ethyne and ethene provide extreme examples of multireference singlet-state chemistry, and they are examined here to test the applicability of several approaches to thermochemical kinetics of systems with large static correlation. Four different multireference diagnostics are applied to measure the multireference characters of the reactants, products, and transition states; all diagnostics indicate significant multireference character in the reactant portion of the potential energy surfaces. We make a more complete estimation of the effect of quadruple excitations than was previously available, and we use this with CCSDT/CBS estimation of Wheeler et al. (Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798.) to make new best estimates of the van der Waals association energy, the barrier height, and the reaction energy to form the cycloadduct for both reactions. Comparing with these best estimates, we present comprehensive mean unsigned errors for a variety of coupled cluster, multilevel, and density functional methods. Several computational aspects of multireference reactions are considered: (i) the applicability of multilevel theory, (ii) the convergence of coupled cluster theory for reaction barrier heights, (iii) the applicability of completely renormalized coupled cluster methods to multireference systems, (iv) the treatment by density functional theory, (v) the multireference perturbation theory for multireference reactions, and (vi) the relative accuracy of scaling-type multilevel methods as compared with additive ones. It is found that scaling-type multilevel methods do not perform better than the additive-type multilevel methods. Among the 48 tested density functionals, only M05 reproduces the best estimates within their uncertainty. Multireference perturbation theory based on the complete-active-space reference wave functions constructed using a small number of reaction-specific active orbitals

  3. The role of hydrogen-bonding interactions in acidic sugar reaction pathways.

    PubMed

    Qian, Xianghong; Johnson, David K; Himmel, Michael E; Nimlos, Mark R

    2010-09-01

    Previously, theoretical multiple sugar (beta-d-xylose and beta-d-glucose) reaction pathways were discovered that depended on the initial protonation site on the sugar molecules using Car-Parrinello-based molecular dynamics (CPMD) simulations [Qian, X. H.; Nimlos, M. R.; Davis, M.; Johnson, D. K.; Himmel, M. E. Carbohydr. Res.2005, 340, 2319-2327]. In addition, simulation results showed that water molecules could participate in the sugar reactions, thus altering the reaction pathways. In the present study, the temperature and water density effects on the sugar degradation pathways were investigated with CPMD. We found that changes in both temperature and water density could profoundly affect the mechanisms and pathways. We attributed these effects to both the strength of hydrogen bonding and proton affinity of water. PMID:20667524

  4. Efficient transition path sampling for systems with multiple reaction pathways

    NASA Astrophysics Data System (ADS)

    Chen, L. Y.; Nash, P. L.; Horing, N. J. M.

    2005-09-01

    A new algorithm is developed for sampling transition paths and computing reaction rates. To illustrate the use of this method, we study a two-dimensional system that has two reaction pathways: one pathway is straight with a relatively high barrier and the other is roundabout with a lower barrier. The transition rate and the ratio between the numbers of the straight and roundabout transition paths are computed for a wide range of temperatures. Our study shows that the harmonic approximation for fluctuations about the steepest-descent paths is not valid even at relatively low temperatures and, furthermore, that factors related to entropy have to be determined by the global geometry of the potential-energy surface (rather than just the local curvatures alone) for complex reaction systems. It is reasonable to expect that this algorithm is also applicable to higher dimensional systems.

  5. A chain reaction approach to modelling gene pathways.

    PubMed

    Cheng, Gary C; Chen, Dung-Tsa; Chen, James J; Soong, Seng-Jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-08-01

    BACKGROUND: Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. RESULTS: In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By

  6. Branching ratios between the abstraction and addition channels in the reactions of OH radicals with monoterpenes

    NASA Astrophysics Data System (ADS)

    Rio, C.; Loison, J. C.; Caralp, F.; Flaud, P. M.; Villenave, E.

    2009-04-01

    Secondary Organic Aerosol (SOA) formation in the atmosphere is described as a mass transfer of volatile organic compound oxidation products with low vapour pressures in particular phases. Among the different aerosol components, the SOA represent an important fraction, but, the fundamental processes governing their physics and chemistry in the atmosphere are poorly understood. So it is important to characterize and understand the mechanisms of their formation. It is well-known that atmospheric oxidation of monoterpenes is an important process in tropospheric SOA formation. Consequently, the identification and quantification of reaction products from the oxidation of monoterpenes in the gas phase have been receiving great attention over the past years. However, the atmospheric degradation leads to the formation of a plethora of reaction products and proceeds through a very complex mechanism that is still not fully characterised. In our study, we have focused on SOA formation from OH + monoterpene reactions and more precisely on the primary oxidation steps of γ-terpinene and d-limonene by OH radicals. Indeed, the primary reaction of monoterpenes with hydroxyl radicals can in principle occur by two reaction pathways: OH-addition and H-abstraction. In this work, we have determined branching ratios of these reactions. Although there seems to be a consensus in the literature that OH-monoterpene reactions proceed almost exclusively by addition, several measurements have shown that in some case H-abstraction can represent up to 30% of the total reaction rate constant. Therefore it is necessary to determine this branching ratio in order to know, in particular, the main peroxy radicals formed and propose a mechanism for the gas phase oxidation of terpene by hydroxyl radicals. (γ-terpinene + OH) and (d-limonene + OH) reactions have been studied i) at atmospheric pressure, using laser photolysis coupled with UV absorption radical detection, and ii) at low pressure, using

  7. Photocatalytic activation of pyridine for addition reactions: an unconventional reaction feature between a photo-induced hole and electron on TiO2.

    PubMed

    Ma, Dongge; Yan, Yan; Ji, Hongwei; Chen, Chuncheng; Zhao, Jincai

    2015-12-21

    TiO2 photocatalysis can be performed for the addition of pyridines to vinylarenes in an anti-Markovnikov manner. Seven examples with considerable yields (56-91%) and selectivity were demonstrated. A comparative survey of the involved process through ESR revealed a novel concerted two electron transfer pathway for these photocatalytic bimolecular addition reactions.

  8. A multi-pathway model for photosynthetic reaction center.

    PubMed

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

    2016-03-28

    Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments. PMID:27036480

  9. A multi-pathway model for photosynthetic reaction center

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  10. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    DOE PAGES

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; et al

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS).more » Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have implications on atmospheric gas-phase chemistry and the oxidative stability of organic substances.« less

  11. Polynuclear aromatic hydrocarbons hydrogenation. 1: Experimental reaction pathways and kinetics

    SciTech Connect

    Korre, S.C.; Klein, M.T. . Dept. of Chemical Engineering); Quann, R.J. . Paulsboro Research Lab.)

    1995-01-01

    The relationship between molecular structure and hydrogenation reactivity in heavy oil hydroprocessing was sought via the elucidation of the controlling reaction pathways and kinetics of one-, two-, three-, and four-fused ring compounds. Hydrogenation reactions of o-xylene, tetralin, naphthalene, phenanthrene, anthracene, pyrene, and chrysene and their multicomponent mixtures were studied in cyclohexane solvent using a presulfided CoMo/Al[sub 2]O[sub 3] catalyst in a 1-liter batch autoclave at P[sub H[sub 2

  12. Reaction pathways for the deoxygenation of vegetable oils and related model compounds.

    PubMed

    Gosselink, Robert W; Hollak, Stefan A W; Chang, Shu-Wei; van Haveren, Jacco; de Jong, Krijn P; Bitter, Johannes H; van Es, Daan S

    2013-09-01

    Vegetable oil-based feeds are regarded as an alternative source for the production of fuels and chemicals. Paraffins and olefins can be produced from these feeds through catalytic deoxygenation. The fundamentals of this process are mostly studied by using model compounds such as fatty acids, fatty acid esters, and specific triglycerides because of their structural similarity to vegetable oils. In this Review we discuss the impact of feedstock, reaction conditions, and nature of the catalyst on the reaction pathways of the deoxygenation of vegetable oils and its derivatives. As such, we conclude on the suitability of model compounds for this reaction. It is shown that the type of catalyst has a significant effect on the deoxygenation pathway, that is, group 10 metal catalysts are active in decarbonylation/decarboxylation whereas metal sulfide catalysts are more selective to hydrodeoxygenation. Deoxygenation studies performed under H2 showed similar pathways for fatty acids, fatty acid esters, triglycerides, and vegetable oils, as mostly deoxygenation occurs indirectly via the formation of fatty acids. Deoxygenation in the absence of H2 results in significant differences in reaction pathways and selectivities depending on the feedstock. Additionally, using unsaturated feedstocks under inert gas results in a high selectivity to undesired reactions such as cracking and the formation of heavies. Therefore, addition of H2 is proposed to be essential for the catalytic deoxygenation of vegetable oil feeds.

  13. Biothiol Xenon MRI Sensor Based on Thiol-Addition Reaction.

    PubMed

    Yang, Shengjun; Jiang, Weiping; Ren, Lili; Yuan, Yaping; Zhang, Bin; Luo, Qing; Guo, Qianni; Bouchard, Louis-S; Liu, Maili; Zhou, Xin

    2016-06-01

    Biothiols such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH) play an important role in regulating the vital functions of living organisms. Knowledge of their biodistribution in real-time could help diagnose a variety of conditions. However, existing methods of biothiol detection are invasive and require assays. Herein we report a molecular biosensor for biothiol detection using the nuclear spin resonance of (129)Xe. The (129)Xe biosensor consists of a cryptophane cage encapsulating a xenon atom and an acrylate group. The latter serves as a reactive site to covalently bond biothiols through a thiol-addition reaction. The biosensor enables discrimination of Cys from Hcy and GSH through the chemical shift and average reaction rate. This biosensor can be detected at a concentration of 10 μM in a single scan and it has been applied to detect biothiols in bovine serum solution. Our results indicate that this biosensor is a promising tool for the real-time imaging of biothiol distributions. PMID:27128102

  14. Oxygen switch in visible-light photoredox catalysis: radical additions and cyclizations and unexpected C-C-bond cleavage reactions.

    PubMed

    Zhu, Shaoqun; Das, Arindam; Bui, Lan; Zhou, Hanjun; Curran, Dennis P; Rueping, Magnus

    2013-02-01

    Visible light photoredox catalyzed inter- and intramolecular C-H functionalization reactions of tertiary amines have been developed. Oxygen was found to act as chemical switch to trigger two different reaction pathways and to obtain two different types of products from the same starting material. In the absence of oxygen, the intermolecular addition of N,N-dimethyl-anilines to electron-deficient alkenes provided γ-amino nitriles in good to high yields. In the presence of oxygen, a radical addition/cyclization reaction occurred which resulted in the formation of tetrahydroquinoline derivatives in good yields under mild reaction conditions. The intramolecular version of the radical addition led to the unexpected formation of indole-3-carboxaldehyde derivatives. Mechanistic investigations of this reaction cascade uncovered a new photoredox catalyzed C-C bond cleavage reaction.

  15. Diels-Alder reactions: The effects of catalyst on the addition reaction

    NASA Astrophysics Data System (ADS)

    Yilmaz, Özgür; Kus, Nermin Simsek; Tunç, Tuncay; Sahin, Ertan

    2015-10-01

    The reaction between 2,3-dimethyl-1,3-butadiene and dimethyl 7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate is efficiently achieved with small amounts of catalyst, i.e. phenol, AcOH, nafion, and β-cyclodextrin. Exo-diastereoselective cycloaddition reactions were observed both without catalyst and different catalysts for 48 days. As a result, different products (tricyclicmolecule 5, retro-Diels-Alder product 6, and oxidation product 7) were obtained with different catalysts. In addition, we synthesized Diels-Alders product 8 and tricyclocyclitol 10 via Diels-Alder reaction. The structures of these products were characterized by 1H NMR, 13C NMR, MS and IR spectroscopy.

  16. Membrane Fission Reactions of the Mammalian ESCRT Pathway

    PubMed Central

    McCullough, John; Colf, Leremy A.; Sundquist, Wesley I.

    2014-01-01

    The endosomal sorting complexes required for transport (ESCRT) pathway was initially defined in yeast genetic screens that identified the factors necessary to sort membrane proteins into intraluminal endosomal vesicles. Subsequent studies have revealed that the mammalian ESCRT pathway also functions in a series of other key cellular processes, including formation of extracellular microvesicles, enveloped virus budding, and the abscission stage of cytokinesis. The core ESCRT machinery comprises Bro1 family proteins and ESCRT-I, ESCRT-II, ESCRT-III, and VPS4. Site-specific adaptors recruit these soluble factors to assemble on different cellular membranes, where they carry out membrane fission reactions. ESCRT-III proteins form filaments that draw membranes together from the cytoplasmic face, and mechanistic models have been advanced to explain how ESCRT-III filaments and the VPS4 ATPase can work together to catalyze membrane fission. PMID:23527693

  17. Theoretical Studies on the Reaction Pathways of Electronically Excited Daaf

    NASA Astrophysics Data System (ADS)

    Quenneville, J.; Moore, D. S.

    2009-12-01

    The use of temporally and spectrally shaped ultrafast laser pulses to initiate, as well as detect, high explosives is being explored at Los Alamos. High level ab initio calculations, presented here, are employed to help guide and interpret the experiments. The ground and first excited electronic states of 3, 3'-diamino-4, 4'-azoxyfurazan (DAAF) are investigated using complete active space self-consistent field (CASSCF) and time-dependent density functional theory (TD-DFT). The geometrical and energetic character of the excited state minima, conical intersections and reaction pathways of DAAF are described. Two radiative and two non-radiative excited state population quenching mechanisms are outlined, and possible pathways for photochemical and spectroscopic control are discussed.

  18. Theoretical investigation of the methane cracking reaction pathways on Ni (1 1 1) surface

    NASA Astrophysics Data System (ADS)

    Li, Jingde; Croiset, Eric; Ricardez-Sandoval, Luis

    2015-10-01

    A comprehensive methane cracking reaction pathway was investigated by performing density functional theory (DFT) calculations. In addition to the sequential dissociation reaction, i.e. CH4 → CHx + (4 - x)H → C + 2H2, a more sophisticated surface reaction network was studied, i.e. CHx + C → CHx - 1 + CH. The results show that CHx dehydrogenation is promoted with a low energy barrier through bimolecular reaction and provide an alternative kinetic favorable route for methane cracking. This study also demonstrates that the production of gas phase C2 hydrocarbon species, e.g. C2H2 and C2H4, in methane cracking reaction is unlikely due to the high barrier energy of C2H3 formation and their strong adsorption energy on Ni (1 1 1).

  19. Theoretical study of the oxidation mechanisms of naphthalene initiated by hydroxyl radicals: the OH-addition pathway.

    PubMed

    Shiroudi, Abolfazl; Deleuze, Michael S; Canneaux, Sébastien

    2014-07-01

    The oxidation mechanisms of naphthalene by OH radicals under inert (He) conditions have been studied using density functional theory along with various exchange-correlation functionals. Comparison has been made with benchmark CBS-QB3 theoretical results. Kinetic rate constants were correspondingly estimated by means of transition state theory and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Comparison with experiment confirms that, on the OH-addition reaction pathway leading to 1-naphthol, the first bimolecular reaction step has an effective negative activation energy around -1.5 kcal mol(-1), whereas this step is characterized by an activation energy around 1 kcal mol(-1) on the OH-addition reaction pathway leading to 2-naphthol. Effective rate constants have been calculated according to a steady state analysis upon a two-step model reaction mechanism. In line with experiment, the correspondingly obtained branching ratios indicate that, at temperatures lower than 410 K, the most abundant product resulting from the oxidation of naphthalene by OH radicals must be 1-naphthol. The regioselectivity of the OH(•)-addition onto naphthalene decreases with increasing temperatures and decreasing pressures. Because of slightly positive or even negative activation energies, the RRKM calculations demonstrate that the transition state approximation breaks down at ambient pressure (1 bar) for the first bimolecular reaction steps. Overwhelmingly high pressures, larger than 10(5) bar, would be required for restoring to some extent (within ∼5% accuracy) the validity of this approximation for all the reaction channels that are involved in the OH-addition pathway. Analysis of the computed structures, bond orders, and free energy profiles demonstrate that all reaction steps involved in the oxidation of naphthalene by OH radicals satisfy Leffler-Hammond's principle. Nucleus independent chemical shift indices and natural bond orbital analysis also show that the computed

  20. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    SciTech Connect

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Sarathy, S. Mani

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS). Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have

  1. Reaction rates in a theory of mechanochemical pathways.

    PubMed

    Quapp, Wolfgang; Bofill, Josep Maria

    2016-10-15

    If one applies mechanical stress to a molecule in a defined direction then one generates a new, effective potential energy surface (PES). Changes for minima and saddle points (SP) by the stress are described by Newton trajectories on the original PES (Quapp and Bofill, Theor. Chem. Acc. 2016, 135, 113). The barrier of a reaction fully breaks down for the maximal value of the norm of the gradient of the PES along a pulling Newton trajectory. This point is named barrier breakdown point (BBP). Depending on the pulling direction, different reaction pathways can be enforced. If the exit SP of the chosen pulling direction is not the lowest SP of the reactant valley, on the original PES, then the SPs must change their role anywhere: in this case the curve of the log(rate) over the pulling force of a forward reaction can show a deviation from the normal concave curvature. We discuss simple, two-dimensional examples for this model to understand more deeply the mechanochemistry of molecular systems under a mechanical stress. © 2016 Wiley Periodicals, Inc.

  2. Reaction rates in a theory of mechanochemical pathways.

    PubMed

    Quapp, Wolfgang; Bofill, Josep Maria

    2016-10-15

    If one applies mechanical stress to a molecule in a defined direction then one generates a new, effective potential energy surface (PES). Changes for minima and saddle points (SP) by the stress are described by Newton trajectories on the original PES (Quapp and Bofill, Theor. Chem. Acc. 2016, 135, 113). The barrier of a reaction fully breaks down for the maximal value of the norm of the gradient of the PES along a pulling Newton trajectory. This point is named barrier breakdown point (BBP). Depending on the pulling direction, different reaction pathways can be enforced. If the exit SP of the chosen pulling direction is not the lowest SP of the reactant valley, on the original PES, then the SPs must change their role anywhere: in this case the curve of the log(rate) over the pulling force of a forward reaction can show a deviation from the normal concave curvature. We discuss simple, two-dimensional examples for this model to understand more deeply the mechanochemistry of molecular systems under a mechanical stress. © 2016 Wiley Periodicals, Inc. PMID:27556915

  3. 78 FR 41703 - Regulation of Fuels and Fuel Additives: Additional Qualifying Renewable Fuel Pathways Under the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-11

    ... renewable fuels they produce through approved fuel pathways. See 75 FR 14670 (March 26, 2010); 75 FR 26026 (May 10, 2010); 75 FR 37733 (June 30, 2010); 75 FR 59622 (September 28, 2010); 75 FR 76790 (December 9, 2010); 75 FR 79964 (December 21, 2010); 77 FR 1320 (January 9, 2012); 77 FR 74592 (December 17,...

  4. Roaming dynamics in ion-molecule reactions: Phase space reaction pathways and geometrical interpretation

    NASA Astrophysics Data System (ADS)

    Mauguière, Frédéric A. L.; Collins, Peter; Ezra, Gregory S.; Farantos, Stavros C.; Wiggins, Stephen

    2014-04-01

    A model Hamiltonian for the reaction CH_4^+ rArr CH_3^+ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom NHIMS are unstable periodic orbits which, in conjunction with their stable and unstable manifolds, unambiguously define the (locally) non-recrossing dividing surfaces assumed in statistical theories of reaction rates. By constructing periodic orbit continuation/bifurcation diagrams for two values of the potential function parameter corresponding to late and early transition states, respectively, and using the total energy as another parameter, we dynamically assign different regions of phase space to reactants and products as well as to conventional and roaming reaction pathways. The classical dynamics of the system are investigated by uniformly sampling trajectory initial conditions on the dividing surfaces. Trajectories are classified into four different categories: direct reactive and non-reactive trajectories, which lead to the formation of molecular and radical products respectively, and roaming reactive and non-reactive orbiting trajectories, which represent alternative pathways to form molecular and radical products. By analysing gap time distributions at several energies, we demonstrate that the phase space structure of the roaming region, which is strongly influenced by nonlinear resonances between the two degrees of freedom, results in nonexponential (nonstatistical) decay.

  5. Tracing Abiotic Redox Reaction Pathways From Changes in Loess Magnetism

    NASA Astrophysics Data System (ADS)

    Lagroix, F.; Guyodo, Y. J.

    2009-12-01

    Loess magnetism has thrived over the last thirty years and has produced valuable paleoclimate records and provided many insights into past climate on continental surfaces. One major hurdle remaining is the quantification of loess magnetism to climate or environment connection(s). Previous studies by others have revealed a relationship in top soils developing over loess in China, the Russian Steppe and the Midwest US between the enhanced magnetism, with respect to the underlying parent loess, and present day rainfall. However from one area to another the relationship differs and therefore whether the relationship observed in for the topsoil at a given site holds for the underlying paleosols is uncertain and difficult to verify. Our efforts are focused here on tracing the abiotic redox reaction pathways of natural samples of parent loess and of its overlying topsoil and underlying paleosol from changes in their magnetic behavior at low-temperature. By forcing the natural samples to their limits, i.e., most oxidized and most reduced states, under controlled laboratory conditions, our goal is to determine the range of alteration and its impact on the bulk magnetic properties. Moreover, by cycling from one end-member state to the other, the pathway of alteration is traced and whether this pathway is reversible or hysteretic is revealed. Our approach is voluntarily simplistic, involving a limited number of variables. Experiments are all conducted at 250°C and in air for oxidizing experiments or a mixture of carbon monoxide (20 %) and carbon dioxide (80 %) for reduction experiments. Starting sample type is the only variable that changes introducing increasing complexity as we go from the parent loess to the paleosol to the topsoil samples with, for example, increasing amounts of organic matter and clays.

  6. Eco-friendly polyethylene glycol promoted Michael addition reactions of α,β-unsaturated carbonyl compounds

    EPA Science Inventory

    Abstract- Intra- and inter-nucleophilic addition reactions of different unsaturated compounds were found to be highly effective without any additives in PEG-400 as a recyclable reaction medium under neutral conditions.

  7. Probing Complex Free-Radical Reaction Pathways of Fuel Model Compounds

    SciTech Connect

    Buchanan III, A C; Kidder, Michelle; Beste, Ariana; Britt, Phillip F

    2012-01-01

    Fossil (e.g. coal) and renewable (e.g. woody biomass) organic energy resources have received considerable attention as possible sources of liquid transportation fuels and commodity chemicals. Knowledge of the reactivity of these complex materials has been advanced through fundamental studies of organic compounds that model constituent substructures. In particular, an improved understanding of thermochemical reaction pathways involving free-radical intermediates has arisen from detailed experimental kinetic studies and, more recently, advanced computational investigations. In this presentation, we will discuss our recent investigations of the fundamental pyrolysis pathways of model compounds that represent key substructures in the lignin component of woody biomass with a focus on molecules representative of the dominant beta-O-4 aryl ether linkages. Additional mechanistic insights gleaned from DFT calculations on the kinetics of key elementary reaction steps will also be presented, as well as a few thoughts on the significant contributions of Jim Franz to this area of free radical chemistry.

  8. Reactions of the alkoxy radicals formed following OH-addition to alpha-pinene and beta-pinene. C-C bond scission reactions.

    PubMed

    Dibble, T S

    2001-05-01

    The atmospheric degradation pathways of the atmospherically important terpenes alpha-pinene and beta-pinene are studied using density functional theory. We employ the correlation functional of Lee, Yang, and Parr and the three-parameter HF exchange functional of Becke (B3LYP) together with the 6-31G(d) basis set. The C-C bond scission reactions of the beta-hydroxyalkoxy radicals that are formed after OH addition to alpha-pinene and beta-pinene are investigated. Both of the alkoxy radicals formed from the alpha-pinene-OH adduct possess a single favored C-C scission pathway with an extremely low barrier (approximately 3 kcal/mol) leading to the formation of pinonaldehyde. Neither of these pathways produces formaldehyde, and preliminary computational results offer some support for suggestions that 1,5 or 1,6 H-shift (isomerization) reactions of alkoxy radicals contribute to formaldehyde production. In the case of the alkoxy radical formed following OH addition to the methylene group of beta-pinene, there exists two C-C scission reactions with nearly identical barrier heights (approximately 7.5 kcal/mol); one leads to known products (nopinone and formaldehyde) but the ultimate products of the competing reaction are unknown. The single C-C scission pathway of the other alkoxy radical from beta-pinene possesses a very low (approximately 4 kcal/mol) barrier. The kinetically favored C-C scission reactions of all four alkoxy radicals appear to be far faster than expected rates of reaction with O2. The rearrangement of the alpha-pinene-OH adduct, a key step in the proposed mechanism of formation of acetone from alpha-pinene, is determined to possess a barrier of 11.6 kcal/mol. This value is consistent with another computational result and is broadly consistent with the modest acetone yields observed in product yield studies.

  9. Reaction pathway of methylenation of carbonyl compounds with bis(iodozincio)methane.

    PubMed

    Sada, Mutsumi; Komagawa, Shinsuke; Uchiyama, Masanobu; Kobata, Masami; Mizuno, Tsuyoshi; Utimoto, Kiitiro; Oshima, Koichiro; Matsubara, Seijiro

    2010-12-15

    About 40 years have passed since methylene dizinc reagent was discovered as a substitute for Wittig reagent. Density functional theory (DFT) calculations have been performed to understand the reaction pathways of methylenation of carbonyl compounds with bis(iodozincio)methane. The present computational/theoretical study concluded that the methylenation reaction with gem-dizinc reagent proceeds as a two-step reaction, that is, methylene addition (RDS) and olefination. In the first step, the nucleophilic attack of the CH2 group enhanced by two Zn proceeds under the assistance of the electrophilic activation of the carbonyl group with the Zn atom. In the second step, the olefination is facilitated by both Zn atoms of the gem-dizinc reagent without an electron transfer process. PMID:21082850

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  11. Double-Ended Surface Walking Method for Pathway Building and Transition State Location of Complex Reactions.

    PubMed

    Zhang, Xiao-Jie; Shang, Cheng; Liu, Zhi-Pan

    2013-12-10

    Toward the activity prediction with large-scale computations, here a double-ended surface walking (DESW) method is developed for connecting two minima on a potential energy surface (PES) and locating the associated transition state (TS) using only the first derivatives. The method operates two images starting from the initial and the final states, respectively, to walk in a stepwise manner toward each other. The surface walking involves repeated bias potential addition and local relaxation with the constrained Broyden dimer method to correct the walking direction. We apply the method to a model PES, a large set of gas phase Baker reactions, and complex surface catalytic reactions, which demonstrates that the DESW method can establish a low energy pathway linking two minima even without iterative optimization of the pathway, from which the TS can be located readily. By comparing the efficiency of the new method with the existing methods, we show that the DESW method is much less computationally demanding and is applicable for reactions with complex PESs. We hope that the DESW method may be integrated with the PES sampling methods for automated reaction prediction.

  12. Heterogeneous Chemistry of Lipopolysaccharides with Gas-Phase Nitric Acid: Reactive Sites and Reaction Pathways.

    PubMed

    Trueblood, Jonathan V; Estillore, Armando D; Lee, Christopher; Dowling, Jacqueline A; Prather, Kimberly A; Grassian, Vicki H

    2016-08-18

    Recent studies have shown that sea spray aerosol (SSA) has a size-dependent, complex composition consisting of biomolecules and biologically derived organic compounds in addition to salts. This additional chemical complexity most likely influences the heterogeneous reactivity of SSA, as these other components will have different reactive sites and reaction pathways. In this study, we focus on the reactivity of a class of particles derived from some of the biological components of sea spray aerosol including lipopolysaccharides (LPS) that undergo heterogeneous chemistry within the reactive sites of the biological molecule. Examples of these reactions and the relevant reactive sites are proposed as follows: R-COONa(s) + HNO3(g) → NaNO3 + R-COOH and R-HPO4Na(s) + HNO3(g) → NaNO3 + R-H2PO4. These reactions may be a heterogeneous pathway not only for sea spray aerosol but also for a variety of other types of atmospheric aerosol as well.

  13. Conjugate addition reactions of N-carbamoyl-4-pyridones and 2,3-dihydropyridones with Grignard reagents in the absence of Cu(I) salts.

    PubMed

    Guo, Fenghai; Dhakal, Ramesh C; Dieter, R Karl

    2013-09-01

    N-Boc- and N-ethoxycarbonyl-4-pyridones and the resulting 2,3-dihydropyridones undergo 1,4-addition reactions with Grignard reagents in the presence of chlorotrimethylsilane (TMSCl) or BF3·Et2O in excellent yields. Copper catalysis is not required, and mechanistic considerations suggest that the reaction is proceeding by a conjugate addition pathway rather than by a pathway involving 1,2-addition to an intermediate pyridinium ion. TMSCl-mediated conjugate addition of Grignard reagents to 2-substituted-2,3-dihydropyridones gives the trans-2,6-disubstitued piperidinones stereoselectively, while cuprate reagents give either the trans or cis diastereomers or mixtures.

  14. Theoretical investigation of the addition reaction of the aluminum chlorosilylenoid H2SiAlCl3 with ethylene.

    PubMed

    Zhang, Mingxia; Li, Wenzuo; Liu, Zhenbo; Li, Qingzhong; Cheng, Jianbo

    2016-07-01

    The addition reaction of the aluminum chlorosilylenoid H2SiAlCl3 with ethylene was investigated using the M06-2X and QCISD methods for the first time. The calculated results demonstrate that the addition reaction proceeds via two pathways: path I involves just one transition state, while path II involves two transition states. Path I is more feasible dynamically, as it has a lower barrier height than path II. The effect of the solvent CH2Cl2 was taken into consideration using the PCM model. The results indicated that the addition reaction is less likely to occur in CH2Cl2 solvent than in vacuum. This work has therefore highlighted a new pathway for the synthesis of silicon heterocyclic compounds. Graphical Abstract Relative energies (in kJ·mol(-1)) of the stationary points along the potential energy surfaces of the addition reaction of H2SiAlCl3 with C2H4 (values in parentheses were calculated in CH2Cl2 solvent). PMID:27271163

  15. Diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams.

    PubMed

    Byrd, Katherine M

    2015-01-01

    The conjugate addition reaction has been a useful tool in the formation of carbon-carbon bonds. The utility of this reaction has been demonstrated in the synthesis of many natural products, materials, and pharmacological agents. In the last three decades, there has been a significant increase in the development of asymmetric variants of this reaction. Unfortunately, conjugate addition reactions using α,β-unsaturated amides and lactams remain underdeveloped due to their inherently low reactivity. This review highlights the work that has been done on both diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams.

  16. Diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams

    PubMed Central

    2015-01-01

    Summary The conjugate addition reaction has been a useful tool in the formation of carbon–carbon bonds. The utility of this reaction has been demonstrated in the synthesis of many natural products, materials, and pharmacological agents. In the last three decades, there has been a significant increase in the development of asymmetric variants of this reaction. Unfortunately, conjugate addition reactions using α,β-unsaturated amides and lactams remain underdeveloped due to their inherently low reactivity. This review highlights the work that has been done on both diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams. PMID:25977728

  17. The reaction pathways of the oxygen plasma pulse in the hafnium oxide atomic layer deposition process

    SciTech Connect

    Jeon, Hyeongtag; Won, Youngdo

    2008-09-22

    The plasma enhanced atomic layer deposition process for the HfO{sub 2} thin film is modeled as simple reactions between Hf(OH){sub 3}NH{sub 2} and reactive oxygen species. The density functional theory calculation was performed for plausible reaction pathways to construct the reaction profile. While the triplet molecular oxygen is unlikely to form a reactive complex, the singlet molecular oxygen forms the stable adduct that goes through the transition state and completes the reaction pathway to the products. Either two singlet or two triplet oxygen atoms make the singlet adduct complex, which follows the same pathway to the product as the singlet molecular oxygen reacts.

  18. WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways.

    PubMed

    Sekiguchi, Tatsuya; Okamoto, Masahiro

    2006-06-01

    We have implemented an efficient, user-friendly biochemical reaction simulator called Web-based BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing large-scale nonlinear networks such as metabolic pathways. Users can easily design and analyze an arbitrary reaction scheme through the Internet and an efficient graphical user interface without considering the mathematical equations. The reaction scheme can include several reaction types, which are represented by both the mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state, such as Michaelis-Menten, Hill cooperative, Competitive inhibition. However, since all modules in Web-based BEST-KIT have been developed in Java applet style, users cannot optionally make use of original mathematical equations in addition to the prepared equations. In the present study, we have developed a new version of BEST-KIT (for Microsoft Windows called WinBEST-KIT) to allow users to define original mathematical equations and to customize these equations very easily as user-defined reaction symbols. The following powerful system-analytical methods are prepared for system analysis: time-course calculation, parameter scanning, estimation of the values of unknown kinetic parameters based on experimentally observed time-course data of reactants, dynamic response of reactants against virtual external perturbations, and real-time simulation (Virtual Dry Lab). PMID:16960966

  19. ReactionFlow: an interactive visualization tool for causality analysis in biological pathways

    PubMed Central

    2015-01-01

    Background Molecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins. Results We introduce ReactionFlow, a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway. To support the identified causality analysis tasks, user interactions allow an analyst to filter, cluster, and select pathway components across linked views. Animation is used to highlight the flow of activity through a pathway. Conclusions We evaluated ReactionFlow by providing our application to two domain experts who have significant experience with biomolecular pathways, after which we conducted a series of in-depth interviews focused on each of the four causality analysis tasks. Their feedback leads us to believe that our techniques could be useful to researchers who must be able to understand and analyze the complex nature of biological pathways. ReactionFlow is available at https://github.com/CreativeCodingLab/ReactionFlow. PMID:26361502

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

    NASA Astrophysics Data System (ADS)

    Samoilov, Michael; Arkin, Adam; Ross, John

    2001-03-01

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

  1. Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

    PubMed Central

    2012-01-01

    Background The representation of a biochemical system as a network is the precursor of any mathematical model of the processes driving the dynamics of that system. Pharmacokinetics uses mathematical models to describe the interactions between drug, and drug metabolites and targets and through the simulation of these models predicts drug levels and/or dynamic behaviors of drug entities in the body. Therefore, the development of computational techniques for inferring the interaction network of the drug entities and its kinetic parameters from observational data is raising great interest in the scientific community of pharmacologists. In fact, the network inference is a set of mathematical procedures deducing the structure of a model from the experimental data associated to the nodes of the network of interactions. In this paper, we deal with the inference of a pharmacokinetic network from the concentrations of the drug and its metabolites observed at discrete time points. Results The method of network inference presented in this paper is inspired by the theory of time-lagged correlation inference with regard to the deduction of the interaction network, and on a maximum likelihood approach with regard to the estimation of the kinetic parameters of the network. Both network inference and parameter estimation have been designed specifically to identify systems of biotransformations, at the biochemical level, from noisy time-resolved experimental data. We use our inference method to deduce the metabolic pathway of the gemcitabine. The inputs to our inference algorithm are the experimental time series of the concentration of gemcitabine and its metabolites. The output is the set of reactions of the metabolic network of the gemcitabine. Conclusions Time-lagged correlation based inference pairs up to a probabilistic model of parameter inference from metabolites time series allows the identification of the microscopic pharmacokinetics and pharmacodynamics of a drug with a

  2. General low-temperature reaction pathway from precursors to monomers before nucleation of compound semiconductor nanocrystals

    PubMed Central

    Yu, Kui; Liu, Xiangyang; Qi, Ting; Yang, Huaqing; Whitfield, Dennis M.; Y. Chen, Queena; Huisman, Erik J. C.; Hu, Changwei

    2016-01-01

    Little is known about the molecular pathway to monomers of semiconductor nanocrystals. Here we report a general reaction pathway, which is based on hydrogen-mediated ligand loss for the precursor conversion to ‘monomers' at low temperature before nucleation. We apply 31P nuclear magnetic resonance spectroscopy to monitor the key phosphorous-containing products that evolve from MXn+E=PPh2H+HY mixtures, where MXn, E=PPh2H, and HY are metal precursors, chalcogenide precursors, and additives, respectively. Surprisingly, the phosphorous-containing products detected can be categorized into two groups, Ph2P–Y and Ph2P(E)–Y. On the basis of our experimental and theoretical results, we propose two competing pathways to the formation of M2En monomers, each of which is accompanied by one of the two products. Our study unravels the pathway of precursor evolution into M2En monomers, the stoichiometry of which directly correlates with the atomic composition of the final compound nanocrystals. PMID:27531507

  3. General low-temperature reaction pathway from precursors to monomers before nucleation of compound semiconductor nanocrystals.

    PubMed

    Yu, Kui; Liu, Xiangyang; Qi, Ting; Yang, Huaqing; Whitfield, Dennis M; Y Chen, Queena; Huisman, Erik J C; Hu, Changwei

    2016-01-01

    Little is known about the molecular pathway to monomers of semiconductor nanocrystals. Here we report a general reaction pathway, which is based on hydrogen-mediated ligand loss for the precursor conversion to 'monomers' at low temperature before nucleation. We apply (31)P nuclear magnetic resonance spectroscopy to monitor the key phosphorous-containing products that evolve from MXn+E=PPh2H+HY mixtures, where MXn, E=PPh2H, and HY are metal precursors, chalcogenide precursors, and additives, respectively. Surprisingly, the phosphorous-containing products detected can be categorized into two groups, Ph2P-Y and Ph2P(E)-Y. On the basis of our experimental and theoretical results, we propose two competing pathways to the formation of M2En monomers, each of which is accompanied by one of the two products. Our study unravels the pathway of precursor evolution into M2En monomers, the stoichiometry of which directly correlates with the atomic composition of the final compound nanocrystals. PMID:27531507

  4. General low-temperature reaction pathway from precursors to monomers before nucleation of compound semiconductor nanocrystals

    NASA Astrophysics Data System (ADS)

    Yu, Kui; Liu, Xiangyang; Qi, Ting; Yang, Huaqing; Whitfield, Dennis M.; Y. Chen, Queena; Huisman, Erik J. C.; Hu, Changwei

    2016-08-01

    Little is known about the molecular pathway to monomers of semiconductor nanocrystals. Here we report a general reaction pathway, which is based on hydrogen-mediated ligand loss for the precursor conversion to `monomers' at low temperature before nucleation. We apply 31P nuclear magnetic resonance spectroscopy to monitor the key phosphorous-containing products that evolve from MXn+E=PPh2H+HY mixtures, where MXn, E=PPh2H, and HY are metal precursors, chalcogenide precursors, and additives, respectively. Surprisingly, the phosphorous-containing products detected can be categorized into two groups, Ph2P-Y and Ph2P(E)-Y. On the basis of our experimental and theoretical results, we propose two competing pathways to the formation of M2En monomers, each of which is accompanied by one of the two products. Our study unravels the pathway of precursor evolution into M2En monomers, the stoichiometry of which directly correlates with the atomic composition of the final compound nanocrystals.

  5. [Risk hidden in the small print? : Some food additives may trigger pseudoallergic reactions].

    PubMed

    Zuberbier, Torsten; Hengstenberg, Claudine

    2016-06-01

    Some food additives may trigger pseudoallergenic reactions. However, the prevalence of such an overreaction is - despite the increasing number of food additives - rather low in the general population. The most common triggers of pseudoallergic reactions to food are naturally occurring ingredients. However, symptoms in patients with chronic urticaria should improve significantly on a pseudoallergen-free diet. In addition, some studies indicate that certain food additives may also have an impact on the symptoms of patients with neurodermatitis and asthma. PMID:27173908

  6. [Risk hidden in the small print? : Some food additives may trigger pseudoallergic reactions].

    PubMed

    Zuberbier, Torsten; Hengstenberg, Claudine

    2016-06-01

    Some food additives may trigger pseudoallergenic reactions. However, the prevalence of such an overreaction is - despite the increasing number of food additives - rather low in the general population. The most common triggers of pseudoallergic reactions to food are naturally occurring ingredients. However, symptoms in patients with chronic urticaria should improve significantly on a pseudoallergen-free diet. In addition, some studies indicate that certain food additives may also have an impact on the symptoms of patients with neurodermatitis and asthma.

  7. A mechanistic study of the addition of alcohol to a five-membered ring silene via a photochemical reaction.

    PubMed

    Su, Ming-Der

    2016-03-21

    The mechanism for the photochemical rearrangement of a cyclic divinyldisilane (1-Si) in its first excited state ((1)π → (1)π*) is determined using the CAS/6-311G(d) and MP2-CAS/6-311++G(3df,3pd) levels of theory. The photoproduct, a cyclic silene, reacts with various alcohols to yield a mixture of cis- and trans- adducts. The two reaction pathways are denoted as the cis- addition path (path A) and the trans-addition path (path B). These model studies demonstrate that conical intersections play a crucial role in the photo-rearrangements of cyclic divinyldisilanes. The theoretical evidence also demonstrates that the addition of alcohol to a cyclic divinyldisilane follows the reaction path: cyclic divinyldisilane → Franck-Condon region → conical intersection → photoproduct (cyclic silene) → local intermediate (with alcohol) → transition state → cis- or trans-adduct. The theoretical studies demonstrate that the steric effects as well as the concentrations of CH3OH must have a dominant role in determining the yields of the final adducts by stereochemistry. The same mechanism for the carbon derivative (1-C) is also considered in this work. However, the theoretical results indicate that 1-C does not undergo a methanol addition reaction via the photochemical reaction pathway, since its energy of conical intersection (S1/S0-CI-C) is more than that of its FC (FC-C). The reason for these phenomena could be that the atomic radius of carbon is much smaller than that of silicon (77 and 117 pm, respectively). As a result, the conformation for 1-C is more sterically congested than that for 1-Si, along the 1,3-silyl-migration pathway. PMID:26928893

  8. On the role of DNA in DNA-based catalytic enantioselective conjugate addition reactions.

    PubMed

    Dijk, Ewold W; Boersma, Arnold J; Feringa, Ben L; Roelfes, Gerard

    2010-09-01

    A kinetic study of DNA-based catalytic enantioselective Friedel-Crafts alkylation and Michael addition reactions showed that DNA affects the rate of these reactions significantly. Whereas in the presence of DNA, a large acceleration was found for the Friedel-Crafts alkylation and a modest acceleration in the Michael addition of dimethyl malonate, a deceleration was observed when using nitromethane as nucleophile. Also, the enantioselectivities proved to be dependent on the DNA sequence. In comparison with the previously reported Diels-Alder reaction, the results presented here suggest that DNA plays a similar role in both cycloaddition and conjugate addition reactions.

  9. Peptide-catalyzed 1,4-addition reactions of aldehydes to nitroolefins.

    PubMed

    Kastl, Robert; Arakawa, Yukihiro; Duschmalé, Jörg; Wiesner, Markus; Wennemers, Helma

    2013-01-01

    Conjugate addition reactions of aldehydes to nitroolefins provide synthetically useful gamma-nitroaldehydes. Here we summarize our research on peptide-catalyzed conjugate addition reactions of aldehydes to differently substituted nitroolefins. We show that peptides of the general type Pro-Pro-Xaa (Xaa = acidic amino acid) are not only highly active, robust and stereoselective catalysts but have also remarkable chemoselectivities.

  10. Intermolecular addition reactions of N-alkyl-N-chlorosulfonamides to unsaturated compounds.

    PubMed

    Heuger, Gerold; Göttlich, Richard

    2015-01-01

    N-Alkyl-N-chlorosulfonamides add to alkenes under copper(I) catalysis. In reactions of styrene derivatives with terminal double bonds the addition products were obtained in excellent yield and high regioselectivity. Lower yields are obtained in addition reactions to non-aromatic alkenes. The reaction most likely proceeds via a redox catalysis and amidyl radicals, a concerted mechanism has been ruled out and a polar mechanism via chloronium ions would lead to the opposite regiochemistry.

  11. Olefin Metathesis Reaction in Water and in Air Improved by Supramolecular Additives.

    PubMed

    Tomasek, Jasmine; Seßler, Miriam; Gröger, Harald; Schatz, Jürgen

    2015-10-21

    A range of water-immiscible commercially available Grubbs-type precatalysts can be used in ring-closing olefin metathesis reaction in high yields. The synthetic transformation is possible in pure water under ambient conditions. Sulfocalixarenes can help to boost the reactivity of the metathesis reaction by catalyst activation, improved mass transfer, and solubility of reactants in the aqueous reaction media. Additionally, the use of supramolecular additives allows lower catalyst loadings, but still high activity in pure water under aerobic conditions.

  12. Intermolecular addition reactions of N-alkyl-N-chlorosulfonamides to unsaturated compounds

    PubMed Central

    Heuger, Gerold

    2015-01-01

    Summary N-Alkyl-N-chlorosulfonamides add to alkenes under copper(I) catalysis. In reactions of styrene derivatives with terminal double bonds the addition products were obtained in excellent yield and high regioselectivity. Lower yields are obtained in addition reactions to non-aromatic alkenes. The reaction most likely proceeds via a redox catalysis and amidyl radicals, a concerted mechanism has been ruled out and a polar mechanism via chloronium ions would lead to the opposite regiochemistry. PMID:26425180

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

    PubMed Central

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

    2016-01-01

    Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway. PMID:26922910

  14. Multiple reaction pathways of metallofullerenes investigated by transmission electron microscopy.

    PubMed

    Koshino, Masanori

    2014-05-28

    Recent advances in molecule-by-molecule transmission electron microscopy (TEM) have provided time-series structural information of individual molecules supported by nano-carbon materials, enabling researchers to trace their motions and reactions. In this paper, the chemical reactions of fullerenes and metallofullerene derivatives, focusing on their deformation process, are reviewed and discussed based on the single-molecule-resolved TEM analysis.

  15. Chemical pathways in ultracold reactions of SrF molecules

    SciTech Connect

    Meyer, Edmund R.; Bohn, John L.

    2011-03-15

    We present a theoretical investigation of the chemical reaction SrF + SrF {yields} products, focusing on reactions at ultralow temperatures. We find that bond swapping SrF + SrF {yields} Sr{sub 2} + F{sub 2} is energetically forbidden at these temperatures. Rather, the only energetically allowed reaction is SrF + SrF {yields} SrF{sub 2} + Sr, and even then only singlet states of the SrF{sub 2} trimer can form. A calculation along a reduced reaction path demonstrates that this abstraction reaction is barrierless and proceeds by one SrF molecule ''handing off'' a fluorine atom to the other molecule.

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

    PubMed

    Li, Huanxuan; Wan, Jinquan; Ma, Yongwen; Wang, Yan

    2016-08-15

    This study investigated reaction pathway and oxidation mechanisms of dibutyl phthalate (DBP) by persulfate (PS) activated with zero-valent iron (ZVI). The DBP degradation was studied at three pH values (acidic, neutral and basic) in the presence of different organic scavengers. Using a chemical probe method, both sulfate radical (SO4(-)) and hydroxyl radical (·OH) were found to be primary oxidants at pH3.0 and pH7.0, respectively while ·OH was the major specie to oxidize DBP at pH11.0. A similar result was found in an experiment of Electron Spin Resonance spin-trapping where in addition to OH, superoxide radical (O2(-)) was detected at pH11.0. 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 pH3.0 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 pH3.0. PMID:27125682

  17. Copper-catalyzed alkyl-alkyl cross-coupling reactions using hydrocarbon additives: efficiency of catalyst and roles of additives.

    PubMed

    Iwasaki, Takanori; Imanishi, Reiko; Shimizu, Ryohei; Kuniyasu, Hitoshi; Terao, Jun; Kambe, Nobuaki

    2014-09-19

    Cross-coupling of alkyl halides with alkyl Grignard reagents proceeds with extremely high TONs of up to 1230000 using a Cu/unsaturated hydrocarbon catalytic system. Alkyl fluorides, chlorides, bromides, and tosylates are all suitable electrophiles, and a TOF as high as 31200 h(-1) was attained using an alkyl iodide. Side reactions of this catalytic system, i.e., reduction, dehydrohalogenation (elimination), and the homocoupling of alkyl halides, occur in the absence of additives. It appears that the reaction involves the β-hydrogen elimination of alkylcopper intermediates, giving rise to olefins and Cu-H species, and that this process triggers both side reactions and the degradation of the Cu catalyst. The formed Cu-H promotes the reduction of alkyl halides to give alkanes and Cu-X or the generation of Cu(0), probably by disproportionation, which can oxidatively add to alkyl halides to yield olefins and, in some cases, homocoupling products. Unsaturated hydrocarbon additives such as 1,3-butadiene and phenylpropyne play important roles in achieving highly efficient cross-coupling by suppressing β-hydrogen elimination, which inhibits both the degradation of the Cu catalyst and undesirable side reactions.

  18. Copper-catalyzed alkyl-alkyl cross-coupling reactions using hydrocarbon additives: efficiency of catalyst and roles of additives.

    PubMed

    Iwasaki, Takanori; Imanishi, Reiko; Shimizu, Ryohei; Kuniyasu, Hitoshi; Terao, Jun; Kambe, Nobuaki

    2014-09-19

    Cross-coupling of alkyl halides with alkyl Grignard reagents proceeds with extremely high TONs of up to 1230000 using a Cu/unsaturated hydrocarbon catalytic system. Alkyl fluorides, chlorides, bromides, and tosylates are all suitable electrophiles, and a TOF as high as 31200 h(-1) was attained using an alkyl iodide. Side reactions of this catalytic system, i.e., reduction, dehydrohalogenation (elimination), and the homocoupling of alkyl halides, occur in the absence of additives. It appears that the reaction involves the β-hydrogen elimination of alkylcopper intermediates, giving rise to olefins and Cu-H species, and that this process triggers both side reactions and the degradation of the Cu catalyst. The formed Cu-H promotes the reduction of alkyl halides to give alkanes and Cu-X or the generation of Cu(0), probably by disproportionation, which can oxidatively add to alkyl halides to yield olefins and, in some cases, homocoupling products. Unsaturated hydrocarbon additives such as 1,3-butadiene and phenylpropyne play important roles in achieving highly efficient cross-coupling by suppressing β-hydrogen elimination, which inhibits both the degradation of the Cu catalyst and undesirable side reactions. PMID:25010426

  19. Transformation and removal of tetrabromobisphenol A from water in the presence of natural organic matter via laccase-catalyzed reactions: reaction rates, products, and pathways.

    PubMed

    Feng, Yiping; Colosi, Lisa M; Gao, Shixiang; Huang, Qingguo; Mao, Liang

    2013-01-15

    The widespread occurrence of the brominated flame retardant tetrabromobisphenol A (TBBPA) makes it a possible source of concern. Our experiments suggest that TBBPA can be effectively transformed by the naturally occurring laccase enzyme from Trametes versicolor. These reactions follow second-order kinetics, whereby apparent removal rate is a function of both substrate and enzyme concentrations. For reactions at different initial concentrations and with or without natural organic matter (NOM), reaction products are identified using liquid or gas chromatography with mass spectrometry. Detailed reaction pathways are proposed. It is postulated that two TBBPA radicals resulting from a laccase-mediated reaction are coupled together via interaction of an oxygen atom on one radical and a propyl-substituted aromatic carbon atom on the other. A 2,6-dibromo-4-isopropylphenol carbocation is then eliminated from the radical dimer. All but one of the detected products arise from either substitution or proton elimination of the 2,6-dibromo-4-isopropylphenol carbocation. Three additional products are identified for reactions in the presence of NOM, which suggests that reaction occurs between NOM and TBBPA radical. Data from acute immobilization tests with Daphnia confirm that TBBPA toxicity is effectively eliminated by laccase-catalyzed TBBPA removal. These findings are useful for understanding laccase-mediated TBBPA reactions and could eventually lead to development of novel methods to control TBBPA contamination. PMID:23256593

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

    PubMed

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

    2016-11-01

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

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

    PubMed

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

    2016-11-01

    As active agents in cleaning and disinfecting products, antimicrobials have been widely spread in the environment and have drawn extensive attention as potential threats to the ecological system and human health. In this study, the laccase-catalyzed removal of two emerging antimicrobials, chlorophene (CP) and dichlorophen (DCP), was investigated under simulated environmental conditions. Intrinsic reaction kinetics showed that the removal of CP and DCP followed second-order reaction kinetics, first-order with respect to both the enzyme and the substrate concentration. It was also found that fulvic acid could suppress the transformation of CP and DCP by reversing the oxidation reactions through its action as a scavenger of the free radical intermediates produced from reactions between laccase and the substrates. Several reaction products were identified by a quadrupole time-of-flight mass spectrometer, and detailed reaction pathways were proposed. For both CP and DCP, direct polymerization was the principal pathway, and the coupling patterns were further corroborated based on molecular modeling. The nucleophilic substitution of chlorine by the hydroxyl group was observed, and further oxidation products capable of coupling with each other were also found. Additionally, toxicity evaluation tests using Scenedesmus obliquus confirmed that the toxicity of CP and DCP was effectively eliminated during the reaction processes. PMID:27262275

  2. Effect of bromide ion on the reaction pathway between hydroxyl radical and glycine.

    PubMed

    Ying, Liwen; Dong, Wenbo; Yuan, Haixia; Liu, Yan; Ma, Luming

    2015-06-01

    Br(-) and nitrogen-containing organic pollutants, such as amino acids, protein, etc., were often detected in water and wastewater treatment plants using advanced oxidation technologies. All these technologies have one common characteristic, that is, the removal processes involve ·OH. Therefore, it is necessary to study the different reaction pathways among ·OH, Br(-), and amino acids. In this research, glycine was chosen as the representative of amino acids and H2O2 was selected as ·OH precursor. Results showed that Br(-) had a shielding effect on [Formula: see text] of α-carbon in glycine, when it was abstracted by ·OH. The main reaction pathway in the system containing Br(-) was the abstraction of H from amino group in glycine by ·OH, contributing 85 % of total abstracted H. This system had a prominent phenomenon of decarboxylation and performed as alkali production dominating. However, in the system not containing Br(-), the main reaction pathway was the abstraction of H from α-carbon in glycine by ·OH, contributing 97 % of total abstracted H. This system performed as acid production dominating. By laser flash photolysis, the second-order rate constants of abstraction of H from both α-carbon and amino group in glycine by ·OH were obtained as (3.3 ± 0.5) × 10(7) M(-1)·s(-1) and (8.2 ± 0.8) × 10(8) M(-1)·s(-1), respectively. The second-order rate constants of the reaction between [Formula: see text], HṄCH2COO(-) and H2O2 were (1.5 ± 1.1) × 10(7) M(-1)·s(-1) and (4.4 ± 0.3) × 10(7) M(-1)·s(-1), respectively. In addition, Br(-) was found to play a catalytic role in the decomposition of H2O2 under UV radiation. The results mentioned above were significant for the application of advanced oxidation technologies for water containing both amino acids and Br(-) in water and wastewater treatment plants.

  3. Effect of bromide ion on the reaction pathway between hydroxyl radical and glycine.

    PubMed

    Ying, Liwen; Dong, Wenbo; Yuan, Haixia; Liu, Yan; Ma, Luming

    2015-06-01

    Br(-) and nitrogen-containing organic pollutants, such as amino acids, protein, etc., were often detected in water and wastewater treatment plants using advanced oxidation technologies. All these technologies have one common characteristic, that is, the removal processes involve ·OH. Therefore, it is necessary to study the different reaction pathways among ·OH, Br(-), and amino acids. In this research, glycine was chosen as the representative of amino acids and H2O2 was selected as ·OH precursor. Results showed that Br(-) had a shielding effect on [Formula: see text] of α-carbon in glycine, when it was abstracted by ·OH. The main reaction pathway in the system containing Br(-) was the abstraction of H from amino group in glycine by ·OH, contributing 85 % of total abstracted H. This system had a prominent phenomenon of decarboxylation and performed as alkali production dominating. However, in the system not containing Br(-), the main reaction pathway was the abstraction of H from α-carbon in glycine by ·OH, contributing 97 % of total abstracted H. This system performed as acid production dominating. By laser flash photolysis, the second-order rate constants of abstraction of H from both α-carbon and amino group in glycine by ·OH were obtained as (3.3 ± 0.5) × 10(7) M(-1)·s(-1) and (8.2 ± 0.8) × 10(8) M(-1)·s(-1), respectively. The second-order rate constants of the reaction between [Formula: see text], HṄCH2COO(-) and H2O2 were (1.5 ± 1.1) × 10(7) M(-1)·s(-1) and (4.4 ± 0.3) × 10(7) M(-1)·s(-1), respectively. In addition, Br(-) was found to play a catalytic role in the decomposition of H2O2 under UV radiation. The results mentioned above were significant for the application of advanced oxidation technologies for water containing both amino acids and Br(-) in water and wastewater treatment plants. PMID:25548016

  4. A summary of seven- and eight-membered ring sultam syntheses via three Michael addition reactions.

    PubMed

    Niu, Ben; Xie, Ping; Wang, Min; Wang, Yanjie; Zhao, Wannian; Pittman, Charles U; Zhou, Aihua

    2015-08-01

    A series of seven- and eight-membered ring -N,O-, -N,N-, and -N,S-sultams were effectively synthesized via tandem reactions involving oxa-, aza-, and thia-Michael addition to vinyl sulfonamides. These reactions are summarized here since they enrich current synthetic methodologies for sultams and provide a good example of sultam diversity-oriented synthesis. All reactions proceeded under relatively mild and environmentally friendly conditions, and all these reactions are quite suitable for the rapid preparation of sultam compound libraries, which are valuable for biological activity explorations.

  5. Borohydride-mediated radical addition reactions of organic iodides to electron-deficient alkenes.

    PubMed

    Kawamoto, Takuji; Uehara, Shohei; Hirao, Hidefumi; Fukuyama, Takahide; Matsubara, Hiroshi; Ryu, Ilhyong

    2014-05-01

    Cyanoborohydrides are efficient reagents in the reductive addition reactions of alkyl iodides and electron-deficient olefins. In contrast to using tin reagents, the reaction took place chemoselectively at the carbon-iodine bond but not at the carbon-bromine or carbon-chlorine bond. The reaction system was successfully applied to three-component reactions, including radical carbonylation. The rate constant for the hydrogen abstraction of a primary alkyl radical from tetrabutylammonium cyanoborohydride was estimated to be <1 × 10(4) M(-1) s(-1) at 25 °C by a kinetic competition method. This value is 3 orders of magnitude smaller than that of tributyltin hydride.

  6. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

    PubMed Central

    Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei

    2016-01-01

    Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

  7. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.

    PubMed

    Wu, D; Fajer, M I; Cao, L; Cheng, X; Yang, W

    2016-01-01

    Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this minipresentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study.

  8. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.

    PubMed

    Wu, D; Fajer, M I; Cao, L; Cheng, X; Yang, W

    2016-01-01

    Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this minipresentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

  9. Olefin Metathesis Reaction in Water and in Air Improved by Supramolecular Additives.

    PubMed

    Tomasek, Jasmine; Seßler, Miriam; Gröger, Harald; Schatz, Jürgen

    2015-01-01

    A range of water-immiscible commercially available Grubbs-type precatalysts can be used in ring-closing olefin metathesis reaction in high yields. The synthetic transformation is possible in pure water under ambient conditions. Sulfocalixarenes can help to boost the reactivity of the metathesis reaction by catalyst activation, improved mass transfer, and solubility of reactants in the aqueous reaction media. Additionally, the use of supramolecular additives allows lower catalyst loadings, but still high activity in pure water under aerobic conditions. PMID:26506329

  10. Michael addition reactions for the modification of gold nanoparticles facilitated by hyperbaric conditions.

    PubMed

    Hartlen, Kurtis D; Ismaili, Hossein; Zhu, Jun; Workentin, Mark S

    2012-01-10

    The chemical interfacial modification of organic solvent soluble 2.4 ± 0.5 nm maleimide-modified monolayer protected gold nanoparticles (2-C(12)AuNPs) with primary or secondary amines via Michael addition reactions is demonstrated. Michael addition reactions between 2-C(12)AuNPs and primary or secondary amines at ambient temperature and pressure and under the conditions where the AuNP is soluble and stable are possible albeit sluggish, often taking days to weeks to go to completion. The rates and efficacies of the these same reactions are drastically increased at hyperbaric pressure conditions (11 000 atm) with no observed adverse effect to the gold nanoparticle stability. The resulting Michael addition adducts (3-C(12)AuNPs) formed from 2-C(12)AuNPs and the corresponding amines were characterized by TEM and by comparison of the (1)H NMR spectra of the 3-C(12)AuNPs with those of model reactions of the same amines with N-dodecylmaleimide, 2. The Michael addition reactions occur more readily with 2 rather than 2-C(12)AuNPs, consistent with the local environment of the latter imposing additional steric or other barriers to the reaction. The use of hyperbaric conditions makes the reaction of the organic solvent soluble 2-C(12)AuNP via Michael addition a viable interfacial modification process that is otherwise impractical. The results also suggest that it is a useful protocol for facilitating Michael addition reactions generally in solution at low temperatures.

  11. Ring Substituent Effects on the Thiol Addition and Hydrolysis Reactions of N-Arylmaleimides.

    PubMed

    Chen, Yingche; Tsao, Kelvin; De Francesco, Élise; Keillor, Jeffrey W

    2015-12-18

    Maleimide groups are used extensively in bioconjugation reactions, but limited kinetic information is available regarding their thiol addition and hydrolysis reactions. We prepared a series of fluorogenic coumarin maleimide derivatives that differ by the substituent on their maleimide C═C bond. Fluorescence-based kinetic studies of the reaction with β-mercaptoethanol (BME) yielded the second-order rate constants (k2), while pH-rate studies from pH 7 to 9 gave base-catalyzed hydrolysis rate constants (kOH). Linear free-energy relationships were studied through the correlation of log k2 and log kOH to both electronic (σ(+)) and steric (Es(norm)) parameters of the C═C substituent. These correlations revealed the thiol addition reaction is primarily sensitive to the electronic effects, while steric effects dominate the hydrolysis reaction. These mechanistic studies provide the basis for the design of novel bioconjugation reactants or fluorogenic labeling agents.

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

    PubMed

    Perez-Benito, Joaquin F

    2011-09-01

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

  13. Cross-reactions between engineered xylose and galactose pathways in recombinant Saccharomyces cerevisiae

    PubMed Central

    2010-01-01

    Background Overexpression of the PGM2 gene encoding phosphoglucomutase (Pgm2p) has been shown to improve galactose utilization both under aerobic and under anaerobic conditions. Similarly, xylose utilization has been improved by overexpression of genes encoding xylulokinase (XK), enzymes from the non-oxidative pentose phosphate pathway (non-ox PPP) and deletion of the endogenous aldose reductase GRE3 gene in engineered Saccharomyces cerevisiae strains carrying either fungal or bacterial xylose pathways. In the present study, we investigated how the combination of these traits affect xylose and galactose utilization in the presence or absence of glucose in S. cerevisiae strains engineered with the xylose reductase (XR)-xylitol dehydrogenase (XDH) pathway. Results In the absence of PGM2 overexpression, the combined overexpression of XK, the non-ox PPP and deletion of the GRE3 gene significantly delayed aerobic growth on galactose, whereas no difference was observed between the control strain and the xylose-engineered strain when the PGM2 gene was overexpressed. Under anaerobic conditions, the overexpression of the PGM2 gene increased the ethanol yield and the xylose consumption rate in medium containing xylose as the only carbon source. The possibility of Pgm2p acting as a xylose isomerase (XI) could be excluded by measuring the XI activity in both strains. The additional copy of the PGM2 gene also resulted in a shorter fermentation time during the co-consumption of galactose and xylose. However, the effect was lost upon addition of glucose to the growth medium. Conclusions PGM2 overexpression was shown to benefit xylose and galactose fermentation, alone and in combination. In contrast, galactose fermentation was impaired in the engineered xylose-utilizing strain harbouring extra copies of the non-ox PPP genes and a deletion of the GRE3 gene, unless PGM2 was overexpressed. These cross-reactions are of particular relevance for the fermentation of mixed sugars from

  14. Monitoring adverse reactions to food additives in the U.S. Food and Drug Administration.

    PubMed

    Tollefson, L

    1988-12-01

    Technological advances in food science have resulted in the development of numerous food additives, most of which require premarket approval by the Food and Drug Administration (FDA). Concomitant with the benefits of these additives, such as extending the shelf life of certain food commodities, is the potential for various risks. These potential risks include the possibility of the consumer experiencing an adverse reaction to the additive. In order to ascertain the character and the gravity of alleged adverse reactions to food products which it regulates, the FDA's Center for Food Safety and Applied Nutrition has developed the Adverse Reaction Monitoring System (ARMS). This postmarketing surveillance system for food additives is designed to analyze consumer reports of adverse reactions in order to alert FDA officials about any potential public health hazard associated with an approved food additive, and to delineate specific syndromes which may lead to focused clinical investigations. To date, among the products routinely monitored in the ARMS, sulfiting agents and the artificial sweetener aspartame have generated the largest volume of consumer reports describing adverse reactions. An overview of the analyses of the sulfite and aspartame adverse reaction reports is presented, along with a description of the mechanics of the postmarketing surveillance system, and a detailed discussion of its limitations.

  15. Photochemical Reactions of Fluorinated Pyridines at Half-Sandwich Rhodium Complexes: Competing Pathways of Reaction

    PubMed Central

    2013-01-01

    Irradiation of CpRh(PMe3)(C2H4) (1; Cp = η5-C5H5) in the presence of pentafluoropyridine in hexane solution at low temperature yields an isolable η2-C,C-coordinated pentafluoropyridine complex, CpRh(PMe3)(η2-C,C-C5NF4) (2). The molecular structure of 2 was determined by single-crystal X-ray diffraction, showing coordination by C3–C4, unlike previous structures of pentafluoropyridine complexes that show N-coordination. Corresponding experiments with 2,3,5,6-tetrafluoropyridine yield the C–H oxidative addition product CpRh(PMe3)(C5NF4)H (3). In contrast, UV irradiation of 1 in hexane, in the presence of 4-substituted tetrafluoropyridines C5NF4X, where X = NMe2, OMe, results in elimination of C2H4 and HF to form the metallacycles CpRh(PMe3)(κ2-C,C-CH2N(CH3)C5NF3) (4) and CpRh(PMe3)(κ2-C,C-CH2OC5NF3) (5), respectively. The X-ray structure of 4 shows a planar RhCCNC-five-membered ring. Complexes 2–5 may also be formed by thermal reaction of CpRh(PMe3)(Ph)H with the respective pyridines at 50 °C. PMID:24563575

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

    PubMed Central

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

    2013-01-01

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

  17. Markovnikov free radical addition reactions, a sleeping beauty kissed to life.

    PubMed

    Hoffmann, Reinhard W

    2016-02-01

    This review covers free radical additions, which are initiated by the formal addition of a hydrogen atom to a C[double bond, length as m-dash]C double bond. These reactions originated in the realms of inorganic chemistry, polymer chemistry, and organic chemistry, whereby barriers between these disciplines impeded the rapid implementation of the findings.

  18. Markovnikov free radical addition reactions, a sleeping beauty kissed to life.

    PubMed

    Hoffmann, Reinhard W

    2016-02-01

    This review covers free radical additions, which are initiated by the formal addition of a hydrogen atom to a C[double bond, length as m-dash]C double bond. These reactions originated in the realms of inorganic chemistry, polymer chemistry, and organic chemistry, whereby barriers between these disciplines impeded the rapid implementation of the findings. PMID:26753913

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

    PubMed

    Qu, Ruijuan; Feng, Mingbao; Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

    2015-01-01

    Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733

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

    PubMed Central

    Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

    2015-01-01

    Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733

  1. Density Functional Theory Calculations and Analysis of Reaction Pathways for Reduction of Nitric Oxide by Hydrogen on Pt(111)

    SciTech Connect

    Farberow, Carrie A.; Dumesic, James A.; Mavrikakis, Manos

    2014-10-03

    Reaction pathways are explored for low temperature (e.g., 400 K) reduction of nitric oxide by hydrogen on Pt(111). First-principles electronic structure calculations based on periodic, self-consistent density functional theory(DFT-GGA, PW91) are employed to obtain thermodynamic and kinetic parameters for proposed reaction schemes on Pt(111). The surface of Pt(111) during NO reduction by H₂ at low temperatures is predicted to operate at a high NO coverage, and this environment is explicitly taken into account in the DFT calculations. Maximum rate analyses are performed to assess the most likely reaction mechanisms leading to formation of N₂O, the major product observed experimentally at low temperatures. The results of these analyses suggest that the reaction most likely proceeds via the addition of at least two H atoms to adsorbed NO, followed by cleavage of the N-O bond.

  2. Photocatalytic decomposition behavior and reaction pathway of sulfamethazine antibiotic using TiO2.

    PubMed

    Fukahori, Shuji; Fujiwara, Taku

    2015-07-01

    The photocatalytic degradation of sulfanethazine (SMT), one of the sulfonamide antibiotics, in aqueous solution by TiO2 was investigated. The time courses of SMT concentration, the amount of non-purgeable organic carbon, and the concentrations of ions such as SO4(2-), NH4(+), and NO3(-) formed during the photocatalytic reaction were measured and the structures of seven intermediates formed with the disappearance of SMT were also estimated by LC/MS/MS analyses. In addition to that of SMT, the decomposition behaviors of model compounds sulfanilic acid (SA) and 4-amino-2, 6-dimethylpyrimidine (ADMP) were investigated using the TiO2/UV system. The observed photocatalytic degradation behaviors of SMT, SA, and ADMP gave new insight into the degradation pathway of SMT. Especially, the formation of p-aminophenol during SMT decomposition, which until now has not been reported in previous studies concerning the photocatalytic decomposition of SMT and other sulfonamide antibiotics. These results indicate the existence of a novel photocatalytic degradation pathway for sulfonamides. The direct substitution of the sulfonamide group with a hydroxyl group is suggested.

  3. O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

    NASA Technical Reports Server (NTRS)

    Slanger, T. G.; Black, G.

    1978-01-01

    The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

  4. Bu4N+ alkoxide-initiated/autocatalytic addition reactions with organotrimethylsilanes.

    PubMed

    Das, Manas; O'Shea, Donal F

    2014-06-20

    The use of Me3SiO(-)/Bu4N(+) as a general activator of organotrimethylsilanes for addition reactions has been established. The broad scope of the method offers trimethylsilanes (including acetate, allyl, propargyl, benzyl, dithiane, heteroaryl, and aryl derivatives) as bench-stable organometallics that can be readily utilized as carbanion equivalents for synthesis. Reactions are achieved at rt without the requirement of specialized precautions that are commonplace for other organometallics.

  5. Synthesis of trifluoromethyl-containing vicinal diamines by asymmetric decarboxylative mannich addition reactions.

    PubMed

    Wu, Lingmin; Xie, Chen; Mei, Haibo; Dai, Yanling; Han, Jianlin; Soloshonok, Vadim A; Pan, Yi

    2015-03-20

    Herein is reported a study of asymmetric decarboxylative Mannich addition reactions between (Ss)-N-t-butylsulfinyl-3,3,3-trifluoroacetaldimine and Schiff bases derived from various aldehydes and lithium 2,2-diphenylglycinate. These reactions proceed with excellent diastereoselectivities and good chemical yields, providing a practical method for preparation of trifluoromethyl-containing vicinal diamines. The procedures can be conducted under convenient conditions, rendering this approach of high synthetic value.

  6. A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate.

    SciTech Connect

    Wu, D.; Wang, Q.; Assary, R. S.; Broadbelt, L. J.; Krilov, G.

    2011-01-01

    We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.

  7. A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate.

    PubMed

    Wu, Di; Wang, Qin; Assary, Rajeev S; Broadbelt, Linda J; Krilov, Goran

    2011-07-25

    We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.

  8. A Computational Approach to Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate

    SciTech Connect

    Wu, Di; Wang, Qin; Assary, Rajeev S.; Broadbelt, Linda J.; Krilov, Goran

    2011-07-25

    We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.

  9. Covalent binding of aniline to humic substances. 2. 15N NMR studies of nucleophilic addition reactions

    USGS Publications Warehouse

    Thorn, K.A.; Pettigrew, P.J.; Goldenberg, W.S.; Weber, E.J.

    1996-01-01

    Aromatic amines are known to undergo covalent binding with humic substances in the environment. Although previous studies have examined reaction conditions and proposed mechanisms, there has been no direct spectroscopic evidence for the covalent binding of the amines to the functional groups in humic substances. In order to further elucidate the reaction mechanisms, the Suwannee River and IHSS soil fulvic and humic acids were reacted with 15N-labeled aniline at pH 6 and analyzed using 15N NMR spectrometry. Aniline underwent nucleophilic addition reactions with the quinone and other carbonyl groups in the samples and became incorporated in the form of anilinohydroquinone, anilinoquinone, anilide, imine, and heterocyclic nitrogen, the latter comprising 50% or more of the bound amine. The anilide and anilinohydroquinone nitrogens were determined to be susceptible to chemical exchange by ammonia. In the case of Suwannee River fulvic acid, reaction under anoxic conditions and pretreatment with sodium borohydride or hydroxylamine prior to reaction under oxic conditions resulted in a decrease in the proportion of anilinohydroquinone nitrogen incorporated. The relative decrease in the incorporation of anilinohydroquinone nitrogen with respect to anilinoquinone nitrogen under anoxic conditions suggested that inter- or intramolecular redox reactions accompanied the nucleophilic addition reactions.

  10. [Use of the granulocytic myeloperoxidase release reaction to diagnose food additive allergies].

    PubMed

    Titova, N D

    2011-03-01

    Adverse reactions to food additives are difficult to diagnose due to the diversity of mechanisms involved in their realization and to the absence of reasonably reliable methods for their determination. Eighty-three patients with allergic diseases were examined using the granulocytic myeloperoxidase release reaction (MRR) to diagnose intolerance reactions to food additives (E102, E122, E124, E132, E110, E2111). MRR revealed leukocyte hypersensitivity to tartrazine in 10.8%, sunset yellow in 4.8%, ponceau in 13.2%, indigo carmine in 8.4%, carmoisine and benzoate in 9.6%. The findings were correlated with history data and the levels of IgE antibodies to these dyes. The practical use of the proposed MRR method makes it possible to enhance the accuracy of diagnosis of allergy to food additives. PMID:21584968

  11. Origin of fatty acid synthesis - Thermodynamics and kinetics of reaction pathways

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.

    1991-01-01

    The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, an alternative pathway of primitive fatty acid synthesis is proposed that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy. Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

  12. Conjugate addition reactions of N-carbamoyl-4-pyridones and 2,3-dihydropyridones with Grignard reagents in the absence of Cu(I) salts.

    PubMed

    Guo, Fenghai; Dhakal, Ramesh C; Dieter, R Karl

    2013-09-01

    N-Boc- and N-ethoxycarbonyl-4-pyridones and the resulting 2,3-dihydropyridones undergo 1,4-addition reactions with Grignard reagents in the presence of chlorotrimethylsilane (TMSCl) or BF3·Et2O in excellent yields. Copper catalysis is not required, and mechanistic considerations suggest that the reaction is proceeding by a conjugate addition pathway rather than by a pathway involving 1,2-addition to an intermediate pyridinium ion. TMSCl-mediated conjugate addition of Grignard reagents to 2-substituted-2,3-dihydropyridones gives the trans-2,6-disubstitued piperidinones stereoselectively, while cuprate reagents give either the trans or cis diastereomers or mixtures. PMID:23937057

  13. Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean.

    PubMed

    Keller, Markus A; Turchyn, Alexandra V; Ralser, Markus

    2014-04-25

    The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose-5-phosphate and the amino acid precursor erythrose-4-phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron-rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world.

  14. On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis

    PubMed Central

    Li, Bing; Chun, Hyonho; Zhao, Hongyu

    2014-01-01

    We introduce a nonparametric method for estimating non-gaussian graphical models based on a new statistical relation called additive conditional independence, which is a three-way relation among random vectors that resembles the logical structure of conditional independence. Additive conditional independence allows us to use one-dimensional kernel regardless of the dimension of the graph, which not only avoids the curse of dimensionality but also simplifies computation. It also gives rise to a parallel structure to the gaussian graphical model that replaces the precision matrix by an additive precision operator. The estimators derived from additive conditional independence cover the recently introduced nonparanormal graphical model as a special case, but outperform it when the gaussian copula assumption is violated. We compare the new method with existing ones by simulations and in genetic pathway analysis. PMID:26401064

  15. New Direction in Hydrogeochemical Transport Modeling: Incorporating Multiple Kinetic and Equilibrium Reaction Pathways

    SciTech Connect

    Steefel, C.I.

    2000-02-02

    At least two distinct kinds of hydrogeochemical models have evolved historically for use in analyzing contaminant transport, but each has important limitations. One kind, focusing on organic contaminants, treats biodegradation reactions as parts of relatively simple kinetic reaction networks with no or limited coupling to aqueous and surface complexation and mineral dissolution/precipitation reactions. A second kind, evolving out of the speciation and reaction path codes, is capable of handling a comprehensive suite of multicomponent complexation (aqueous and surface) and mineral precipitation and dissolution reactions, but has not been able to treat reaction networks characterized by partial redox disequilibrium and multiple kinetic pathways. More recently, various investigators have begun to consider biodegradation reactions in the context of comprehensive equilibrium and kinetic reaction networks (e.g. Hunter et al. 1998, Mayer 1999). Here we explore two examples of multiple equilibrium and kinetic reaction pathways using the reactive transport code GIMRT98 (Steefel, in prep.): (1) a computational example involving the generation of acid mine drainage due to oxidation of pyrite, and (2) a computational/field example where the rates of chlorinated VOC degradation are linked to the rates of major redox processes occurring in organic-rich wetland sediments overlying a contaminated aerobic aquifer.

  16. Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.

    PubMed

    Haines, Brandon E; Steussy, C Nicklaus; Stauffacher, Cynthia V; Wiest, Olaf

    2012-10-01

    HMG-CoA reductase catalyzes the four-electron reduction of HMG-CoA to mevalonate and is an enzyme of considerable biomedical relevance because of the impact of its statin inhibitors on public health. Although the reaction has been studied extensively using X-ray crystallography, there are surprisingly no computational studies that test the mechanistic hypotheses suggested for this complex reaction. Theozyme and quantum mechanical (QM)/molecular mechanical (MM) calculations up to the B3LYP/6-31g(d,p)//B3LYP/6-311++g(2d,2p) level of theory were employed to generate an atomistic description of the enzymatic reaction process and its energy profile. The models generated here predict that the catalytically important Glu83 is protonated prior to hydride transfer and that it acts as the general acid or base in the reaction. With Glu83 protonated, the activation energies calculated for the sequential hydride transfer reactions, 21.8 and 19.3 kcal/mol, are in qualitative agreement with the experimentally determined rate constant for the entire reaction (1 s(-1) to 1 min(-1)). When Glu83 is not protonated, the first hydride transfer reaction is predicted to be disfavored by >20 kcal/mol, and the activation energy is predicted to be higher by >10 kcal/mol. While not involved in the reaction as an acid or base, Lys267 is critical for stabilization of the transition state in forming an oxyanion hole with the protonated Glu83. Molecular dynamics simulations and MM/Poisson-Boltzmann surface area free energy calculations predict that the enzyme active site stabilizes the hemithioacetal intermediate better than the aldehyde intermediate. This suggests a mechanism in which cofactor exchange occurs before the breakdown of the hemithioacetal. Slowing the conversion to aldehyde would provide the enzyme with a mechanism to protect it from solvent and explain why the free aldehyde is not observed experimentally. Our results support the hypothesis that the pK(a) of an active site acidic

  17. Fundamental reaction pathway and free energy profile for proteasome inhibition by syringolin A (SylA)

    PubMed Central

    Wei, Donghui; Tang, Mingsheng; Zhan, Chang-Guo

    2015-01-01

    In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-Oγ directly by Thr1-Nz to form a zwitterionic intermediate. The next step is nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-Oγ atom. The last step is a proton transfer from Thr1-Nz to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal/mol, which is reasonably close to the activation free energy (∼22.4 – 23.0 kcal/mol) derived from available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome. PMID:26018983

  18. Formation Of Cometary Hydrocarbons By Hydrogen Addition Reactions On Cold Grains

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hitomi; Watanabe, N.; Kawakita, H.; Fukushima, T.

    2012-10-01

    Hydrogen addition reactions on cold grains are considered to play an important role to form many kinds of volatiles in low temperature conditions like molecular clouds or early solar nebula. We can investigate the physical conditions (e.g., temperature, gas density, and etc.) of the early solar nebula via chemical properties of the pristine bodies like comets. The hydrocarbons like C2H2 and C2H6 have been studied so far and C2H6 might be a product of successive hydrogen addition of C2H2 on the cold grain. To evaluate the efficiency of hydrogen addition reactions from C2H2 to C2H6 quantitatively, we conducted laboratory measurements of those reactions under multiple conditions of the samples (on H2O ice) at different temperatures (10, 20, 30 K) with the LASSIE apparatus at Hokkaido University. Our results provide more detailed information about those reactions than previous quantitative studies. We discuss about the reaction rates with different samples and conditions.

  19. Effects of Ga Addition on Interfacial Reactions Between Sn-Based Solders and Ni

    NASA Astrophysics Data System (ADS)

    Wang, Chao-Hong; Li, Kuan-Ting

    2016-07-01

    The use of Ga as a micro-alloying element in Sn-based solders can change the microstructure of solder joints to improve the mechanical properties, and even suppress the interfacial intermetallic compound (IMC) growth. This research investigated the effects of Ga addition (0.2-1 wt.%Ga) on the IMC formation and morphological evolution in the Sn-based solder joints with Ni substrate. In the soldering reaction at 250°C and with less than 0.2 wt.%Ga addition, the formed phase was Ni3Sn4. When the Ga addition increased to 0.5 wt.%, it changed to a thin Ni2Ga3 layer of ˜1 μm thick, which stably existed at the interface in the initial 1-h reaction. Subsequently, the whole Ni2Ga3 layer detached from the Ni substrate and drifted into the molten solder. The Ni3Sn4 phase became dominant in the later stage. Notably, the Ga addition significantly reduced the grain size of Ni3Sn4, resulting in the massive spalling of Ni3Sn4 grains. With 1 wt.%Ga addition, the Ni2Ga3 layer remained very thin with no significant growth, and it stably existed at the interface for more than 10 h. In addition, the solid-state reactions were examined at temperatures of 160°C to 200°C. With addition of 0.5 wt.%Ga, the Ni3Sn4 phase dominated the whole reaction. By contrast, with increasing to 1 wt.%Ga, only a thin Ni2Ga3 layer was found even after aging at 160°C for more than 1200 h. The 1 wt.%Ga addition in solder can effectively inhibit the Ni3Sn4 formation in soldering and the long-term aging process.

  20. Catalytic asymmetric direct-type 1,4-addition reactions of simple amides.

    PubMed

    Suzuki, Hirotsugu; Sato, Io; Yamashita, Yasuhiro; Kobayashi, Shū

    2015-04-01

    The development of catalytic asymmetric direct-type reactions of less acidic carbonyl compounds such as amides and esters has been a challenging theme in organic chemistry for decades. Here we describe the asymmetric direct 1,4-addition reactions of simple amides with α,β-unsaturated carbonyl compounds using a catalytic amount of a novel chiral catalyst consisting of a potassium base and a macrocyclic chiral crown ether. The desired 1,5-dicarbonyl compounds were obtained in high yields with excellent diastereo- and enantioselectivities. This is the first example of a highly enantioselective catalytic direct-type reaction of simple amides. In addition, the structure of the chiral potassium catalyst has been investigated by X-ray crystallographic, dynamic (1)H NMR, and MALDI-TOF MS analyses.

  1. Asymmetric Michael addition reactions of nitroalkanes to 2-furanones catalyzed by bifunctional thiourea catalysts.

    PubMed

    Bai, Zhushuang; Ji, Ling; Ge, Zemei; Wang, Xin; Li, Runtao

    2015-05-21

    The first bifunctional thiourea catalyzed asymmetric Michael addition reactions of nitroalkanes to 2-furanones are described. The highly functionalized γ-lactones with two or three consecutive stereogenic carbons were obtained in high yields (up to 99%), high diastereoselectivities (up to >20 : 1 dr) and enantioselectivities (up to >99% ee).

  2. Reaction pathways of biomass-derived oxygenates on noble metal surfaces

    NASA Astrophysics Data System (ADS)

    McManus, Jesse R.

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

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

    PubMed Central

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

    2015-01-01

    As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482

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

    PubMed

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

    2015-01-01

    As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482

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

    PubMed

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

    2015-04-10

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

  6. Electrode Reaction Pathway in Oxide Anode for Solid Oxide Fuel Cells

    NASA Astrophysics Data System (ADS)

    Li, Wenyuan

    Oxide anodes for solid oxide fuel cells (SOFC) with the advantage of fuel flexibility, resistance to coarsening, small chemical expansion and etc. have been attracting increasing interest. Good performance has been reported with a few of perovskite structure anodes, such as (LaSr)(CrMn)O3. However, more improvements need to be made before meeting the application requirement. Understanding the oxidation mechanism is crucial for a directed optimization, but it is still on the early stage of investigation. In this study, reaction mechanism of oxide anodes is investigated on doped YCrO 3 with H2 fuel, in terms of the origin of electrochemical activity, rate-determining steps (RDS), extension of reactive zone, and the impact from overpotential under service condition to those properties. H2 oxidation on the YCs anodes is found to be limited by charge transfer and H surface diffusion. A model is presented to describe the elementary steps in H2 oxidation. From the reaction order results, it is suggested that any models without taking H into the charge transfer step are invalid. The nature of B site element determines the H2 oxidation kinetics primarily. Ni displays better adsorption ability than Co. However, H adsorption ability of such oxide anode is inferior to that of Ni metal anode. In addition, the charge transfer step is directly associated with the activity of electrons in the anode; therefore it can be significantly promoted by enhancement of the electron activity. It is found that A site Ca doping improves the polarization resistance about 10 times, by increasing the activity of electrons to promote the charge transfer process. For the active area in the oxide anode, besides the traditional three-phase boundary (3PB), the internal anode surface as two-phase boundary (2PB) is proven to be capable of catalytically oxidizing the H2 fuel also when the bulk lattice is activated depending on the B site elements. The contribution from each part is estimated by switching

  7. Role of Carbon-Addition and Hydrogen-Migration Reactions in Soot Surface Growth.

    PubMed

    Zhang, Hong-Bo; Hou, Dingyu; Law, Chung K; You, Xiaoqing

    2016-02-11

    Using density functional theory and master equation modeling, we have studied the kinetics of small unsaturated aliphatic molecules reacting with polycyclic aromatic hydrocarbon (PAH) molecules having a diradical character. We have found that these reactions follow the mechanism of carbon addition and hydrogen migration (CAHM) on both spin-triplet and open-shell singlet potential energy surfaces at a rate that is about ten times those of the hydrogen-abstraction-carbon-addition (HACA) reactions at 1500 K in the fuel-rich postflame region. The results also show that the most active reaction sites are in the center of the zigzag edges of the PAHs. Furthermore, the reaction products are more likely to form straight rather than branched aliphatic side chains in the case of reacting with diacetylene. The computed rate constants are also found to be independent of pressure at conditions of interest in soot formation, and the activation barriers of the CAHM reactions are linearly correlated with the diradical characters.

  8. Role of Carbon-Addition and Hydrogen-Migration Reactions in Soot Surface Growth.

    PubMed

    Zhang, Hong-Bo; Hou, Dingyu; Law, Chung K; You, Xiaoqing

    2016-02-11

    Using density functional theory and master equation modeling, we have studied the kinetics of small unsaturated aliphatic molecules reacting with polycyclic aromatic hydrocarbon (PAH) molecules having a diradical character. We have found that these reactions follow the mechanism of carbon addition and hydrogen migration (CAHM) on both spin-triplet and open-shell singlet potential energy surfaces at a rate that is about ten times those of the hydrogen-abstraction-carbon-addition (HACA) reactions at 1500 K in the fuel-rich postflame region. The results also show that the most active reaction sites are in the center of the zigzag edges of the PAHs. Furthermore, the reaction products are more likely to form straight rather than branched aliphatic side chains in the case of reacting with diacetylene. The computed rate constants are also found to be independent of pressure at conditions of interest in soot formation, and the activation barriers of the CAHM reactions are linearly correlated with the diradical characters. PMID:26799641

  9. Reaction products of amido-amine and epoxide useful as fuel additives

    SciTech Connect

    Efner, H.F.

    1988-04-12

    A method for reducing engine deposits in an internal combustion engine is described comprising the addition of a detergent fuel additive package to a hydrocarbon fuel for the engine. The fuel detergent is added in an amount effective to reduce deposits and the hydrocarbon fuel is used with detergent additive as fuel in an internal combustion engine. The detergent fuel additive package comprises: (1) a fuel detergent additive that is the reaction product prepared by reacting (a) vegetable oil or (b) higher carboxylic acid chosen from (i) aliphatic fatty acids having 10-25 carbon atoms and (ii) aralkyl acids having 12-42 carbon atoms with (c) multiamine to obtain a fist product mixture with the first product mixture reacted with alklylene oxide to produce a second product mixture and (2) a fuel detergent additive solvent compatible with the fuels.

  10. The role of grain boundaries and transient porosity in rocks as fluid pathways for reaction front propagation

    NASA Astrophysics Data System (ADS)

    Jonas, Laura; John, Timm; King, Helen E.; Geisler, Thorsten; Putnis, Andrew

    2014-01-01

    The pseudomorphic replacement of Carrara marble by calcium phosphates was used as a model system in order to study the influence of different fluid pathways for reaction front propagation induced by fluid-rock interaction. In this model, grain boundaries present in the rock as well as the transient porosity structures developing throughout the replacement reaction enable the reaction front to progress further into the rock as well as to the center of each single grain until transformation is complete. Hydrothermal treatment of the marble using phosphate bearing solutions led to the formation of hydroxylapatite and β-TCP; the formation of the latter phase was probably promoted by the presence of ∼0.6 wt.% Mg in the parent carbonate phase. Completely transformed single grains show a distinctive zoning, both in composition and texture. Whereas areas next to the grain boundary consist of nearly pure hydroxylapatite and show a coarse porosity, areas close to the center of the single grains show a high amount of β-TCP and a very fine porous microstructure. If fluorine was added as an additional solution component, up to 3 wt.% of F were incorporated into the product apatite and the formation of β-TCP was avoided. The use of the isotope 18O as a chronometer for the replacement reaction makes it possible to reconstruct the chronological development of the calcium phosphate reaction front. Raman analysis revealed that the incorporation of 18O in the PO4 tetrahedron of hydroxylapatite results in the development of distinct profiles in the calcium phosphate reaction front perpendicular to the grain boundaries of the marble. Through the use of the 18O chronometer, it is possible to estimate and compare the time effectiveness of the different fluid pathways in this model system. The results demonstrate that the grain boundaries are an effective pathway enabling the fluid to penetrate the rock more than one order of magnitude faster compared to the newly developing channel

  11. Ion/molecule reactions of arsenic and phosphorus cluster ions: Ionization potentials and novel reaction pathways

    SciTech Connect

    Zimmerman, J.A.; Bach, S.B.H.; Watson, C.H.; Eyler, J.R. )

    1991-01-10

    Ionization potentials (IP's) for arsenic and phosphorus clusters (As{sub n}, n = 1-5; P{sub n}, n = 1-4) have been determined by gas-phase charge-transfer reactions. Arsenic and phosphorus cluster ions were generated by pulsed CO{sub 2} laser desorption from GaAs and InP substrates, mass-selected, thermalized, and allowed to react with compounds of known ionization potential in a Fourier transform ion cyclotron resonance mass spectrometer. The IP's for As{sub 3} and As{sub 5} previously unreported, as well as more accurate IP values for several of the other clusters, have been determined. Products and rate coefficients of some interesting reactions of the cluster ions with the charge-transfer agents are also reported.

  12. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

    PubMed

    Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

    2016-09-19

    Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions. PMID:27573794

  13. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

    PubMed

    Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

    2016-09-19

    Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions.

  14. Peptide-Catalyzed Stereoselective Conjugate Addition Reactions of Aldehydes to Maleimide.

    PubMed

    Grünenfelder, Claudio E; Kisunzu, Jessica K; Wennemers, Helma

    2016-07-18

    The tripeptide H-dPro-Pro-Asn-NH2 is presented as a catalyst for asymmetric conjugate addition reactions of aldehydes to maleimide. The peptidic catalyst promotes the reaction between various aldehydes and unprotected maleimide with high stereoselectivities and yields. The obtained products were readily derivatized to the corresponding pyrrolidines, lactams, lactones, and peptide-like compounds. (1) H NMR spectroscopic, crystallographic, and computational investigations provided insight into the conformational properties of H-dPro-Pro-Asn-NH2 and revealed the importance of hydrogen bonding between the peptide and maleimide for catalyzing the stereoselective C-C bond formation.

  15. Helical inversion reaction pathway for π/ π stacking in aromatic compounds

    NASA Astrophysics Data System (ADS)

    Muraoka, Azusa; Ushiyama, Hiroshi; Yamashita, Koichi

    2013-03-01

    Polyaromatics have the π/ π stacking interaction, which shows that two aromatic units preferentially interact in a parallel-displaced orientation, such as the crystal packing of organic molecules. Recently, π/ π stacking compounds have become of interest in the photocatalysis solor energy transformational materials. In particular, the stable configurations of neutral and cationic o-phenylenes have helical tightly packed n-phenylenes with π/ π stacking interactions. To investigate helical inversion pathways, we have studied theoretically the stable and transition-state geometries of neutral and cationic o-phenylenes using the density functional theory method. We have found that o-phenylenes follow an inversion reaction pathway with three transition-states in which the configuration of each phenylene is inverted. This means that o-phenylenes cannot convert from right- to left-handed geometry at once; however, we suggest a step-by-step reaction pathway through the three transition-state structures.

  16. Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  17. Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: Unexpected substituent effects

    PubMed Central

    Yao, Min; Tu, Wenlong; Chen, Xi; Zhan, Chang-Guo

    2013-01-01

    It has been difficult to directly measure the spontaneous hydrolysis rate of urea and, thus, 1,1,3,3-tetramethylurea (Me4U) was used as a model to determine the “experimental” rate constant for urea hydrolysis. The use of Me4U was based on an assumption that the rate of urea hydrolysis should be 2.8 times that of Me4U hydrolysis because the rate of acetamide hydrolysis is 2.8 times that of N,N-dimethyl-acetamide hydrolysis. The present first-principles electronic-structure calculations on the competing non-enzymatic hydrolysis pathways have demonstrated that the dominant pathway is the neutral hydrolysis via the CN addition for both urea (when pH<~11.6) and Me4U (regardless of pH), unlike the non-enzymatic hydrolysis of amides where alkaline hydrolysis is dominant. Based on the computational data, the substituent shift of free energy barrier calculated for the neutral hydrolysis is remarkably different from that for the alkaline hydrolysis, and the rate constant for the urea hydrolysis should be ~1.3×109-fold lower than that (4.2×10−12 s−1) measured for the Me4U hydrolysis. As a result, the rate enhancement and catalytic proficiency of urease should be 1.2×1025 and 3×1027 M−1, respectively, suggesting that urease surpasses proteases and all other enzymes in its power to enhance the rate of reaction. All of the computational results are consistent with available experimental data for Me4U, suggesting that the computational prediction for urea is reliable. PMID:24097048

  18. Fluorescent probes for tracking the transfer of iron-sulfur cluster and other metal cofactors in biosynthetic reaction pathways.

    PubMed

    Vranish, James N; Russell, William K; Yu, Lusa E; Cox, Rachael M; Russell, David H; Barondeau, David P

    2015-01-14

    Iron-sulfur (Fe-S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe-S cluster synthesis and transfer reactions. Here we present fusion protein- and intein-based fluorescent labeling strategies that can probe Fe-S cluster binding. The fluorescence is sensitive to different cluster types ([2Fe-2S] and [4Fe-4S] clusters), ligand environments ([2Fe-2S] clusters on Rieske, ferredoxin (Fdx), and glutaredoxin), and cluster oxidation states. The power of this approach is highlighted with an extreme example in which the kinetics of Fe-S cluster transfer reactions are monitored between two Fdx molecules that have identical Fe-S spectroscopic properties. This exchange reaction between labeled and unlabeled Fdx is catalyzed by dithiothreitol (DTT), a result that was confirmed by mass spectrometry. DTT likely functions in a ligand substitution reaction that generates a [2Fe-2S]-DTT species, which can transfer the cluster to either labeled or unlabeled Fdx. The ability to monitor this challenging cluster exchange reaction indicates that real-time Fe-S cluster incorporation can be tracked for a specific labeled protein in multicomponent assays that include several unlabeled Fe-S binding proteins or other chromophores. Such advanced kinetic experiments are required to untangle the intricate networks of transfer pathways and the factors affecting flux through branch points. High sensitivity and suitability with high-throughput methodology are additional benefits of this approach. We anticipate that this cluster detection methodology will transform the study of Fe-S cluster pathways and potentially other metal cofactor biosynthetic pathways.

  19. 4-Trifluoromethyl-p-quinols as dielectrophiles: three-component, double nucleophilic addition/aromatization reactions

    PubMed Central

    Dong, Jinhuan; Shi, Lou; Pan, Ling; Xu, Xianxiu; Liu, Qun

    2016-01-01

    In recent years, numerous methods have emerged for the synthesis of trifluoromethylated arenes based on the late-stage introduction of a trifluoromethyl group onto an aryl ring. In sharp comparison, the synthesis of trifluoromethylated arenes based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon has rarely been addressed. It has been found that 4-trifluoromethyl-p-quinol silyl ethers, the readily available and relatively stable compounds, can act as dielectrophiles to be applied to multi-component reactions for the synthesis of various trifluoromethylated arenes. Catalyzed by In(OTf)3, 4-trifluoromethyl-p-quinol silyl ethers react with C-, N-, and S-nucleophiles, respectively, in a regiospecific 1,2-addition manner to generate the corresponding highly reactive electrophilic intermediates. Further reaction of the in-situ generated electrophiles with a C-nucleophile followed by spontaneous aromatization enables the construction of functionalized trifluoromethyl arenes. This three-component, double nucleophilic addition/aromatization reaction based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon provides a divergent strategy for the synthesis of trifluoromethylated arenes under mild reaction conditions in a single operation. PMID:27246540

  20. 4-Trifluoromethyl-p-quinols as dielectrophiles: three-component, double nucleophilic addition/aromatization reactions.

    PubMed

    Dong, Jinhuan; Shi, Lou; Pan, Ling; Xu, Xianxiu; Liu, Qun

    2016-06-01

    In recent years, numerous methods have emerged for the synthesis of trifluoromethylated arenes based on the late-stage introduction of a trifluoromethyl group onto an aryl ring. In sharp comparison, the synthesis of trifluoromethylated arenes based on the pre-introduction of a trifluoromethyl group onto an "aromatic to be" carbon has rarely been addressed. It has been found that 4-trifluoromethyl-p-quinol silyl ethers, the readily available and relatively stable compounds, can act as dielectrophiles to be applied to multi-component reactions for the synthesis of various trifluoromethylated arenes. Catalyzed by In(OTf)3, 4-trifluoromethyl-p-quinol silyl ethers react with C-, N-, and S-nucleophiles, respectively, in a regiospecific 1,2-addition manner to generate the corresponding highly reactive electrophilic intermediates. Further reaction of the in-situ generated electrophiles with a C-nucleophile followed by spontaneous aromatization enables the construction of functionalized trifluoromethyl arenes. This three-component, double nucleophilic addition/aromatization reaction based on the pre-introduction of a trifluoromethyl group onto an "aromatic to be" carbon provides a divergent strategy for the synthesis of trifluoromethylated arenes under mild reaction conditions in a single operation.

  1. Dynamic effect of sodium-water reaction in fast flux test facility power addition sodium pipes

    SciTech Connect

    Huang, S.N.; Anderson, M.J.

    1990-03-01

    The Fast Flux Facility (FFTF) is a demonstration and test facility of the sodium-cooled fast breeder reactor. A power addition'' to the facility is being considered to convert some of the dumped, unused heat into electricity generation. Components and piping systems to be added are sodium-water steam generators, sodium loop extensions from existing dump heat exchangers to sodium-water steam generators, and conventional water/steam loops. The sodium loops can be subjected to the dynamic loadings of pressure pulses that are caused by postulated sodium leaks and subsequent sodium-water reaction in the steam generator. The existing FFTF secondary pipes and the new power addition sodium loops were evaluated for exposure to the dynamic effect of the sodium-water reaction. Elastic and simplified inelastic dynamic analyses were used in this feasibility study. The results indicate that both the maximum strain and strain range are within the allowable limits. Several cycles of the sodium-water reaction can be sustained by the sodium pipes that are supported by ordinary pipe supports and seismic restraints. Expensive axial pipe restraints to withstand the sodium-water reaction loads are not needed, because the pressure-pulse-induced alternating bending stresses act as secondary stresses and the pressure pulse dynamic effect is a deformation-controlled quantity and is self-limiting. 14 refs., 7 figs., 3 tabs.

  2. 4-Trifluoromethyl-p-quinols as dielectrophiles: three-component, double nucleophilic addition/aromatization reactions

    NASA Astrophysics Data System (ADS)

    Dong, Jinhuan; Shi, Lou; Pan, Ling; Xu, Xianxiu; Liu, Qun

    2016-06-01

    In recent years, numerous methods have emerged for the synthesis of trifluoromethylated arenes based on the late-stage introduction of a trifluoromethyl group onto an aryl ring. In sharp comparison, the synthesis of trifluoromethylated arenes based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon has rarely been addressed. It has been found that 4-trifluoromethyl-p-quinol silyl ethers, the readily available and relatively stable compounds, can act as dielectrophiles to be applied to multi-component reactions for the synthesis of various trifluoromethylated arenes. Catalyzed by In(OTf)3, 4-trifluoromethyl-p-quinol silyl ethers react with C-, N-, and S-nucleophiles, respectively, in a regiospecific 1,2-addition manner to generate the corresponding highly reactive electrophilic intermediates. Further reaction of the in-situ generated electrophiles with a C-nucleophile followed by spontaneous aromatization enables the construction of functionalized trifluoromethyl arenes. This three-component, double nucleophilic addition/aromatization reaction based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon provides a divergent strategy for the synthesis of trifluoromethylated arenes under mild reaction conditions in a single operation.

  3. Exploration of Unimolecular Gas-Phase Detoxication Pathways of Sarin and Soman: A Computational Study from the Perspective of Reaction Energetics and Kinetics.

    PubMed

    Ash, Tamalika; Debnath, Tanay; Banu, Tahamida; Das, Abhijit Kumar

    2016-09-19

    A mechanistic investigation has been carried out to explore all possible gas phase unimolecular isomerization as well as decomposition pathways of toxic organophosphorus compounds (OPCs), namely, sarin (GB) and soman (GD), which are better known as nerve agents. We have identified a total of 13 detoxication pathways for sarin, where the α-H, β-H, and γ-H take part in the H-transfer process. However, for soman, due to the presence of ω-H, three additional detoxication pathways are obtained, where the ω-H is involved in the H-transfer process. Among all the pathways, the D3 decomposition pathway, where the phosphorus oxoacid derivative and alkene are generated via the formation of a six-membered ring in the transition state, is identified as the most feasible pathway from the perspective of both activation barrier and reaction enthalpy values. Moreover, we have studied the feasibility of the isomerization and decomposition pathways by performing the reaction kinetics in the temperature range of 300 K-1000 K using the one-dimensional Rice-Ramsperger-Kassel-Marcus (RRKM) master equation. From the RRKM calculation also, D3 pathway is confirmed as the most feasible pathway for both OPCs. The rate constant values associated with the D3 pathway within the temperature range of 600 K-700 K imply that the degradation of the OPCs is possible within this temperature range via the D3 pathway, which is in good agreement with the earlier reported experimental result. It is also observed that at higher temperature range (∼900 K), the increased rate constant values of other detoxication pathways indicate that along with D3, all other pathways become more or less equally feasible. Therefore, the entire work provides a widespread idea about the kinetic as well as thermodynamic feasibility of the explored detoxication pathways of the titled OPCs. PMID:27509164

  4. Effect of method of heterogenization of ephedrine and reaction conditions on the enantioselectivity of Michael additions

    SciTech Connect

    Krotov, V.V.; Staroverov, S.M.; Nesterenko, P.N.; Lisichkin. G.V.

    1987-11-10

    A series of heterogeneous catalysts for asymmetric Michael additions was synthesized based on ephedrine chemically bound to the surface of silica. The length of the hydrocarbon chain binding the active center to the support surface affects the sign of rotation of the reaction product from the asymmetric addition of thiophenol to benzylideneacetophenone. Grafting ephedrine to the silica surface via a short hydrocarbon chain results in a change in the configuration of the reaction product. Silanol groups on the silica surface are involved in the transition state, as evidenced by data obtained using silica which has been exhaustively treated with trimethylchlorosilane. The absolute specific rotation of 1,3-diphenyl-3-thiophenylpropan-1-one has been established.

  5. Metal-Catalyzed β-Functionalization of Michael Acceptors through Reductive Radical Addition Reactions.

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

    Transition-metal-catalyzed radical reactions are becoming increasingly important in modern organic chemistry. They offer fascinating and unconventional ways for connecting molecular fragments that are often complementary to traditional methods. In particular, reductive radical additions to α,β-unsaturated compounds have recently gained substantial attention as a result of their broad applicability in organic synthesis. This Minireview critically discusses the recent landmark achievements in this field in context with earlier reports that laid the foundation for today's developments.

  6. Deracemizing organocatalyzed Michael addition reactions of 2-(arylthio)cyclobutanones with β-nitrostyrenes.

    PubMed

    Luridiana, Alberto; Frongia, Angelo; Aitken, David J; Guillot, Regis; Sarais, Giorgia; Secci, Francesco

    2016-04-01

    Organocatalyzed Michael addition reactions of 2-(arylthio)cyclobutanones with trans-β-nitrostyrenes have been carried out using a bifunctional thiourea-primary amine catalyst, providing diastereoisomerically and enantiomerically enriched 2-alkyl-2-(arylthio)cyclobutanones having two contiguous stereocenters of which one is a chiral quaternary center. The absolute configuration of these novel adducts was assigned by X-ray diffraction analysis and a transition-state model is proposed to explain the observed stereoselectivities.

  7. Metal-Catalyzed β-Functionalization of Michael Acceptors through Reductive Radical Addition Reactions.

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

    Transition-metal-catalyzed radical reactions are becoming increasingly important in modern organic chemistry. They offer fascinating and unconventional ways for connecting molecular fragments that are often complementary to traditional methods. In particular, reductive radical additions to α,β-unsaturated compounds have recently gained substantial attention as a result of their broad applicability in organic synthesis. This Minireview critically discusses the recent landmark achievements in this field in context with earlier reports that laid the foundation for today's developments. PMID:26471460

  8. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  9. Lewis base activation of Lewis acids: catalytic, enantioselective vinylogous aldol addition reactions.

    PubMed

    Denmark, Scott E; Heemstra, John R

    2007-07-20

    The generality of Lewis base catalyzed, Lewis acid mediated, enantioselective vinylogous aldol addition reactions has been investigated. The combination of silicon tetrachloride and chiral phosphoramides is a competent catalyst for highly selective additions of a variety of alpha,beta-unsaturated ketone-, 1,3-diketone-, and alpha,beta-unsaturated amide-derived dienolates to aldehydes. These reactions provided high levels of gamma-site selectivity for a variety of substitution patterns on the dienyl unit. Both ketone- and morpholine amide-derived dienol ethers afforded high enantio- and diastereoselectivity in the addition to conjugated aldehydes. Although alpha,beta-unsaturated ketone-derived dienolate did not react with aliphatic aldehydes, alpha,beta-unsaturated amide-derived dienolates underwent addition at reasonable rates affording high yields of vinylogous aldol product. The enantioselectivities achieved with the morpholine derived-dienolate in the addition to aliphatic aldehydes was the highest afforded to date with the silicon tetrachloride-chiral phosphoramide system. Furthermore, the ability to cleanly convert the morpholine amide to a methyl ketone was demonstrated.

  10. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface

    NASA Astrophysics Data System (ADS)

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-01

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH4) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH4 over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH4 decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C2) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface.

  11. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities.

    PubMed Central

    Ninio, J

    1987-01-01

    An alternative method for deriving rate equations in enzyme kinetics is presented. An enzyme is followed as it moves along the various pathways allowed by the reaction scheme. The times spent in various sections of the scheme and the pathway probabilities are computed, using simple rules. The rate equation obtains as a function of times and probabilities. The results are equivalent to those provided by the steady-state formalism. While the latter applies uniformly to all schemes, the formalism presented here requires adaptation to each additional class of schemes. However, it has the merit of allowing one to leave unspecified many details of the scheme, including topological ones. Furthermore, it allows one to decompose a scheme into subschemes, analyze the parts separately, and use the intermediate results to derive the rate equation of the complete scheme. The method is applied here to derive general equations for one- and two-entry site enzymes. PMID:3468503

  12. Influence of the heterogeneous reaction HCL + HOCl on an ozone hole model with hydrocarbon additions

    SciTech Connect

    Elliott, S.; Cicerone, R.J.; Turco, R.P.

    1994-02-20

    Injection of ethane or propane has been suggested as a means for reducing ozone loss within the Antarctic vortex because alkanes can convert active chlorine radicals into hydrochloric acid. In kinetic models of vortex chemistry including as heterogeneous processes only the hydrolysis and HCl reactions of ClONO{sub 2} and N{sub 2}O{sub 5}, parts per billion by volume levels of the light alkanes counteract ozone depletion by sequestering chlorine atoms. Introduction of the surface reaction of HCl with HOCl causes ethane to deepen baseline ozone holes and generally works to impede any mitigation by hydrocarbons. The increased depletion occurs because HCl + HOCl can be driven by HO{sub x} radicals released during organic oxidation. Following initial hydrogen abstraction by chlorine, alkane breakdown leads to a net hydrochloric acid activation as the remaining hydrogen atoms enter the photochemical system. Lowering the rate constant for reactions of organic peroxy radicals with ClO to 10{sup {minus}13} cm{sup 3} molecule{sup {minus}1} s{sup {minus}1} does not alter results, and the major conclusions are insensitive to the timing of the ethane additions. Ignoring the organic peroxy radical plus ClO reactions entirely restores remediation capabilities by allowing HO{sub x} removal independent of HCl. Remediation also returns if early evaporation of polar stratospheric clouds leaves hydrogen atoms trapped in aldehyde intermediates, but real ozone losses are small in such cases. 95 refs., 4 figs., 7 tabs.

  13. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes

    NASA Astrophysics Data System (ADS)

    Niemeyer, Zachary L.; Milo, Anat; Hickey, David P.; Sigman, Matthew S.

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands.

  14. A Simple and Inexpensive Device for Slow, Controlled Addition of a Solution to a Reaction Mixture

    NASA Astrophysics Data System (ADS)

    Osvath, Peter

    1995-07-01

    A number of reactions require the slow and controlled addition of a solution containing one reagent to another. Attempting to control the flow rate over a number of hours using a conventional constant pressure addition funnel is a frustrating exercise; commercially available constant volume addition funnels are expensive and must be adjusted by trial and error each time a reaction is carried out. The use of an (expensive) peristaltic pump or syringe pump overcomes these problems but can introduce other complications. We have recently had occasion to carry out the synthesis of thioether macrocycles and cages requiring the slow and controlled addition of DMF solutions of (offensively odoriferous) thiols or (air-sensitive) thiolates to a reactant solution under nitrogen(1), Although the use of a syringe pump was called for, there are obvious difficulties associated with purging the solution and assembling such an apparatus under nitrogen, and we report a simple and inexpensive solution. A Male Luer Lock tip (recovered from a broken syringe) was sweated onto the flattened tip of a pressure-equalizing addition funnel and a syringe needle was attached. Judicious selection of needle length, bore size, and reactant volume can be used to control the addition time simply and reproducibly. With a 250-mL funnel, the flow rate changes by <25% from the beginning to the end of the addition. (In fact, a reduction in the rate of addition may even be advantageous as the reaction proceeds, the reagent in the receiving flask is consumed, its concentration drops, and the rate of reaction will decrease). A piece of fine Teflon tubing of appropriate length attached to the needle can be used to reduce the flow rate even further, but this is only necessary for very slow rates of addition. For example, the time of addition of 200 mL, of an ethanolic solution could be varied from approximately 5 minutes (150mm/17 gauge) to approximately 5 h (200mm/22 gauge), and once the addition time for a

  15. Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  16. S3S63 Terminal Ynamides: Synthesis, Coupling Reactions and Additions to Common Electrophiles

    PubMed Central

    Cook, Andrea M.

    2015-01-01

    Ynamides consist of a polarized triple bond that is directly attached to a nitrogen atom carrying a sulfonyl, an alkoxycarbonyl, an acyl or another electron withdrawing group. The triple bond polarization renders ynamides broadly useful building blocks with synthetic opportunities that go far beyond traditional alkyne chemistry. The versatile reactivity of ynamides in cycloadditions, cycloisomerizations, regioselective additions with various nucleophiles or electrophiles, ring-closing metathesis, and many other reactions has been investigated in detail during the past decades. A common feature of these methods is that the triple bond is consumed and either cleaved or transformed to a new functionality. The wealth of reports on these ynamide reactions is in stark contrast to the dearth of carbon-carbon bond formations that leave the triple bond of terminal ynamides intact. The recent introduction of effective synthetic methods for the preparation of terminal ynamides has set the stage to fully explore the synthetic potential of this intriguing class of compounds. This digest letter summarizes the most effective routes to terminal ynamides and the current state of selective nucleophilic addition, substitution and coupling reactions, including the first examples of asymmetric synthesis. PMID:26085692

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

    NASA Astrophysics Data System (ADS)

    Yu, Weiting; Chen, Jingguang G.

    2015-10-01

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

  18. Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage

    PubMed Central

    Radhakrishnan, Ravi

    2007-01-01

    By employing classical molecular dynamics, correlation analysis of coupling between slow and fast dynamical modes, and free energy (umbrella) sampling using classical as well as mixed quantum mechanics molecular mechanics force fields, we uncover a possible pathway for phosphoryl transfer in the self-cleaving reaction of the minimal hammerhead ribozyme. The significance of this pathway is that it initiates from the minimal hammerhead crystal structure and describes the reaction landscape as a conformational rearrangement followed by a covalent transformation. The delineated mechanism is catalyzed by two metal (Mg2+) ions, proceeds via an in-line-attack by CYT 17 O2′ on the scissile phosphorous (ADE 1.1 P), and is therefore consistent with the experimentally observed inversion configuration. According to the delineated mechanism, the coupling between slow modes involving the hammerhead backbone with fast modes in the cleavage site appears to be crucial for setting up the in-line nucleophilic attack. PMID:17545240

  19. Bimetallic oxidative addition involving radical intermediates in nickel-catalyzed alkyl-alkyl Kumada coupling reactions.

    PubMed

    Breitenfeld, Jan; Ruiz, Jesus; Wodrich, Matthew D; Hu, Xile

    2013-08-14

    Many nickel-based catalysts have been reported for cross-coupling reactions of nonactivated alkyl halides. The mechanistic understanding of these reactions is still primitive. Here we report a mechanistic study of alkyl-alkyl Kumada coupling catalyzed by a preformed nickel(II) pincer complex ([(N2N)Ni-Cl]). The coupling proceeds through a radical process, involving two nickel centers for the oxidative addition of alkyl halide. The catalysis is second-order in Grignard reagent, first-order in catalyst, and zero-order in alkyl halide. A transient species, [(N2N)Ni-alkyl(2)](alkyl(2)-MgCl), is identified as the key intermediate responsible for the activation of alkyl halide, the formation of which is the turnover-determining step of the catalysis.

  20. Enantioselective Visible-Light-Induced Radical-Addition Reactions to 3-Alkylidene Indolin-2-ones.

    PubMed

    Lenhart, Dominik; Bauer, Andreas; Pöthig, Alexander; Bach, Thorsten

    2016-05-01

    The title compounds underwent a facile and high-yielding addition reaction (19 examples, 66-99% yield) with various N-(trimethylsilyl)methyl-substituted amines upon irradiation with visible light and catalysis by a metal complex. If the alkylidene substituent is non-symmetric and if the reaction is performed in the presence of a chiral hydrogen-bonding template, products are obtained with significant enantioselectivity (58-72% ee) as a mixture of diastereoisomers. Mechanistic studies suggest a closed catalytic cycle for the photoactive metal complex. However, the silyl transfer from the amine occurs not only to the product, but also to the substrate, and interferes with the desired chirality transfer.

  1. Bimetallic oxidative addition involving radical intermediates in nickel-catalyzed alkyl-alkyl Kumada coupling reactions.

    PubMed

    Breitenfeld, Jan; Ruiz, Jesus; Wodrich, Matthew D; Hu, Xile

    2013-08-14

    Many nickel-based catalysts have been reported for cross-coupling reactions of nonactivated alkyl halides. The mechanistic understanding of these reactions is still primitive. Here we report a mechanistic study of alkyl-alkyl Kumada coupling catalyzed by a preformed nickel(II) pincer complex ([(N2N)Ni-Cl]). The coupling proceeds through a radical process, involving two nickel centers for the oxidative addition of alkyl halide. The catalysis is second-order in Grignard reagent, first-order in catalyst, and zero-order in alkyl halide. A transient species, [(N2N)Ni-alkyl(2)](alkyl(2)-MgCl), is identified as the key intermediate responsible for the activation of alkyl halide, the formation of which is the turnover-determining step of the catalysis. PMID:23865460

  2. Divergent Reaction Pathways for Phenol Arylation by Arynes: Synthesis of Helicenes and 2-Arylphenols

    PubMed Central

    Truong, Thanh; Daugulis, Olafs

    2013-01-01

    Two reactions of phenols with arynes have been developed. If LiTMP base is employed, arynes generated from aryl chlorides react with phenols to form helicenes. o-Arylation of phenols can be achieved by employing tBuONa base in the presence of AgOAc. Direct arylation of binol was achieved leading to the shortest pathway to o,o’-diarylbinols. PMID:24077102

  3. Carbenic vs. ionic mechanistic pathway in reaction of cyclohexanone with bromoform.

    PubMed

    Vitnik, Vesna D; Vitnik, Zeljko J; Juranić, Ivan O

    2012-10-01

    The extensive computation study was done to elucidate the mechanism of formation dibromoepoxide from cyclohexanone and bromoform. In this reaction, the formation of dihaloepoxide 2 is postulated as a key step that determines the distribution and stereochemistry of products. Two mechanistic paths of reaction were investigated: the addition of dibromocarbene to carbonyl group of ketone, and the addition of tribromomethyl carbanion to the same (C=O) group. The mechanisms for the addition reactions of dibromocarbenes and tribromomethyl carbanions with cyclohexanone have been investigated using ab initio HF/6-311++G** and MP2/6-311+G* level of theory. Solvent effects on these reactions have been explored by calculations which included a continuum polarizable conductor model (CPCM) for the solvent (H₂O). The calculations showed that both mechanisms are possible and are exothermic, but have markedly different activation energies.

  4. Glucose and fructose decomposition in subcritical and supercritical water: Detailed reaction pathway, mechanisms, and kinetics

    SciTech Connect

    Kabyemela, B.M.; Adschiri, T.; Malaluan, R.M.; Arai, K.

    1999-08-01

    The authors are developing a new catalyst-free process of cellulose decomposition in supercritical water. In their initial study on the cellulose decomposition in supercritical water, the main products of cellulose decomposition were found to be oligomers of glucose (cellobiose, cellotriose, etc.) and glucose at short residence times (400 C, 25 MPa, 0.05 s). The kinetics of glucose at these conditions can be useful in understanding the reaction pathways of cellulose. Experiments were performed on the products of glucose decomposition at short residence times to elucidate the reaction pathways and evaluate kinetics of glucose and fructose decomposition in sub- and supercritical water. The conditions were a temperature of 300--400 C and pressure of 25--40 MPa for extremely short residence times between 0.02 and 2 s. The products of glucose decomposition were fructose, a product of isomerization, 1,6-anhydroglucose, a product of dehydration, and erythrose and glyceraldehyde, products of C-C bond cleavage. Fructose underwent reactions similar to glucose except that it did not form 1,6-anhydroglucose and isomerization to glucose is negligible. The mechanism for the products formed from C-C bond cleavage could be explained by reverse aldol condensation and the double-bond rule of the respective enediols formed during the Lobry de Bruyn Alberda van Ekenstein transformation. The differential equations resulting from the proposed pathways were fit to experimental results to obtain the kinetic rate constants.

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

    PubMed

    Jin, Biao; Rolle, Massimo

    2016-03-01

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

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

    PubMed

    Jin, Biao; Rolle, Massimo

    2016-03-01

    The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces the multi-element isotope data observed in previous experimental studies. Furthermore, it precisely captures the dual element isotope trends characteristic of different reaction pathways as well as their range of variation consistent with observed bulk isotope fractionation. It was also possible to directly validate the model capability to predict the evolution of position-specific isotope ratios with available experimental data. Therefore, the approach is useful both for a mechanism-based evaluation of experimental results and as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. PMID:26708763

  7. High-resolution mineralogical characterization and biogeochemical modeling of uranium reaction pathways at the FRC

    SciTech Connect

    Chen Zhu

    2006-06-15

    High-Resolution Mineralogical Characterization and Biogeochemical Modeling of Uranium Reduction Pathways at the Oak Ridge Field-Research Center (FRC) Chen Zhu, Indiana University, David R. Veblen, Johns Hopkins University We have successfully completed a proof-of-concept, one-year grant on a three-year proposal from the former NABIR program, and here we seek additional two-year funding to complete and publish the research. Using a state-of-the-art 300-kV, atomic resolution, Field Emission Gun Transmission Electron Microscope (TEM), we have successfully identified three categories of mineral hosts for uranium in contaminated soils: (1) iron oxides; (2) mixed manganese-iron oxides; and (3) uranium phosphates. Method development using parallel electron energy loss spectroscopy (EELS) associated with the TEM shows great promise for characterizing the valence states of immobilized U during bioremediation. We have also collected 27 groundwater samples from two push-pull field biostimulation tests, which form two time series from zero to approximately 600 hours. The temporal evolution in major cations, anions, trace elements, and the stable isotopes 34S, 18O in sulfate, 15N in nitrate, and 13C in dissolved inorganic carbon (DIC) clearly show that biostimulation resulted in reduction of nitrate, Mn(IV), Fe(III), U(VI), sulfate, and Tc(VII), and these reduction reactions were intimately coupled with a complex network of inorganic reactions evident from alkalinity, pH, Na, K, Mg, and Ca concentrations. From these temporal trends, apparent zero order rates were regressed. However, our extensive suite of chemical and isotopic data sets, perhaps the first and only comprehensive data set available at the FRC, show that the derived rates from these field biostimulation experiments are composite and lump-sum rates. There were several reactions that were occurring at the same time but were masked by these pseudo-zero order rates. A reaction-path model comprising a total of nine

  8. Multiple Pathways Suppress Telomere Addition to DNA Breaks in the Drosophila Germline

    PubMed Central

    Beaucher, Michelle; Zheng, Xiao-Feng; Amariei, Flavia; Rong, Yikang S.

    2012-01-01

    Telomeres protect chromosome ends from being repaired as double-strand breaks (DSBs). Just as DSB repair is suppressed at telomeres, de novo telomere addition is suppressed at the site of DSBs. To identify factors responsible for this suppression, we developed an assay to monitor de novo telomere formation in Drosophila, an organism in which telomeres can be established on chromosome ends with essentially any sequence. Germline expression of the I-SceI endonuclease resulted in precise telomere formation at its cut site with high efficiency. Using this assay, we quantified the frequency of telomere formation in different genetic backgrounds with known or possible defects in DNA damage repair. We showed that disruption of DSB repair factors (Rad51 or DNA ligase IV) or DSB sensing factors (ATRIP or MDC1) resulted in more efficient telomere formation. Interestingly, partial disruption of factors that normally regulate telomere protection (ATM or NBS) also led to higher frequencies of telomere formation, suggesting that these proteins have opposing roles in telomere maintenance vs. establishment. In the ku70 mutant background, telomere establishment was preceded by excessive degradation of DSB ends, which were stabilized upon telomere formation. Most strikingly, the removal of ATRIP caused a dramatic increase in telomeric retrotransposon attachment to broken ends. Our study identifies several pathways thatsuppress telomere addition at DSBs, paving the way for future mechanistic studies. PMID:22446318

  9. Oxidative degradation of decabromodiphenyl ether (BDE 209) by potassium permanganate: reaction pathways, kinetics, and mechanisms assisted by density functional theory calculations.

    PubMed

    Shi, Jiaqi; Qu, Ruijuan; Feng, Mingbao; Wang, Xinghao; Wang, Liansheng; Yang, Shaogui; Wang, Zunyao

    2015-04-01

    This study found that decabromodiphenyl ether (BDE 209) could be oxidized effectively by potassium permanganate (KMnO4) in sulfuric acid medium. A total of 15 intermediate oxidative products were detected. The reaction pathways were proposed, which primarily included cleavage of the ether bond to form pentabromophenol. Direct oxidation on the benzene ring also played an important role because hydroxylated polybrominated diphenyl ethers (PBDEs) were produced during the oxidation process. The degradation occurred dramatically in the first few minutes and fitted pseudo-first-order kinetics. Increasing the water content decelerated the reaction rate, whereas increasing the temperature facilitated the reaction. In addition, density functional theory (DFT) was employed to determine the frontier molecular orbital (FMO) and frontier electron density (FED) of BDE 209 and the oxidative products. The theoretical calculation results confirmed the proposed reaction pathways. PMID:25751737

  10. Oxidative degradation of decabromodiphenyl ether (BDE 209) by potassium permanganate: reaction pathways, kinetics, and mechanisms assisted by density functional theory calculations.

    PubMed

    Shi, Jiaqi; Qu, Ruijuan; Feng, Mingbao; Wang, Xinghao; Wang, Liansheng; Yang, Shaogui; Wang, Zunyao

    2015-04-01

    This study found that decabromodiphenyl ether (BDE 209) could be oxidized effectively by potassium permanganate (KMnO4) in sulfuric acid medium. A total of 15 intermediate oxidative products were detected. The reaction pathways were proposed, which primarily included cleavage of the ether bond to form pentabromophenol. Direct oxidation on the benzene ring also played an important role because hydroxylated polybrominated diphenyl ethers (PBDEs) were produced during the oxidation process. The degradation occurred dramatically in the first few minutes and fitted pseudo-first-order kinetics. Increasing the water content decelerated the reaction rate, whereas increasing the temperature facilitated the reaction. In addition, density functional theory (DFT) was employed to determine the frontier molecular orbital (FMO) and frontier electron density (FED) of BDE 209 and the oxidative products. The theoretical calculation results confirmed the proposed reaction pathways.

  11. Hydrogen generation from alcohols catalyzed by ruthenium-triphenylphosphine complexes: multiple reaction pathways.

    PubMed

    Sieffert, Nicolas; Bühl, Michael

    2010-06-16

    We report a comprehensive density functional theory (DFT) study of the mechanism of the methanol dehydrogenation reaction catalyzed by [RuH(2)(H(2))(PPh(3))(3)]. Using the B97-D dispersion-corrected functional, four pathways have been fully characterized, which differ in the way the critical beta-hydrogen transfer step is brought about (e.g., by prior dissociation of one PPh(3) ligand). All these pathways are found to be competitive (DeltaG(++) = 27.0-32.1 kcal/mol at 150 degrees C) and strongly interlocked. The reaction can thus follow multiple reaction channels, a feature which is expected to be at the origin of the good kinetics of this system. Our results also point to the active role of PPh(3) ligands, which undergo significant conformational changes as the reaction occurs, and provide insights into the role of the base, which acts as a "co-catalyst" by facilitating proton transfers within active species. Activation barriers decrease on going from methanol to ethanol and 2-propanol substrates, in accord with experiment. PMID:20481632

  12. Oxidation of antibiotics during water treatment with potassium permanganate: reaction pathways and deactivation.

    PubMed

    Hu, Lanhua; Stemig, Amanda M; Wammer, Kristine H; Strathmann, Timothy J

    2011-04-15

    Recent work demonstrates that three widely administered antibiotics (ciprofloxacin, lincomycin, and trimethoprim) are oxidized by potassium permanganate [KMnO(4), Mn(VII)] under conditions relevant to water treatment operations. However, tests show that little to no mineralization occurs during reactions with Mn(VII), so studies were undertaken to characterize the reaction products and pathways and to assess the effects of Mn(VII)-mediated transformations on the antibacterial activity of solutions. Several oxidation products were identified for each antibiotic by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For ciprofloxacin, 12 products were identified, consistent with oxidation of the tertiary aromatic and secondary aliphatic amine groups on the piperazine ring and the cyclopropyl group. For lincomycin, seven products were identified that indicate structural changes to the pyrrolidine ring and thioether group. For trimethoprim, seven products were identified, consistent with Mn(VII) reaction at C═C double bonds on the pyrimidine ring and the bridging methylene group. Oxidation pathways are proposed based on the identified products. Bacterial growth inhibition bioassays (E. coli DH5α) show that the mixture of products resulting from Mn(VII) reactions with the antibiotics collectively retain negligible antibacterial potency in comparison to the parent antibiotics. These results suggest that permanganate can be an effective reagent for eliminating the pharmaceutical activity of selected micropollutants during drinking water treatment.

  13. Ligand- and base-free Pd(II)-catalyzed controlled switching between oxidative Heck and conjugate addition reactions.

    PubMed

    Walker, Sarah E; Boehnke, Julian; Glen, Pauline E; Levey, Steven; Patrick, Lisa; Jordan-Hore, James A; Lee, Ai-Lan

    2013-04-19

    A simple change of solvent allows controlled and efficient switching between oxidative Heck and conjugate addition reactions on cyclic Michael acceptor substrates, catalyzed by a cationic Pd(II) catalyst system. Both reactions are ligand- and base-free and tolerant of air and moisture, and the controlled switching sheds light on some of the factors which favor one reaction over the other.

  14. Precipitation Reactions in Age-Hardenable Alloys During Laser Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Jägle, Eric A.; Sheng, Zhendong; Wu, Liang; Lu, Lin; Risse, Jeroen; Weisheit, Andreas; Raabe, Dierk

    2016-03-01

    We describe and study the thermal profiles experienced by various age-hardenable alloys during laser additive manufacturing (LAM), employing two different manufacturing techniques: selective laser melting and laser metal deposition. Using scanning electron microscopy and atom probe tomography, we reveal at which stages during the manufacturing process desired and undesired precipitation reactions can occur in age-hardenable alloys. Using examples from a maraging steel, a nickel-base superalloy and a scandium-containing aluminium alloy, we demonstrate that precipitation can already occur during the production of the powders used as starting material, during the deposition of material (i.e. during solidification and subsequent cooling), during the intrinsic heat treatment effected by LAM (i.e. in the heat affected zones) and, naturally, during an ageing post-heat treatment. These examples demonstrate the importance of understanding and controlling the thermal profile during the entire additive manufacturing cycle of age-hardenable materials including powder synthesis.

  15. Resonant-pattern formation induced by additive noise in periodically forced reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Wang, Hongli; Zhang, Ke; Ouyang, Qi

    2006-09-01

    We report frequency-locked resonant patterns induced by additive noise in periodically forced reaction-diffusion Brusselator model. In the regime of 2:1 frequency-locking and homogeneous oscillation, the introduction of additive noise, which is colored in time and white in space, generates and sustains resonant patterns of hexagons, stripes, and labyrinths which oscillate at half of the forcing frequency. Both the noise strength and the correlation time control the pattern formation. The system transits from homogeneous to hexagons, stripes, and to labyrinths successively as the noise strength is adjusted. Good frequency-locked patterns are only sustained by the colored noise and a finite time correlation is necessary. At the limit of white noise with zero temporal correlation, irregular patterns which are only nearly resonant come out as the noise strength is adjusted. The phenomenon induced by colored noise in the forced reaction-diffusion system is demonstrated to correspond to noise-induced Turing instability in the corresponding forced complex Ginzburg-Landau equation.

  16. Resonant-pattern formation induced by additive noise in periodically forced reaction-diffusion systems.

    PubMed

    Wang, Hongli; Zhang, Ke; Ouyang, Qi

    2006-09-01

    We report frequency-locked resonant patterns induced by additive noise in periodically forced reaction-diffusion Brusselator model. In the regime of 2:1 frequency-locking and homogeneous oscillation, the introduction of additive noise, which is colored in time and white in space, generates and sustains resonant patterns of hexagons, stripes, and labyrinths which oscillate at half of the forcing frequency. Both the noise strength and the correlation time control the pattern formation. The system transits from homogeneous to hexagons, stripes, and to labyrinths successively as the noise strength is adjusted. Good frequency-locked patterns are only sustained by the colored noise and a finite time correlation is necessary. At the limit of white noise with zero temporal correlation, irregular patterns which are only nearly resonant come out as the noise strength is adjusted. The phenomenon induced by colored noise in the forced reaction-diffusion system is demonstrated to correspond to noise-induced Turing instability in the corresponding forced complex Ginzburg-Landau equation. PMID:17025732

  17. Evaluating reaction pathways of hydrothermal abiotic organic synthesis at elevated temperatures and pressures using carbon isotopes

    NASA Astrophysics Data System (ADS)

    Fu, Qi; Socki, Richard A.; Niles, Paul B.

    2015-04-01

    Experiments were performed to better understand the role of environmental factors on reaction pathways and corresponding carbon isotope fractionations during abiotic hydrothermal synthesis of organic compounds using piston cylinder apparatus at 750 °C and 5.5 kbars. Chemical compositions of experimental products and corresponding carbon isotopic values were obtained by a Pyrolysis-GC-MS-IRMS system. Alkanes (methane and ethane), straight-chain saturated alcohols (ethanol and n-butanol) and monocarboxylic acids (formic and acetic acids) were generated with ethanol being the only organic compound with higher δ13C than CO2. CO was not detected in experimental products owing to the favorable water-gas shift reaction under high water pressure conditions. The pattern of δ13C values of CO2, carboxylic acids and alkanes are consistent with their equilibrium isotope relationships: CO2 > carboxylic acids > alkanes, but the magnitude of the fractionation among them is higher than predicted isotope equilibrium values. In particular, the isotopic fractionation between CO2 and CH4 remained constant at ∼31‰, indicating a kinetic effect during CO2 reduction processes. No "isotope reversal" of δ13C values for alkanes or carboxylic acids was observed, which indicates a different reaction pathway than what is typically observed during Fischer-Tropsch synthesis under gas phase conditions. Under constraints imposed in experiments, the anomalous 13C isotope enrichment in ethanol suggests that hydroxymethylene is the organic intermediate, and that the generation of other organic compounds enriched in 12C were facilitated by subsequent Rayleigh fractionation of hydroxymethylene reacting with H2 and/or H2O. Carbon isotope fractionation data obtained in this study are instrumental in assessing the controlling factors on abiotic formation of organic compounds in hydrothermal systems. Knowledge on how environmental conditions affect reaction pathways of abiotic synthesis of organic

  18. Influence of Catalyst Structure and Reaction Conditions on Anti- vs. Syn-Aminopalladation Pathways in Pd-Catalyzed Alkene Carboamination Reactions of N-Allyl Sulfamides

    PubMed Central

    Fornwald, Ryan M.; Fritz, Jonathan A.

    2014-01-01

    The Pd-catalyzed coupling of N-allyl sulfamides with aryl and alkenyl triflates to afford cyclic sulfamide products is described. In contrast to other known Pd-catalyzed alkene carboamination reactions, these transformations may be selectively induced to occur by way of either anti- or syn-aminopalladation mechanistic pathways by modifying catalyst structure and reaction conditions. PMID:24938206

  19. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane

    DOE PAGES

    Rotavera, Brandon; Zádor, Judit; Welz, Oliver; Sheps, Leonid; Scheer, Adam M.; Savee, John D.; Akbar Ali, Mohamad; Lee, Taek Soon; Simmons, Blake A.; Osborn, David L.; et al

    2014-09-19

    The product formation from R + O2 reactions relevant to low-temperature autoignition chemistry was studied for 2,5-dimethylhexane, a symmetrically branched octane isomer, at 550 and 650 K using Cl-atom initiated oxidation and multiplexed photoionization mass spectrometry (MPIMS). The interpretation of time- and photon-energy-resolved mass spectra led to three specific results important to characterizing the initial oxidation steps: (1) quantified isomer-resolved branching ratios for HO2 + alkene channels; (2) 2,2,5,5-tetramethyltetrahydrofuran is formed in substantial yield from addition of O2 to tertiary 2,5-dimethylhex-2-yl followed by isomerization of the resulting ROO adduct to tertiary hydroperoxyalkyl (QOOH) and exhibits a positive dependence on temperaturemore » over the range covered leading to a higher flux relative to aggregate cyclic ether yield. The higher relative flux is explained by a 1,5-hydrogen atom shift reaction that converts the initial primary alkyl radical (2,5-dimethylhex-1-yl) to the tertiary alkyl radical 2,5-dimethylhex-2-yl, providing an additional source of tertiary alkyl radicals. Furthermore, quantum-chemical and master-equation calculations of the unimolecular decomposition of the primary alkyl radical reveal that isomerization to the tertiary alkyl radical is the most favorable pathway, and is favored over O2-addition at 650 K under the conditions herein. The isomerization pathway to tertiary alkyl radicals therefore contributes an additional mechanism to 2,2,5,5-tetramethyltetrahydrofuran formation; (3) carbonyl species (acetone, propanal, and methylpropanal) consistent with β-scission of QOOH radicals were formed in significant yield, indicating unimolecular QOOH decomposition into carbonyl + alkene + OH.« less

  20. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane

    SciTech Connect

    Rotavera, Brandon; Zádor, Judit; Welz, Oliver; Sheps, Leonid; Scheer, Adam M.; Savee, John D.; Akbar Ali, Mohamad; Lee, Taek Soon; Simmons, Blake A.; Osborn, David L.; Violi, Angela; Taatjes, Craig A.

    2014-09-19

    The product formation from R + O2 reactions relevant to low-temperature autoignition chemistry was studied for 2,5-dimethylhexane, a symmetrically branched octane isomer, at 550 and 650 K using Cl-atom initiated oxidation and multiplexed photoionization mass spectrometry (MPIMS). The interpretation of time- and photon-energy-resolved mass spectra led to three specific results important to characterizing the initial oxidation steps: (1) quantified isomer-resolved branching ratios for HO2 + alkene channels; (2) 2,2,5,5-tetramethyltetrahydrofuran is formed in substantial yield from addition of O2 to tertiary 2,5-dimethylhex-2-yl followed by isomerization of the resulting ROO adduct to tertiary hydroperoxyalkyl (QOOH) and exhibits a positive dependence on temperature over the range covered leading to a higher flux relative to aggregate cyclic ether yield. The higher relative flux is explained by a 1,5-hydrogen atom shift reaction that converts the initial primary alkyl radical (2,5-dimethylhex-1-yl) to the tertiary alkyl radical 2,5-dimethylhex-2-yl, providing an additional source of tertiary alkyl radicals. Furthermore, quantum-chemical and master-equation calculations of the unimolecular decomposition of the primary alkyl radical reveal that isomerization to the tertiary alkyl radical is the most favorable pathway, and is favored over O2-addition at 650 K under the conditions herein. The isomerization pathway to tertiary alkyl radicals therefore contributes an additional mechanism to 2,2,5,5-tetramethyltetrahydrofuran formation; (3) carbonyl species (acetone, propanal, and methylpropanal) consistent with β-scission of QOOH radicals were formed in significant yield, indicating unimolecular QOOH decomposition into carbonyl + alkene + OH.

  1. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane.

    PubMed

    Rotavera, Brandon; Zádor, Judit; Welz, Oliver; Sheps, Leonid; Scheer, Adam M; Savee, John D; Akbar Ali, Mohamad; Lee, Taek Soon; Simmons, Blake A; Osborn, David L; Violi, Angela; Taatjes, Craig A

    2014-11-01

    Product formation from R + O2 reactions relevant to low-temperature autoignition chemistry was studied for 2,5-dimethylhexane, a symmetrically branched octane isomer, at 550 and 650 K using Cl-atom initiated oxidation and multiplexed photoionization mass spectrometry (MPIMS). Interpretation of time- and photon-energy-resolved mass spectra led to three specific results important to characterizing the initial oxidation steps: (1) quantified isomer-resolved branching ratios for HO2 + alkene channels; (2) 2,2,5,5-tetramethyltetrahydrofuran is formed in substantial yield from addition of O2 to tertiary 2,5-dimethylhex-2-yl followed by isomerization of the resulting ROO adduct to tertiary hydroperoxyalkyl (QOOH) and exhibits a positive dependence on temperature over the range covered leading to a higher flux relative to aggregate cyclic ether yield. The higher relative flux is explained by a 1,5-hydrogen atom shift reaction that converts the initial primary alkyl radical (2,5-dimethylhex-1-yl) to the tertiary alkyl radical 2,5-dimethylhex-2-yl, providing an additional source of tertiary alkyl radicals. Quantum-chemical and master-equation calculations of the unimolecular decomposition of the primary alkyl radical reveal that isomerization to the tertiary alkyl radical is the most favorable pathway, and is favored over O2-addition at 650 K under the conditions herein. The isomerization pathway to tertiary alkyl radicals therefore contributes an additional mechanism to 2,2,5,5-tetramethyltetrahydrofuran formation; (3) carbonyl species (acetone, propanal, and methylpropanal) consistent with β-scission of QOOH radicals were formed in significant yield, indicating unimolecular QOOH decomposition into carbonyl + alkene + OH.

  2. Reaction Pathways and Energetics of Etheric C–O Bond Cleavage Catalyzed by Lanthanide Triflates

    SciTech Connect

    Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.

    2013-09-06

    Efficient and selective cleavage of etheric C-O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C-O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C-O cleavage occurs via a C-H → O-H proton transfer in concert with weakening of the C-O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C-O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.

  3. On the use of isovalued surfaces to determine molecule shape and reaction pathways.

    PubMed

    Purvis, G D

    1991-02-01

    Novel insights into local molecule structure and reactivity can be gained from viewing isovalued surfaces of the molecular electron density, electrostatic potential and molecular orbitals rendered as colored, 3-D objects. For example, drawing positive and negative electrostatic isopotential surfaces partitions the molecule into regions subject to nucleophilic or electrophilic attack. Similarly, coloring isodensity surfaces to indicate the magnitude of the gradient of the electron density maps the molecule surface into regions of high and low electronegativity. A basic understanding of reaction mechanisms can also come from viewing and manipulating isovalued surfaces. A theory of molecular interactions, based upon second-order perturbation theory, provides for the decomposition of the intermolecular interaction energy into steric, electrostatic and orbital interactions. Color figures illustrate the docking of reactant molecular densities, electrostatic potentials and orbitals on low-energy pathways. The figures are used to visualize the steric, electrostatic and orbital contributions to molecular interaction energy. The visualization not only identifies low-energy reaction pathways, but it frequently reveals local interactions which determine the magnitude of the total interaction energy. Similar insight is not easily obtained by simple evaluation of the total interaction energy. Approximate transition states, built from structures along low-energy approach pathways, are excellent starting points for transition state searches. PMID:2072126

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

    PubMed

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

    2007-05-17

    The Utah Surrogate Mechanism was extended in order to model a stoichiometric premixed cyclohexane flame (P = 30 Torr). Generic rates were assigned to reaction classes of hydrogen abstraction, beta scission, and isomerization, and the resulting mechanism was found to be adequate in describing the combustion chemistry of cyclohexane. Satisfactory results were obtained in comparison with the experimental data of oxygen, major products and important intermediates, which include major soot precursors of C2-C5 unsaturated species. Measured concentrations of immediate products of fuel decomposition were also successfully reproduced. For example, the maximum concentrations of benzene and 1,3-butadiene, two major fuel decomposition products via competing pathways, were predicted within 10% of the measured values. Ring-opening reactions compete with those of cascading dehydrogenation for the decomposition of the conjugate cyclohexyl radical. The major ring-opening pathways produce 1-buten-4-yl radical, molecular ethylene, and 1,3-butadiene. The butadiene species is formed via beta scission after a 1-4 internal hydrogen migration of 1-hexen-6-yl radical. Cascading dehydrogenation also makes an important contribution to the fuel decomposition and provides the exclusive formation pathway of benzene. Benzene formation routes via combination of C2-C4 hydrocarbon fragments were found to be insignificant under current flame conditions, inferred by the later concentration peak of fulvene, in comparison with benzene, because the analogous species series for benzene formation via dehydrogenation was found to be precursors with regard to parent species of fulvene. PMID:17388269

  5. Ring Walking/Oxidative Addition Reactions for the Controlled Synthesis of Conjugated Polymers

    SciTech Connect

    Bazan, Guillermo C

    2012-04-03

    Power conversion efficiencies of plastic solar cells depend strongly on the molecular weight characteristics of the semiconducting polymers used for their fabrication. The synthesis of these materials typically relies on transition metal mediated catalytic reactions. In many instances, the ideal structures cannot be attained because of deficiencies in these reactions, particularly when it comes to being able to achieve high number average molecular weights and narrow molecular weight distributions. Another important conjugated polymer structure of interest is one in which a single functional group is attached at the end group of the chain. Such systems would be ideal for modifying surface properties at interfaces and for labeling biomolecular probes used in fluorescent biosensors. To respond to the challenges above, our efforts have centered on the design of homogenous transition metal complexes that are easy to prepare and effective in carrying out living, or quasi-living, condensative chain polymerization reactions. The key mechanistic challenge for the success of this reaction is to force the insertion of one monomer unit at a time via a process that involves migration of the transition metal-containing fragment to one terminus of the polymer chain. Chain growth characteristics are therefore favored when the metal does not dissociate from the newly formed reductive elimination product. We have proposed that dissociation is disfavored by the formation of a -complex, in which the metal can sample various locations of the electronically delocalized framework, a process that we term ring-walking , and find the functionality where oxidative addition takes place. Success has been achieved in the nickel-mediated cross coupling reaction of Grignard reagents with aromatic halides by using bromo[1,2-bis(diphenylphosphino)ethane]phenylnickel. This reagent can yield poly(thiophene)s (one of the most widely used type of polymer in plastic solar cells) with excellent

  6. Direct vs. indirect pathway for nitrobenzene reduction reaction on a Ni catalyst surface: a density functional study.

    PubMed

    Mahata, Arup; Rai, Rohit K; Choudhuri, Indrani; Singh, Sanjay K; Pathak, Biswarup

    2014-12-21

    Density functional theory (DFT) calculations are performed to understand and address the previous experimental results that showed the reduction of nitrobenzene to aniline prefers direct over indirect reaction pathways irrespective of the catalyst surface. Nitrobenzene to aniline conversion occurs via the hydroxyl amine intermediate (direct pathway) or via the azoxybenzene intermediate (indirect pathway). Through our computational study we calculated the spin polarized and dispersion corrected reaction energies and activation barriers corresponding to various reaction pathways for the reduction of nitrobenzene to aniline over a Ni catalyst surface. The adsorption behaviour of the substrate, nitrobenzene, on the catalyst surface was also considered and the energetically most preferable structural orientation was elucidated. Our study indicates that the parallel adsorption behaviour of the molecules over a catalyst surface is preferable over vertical adsorption behaviour. Based on the reaction energies and activation barrier of the various elementary steps involved in direct or indirect reaction pathways, we find that the direct reduction pathway of nitrobenzene over the Ni(111) catalyst surface is more favourable than the indirect reaction pathway. PMID:25367892

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

    PubMed

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

    2016-03-01

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

  8. Carbonylation of myofibrillar proteins through the maillard pathway: effect of reducing sugars and reaction temperature.

    PubMed

    Villaverde, Adriana; Estévez, Mario

    2013-03-27

    Carbonylation is recognized as one of the most remarkable chemical modifications in oxidized proteins and is generally ascribed to the direct attack of free radicals to basic amino acid residues. The purpose of this work was to investigate the formation of specific carbonyls, α-aminoadipic and γ-glutamic semialdehydes (AAS and GGS, respectively), in myofibrillar proteins (MP) through a Maillard-type pathway in the presence of reducing sugars. The present study confirmed the concurrent formation of protein carbonyls and advanced glycation end-products (AGEs) during incubation (80 °C/48 h) of MP (4 mg/mL) in the presence of reducing sugars (0.5 M). Copper irons (10 μM) were found to promote the formation of protein carbonyls, and a specific inhibitor of the Maillard reaction (0.02 M pyridoxamine) blocked the carbonylation process which emphasize the occurrence of a Maillard-type pathway. The Maillard-mediated carbonylation occurred in a range of reducing sugars (0.02-0.5 M) and reaction temperatures (4-110 °C) compatible with food systems. Upcoming studies on this topic may contribute further to shed light on the complex interactions between protein oxidation and the Maillard reaction and the impact of the protein damage on food quality and human health.

  9. Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetics, and Rate Rule Optimizations for 2-Methylhexane.

    PubMed

    Mohamed, Samah Y; Cai, Liming; Khaled, Fethi; Banyon, Colin; Wang, Zhandong; Al Rashidi, Mariam J; Pitsch, Heinz; Curran, Henry J; Farooq, Aamir; Sarathy, S Mani

    2016-04-14

    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model's performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

  10. Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F(-) + CH3I.

    PubMed

    Carrascosa, Eduardo; Michaelsen, Tim; Stei, Martin; Bastian, Björn; Meyer, Jennifer; Mikosch, Jochen; Wester, Roland

    2016-07-14

    Ion-molecule reactions of the type X(-) + CH3Y are commonly assumed to produce Y(-) through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F(-) + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I(-) is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF(-) via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI](-) product ion. This [FHI](-) product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I(-). A similar trend is observed for the isoelectronic OH(-) + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy. PMID:26799548

  11. Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F– + CH3I

    PubMed Central

    2016-01-01

    Ion–molecule reactions of the type X– + CH3Y are commonly assumed to produce Y– through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F– + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I– is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF– via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI]− product ion. This [FHI]− product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I–. A similar trend is observed for the isoelectronic OH– + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy. PMID:26799548

  12. Reaction pathways and sources of OH groups in low temperature remote PECVD silicon dioxide thin films

    NASA Astrophysics Data System (ADS)

    Theil, J. A.; Tsu, D. V.; Lucovsky, G.

    1990-02-01

    Silicon oxides deposited by remote plasma-enhanced chemical-vapor deposition (Remote PECVD) can be grown under conditions which produce hydrogen-free SiO2, and under conditions which promote the incorporation of bonded-hydrogen in either SiH or SiOH groups, but generally not in both. In this paper, we investigate the relationship between the deposition conditions leading to OH incorporation, and other post-deposition pathway(s) by which OH can also be incorporated. Two ways by which OH can be incorporated into the oxides are by: (i) intrinsic pathways which are associated with the heterogeneous chemical reactions responsible for film growth; and (ii) extrinsic pathways which refer to incorporation after film deposition stops. The results of our experiments to date show no evidence to support the intrinsic process; all of the infrared (ir) detectable OH is shown to derive from post-deposition or extrinsic sources. We have found two distinct post-deposition sources, one from the deposition chamber ambient during cool-down and one from atmospheric moisture. Each of these sources has a particular spectroscopic signature. We show that OH incorporated from atmospheric moisture occurs as spatially correlated near-neighbor Si-OH groups, whereas OH groups incorporated in the deposition chamber ambient are randomly distributed in the SiO2 host material.

  13. Innocuous oil as an additive for reductive reactions involving zero valence iron

    SciTech Connect

    Cary, J.W.; Cantrell, K.J.

    1994-11-01

    Reductive reactions involving zero valence iron appear to hold promise for in situ remediation of sites containing chlorinated hydrocarbon solvents and certain reducible metals and radionuclides. Treatment involves the injection of metallic iron and the creation of low levels of dissolved oxygen in the aqueous phase through oxidation of the metallic iron. The use of a biodegradable immiscible and innocuous organic liquid such as vegetable oil as an additive offers several intriguing possibilities. The oil phase creates a large oil-water interface that is immobile with respect to flow in the aqueous phase. This phase will act as a trap for chlorinated hydrocarbons and could potentially increase the reaction efficiency of reductive dehalogenation of chlorinated hydrocarbons by the metallic iron. When iron particles are suspended in the oil before injection they are preferentially held in the oil phase and tend to accumulate at the oil-water interface. Thus oil injection can serve as a mechanism for creating a stable porous curtain of metallic iron in the vadose to maintain a low oxygen environment which will minimize the consumption of the iron by molecular oxygen.

  14. FORMATION OF POLYCYCLIC AROMATIC HYDROCARBONS AND THEIR GROWTH TO SOOT -A REVIEW OF CHEMICAL REACTION PATHWAYS. (R824970)

    EPA Science Inventory

    The generation by combustion processes of airborne species of current health concern such as polycyclic aromatic hydrocarbons (PAH) and soot particles necessitates a detailed understanding of chemical reaction pathways responsible for their formation. The present review discus...

  15. Helical-Peptide-Catalyzed Enantioselective Michael Addition Reactions and Their Mechanistic Insights.

    PubMed

    Ueda, Atsushi; Umeno, Tomohiro; Doi, Mitsunobu; Akagawa, Kengo; Kudo, Kazuaki; Tanaka, Masakazu

    2016-08-01

    Helical peptide foldamer catalyzed Michael addition reactions of nitroalkane or dialkyl malonate to α,β-unsaturated ketones are reported along with the mechanistic considerations of the enantio-induction. A wide variety of α,β-unsaturated ketones, including β-aryl, β-alkyl enones, and cyclic enones, were found to be catalyzed by the helical peptide to give Michael adducts with high enantioselectivities (up to 99%). On the basis of X-ray crystallographic analysis and depsipeptide study, the amide protons, N(2)-H and N(3)-H, at the N terminus in the α-helical peptide catalyst were crucial for activating Michael donors, while the N-terminal primary amine activated Michael acceptors through the formation of iminium ion intermediates.

  16. Pd(Quinox)-Catalyzed Allylic Relay Suzuki Reactions of Secondary Homostyrenyl Tosylates via Alkene-Assisted Oxidative Addition.

    PubMed

    Stokes, Benjamin J; Bischoff, Amanda J; Sigman, Matthew S

    2014-06-01

    Pd-catalyzed allylic relay Suzuki cross-coupling reactions of secondary alkyl tosylates, featuring a sterically-hindered oxidative addition and precise control of β-hydride elimination, are reported. The identification of a linear free energy relationship between the relative rates of substrate consumption and the electronic nature of the substrate alkene suggests that the oxidative addition requires direct alkene involvement. A study of the effect of chain length on the reaction outcome supports a chelation-controlled oxidative addition.

  17. Sequential aldol condensation-transition metal-catalyzed addition reactions of aldehydes, methyl ketones, and arylboronic acids.

    PubMed

    Liao, Yuan-Xi; Xing, Chun-Hui; Israel, Matthew; Hu, Qiao-Sheng

    2011-04-15

    Sequential aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reactions of arylboronic acids to form β-substituted ketones is described. By using the 1,1'-spirobiindane-7,7'-diol (SPINOL)-based phosphite, an asymmetric version of this type of sequential reaction, with up to 92% ee, was also realized. Our study provided an efficient method to access β-substituted ketones and might lead to the development of other sequential/tandem reactions with transition metal-catalyzed addition reactions as the key step.

  18. Secondary Pollutants from Ozone Reaction with Ventilation Filters and Degradation of Filter Media Additives

    SciTech Connect

    Destaillats, Hugo; Chen, Wenhao; Apte, Michael; Li, Nuan; Spears, Michael; Almosni, Jérémie; Brunner, Gregory; Zhang, Jianshun; Fisk, William J.

    2011-05-01

    Prior research suggests that chemical processes taking place on the surface of particle filters employed in buildings may lead to the formation of harmful secondary byproducts. We investigated ozone reactions with fiberglass, polyester, cotton/polyester and polyolefin filter media, as well as hydrolysis of filter media additives. Studies were carried out on unused media, and on filters that were installed for 3 months in buildings at two different locations in the San Francisco Bay Area. Specimens from each filter media were exposed to {approx}150 ppbv ozone in a flow tube under a constant flow of dry or humidified air (50percent RH). Ozone breakthrough was recorded for each sample over periods of {approx}1000 min; the ozone uptake rate was calculated for an initial transient period and for steady-state conditions. While ozone uptake was observed in all cases, we did not observe significant differences in the uptake rate and capacity for the various types of filter media tested. Most experiments were performed at an airflow rate of 1.3 L/min (face velocity = 0.013 m/s), and a few tests were also run at higher rates (8 to 10 L/min). Formaldehyde and acetaldehyde, two oxidation byproducts, were quantified downstream of each sample. Those aldehydes (m/z 31 and 45) and other volatile byproducts (m/z 57, 59, 61 and 101) were also detected in real-time using Proton-Transfer Reaction - Mass Spectrometry (PTR-MS). Low-ppbv byproduct emissions were consistently higher under humidified air than under dry conditions, and were higher when the filters were loaded with particles, as compared with unused filters. No significant differences were observed when ozone reacted over various types of filter media. Fiberglass filters heavily coated with impaction oil (tackifier) showed higher formaldehyde emissions than other samples. Those emissions were particularly high in the case of used filters, and were observed even in the absence of ozone, suggesting that hydrolysis of additives

  19. Shining Light on Copper: Unique Opportunities for Visible-Light-Catalyzed Atom Transfer Radical Addition Reactions and Related Processes.

    PubMed

    Reiser, Oliver

    2016-09-20

    Visible-light photoredox catalysis offers exciting opportunities to achieve challenging carbon-carbon bond formations under mild and ecologically benign conditions. Desired features of photoredox catalysts are photostability, long excited-state lifetimes, strong absorption in the visible region, and high reduction or oxidation potentials to achieve electron transfer to substrates, thus generating radicals that can undergo synthetic organic transformations. These requirements are met in a convincing way by Ru(II)(phenanthroline)3- and Ir(III)(phenylpyridine)3-type complexes and, as a low-cost alternative, by organic dyes that offer a metal-free catalyst but suffer in general from lower photostability. Cu(I)(phenanthroline)2 complexes have been recognized for more than 30 years as photoresponsive compounds with highly negative Cu(I)* → Cu(II) oxidation potentials, but nevertheless, they have not been widely considered as suitable photoredox catalysts, mainly because their excited lifetimes are shorter by a factor of 5 to 10 compared with Ru(II) and Ir(III) complexes, their absorption in the visible region is weak, and their low Cu(II) → Cu(I) reduction potentials might impede the closure of a catalytic cycle for a given process. Contrasting again with Ru(II)L3 and Ir(III)L3 complexes, Cu(I)L2 assemblies undergo more rapid ligand exchange in solution, thus potentially reducing the concentration of the photoactive species. Focusing on atom transfer radical addition (ATRA) reactions and related processes, we highlight recent developments that show the utility of Cu(I)(phenanthroline)2 complexes as photoredox catalysts, demonstrating that despite their short excited-state lifetimes and weak absorption such complexes are efficient at low catalyst loadings. Moreover, some of the inherent disadvantages stated above can even be turned to advantages: (1) the low Cu(II) → Cu(I) reduction potential might efficiently promote reactions via a radical chain pathway, and (2

  20. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface.

    PubMed

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-14

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH(4)) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH(4) over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH(4) decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C(2)) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface. PMID:21842949

  1. [Adaptive reactions of dehydrogenation processes in root voles during additional impacts of the physical nature].

    PubMed

    Kudiasheva, A G; Taskaev, A I

    2011-01-01

    Variations of the dehydrogenation enzyme activity (succinate dehydrogenase, pyruvate dehydrogenase, lactate dehydrogenase) in the heart muscle, liver and brain of root voles (Microtus oeconomus Pall.) and their progeny associated with additional stress effects (chronic low-level gamma-irradiation, short-term exposure to cold) have been studied. Root voles (parents) were caught in the areas with a normal and high-level natural radioactivity in the Republic of Komi. It has been revealed that the direction of shifts of the dehydrogenation enzyme activity in response to the factors of the physical nature is determined by the initial level of the oxidation process in tissues of root voles and their progeny that haven't been subjected to these actions. The reaction of root voles and their progeny (1-3 generations) from the radium zone has lower reserve functional possibilities in relation to the additional exposure as compared with the animals from the control zone. In some cases, chronic low-level irradiation and short-term cooling lead to leveling of differences between groups of animals which initially varied from each other in biochemical indexes. PMID:22279768

  2. Cinchona Alkaloid Catalyzed Sulfa-Michael Addition Reactions Leading to Enantiopure β-Functionalized Cysteines.

    PubMed

    Breman, Arjen C; Telderman, Suze E M; van Santen, Roy P M; Scott, Jamie I; van Maarseveen, Jan H; Ingemann, Steen; Hiemstra, Henk

    2015-11-01

    Sulfa-Michael additions to α,β-unsaturated N-acylated oxazolidin-2-ones and related α,β-unsaturated α-amino acid derivatives have been enantioselectively catalyzed by Cinchona alkaloids functionalized with a hydrogen bond donating group at the C6' position. The series of Cinchona alkaloids includes known C6' (thio)urea and sulfonamide derivatives and several novel species with a benzimidazole, squaramide or a benzamide group at the C6' position. The sulfonamides were especially suited as bifunctional organocatalysts as they gave the products in very good diastereoselectivity and high enantioselectivity. In particular, the C6' sulfonamides catalyzed the reaction with the α,β-unsaturated α-amino acid derivatives to afford the products in a diastereomeric ratio as good as 93:7, with the major isomer being formed in an ee of up to 99%. The products of the organocatalytic sulfa-Michael addition to α,β-unsaturated α-amino acid derivatives were subsequently converted in high yields to enantiopure β-functionalized cysteines suitable for native chemical ligation.

  3. UV light-mediated difunctionalization of alkenes through aroyl radical addition/1,4-/1,2-aryl shift cascade reactions.

    PubMed

    Zheng, Lewei; Huang, Hongli; Yang, Chao; Xia, Wujiong

    2015-02-20

    UV light-mediated difunctionalization of alkenes through an aroyl radical addition/1,4-/1,2-aryl shift has been described. The resulted aroyl radical from a photocleavage reaction added to acrylamide compounds followed by cyclization led to the formation of oxindoles, whereas the addition to cinnamic amides aroused a unique 1,4-aryl shift reaction. Furthermore, the difunctionalization of alkenes of prop-2-en-1-ols was also achieved through aroyl radical addition and a sequential 1,2-aryl shift cascade reaction.

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

    SciTech Connect

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

    2014-10-01

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

  5. Extractive phase vanishing reactions with dichloromethane, perfluorohexanes, and dibromoethane: slow addition in a test tube.

    PubMed

    Curran, Dennis P; Werner, Stefan

    2004-03-18

    [reaction: see text] Partition coefficient measurements and experiments with a dye show that a new fluorous "phase vanishing reaction" described by Jana and Verkade occurs by an extractive mechanism. This mechanism is contrasted with the original diffusive phase-vanishing reactions introduced by Ryu and co-workers.

  6. Chemical and Physical Reactions of Wellbore Cement under CO2 Storage Conditions: Effects of Cement Additives

    NASA Astrophysics Data System (ADS)

    Kutchko, B. G.; Strazisar, B. R.; Huerta, N.; Lowry, G. V.; Dzombak, D. A.; Thaulow, N.

    2008-12-01

    Sequestration of CO2 into geologic formations requires long-term storage and low leakage rates to be effective. Active and abandoned wells in candidate storage formations must be evaluated as potential leakage points. Wellbore integrity is an important part of an overall integrated assessment program being developed at NETL to assess potential risks at CO2 storage sites. Such a program is needed for ongoing policy and regulatory decisions for geologic carbon sequestration. The permeability and integrity of the cement in the well is a primary factor affecting its ability to prevent leakage. Cement must be able to maintain low permeability over lengthy exposure to reservoir conditions in a CO2 injection and storage scenario. Although it is known that cement may be altered by exposure to CO2, the results of ongoing research indicate that cement curing conditions, fluid properties, and cement additives play a significant role in the rate of alteration and reaction. The objective of this study is to improve understanding of the factors affecting wellbore cement integrity for large-scale geologic carbon sequestration projects. Due to the high frequency use of additives (pozzolan) in wellbore cement, it is also essential to understand the reaction of these cement-pozzolan systems upon exposure to CO2 under sequestration conditions (15.5 MPa and 50°C). Laboratory experiments were performed to determine the physical and chemical changes, as well as the rate of alteration of commonly used pozzolan-cement systems under simulated sequestration reservoir conditions, including both supercritical CO2 and CO2-saturated brine. The rate of alteration of the cement-pozzolan systems is considerably faster than with neat cement. However, the alteration of physical properties is much less significant with the pozzolanic blends. Permeability of a carbonated pozzolanic cement paste remains sufficiently small to block significant vertical migration of CO2 in a wellbore. All of the

  7. Seeding the Pregenetic Earth: Meteoritic Abundances of Nucleobases and Potential Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Pearce, Ben K. D.; Pudritz, Ralph E.

    2015-07-01

    Carbonaceous chondrites are a class of meteorite known for having high contents of water and organics. In this study, the abundances of the nucleobases, i.e., the building blocks of RNA and DNA, found in carbonaceous chondrites are collated from a variety of published data and compared across various meteorite classes. An extensive review of abiotic chemical reactions producing nucleobases is then performed. These reactions are then reduced to a list of 15 individual reaction pathways that could potentially occur within meteorite parent bodies. The nucleobases guanine, adenine, and uracil are found in carbonaceous chondrites in amounts of 1–500 ppb. It is currently unknown which reaction is responsible for their synthesis within the meteorite parent bodies. One class of carbonaceous meteorite dominates the abundances of both amino acids and nucleobases—the so-called CM2 (e.g., Murchison meteorite). CR2 meteorites (e.g., Graves Nunataks) also dominate the abundances of amino acids, but are the least abundant in nucleobases. The abundances of total nucleobases in these two classes are 330 ± 250 and 16 ± 13 ppb, respectively. Guanine most often has the greatest abundances in carbonaceous chondrites with respect to the other nucleobases, but is 1–2 orders of magnitude less abundant in CM2 meteorites than glycine (the most abundant amino acid). Our survey of the reaction mechanisms for nucleobase formation suggests that Fischer–Tropsch synthesis (i.e., CO, H2, and NH3 gases reacting in the presence of a catalyst such as alumina or silica) is the most likely candidate for conditions that characterize the early states of planetesimals.

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

    PubMed

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

    2016-01-01

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

  9. Seeding the Pregenetic Earth: Meteoritic Abundances of Nucleobases and Potential Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Pearce, Ben K. D.; Pudritz, Ralph E.

    2015-07-01

    Carbonaceous chondrites are a class of meteorite known for having high contents of water and organics. In this study, the abundances of the nucleobases, i.e., the building blocks of RNA and DNA, found in carbonaceous chondrites are collated from a variety of published data and compared across various meteorite classes. An extensive review of abiotic chemical reactions producing nucleobases is then performed. These reactions are then reduced to a list of 15 individual reaction pathways that could potentially occur within meteorite parent bodies. The nucleobases guanine, adenine, and uracil are found in carbonaceous chondrites in amounts of 1-500 ppb. It is currently unknown which reaction is responsible for their synthesis within the meteorite parent bodies. One class of carbonaceous meteorite dominates the abundances of both amino acids and nucleobases—the so-called CM2 (e.g., Murchison meteorite). CR2 meteorites (e.g., Graves Nunataks) also dominate the abundances of amino acids, but are the least abundant in nucleobases. The abundances of total nucleobases in these two classes are 330 ± 250 and 16 ± 13 ppb, respectively. Guanine most often has the greatest abundances in carbonaceous chondrites with respect to the other nucleobases, but is 1-2 orders of magnitude less abundant in CM2 meteorites than glycine (the most abundant amino acid). Our survey of the reaction mechanisms for nucleobase formation suggests that Fischer-Tropsch synthesis (i.e., CO, H2, and NH3 gases reacting in the presence of a catalyst such as alumina or silica) is the most likely candidate for conditions that characterize the early states of planetesimals.

  10. HIGHLY DIASTEREOSELECTIVE MICHAEL REACTION UNDER SOLVENT-FREE CONDITIONS USING MICROWAVES: CONJUGATE ADDITION OF FLAVANONE TO ITS CHALCONE PRECURSOR

    EPA Science Inventory

    Microwave-assisted reaction of 2'-hydroxychalcones in the presence of DBU resulted in the formation of hitherto unknown dimers by conjugate addition of the intermediate cyclic ketone to the starting enone.

  11. Competitive reaction pathways for the gas-phase reactivity of [Me2 AlNH2 ]3.

    PubMed

    Davydova, Elena I; Frenking, Gernot; Timoshkin, Alexey Y

    2014-09-15

    Reaction energy profiles for [Me2 AlNH2 ]3 have been computationally explored by using density functional theory. Both intra- and intermolecular methane elimination reactions, as well as Al-N bond-breaking pathways, were considered. The results show that the energy required for Al-N bond breaking in cyclic [Me2 AlNH2 ]3 is of the same order of magnitude as the activation energies for the first (limiting) step of methane elimination (for both mono- and bimolecular mechanisms). Thus, dissociative and associative reaction pathways are competitive. Low-temperature/high-pressure conditions will favor the bimolecular pathway, whereas at high temperatures, either intramolecular methane elimination or Al-N bond-breaking dissociative pathways will be operational. PMID:24976567

  12. Unified reaction pathways for the prebiotic formation of RNA and DNA nucleobases.

    PubMed

    Jeilani, Yassin Aweis; Williams, Phoenix N; Walton, Sofia; Nguyen, Minh Tho

    2016-07-27

    The reaction pathways for the prebiotic formation of nucleobases are complex and lead to the formation of a mixture of products. In the past 50 years, there has been a concerted effort for identifying a unified mechanism for the abiotic origin of the biomolecules but with little success. In the present theoretical study, we identified two prominent precursors for the building up of RNA and DNA nucleobases under prebiotic conditions: (a) 1,2-diaminomaleonitrile (DAMN), which is a tetramer of hydrogen cyanide (HCN), and (b) formamide, a hydrolysis product of HCN; it is important to emphasize that HCN is the source of both precursors. We find that free radical pathways are potentially appropriate to account for the origin of nucleobases from HCN. The current study unites the formamide pathways with the DAMN pathways. The mechanisms for the formation of the RNA and DNA nucleobases (uracil, adenine, purine, cytosine) were studied by quantum chemical computations using density functional theory at the B3LYP/6-311G(d,p) level. All the routes involved proceed with relatively low energy barriers (within the error margin of DFT methods). We showed that the radical mechanisms for the formation of nucleobases could be unified through common precursors. The results demonstrated that 4-aminoimidazole-5-carbonitrile (AICN), which is a known precursor for nucleobases, is a product of DAMN. The overall mechanisms are internally consistent with the abiotic formation of the nucleobases, namely (a) under a meteoritic impact scenario on the early Earth's surface that generated high internal energy, and/or (b) in the (gas phase) interstellar regions without the presence of catalysts.

  13. Additive Runge-Kutta Schemes for Convection-Diffusion-Reaction Equations

    NASA Technical Reports Server (NTRS)

    Kennedy, Christopher A.; Carpenter, Mark H.

    2001-01-01

    Additive Runge-Kutta (ARK) methods are investigated for application to the spatially discretized one-dimensional convection-diffusion-reaction (CDR) equations. First, accuracy, stability, conservation, and dense output are considered for the general case when N different Runge-Kutta methods are grouped into a single composite method. Then, implicit-explicit, N = 2, additive Runge-Kutta ARK2 methods from third- to fifth-order are presented that allow for integration of stiff terms by an L-stable, stiffly-accurate explicit, singly diagonally implicit Runge-Kutta (ESDIRK) method while the nonstiff terms are integrated with a traditional explicit Runge-Kutta method (ERK). Coupling error terms are of equal order to those of the elemental methods. Derived ARK2 methods have vanishing stability functions for very large values of the stiff scaled eigenvalue, z(exp [I]) goes to infinity, and retain high stability efficiency in the absence of stiffness, z(exp [I]) goes to zero. Extrapolation-type stage-value predictors are provided based on dense-output formulae. Optimized methods minimize both leading order ARK2 error terms and Butcher coefficient magnitudes as well as maximize conservation properties. Numerical tests of the new schemes on a CDR problem show negligible stiffness leakage and near classical order convergence rates. However, tests on three simple singular-perturbation problems reveal generally predictable order reduction. Error control is best managed with a PID-controller. While results for the fifth-order method are disappointing, both the new third- and fourth-order methods are at least as efficient as existing ARK2 methods while offering error control and stage-value predictors.

  14. Reaction pathways towards the formation of dolomite-analogues at ambient conditions

    NASA Astrophysics Data System (ADS)

    Pimentel, Carlos; Pina, Carlos M.

    2016-04-01

    In this paper we present results of a study of the crystallisation behaviour of the dolomite-analogues norsethite and PbMg(CO3)2 at room temperature and atmospheric pressure. Whereas precipitation of norsethite was previously obtained by mixing solutions (Hood et al., 1974; Pimentel and Pina, 2014a,b), we report, for the first time, the synthesis of PbMg(CO3)2 by using the same method. The formation of both phases was promoted by ageing slurries for periods of time ranging from a few days (norsethite) up to 6 months (PbMg(CO3)2). The crystallisation of both norsethite and PbMg(CO3)2 occurs by sequences of dissolution-precipitation reactions involving several amorphous and crystalline precursor phases, which were identified and characterised by X-ray diffraction and scanning electron microscopy. Depending on the initial composition and Ba:Mg and Pb:Mg ratios in the slurries, different precursors and reaction kinetics were observed. This demonstrates the existence of different reaction pathways towards the formation of the investigated dolomite-analogues. Our experimental results provide new insights into the possible mechanisms of formation of dolomite and other double carbonates in nature.

  15. Reaction pathways for ethanol on model Co/ZnO(0001) catalysts.

    PubMed

    Martono, Eddie; Hyman, Matthew P; Vohs, John M

    2011-05-28

    The pathways for the reaction of ethanol on model catalysts consisting of Co and CoO films and particles supported on single crystal ZnO(0001) surfaces were studied using X-ray Photoelectron Spectroscopy (XPS) and Temperature Programmed Desorption (TPD). On supported metallic Co films and particles ethanol was found to primarily undergo decarbonylation forming CO, H(2), and adsorbed methyl groups. In contrast, supported CoO particles were found to be largely unreactive toward ethanol. High selectivity to the dehydrogenation product, acetaldehyde, was only observed when the supported Co was partially oxidized and contained both Co(0) and Co(2+). Since acetaldehyde is thought to be a critical intermediate during steam reforming of ethanol (SRE) to produce H(2) and CO(2), the results of this study suggest that partially oxidized Co species provide the active sites for this reaction. This result is consistent with studies of high surface area Co/ZnO catalysts which also suggest that both Co(0) and Co(2+) species are present under typical SRE reaction conditions. PMID:21475754

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

    SciTech Connect

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

    2013-12-14

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

  17. Development of catalytic asymmetric 1,4-addition and [3 + 2] cycloaddition reactions using chiral calcium complexes.

    PubMed

    Tsubogo, Tetsu; Saito, Susumu; Seki, Kazutaka; Yamashita, Yasuhiro; Kobayashi, Shu

    2008-10-01

    Catalytic asymmetric 1,4-addition and [3 + 2] cycloaddition reactions using chiral calcium species prepared from calcium isopropoxide and chiral bisoxazoline ligands have been developed. Glycine Schiff bases reacted with acrylic esters to afford 1,4-addition products, glutamic acid derivatives, in high yields with high enantioselectivities. During the investigation of the 1,4-addition reactions, we unexpectedly found that a [3 + 2] cycloaddition occurred in the reactions with crotonate derivatives, affording substituted pyrrolidine derivatives in high yields with high enantioselectivities. On the basis of this finding, we investigated asymmetric [3 + 2] cycloadditions, and it was revealed that several kinds of optically active substituted pyrrolidine derivatives containing contiguous stereogenic tertiary and quaternary carbon centers were obtained with high diastereo- and enantioselectivities. In addition, optically active pyrrolidine cores of hepatitis C virus RNA-dependent polymerase inhibitors and potential effective antiviral agents have been synthesized using this [3 + 2] cycloaddition reaction. NMR spectroscopic analysis and observation of nonamplification of enantioselectivity in nonlinear effect experiments suggested that a monomeric calcium species with an anionic ligand was formed as an active catalyst. A stepwise mechanism of the [3 + 2] cycloaddition, consisting of 1,4-addition and successive intramolecular Mannich-type reaction was suggested. Furthermore, modification of the Schiff base structure resulted in a modification of the reaction course from a [3 + 2] cycloaddition to a 1,4-addition, affording 3-substituted glutamic acid derivatives with high diasterero- and enantioselectivities.

  18. Development of catalytic asymmetric 1,4-addition and [3 + 2] cycloaddition reactions using chiral calcium complexes.

    PubMed

    Tsubogo, Tetsu; Saito, Susumu; Seki, Kazutaka; Yamashita, Yasuhiro; Kobayashi, Shu

    2008-10-01

    Catalytic asymmetric 1,4-addition and [3 + 2] cycloaddition reactions using chiral calcium species prepared from calcium isopropoxide and chiral bisoxazoline ligands have been developed. Glycine Schiff bases reacted with acrylic esters to afford 1,4-addition products, glutamic acid derivatives, in high yields with high enantioselectivities. During the investigation of the 1,4-addition reactions, we unexpectedly found that a [3 + 2] cycloaddition occurred in the reactions with crotonate derivatives, affording substituted pyrrolidine derivatives in high yields with high enantioselectivities. On the basis of this finding, we investigated asymmetric [3 + 2] cycloadditions, and it was revealed that several kinds of optically active substituted pyrrolidine derivatives containing contiguous stereogenic tertiary and quaternary carbon centers were obtained with high diastereo- and enantioselectivities. In addition, optically active pyrrolidine cores of hepatitis C virus RNA-dependent polymerase inhibitors and potential effective antiviral agents have been synthesized using this [3 + 2] cycloaddition reaction. NMR spectroscopic analysis and observation of nonamplification of enantioselectivity in nonlinear effect experiments suggested that a monomeric calcium species with an anionic ligand was formed as an active catalyst. A stepwise mechanism of the [3 + 2] cycloaddition, consisting of 1,4-addition and successive intramolecular Mannich-type reaction was suggested. Furthermore, modification of the Schiff base structure resulted in a modification of the reaction course from a [3 + 2] cycloaddition to a 1,4-addition, affording 3-substituted glutamic acid derivatives with high diasterero- and enantioselectivities. PMID:18783222

  19. Addition reaction of alkyl radical to C60 fullerene: Density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-02-01

    Functionalized fullerenes are known as a high-performance molecules. In this study, the alkyl-functionalized fullerenes (denoted by R-C60) have been investigated by means of the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of fullerene. Also, the reaction mechanism of alkyl radicals with C60 was investigated. The methyl, ethyl, propyl, and butyl radicals (denoted by n = 1-4, where n means the number of carbon atoms in the alkyl radical) were examined as alkyl radicals. The DFT calculation showed that the alkyl radical binds to the carbon atom of C60 at the on-top site, and a strong C-C single bond is formed. The binding energies of alkyl radicals to C60 were distributed in the range of 31.8-35.1 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists before alkyl addition, the barrier heights were calculated to be 2.1-2.8 kcal mol-1. The electronic states of R-C60 complexes were discussed on the basis of the theoretical results.

  20. Synthesis of the Hemoglobin-Conjugated Polymer Micelles by Thiol Michael Addition Reactions.

    PubMed

    Qi, Yanxin; Li, Taihang; Wang, Yupeng; Wei, Xing; Li, Bin; Chen, Xuesi; Xie, Zhigang; Jing, Xiabin; Huang, Yubin

    2016-06-01

    Amphiphilic triblock copolymers mPEG-b-PMAC-b-PCL are synthesized using methoxyl poly(ethylene glycol), cyclic carbonic ester monomer including acryloyl group, and ε-caprolactone. Copolymers are self-assembled into core-shell micelles in aqueous solution. Thiolated hemoglobin (Hb) is conjugated with micelles sufficiently through thiol Michael addition reaction to form hemoglobin nanoparticles (HbNs) with 200 nm in diameter. The conjugation of Hb onto the micelle surface is further confirmed by X-ray photoelectron spectroscopy. Feeding ratio of copolymer micelles to Hb at 1:3 would lead to the highest hemoglobin loading efficiency 36.7 wt%. The UV results demonstrate that the gas transporting capacity of HbNs is well remained after Hb is conjugated with polymeric micelles. Furthermore, the obtained HbNs have no obvious detrimental effects on blood components in vitro. This system may thus have great potential as one of the candidates to be developed as oxygen carriers and provide a reference for the modification of protein drugs.

  1. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies.

    PubMed

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M; Wells, George F

    2012-01-01

    Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial

  2. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    PubMed Central

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  3. Reaction dynamics in astrochemistry: low-temperature pathways to polycyclic aromatic hydrocarbons in the interstellar medium.

    PubMed

    Kaiser, Ralf I; Parker, Dorian S N; Mebel, Alexander M

    2015-04-01

    Bimolecular reactions of phenyl-type radicals with the C4 and C5 hydrocarbons vinylacetylene and (methyl-substituted) 1,3-butadiene have been found to synthesize polycyclic aromatic hydrocarbons (PAHs) with naphthalene and 1,4-dihydronaphthalene cores in exoergic and entrance barrierless reactions under single-collision conditions. The reaction mechanism involves the initial formation of a van der Waals complex and addition of a phenyl-type radical to the C1 position of a vinyl-type group through a submerged barrier. Investigations suggest that in the hydrocarbon reactant, the vinyl-type group must be in conjugation with a -C≡CH or -HC=CH2 group to form a resonantly stabilized free radical intermediate, which eventually isomerizes to a cyclic intermediate followed by hydrogen loss and aromatization (PAH formation). The vinylacetylene-mediated formation of PAHs might be expanded to more complex PAHs, such as anthracene and phenanthrene, in cold molecular clouds via barrierless reactions involving phenyl-type radicals, such as naphthyl, which cannot be accounted for by the classical hydrogen abstraction-acetylene addition mechanism.

  4. Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study.

    PubMed

    Kumari, Manju; Kozmon, Stanislav; Kulhánek, Petr; Štepán, Jakub; Tvaroška, Igor; Koča, Jaroslav

    2015-03-26

    The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to the hydroxyl group of the Ser/Thr of cytoplasmic, nuclear, and mitochondrial proteins. In the past, three different catalytic bases were proposed for the reaction: His498, α-phosphate, and Asp554. In this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello molecular dynamics to investigate reaction paths using α-phosphate and Asp554 as the catalytic bases. The string method was used to calculate the free-energy reaction profiles of the tested mechanisms. During the investigations, an additional mechanism was observed. In this mechanism, a proton is transferred to α-phosphate via a water molecule. Our calculations show that the mechanism with α-phosphate acting as the base is favorable. This reaction has a rate-limiting free-energy barrier of 23.5 kcal/mol, whereas reactions utilizing Asp554 and water-assisted α-phosphate have barriers of 41.7 and 40.9 kcal/mol, respectively. Our simulations provide a new insight into the catalysis of OGT and may thus guide rational drug design of transition-state analogue inhibitors with potential therapeutic use. PMID:25731954

  5. Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study.

    PubMed

    Kumari, Manju; Kozmon, Stanislav; Kulhánek, Petr; Štepán, Jakub; Tvaroška, Igor; Koča, Jaroslav

    2015-03-26

    The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to the hydroxyl group of the Ser/Thr of cytoplasmic, nuclear, and mitochondrial proteins. In the past, three different catalytic bases were proposed for the reaction: His498, α-phosphate, and Asp554. In this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello molecular dynamics to investigate reaction paths using α-phosphate and Asp554 as the catalytic bases. The string method was used to calculate the free-energy reaction profiles of the tested mechanisms. During the investigations, an additional mechanism was observed. In this mechanism, a proton is transferred to α-phosphate via a water molecule. Our calculations show that the mechanism with α-phosphate acting as the base is favorable. This reaction has a rate-limiting free-energy barrier of 23.5 kcal/mol, whereas reactions utilizing Asp554 and water-assisted α-phosphate have barriers of 41.7 and 40.9 kcal/mol, respectively. Our simulations provide a new insight into the catalysis of OGT and may thus guide rational drug design of transition-state analogue inhibitors with potential therapeutic use.

  6. Reactions of Propylene Oxide on Supported Silver Catalysts: Insights into Pathways Limiting Epoxidation Selectivity

    SciTech Connect

    Kulkarni, Apoorva; Bedolla-Pantoja, Marco; Singh, Suyash; Lobo, Raul F.; Mavrikakis, Manos; Barteau, Mark A.

    2012-02-04

    The reactions of propylene oxide (PO) on silver catalysts were studied to understand the network of parallel and sequential reactions that may limit the selectivity of propylene epoxidation by these catalysts. The products of the anaerobic reaction of PO on Ag/a-Al2O3 were propanal, acetone and allyl alcohol for PO conversions below 2–3%. As the conversion of PO was increased either by increasing the temperature or the contact time, acrolein was formed at the expense of propanal, indicating that acrolein is a secondary reaction product in PO decomposition. With addition of oxygen to the feedstream the conversion of PO increased moderately. In contrast to the experiments in absence of oxygen, CO2 was a significant product while the selectivity to propanal decreased as soon as oxygen was introduced in the system. Allyl alcohol disappeared completely from the product stream in the presence of oxygen, reacting to form acrolein and CO2. The product distribution may be explained by a network of reactions involving two types of oxametallacycles formed by ring opening of PO: one with the oxygen bonded to C1 (OMC1, linear) and the other with oxygen bonded to C2 (OMC2, branched). OMC1 reacts to form PO, propanal, and allyl alcohol.

  7. Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase.

    PubMed

    Cornish, Adam J; Ginovska, Bojana; Thelen, Adam; da Silva, Julio C S; Soares, Thereza A; Raugei, Simone; Dupuis, Michel; Shaw, Wendy J; Hegg, Eric L

    2016-06-01

    The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a water molecule. A computational analysis of this pathway in the [FeFe]-hydrogenase from Clostridium pasteurianum revealed that the solvent-exposed residue of the pathway (Glu282) forms hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implying that these residues could function in regulating proton transfer. In this study, we show that substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in an ∼3-fold enhancement of H2 production activity when methyl viologen is used as an electron donor, suggesting that Arg286 may help control the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate ∼5-fold, implying that it either acts as a member of the pathway or influences Glu282 to permit proton transfer. Interestingly, quantum mechanics/molecular mechanics and molecular dynamics calculations indicate that Ser320 does not play a structural role or indirectly influence the barrier for proton movement at the entrance of the channel. Rather, it may act as an additional proton acceptor for the pathway or serve in a regulatory role. While further studies are needed to elucidate the role of Ser320, collectively these data provide insights into the complex proton transport process. PMID:27186945

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

    NASA Astrophysics Data System (ADS)

    Jin, Biao; Rolle, Massimo

    2016-04-01

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

  9. The molecular basis for the post-translational addition of amino acids by L/F transferase in the N-end rule pathway.

    PubMed

    Fung, Angela Wai S; Fahlman, Richard P

    2015-01-01

    The N-end rule pathway is a conserved targeted proteolytic process observed in organisms ranging from eubacteria to mammals. The N-end rule relates the metabolic stability of a protein to its N-terminal amino acid residue. The identity of the N-terminal amino acid residue is a primary degradation signal, often referred to as an N-degron, which is recognized by the components of the N-end rule when it is a destabilizing N-terminus. N-degrons may be exposed by non-processive proteolytic cleavages or by post-translational modifications. One modification is the post-translational addition of amino acids to the N-termini of proteins, a reaction catalyzed by aminoacyl-tRNA protein transferases. The aminoacyl-tRNA protein transferase in eubacteria like Escherichia coli is L/F transferase. Recent investigations have reported unexpected observations regarding the L/F transferase catalytic mechanism and its mechanisms of substrate recognition. Additionally, recent proteome-wide identification of putative in vivo substrates facilitates hypothesis into the yet elusive biological functions of the prokaryotic N-end rule pathway. Here we summarize the recent findings on the molecular mechanisms of catalysis and substrate recognition by the E. coli L/F transferase in the prokaryotic N-end rule pathway.

  10. Insights into the Halogen Oxidative Addition Reaction to Dinuclear Gold(I) Di(NHC) Complexes.

    PubMed

    Baron, Marco; Tubaro, Cristina; Basato, Marino; Isse, Abdirisak Ahmed; Gennaro, Armando; Cavallo, Luigi; Graiff, Claudia; Dolmella, Alessandro; Falivene, Laura; Caporaso, Lucia

    2016-07-11

    Gold(I) dicarbene complexes [Au2 (MeIm-Y-ImMe)2 ](PF6 )2 (Y=CH2 (1), (CH2 )2 (2), (CH2 )4 (4), MeIm=1-methylimidazol-2-ylidene) react with iodine to give the mixed-valence complex [Au(MeIm-CH2 -ImMe)2 AuI2 ](PF6 )2 (1 a(I) ) and the gold(III) complexes [Au2 I4 (MeIm-Y-ImMe)2 ](PF6 )2 (2 c(I) and 4 c(I) ). Reaction of complexes 1 and 2 with an excess of ICl allows the isolation of the tetrachloro gold(III) complexes [Au2 Cl4 (MeIm-CH2 -ImMe)2 ](PF6 )2 (1 c(Cl) ) and [Au2 Cl4 (MeIm-(CH2 )2 -ImMe)2 ](Cl)2 (2 c(Cl) -Cl) (as main product); remarkably in the case of complex 2, the X-ray molecular structure of the crystals also shows the presence of I-Au-Cl mixed-sphere coordination. The same type of coordination has been observed in the main product of the reaction of complexes 3 or 4 with ICl. The study of the reactivity towards the oxidative addition of halogens to a large series of dinuclear bis(dicarbene) gold(I) complexes has been extended and reviewed. The complexes react with Cl2 , Br2 and I2 to give the successive formation of the mixed-valence gold(I)/gold(III) n a(X) and gold(III) n c(X) (excluding compound 1 c(I) ) complexes. However, complex 3 affords with Cl2 and Br2 the gold(II) complex 3 b(X) [Au2 X2 (MeIm-(CH2 )3 -ImMe)2 ](PF6 )2 (X=Cl, Br), which is the predominant species over compound 3 c(X) even in the presence of free halogen. The observed different relative stabilities of the oxidised complexes of compounds 1 and 3 have also been confirmed by DFT calculations. PMID:27297191

  11. Pre-steady-state kinetic analysis of the trichodiene synthase reaction pathway.

    PubMed

    Cane, D E; Chiu, H T; Liang, P H; Anderson, K S

    1997-07-01

    The pre-steady-state kinetics of the trichodiene synthase reaction were investigated by rapid chemical quench methods. The single-turnover rate was found to be 3.5-3.8 s-1, a rate 40 times faster than the steady-state catalytic rate (kcat = 0.09 s-1) for trichodiene synthase-catalyzed conversion of farnesyl diphosphate (FPP) to trichodiene at 15 degrees C. In a multiturnover experiment, a burst phase (kb = 4.2 s-1) corresponding to the accumulation of trichodiene on the surface of the enzyme was followed by a slower, steady-state release of products (klin = 0.086 s-1) which corresponds to kcat. These results strongly suggest that the release of trichodiene from the enzyme active site is the rate-limiting step in the overall reaction, while the consumption of FPP is the step which limits chemical catalysis at the active site. Single-turnover experiments with trichodiene synthase mutant D101E, for which the steady-state rate constant kcat is 1/3 of that of wild type, revealed that the mutation actually depresses the rate of FPP consumption by a factor of 100. The deuterium isotope effect on the consumption of [1-2H,1,2-14C]FPP was found to be 1.11 +/- 0.06. Single turnover reactions of [1,2-14C]FPP catalyzed by trichodiene synthase were carried out at 4, 15, or 30 degrees C in an effort to provide direct observation of the proposed intermediate nerolidyl diphosphate (NPP). However, no NPP was detected, indicating that the conversion of NPP must be too fast to be observed within the detection limits of the assay. Taken together, these observations suggest that the isomerization of FPP to NPP is the step which limits the rate of chemical catalysis in the trichodiene synthase reaction pathway. PMID:9204880

  12. Evidence of additional excitation energy transfer pathways in the phycobiliprotein antenna system of Acaryochloris marina.

    PubMed

    Nganou, A C; David, L; Adir, N; Pouhe, D; Deen, M J; Mkandawire, M

    2015-02-01

    To improve the energy conversion efficiency of solar organic cells, the clue may lie in the development of devices inspired by an efficient light harvesting mechanism of some aquatic photosynthetic microorganisms that are adapted to low light intensity. Consequently, we investigated the pathways of excitation energy transfer (EET) from successive light harvesting pigments to the low energy level inside the phycobiliprotein antenna system of Acaryochloris marina, a cyanobacterium, using a time resolved absorption difference spectroscopy with a resolution time of 200 fs. The objective was to understand the actual biochemical process and pathways that determine the EET mechanism. Anisotropy of the EET pathway was calculated from the absorption change trace in order to determine the contribution of excitonic coupling. The results reveal a new electron energy relaxation pathway of 14 ps inside the phycocyanin component, which runs from phycocyanin to the terminal emitter. The bleaching of the 660 nm band suggests a broader absorption of the terminal emitter between 660 nm and 675 nm. Further, there are trimer depolarization kinetics of 450 fs and 500 fs in high and low ionic strength, respectively, which arise from the relaxation of the β84 and α84 in adjacent monomers of phycocyanin. Under conditions of low ionic strength buffer solution, the evolution of the kinetic amplitude during the depolarization of the trimer is suggestive of trimer conservation within the phycocyanin hexamer. The anisotropy values were 0.38 and 0.40 in high and in low ionic strength, respectively, indicating that there is no excitonic delocalization in the high energy level of phycocyanin hexamers.

  13. Kinetics and reaction pathways of formaldehyde degradation using the UV-fenton method.

    PubMed

    Liu, Xiangxuan; Liang, Jiantao; Wang, Xuanjun

    2011-05-01

    This study was based on the purpose of investigating the reaction rules of formaldehyde (HCHO) as an intermediate product in the degradation of many other organic wastewaters. The process conditions of UV-Fenton method for the degradation of the low concentrations of HCHO were studied in a batch photochemical reactor. The results showed that, when the original HCHO concentration was 30 mg/L, at an operating temperature of 23 degrees C, pH = 3, an H202 dosage of 68 mg/L, and an H2O2-to-Fe2+ mole ratio (H2O2:Fe2+) of 5, 91.89% of the HCHO was removed after 30 minutes. The degradation of HCHO in the UV-Fenton system was basically in accordance with the exponential decay. The kinetic study results showed that the reaction orders of HCHO, Fe2+, and H2O2 in the system were 1.054, 0.510, and 0.728, respectively, and the activation energy (Ea) was 9.85 kJ/mol. The comparison of UV/H2O2, Fenton, and UV-Fenton systems for the degradation of HCHO, and the results of iron catalyst tests showed that the mechanism of UV-Fenton on the degradation of HCHO was through a synergistic effect of Fe2+ and UV light to catalyze the decomposition of H2O2. The introduction of UV irradiation to the Fenton system largely increased the degradation rate of HCHO, mainly as a result of the accelerating effect on the formation of the Fe2+/Fe3+ cycle. The reaction products were analyzed by gas chromatography-mass spectrometry and a chemical oxygen demand (COD) analyzer. The effluent gases also were analyzed by gas chromatography. Based on those results, the reaction pathways of HCHO in the UV-Fenton system were proposed. The qualitative and quantitative analysis of the reaction products and the COD showed that the main intermediate product of the reaction was formic acid, and the further oxidation of it was the rate-limiting step for the degradation of HCHO.

  14. Catalysts and Reaction Pathways for the Electrochemical Reduction of Carbon Dioxide.

    PubMed

    Kortlever, Ruud; Shen, Jing; Schouten, Klaas Jan P; Calle-Vallejo, Federico; Koper, Marc T M

    2015-10-15

    The electrochemical reduction of CO2 has gained significant interest recently as it has the potential to trigger a sustainable solar-fuel-based economy. In this Perspective, we highlight several heterogeneous and molecular electrocatalysts for the reduction of CO2 and discuss the reaction pathways through which they form various products. Among those, copper is a unique catalyst as it yields hydrocarbon products, mostly methane, ethylene, and ethanol, with acceptable efficiencies. As a result, substantial effort has been invested to determine the special catalytic properties of copper and to elucidate the mechanism through which hydrocarbons are formed. These mechanistic insights, together with mechanistic insights of CO2 reduction on other metals and molecular complexes, can provide crucial guidelines for the design of future catalyst materials able to efficiently and selectively reduce CO2 to useful products. PMID:26722779

  15. Oxidation of Annelated Diarylamines: Analysis of Reaction Pathways to Nitroxide Diradical and Spirocyclic Products

    SciTech Connect

    Rajca, Andrzej; Shiraishi, Kouichi; Boraty; #324; ski, Przemyslaw J.; Pink, Maren; Miyasaka, Makoto; Rajca, Suchada

    2012-02-06

    Oxidation of diaryldiamine 2, a tetrahydrodiazapentacene derivative, provides diarylnitroxide diradical 1 accompanied by an intermediate nitroxide monoradical and a multitude of isolable diamagnetic products. DFT-computed tensors for EPR spectra and paramagnetic {sup 1}H NMR isotropic shifts for nitroxide diradical 1 show good agreement with the experimental EPR spectra in rigid matrices and paramagnetic {sup 1}H NMR spectra in solution, respectively. Examination of the diamagnetic products elucidates their formation via distinct pathways involving C-O bond-forming reactions, including Baeyer-Villiger-type oxidations. An unusual diiminoketone structure and two spirocyclic structures of the predominant diamagnetic products are confirmed by either X-ray crystallography or correlations between DFT-computed and experimental spectroscopic data such as {sup 1}H, {sup 13}C, and {sup 15}N NMR chemical shifts and electronic absorption spectra.

  16. Chlorhexidine gluconate mouthwashes as a surfactant for addition-reaction silicone impressions.

    PubMed

    Reshad, Mamaly; Nesbit, Michael; Petrie, Aviva; Setchell, Derrick

    2009-03-01

    Addition-reaction silicone impression (PVS) materials are hydrophobic. Hydrophobicity of the impression material may interfere with the wetting of the tooth, resulting in void formation. The study investigates whether conditioning teeth with Chlorhexidine-gluconate based mouthwashes can reduce the hydrophobicity and the number of voids on PVS impressions. Impression material contact angle specimens on bovine tooth surfaces were measured using a Reflex Microscope. PVS impressions (President) were made of untreated bovine teeth in three groups (1, 2 and 3) and fourth group used Impregum polyether impression material: Group I was used as a control group, and original and mint flavoured Corsodyl (Chlorhexidine) mouthwashes were used as clinical surfactants in Groups 2 and 3, respectively. Contact angle readings were recorded on each side of every impression in each of the four groups and compared by an analysis of variance. In the second part of the study, the numbers of air voids on impression surfaces were visually recorded. The proportions of air voids in the groups were compared using a Chi-squared test. The mean angle for Group 3 with mint flavoured Corsodyl mouthwash was significantly smaller than that of any of the other groups (P < 0.05). The only statistically significant (P < 0.01) comparisons of the proportions of air voids were between Group 4 and each of the other experimental groups, with the percentage of voids being significantly greater in Group 4. Although Corsodyl mint significantly reduced the mean contact angle it did not significantly reduce the percentage of voids on impression surfaces. PMID:19378615

  17. The NBS Reaction: A Simple Explanation for the Predominance of Allylic Substitution over Olefin Addition by Bromine at Low Concentrations.

    ERIC Educational Resources Information Center

    Wamser, Carl C.; Scott, Lawrence T.

    1985-01-01

    Examines mechanisms related to use of N-bromosuccinimide (NBS) for bromination at an allylic position. Also presents derived rate laws for three possible reactions of molecular bromine with an alkene: (1) free radical substitution; (2) free radical addition; and (3) electrophilic addition. (JN)

  18. Oxidation of ofloxacin by Oxone/Co(2+): identification of reaction products and pathways.

    PubMed

    Pi, Yunqing; Feng, Jinglan; Sun, Jingyu; Song, Mengke; Sun, Jianhui

    2014-02-01

    Oxidative degradation of ofloxacin (OFX) by sulfate free radicals (SO4 (-•)) in the UV/Oxone/Co(2+)oxidation process was investigated for the first time, with a special focus upon identifying the transformation products as well as understanding the reaction pathways. Thirteen main compounds were identified after the initial transformation of OFX; the detailed structural information of which were characterized by high-performance liquid chromatography-high resolution mass spectrometry and MS fragmentation analysis. The degradation pathways mainly encompassed ring openings at both the piperazinyl substituent and the quinolone moiety, indicating that the usage of SO4 (-•) aided the oxidative degradation of OFX to undergo more facile routes compared to those in previous reports by using OH(•)/h(+) as the oxidant, where the initial transformation attacks were mainly confined to the piperazine moiety. Moreover, in this study, smart control over the pH conditions of the oxidation system via different modes of Oxone dosage resulted in the selective degradation of the functional sites of OFX molecule, where it was shown that the SO4 (-•)-driven destruction of the quinolone moiety of OFX molecule favored the neutral pH conditions. This would be beneficial for the reduction of bacterial resistance against quinolones in the aqueous environment.

  19. Modeling reaction histories to study chemical pathways in condensed phase detonation

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  20. Reaction pathways of furfural, furfuryl alcohol and 2-methylfuran on Cu(111) and NiCu bimetallic surfaces

    NASA Astrophysics Data System (ADS)

    Xiong, Ke; Wan, Weiming; Chen, Jingguang G.

    2016-10-01

    Hydrodeoxygenation (HDO) is an important reaction for converting biomass-derived furfural to value-added 2-methylfuran, which is a promising fuel additive. In this work, the HDO of furfural to produce 2-methylfuran occurred on the NiCu bimetallic surfaces prepared on either Ni(111) or Cu(111). The reaction pathways of furfural were investigated on Cu(111) and Ni/Cu(111) surfaces using density functional theory (DFT) calculations, temperature-programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) experiments. These studies provided mechanistic insights into the effects of bimetallic formation on enhancing the HDO activity. Specifically, furfural weakly adsorbed on Cu(111), while it strongly adsorbed on Ni/Cu(111) through an η2(C,O) configuration, which led to the HDO of furfural on Ni/Cu(111). The ability to dissociate H2 on Ni/Cu(111) is also an important factor for enhancing the HDO activity over Cu(111).

  1. Highly efficient "on water" catalyst-free nucleophilic addition reactions using difluoroenoxysilanes: dramatic fluorine effects.

    PubMed

    Yu, Jin-Sheng; Liu, Yun-Lin; Tang, Jing; Wang, Xin; Zhou, Jian

    2014-09-01

    A remarkable fluorine effect on "on water" reactions is reported. The CF⋅⋅⋅HO interactions between suitably fluorinated nucleophiles and the hydrogen-bond network at the phase boundary of oil droplets enable the formation of a unique microstructure to facilitate on water catalyst-free reactions, which are difficult to realize using nonfluorinated substrates. Accordingly, a highly efficient on water, catalyst-free reaction of difluoroenoxysilanes with aldehydes, activated ketones, and isatylidene malononitriles was developed, thus leading to the highly efficient synthesis of a variety of α,α-difluoro-β-hydroxy ketones and quaternary oxindoles.

  2. Fundamental reaction pathways during coprocessing. Thirteenth quarterly technical progress report and milestone status report

    SciTech Connect

    Stock, L.M.; Gatsis, J.

    1991-12-31

    We have been carrying out an investigation that is studying the role of dihydrogen in the coprocessing reaction. The initial research on this part of the project has been reported. In that contribution, Illinois No. 6 coal or Wyodak coal and Lloydminster resid or Hondo resid was mixed with a molybdenum based UOP proprietary catalyst was carried out under a 3000 psi dideuterium atmosphere at 420{degrees}C with a heat up time of 120 minutes and a residence time of 120 minutes. Quantitative 1H and 2H NMR analyses yielded similar results for the four combinations of coals and resids. Specifically, the degree of deuteration, (D/H+D), of the coprocessed products approached 0.25, the value that was expected for complete equilibration of the isotopes among the available positions in the oil, resin, and asphaltene. These results established the ultimate unselective character of the severe coprocessing reaction. However, we sought information on the limiting processes. Accordingly, additional coprocessing reactions with Illinois No. 6 coal and Lloydminster resid have been carried out under less severe conditions to investigate how the dideuterium utilization in the reaction products is affected by changes in the temperature and pressure.

  3. In search of a viable reaction pathway in the chelation of a metallo-protein

    NASA Astrophysics Data System (ADS)

    Rose, Frisco; Hodak, Miroslav; Bernholc, Jerry

    2010-03-01

    Misfolded metallo-proteins are potential causal agents in the onset of neuro-degenerative diseases, such as Alzheimer's and Parkinson's Diseases (PD). Experimental results involving metal chelation have shown significant promise in symptom reduction and misfolding reversal. We explore, through atomistic simulations, potential reaction pathways for the chelation of Cu^2+ from the metal binding site in our representation of a partially misfolded α-synuclein, the protein implicated in PD. Our ab initio simulations use Density Functional Theory (DFT) and nudged elastic band to obtain the minimized energy coordinates of this reaction. Our simulations include ab initio water at the interaction site and in its first solvation shells, while the remainder is fully solvated with orbital-free DFT water representation [1]. Our ongoing studies of viable chelation agents include nicotine, caffeine and other potential reagents, we will review the best case agents in this presentation. [4pt] [1] Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J. Chem. Phys. 2008 Jan;128(1):014101-9.

  4. Structural Snapshots of Escherichia coli Histidinol Phosphate Phosphatase along the Reaction Pathway

    SciTech Connect

    Rangarajan,E.; Proteau, A.; Wagner, J.; Hung, M.; Matte, A.; Cygler, M.

    2006-01-01

    HisB from Escherichia coli is a bifunctional enzyme catalyzing the sixth and eighth steps of L-histidine biosynthesis. The N-terminal domain (HisB-N) possesses histidinol phosphate phosphatase activity, and its crystal structure shows a single domain with fold similarity to the haloacid dehalogenase (HAD) enzyme family. HisB-N forms dimers in the crystal and in solution. The structure shows the presence of a structural Zn{sup 2+} ion stabilizing the conformation of an extended loop. Two metal binding sites were also identified in the active site. Their presence was further confirmed by isothermal titration calorimetry. HisB-N is active in the presence of Mg{sup 2+}, Mn{sup 2+}, Co{sup 2+}, or Zn{sup 2+}, but Ca{sup 2+} has an inhibitory effect. We have determined structures of several intermediate states corresponding to snapshots along the reaction pathway, including that of the phosphoaspartate intermediate. A catalytic mechanism, different from that described for other HAD enzymes, is proposed requiring the presence of the second metal ion not found in the active sites of previously characterized HAD enzymes, to complete the second half-reaction. The proposed mechanism is reminiscent of two-Mg{sup 2+} ion catalysis utilized by DNA and RNA polymerases and many nucleases. The structure also provides an explanation for the inhibitory effect of Ca{sup 2+}.

  5. Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied.

    PubMed

    Bai, Shirong; Davis, Michael J; Skodje, Rex T

    2015-11-12

    The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of how that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux.

  6. Reaction pathway in vapour phase hydrogenation of maleic anhydride and its esters to {gamma}-butyrolactone

    SciTech Connect

    Messori, M.; Vaccari, A.

    1994-11-01

    The catalytic reactivity of maleic anhydride (MA), succinic anhydride (SA) and their dimethyl esters (dimethyl maleate and dimethyl succinate) in the vapour phase hydrogenation to {gamma}-butyrolacetone (GBL) was investigated. In order to obtain general data, both a multicomponent catalyst (CAT 1: Cu/Zn/Mg/Cr = 40:5:5:50, atomic ratio %), obtained by reduction of a nonstoichiometric spinel-type precursor, and a commercial catalyst (CAT 2: Cu/Mn/Ba/Cr = 44:8:1:47, atomic ratio %) were used. The MA/GBL solution exhibited the highest GBL production, while the SA/GBL solution was converted only partially due to a competitive adsorption of GBL on the active sites, as evidenced by the similar reactivities observed with pure anhydrides. The best carbon balances were observed with the esters, probably the result of lowest light hydrocarbon synthesis and tar formation. With all the feedstocks, the activity of CAT 2 is higher than that of CAT 1, which, however, gives the best yield in GBL due its lower activity in the overhydrogenation and hydrogenolysis reaction. It was found that n-butanol (BuOH) and butyric acid (BuA) derived mainly from GBL. On this basis, the reactivities of the main products observed were investigated separately, confirming the stability of tetrahydrofuran (THF), which reacted only at high temperature with low conversions to ethanol. On the other hand, GBL gave rise to overhydrogenation and/or hydrogenolysis, with high conversion (mainly with CAT 2), confirming its key role in both reactions. Furthermore, the formation in the catalytic tests with BuA and BuOH of n-butanal, notwithstanding the high H{sub 2}/organic ratio, implies that it is the main intermediate in the hydrogenolysis reactions. A new reaction scheme is proposed, pointing out the key role of GBL as the {open_quotes}intersection{close_quotes} of two possible reaction pathways, giving rise to THF or overhydrogenation and hydrogenolysis products, respectively. 44 refs., 4 figs., 6 tabs.

  7. Carbocations as Lewis acid catalysts in Diels-Alder and Michael addition reactions.

    PubMed

    Bah, Juho; Franzén, Johan

    2014-01-20

    In general, Lewis acid catalysts are metal-based compounds that owe their reactivity to a low-lying empty orbital. However, one potential Lewis acid that has received negligible attention as a catalyst is the carbocation. We have demonstrated the potential of the carbocation as a highly powerful Lewis acid catalyst for organic reactions. The stable and easily available triphenylmethyl (trityl) cation was found to be a highly efficient catalyst for the Diels-Alder reaction for a range of substrates. Catalyst loadings as low as 500 ppm, excellent yields, and good endo/exo selectivities were achieved. Furthermore, by changing the electronic properties of the substituents on the tritylium ion, the Lewis acidity of the catalyst could be tuned to control the outcome of the reaction. The ability of this carbocation as a Lewis acid catalyst was also further extended to the Michael reaction.

  8. Atmospheric transport and deposition, an additional input pathway for triazine herbicides to surface waters

    SciTech Connect

    Muir, D.C.G.; Rawn, D.F.

    1996-10-01

    Although surface runoff from treated fields is regarded as the major route of entry of triazine herbicides to surface waters, other pathways such as deposition via precipitation, gas absorption and dryfall may also be important. Triazine herbicides have been detected in precipitation but there has been only a very limited amount of work on gas phase and aerosols. To examine the importance of atmospheric inputs concentrations of atrazine, cyanazine and terbuthylazine in gas phase/aerosols, precipitation, and surface waters were determined (along with other herbicides) using selected ion GC-MS. Atrazine was detected at low ng/L concentrations in surface waters (<0.04-5.3 ng/L) and precipitation (0.1-53 ng/L), and at 0.02-0.1 ng/m{sup 3} in air. Cyanazine and terbuthylazine were detected in air and infrequently in water. Highest atrazine concentrations in air were found during June each year on both gas phase and particles. Concentrations of atrazine in surface waters at both locations increased during June, even in the absence of precipitation or overland flow, presumably due to inputs from dryfall and to gas areas and boreal forest lakes due to transport and deposition. Ecological risk assessment of triazines, especially for pristine aquatic environments should include consideration of this atmospheric pathway.

  9. Reactions of diborane with ammonia and ammonia borane: catalytic effects for multiple pathways for hydrogen release.

    PubMed

    Nguyen, Vinh Son; Matus, Myrna H; Nguyen, Minh Tho; Dixon, David A

    2008-10-01

    High-level electronic structure calculations have been used to construct portions of the potential energy surfaces related to the reaction of diborane with ammonia and ammonia borane (B2H6 + NH3 and B2H6 + BH3NH3)to probe the molecular mechanism of H2 release. Geometries of stationary points were optimized at the MP2/aug-cc-pVTZ level. Total energies were computed at the coupled-cluster CCSD(T) theory level with the correlation-consistent basis sets. The results show a wide range of reaction pathways for H2 elimination. The initial interaction of B2H6 + NH3 leads to a weak preassociation complex, from which a B-H-B bridge bond is broken giving rise to a more stable H3BHBH2NH3 adduct. This intermediate, which is also formed from BH3NH3 + BH3, is connected with at least six transition states for H2 release with energies 18-93 kal/mol above the separated reactants. The lowest-lying transition state is a six-member cycle, in which BH3exerts a bifunctional catalytic effect accelerating H2 generation within a B-H-H-N framework. Diborane also induces a catalytic effect for H2 elimination from BH3NH3 via a three-step pathway with cyclic transition states. Following conformational changes, the rate-determining transition state for H2 release is approximately 27 kcal/mol above the B2H6 + BH3NH3 reactants, as compared with an energy barrier of approximately 37 kcal/mol for H2 release from BH3NH3. The behavior of two separated BH3 molecules is more complex and involves multiple reaction pathways. Channels from diborane or borane initially converge to a complex comprising the H3BHBH2NH3adduct plus BH3. The interaction of free BH3 with the BH3 moiety of BH3NH3 via a six-member transition state with diborane type of bonding leads to a lower-energy transition state. The corresponding energy barrier is approximately 8 kcal/mol, relative to the reference point H3BHBH2NH3 adduct + BH3. These transition states are 27-36 kcal/mol above BH3NH3 + B2H6, but 1-9 kcal/mol below the

  10. Shining Light on Copper: Unique Opportunities for Visible-Light-Catalyzed Atom Transfer Radical Addition Reactions and Related Processes.

    PubMed

    Reiser, Oliver

    2016-09-20

    Visible-light photoredox catalysis offers exciting opportunities to achieve challenging carbon-carbon bond formations under mild and ecologically benign conditions. Desired features of photoredox catalysts are photostability, long excited-state lifetimes, strong absorption in the visible region, and high reduction or oxidation potentials to achieve electron transfer to substrates, thus generating radicals that can undergo synthetic organic transformations. These requirements are met in a convincing way by Ru(II)(phenanthroline)3- and Ir(III)(phenylpyridine)3-type complexes and, as a low-cost alternative, by organic dyes that offer a metal-free catalyst but suffer in general from lower photostability. Cu(I)(phenanthroline)2 complexes have been recognized for more than 30 years as photoresponsive compounds with highly negative Cu(I)* → Cu(II) oxidation potentials, but nevertheless, they have not been widely considered as suitable photoredox catalysts, mainly because their excited lifetimes are shorter by a factor of 5 to 10 compared with Ru(II) and Ir(III) complexes, their absorption in the visible region is weak, and their low Cu(II) → Cu(I) reduction potentials might impede the closure of a catalytic cycle for a given process. Contrasting again with Ru(II)L3 and Ir(III)L3 complexes, Cu(I)L2 assemblies undergo more rapid ligand exchange in solution, thus potentially reducing the concentration of the photoactive species. Focusing on atom transfer radical addition (ATRA) reactions and related processes, we highlight recent developments that show the utility of Cu(I)(phenanthroline)2 complexes as photoredox catalysts, demonstrating that despite their short excited-state lifetimes and weak absorption such complexes are efficient at low catalyst loadings. Moreover, some of the inherent disadvantages stated above can even be turned to advantages: (1) the low Cu(II) → Cu(I) reduction potential might efficiently promote reactions via a radical chain pathway, and (2

  11. Ratiometric fluorescent probe for rapid detection of bisulfite through 1,4-addition reaction in aqueous solution.

    PubMed

    Sun, Yue; Zhao, Dong; Fan, Shanwei; Duan, Lian; Li, Ruifeng

    2014-04-16

    A ratiometric fluorescent probe based on a positively charged benzo[e]indolium moiety for bisulfite is reported. The bisulfite underwent a 1,4-addition reaction with the C-4 atom in the ethylene group. This reaction resulted in a large emission wavelength shift (Δλ = 106 nm) and an observable fluorescent color change from orange to cyan. The reaction could be completed in 90 s in a PBS buffer solution and displayed high selectivity and sensitivity for bisulfite. A simple paper test strip system was developed to detect bisulfite rapidly. Probe 1 was used to detect bisulfite in real samples with good recovery.

  12. Effects of aluminum additions to gas atomized reaction synthesis produced oxide dispersion strengthened alloys

    NASA Astrophysics Data System (ADS)

    Spicher, Alexander Lee

    The production of an aluminum containing ferritic oxide dispersion strengthened (ODS) alloy was investigated. The production method used in this study was gas atomization reaction synthesis (GARS). GARS was chosen over the previously commercial method of mechanical alloying (MA) process due to complications from this process. The alloy compositions was determined from three main components; corrosion resistance, dispersoid formation, and additional elements. A combination of Cr and Al were necessary in order to create a protective oxide in the steam atmosphere that the boiler tubing in the next generation of coal-fired power plants would be exposed to. Hf and Y were chosen as dispersoid forming elements due to their increased thermal stability and potential to avoid decreased strength caused by additions of Al to traditional ODS materials. W was used as an additive due to benefits as a strengthener as well as its benefits for creep rupture time. The final composition chosen for the alloy was Fe-16Cr-12Al-0.9W-0.25Hf-0.2Y at%. The aforementioned alloy, GA-1-198, was created through gas atomization with atomization gas of Ar-300ppm O2. The actual composition created was found to be Fe-15Cr-12.3Al-0.9W-0.24Hf-0.19Y at%. An additional alloy that was nominally the same without the inclusion of aluminum was created as a comparison for the effects on mechanical and corrosion properties. The actual composition of the comparison alloy, GA-1-204, was Fe-16Cr-0Al-0.9W-0.25Hf-0.24Y at%. An investigation on the processing parameters for these alloys was conducted on the GA-1-198 alloy. In order to predict the necessary amount of time for heat treatment, a diffusion study was used to find the diffusion rate of oxygen in cast alloys with similar composition. The diffusion rate was found to be similar to that of other GARS compositions that have been created without the inclusion of aluminum. The effect of heat treatment time was investigated with temperatures of 950°C, 1000

  13. Fast removal of the antibiotic flumequine from aqueous solution by ozonation: Influencing factors, reaction pathways, and toxicity evaluation.

    PubMed

    Feng, Mingbao; Yan, Liqing; Zhang, Xiaoling; Sun, Ping; Yang, Shaogui; Wang, Liansheng; Wang, Zunyao

    2016-01-15

    As one of the first generation of fluoroquinolone antibiotics, flumequine (FLU) has been detected ubiquitously in surface waters and municipal wastewaters. In light of FLU's possible adverse effects on aquatic species, the removal of this antibiotic has received worldwide attention. In this study, the kinetics, transformation products, mechanisms and toxicity variations of the ozonation process for FLU were systematically determined. The possible effects of solution pH, addition of inorganic ions, dissolved organic matter, and tert-butyl-alcohol (a radical scavenger), as well as the type of water matrices on FLU removal by ozonation, were studied from the perspective of the degradation kinetics. The data obtained suggested that ozone can be used as an effective oxidant for the fast removal of FLU from natural waters. Using liquid chromatography-mass spectrometry, a total of thirteen transformation products of FLU during ozonation were identified, and their specific reaction mechanisms were also proposed. The degradation pathways involving the hydroxylation, decarboxylation and defluorination were tentatively proposed. Meanwhile, the generation of three low-molecular-weight carboxylic acids was also observed. In addition, the potential toxicity of the transformation mixtures of FLU by ozone was evaluated. Overall, this paper can be a unique contribution to the systematic elucidation of the ozonation process of this antibiotic in water. PMID:26409146

  14. Fast removal of the antibiotic flumequine from aqueous solution by ozonation: Influencing factors, reaction pathways, and toxicity evaluation.

    PubMed

    Feng, Mingbao; Yan, Liqing; Zhang, Xiaoling; Sun, Ping; Yang, Shaogui; Wang, Liansheng; Wang, Zunyao

    2016-01-15

    As one of the first generation of fluoroquinolone antibiotics, flumequine (FLU) has been detected ubiquitously in surface waters and municipal wastewaters. In light of FLU's possible adverse effects on aquatic species, the removal of this antibiotic has received worldwide attention. In this study, the kinetics, transformation products, mechanisms and toxicity variations of the ozonation process for FLU were systematically determined. The possible effects of solution pH, addition of inorganic ions, dissolved organic matter, and tert-butyl-alcohol (a radical scavenger), as well as the type of water matrices on FLU removal by ozonation, were studied from the perspective of the degradation kinetics. The data obtained suggested that ozone can be used as an effective oxidant for the fast removal of FLU from natural waters. Using liquid chromatography-mass spectrometry, a total of thirteen transformation products of FLU during ozonation were identified, and their specific reaction mechanisms were also proposed. The degradation pathways involving the hydroxylation, decarboxylation and defluorination were tentatively proposed. Meanwhile, the generation of three low-molecular-weight carboxylic acids was also observed. In addition, the potential toxicity of the transformation mixtures of FLU by ozone was evaluated. Overall, this paper can be a unique contribution to the systematic elucidation of the ozonation process of this antibiotic in water.

  15. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-08-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of a similar magnitude, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity-dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  16. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-12-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  17. Nucleophilic lewis base dependent addition reactions of allenoates with trifluoromethylated cyclic ketimines.

    PubMed

    Yang, Li-Jun; Li, Shen; Wang, Shuai; Nie, Jing; Ma, Jun-An

    2014-04-18

    A detailed investigation on the different reactivity patterns shown by phosphorus- and nitrogen-containing Lewis base catalysts in the reactions of allenoates with cyclic trifluoromethyl ketimines was accomplished. With PPh3, [3 + 2] annulations proceeded smoothly to afford dihydropyrrole derivatives in excellent yields. Under the catalysis of DABCO, [2 + 2] annulations occurred, producing azetidine derivatives in good to high yields. However, in the presence of pyridine, α,α'-disubstituted allenoates were obtained in very high yields via aza-Morita-Baylis-Hillman reactions. These studies provide an opportunity for diverse synthesis of a variety of N-heterocyclic compounds from the same starting materials.

  18. Pulse radiolytic and product analysis studies of the reaction of hydroxyl radicals with cinnamic acid. The relative extent of addition to the ring and side chain

    SciTech Connect

    Bobrowski, K.; Raghavan, N.V.

    1982-10-28

    Using pulse radiolysis with optical detection and high-pressure liquid chromatography (HPCL), it has been shown that reaction of OH radicals with cinnamic acid (CA in aqueous solutions leads to addition to both the ring and the olefinic group. The relative extent of the above two pathways was estimated as 3:7, respectively. Benzyl- and hydroxycyclohexadienyl-type radicals were observed with absorption maxima at 320 (310) and 370 (365) nm depending on the pH of the solution. In the pH region 4.9 to 5.7 the absorption at 305 to 315 nm decays during the first 5 ..mu..s after the pulse. The dependence of the rate constants and absorption spectra on pH suggests that this decay is due to an equilibration process between acid-base forms of benzyl-type radicals formed through OH addition to te olefinic group.

  19. A tyrosine decarboxylase catalyzes the initial reaction of the salidroside biosynthesis pathway in Rhodiola sachalinensis.

    PubMed

    Zhang, Ji-Xing; Ma, Lan-Qing; Yu, Han-Song; Zhang, Hong; Wang, Hao-Tian; Qin, Yun-Fei; Shi, Guang-Lu; Wang, You-Nian

    2011-08-01

    Salidroside, the 8-O-β-D-glucoside of tyrosol, is the main bioactive component of Rhodiola species and is found mainly in the plant roots. It is well known that glucosylation of tyrosol is the final step in the biosynthesis of salidroside; however, the biosynthetic pathway of tyrosol and its regulation are less well understood. A summary of the results of related studies revealed that the precursor of tyrosol might be tyramine, which is synthesized from tyrosine. In this study, a cDNA clone encoding tyrosine decarboxylase (TyrDC) was isolated from Rhodiola sachalinensis A. Bor using rapid amplification of cDNA ends. The resulting cDNA was designated RsTyrDC. RNA gel-blot analysis revealed that the predominant sites of expression in plants are the roots and high levels of transcripts are also found in callus tissue culture. Functional analysis revealed that tyrosine was best substrate of recombinant RsTyrDC. The over-expression of the sense-RsTyrDC resulted in a marked increase of tyrosol and salidroside content, but the levels of tyrosol and salidroside were 274 and 412%, respectively, lower in the antisense-RsTyrDC transformed lines than those in the controls. The data presented here provide in vitro and in vivo evidence that the RsTyrDC can regulate the tyrosol and salidroside biosynthesis, and the RsTyrDC is most likely to have an important function in the initial reaction of the salidroside biosynthesis pathway in R. sachalinensis.

  20. Enantio- and diastereoselective Michael addition reactions of unmodified aldehydes and ketones with nitroolefins catalyzed by a pyrrolidine sulfonamide.

    PubMed

    Wang, Jian; Li, Hao; Lou, Bihshow; Zu, Liansuo; Guo, Hua; Wang, Wei

    2006-05-24

    Chiral (S)-pyrrolidine trifluoromethanesulfonamide has been shown to serve as an effective catalyst for direct Michael addition reactions of aldehydes and ketones with nitroolefins. A wide range of aldehydes and ketones as Michael donors and nitroolefins as acceptors participate in the process, which proceeds with high levels of enantioselectivity (up to 99 % ee) and diastereoselectivity (up to 50:1 d.r.). The methodology has been employed successfully in an efficient synthesis of the potent H(3) agonist Sch 50917. In addition, a practical three-step procedure for the preparation of (S)-pyrrolidine trifluoromethanesulfonamide has been developed. The high levels of stereochemical control attending Michael addition reactions catalyzed by this pyrrolidine sulfonamide, have been investigated by using ab initio and density functional methods. Transition state structures for the rate-limiting C--C bond-forming step, corresponding to re- and si-face addition to the reactive conformation of the key enamine intermediates have been calculated. Analysis of these structures indicates that hydrogen bonding plays an important role in catalysis and that the energy barrier for si-face attack in reactions of aldehydes to form 2R,3S products is lower than that for the re-face attack leading to 2S,3R products. In contrast, the energy barrier for re-face addition is lower than that for si-face addition in reactions of ketones. The computational results, which are in good agreement with the experimental observations, are discussed in the context of the stereochemical course of these Michael addition reactions.

  1. Bromine radical-mediated sequential radical rearrangement and addition reaction of alkylidenecyclopropanes.

    PubMed

    Kippo, Takashi; Hamaoka, Kanako; Ryu, Ilhyong

    2013-01-16

    Bromine radical-mediated cyclopropylcarbinyl-homoallyl rearrangement of alkylidenecyclopropanes was effectively accomplished by C-C bond formation with allylic bromides, which led to the syntheses of 2-bromo-1,6-dienes. A three-component coupling reaction comprising alkylidenecyclopropanes, allylic bromides, and carbon monoxide also proceeded well to give 2-bromo-1,7-dien-5-ones in good yield.

  2. Guided ion beam studies of the reactions of Vn+ (n=2-17) with O2: Bond energies and dissociation pathways

    NASA Astrophysics Data System (ADS)

    Xu, J.; Rodgers, M. T.; Griffin, J. B.; Armentrout, P. B.

    1998-06-01

    The kinetic energy dependence of the reactions of Vn+ (n=2-17) with oxygen is studied using a guided ion beam mass spectrometer. In all but the smallest clusters, the primary reaction process at low energies is the formation of a vanadium cluster dioxide ion which then loses one or two vanadium atoms or a vanadium oxide diatom (VO). Vanadium atom loss is the preferred reaction pathway for large clusters (n⩾5), whereas loss of VO is more favorable for the smallest reactant clusters (n⩽4). As the collision energy is increased, these primary products dissociate further by loss of additional vanadium atoms. Bond dissociation energies of the vanadium cluster oxides are determined by analysis of the kinetic energy dependence of several different products. The effect of oxygen atoms on the stabilities of vanadium cluster ions is discussed and compared with bulk phase thermochemistry.

  3. Oxidation of flame retardant tetrabromobisphenol a by aqueous permanganate: reaction kinetics, brominated products, and pathways.

    PubMed

    Pang, Su-Yan; Jiang, Jin; Gao, Yuan; Zhou, Yang; Huangfu, Xiaoliu; Liu, Yongze; Ma, Jun

    2014-01-01

    In this work, the most widely used brominated flame retardant tetrabromobisphenol A (TBrBPA) was shown to exhibit appreciable reactivity toward potassium permanganate [Mn(VII)] in water over a wide pH range of 5-10 with the maxima of second-order rate constants (kMn(VII) = 15-700 M(-1) s(-1)) at pH near its pKa values (7.5/8.5). A novel precursor ion scan (PIS) approach using negative electrospray ionization-triple quadrupole mass spectrometry (ESI-QqQMS) was adopted and further optimized for fast selective detection of brominated oxidation products of TBrBPA by Mn(VII). By setting PIS of m/z 79 and 81, two major products (i.e., 4-(2-hydroxyisopropyl)-2,6-dibromophenol and 4-isopropylene-2,6-dibromophenol) and five minor ones (including 2,6-dibromophenol, 2,6-dibromo-1,4-benzoquinone, and three dimers) were detected and suggested with chemical structures from their product ion spectra and bromine isotope patterns. Reaction pathways mainly involving the initial one-electron oxidation of TBrBPA and subsequent release and further reactions of 2,6-dibromo-4-isopropylphenol carbocation intermediate were proposed. The effectiveness of Mn(VII) for treatment of TBrBPA in real waters was confirmed. It is important to better understand the reactivity and toxicity of primary brominated products before Mn(VII) can be applied for treatment of TBrBPA-contaminated wastewater and source water. PMID:24295083

  4. Muonium Addition Reactions and Kinetic Isotope Effects in the Gas Phase: k∞ Rate Constants for Mu + C2H2.

    PubMed

    Arseneau, Donald J; Garner, David M; Reid, Ivan D; Fleming, Donald G

    2015-07-16

    The kinetics of the addition reaction of muonium (Mu) to acetylene have been studied in the gas phase at N2 moderator pressures mainly from ∼800 to 1000 Torr and over the temperature range from 168 to 446 K, but also down to 200 Torr at 168 K and over a much higher range of pressures, from 10 to 44 bar at 295 K, demonstrating pressure-independent rate constants, kMu(T). Even at 200 Torr moderator pressure, the kinetics for Mu + C2H2 addition behave as if effectively in the high-pressure limit, giving k∞ = kMu due to depolarization of the muon spin in the MuC2H2 radical formed in the addition step. The rate constants kMu(T) exhibit modest Arrhenius curvature over the range of measured temperatures. Comparisons with data and with calculations for the corresponding H(D) + C2H2 addition reactions reveal a much faster rate for the Mu reaction at the lowest temperatures, by 2 orders of magnitude, in accord with the propensity of Mu to undergo quantum tunneling. Moreover, isotopic atom exchange, which contributes in a major way to the analogous D atom reaction, forming C2HD + H, is expected to be unimportant in the case of Mu addition, a consequence of the much higher zero-point energy and hence weaker C-Mu bond that would form, meaning that the present report of the Mu + C2H2 reaction is effectively the only experimental study of kinetic isotope effects in the high-pressure limit for H-atom addition to acetylene.

  5. Muonium Addition Reactions and Kinetic Isotope Effects in the Gas Phase: k∞ Rate Constants for Mu + C2H2.

    PubMed

    Arseneau, Donald J; Garner, David M; Reid, Ivan D; Fleming, Donald G

    2015-07-16

    The kinetics of the addition reaction of muonium (Mu) to acetylene have been studied in the gas phase at N2 moderator pressures mainly from ∼800 to 1000 Torr and over the temperature range from 168 to 446 K, but also down to 200 Torr at 168 K and over a much higher range of pressures, from 10 to 44 bar at 295 K, demonstrating pressure-independent rate constants, kMu(T). Even at 200 Torr moderator pressure, the kinetics for Mu + C2H2 addition behave as if effectively in the high-pressure limit, giving k∞ = kMu due to depolarization of the muon spin in the MuC2H2 radical formed in the addition step. The rate constants kMu(T) exhibit modest Arrhenius curvature over the range of measured temperatures. Comparisons with data and with calculations for the corresponding H(D) + C2H2 addition reactions reveal a much faster rate for the Mu reaction at the lowest temperatures, by 2 orders of magnitude, in accord with the propensity of Mu to undergo quantum tunneling. Moreover, isotopic atom exchange, which contributes in a major way to the analogous D atom reaction, forming C2HD + H, is expected to be unimportant in the case of Mu addition, a consequence of the much higher zero-point energy and hence weaker C-Mu bond that would form, meaning that the present report of the Mu + C2H2 reaction is effectively the only experimental study of kinetic isotope effects in the high-pressure limit for H-atom addition to acetylene. PMID:25664674

  6. A Fluorescent Molecular Probe for the Detection of Hydrogen Based on Oxidative Addition Reactions with Crabtree-Type Hydrogenation Catalysts.

    PubMed

    Kos, Pavlo; Plenio, Herbert

    2015-11-01

    A Crabtree-type Ir(I) complex tagged with a fluorescent dye (bodipy) was synthesized. The oxidative addition of H2 converts the weakly fluorescent Ir(I) complex (Φ=0.038) into a highly fluorescent Ir(III) species (Φ=0.51). This fluorogenic reaction can be utilized for the detection of H2 and to probe the oxidative addition step in the catalytic hydrogenation of olefins.

  7. Synthesis of Heterocycles Through Classical Ugi and Passerini Reactions Followed by Secondary Transformations Involving One or Two Additional Functional Groups

    NASA Astrophysics Data System (ADS)

    Banfi, Luca; Basso, Andrea; Riva, Renata

    The combination of classical isocyanide-based multicomponent reactions (Ugi and Passerini) with a variety of post-condensation transformations, which take advantage of suitably positioned additional functional groups, allows the straightforward synthesis, often in 1-2 synthetic steps, of many diverse nitrogen-containing heterocycles. This review will cover all the applications of this strategy reported to date (September 2009).

  8. Highly enantioselective Michael addition reactions of 2-substituted benzofuran-3(2H)-ones to nitroolefins.

    PubMed

    Zhang, Zhi-Pei; Dong, Nan; Li, Xin; Cheng, Jin-Pei

    2015-10-21

    A highly enantioselective Michael addition reaction of 2-substituted benzofuran-3(2H)-ones to nitroolefins was promoted by a bifunctional squaramide catalyst. As a result, a number of chiral 2,2'-substituted benzofuran-3-one derivatives, bearing adjacent quaternary-tertiary stereocenters, were efficiently synthesized with excellent enantioselectivities.

  9. Addition of CFCl3 to Aromatic Aldehydes via in Situ Grignard Reaction

    DOE PAGES

    Barkakaty, Balaka; Talukdar, Bandana; Lokitz, Bradley

    2015-08-18

    In the case of synthetic modification of trichlorofluoromethane (CFCl3) to non-volatile and useful fluorinated precursors, we realized that it is a cost-effective and an environmentally benign strategy for the safe consumption/destruction of the ozone depleting potential of the reagent. In our report, we present a novel method for in situ Grignard reaction using magnesium powder and CFCl3 for synthesis of dichlorofluoromethyl aromatic alcohols.

  10. Addition of CFCl3 to Aromatic Aldehydes via in Situ Grignard Reaction

    SciTech Connect

    Barkakaty, Balaka; Talukdar, Bandana; Lokitz, Bradley

    2015-08-18

    In the case of synthetic modification of trichlorofluoromethane (CFCl3) to non-volatile and useful fluorinated precursors, we realized that it is a cost-effective and an environmentally benign strategy for the safe consumption/destruction of the ozone depleting potential of the reagent. In our report, we present a novel method for in situ Grignard reaction using magnesium powder and CFCl3 for synthesis of dichlorofluoromethyl aromatic alcohols.

  11. Addition of CFCl3 to Aromatic Aldehydes via in Situ Grignard Reaction.

    PubMed

    Barkakaty, Balaka; Talukdar, Bandana; Lokitz, Bradley S

    2015-01-01

    Synthetic modification of trichlorofluoromethane (CFCl3) to non-volatile and useful fluorinated precursors is a cost-effective and an environmentally benign strategy for the safe consumption/destruction of the ozone depleting potential of the reagent. In this report, we present a novel method for in situ Grignard reaction using magnesium powder and CFCl3 for synthesis of dichlorofluoromethyl aromatic alcohols. PMID:26295221

  12. Reaction pathway of tryptophanase-catalyzed L-tryptophan synthesis from D-serine.

    PubMed

    Shimada, Akihiko; Ozaki, Haruka; Saito, Takeshi; Fujii, Noriko

    2011-11-01

    Tryptophanase, L-tryptophan indole-lyase with extremely absolute stereospecificity, can change the stereospecificity in concentrated diammonium hydrogenphosphate solution. While tryptophanase is not inert to D-serine in the absence of diammonium hydrogenphosphate, it can undergo L-tryptophan synthesis from D-serine along with indole in the presence of it. It has been well known that tryptophanase synthesizes L-tryptophan from L-serine through a β-substitution mechanism of the ping-pong type. However, a metabolic pathway of L-tryptophan synthesis from D-serine has remained unclear. The present study aims to elucidate it. Diammonium hydrogenphosphate plays a role in the emergence of catalytic activity on D-serine. The salt gives tryptophanase a small conformational change, which makes it possible to catalyze D-serine. Tryptophanase-bound D-serine produces L-tryptophan synthesis by β-replacement reaction via the enzyme-bound aminoacrylate intermediate. Our result will be valuable in studying the origin of homochirality.

  13. Exploring two-state reaction pathways in the photodimerization of cyclohexadiene.

    PubMed

    Domingo, Luis R; Pérez-Prieto, Julia

    2006-03-13

    The ground- (S0) and lowest triplet-state (T1) pathways associated with dimerization of cyclohexadiene to give [2+2] and [4+2] cycloadducts have been theoretically studied at the UBLYP and UB3LYP levels of theory with the 6-31G* basis set. The DFT energies were validated by CCSD(T) single-point energy calculations. These cycloaddition reactions follow stepwise mechanisms with formation of bis-allylic biradical (BB) intermediates. In the S0 ground state, the interaction between two cyclohexadiene molecules with formation of BB intermediate IN(S0) has a large activation enthalpy of 32.0 kcal mol(-1). On the other hand, C-C bond-formation in the lowest triplet state (T1) leading to BB intermediate IN(T1) has a low activation enthalpy of 5.0 kcal mol(-1), but the subsequent ring closure involves a very large activation enthalpy of 43.4 kcal mol(-1). Triplet-to-singlet intersystem crossing from IN(T1) to IN(S0) favors cyclization to give the corresponding [2+2] and [4+2] cycloadducts.

  14. p53 and ATF4 mediate distinct and additive pathways to skeletal muscle atrophy during limb immobilization.

    PubMed

    Fox, Daniel K; Ebert, Scott M; Bongers, Kale S; Dyle, Michael C; Bullard, Steven A; Dierdorff, Jason M; Kunkel, Steven D; Adams, Christopher M

    2014-08-01

    Immobilization causes skeletal muscle atrophy via complex signaling pathways that are not well understood. To better understand these pathways, we investigated the roles of p53 and ATF4, two transcription factors that mediate adaptations to a variety of cellular stresses. Using mouse models, we demonstrate that 3 days of muscle immobilization induces muscle atrophy and increases expression of p53 and ATF4. Furthermore, muscle fibers lacking p53 or ATF4 are partially resistant to immobilization-induced muscle atrophy, and forced expression of p53 or ATF4 induces muscle fiber atrophy in the absence of immobilization. Importantly, however, p53 and ATF4 do not require each other to promote atrophy, and coexpression of p53 and ATF4 induces more atrophy than either transcription factor alone. Moreover, muscle fibers lacking both p53 and ATF4 are more resistant to immobilization-induced atrophy than fibers lacking only p53 or ATF4. Interestingly, the independent and additive nature of the p53 and ATF4 pathways allows for combinatorial control of at least one downstream effector, p21. Using genome-wide mRNA expression arrays, we identified p21 mRNA as a skeletal muscle transcript that is highly induced in immobilized muscle via the combined actions of p53 and ATF4. Additionally, in mouse muscle, p21 induces atrophy in a manner that does not require immobilization, p53 or ATF4, and p21 is required for atrophy induced by immobilization, p53, and ATF4. Collectively, these results identify p53 and ATF4 as essential and complementary mediators of immobilization-induced muscle atrophy and discover p21 as a critical downstream effector of the p53 and ATF4 pathways.

  15. Rate and pathways for the reaction of OH with the biogenic p-cymene, an alkylated aromatic

    NASA Astrophysics Data System (ADS)

    Strekowski, R.; Rayez, M.-T.; Rayez, J.-C.; Zetzsch, C.

    2009-04-01

    Aromatics are known to contribute strongly to tropospheric formation of ozone, and p-cymene (4-isopropyltoluene) is one of only a few biogenic, volatile aromatic hydrocarbons. In spite of its symmetry, this molecule (CH3 - °-CH(CH3)2) has a multitude of potential pathways of its reaction with OH radicals. Addition of OH is well-known to be the predominating primary step in the tropospheric transformation of aromatic hydrocarbons. The addition is expected to occur preferably at a non-occupied position, where four positions are available: two equivalent ones ortho to the methyl group and two equivalent ones ortho to the isopropyl group. Furthermore, various C-H bonds (4 aromatic and 10 aliphatic) are available for abstraction, leading to benzyl-type radicals in two cases. The present study combines theoretical calculations with kinetic experiments in the gas phase. The theoretical calculations are based on electronic quantum chemistry DFT method for the investigation of the possible pathways in the potential energy surface of the reaction. The experiments are carried out by the flash photolysis/resonance fluorescence technique. OH radicals are produced by pulsed vacuum-UV photolysis of H2O (> 115 nm) in the presence of p-cymene in a slow flow of He as carrier gas. Their pseudo-first-order decays are monitored by resonance fluorescence, storing the photon counts by multichannel scaling in a PC and accumulating 50 decays each; see Koch et al. (2007) for details of the technique and evaluation of data. The temperature was varied between room temperature (295 K) and 345K, the He pressure was 250 mbar, and the level of p-cymene was increased stepwise, up to 3 x 1013 molecules/cm3. The decays of OH were observed to be exponential at room temperature, becoming clearly biexponential at higher temperatures, thus indicating reversible addition of OH according to the equilibration OH + p-cymene ⇔ p-cymene-OH (1, -1) These reactions might be accompanied by various

  16. Monitoring Wnt Protein Acylation Using an In Vitro Cyclo-Addition Reaction

    PubMed Central

    Tuladhar, Rubina; Yarravarapu, Nageswari; Lum, Lawrence

    2016-01-01

    We describe here a technique for visualizing the lipidation status of Wnt proteins using azide-alkyne cycloaddition chemistry (click chemistry) and SDS-PAGE. This protocol incorporates in vivo labeling of a Wnt-IgG Fc fusion protein using an alkynylated palmitate probe but departs from a traditional approach by incorporating a secondary cycloaddition reaction performed on single-step purified Wnt protein immobilized on protein A resin. This approach mitigates experimental noise by decreasing the contribution of labeling from other palmitoylated proteins and by providing a robust method for normalizing labeling efficiency based on protein abundance. PMID:27590147

  17. Monitoring Wnt Protein Acylation Using an In Vitro Cyclo-Addition Reaction.

    PubMed

    Tuladhar, Rubina; Yarravarapu, Nageswari; Lum, Lawrence

    2016-01-01

    We describe here a technique for visualizing the lipidation status of Wnt proteins using azide-alkyne cycloaddition chemistry (click chemistry) and SDS-PAGE. This protocol incorporates in vivo labeling of a Wnt-IgG Fc fusion protein using an alkynylated palmitate probe but departs from a traditional approach by incorporating a secondary cycloaddition reaction performed on single-step purified Wnt protein immobilized on protein A resin. This approach mitigates experimental noise by decreasing the contribution of labeling from other palmitoylated proteins and by providing a robust method for normalizing labeling efficiency based on protein abundance. PMID:27590147

  18. Tandem bis-aza-Michael addition reaction of amines in aqueous medium promoted by polystyrenesulfonic Acid

    EPA Science Inventory

    An efficient and environmentally benign tandem bis-aza-Michael addition of amines catalyzed by polystyrene sulfonic acid (PSSA) is described. This operationally simple high yielding microwave assisted synthetic protocol proceeded in water in the absence of any organic solvent.

  19. Insight into the reaction mechanisms for oxidative addition of strong σ bonds to an Al(i) center.

    PubMed

    Zhang, Xiangfei; Cao, Zexing

    2016-06-21

    The oxidation addition of a series of σ H-X bonds (X = H, B, C, Si, N, P, and O) to a single Al(i) supported by a (NacNac)(-) bidentate ligand ((NacNac)(-) = [ArNC(Me)CHC(Me)NAr](-) and Ar = 2,6-(i)Pr2C6H3) has been explored through extensive DFT calculations. The presented results show that activation and addition of these σ bonds follow various reaction mechanisms, in which hydride transfer, proton transfer, and Al-X bond coupling steps are involved. The predicted free energy barriers for these oxidative additions range from 8 to 32 kcal mol(-1), and all the reactions are remarkably favorable thermodynamically. However, sterically hindered ligands, for most reactants, make the formation of the initial reactant complex difficult and may reduce the efficiency of the reaction. Calculations reveal a strong dependence of the reaction mechanism and low-energy channel on the bonding features of X-H and the local structural environments. PMID:27249667

  20. Effect of Reaction Pathway on the Extent and Mechanism of Uranium(VI) Immobilization with Calcium and Phosphate.

    PubMed

    Mehta, Vrajesh S; Maillot, Fabien; Wang, Zheming; Catalano, Jeffrey G; Giammar, Daniel E

    2016-03-15

    Phosphate addition to subsurface environments contaminated with uranium can be used as an in situ remediation approach. Batch experiments were conducted to evaluate the dependence of the extent and mechanism of uranium uptake on the pathway for reaction with calcium phosphates. At pH 4.0 and 6.0 uranium uptake from solution occurred via autunite (Ca(UO2)2(PO4)2) precipitation irrespective of the starting forms of calcium and phosphate. At pH 7.5, a condition at which calcium phosphate solids could form, the uptake mechanism depended on the nature of the calcium and phosphate as determined by X-ray absorption spectroscopy and laser-induced fluorescence spectroscopy. When dissolved uranium, calcium, and phosphate were added simultaneously, uranium was structurally incorporated into a newly formed amorphous calcium phosphate solid. Adsorption was the dominant removal mechanism for uranium contacted with preformed amorphous calcium phosphate solids. When U(VI) was added to a suspension containing amorphous calcium phosphate solids as well as dissolved calcium and phosphate, then removal occurred through precipitation (57 ± 4%) of autunite and adsorption (43 ± 4%) onto calcium phosphate. Dissolved uranium, calcium, and phosphate concentrations with saturation index calculations helped identify removal mechanisms and determine thermodynamically favorable solid phases. PMID:26934085

  1. Characterizing the Mechanistic Pathways of the Instant Blood-Mediated Inflammatory Reaction in Xenogeneic Neonatal Islet Cell Transplantation

    PubMed Central

    Liuwantara, David; Chew, Yi Vee; Favaloro, Emmanuel J.; Hawkes, Joanne M.; Burns, Heather L.; O'Connell, Philip J.; Hawthorne, Wayne J.

    2016-01-01

    Introduction The instant blood-mediated inflammatory reaction (IBMIR) causes major loss of islets after transplantation and consequently represents the initial barrier to survival of porcine neonatal islet cell clusters (NICC) after xenotransplantation. Methods This study used novel assays designed to characterize the various immunologic components responsible for xenogeneic IBMIR to identify initiators and investigate processes of IBMIR-associated coagulation, complement activation and neutrophil infiltration. The IBMIR was induced in vitro by exposing NICC to platelet-poor or platelet-rich human plasma or isolated neutrophils. Results We found that xenogeneic IBMIR was characterized by rapid, platelet-independent thrombin generation, with addition of platelets both accelerating and exacerbating this response. Platelet-independent complement activation was observed as early as 30 minutes after NICC exposure to plasma. However, membrane attack complex formation was not observed in NICC histopathology sections until after 60 minutes. We demonstrated for the first time that NICC-mediated complement activation was necessary for neutrophil activation in the xenogeneic IBMIR setting. Finally, using the Seahorse extracellular flux analyzer, we identified substantial loss of islet function (up to 40%) after IBMIR with surviving NICC showing evidence of mitochondrial damage. Conclusions This study used novel assays to describe multiple key pathways by which xenogeneic IBMIR causes islet destruction, allowing further refinement of future interventions aimed at resolving the issue of IBMIR in xenotransplantation. PMID:27500267

  2. Organocatalytic Domino Oxa-Michael/1,6-Addition Reactions: Asymmetric Synthesis of Chromans Bearing Oxindole Scaffolds.

    PubMed

    Zhao, Kun; Zhi, Ying; Shu, Tao; Valkonen, Arto; Rissanen, Kari; Enders, Dieter

    2016-09-19

    An asymmetric organocatalytic domino oxa-Michael/1,6-addition reaction of ortho-hydroxyphenyl-substituted para-quinone methides and isatin-derived enoates has been developed. In the presence of 5 mol % of a bifunctional thiourea organocatalyst, this scalable domino reaction affords 4-phenyl-substituted chromans bearing spiro-connected oxindole scaffolds and three adjacent stereogenic centers in good to excellent yields (up to 98 %) and with very high stereoselectivities (up to >20:1 d.r., >99 % ee). PMID:27600477

  3. Organocatalytic Domino Oxa-Michael/1,6-Addition Reactions: Asymmetric Synthesis of Chromans Bearing Oxindole Scaffolds.

    PubMed

    Zhao, Kun; Zhi, Ying; Shu, Tao; Valkonen, Arto; Rissanen, Kari; Enders, Dieter

    2016-09-19

    An asymmetric organocatalytic domino oxa-Michael/1,6-addition reaction of ortho-hydroxyphenyl-substituted para-quinone methides and isatin-derived enoates has been developed. In the presence of 5 mol % of a bifunctional thiourea organocatalyst, this scalable domino reaction affords 4-phenyl-substituted chromans bearing spiro-connected oxindole scaffolds and three adjacent stereogenic centers in good to excellent yields (up to 98 %) and with very high stereoselectivities (up to >20:1 d.r., >99 % ee).

  4. Evaluation of lead anode reactions in acid sulfate electrolytes. 1: Lead alloys with cobalt additives

    SciTech Connect

    Yu, P.; O`Keefe, T.J.

    1999-04-01

    Lead alloys, such as lead-calcium-tin and lead-silver, are the primary insoluble anodes used in the electrowinning of metals. While some difficulties are encountered in their use, there is no obvious replacement that is economically and technically competitive. Two of the specific problems with lead include decreased cathode purity due to incorporation from corrosion products and the relatively high overpotential which increases cell voltage. To gain an improved understanding of the fundamental behavior of lead anodes, the polarization behavior of six different alloys in sulfuric acid was evaluated. Some tests were also made with Co(II) in the acid sulfate electrolyte. Notable differences were found in the multiple activation-passivation cycles, stability, and relative activity for oxygen evolution for the alloys, and the relative trends in behavior were established. Electrochemical impedance spectroscopy studies were also conducted at selected potentials. Overall, the data show that the electrochemical response, particularly the degree of polarization for the oxygen evolution reaction, of the lead alloy anodes are dependent on the surface phases and structures present. The ability to depolarize the anode reaction using Co(II) was particularly sensitive to the lead composition.

  5. Reaction pathways for bio-active species in a He/H2O atmospheric pressure capacitive discharge

    NASA Astrophysics Data System (ADS)

    Ding, Ke; Lieberman, M. A.

    2015-01-01

    Helium/trace gas atmospheric pressure radio-frequency (rf) capacitive discharges have increasing biomedical applications. We have performed a principal pathway analysis for a chemically complex, bounded He/H2O atmospheric pressure, planar capacitive discharge, with a discharge gap of 0.5 mm and a power of 0.85 W cm-2 at 13.56 MHz (ne ≈ 1.6 × 1017 m-3). The discharge is embedded in a larger volume in which the H2O fraction is controlled to be 0.001. The generation and loss pathways for eleven species of interest for discharge maintenance and biomedical applications have been determined. The production and consumption pathways of He*, H2O, {{\\text{H}}11}\\text{O}5+ and electrons are found to be tightly coupled. The metastable He* generated by electron impact excitation of He is mostly consumed by Penning reactions with H2O, followed by subsequent three-body association reactions with H2O, to form the dominant positive ion, {{\\text{H}}11}\\text{O}5+ . The main loss pathways for {{\\text{H}}11}\\text{O}5+ are ion cluster fragmentations at the wall, which are important generation pathways for H2O. The generation and loss pathways for electrons are almost the same as for {{\\text{H}}11}\\text{O}5+ . OH and H2O2 generation and loss are strongly coupled, and they are important intermediate species in the generation pathways for the purely O-containing bio-active species: O2(a), O, O3 and O*. The generation and loss pathways for the latter four species were found to be strongly coupled by volume and surface processes, with O2 as an important precursor. The generation of O2 from H2O involves H2O2 as a key long-lived intermediate.

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

    NASA Astrophysics Data System (ADS)

    McCaig, Andrew; Castelain, Teddy; Klein, Frieder

    2013-04-01

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

  7. Heterogeneous versus homogeneous copper(II) catalysis in enantioselective conjugate-addition reactions of boron in water.

    PubMed

    Kitanosono, Taku; Xu, Pengyu; Kobayashi, Shū

    2014-01-01

    We have developed Cu(II)-catalyzed enantioselective conjugate-addition reactions of boron to α,β-unsaturated carbonyl compounds and α,β,γ,δ-unsaturated carbonyl compounds in water. In contrast to the previously reported Cu(I) catalysis that required organic solvents, chiral Cu(II) catalysis was found to proceed efficiently in water. Three catalyst systems have been exploited: cat. 1: Cu(OH)2 with chiral ligand L1; cat. 2: Cu(OH)2 and acetic acid with ligand L1; and cat. 3: Cu(OAc)2 with ligand L1. Whereas cat. 1 is a heterogeneous system, cat. 2 and cat. 3 are homogeneous systems. We tested 27 α,β-unsaturated carbonyl compounds and an α,β-unsaturated nitrile compound, including acyclic and cyclic α,β-unsaturated ketones, acyclic and cyclic β,β-disubstituted enones, acyclic and cyclic α,β-unsaturated esters (including their β,β-disubstituted forms), and acyclic α,β-unsaturated amides (including their β,β-disubstituted forms). We found that cat. 2 and cat. 3 showed high yields and enantioselectivities for almost all substrates. Notably, no catalysts that can tolerate all of these substrates with high yields and high enantioselectivities have been reported for the conjugate addition of boron. Heterogeneous cat. 1 also gave high yields and enantioselectivities with some substrates and also gave the highest TOF (43,200 h(-1) ) for an asymmetric conjugate-addition reaction of boron. In addition, the catalyst systems were also applicable to the conjugate addition of boron to α,β,γ,δ-unsaturated carbonyl compounds, although such reactions have previously been very limited in the literature, even in organic solvents. 1,4-Addition products were obtained in high yields and enantioselectivities in the reactions of acyclic α,β,γ,δ-unsaturated carbonyl compounds with diboron 2 by using cat. 1, cat. 2, or cat. 3. On the other hand, in the reactions of cyclic α,β,γ,δ-unsaturated carbonyl compounds with compound 2, whereas 1,4-addition products

  8. Heterogeneous versus homogeneous copper(II) catalysis in enantioselective conjugate-addition reactions of boron in water.

    PubMed

    Kitanosono, Taku; Xu, Pengyu; Kobayashi, Shū

    2014-01-01

    We have developed Cu(II)-catalyzed enantioselective conjugate-addition reactions of boron to α,β-unsaturated carbonyl compounds and α,β,γ,δ-unsaturated carbonyl compounds in water. In contrast to the previously reported Cu(I) catalysis that required organic solvents, chiral Cu(II) catalysis was found to proceed efficiently in water. Three catalyst systems have been exploited: cat. 1: Cu(OH)2 with chiral ligand L1; cat. 2: Cu(OH)2 and acetic acid with ligand L1; and cat. 3: Cu(OAc)2 with ligand L1. Whereas cat. 1 is a heterogeneous system, cat. 2 and cat. 3 are homogeneous systems. We tested 27 α,β-unsaturated carbonyl compounds and an α,β-unsaturated nitrile compound, including acyclic and cyclic α,β-unsaturated ketones, acyclic and cyclic β,β-disubstituted enones, acyclic and cyclic α,β-unsaturated esters (including their β,β-disubstituted forms), and acyclic α,β-unsaturated amides (including their β,β-disubstituted forms). We found that cat. 2 and cat. 3 showed high yields and enantioselectivities for almost all substrates. Notably, no catalysts that can tolerate all of these substrates with high yields and high enantioselectivities have been reported for the conjugate addition of boron. Heterogeneous cat. 1 also gave high yields and enantioselectivities with some substrates and also gave the highest TOF (43,200 h(-1) ) for an asymmetric conjugate-addition reaction of boron. In addition, the catalyst systems were also applicable to the conjugate addition of boron to α,β,γ,δ-unsaturated carbonyl compounds, although such reactions have previously been very limited in the literature, even in organic solvents. 1,4-Addition products were obtained in high yields and enantioselectivities in the reactions of acyclic α,β,γ,δ-unsaturated carbonyl compounds with diboron 2 by using cat. 1, cat. 2, or cat. 3. On the other hand, in the reactions of cyclic α,β,γ,δ-unsaturated carbonyl compounds with compound 2, whereas 1,4-addition products

  9. Synthesis of Diverse Heterocyclic Scaffolds via Tandem Additions to Imine Derivatives and Ring-Forming Reactions

    PubMed Central

    Sunderhaus, James D.; Dockendorff, Chris; Martin, Stephen F.

    2009-01-01

    A novel strategy has been developed for the efficient syntheses of diverse arrays of heterocyclic compounds. The key elements of the approach comprise a Mannich-type, multicomponent coupling reaction in which functionalized amines, aromatic aldehydes, acylating agents, and π- and organometallic nucleophiles are combined to generate intermediates that are then further transformed into diverse heterocyclic scaffolds via a variety of cyclization manifolds. Significantly, many of these scaffolds bear functionality that may be exploited by further manipulation to create diverse collections of compounds having substructures found in biologically active natural products and clinically useful drugs. The practical utility of this strategy was exemplified by its application to the first, and extraordinarily concise synthesis of the isopavine alkaloid roelactamine. PMID:20625454

  10. A combined QM/MM study of the nucleophilic addition reaction of methanethiolate and N-methylacetamide.

    PubMed

    Byun, K; Gao, J

    2000-02-01

    A combined quantum mechanical (QM) and molecular mechanical (MM) method was used to study the nucleophilic addition reaction of methanethiolate to N-methylacetamide (NMA) in the gas phase and aqueous solution. At the B3LYP/aug-cc-pVDZ//HF/6-31 + G(d) level, the ion-dipole complex was found to be the global minimum on the potential energy surface in the gas phase with a binding energy of 21.2 kcal/mol. The complex has a C-S distance of 4.33 A, and no stabilized tetrahedral intermediate was located. The computed potential of mean force in water shows that solvent effects stabilize the reactants over the tetrahedral adduct by 36.5 kcal/mol, and that the tetrahedral intermediate does not exist for the present reaction in water. The present study provides an initial step for modeling the cysteine protease hydrolysis reactions in enzymes.

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

    PubMed

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

    2016-07-01

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

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

    PubMed Central

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

    2016-01-01

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. PMID:27131375

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

    ERIC Educational Resources Information Center

    Latimer, Devin

    2007-01-01

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

  14. Synthesis of a Fluorescent Acridone Using a Grignard Addition, Oxidation, and Nucleophilic Aromatic Substitution Reaction Sequence

    ERIC Educational Resources Information Center

    Goodrich, Samuel; Patel, Miloni; Woydziak, Zachary R.

    2015-01-01

    A three-pot synthesis oriented for an undergraduate organic chemistry laboratory was developed to construct a fluorescent acridone molecule. This laboratory experiment utilizes Grignard addition to an aldehyde, alcohol oxidation, and iterative nucleophilic aromatic substitution steps to produce the final product. Each of the intermediates and the…

  15. Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

    PubMed

    Du, Qingzhang; Tian, Jiaxing; Yang, Xiaohui; Pan, Wei; Xu, Baohua; Li, Bailian; Ingvarsson, Pär K; Zhang, Deqiang

    2015-02-01

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

  16. Stereoselective synthesis of densely functionalized pyrrolidin-2-ones by a conjugate addition/nitro-Mannich/lactamization reaction.

    PubMed

    Anderson, James C; Horsfall, Lisa R; Kalogirou, Andreas S; Mills, Matthew R; Stepney, Gregory J; Tizzard, Graham J

    2012-07-20

    Copper-catalyzed conjugate addition of diorgano zinc reagents to nitroacrylate 1 followed by a subsequent nitro-Mannich reaction and in situ lactamization leads to an efficient one-pot synthesis of 1,3,5-trisubstituted 4-nitropyrrolidin-2-ones (5). The versatility of the reaction is shown for a wide range of N-p-(methoxy)phenyl protected aldimines 3 derived from alkyl, aryl, and heteroaryl aldehydes. The densely functionalized pyrrolidin-2-ones 5 are isolated as single diastereoisomers (40 examples, 33-84% yield). An enantioselective copper-catalyzed conjugate addition of diethylzinc led to highly crystalline products that could be recrystallized to enantiopurity in high yield. A range of successful chemoselective transformations were investigated, which widens the applicability of the pyrrolidn-2-ones as stereochemically pure building blocks for further organic synthesis. PMID:22708711

  17. Michael-type addition reactions for the in situ formation of poly(vinyl alcohol)-based hydrogels.

    PubMed

    Tortora, Mariarosaria; Cavalieri, Francesca; Chiessi, Ester; Paradossi, Gaio

    2007-01-01

    Michael-type addition reactions offer the possibility to obtain in situ formation of polymeric hydrogels in the absence of a radical mechanism for the networking process. We explored such a synthetic route for obtaining a poly(vinyl alcohol) (PVA)-based hydrogel as a potential biomaterial for applications in vitro-retinal replacement surgery. The presence of radicals in the reaction medium can represent a risk for in situ surgical treatment. To circumvent this problem we have applied nucleophilic addition to ad hoc modified PVA macromers. The gel formation has been studied with respect to the timing required in this surgery and in terms of the structural characteristics of the obtained network.

  18. Convergent Synthesis of Diverse Nitrogen Heterocycles via Rh(III)-Catalyzed C-H Conjugate Addition/Cyclization Reactions.

    PubMed

    Weinstein, Adam B; Ellman, Jonathan A

    2016-07-01

    The development of Rh(III)-catalyzed C-H conjugate addition/cyclization reactions that provide access to synthetically useful fused bi- and tricyclic nitrogen heterocycles is reported. A broad scope of C-H functionalization substrates and electrophilic olefin coupling partners is effective, and depending on the nature of the directing group, cyclic imide, amide, or heteroaromatic products are obtained. An efficient synthesis of a pyrrolophenanthridine alkaloid natural product, oxoassoanine, highlights the utility of this method.

  19. Intramolecular 1,1-carboboration versus intermolecular FLP addition in reactions of boranes and bis(phenylethynyl)telluroether.

    PubMed

    Tsao, Fu An; Lough, Alan J; Stephan, Douglas W

    2015-03-11

    Reactions of boranes with Te(CCPh)2 proceed via initial intermolecular 1,1-carboboration followed by either an intramolecular carboboration or an FLP addition to a second molecule of the intermediate, yielding 1-bora-4-tellurocyclohexa-2,5-diene heterocycles or tricylic derivatives of 1,4-ditellurocyclohexa-2,5-diene, respectively. The latter species is also shown to convert to the former upon heating.

  20. Convergent Synthesis of Diverse Nitrogen Heterocycles via Rh(III)-Catalyzed C-H Conjugate Addition/Cyclization Reactions.

    PubMed

    Weinstein, Adam B; Ellman, Jonathan A

    2016-07-01

    The development of Rh(III)-catalyzed C-H conjugate addition/cyclization reactions that provide access to synthetically useful fused bi- and tricyclic nitrogen heterocycles is reported. A broad scope of C-H functionalization substrates and electrophilic olefin coupling partners is effective, and depending on the nature of the directing group, cyclic imide, amide, or heteroaromatic products are obtained. An efficient synthesis of a pyrrolophenanthridine alkaloid natural product, oxoassoanine, highlights the utility of this method. PMID:27337641

  1. C-C Bond Formation via Copper-Catalyzed Conjugate Addition Reactions to Enones in Water at Room Temperature

    PubMed Central

    Lipshutz, Bruce H.; Huang, Shenlin; Leong, Wendy Wen Yi; Isley, Nicholas A.

    2013-01-01

    Conjugate addition reactions to enones can now be done in water at room temperature with in situ-generated organocopper reagents. Mixing an enone, zinc powder, TMEDA, and an alkyl halide in a micellar environemnt containing catalytic amounts of Cu(I), Ag(I), and Au(III), leads to 1,4-adducts in good isolated yields: no organometallic precursor is involved. PMID:23190029

  2. Well-to-Wheels analysis of landfill gas-based pathways and their addition to the GREET model.

    SciTech Connect

    Mintz, M.; Han, J.; Wang, M.; Saricks, C.; Energy Systems

    2010-06-30

    Today, approximately 300 million standard cubic ft/day (mmscfd) of natural gas and 1600 MW of electricity are produced from the decomposition of organic waste at 519 U.S. landfills (EPA 2010a). Since landfill gas (LFG) is a renewable resource, this energy is considered renewable. When used as a vehicle fuel, compressed natural gas (CNG) produced from LFG consumes up to 185,000 Btu of fossil fuel and generates from 1.5 to 18.4 kg of carbon dioxide-equivalent (CO{sub 2}e) emissions per million Btu of fuel on a 'well-to-wheel' (WTW) basis. This compares with approximately 1.1 million Btu and 78.2 kg of CO{sub 2}e per million Btu for CNG from fossil natural gas and 1.2 million Btu and 97.5 kg of CO{sub 2}e per million Btu for petroleum gasoline. Because of the additional energy required for liquefaction, LFG-based liquefied natural gas (LNG) requires more fossil fuel (222,000-227,000 Btu/million Btu WTW) and generates more GHG emissions (approximately 22 kg CO{sub 2}e /MM Btu WTW) if grid electricity is used for the liquefaction process. However, if some of the LFG is used to generate electricity for gas cleanup and liquefaction (or compression, in the case of CNG), vehicle fuel produced from LFG can have no fossil fuel input and only minimal GHG emissions (1.5-7.7 kg CO{sub 2}e /MM Btu) on a WTW basis. Thus, LFG-based natural gas can be one of the lowest GHG-emitting fuels for light- or heavy-duty vehicles. This report discusses the size and scope of biomethane resources from landfills and the pathways by which those resources can be turned into and utilized as vehicle fuel. It includes characterizations of the LFG stream and the processes used to convert low-Btu LFG into high-Btu renewable natural gas (RNG); documents the conversion efficiencies and losses of those processes, the choice of processes modeled in GREET, and other assumptions used to construct GREET pathways; and presents GREET results by pathway stage. GREET estimates of well-to-pump (WTP), pump

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

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Walch, Stephen P.

    2002-01-01

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

  4. Core-structure-inspired asymmetric addition reactions: enantioselective synthesis of dihydrobenzoxazinone- and dihydroquinazolinone-based anti-HIV agents.

    PubMed

    Li, Shen; Ma, Jun-An

    2015-11-01

    Dihydrobenzoxazinones and dihydroquinazolinones are the core units present in many anti-HIV agents, such as Efavirenz, DPC 961, DPC 963, and DPC 083. All these molecules contain a trifluoromethyl moiety at the quaternary stereogenic carbon center with S configuration. The enantioselective addition of carbon nucleophiles to ketones or cyclic ketimines could serve as a key step to access these molecules. This tutorial review provides an overview of significant advances in the synthesis of dihydrobenzoxazinone- and dihydroquinazolinone-based anti-HIV agents and relative analogues, with an emphasis on asymmetric addition reactions for the establishment of the CF3-containing quaternary carbon centers.

  5. Modifying structure-sensitive reactions by addition of Zn to Pd

    SciTech Connect

    Childers, David J.; Schweitzer, Neil M.; Kamali Shahari, Seyed Mehdi; Rioux, Robert M.; Miller, Jeffrey T.; Meyer, Randall J.

    2014-10-01

    Silica-supported Pd and PdZn nanoparticles of a similar size were evaluated for neopentane hydrogenolysis/isomerization and propane hydrogenolysis/dehydrogenation. Monometallic Pd showed high neopentane hydrogenolysis selectivity. Addition of small amounts of Zn to Pd lead Pd–Zn scatters in the EXAFS spectrum and an increase in the linear bonded CO by IR. In addition, the neopentane turnover rate decreased by nearly 10 times with little change in the selectivity. Increasing amounts of Zn lead to greater Pd–Zn interactions, higher linear-to-bridging CO ratios by IR and complete loss of neopentane conversion. Pd NPs also had high selectivity for propane hydrogenolysis and thus were poorly selective for propylene. The PdZn bimetallic catalysts, however, were able to preferentially catalyze dehydrogenation, were not active for propane hydrogenolysis, and thus were highly selective for propylene formation. The decrease in hydrogenolysis selectivity was attributed to the isolation of active Pd atoms by inactive metallic Zn,demonstrating that hydrogenolysis requires a particular reactive ensemble whereas propane dehydrogenation does not.

  6. Effect of temperature on the reaction pathway of calcium carbonate formation via precursor phases

    NASA Astrophysics Data System (ADS)

    Purgstaller, Bettina; Mavromatis, Vasileios; Konrad, Florian; Dietzel, Martin

    2016-04-01

    It has been earlier postulated that some biogenic and sedimentary calcium carbonate (CaCO3) minerals (e.g. calcite and aragonite) are secondary in origin and have originally formed via a metastable calcium carbonate precursor phase (e.g. amorphous CaCO3, [1-2]). Such formation pathways are likely affected by various physicochemical parameters including aqueous Mg and temperature. In an effort to improve our understanding on the formation mechanism of CaCO3 minerals, precipitation experiments were carried out by the addition of a 0.6 M (Ca,Mg)Cl2 solution at distinct Mg/Ca ratios (1/4 and 1/8) into a 1 M NaHCO3 solution under constant pH conditions(8.3 ±0.1). The formation of CaCO3 was systematically examined as a function of temperature (6, 12, 18 and 25 ±0.3° C). During the experimental runs mineral precipitation was monitored by in situ Raman spectroscopy as well as by continuous sampling and analyzing of precipitates and reactive solutions. The results revealed two pathways of CaCO3 formation depending on the initial Mg/Ca ratio and temperature: (i) In experiments with a Mg/Ca ratio of 1/4 at ≤ 12° C as well as in experiments with a Mg/Ca ratio of 1/8 at ≤ 18° C, ikaite (CaCO3 6H2O) acts as a precursor phase for aragonite formation. (ii) In contrast higher temperatures induced the formation of Mg-rich amorphous CaCO3 (Mg-ACC) which was subsequently transformed to Mg-rich calcite. In situ Raman spectra showed that the transformation of Mg-ACC to Mg-calcite occurs at a higher rate (˜ 8 min) compared to that of ikaite to aragonite (> 2 h). Thus, the formation of aragonite rather than of Mg-calcite occurs due to the slower release of Ca2+and CO32- ions into the Mg-rich reactive solution during retarded ikaite dissolution. This behavior is generally consistent with the observation that calcite precipitation is inhibited at elevated aqueous Mg/Ca ratios. [1] Addadi L., Raz S. and Weiner S. (2003) Advanced Materials 15, 959-970. [2] Rodriguez-Blanco J. D

  7. Pathway development and pilot library realization in diversity-oriented synthesis: exploring Ferrier and Pauson-Khand reactions on a glycal template.

    PubMed

    Kubota, Hideki; Lim, Jongwon; Depew, Kristopher M; Schreiber, Stuart L

    2002-02-01

    Through a correlation of the ability of small molecules to bind biological macromolecules and their ability to modulate cellular and organismal processes, chemistry can inform biology and vice versa. Diversity-oriented organic synthesis (DOS), which aims to provide structurally complex and diverse small molecules efficiently, can play a key role in such chemical genetic studies. Here we illustrate the trial-and-error experimentation that can refine an initial pathway-planning exercise and result eventually in an effective diversity pathway. By exploring Ferrier and Pauson-Khand reactions on a glycal template, we have developed efficient and stereoselective syntheses of tricyclic compounds. In this pathway, diversity results from the substituents and their spatial relationships about the tricyclic rings. A pilot split-pool library synthesis of 2500 tricyclic compounds highlights the use of planning considerations in DOS and a "one-bead, one-stock solution" technology platform. Additionally, it illustrates a promising synthetic pathway for future chemical genetic studies. PMID:11880041

  8. Nickel and cobalt-catalyzed coupling of alkyl halides with alkenes via heck reactions and radical conjugate addition.

    PubMed

    Qian, Qun; Zang, Zhenhua; Chen, Yang; Tong, Weiqi; Gong, Hegui

    2013-05-01

    Cross-coupling of alkyl halides with alkenes leading to Heck-type and addition products is summarized. The development of Heck reaction with aliphatic halides although has made significant progress in the past decade and particularly recently, it was much less explored in comparison with the aryl halides. The use of Ni- and Co-catalyzed protocols allowed efficient Heck coupling of activated and unactivated alkenes with 1°, 2° and 3° alkyl halides. In addition, radical conjugate addition to activated alkenes has become a well-established method that has led to efficient construction of many natural products. The utilization of Ni- and Co-catalyzed strategies would avoid toxic tin reagents, and therefore worth exploring. The recent development of Ni- and Co-catalyzed addition of alkyl halides to alkenes displays much improved reactivity and functional group tolerance. In this mini-review, we also attempt to overview the mechanisms that are proposed in the reactions, aiming at providing insight into the nickel and cobalt-catalyzed coupling of alkyl halides with alkenes.

  9. Highly Functionalized Cyclopentane Derivatives by Tandem Michael Addition/Radical Cyclization/Oxygenation Reactions.

    PubMed

    Holan, Martin; Pohl, Radek; Císařová, Ivana; Klepetářová, Blanka; Jones, Peter G; Jahn, Ullrich

    2015-06-26

    Densely functionalized cyclopentane derivatives with up to four consecutive stereocenters are assembled by a tandem Michael addition/single-electron transfer oxidation/radical cyclization/oxygenation strategy mediated by ferrocenium hexafluorophosphate, a recyclable, less toxic single-electron transfer oxidant. Ester enolates were coupled with α-benzylidene and α-alkylidene β-dicarbonyl compounds with switchable diastereoselectivity. This pivotal steering element subsequently controls the diastereoselectivity of the radical cyclization step. The substitution pattern of the radical cyclization acceptor enables a switch of the cyclization mode from a 5-exo pattern for terminally substituted olefin units to a 6-endo mode for internally substituted acceptors. The oxidative anionic/radical strategy also allows efficient termination by oxygenation with the free radical 2,2,6,6-tetramethyl-1-piperidinoxyl, and two C-C bonds and one C-O bond are thus formed in the sequence. A stereochemical model is proposed that accounts for all of the experimental results and allows the prediction of the stereochemical outcome. Further transformations of the synthesized cyclopentanes are reported.

  10. Pathways of nitrobenzene degradation in horizontal subsurface flow constructed wetlands: Effect of intermittent aeration and glucose addition.

    PubMed

    Kirui, Wesley K; Wu, Shubiao; Kizito, Simon; Carvalho, Pedro N; Dong, Renjie

    2016-01-15

    Intermittent aeration and addition of glucose were applied to horizontal subsurface flow constructed wetlands in order to investigate the effect on pathways of nitrobenzene (NB) degradation and interactions with microbial nitrogen and sulphur transformations. The experiment was carried out in three phases A, B and C consisting of different NB loading and glucose dosing. For each phase, the effect of aeration was assessed by intermittently aerating one wetland and leaving one unaerated. Regardless of whether or not the wetland was aerated, at an influent NB concentration of 140 mg/L, both wetlands significantly reduced NB to less than 2 mg/L, a reduction efficiency of 98%. However, once the influent NB concentration was increased to 280 mg/L, the aerated wetland had a higher removal performance 82% compared to that of the unaerated wetland 71%. Addition of glucose further intensified the NB removal to 95% in the aerated wetlands and 92% in the unaerated. Aeration of wetlands enhanced NB degradation, but also resulted in higher NB volatilization of 6 mg m(-2) d(-1). The detected high concentration of sulphide 20-60 mg/L in the unaerated wetland gave a strong indication that NB may act as an electron donor to sulphate-reducing bacteria, but this should be further investigated. Aeration positively improved NB removal in constructed wetlands, but resulted in higher NB volatilization. Glucose addition induced co-metabolism to enhance NB degradation. PMID:26468606

  11. Pathways of nitrobenzene degradation in horizontal subsurface flow constructed wetlands: Effect of intermittent aeration and glucose addition.

    PubMed

    Kirui, Wesley K; Wu, Shubiao; Kizito, Simon; Carvalho, Pedro N; Dong, Renjie

    2016-01-15

    Intermittent aeration and addition of glucose were applied to horizontal subsurface flow constructed wetlands in order to investigate the effect on pathways of nitrobenzene (NB) degradation and interactions with microbial nitrogen and sulphur transformations. The experiment was carried out in three phases A, B and C consisting of different NB loading and glucose dosing. For each phase, the effect of aeration was assessed by intermittently aerating one wetland and leaving one unaerated. Regardless of whether or not the wetland was aerated, at an influent NB concentration of 140 mg/L, both wetlands significantly reduced NB to less than 2 mg/L, a reduction efficiency of 98%. However, once the influent NB concentration was increased to 280 mg/L, the aerated wetland had a higher removal performance 82% compared to that of the unaerated wetland 71%. Addition of glucose further intensified the NB removal to 95% in the aerated wetlands and 92% in the unaerated. Aeration of wetlands enhanced NB degradation, but also resulted in higher NB volatilization of 6 mg m(-2) d(-1). The detected high concentration of sulphide 20-60 mg/L in the unaerated wetland gave a strong indication that NB may act as an electron donor to sulphate-reducing bacteria, but this should be further investigated. Aeration positively improved NB removal in constructed wetlands, but resulted in higher NB volatilization. Glucose addition induced co-metabolism to enhance NB degradation.

  12. Semifluorinated polymers via cycloaddition and nucleophilic addition reactions of aromatic trifluorovinyl ethers

    NASA Astrophysics Data System (ADS)

    Iacono, Scott Thomas

    This dissertation encompasses the synthesis, characterization, and properties of semifluorinated polymers derived from thermal polymerization of aryl trifluorovinyl ether (TFVE) monomers. This work is divided into two parts based on the methodology of thermal polymerization using aryl TFVE monomers. The first part of this work involves the thermal [2 + 2] cyclodimerization of aryl TFVE monomers affording perfluorocyclobutyl (PFCB) aryl ether polymers. Chapter 1 provides an overview of PFCB aryl ether polymers as a next-generation class of high performance fluoropolymers that have been successfully employed for a myriad of technologies. PFCB aryl ether polymers are highly desired because of their high thermal stability, processability, and tailorability for specific material applications. Chapter 2 introduces a general perspective of polyhedral oligomeric silsesquioxanes (POSS) that were modified with PFCB aryl ether polymer for property enhancement, specifically for low surface energy materials. Chapter 3 and 4 show the synthesis, characterization, and properties of POSS modified PFCB aryl ether polymers as blends and a variety of copolymer architectures, respectively. The second portion of this dissertation focuses on the development of a new, facile step-growth polymerization of diols/bisphenols and aryl TFVEs to afford fluoroethylene/vinylene alkyl/aryl ether (FAE) polymers. Chapter 5 is a prelude to the development of FAE polymers which entails optimizing the methodology and mechanistic rationale of nucleophile addition to aryl TFVEs. Chapter 6 details the FAE polymerization kinetics, physical properties, and strategy for functionalization. Chapter 7 illustrates the modular modification of FAE polymers for the development of tunable light emissive materials for potential use as transport layer material for organic light emitting diodes (OLEDs) and also chemical sensors. Chapter 8 introduces postfunctionaliztion of FAE polymers resulting with sulfonated biaryl

  13. Scope and limitations of aliphatic Friedel-Crafts alkylations. Lewis acid catalyzed addition reactions of alkyl chlorides to carbon-carbon double bonds

    SciTech Connect

    Mayr, H.; Striepe, W.

    1983-04-22

    Lewis acid catalyzed addition reactions of alkyl halides with unsaturated hydrocarbons have been studied. 1:1 addition products are formed if the addends dissociate faster than the corresponding products; otherwise, polymerization takes place. For reaction conditions under which these compounds exist mainly undissociated, solvolysis constants of model compounds can be used to predict the outcome of any such addition reactions if systems with considerable steric hindrance are excluded.

  14. Probing the Additional Capacity and Reaction Mechanism of the RuO2 Anode in Lithium Rechargeable Batteries.

    PubMed

    Kim, Yunok; Muhammad, Shoaib; Kim, Hyunchul; Cho, Yong-Hun; Kim, Hansu; Kim, Ji Man; Yoon, Won-Sub

    2015-07-20

    The structural changes and electrochemical behavior of RuO2 are investigated by using in situ XRD, X-ray absorption spectroscopy, and electrochemical techniques to understand the electrochemical reaction mechanism of this metal oxide anode material. Intermediate phase-assisted transformation of RuO2 to LiRuO2 takes place at the start of discharge. Upon further lithiation, LiRuO2 formed by intercalation decomposes to nanosized Ru metal and Li2 O by a conversion reaction. A reversible capacity in addition to its theoretical capacity is observed on discharging below 0.5 V during which no redox activity involving Ru is observed. TEM, X-ray photoelectron spectroscopy, and the galvanostatic intermittent titration technique are used to probe this additional capacity. The results show that the additional capacity is a result of Li storage in the grain boundary between nanosized Ru metal and Li2 O. Findings of this study provide a better understanding of the quantitative share of capacity by a unique combination of intercalation, conversion, and interfacial Li storage in a RuO2 anode.

  15. The phenyl + phenyl reaction as pathway to benzynes: An experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Dürrstein, Steffen H.; Olzmann, Matthias; Aguilera-Iparraguirre, Jorge; Barthel, Robert; Klopper, Wim

    2011-09-01

    Theoretical and experimental results shed light on the phenyl + phenyl reaction. Benzyne formation in the phenyl + phenyl reaction is important. Rate for benzyne formation is one order of magnitude below recombination rate. Coupled-cluster barrier heights differ significantly from CASPT2 results. Satisfactory agreement between B3LYP and coupled-cluster results.

  16. Charting an Alternate Pathway to Reaction Orders and Rate Laws in Introductory Chemistry Courses

    ERIC Educational Resources Information Center

    Rushton, Gregory T.; Criswell, Brett A.; McAllister, Nicole D.; Polizzi, Samuel J.; Moore, Lamesha A.; Pierre, Michelle S.

    2014-01-01

    Reaction kinetics is an axiomatic topic in chemistry that is often addressed as early as the high school course and serves as the foundation for more sophisticated conversations in college-level organic, physical, and biological chemistry courses. Despite the fundamental nature of reaction kinetics, students can struggle with transforming their…

  17. Adapting to substrate challenges: peptides as catalysts for conjugate addition reactions of aldehydes to α,β-disubstituted nitroolefins.

    PubMed

    Duschmalé, Jörg; Wennemers, Helma

    2012-01-23

    Conjugate addition reactions of aldehydes to α,β-disubstituted nitroolefins are important because they provide synthetically useful γ-nitroaldehydes bearing three consecutive stereogenic centers. Such reactions are challenging due to the drastically lower reactivity of α,β-disubstituted nitroolefins compared to, for example, β-monosubstituted nitroolefins. The testing of a small collection of peptides of the type Pro-Pro-Xaa (Xaa=acidic amino acid) led to the identification of H-Pro-Pro-D-Gln-OH and H-Pro-Pro-Asn-OH as excellent stereoselective catalysts for this transformation. In the presence of 5 mol% of these peptides different combinations of aldehydes and α,β-disubstituted nitroolefins react readily with each other providing γ-nitroaldehydes in good yields and diastereoselectivities as well as excellent enantioselectivities. Chiral pyrrolidines as well as fully substituted γ-butyrolactams and γ-amino acids are easily accessible from the γ-nitroaldehydes. Mechanistic studies demonstrate that the configuration at all three stereogenic centers is induced by the peptidic catalysts. Only a minimal amount of products from homo-aldol reactions is observed demonstrating the high chemoselectivity of the peptidic catalysts.

  18. Concise Enantioselective Synthesis of Oxygenated Steroids via Sequential Copper(II)-Catalyzed Michael Addition/Intramolecular Aldol Cyclization Reactions.

    PubMed

    Cichowicz, Nathan R; Kaplan, Will; Khomutnyk, Yaroslav; Bhattarai, Bijay; Sun, Zhankui; Nagorny, Pavel

    2015-11-18

    A new scalable enantioselective approach to functionalized oxygenated steroids is described. This strategy is based on chiral bis(oxazoline) copper(II) complex-catalyzed enantioselective and diastereoselective Michael reactions of cyclic ketoesters and enones to install vicinal quaternary and tertiary stereocenters. In addition, the utility of copper(II) salts as highly active catalysts for the Michael reactions of traditionally unreactive β,β'-enones and substituted β,β'-ketoesters that results in unprecedented Michael adducts containing vicinal all-carbon quaternary centers is also demonstrated. The Michael adducts subsequently undergo base-promoted diastereoselective aldol cascade reactions resulting in the natural or unnatural steroid skeletons. The experimental and computational studies suggest that the torsional strain effects arising from the presence of the Δ(5)-unsaturation are key controlling elements for the formation of the natural cardenolide scaffold. The described method enables expedient generation of polycyclic molecules including modified steroidal scaffolds as well as challenging-to-synthesize Hajos-Parrish and Wieland-Miescher ketones.

  19. Concise Enantioselective Synthesis of Oxygenated Steroids via Sequential Copper(II)-Catalyzed Michael Addition/Intramolecular Aldol Cyclization Reactions

    PubMed Central

    Cichowicz, Nathan R.; Kaplan, Will; Khomutnyk, Yaroslav; Bhattarai, Bijay; Sun, Zhankui; Nagorny, Pavel

    2015-01-01

    A new scalable enantioselective approach to functionalized oxygenated steroids is described. This strategy is based on chiral bis(oxazoline) copper(II) complex-catalyzed enantioselective and diastereoselective Michael reactions of cyclic ketoesters and enones to install vicinal quaternary and tertiary stereocenters. In addition, the utility of copper(II) salts as highly active catalysts for the Michael reactions of traditionally unreactive ββ′-enones and substituted ββ′-ketoesters that results in unprecedented Michael adducts containing vicinal all-carbon quaternary centers is also demonstrated. The Michael adducts subsequently undergo base-promoted diastereoselective aldol cascade reactions resulting in the natural or unnatural steroid skeletons. The experimental and computational studies suggest that the torsional strain effects arising from the presence of the Δ5-unsaturation are key controling elements for the formation of the natural cardenolide scaffold. The described method enables expedient generation of polycyclic molecules including modified steroidal scaffolds as well as challenging-to-synthesize Hajos-Parrish and Wieland-Miescher ketones. PMID:26491886

  20. Composition-Dependent Reaction Pathways and Hydrogen Storage Properties of LiBH₄/Mg(AlH₄)₂ Composites.

    PubMed

    Pang, Yuepeng; Liu, Yongfeng; Zhang, Xin; Li, Qian; Gao, Mingxia; Pan, Hongge

    2015-11-01

    Herein, an initial attempt to understand the relationships between hydrogen storage properties, reaction pathways, and material compositions in LiBH4-x Mg(AlH4)2 composites is demonstrated. The hydrogen storage properties and the reaction pathways for hydrogen release from LiBH4-x Mg(AlH4)2 composites with x=1/6, 1/4, and 1/2 were systematically investigated. All of the composites exhibit a four-step dehydrogenation event upon heating, but the pathways for hydrogen desorption/absorption are varied with decreasing LiBH4/Mg(AlH4)2 molar ratios. Thermodynamic and kinetic investigations reveal that different x values lead to different enthalpy changes for the third and fourth dehydrogenation steps and varied apparent activation energies for the first, second, and third dehydrogenation steps. Thermodynamic and kinetic destabilization caused by the presence of Mg(AlH4)2 is likely to be responsible for the different hydrogen desorption/absorption performances of the LiBH4-x Mg(AlH4)2 composites.

  1. The reaction pathway for the heterogeneous photocatalysis of trichloroethylene in gas phase.

    PubMed

    Wang, Kuo-Hua; Jehng, Jih-Mirn; Hsieh, Yung-Hsu; Chang, Chen-Yu

    2002-02-14

    Trichloroethylene (TCE) has been widely used in industry. It is considered a hazardous and carcinogenic air pollutant. In this investigation, TCE photocatalytic reactions were performed in a packed bed reactor configured as a continuous flow reactor and a FT-IR sample cell used as a batch reactor to determine the intermediates under irradiation by 365 nm UV light. In this study, the intermediates detected during these reactions were phosgene, dichloroacetyl chloride (DCAC), chloroform, hexachloroethane, alcohols, esters, aldehydes, carbon monoxide, and carbon dioxide. The possible reaction mechanisms began with the Cl- subtraction. The Cl radicals then interacted with TCE to form various intermediates and products.

  2. Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation.

    PubMed

    Yang, Xinxing; Duan, Jingqi; Li, Shuang; Wang, Peng; Ma, Shoucai; Ye, Keqiong; Zhao, Xin Sheng

    2012-11-01

    The box H/ACA RNA-guided pseudouridine synthase is a complicated ribonucleoprotein enzyme that recruits substrate via both the guide RNA and the catalytic subunit Cbf5. Structural studies have revealed multiple conformations of the enzyme, but a quantitative description of the reaction pathway is still lacking. Using fluorescence correlation spectroscopy, we here measured the equilibrium dissociation constants and kinetic association and dissociation rates of substrate and product complexes mimicking various reaction intermediate states. These data support a sequential model for substrate loading and product release regulated by the thumb loop of Cbf5. The uridine substrate is first bound primarily through interaction with the guide RNA and then loaded into the active site while progressively interacted with the thumb. After modification, the subtle chemical structure change from uridine to pseudouridine at the target site triggers the release of the thumb, resulting in an intermediate complex with the product bound mainly by the guide RNA. By dissecting the role of Gar1 in individual steps of substrate turnover, we show that Gar1 plays a major role in catalysis and also accelerates product release about 2-fold. Our biophysical results integrate with previous structural knowledge into a coherent reaction pathway of H/ACA RNA-guided pseudouridylation.

  3. Conducting Polymers: Insights Into Reduced Polyparaphenylene Vinylene Materials via Nucleophilic Addition, Proton Abstraction, and Electron Transfer Reactions.

    NASA Astrophysics Data System (ADS)

    Hilker, Brian Lee

    Grignard routes were investigated as methods to produce poly paraphenylene vinylene polymers. Because of coupling problems with these reactions, high molecular weight unsubstituted and dimethyl and dimethoxy substituted poly paraphenylene vinylene polymers were prepared via a literature-proven synthetic route: the sodium hydride dehydrochlorination addition polymerization route. Both the Grignard reactions and the sodium hydride method required dichloromethyl compounds monomers. The syntheses of these dichloromethyl monomers were studied extensively. The three high molecular weight poly paraphenylene vinylene polymer systems prepared in this work were charged with the traditional electron transfer reducing agent potassium/naphthalide. They were also charged via the novel nucleophilic addition of n-butyllithium across the alkenes and subjected to proton abstraction charging in the presence of a strong, complexed base mixture of n-butyllithium and potassium-t-butoxide. Conductivities were obtained via standard four point probe techniques. Characterization of these polymers and their quenched anion derivatives was via FTIR and acid titration. Results of these topics are presented and discussed.

  4. Sequential Addition Reaction of Sulfanylmethyllithiums and Grignard Reagents to Thioformamides Leading to the Formation of 2-Phenyl-2-sulfanylethyl Tertiary Amines.

    PubMed

    Murai, Toshiaki; Mutoh, Natsumi

    2016-09-16

    The reaction of sulfanylmethyllithiums generated from benzylsulfanes and n-BuLi with N,N-dimethylthioformamide followed by the addition of Grignard reagents gave 2-phenyl-2-sulfanyl tertiary amines in moderate to good yields. A range of Grignard reagents involving primary alkyl, aryl, vinyl, and alkynyl Grignard reagents were used. Two carbon-carbon bond-forming reactions were achieved through a one-pot reaction. The reaction showed good to high diastereoselectivity, particularly with alkynyl Grignard reagents. PMID:27565031

  5. Graphene Facilitated Removal of Labetalol in Laccase-ABTS System: Reaction Efficiency, Pathways and Mechanism

    PubMed Central

    Dong, Shipeng; Xiao, Huifang; Huang, Qingguo; Zhang, Jian; Mao, Liang; Gao, Shixiang

    2016-01-01

    The widespread occurrence of the beta-blocker labetalol causes environmental health concern. Enzymatic reactions are highly efficient and specific offering biochemical transformation of trace contaminants with short reaction time and little to none energy consumption. Our experiments indicate that labetalol can be effectively transformed by laccase-catalyzed reaction using 2, 2-Azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as a mediator, while no significant removal of labetalol can be achieved in the absence of ABTS. A total of three products were identified. It is interesting that the presence of graphene greatly increased the reaction rate while not changed the products. In the presence of 100 μg/L graphene, the pseudo-first-order reaction rate constant was increased ~50 times. We found that the enhancement of graphene is probably attributed to the formation and releasing of ABTS2+ which has a much greater reactivity towards labetalol when graphene is present. This study provides fundamental information for laccase-ABTS mediated labetalol reactions and the effect of graphene, which could eventually lead to development of novel methods to control beta-blocker contamination. PMID:26891761

  6. Graphene Facilitated Removal of Labetalol in Laccase-ABTS System: Reaction Efficiency, Pathways and Mechanism

    NASA Astrophysics Data System (ADS)

    Dong, Shipeng; Xiao, Huifang; Huang, Qingguo; Zhang, Jian; Mao, Liang; Gao, Shixiang

    2016-02-01

    The widespread occurrence of the beta-blocker labetalol causes environmental health concern. Enzymatic reactions are highly efficient and specific offering biochemical transformation of trace contaminants with short reaction time and little to none energy consumption. Our experiments indicate that labetalol can be effectively transformed by laccase-catalyzed reaction using 2, 2-Azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as a mediator, while no significant removal of labetalol can be achieved in the absence of ABTS. A total of three products were identified. It is interesting that the presence of graphene greatly increased the reaction rate while not changed the products. In the presence of 100 μg/L graphene, the pseudo-first-order reaction rate constant was increased ~50 times. We found that the enhancement of graphene is probably attributed to the formation and releasing of ABTS2+ which has a much greater reactivity towards labetalol when graphene is present. This study provides fundamental information for laccase-ABTS mediated labetalol reactions and the effect of graphene, which could eventually lead to development of novel methods to control beta-blocker contamination.

  7. The IgE-dependent pathway in allergic transfusion reactions: involvement of donor blood allergens other than plasma proteins.

    PubMed

    Matsuyama, Nobuki; Yasui, Kazuta; Amakishi, Etsuko; Hayashi, Tomoya; Kuroishi, Ayumu; Ishii, Hiroyuki; Matsukura, Harumichi; Tani, Yoshihiko; Furuta, Rika A; Hirayama, Fumiya

    2015-07-01

    On transfusion, several plasma proteins can cause anaphylaxis in patients deficient in the corresponding plasma proteins. However, little is known about other allergens, which are encountered much more infrequently. Although it has been speculated that an allergen-independent pathway underlying allergic transfusion reactions (ATRs) is elicited by biological response modifiers accumulated in blood components during storage, the exact mechanisms remain unresolved. Furthermore, it is difficult even to determine whether ATRs are induced via allergen-dependent or allergen-independent pathways. To distinguish these two pathways in ATR cases, we established a basophil activation test, in which the basophil-activating ability of supernatants of residual transfused blood of ATR cases to whole blood basophils was assessed in the presence or absence of dasatinib, an inhibitor of IgE-mediated basophil activation. Three of 37 supernatants from the platelet concentrates with ATRs activated panel blood basophils in the absence, but not in the presence, of dasatinib. The basophil activation was inhibited by treatment of anti-fish collagen I MoAb in one case, suggesting that the involvement of fish allergens may have been present in donor plasma. We concluded that unknown non-plasma proteins, some of which had epitopes similar to fish antigens, in blood component may be involved in ATRs via an allergen/IgE-dependent pathway. PMID:25840771

  8. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths

    SciTech Connect

    Isegawa, Miho; Liu, Fengyi; Morokuma, Keiji; Maeda, Satoshi

    2014-06-28

    Photodissociation pathways of nitromethane following π → π{sup *} electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH{sub 3} and NO{sub 2} ({sup 2}B{sub 2}) is formed by direct dissociation from the S{sub 1} state. Important pathways involving S{sub 1} and S{sub 0} states for production of various dissociation products CH{sub 3}NO + O ({sup 1}D), CH{sub 3}O(X{sup 2}E) + NO (X{sup 2}Π), CH{sub 2}NO + OH, and CH{sub 2}O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH{sub 3}NO{sub 2}, the OH radical roaming in OH dissociation from CH{sub 2}N(O)(OH), and the NO roaming in NO dissociation from CH{sub 3}ONO.

  9. Functional Organosulfide Electrolyte Promotes an Alternate Reaction Pathway to Achieve High Performance in Lithium-Sulfur Batteries.

    PubMed

    Chen, Shuru; Dai, Fang; Gordin, Mikhail L; Yu, Zhaoxin; Gao, Yue; Song, Jiangxuan; Wang, Donghai

    2016-03-18

    Lithium-sulfur (Li-S) batteries have recently received great attention because they promise to provide energy density far beyond current lithium ion batteries. Typically, Li-S batteries operate by conversion of sulfur to reversibly form different soluble lithium polysulfide intermediates and insoluble lithium sulfides through multistep redox reactions. Herein, we report a functional electrolyte system incorporating dimethyl disulfide as a co-solvent that enables a new electrochemical reduction pathway for sulfur cathodes. This pathway uses soluble dimethyl polysulfides and lithium organosulfides as intermediates and products, which can boost cell capacity and lead to improved discharge-charge reversibility and cycling performance of sulfur cathodes. This electrolyte system can potentially enable Li-S batteries to achieve high energy density.

  10. Densification of Reaction Bonded Silicon Nitride with the Addition of Fine Si Powder Effects on the Sinterability and Mechanical Properties

    SciTech Connect

    Lee, Sea-Hoon; Cho, Chun-Rae; Park, Young-Jo; Ko, Jae-Woong; Kim, Hai-Doo; Lin, Hua-Tay; Becher, Paul F

    2013-01-01

    The densification behavior and strength of sintered reaction bonded silicon nitrides (SRBSN) that contain Lu2O3-SiO2 additives were improved by the addition of fine Si powder. Dense specimens (relative density: 99.5%) were obtained by gas-pressure sintering (GPS) at 1850oC through the addition of fine Si. In contrast, the densification of conventional specimens did not complete at 1950oC. The fine Si decreased the onset temperature of shrinkage and increased the shrinkage rate because the additive helped the compaction of green bodies and induced the formation of fine Si3N4 particles after nitridation and sintering at and above 1600oC. The amount of residual SiO2 within the specimens was not strongly affected by adding fine Si powder because most of the SiO2 layer that had formed on the fine Si particles decomposed during nitridation. The maximum strength and fracture toughness of the specimens were 991 MPa and 8.0 MPa m1/2, respectively.

  11. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity.

    PubMed

    Boesenberg, Ulrike; Marcus, Matthew A; Shukla, Alpesh K; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-01-01

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. The presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale.

  12. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    SciTech Connect

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-11-20

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. Lastly, the presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale.

  13. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    PubMed Central

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-01-01

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. The presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale. PMID:25410966

  14. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity.

    PubMed

    Boesenberg, Ulrike; Marcus, Matthew A; Shukla, Alpesh K; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-01-01

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. The presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale. PMID:25410966

  15. Ab initio characterization of (CH3IO3) isomers and the CH3O2 + IO reaction pathways.

    PubMed

    Drougas, Evangelos; Kosmas, Agnie M

    2007-05-01

    The geometries, harmonic vibrational frequencies, relative energetics, and enthalpies of formation of (CH(3)IO(3)) isomers and the reaction CH(3)O(2) + IO have been investigated using quantum mechanical methods. Optimization has been performed at the MP2 level of theory, using all electron and effective core potential, ECP, computational techniques. The relative energetics has been studied by single-point calculations at the CCSD(T) level. Methyl iodate, CH(3)OIO(2), is found to be the lowest-energy isomer showing particular stabilization. The two nascent association minima, CH(3)OOOI and CH(3)OOIO, show similar stabilities, and they are considerably higher located than CH(3)OIO(2). Interisomerization barriers have been determined, along with the transition states involved in various pathways of the reaction CH(3)O(2) + IO.

  16. Towards quantum-based modeling of enzymatic reaction pathways: Application to the acetylholinesterase catalysis

    NASA Astrophysics Data System (ADS)

    Polyakov, Igor V.; Grigorenko, Bella L.; Moskovsky, Alexander A.; Pentkovski, Vladimir M.; Nemukhin, Alexander V.

    2013-01-01

    We apply computational methods aiming to approach a full quantum mechanical treatment of chemical reactions in proteins. A combination of the quantum mechanical - molecular mechanical methodology for geometry optimization and the fragment molecular orbital approach for energy calculations is examined for an example of acetylcholinesterase catalysis. The codes based on the GAMESS(US) package operational on the 'RSC Tornado' computational cluster are applied to determine that the energy of the reaction intermediate upon hydrolysis of acetylcholine is lower than that of the enzyme-substrate complex. This conclusion is consistent with the experiments and it is free from the empirical force field contributions.

  17. Fundamental kinetics and mechanistic pathways for oxidation reactions in supercritical water

    NASA Technical Reports Server (NTRS)

    Webley, Paul A.; Tester, Jefferson W.

    1988-01-01

    Oxidation of the products of human metabolism in supercritical water has been shown to be an efficient way to accomplish the on-board water/waste recycling in future long-term space flights. Studies of the oxidation kinetics of methane to carbon dioxide in supercritical water are presented in this paper in order to enhance the fundamental understanding of the oxidation of human waste compounds in supercritical water. It is concluded that, although the elementary reaction models remain the best hope for simulating oxidation in supercritical water, several modifications to existing mechanisms need to be made to account for the role of water in the reaction mechanism.

  18. Vesicle-based artificial cells as chemical microreactors with spatially segregated reaction pathways.

    PubMed

    Elani, Yuval; Law, Robert V; Ces, Oscar

    2014-01-01

    In the discipline of bottom-up synthetic biology, vesicles define the boundaries of artificial cells and are increasingly being used as biochemical microreactors operating in physiological environments. As the field matures, there is a need to compartmentalize processes in different spatial localities within vesicles, and for these processes to interact with one another. Here we address this by designing and constructing multi-compartment vesicles within which an engineered multi-step enzymatic pathway is carried out. The individual steps are isolated in distinct compartments, and their products traverse into adjacent compartments with the aid of transmembrane protein pores, initiating subsequent steps. Thus, an engineered signalling cascade is recreated in an artificial cellular system. Importantly, by allowing different steps of a chemical pathway to be separated in space, this platform bridges the gap between table-top chemistry and chemistry that is performed within vesicles. PMID:25351716

  19. Mechanisms and reaction pathways for simultaneous oxidation of NOx and SO₂ by ozone determined by in situ IR measurements.

    PubMed

    Sun, Chenglang; Zhao, Nan; Zhuang, Zhuokai; Wang, Haiqiang; Liu, Yue; Weng, Xiaole; Wu, Zhongbiao

    2014-06-15

    Ozone (O3) oxidation combined with wet scrubbing is a promising method for the simultaneous removal of SO2 and NOx in flue gas. In this study, the O3 oxidation processes of NO and SO2, as well as their coexistence, were investigated using an in situ IR spectrometer. Experimental results showed that the O3 concentration and the reaction temperature played critical roles in the O3 oxidation process of NO. Around 80°C, when inlet molar ratio of O3/NO was less than 1, NO was mainly oxidized to NO2, while when the ratio was greater than 1, NO would be further oxidized to NO3, N2O5, and HNO3. NO3 was the key intermediate product for the formation of N2O5 and HNO3. However, the subsequent reactions of NO3 were temperature dependence. With the increase of reaction temperature above 100°C, the concentration of NO2 increased whereas the concentrations of N2O5 and HNO3 decreased. The oxidation of SO2 by O3 was negligible and SO2 had little influence on the oxidation of NO in the simultaneous oxidation of NO and SO2. Finally, based on the in situ IR results, the oxidation mechanism is discussed and the reaction pathways are proposed. PMID:24801895

  20. Mechanisms and reaction pathways for simultaneous oxidation of NOx and SO₂ by ozone determined by in situ IR measurements.

    PubMed

    Sun, Chenglang; Zhao, Nan; Zhuang, Zhuokai; Wang, Haiqiang; Liu, Yue; Weng, Xiaole; Wu, Zhongbiao

    2014-06-15

    Ozone (O3) oxidation combined with wet scrubbing is a promising method for the simultaneous removal of SO2 and NOx in flue gas. In this study, the O3 oxidation processes of NO and SO2, as well as their coexistence, were investigated using an in situ IR spectrometer. Experimental results showed that the O3 concentration and the reaction temperature played critical roles in the O3 oxidation process of NO. Around 80°C, when inlet molar ratio of O3/NO was less than 1, NO was mainly oxidized to NO2, while when the ratio was greater than 1, NO would be further oxidized to NO3, N2O5, and HNO3. NO3 was the key intermediate product for the formation of N2O5 and HNO3. However, the subsequent reactions of NO3 were temperature dependence. With the increase of reaction temperature above 100°C, the concentration of NO2 increased whereas the concentrations of N2O5 and HNO3 decreased. The oxidation of SO2 by O3 was negligible and SO2 had little influence on the oxidation of NO in the simultaneous oxidation of NO and SO2. Finally, based on the in situ IR results, the oxidation mechanism is discussed and the reaction pathways are proposed.

  1. Quantitative analysis of energy metabolic pathways in MCF-7 breast cancer cells by selected reaction monitoring assay.

    PubMed

    Drabovich, Andrei P; Pavlou, Maria P; Dimitromanolakis, Apostolos; Diamandis, Eleftherios P

    2012-08-01

    To investigate the quantitative response of energy metabolic pathways in human MCF-7 breast cancer cells to hypoxia, glucose deprivation, and estradiol stimulation, we developed a targeted proteomics assay for accurate quantification of protein expression in glycolysis/gluconeogenesis, TCA cycle, and pentose phosphate pathways. Cell growth conditions were selected to roughly mimic the exposure of cells in the cancer tissue to the intermittent hypoxia, glucose deprivation, and hormonal stimulation. Targeted proteomics assay allowed for reproducible quantification of 76 proteins in four different growth conditions after 24 and 48 h of perturbation. Differential expression of a number of control and metabolic pathway proteins in response to the change of growth conditions was found. Elevated expression of the majority of glycolytic enzymes was observed in hypoxia. Cancer cells, as opposed to near-normal MCF-10A cells, exhibited significantly increased expression of key energy metabolic pathway enzymes (FBP1, IDH2, and G6PD) that are known to redirect cellular metabolism and increase carbon flux through the pentose phosphate pathway. Our quantitative proteomic protocol is based on a mass spectrometry-compatible acid-labile detergent and is described in detail. Optimized parameters of a multiplex selected reaction monitoring (SRM) assay for 76 proteins, 134 proteotypic peptides, and 401 transitions are included and can be downloaded and used with any SRM-compatible mass spectrometer. The presented workflow is an integrated tool for hypothesis-driven studies of mammalian cells as well as functional studies of proteins, and can greatly complement experimental methods in systems biology, metabolic engineering, and metabolic transformation of cancer cells.

  2. Vitamin B6 nutritional status and cellular availability of pyridoxal 5'-phosphate govern the function of the transsulfuration pathway's canonical reactions and hydrogen sulfide production via side reactions.

    PubMed

    Gregory, Jesse F; DeRatt, Barbara N; Rios-Avila, Luisa; Ralat, Maria; Stacpoole, Peter W

    2016-07-01

    The transsulfuration pathway (TS) acts in sulfur amino acid metabolism by contributing to the regulation of cellular homocysteine, cysteine production, and the generation of H2S for signaling functions. Regulation of TS pathway kinetics involves stimulation of cystathionine β-synthase (CBS) by S-adenosylmethionine (SAM) and oxidants such as H2O2, and by Michaelis-Menten principles whereby substrate concentrations affect reaction rates. Although pyridoxal phosphate (PLP) serves as coenzyme for both CBS and cystathionine γ-lyase (CSE), CSE exhibits much greater loss of activity than CBS during PLP insufficiency. Thus, cellular and plasma cystathionine concentrations increase in vitamin B6 deficiency mainly due to the bottleneck caused by reduced CSE activity. Because of the increase in cystathionine, the canonical production of cysteine (homocysteine → cystathionine → cysteine) is largely maintained even during vitamin B6 deficiency. Typical whole body transsulfuration flux in humans is 3-7 μmol/h per kg body weight. The in vivo kinetics of H2S production via side reactions of CBS and CSE in humans are unknown but they have been reported for cultured HepG2 cells. In these studies, cells exhibit a pronounced reduction in H2S production capacity and rates of lanthionine and homolanthionine synthesis in deficiency. In humans, plasma concentrations of lanthionine and homolanthionine exhibit little or no mean change due to 4-wk vitamin B6 restriction, nor do they respond to pyridoxine supplementation of subjects in chronically low-vitamin B6 status. Wide individual variation in responses of the H2S biomarkers to such perturbations of human vitamin B6 status suggests that the resulting modulation of H2S production may have physiological consequences in a subset of people. Supported by NIH grant DK072398. This paper refers to data from studies registered at clinicaltrials.gov as NCT01128244 and NCT00877812.

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

    SciTech Connect

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

    2004-04-12

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

  4. Urea degradation by electrochemically generated reactive chlorine species: products and reaction pathways.

    PubMed

    Cho, Kangwoo; Hoffmann, Michael R

    2014-10-01

    This study investigated the transformation of urea by electrochemically generated reactive chlorine species (RCS). Solutions of urea with chloride ions were electrolyzed using a bismuth doped TiO2 (BiOx/TiO2) anode coupled with a stainless steel cathode at applied anodic potentials (Ea) of either +2.2 V or +3.0 V versus the normal hydrogen electrode. In NaCl solution, the current efficiency of RCS generation was near 30% at both potentials. In divided cell experiments, the pseudo-first-order rate of total nitrogen decay was an order of magnitude higher at Ea of +3.0 V than at +2.2 V, presumably because dichlorine radical (Cl2(-)·) ions facilitate the urea transformation primary driven by free chlorine. Quadrupole mass spectrometer analysis of the reactor headspace revealed that N2 and CO2 are the primary gaseous products of the oxidation of urea, whose urea-N was completely transformed into N2 (91%) and NO3(-) (9%). The higher reaction selectivity with respect to N2 production can be ascribed to a low operational ratio of free available chlorine to N. The mass-balance analysis recovered urea-C as CO2 at 77%, while CO generation most likely accounts for the residual carbon. In light of these results, we propose a reaction mechanism involving chloramines and chloramides as reaction intermediates, where the initial chlorination is the rate-determining step in the overall sequence of reactions.

  5. Citrus Peel Additives for One-Pot Triazole Formation by Decarboxylation, Nucleophilic Substitution, and Azide-Alkyne Cycloaddition Reactions

    ERIC Educational Resources Information Center

    Mendes, Desiree E.; Schoffstall, Allen M.

    2011-01-01

    This undergraduate organic laboratory experiment consists of three different reactions occurring in the same flask: a cycloaddition reaction, preceded by decarboxylation and nucleophilic substitution reactions. The decarboxylation and cycloaddition reactions occur using identical Cu(I) catalyst and conditions. Orange, lemon, and other citrus fruit…

  6. Design of Selective Gas Sensors Using Additive-Loaded In2O3 Hollow Spheres Prepared by Combinatorial Hydrothermal Reactions

    PubMed Central

    Kim, Sun-Jung; Hwang, In-Sung; Kang, Yun Chan; Lee, Jong-Heun

    2011-01-01

    A combinatorial hydrothermal reaction has been used to prepare pure and additive (Sb, Cu, Nb, Pd, and Ni)-loaded In2O3 hollow spheres for gas sensor applications. The operation of Pd- and Cu-loaded In2O3 sensors at 371 °C leads to selective H2S detection. Selective detection of CO and NH3 was achieved by the Ni-In2O3 sensor at sensing temperatures of 371 and 440 °C, respectively. The gas responses of six different sensors to NH3, H2S, H2, CO and CH4 produced unique gas sensing patterns that can be used for the artificial recognition of these gases. PMID:22346661

  7. Hydrogenation of O and OH on Pt(111): A comparison between the reaction rates of the first and the second hydrogen addition steps

    SciTech Connect

    Näslund, L.-Å.

    2014-03-14

    The formation of water through hydrogenation of oxygen on platinum occurs at a surprisingly low reaction rate. The reaction rate limited process for this catalytic reaction is, however, yet to be settled. In the present work, the reaction rates of the first and the second hydrogen addition steps are compared when hydrogen is obtained through intense synchrotron radiation that induces proton production in a water overlayer on top of the adsorbed oxygen species. A substantial amount of the produced hydrogen diffuses to the platinum surface and promotes water formation at the two starting conditions O/Pt(111) and (H{sub 2}O+OH)/Pt(111). The comparison shows no significant difference in the reaction rate between the first and the second hydrogen addition steps, which indicates that the rate determining process of the water formation from oxygen on Pt(111) is neither the first nor the second H addition step or, alternatively, that both H addition steps exert rate control.

  8. A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease.

    PubMed

    Holmans, Peter; Moskvina, Valentina; Jones, Lesley; Sharma, Manu; Vedernikov, Alexey; Buchel, Finja; Saad, Mohamad; Sadd, Mohamad; Bras, Jose M; Bettella, Francesco; Nicolaou, Nayia; Simón-Sánchez, Javier; Mittag, Florian; Gibbs, J Raphael; Schulte, Claudia; Durr, Alexandra; Guerreiro, Rita; Hernandez, Dena; Brice, Alexis; Stefánsson, Hreinn; Majamaa, Kari; Gasser, Thomas; Heutink, Peter; Wood, Nicholas W; Martinez, Maria; Singleton, Andrew B; Nalls, Michael A; Hardy, John; Morris, Huw R; Williams, Nigel M

    2013-03-01

    Parkinson's disease (PD) is the second most common neurodegenerative disease affecting 1-2% in people >60 and 3-4% in people >80. Genome-wide association (GWA) studies have now implicated significant evidence for association in at least 18 genomic regions. We have studied a large PD-meta analysis and identified a significant excess of SNPs (P < 1 × 10(-16)) that are associated with PD but fall short of the genome-wide significance threshold. This result was independent of variants at the 18 previously implicated regions and implies the presence of additional polygenic risk alleles. To understand how these loci increase risk of PD, we applied a pathway-based analysis, testing for biological functions that were significantly enriched for genes containing variants associated with PD. Analysing two independent GWA studies, we identified that both had a significant excess in the number of functional categories enriched for PD-associated genes (minimum P = 0.014 and P = 0.006, respectively). Moreover, 58 categories were significantly enriched for associated genes in both GWA studies (P < 0.001), implicating genes involved in the 'regulation of leucocyte/lymphocyte activity' and also 'cytokine-mediated signalling' as conferring an increased susceptibility to PD. These results were unaltered by the exclusion of all 178 genes that were present at the 18 genomic regions previously reported to be strongly associated with PD (including the HLA locus). Our findings, therefore, provide independent support to the strong association signal at the HLA locus and imply that the immune-related genetic susceptibility to PD is likely to be more widespread in the genome than previously appreciated.

  9. Mechanism and Reaction Pathways for Microcystin-LR Degradation through UV/H2O2 Treatment

    PubMed Central

    Liu, Yafeng; Ren, Jing; Wang, Xiangrong; Fan, Zhengqiu

    2016-01-01

    Microcystin-LR (MCLR) is the most common cyanotoxin in contaminated aquatic systems. MCLR inhibits protein phosphatases 1 and 2A, leading to liver damage and tumor formation. MCLR is relatively stable owing to its cyclic structures. The combined UV/H2O2 technology can degrade MCLR efficiently. The second-order rate constant of the reaction between MCLR and hydroxyl radical (·OH) is 2.79(±0.23)×1010 M−1 s−1 based on the competition kinetics model using nitrobenzene as reference compound. The probable degradation pathway was analyzed through liquid chromatography mass spectrometry. Results suggested that the major destruction pathways of MCLR were initiated by ·OH attack on the benzene ring and diene of the Adda side chain. The corresponding aldehyde or ketone peptide residues were formed through further oxidation. Another minor destruction pathway involved ·OH attack on the methoxy group of the Adda side chain, followed by complete removal of the methoxy group. The combined UV/H2O2 system is a promising technology for MCLR removal in contaminated aquatic systems. PMID:27281173

  10. Mechanism and Reaction Pathways for Microcystin-LR Degradation through UV/H2O2 Treatment.

    PubMed

    Liu, Yafeng; Ren, Jing; Wang, Xiangrong; Fan, Zhengqiu

    2016-01-01

    Microcystin-LR (MCLR) is the most common cyanotoxin in contaminated aquatic systems. MCLR inhibits protein phosphatases 1 and 2A, leading to liver damage and tumor formation. MCLR is relatively stable owing to its cyclic structures. The combined UV/H2O2 technology can degrade MCLR efficiently. The second-order rate constant of the reaction between MCLR and hydroxyl radical (·OH) is 2.79(±0.23)×1010 M-1 s-1 based on the competition kinetics model using nitrobenzene as reference compound. The probable degradation pathway was analyzed through liquid chromatography mass spectrometry. Results suggested that the major destruction pathways of MCLR were initiated by ·OH attack on the benzene ring and diene of the Adda side chain. The corresponding aldehyde or ketone peptide residues were formed through further oxidation. Another minor destruction pathway involved ·OH attack on the methoxy group of the Adda side chain, followed by complete removal of the methoxy group. The combined UV/H2O2 system is a promising technology for MCLR removal in contaminated aquatic systems.

  11. Urea-acetylene dicarboxylic acid reaction: A likely pathway for prebiotic uracil formation

    NASA Astrophysics Data System (ADS)

    Subbaraman, A. S.; Kazi, Z. A.; Choughuley, A. S. U.; Chadha, M. S.

    1980-12-01

    A number of routes have been suggested for the prebiotic synthesis of uracil involving the reaction of urea with malic acid, propiolic acid, cyanoacetylene and others. Cyanoacetylene has been detected in the interstellar medium as well as simulated prebiotic experiments. It is therefore plausible that dicyanoacetylene and its hydrolytic product acetylene dicarboxylic acid, (ADCA) may have played a role in chemical evolution. This aspect has been examined in the present work for the synthesis of uracil from ADCA and urea reaction. It was found that when ADCA reacted with urea, uracil was formed only in the presence of phosphoric acid and phosphates. Ammonium phosphates gave higher yields of uracil than other phosphates. In the absence of phosphoric acid or phosphates no uracil formation took place. This type of synthesis could have taken place in prebiotic oceans which contained ammonium phosphates and other salts.

  12. An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase

    PubMed Central

    Nuñez, Sara; Tresadern, Gary; Hillier, Ian H; Burton, Neil A

    2006-01-01

    Computational methods have now become a valuable tool to understand the way in which enzymes catalyse chemical reactions and to aid the interpretation of a diverse set of experimental data. This study focuses on the influence of the condensed-phase environment structure on proton transfer mechanisms, with an aim to understand how C–H bond cleavage is mediated in enzymatic reactions. We shall use a combination of molecular simulation, ab initio or semi-empirical quantum chemistry and semi-classical multidimensional tunnelling methods to consider the primary kinetic isotope effects of the enzyme methylamine dehydrogenase (MADH), with reference to an analogous application to triosephosphate isomerase. Analysis of potentially reactive conformations of the system, and correlation with experimental isotope effects, have highlighted that a quantum tunnelling mechanism in MADH may be modulated by specific amino acid residues, such as Asp428, Thr474 and Asp384. PMID:16873126

  13. Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels.

    PubMed

    Hajjar, Eric; Kumar, Amit; Ruggerone, Paolo; Ceccarelli, Matteo

    2010-11-01

    In Gram-negative bacteria, outer-membrane protein channels, such as OmpF of Escherichia coli, constitute the entry point of various classes of antibiotics. While antibacterial research and development is declining, bacterial resistance to antibiotics is rising and there is an emergency call for a new way to develop potent antibacterial agents and to bring them to the market faster and at reduced cost. An emerging strategy is to follow a bottom-up approach based on microscopically founded computational based screening, however such strategy needs better-tuned methods. Here we propose to use molecular dynamics (MD) simulations combined with the metadynamics algorithm, to study antibiotic translocation through OmpF at a molecular scale. This recently designed algorithm overcomes the time scale problem of classical MD by accelerating some reaction coordinates. It is expected that the initial assumption of the reaction coordinates is a key determinant for the efficiency and accuracy of the simulations. Previous studies using different computational schemes for a similar process only used one reaction coordinate, which is the directionality. Here we go further and see how it is possible to include more informative reaction coordinates, accounting explicitly for: (i) the antibiotic flexibility and (ii) interactions with the channel. As model systems, we select two compounds covering the main classes of antibiotics, ampicillin and moxifloxacine. We decipher the molecular mechanism of translocation of each antibiotic and highlight the important parameters that should be taken into account for improving further simulations. This will benefit the screening and design for antibiotics with better permeation properties.

  14. Oxidation of elemental mercury by chlorine: Gas phase, Surface,and Photo-induced reaction pathways

    SciTech Connect

    Yan, Nai-Qiang; Liu, Shou-Heng; Chang, Shih-Ger

    2004-10-22

    Accurate oxidation rate constants of mercury gas are needed for determining its dispersion and lifetime in the atmosphere. They would also help in developing a technology for the control of mercury emissions from coal-fired power plants. However, it is difficult to establish the accurate rate constants primarily due to the fact that mercury easily adsorbs on solid surface and its reactions can be catalyzed by the surface. We have demonstrated a procedure that allows the determination of gas phase, surface-induced, and photo-induced contributions in the kinetic study of the oxidation of mercury by chlorine gas. The kinetics was studied using reactors with various surface to volume ratios. The effect of the surface and the photo irradiation on the reaction was taken into consideration. The pressure dependent study revealed that the gas phase oxidation was a three-body collision process. The third order rate constant was determined to be 7.5({+-}0.2) x 10{sup -39} mL{sup 2} molecules{sup -2}s{sup -1} with N{sub 2} as the third body at 297 {+-} 1 K. The surface induced reaction on quartz window was second order and the rate constant was 2.7 x 10{sup -17} mL{sup 2} molecules{sup -1} cm{sup -2} sec. Meanwhile, the 253.7 nm photon employed for mercury detection was found to accelerate the reaction. The utilization efficiency of 253.7 nm photon for Hg{sup 0} oxidation was 6.7 x 10{sup -4} molecules photon{sup -1} under the conditions employed in this study.

  15. Reaction Pathways in the Reactive Composite Mg(NH 2)2 + LiH

    NASA Astrophysics Data System (ADS)

    Cakir, Deniz; de Wijs, Gilles A.; Brocks, Geert

    2011-03-01

    Chen et al reported reversible hydrogen storage in a mixture of LiH + Li NH2 with a storage capacity of 6.5 wt %. However, this system requires an operating temperature in excess of 250 C to achieve a hydrogen pressure of 1 bar. Several efforts including cation substitution have been considered in order to improve the operating conditions, which is necessary for onboard applications. For instance, replacing LiH with Mg H2 markedly reduces the operating temperature through the reaction Mg H2 + 2 Li NH2 --> Li 2 Mg(NH)2 + 2 H2 <--> Mg(NH2)2 + 2 LiH. Recent experimental results however indicate that the latter is not a simple one-step reaction and full hydrogenation of Li 2 Mg(NH)2 occurs in a two-step sequence via an intermediate Li 2 Mg 2 (NH)3. In this work we examine the stability and structure of possible intermediates compounds, namely Li 2-2x Mg x NH, Li 1-2x Mg x NH2 , and Li 2-x Mg(NH)2-x (NH2)x , by means of first-principles DFT calculations. All intermediate compounds are thermodynamically stable with respect to the elements. The hydrogenation reaction of Li 2 Mg(NH)2 via the intermediate imides Li 2-2x Mg x NH is energetically favorable compared to other intermediates.

  16. Reaction Mechanism and Regioselectivity of the Bingel-Hirsch Addition of Dimethyl Bromomalonate to La@C2v -C82.

    PubMed

    Martínez, Juan Pablo; Garcia-Borràs, Marc; Osuna, Sílvia; Poater, Jordi; Bickelhaupt, F Matthias; Solà, Miquel

    2016-04-18

    We quantum chemically explore the thermodynamics and kinetics of all 65 possible mechanistic pathways of the Bingel-Hirsch addition of dimethyl bromomalonate to the endohedral metallofullerene La@C2v -C82 that result from the combination of 24 nonequivalent carbon atoms and 35 different bonds present in La@C2v -C82 by using dispersion-corrected DFT calculations. Experimentally, this reaction leads to four singly bonded derivatives and one fulleroid adduct. Of these five products, only the singly bonded derivative on C23 could be experimentally identified unambiguously. Our calculations show that La@C2v -C82 is not particularly regioselective under Bingel-Hirsch conditions. From the obtained results, however, it is possible to make a tentative assignment of the products observed experimentally. We propose that the observed fulleroid adduct results from the attack at bond 19 and that the singly bonded derivatives correspond to the C2, C19, C21, and C23 initial attacks. However, other possibilities cannot be ruled out completely.

  17. A DFT study of addition reaction between fragment ion (CH₂) units and fullerene (C₆₀) molecule.

    PubMed

    Zaragoza, Irineo Pedro; Vergara, Jaime; Pérez-Manríquez, Liliana; Salcedo, Roberto

    2011-05-01

    The theoretical study of the interaction between CH(2) and fullerene (C(60)) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH(2) into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH(2) group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C(60)) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH(2) fragment to attack the CC (6, 5) bond. PMID:20658255

  18. Effects of the method of apatite seed crystals addition on setting reaction of α-tricalcium phosphate based apatite cement.

    PubMed

    Tsuru, Kanji; Ruslin; Maruta, Michito; Matsuya, Shigeki; Ishikawa, Kunio

    2015-10-01

    Appropriate setting time is an important parameter that determines the effectiveness of apatite cement (AC) for clinical application, given the issues of crystalline inflammatory response phenomena if AC fails to set. To this end, the present study analyzes the effects of the method of apatite seed crystals addition on the setting reaction of α-tricalcium phosphate (α-TCP) based AC. Two ACs, both consisting of α-TCP and calcium deficient hydroxyapatite (cdHAp), were analyzed in this study. In one AC, cdHAp was added externally to α-TCP and this AC was abbreviated as AC(EA). In the other AC, α-TCP was partially hydrolyzed to form cdHAp on the surface of α-TCP. This AC was referred to as AC(PH). Results indicate a decrease in the setting time of both ACs with the addition of cdHAp. Among them, for the given amount of added cdHAp, AC(PH) showed relatively shorter setting time than AC(EA). Besides, the mechanical strength of the set AC(PH) was also higher than that of set AC(EA). These properties of AC(PH) were attributed to the predominant crystal growth of cdHAp in the vicinity of the α-TCP particle surface. Accordingly, it can be concluded that the partial hydrolysis of α-TCP may be a better approach to add low crystalline cdHAp onto α-TCP based AC.

  19. Characterization and mechanism insight of accelerated catalytic promiscuity of Sulfolobus tokodaii (ST0779) peptidase for aldol addition reaction.

    PubMed

    Li, Rong; Perez, Bianca; Jian, Hui; Jensen, Mads Mørk; Gao, Renjun; Dong, Mingdong; Glasius, Marianne; Guo, Zheng

    2015-11-01

    A novel peptidase from thermophilic archaea Sulfolobus tokodaii (ST0779) is examined for its catalytic promiscuity of aldol addition, which shows comparable activity as porcine pancreatic lipase (PPL, one of the best enzymes identified for biocatalytic aldol addition) at 30 °C but much accelerated activity at elevated temperature. The molecular catalytic efficiency kcat/Km (M(-1) s(-1)) of this thermostable enzyme at 55 °C adds up to 140 times higher than that of PPL at its optimum temperature 37 °C. The fluorescence quenching analysis depicts that the binding constants of PPL are significantly higher than those of ST0779, and their numbers of binding sites show opposite temperature dependency. Thermodynamic parameters estimated by fluorescence quenching analysis unveil distinctly different substrate-binding modes between PPL and ST0779: the governing binding interaction between PPL and substrates is hydrophobic force, while the dominating substrate-binding forces for ST0779 are van der Waals and H-bonds interactions. A reasonable mechanism for ST0779-catalyzed aldol reaction is proposed based on kinetic study, spectroscopic analysis, and molecular stereostructure simulation. This work represents a successful example to identify a new enzyme for catalytic promiscuity, which demonstrates a huge potential to discover and exploit novel biocatalyst from thermophile microorganism sources. PMID:26169629

  20. Origin of a mixed brominated ethene groundwater plume: contaminant degradation pathways and reactions.

    PubMed

    Patterson, Bradley M; Cohen, Elizabeth; Prommer, Henning; Thomas, David G; Rhodes, Stuart; McKinley, Allan J

    2007-02-15

    On the basis of a combination of laboratory microcosm experiments, column sorption experiments, and the current spatial distribution of groundwater concentrations, the origin of a mixed brominated ethene groundwater plume and its degradation pathway were hypothesized. The contaminant groundwater plume was detected downgradient of a former mineral processing facility, and consisted of tribromoethene (TriBE), cis-1,2-dibromoethene (c-DBE), trans-1,2-dibromoethene (t-DBE), and vinyl bromide (VB). The combined laboratory and field data provided strong evidence that the origin of the mixed brominated ethene plume was a result of dissolution of the dense non-aqueous-phase liquid 1,1,2,2-tetrabromoethane (TBA) atthe presumed source zone, which degraded rapidly (half-life of 0.2 days) to form TriBE in near stoichiometric amounts. TriBE then degraded (half-life of 96 days) to form c-DBE, t-DBE, and VB via a reductive debromination degradation pathway. Slow degradation of c-DBE (half-life >220 days), t-DBE (half-life 220 days), and VB (half-life >220 days) coupled with their low retardation coefficients (1.2, 1.2, and 1.0 respectively) resulted in the formation of an extensive mixed brominated ethene contaminant plume. Without this clearer understanding of the mechanism for TBA degradation, the origin of the mixed brominated ethene groundwater contamination could have been misinterpreted, and inappropriate and ineffective source zone and groundwater remediation techniques could be applied.

  1. A STUDY OF THE ADDITION OF CHOLESTERIN TO THE ALCOHOLIC EXTRACTS OF TISSUES USED FOR ANTIGENS IN THE WASSERMANN REACTION.

    PubMed

    Walker, I C; Swift, H F

    1913-07-01

    1. The addition of cholesterin to an alcoholic extract of heart or fetal liver increases the antigenic value of the extracts in the Wassermann reaction. 2. The optimum amount of cholesterin to be added to heart extract or fetal liver extract was found to be 0.4 per cent. 3. Cholesterin-heart extracts are superior to cholesterin-liver extracts and to alcoholic extracts of syphilitic livers, as well as to ether extracts of dried hearts. 4. Cholesterin-heart extracts prepared from different human hearts are practically equal in anticomplementary and antigenic value. Similar extracts prepared from guinea pig hearts have the same antigenic value as those prepared from human hearts. Both the human heart and the guinea pig heart extracts are superior to beef heart extract when the same amount of cholesterin is added to each of the extracts. 5. In testing blood serum for diagnostic purposes, it is not safe to use more than one fourth of the anticomplementary dose of the 0.4 per cent. cholesterin heart extract. In the work here presented, this consisted of a 1 in 10 emulsion. 6. In testing cerebrospinal fluids, 1 in 10 emulsions give slightly better reactions with smaller quantities of the fluid than do 1 in 6 emulsions. 7. Because of the simple preparation, the superior antigenic property, and the constant antigen value of cholesterin-heart extracts prepared from human hearts, we agree with McIntosh and Fildes that this form of extract fulfills the requirements of a standard antigen.

  2. Communication: From graphite to diamond: reaction pathways of the phase transition.

    PubMed

    Xiao, Penghao; Henkelman, Graeme

    2012-09-14

    Phase transitions between carbon allotropes are calculated using the generalized solid-state nudged elastic band method. We find a new reaction mechanism between graphite and diamond with nucleation characteristics that has a lower activation energy than the concerted mechanism. The calculated barrier from graphite to hexagonal diamond is lower than to cubic diamond, resolving a conflict between theory and experiment. Transitions are calculated to three structures of cold compressed graphite: bct C4, M, and Z-carbon, which are accessible at the experimentally relevant pressures near 17 GPa.

  3. Enzymological studies of one-carbon reactions in the pathway of acetate utilization by methanogenic bacteria

    SciTech Connect

    Ferry, J.G.

    1991-01-01

    Several enzymes in the pathway of acetate conversion to methane and carbon dioxide have been purified from Methanosarcina thermophila. The mechanisms of these enzymes are under investigation utilizing biochemical, biophysical and molecular genetic approaches. Acetate kinase and phosphotransacetylase catalyzes the activation of acetate to acetyl-CoA. The primary structure of these enzymes will be determined through cloning and sequencing of the genes. Two protein components of the CO dehydrogenase complex are under investigations. The metal centers of each component have been characterized using EPR. Cloning and sequencing of the genes for the two subunits of each component is in progress. Results indicate that the Ni/Fe-S component cleaves the C-C and C-S bonds of acetyl-CoA followed by oxidation of the carbonyl group to carbon dioxide and transfer of the methyl group to the Co/Fe-S component. The enzymes and cofactors involved in transfer of the methyl group from the Co/Fe-S component to coenzyme M will be purified and characterized. Ferredoxin is an electron acceptor for the Ni/Fe-S component and also serves to reductively reactivate methylreductase which catalyzes the demethylation of methyl coenzyme M to methane. This ferredoxin is being characterized utilizing EPR and RR spectroscopic methods to determine the properties of the Fe-S centers. Genes encoding this and other ferredoxins have been cloned and sequenced to determine the primary structures. Carbonic anhydrase is being purified and characterized to determine the function of this enzyme in the pathway.

  4. Enzymological studies of one-carbon reactions in the pathway of acetate utilization by methanogenic bacteria

    SciTech Connect

    Ferry, J.G.

    1991-12-31

    Several enzymes in the pathway of acetate conversion to methane and carbon dioxide have been purified from Methanosarcina thermophila. The mechanisms of these enzymes are under investigation utilizing biochemical, biophysical and molecular genetic approaches. Acetate kinase and phosphotransacetylase catalyzes the activation of acetate to acetyl-CoA. The primary structure of these enzymes will be determined through cloning and sequencing of the genes. Two protein components of the CO dehydrogenase complex are under investigations. The metal centers of each component have been characterized using EPR. Cloning and sequencing of the genes for the two subunits of each component is in progress. Results indicate that the Ni/Fe-S component cleaves the C-C and C-S bonds of acetyl-CoA followed by oxidation of the carbonyl group to carbon dioxide and transfer of the methyl group to the Co/Fe-S component. The enzymes and cofactors involved in transfer of the methyl group from the Co/Fe-S component to coenzyme M will be purified and characterized. Ferredoxin is an electron acceptor for the Ni/Fe-S component and also serves to reductively reactivate methylreductase which catalyzes the demethylation of methyl coenzyme M to methane. This ferredoxin is being characterized utilizing EPR and RR spectroscopic methods to determine the properties of the Fe-S centers. Genes encoding this and other ferredoxins have been cloned and sequenced to determine the primary structures. Carbonic anhydrase is being purified and characterized to determine the function of this enzyme in the pathway.

  5. Adsorption structure, thermal reaction and initial pathways of 1,2-benzyne on Cu(100)

    NASA Astrophysics Data System (ADS)

    Lin, Jong-Liang; Lin, Yi-Shiue; Lin, Bo-Chiuan; Liao, Yuan-Hsuan; Chen, Yi-Ting; Chen, Shang-Wei; Jhuang, Jyun-Yi; Lee, Yarong; Lin, Jiing-Chyuan

    2016-10-01

    1,2-C6H4I2 is used as precursor to generate 1,2-C6H4 (ortho-C6H4) on Cu(100). The reflection-absorption infrared spectroscopy (RAIRS) confirms the vertical adsorption geometry of 1,2-C6H4 on Cu(100), which agrees with that predicted theoretically. H2 evolving between 620 K and 870 K is the only reaction product detected from the 1,2-C6H4 decomposition in temperature-programmed reaction/desorption (TPR/D). Our calculations indicate that the 1,2-C6H4 primarily undergoes C3-H bond scission, forming 1,2,3-C6H3, with distorted C6 ring, and H atom on the surface without ring rupture (C1-C2 bond dissociation) prior to H loss. Furthermore, isomerization of the 1,2-C6H4, if it does occur, may proceed via dehydrogenation-hydrogenation, instead of H-shift.

  6. Evidence for Different Reaction Pathways for Liquid and Granular Micronutrients in a Calcareous Soil

    SciTech Connect

    Hettiarachchi, Ganga M.; McLaughlin, Mike J.; Scheckel, Kirk G.; Chittleborough, David J.; Newville, Mathew; Sutton, Steve; Lombi, Enzo

    2008-06-16

    The benefits of Mn and Zn fluid fertilizers over conventional granular products in calcareous sandy loam soils have been agronomically demonstrated. We hypothesized that the differences in the effectiveness between granular and fluid Mn and Zn fertilizers is due to different Mn and Zn reaction processes in and around fertilizer granules and fluid fertilizer bands. We used a combination of several synchrotron-based x-ray techniques, namely, spatially resolved micro-x-ray fluorescence (?-XRF), micro-x-ray absorption near edge structure spectroscopy (?-XANES), and bulk-XANES and -extended x-ray absorption fine structure (EXAFS) spectroscopy, along with several laboratory-based x-ray techniques to speciate different fertilizer-derived Mn and Zn species in highly calcareous soils to understand the chemistry underlying the observed differential behavior of fluid and granular micronutrient forms. Micro-XRF mapping of soil-fertilizer reactions zones indicated that the mobility of Mn and Zn from liquid fertilizer was greater than that observed for equivalent granular sources of these micronutrients in soil. After application of these micronutrient fertilizers to soil, Mn and Zn from liquid fertilizers were found to remain in comparatively more soluble solid forms, such as hydrated Mn phosphate-like, Mn calcite-like, adsorbed Zn-like, and Zn silicate-like phases, whereas Mn and Zn from equivalent granular sources tended to transform into comparatively less soluble solid forms such as Mn oxide-like, Mn carbonate-like, and Zn phosphate-like phases.

  7. Formally direct pathways and low-temperature chain branching in hydrocarbon autoignition : the cyclohexyl + O2 reaction at high pressure.

    SciTech Connect

    Taatjes, Craig A.; Jusinski, Leonard E.; Zador, Judit; Fernandes, Ravi X.; Miller, James A.

    2008-10-01

    The OH concentration in the Cl-initiated oxidation of cyclohexane has been measured between 6.5-20.3 bar and in the 586-828 K temperature range by a pulsed-laser photolytic initiation--laser-induced fluorescence method. The experimental OH profiles are modeled by using a master-equation-based kinetic model as well as a comprehensive literature mechanism. Below 700 K OH formation takes place on two distinct time-scales, one on the order of microseconds and the other over milliseconds. Detailed modeling demonstrates that formally direct chemical activation pathways are responsible for the OH formation on short timescales. These results establish that formally direct pathways are surprisingly important even for relatively large molecules at the pressures of practical combustors. It is also shown that remaining discrepancies between model and experiment are attributable to low-temperature chain branching from the addition of the second oxygen to hydroperoxycyclohexyl radicals.

  8. Mechanism for the Direct Synthesis of H2O2 on Pd Clusters: Heterolytic Reaction Pathways at the Liquid-Solid Interface.

    PubMed

    Wilson, Neil M; Flaherty, David W

    2016-01-20

    Direct synthesis (H2 + O2 → H2O2) is a promising reaction for producing H2O2, which can replace chlorinated oxidants in industrial processes. The mechanism of this reaction and the reasons for the importance of seemingly unrelated factors (e.g., Pd cluster size and solvent pH) remain unclear despite significant research. We propose a mechanism for H2O2 formation on Pd clusters consistent with steady-state H2O2 and H2O formation rates measured as functions of reactant pressures and temperature and the interpretations of proton concentration effects. H2O2 forms by sequential proton-electron transfer to O2 and OOH surface intermediates, whereas H2O forms by O-O bond rupture within OOH surface species. Direct synthesis, therefore, does not proceed by the Langmuir-Hinshelwood mechanism often invoked. Rather, H2O2 forms by heterolytic reaction pathways resembling the two-electron oxygen reduction reaction (ORR); however, the chemical potential of H2 replaces an external electrical potential as the thermodynamic driving force. Activation enthalpies (ΔH(⧧)) for H2O formation increase by 14 kJ mol(-1) when Pd cluster diameters increase from 0.7 to 7 nm because changes in the electronic structure of Pd surface atoms decrease their propensity to cleave O-O bonds. ΔH(⧧) values for H2O2 remain nearly constant because barriers for proton-electron transfer depend weakly on the coordinative saturation of Pd surface atoms. Collectively, these results provide a self-consistent mechanism, which clarifies many studies in which H2O2 rates and selectivities were shown to depend on the concentration of acid/halide additives and Pd cluster size. These findings will guide the rational design of selective catalysts for direct synthesis.

  9. Mechanism for the Direct Synthesis of H2O2 on Pd Clusters: Heterolytic Reaction Pathways at the Liquid-Solid Interface.

    PubMed

    Wilson, Neil M; Flaherty, David W

    2016-01-20

    Direct synthesis (H2 + O2 → H2O2) is a promising reaction for producing H2O2, which can replace chlorinated oxidants in industrial processes. The mechanism of this reaction and the reasons for the importance of seemingly unrelated factors (e.g., Pd cluster size and solvent pH) remain unclear despite significant research. We propose a mechanism for H2O2 formation on Pd clusters consistent with steady-state H2O2 and H2O formation rates measured as functions of reactant pressures and temperature and the interpretations of proton concentration effects. H2O2 forms by sequential proton-electron transfer to O2 and OOH surface intermediates, whereas H2O forms by O-O bond rupture within OOH surface species. Direct synthesis, therefore, does not proceed by the Langmuir-Hinshelwood mechanism often invoked. Rather, H2O2 forms by heterolytic reaction pathways resembling the two-electron oxygen reduction reaction (ORR); however, the chemical potential of H2 replaces an external electrical potential as the thermodynamic driving force. Activation enthalpies (ΔH(⧧)) for H2O formation increase by 14 kJ mol(-1) when Pd cluster diameters increase from 0.7 to 7 nm because changes in the electronic structure of Pd surface atoms decrease their propensity to cleave O-O bonds. ΔH(⧧) values for H2O2 remain nearly constant because barriers for proton-electron transfer depend weakly on the coordinative saturation of Pd surface atoms. Collectively, these results provide a self-consistent mechanism, which clarifies many studies in which H2O2 rates and selectivities were shown to depend on the concentration of acid/halide additives and Pd cluster size. These findings will guide the rational design of selective catalysts for direct synthesis. PMID:26597848

  10. Multiple pathways to compliance: mothers' willingness to cooperate and knowledge of their children's reactions to discipline.

    PubMed

    Davidov, Maayan; Grusec, Joan E

    2006-12-01

    Mothers of 59 children with ages from 6 to 9 years were assessed for their general willingness to cooperate with their children's desires and their accurate predictions of their children's evaluations of different discipline strategies. Mothers asked their children to clean up a playroom in their absence, with some children protesting and others not protesting. Results showed that maternal willing cooperation predicted children's compliance in the absence but not in the presence of protest. Conversely, maternal accuracy concerning their children's evaluations of discipline facilitated children's compliance in dyads in which children expressed initial resistance but not if children indicated no opposition. Mothers' responsive reactions to protest mediated between maternal accuracy and children's ultimate compliance. Results indicate that specific features of parenting facilitate compliance in specific situations. PMID:17176207

  11. Wavelength-dependent photoproduct formation of phycocyanobilin in solution - Indications for competing reaction pathways

    NASA Astrophysics Data System (ADS)

    Dietzek, Benjamin; Fey, Sonja; Matute, Ricardo A.; González, Leticia; Schmitt, Michael; Popp, Jürgen; Yartsev, Arkady; Hermann, Gudrun

    2011-10-01

    Phycocyanobilin (PCB), an open-chain tetrapyrrole, makes up - slightly modified - the chromophore in phytochromes, the importance of which triggered model studies on the photochemistry of PCB in solution. We use pump-wavelength dependent femtosecond transient absorption spectroscopy including the near-IR region for probing to gain new insight into the photoreaction. The data reveal the coexistence of three ground state species: The dominant species PCB A undergoes photoreaction into PCB B and PCB C indicating a branching of the initial reaction path leading to formation of PCB B and PCB C. On this basis the photoreaction involves fast structural rearrangements within the tetrapyrrolic macrocycle, which are followed by slower rate-limiting changes in the protonation state of the pyrrolenine/pyrrole rings.

  12. Mixed N-Heterocyclic Carbene-Bis(oxazolinyl)borato Rhodium and Iridium Complexes in Photochemical and Thermal Oxidative Addition Reactions

    SciTech Connect

    Xu, Songchen; Manna, Kuntal; Ellern, Arkady; Sadow, Aaron D

    2014-12-08

    In order to facilitate oxidative addition chemistry of fac-coordinated rhodium(I) and iridium(I) compounds, carbene–bis(oxazolinyl)phenylborate proligands have been synthesized and reacted with organometallic precursors. Two proligands, PhB(OxMe2)2(ImtBuH) (H[1]; OxMe2 = 4,4-dimethyl-2-oxazoline; ImtBuH = 1-tert-butylimidazole) and PhB(OxMe2)2(ImMesH) (H[2]; ImMesH = 1-mesitylimidazole), are deprotonated with potassium benzyl to generate K[1] and K[2], and these potassium compounds serve as reagents for the synthesis of a series of rhodium and iridium complexes. Cyclooctadiene and dicarbonyl compounds {PhB(OxMe2)2ImtBu}Rh(η4-C8H12) (3), {PhB(OxMe2)2ImMes}Rh(η4-C8H12) (4), {PhB(OxMe2)2ImMes}Rh(CO)2 (5), {PhB(OxMe2)2ImMes}Ir(η4-C8H12) (6), and {PhB(OxMe2)2ImMes}Ir(CO)2 (7) are synthesized along with ToMM(η4-C8H12) (M = Rh (8); M = Ir (9); ToM = tris(4,4-dimethyl-2-oxazolinyl)phenylborate). The spectroscopic and structural properties and reactivity of this series of compounds show electronic and steric effects of substituents on the imidazole (tert-butyl vs mesityl), effects of replacing an oxazoline in ToM with a carbene donor, and the influence of the donor ligand (CO vs C8H12). The reactions of K[2] and [M(μ-Cl)(η2-C8H14)2]2 (M = Rh, Ir) provide {κ4-PhB(OxMe2)2ImMes'CH2}Rh(μ-H)(μ-Cl)Rh(η2-C8H14)2 (10) and {PhB(OxMe2)2ImMes}IrH(η3-C8H13) (11). In the former compound, a spontaneous oxidative addition of a mesityl ortho-methyl to give a mixed-valent dirhodium species is observed, while the iridium compound forms a monometallic allyl hydride. Photochemical reactions of dicarbonyl compounds 5 and 7 result in C–H bond oxidative addition providing the compounds {κ4-PhB(OxMe2)2ImMes'CH2}RhH(CO) (12) and {PhB(OxMe2)2ImMes}IrH(Ph)CO (13). In 12, oxidative addition results in cyclometalation of the mesityl ortho-methyl similar to 10, whereas the iridium compound reacts with the benzene solvent to give a rare crystallographically characterized cis

  13. Bifunctional heterogeneous catalysis of silica-alumina-supported tertiary amines with controlled acid-base interactions for efficient 1,4-addition reactions.

    PubMed

    Motokura, Ken; Tanaka, Satoka; Tada, Mizuki; Iwasawa, Yasuhiro

    2009-10-19

    We report the first tunable bifunctional surface of silica-alumina-supported tertiary amines (SA-NEt(2)) active for catalytic 1,4-addition reactions of nitroalkanes and thiols to electron-deficient alkenes. The 1,4-addition reaction of nitroalkanes to electron-deficient alkenes is one of the most useful carbon-carbon bond-forming reactions and applicable toward a wide range of organic syntheses. The reaction between nitroethane and methyl vinyl ketone scarcely proceeded with either SA or homogeneous amines, and a mixture of SA and amines showed very low catalytic activity. In addition, undesirable side reactions occurred in the case of a strong base like sodium ethoxide employed as a catalytic reagent. Only the present SA-supported amine (SA-NEt(2)) catalyst enabled selective formation of a double-alkylated product without promotions of side reactions such as an intramolecular cyclization reaction. The heterogeneous SA-NEt(2) catalyst was easily recovered from the reaction mixture by simple filtration and reusable with retention of its catalytic activity and selectivity. Furthermore, the SA-NEt(2) catalyst system was applicable to the addition reaction of other nitroalkanes and thiols to various electron-deficient alkenes. The solid-state magic-angle spinning (MAS) NMR spectroscopic analyses, including variable-contact-time (13)C cross-polarization (CP)/MAS NMR spectroscopy, revealed that acid-base interactions between surface acid sites and immobilized amines can be controlled by pretreatment of SA at different temperatures. The catalytic activities for these addition reactions were strongly affected by the surface acid-base interactions.

  14. Facile preparation and biological imaging of luminescent polymeric nanoprobes with aggregation-induced emission characteristics through Michael addition reaction.

    PubMed

    Lv, Qiulan; Wang, Ke; Xu, Dazhuang; Liu, Meiying; Wan, Qing; Huang, Hongye; Liang, Shangdong; Zhang, Xiaoyong; Wei, Yen

    2016-09-01

    Water dispersion aggregation-induced emission (AIE) dyes based nanomaterials have recently attracted increasing attention in the biomedical fields because of their unique optical properties, outstanding performance as imaging and therapeutic agents. The methods to conjugate hydrophilic polymers with AIE dyes to solve the hydrophobic nature of AIE dyes and makeS them widely used in biomedicine, which have been extensively explored and paid great effort previously. Although great advance has been made in the fabrication and biomedical applications of AIE-active polymeric nanoprobes, facile and efficient strategies for fabrication of biodegradable AIE-active nanoprobes are still high desirable. In this work, amphiphilic biodegradable fluorescent organic nanoparticles (PLL-TPE-O-E FONs) have been fabricated for the first time by conjugation of AIE dye tetraphenylethene acrylate (TPE-O-E) with Poly-l-Lysine (PLL) through a facile one-step Michael addition reaction, which was carried out under rather mild conditions, included air atmosphere, near room temperature and absent of metal catalysts or hazardous reagents. Due to the unique AIE properties, these amphiphilic copolymers tend to self-assemble into high luminescent water dispersible nanoparticles with size range from 400 to 600nm. Laser scanning microscope and cytotoxicity results revealed that PLL-TPE-O-E FONs can be internalized into cytoplasm with negative cytotoxicity, which implied that PLL-TPE-O-E FONs are promising for biological applications. PMID:27311129

  15. Competitive reaction pathways in vibrationally induced photodissociation of H2SO4.

    PubMed

    Yosa Reyes, Juvenal; Nagy, Tibor; Meuwly, Markus

    2014-09-14

    Vibrationally induced photodissociation of sulfuric acid into H2O + SO3 is investigated based on reactive molecular dynamics (MD) simulations. Multisurface adiabatic reactive MD simulations allow us to follow both, H-transfer and water elimination after excitation of the ν9 OH-stretching mode. Analysis of several thousand trajectories finds that the H2O and SO3 fragments have distinct final state distributions with respect to translational, rotational, and vibrational degrees of freedom. Rotational distributions peak at quantum numbers j ≤ 5 for water and j ≈ 60 for SO3. The final state distributions should be useful in identifying products in forthcoming experiments. Based on the MD trajectories, a kinetic scheme has been developed which is able to explain most of the trajectory data and suggests that IVR is very rapid. Typical lifetimes of the excited complex range from several 10 picoseconds to hundreds of nanoseconds, depending on the excitation level. Including temperature and pressure profiles characteristic for the stratosphere in the kinetic model shows that excitations higher than ν9 = 4 can significantly contribute to the photolysis rate. This extends and specifies earlier work in that multi-level modeling is required to understand the significance of vibrationally induced decomposition pathways of sulfuric acid in the middle atmosphere. PMID:25072517

  16. Cobalt-catalyzed cyclotrimerization of alkynes: the answer to the puzzle of parallel reaction pathways.

    PubMed

    Agenet, Nicolas; Gandon, Vincent; Vollhardt, K Peter C; Malacria, Max; Aubert, Corinne

    2007-07-18

    To understand some experimental data at odds with the computed mechanism of the CpCo(L2)-catalyzed [2 + 2 + 2] cyclotrimerization of ethyne, DFT computations were carried out following the fate of methyl- and hydroxycarbonyl-substituted alkynes to give the corresponding arenes. The key intermediate in all cases is a triplet cobaltacyclopentadiene obtained by oxidative coupling of the corresponding CpCo(bisalkyne) complex and subsequent spin change via a minimum energy crossing point (MECP). From that species, two different catalytic cycles lead to an arene product, depending on the nature of the alkyne and other ligands present: either alkyne ligation to furnish a cobaltacyclopentadiene(alkyne) intermediate or trapping by a sigma-donor ligand to generate a coordinatively saturated cobaltacyclopentadiene(PR3) complex. The former leads to the CpCo-complexed arene product via intramolecular cobalt-assisted [4 + 2] cycloaddition, whereas the latter may, in the case of a reactive dienophile (butynedioic acid), undergo direct intermolecular [4 + 2] cycloaddition to generate a cobaltanorbornene. The bridgehead cobalt atom is then reductively eliminated after another change in spin state from singlet to triplet. The necessary conditions for one or the other mechanistic pathway are elaborated.

  17. Theoretical and Experimental Investigation of Thermodynamics and Kinetics of Thiol-Michael Addition Reactions: A Case Study of Reversible Fluorescent Probes for Glutathione Imaging in Single Cells.

    PubMed

    Chen, Jianwei; Jiang, Xiqian; Carroll, Shaina L; Huang, Jia; Wang, Jin

    2015-12-18

    Density functional theory (DFT) was applied to study the thermodynamics and kinetics of reversible thiol-Michael addition reactions. M06-2X/6-31G(d) with the SMD solvation model can reliably predict the Gibbs free energy changes (ΔG) of thiol-Michael addition reactions with an error of less than 1 kcal·mol(-1) compared with the experimental benchmarks. Taking advantage of this computational model, the first reversible reaction-based fluorescent probe was developed that can monitor the changes in glutathione levels in single living cells.

  18. Prediction of CL-20 chemical degradation pathways, theoretical and experimental evidence for dependence on competing modes of reaction

    SciTech Connect

    Qasim, Mohammad M.; Fredrickson, Herbert L.; Honea, P.; Furey, John; Leszczynski, Jerzy; Okovytyy, S.; Szecsody, Jim E.; Kholod, Y.

    2005-10-01

    Highest occupied and lowest unoccupied molecular orbital energies, formation energies, bond lengths and FTIR spectra all suggest competing CL-20 degradation mechanisms. This second of two studies investigates recalcitrant, toxic, aromatic CL-20 intermediates that absorb from 370 to 430 nm. Our earlier study (Struct. Chem., 15, 2004) revealed that these intermediates were formed at high OH- concentrations via the chemically preferred pathway of breaking the C-C bond between the two cyclopentanes, thereby eliminating nitro groups, forming conjugated π bonds, and resulting in a pyrazine three-ring aromatic intermediate. In attempting to find and make dominant a more benign CL-20 transformation pathway, this current research validates hydroxylation results from both studies and examines CL-20 transformations via photo-induced free radical reactions. This article discusses CL-20 competing modes of degradation revealed through: computational calculation; UV/VIS and SF spectroscopy following alkaline hydrolysis; and photochemical irradiation to degrade CL-20 and its byproducts at their respective wavelengths of maximum absorption.

  19. Prediction of CL-20 chemical degradation pathways, theoretical and experimental evidence for dependence on competing modes of reaction.

    PubMed

    Qasim, M; Fredrickson, H; Honea, P; Furey, J; Leszczynski, J; Okovytyy, S; Szecsody, J; Kholod, Y

    2005-10-01

    Highest occupied and lowest unoccupied molecular orbital energies, formation energies, bond lengths and FTIR spectra all suggest competing CL-20 degradation mechanisms. This second of two studies investigates recalcitrant, toxic, aromatic CL-20 intermediates that absorb from 370 to 430 nm. Our earlier study (Struct. Chem., 15, 2004) revealed that these intermediates were formed at high OH(-) concentrations via the chemically preferred pathway of breaking the C-C bond between the two cyclopentanes, thereby eliminating nitro groups, forming conjugated pi bonds, and resulting in a pyrazine three-ring aromatic intermediate. In attempting to find and make dominant a more benign CL-20 transformation pathway, this current research validates hydroxylation results from both studies and examines CL-20 transformations via photo-induced free radical reactions. This article discusses CL-20 competing modes of degradation revealed through: computational calculation; UV/VIS and SF spectroscopy following alkaline hydrolysis; and photochemical irradiation to degrade CL-20 and its byproducts at their respective wavelengths of maximum absorption. PMID:16272046

  20. Polyphenol-enriched cocoa protects the diabetic retina from glial reaction through the sirtuin pathway.

    PubMed

    Duarte, Diego A; Rosales, Mariana Ap B; Papadimitriou, Alexandros; Silva, Kamila C; Amancio, Vitor Hugo O; Mendonça, Jacqueline N; Lopes, Norberto P; de Faria, José B Lopes; de Faria, Jacqueline M Lopes

    2015-01-01

    Cocoa is rich in flavonoids, which are potent antioxidants with established benefits for cardiovascular health but unproven effects on neurodegeneration. Sirtuins (SIRTs), which make up a family of deacetylases, are thought to be sensitive to oxidation. In this study, the possible protective effects of cocoa in the diabetic retina were assessed. Rat Müller cells (rMCs) exposed to normal or high glucose (HG) or H2O2 were submitted to cocoa treatment in the presence or absence of SIRT-1 inhibitor and small interfering RNA The experimental animal study was conducted in streptozotocin-induced diabetic rats randomized to receive low-, intermediate-, or high-polyphenol cocoa treatments via daily gavage for 16 weeks (i.e., 0.12, 2.9 or 22.9 mg/kg/day of polyphenols). The rMCs exposed to HG or H2O2 exhibited increased glial fibrillary acidic protein (GFAP) and acetyl-RelA/p65 and decreased SIRT1 activity/expression. These effects were cancelled out by cocoa, which decreased reactive oxygen species production and PARP-1 activity, augmented the intracellular pool of NAD(+), and improved SIRT1 activity. The rat diabetic retinas displayed the early markers of retinopathy accompanied by markedly impaired electroretinogram. The presence of diabetes activated PARP-1 and lowered NAD(+) levels, resulting in SIRT1 impairment. This augmented acetyl RelA/p65 had the effect of up-regulated GFAP. Oral administration of polyphenol cocoa restored the above alterations in a dose-dependent manner. This study reveals that cocoa enriched with polyphenol improves the retinal SIRT-1 pathway, thereby protecting the retina from diabetic milieu insult.

  1. Polyphenol-enriched cocoa protects the diabetic retina from glial reaction through the sirtuin pathway.

    PubMed

    Duarte, Diego A; Rosales, Mariana Ap B; Papadimitriou, Alexandros; Silva, Kamila C; Amancio, Vitor Hugo O; Mendonça, Jacqueline N; Lopes, Norberto P; de Faria, José B Lopes; de Faria, Jacqueline M Lopes

    2015-01-01

    Cocoa is rich in flavonoids, which are potent antioxidants with established benefits for cardiovascular health but unproven effects on neurodegeneration. Sirtuins (SIRTs), which make up a family of deacetylases, are thought to be sensitive to oxidation. In this study, the possible protective effects of cocoa in the diabetic retina were assessed. Rat Müller cells (rMCs) exposed to normal or high glucose (HG) or H2O2 were submitted to cocoa treatment in the presence or absence of SIRT-1 inhibitor and small interfering RNA The experimental animal study was conducted in streptozotocin-induced diabetic rats randomized to receive low-, intermediate-, or high-polyphenol cocoa treatments via daily gavage for 16 weeks (i.e., 0.12, 2.9 or 22.9 mg/kg/day of polyphenols). The rMCs exposed to HG or H2O2 exhibited increased glial fibrillary acidic protein (GFAP) and acetyl-RelA/p65 and decreased SIRT1 activity/expression. These effects were cancelled out by cocoa, which decreased reactive oxygen species production and PARP-1 activity, augmented the intracellular pool of NAD(+), and improved SIRT1 activity. The rat diabetic retinas displayed the early markers of retinopathy accompanied by markedly impaired electroretinogram. The presence of diabetes activated PARP-1 and lowered NAD(+) levels, resulting in SIRT1 impairment. This augmented acetyl RelA/p65 had the effect of up-regulated GFAP. Oral administration of polyphenol cocoa restored the above alterations in a dose-dependent manner. This study reveals that cocoa enriched with polyphenol improves the retinal SIRT-1 pathway, thereby protecting the retina from diabetic milieu insult. PMID:25448608

  2. Effects of Bond Location on the Ignition and Reaction Pathways of trans-Hexene Isomers.

    PubMed

    Wagnon, Scott W; Barraza-Botet, Cesar L; Wooldridge, Margaret S

    2015-07-16

    Chemical structure and bond location are well-known to impact combustion reactivity. The current work presents new experimental autoignition and speciation data on the three trans-hexene isomers (1-hexene, trans-2-hexene, and trans-3-hexene), which describe the effects of the location of the carbon-carbon double bond. Experiments were conducted with the University of Michigan rapid compression facility to determine ignition delay times from pressure time histories. Stoichiometric (ϕ = 1.0) mixtures at dilution levels of buffer gas:O2 = 7.5 (mole basis) were investigated at an average pressure of 11 atm and temperatures from 837 to 1086 K. Fast gas sampling and gas chromatography were also used to quantitatively measure 13 stable intermediate species formed during the ignition delay period of each isomer at a temperature of ∼900 K. The measured ignition delay times and species measurements were in good agreement with previous experimental studies at overlapping conditions. The results were modeled using a gasoline surrogate reaction mechanism from Lawrence Livermore National Laboratory, which contains a submechanism for the trans-hexene isomers. The model predictions captured the overall autoignition characteristics of the hexene isomers well (within a factor of 2), as well as the time histories of several of the intermediate species (e.g., propene). However, there were discrepancies between the model predictions and the experimental data for some species, particularly for the 3-hexene isomer.

  3. Interleukin-13 Activates Distinct Cellular Pathways Leading to Ductular Reaction, Steatosis, and Fibrosis.

    PubMed

    Gieseck, Richard L; Ramalingam, Thirumalai R; Hart, Kevin M; Vannella, Kevin M; Cantu, David A; Lu, Wei-Yu; Ferreira-González, Sofía; Forbes, Stuart J; Vallier, Ludovic; Wynn, Thomas A

    2016-07-19

    Fibroproliferative diseases are driven by dysregulated tissue repair responses and are a major cause of morbidity and mortality because they affect nearly every organ system. Type 2 cytokine responses are critically involved in tissue repair; however, the mechanisms that regulate beneficial regeneration versus pathological fibrosis are not well understood. Here, we have shown that the type 2 effector cytokine interleukin-13 simultaneously, yet independently, directed hepatic fibrosis and the compensatory proliferation of hepatocytes and biliary cells in progressive models of liver disease induced by interleukin-13 overexpression or after infection with Schistosoma mansoni. Using transgenic mice with interleukin-13 signaling genetically disrupted in hepatocytes, cholangiocytes, or resident tissue fibroblasts, we have revealed direct and distinct roles for interleukin-13 in fibrosis, steatosis, cholestasis, and ductular reaction. Together, these studies show that these mechanisms are simultaneously controlled but distinctly regulated by interleukin-13 signaling. Thus, it may be possible to promote interleukin-13-dependent hepatobiliary expansion without generating pathological fibrosis. VIDEO ABSTRACT. PMID:27421703

  4. Hafnium oxide and zirconium oxide atomic layer deposition: initial precursor and potential side-reaction product pathways with H/Si(100)-2 x 1.

    PubMed

    Fenno, Ryan D; Halls, Mathew D; Raghavachari, Krishnan

    2005-03-24

    Hybrid density functional calculations have been carried out using cluster models of the H/Si(100)-2 x 1 surface to investigate the mechanistic details of the initial surface reactions occurring in the atomic layer deposition of hafnium and zirconium oxides (HfO2 and ZrO2). Reaction pathways involving the metal precursors ZrCl4, Zr(CH3)4, HfCl4, and Hf(CH3)4 have been examined. Pathways leading to the formation of a Zr-Si or Hf-Si linkage show a significant sensitivity to the identity of the leaving group, with chloride loss reactions being both kinetically and thermodynamically less favorable than reactions leading to the loss of a methyl group. The energetics of the Zr(CH3)4 and Hf(CH3)4 reactions are similar with an overall exothermicity of 0.3-0.4 eV and a classical barrier height of 1.1-1.2 eV. For the reaction between H2O and the H/Si(100)-2 x 1 surface, the activation energy and overall reaction enthalpy are 1.6 and -0.8 eV, respectively. Due to contamination, trace amounts of H2O may be encountered by metal precursors, leading to the formation of minor species that can lead to unanticipated side-reaction pathways. Such gas-phase reactions between the halogenated and alkylated metal precursors and H2O are exothermic with small or no reaction barriers, allowing for the possibility of metal precursor hydroxylation before the H/Si surface is encountered. Of the contaminant surface reaction pathways, the most kinetically favorable corresponds to the surface -OH deposition. Interestingly, for the hydroxylated metal precursors, a unique reaction pathway resulting in the direct formation of Si-O-Zr and Si-O-Hf linkages has been identified and found to be the most thermodynamically stable pathway available, being exothermic by approximately 1.0 eV.

  5. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    DOE PAGES

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-11-20

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, ismore » likely to apply to other transition metal oxide systems. Lastly, the presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale.« less

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

    SciTech Connect

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

    2014-04-01

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

  7. The photoinitiated reaction pathway of full-length cyanobacteriochrome Tlr0924 monitored over 12 orders of magnitude.

    PubMed

    Hauck, Anna F E; Hardman, Samantha J O; Kutta, Roger J; Greetham, Gregory M; Heyes, Derren J; Scrutton, Nigel S

    2014-06-20

    The coupling of photochemistry to protein chemical and structural change is crucial to biological light-activated signaling mechanisms. This is typified by cyanobacteriochromes (CBCRs), members of the phytochrome superfamily of photoreceptors that exhibit a high degree of spectral diversity, collectively spanning the entire visible spectrum. CBCRs utilize a basic E/Z isomerization of the bilin chromophore as the primary step in their photocycle, which consists of reversible photoconversion between two photostates. Despite intense interest in these photoreceptors as signal transduction modules a complete description of light-activated chemical and structural changes has not been reported. The CBCR Tlr0924 contains both phycocyanobilin and phycoviolobilin chromophores, and these two species photoisomerize in parallel via spectrally and kinetically equivalent intermediates before the second step of the photoreaction where the reaction pathways diverge, the loss of a thioether linkage to a conserved cysteine residue occurs, and the phycocyanobilin reaction terminates in a red-absorbing state, whereas the phycoviolobilin reaction proceeds more rapidly to a final green-absorbing state. Here time-resolved visible transient absorption spectroscopy (femtosecond to second) has been used, in conjunction with time-resolved IR spectroscopy (femtosecond to nanosecond) and cryotrapping techniques, to follow the entire photoconversion of the blue-absorbing states to the green- and red-absorbing states of the full-length form of Tlr0924 CBCR. Our analysis shows that Tlr0924 undergoes an unprecedented long photoreaction that spans from picoseconds to seconds. We show that the thermally driven, long timescale changes are less complex than those reported for the red/far-red photocycles of the related phytochrome photoreceptors. PMID:24817121

  8. Macrocyclic cyclooctene-supported AlCl-salen catalysts for conjugated addition reactions: effect of linker and support structure on catalysis.

    PubMed

    Madhavan, Nandita; Takatani, Tait; Sherrill, C David; Weck, Marcus

    2009-01-01

    AlCl-salen (salen=N,N'-bis(salicylidene)ethylenediamine dianion) catalysts supported onto macrocyclic oligomeric cyclooctene through linkers of varying length and flexibility have been developed to demonstrate the importance of support architecture on catalyst activity. The role played by the support and the linkers in dictating catalyst activity was found to vary for reactions with contrasting mechanisms, such as the bimetallic cyanide and the monometallic indole addition reactions. While the flexible support significantly enhanced the cyanide addition reaction, most likely by improving salen-salen interactions in the transition state, it lowered the reaction rate for the monometallic indole reaction. For both reactions, significant increase in catalytic activity was observed for catalysts with the longest linkers. The effect of the flexible macrocyclic support on catalysis was further exemplified by the enhanced activity of the supported catalyst in comparison with its unsupported analogue for the conjugate addition of tetrazoles, which is known to be catalyzed by dimeric mu-oxo-salen catalysts. Our studies with the cyclooctene supported AlCl-salen catalysts provides significant insights for rationally designing highly efficient AlCl-salen catalysts for a diverse set of reactions.

  9. Identification in Haloferax volcanii of phosphomevalonate decarboxylase and isopentenyl phosphate kinase as catalysts of the terminal enzyme reactions in an archaeal alternate mevalonate pathway.

    PubMed

    Vannice, John C; Skaff, D Andrew; Keightley, Andrew; Addo, James K; Wyckoff, Gerald J; Miziorko, Henry M

    2014-03-01

    Mevalonate (MVA) metabolism provides the isoprenoids used in archaeal lipid biosynthesis. In synthesis of isopentenyl diphosphate, the classical MVA pathway involves decarboxylation of mevalonate diphosphate, while an alternate pathway has been proposed to involve decarboxylation of mevalonate monophosphate. To identify the enzymes responsible for metabolism of mevalonate 5-phosphate to isopentenyl diphosphate in Haloferax volcanii, two open reading frames (HVO_2762 and HVO_1412) were selected for expression and characterization. Characterization of these proteins indicated that one enzyme is an isopentenyl phosphate kinase that forms isopentenyl diphosphate (in a reaction analogous to that of Methanococcus jannaschii MJ0044). The second enzyme exhibits a decarboxylase activity that has never been directly attributed to this protein or any homologous protein. It catalyzes the synthesis of isopentenyl phosphate from mevalonate monophosphate, a reaction that has been proposed but never demonstrated by direct experimental proof, which is provided in this account. This enzyme, phosphomevalonate decarboxylase (PMD), exhibits strong inhibition by 6-fluoromevalonate monophosphate but negligible inhibition by 6-fluoromevalonate diphosphate (a potent inhibitor of the classical mevalonate pathway), reinforcing its selectivity for monophosphorylated ligands. Inhibition by the fluorinated analog also suggests that the PMD utilizes a reaction mechanism similar to that demonstrated for the classical MVA pathway decarboxylase. These observations represent the first experimental demonstration in H. volcanii of both the phosphomevalonate decarboxylase and isopentenyl phosphate kinase reactions that are required for an alternate mevalonate pathway in an archaeon. These results also represent, to our knowledge, the first identification and characterization of any phosphomevalonate decarboxylase. PMID:24375100

  10. Photoreversible oxidative-addition, reductive-elimination reactions Fe + H/sub 2/ in equilibrium FeH/sub 2/ in low-temperature matrices

    SciTech Connect

    Ozin, G.A.; McCaffrey, J.G.

    1984-02-16

    307-nm photoexcited Fe atoms in H/sub 2//rare gas 12 K matrices undergo an activated and concerted insertion reaction into the H-H bond of H/sub 2/ to form iron dihydride, FeH/sub 2/, having a nonlinear geometry, with no detectable involvement of H-atom abstraction products FeH + H, higher iron hydrides FeH/sub x/ (x greater than or equal to 3), or molecular dihydrogen complexes, Fe(H/sub 2/). The microscopic reverse of the photoinsertion reaction can be induced by 440-nm photoexcitation of FeH/sub 2/ at 12 K and proceeds by a nonactivated and concerted reductive-elimination pathway with no observable participation of FeH, H, FeH/sub x/ (x greater than or equal to 3), or Fe(H/sub 2/) reaction intermediates.

  11. Application of a C-C Bond-Forming Conjugate Addition Reaction in Asymmetric Dearomatization of β-Naphthols.

    PubMed

    Yang, Dongxu; Wang, Linqing; Kai, Ming; Li, Dan; Yao, Xiaojun; Wang, Rui

    2015-08-10

    A C-C bond-forming conjugate reaction was successfully applied to the enantioselective dearomatization of β-naphthols. A C(sp2)-C(sp3) bond is formed by using propargylic ketones as reactive partners. Good to excellent Z/E ratios and ee values were obtained by employing an in situ generated magnesium catalyst. Further transformations of the Z-configured C-C double bond in the products were achieved under mild reaction conditions. Moreover, the stereocontrolling element of this magnesium-catalyzed dearomatization reaction was explored by computational chemistry. PMID:26173841

  12. Toward Additive-Free Small-Molecule Organic Solar Cells: Roles of the Donor Crystallization Pathway and Dynamics.

    PubMed

    Abdelsamie, Maged; Treat, Neil D; Zhao, Kui; McDowell, Caitlin; Burgers, Mark A; Li, Ruipeng; Smilgies, Detlef-M; Stingelin, Natalie; Bazan, Guillermo C; Amassian, Aram

    2015-12-01

    The ease with which small-molecule donors crystallize during solution processing is directly linked to the need for solvent additives. Donor molecules that get trapped in disordered (H1) or liquid crystalline (T1) mesophases require additive processing to promote crystallization, phase separation, and efficient light harvesting. A donor material (X2) that crystallizes directly from solution yields additive-free solar cells with an efficiency of 7.6%.

  13. Lewis acid-base 1,2-addition reactions: synthesis of pyrylium borates from en-ynoate precursors.

    PubMed

    Wilkins, Lewis C; Hamilton, Hugh B; Kariuki, Benson M; Hashmi, A Stephen K; Hansmann, Max M; Melen, Rebecca L

    2016-04-14

    Treatment of methyl (Z)-2-alken-4-ynoates with the strong Lewis acid tris(pentafluorophenyl) borane, B(C6F5)3, yield substituted zwitterionic pyrylium borate species via an intramolecular 6-endo-dig cyclisation reaction.

  14. A STUDY OF FUNDAMENTAL REACTION PATHWAYS FOR TRANSITION METAL ALKYL COMPLEXES. I. THE REACTION OF A NICKEL METHYL COMPLEX WITH ALKYNES. II. THE MECHANISM OF ALDEHYDE FORMATION IN THE REACTION OF A MOLYBDENUM HYDRIDE WITH MOLYBDENUM ALKYLS

    SciTech Connect

    Huggins, John Mitchell

    1980-06-01

    I. This study reports the rapid reaction under mild conditions of internal or terminal alkynes with methyl (acetyl~ acetonato) (triphenylphosphine) nickel (1) in either aromatic or ether solvents. In all cases vinylnickel products 2 are formed by insertion of the alkyne into the nickel=methyl bond. These complexes may be converted into a variety of organic products (e.g. alkenes, esters, vinyl halides) by treatment with appropriate reagents. Unsymmetrical alkynes give selectively the one regioisomer with the sterically largest substituent next to the nickel atom. In order to investigate the stereochemistry of the initial insertion, a x-ray diffraction study of the reaction of 1 with diphenylacetylene was carried out. This showed that the vinylnickel complex formed by overall trans insertion was the product of the reaction. Furthermore, subsequent slow isomerization of this complex, to a mixture of it and the corresponding cis isomer, demonstrated that this trans addition product is the kinetic product of the reaction. In studies with other alkynes, the product of trans addition was not always exclusively (or even predominantly) formed, but the ratio of the stereoisomers formed kinetically was substantially different from the thermodynamic ratio. Isotope labeling, added phosphine, and other experiments have allowed us to conclude that the mechanism of this reaction does involve initial cis addition. However, a coordinatively unsaturated vinylnickel complex is initially formed which can undergo rapid, phosphine-catalyzed cis-trans isomerization in competition with its conversion to the isolable phosphine-substituted kinetic reaction products. II. The reaction of CpMo(CO){sub 3}H (1a) with CpMo(CO){sub 3}R (2, R= CH{sub 3}, C{sub 2}H{sub 5}) at 50{degrees} C in THF gives the aldehyde RCHO and the dimers [CpMo(CO){sub 3}]{sub 2} (3a) and [CpMo(CO){sub 2}]{sub 2} (4a). Labeling one of the reactants with a methylcyclopentadienyl ligand it was possible to show that the

  15. Physical Properties and CO2 Reaction Pathway of 1-Ethyl-3-Methylimidazolium Ionic Liquids with Aprotic Heterocyclic Anions

    SciTech Connect

    Seo, S; DeSilva, MA; Brennecke, JF

    2014-12-25

    Ionic liquids (ILs) with aprotic heterocyclic anions (AHA) are attractive candidates for CO2 capture technologies. In this study, a series of AHA ILs with 1-ethyl-3-methylimidazolium ([emim](+)) cations were synthesized, and their physical properties (density, viscosity, and ionic conductivity) were measured. In addition, CO2 solubility in each IL was determined at room temperature using a volumetric method at pressures between 0 and 1 bar. The AHAs are basic anions that are capable of reacting stoichiometrically with CO2 to form carbamate species. An interesting CO2 uptake isotherm behavior was observed, and this may be attributed to a parallel, equilibrium proton exchange process between the imidazolium cation and the basic AHA in the presence of CO2, followed by the formation of "transient" carbene species that react rapidly with CO2. The presence of the imidazolium-carboxylate species and carbamate anion species was verified using H-1 and C-13 NMR spectroscopy. While the reaction between CO2 and the proposed transient carbene resulted in cation-CO2 binding that is stronger than the anion-CO2 reaction, the reactions of the imidazolium AHA ILs were fully reversible upon regeneration at 80 degrees C with nitrogen purging. The presence of water decreased the CO2 uptake due to the inhibiting effect of the neutral species (protonated form of AHA) that is formed.

  16. Methyl iodide oxidative addition to [Rh(acac)(CO)(PPh3)]: an experimental and theoretical study of the stereochemistry of the products and the reaction mechanism.

    PubMed

    Conradie, Marrigje M; Conradie, Jeanet

    2011-08-28

    Density functional theory was used to investigate the oxidative addition and subsequent carbonyl insertion and deinsertion steps of the reaction of methyl iodide to a rhodium(I) acetylacetonato complex of the formula [Rh(acac)(CO)(PPh(3))] (Hacac = acetylacetone). This process has been studied experimentally for many rhodium β-diketonato complexes, but, to the best of our knowledge, this is the first systematic computational study of the complete reaction sequence. Experimental (1)H techniques complement the theoretical results on the stereochemistry of the reaction intermediates and products. (1)H NMR also revealed the existence of a second rhodium(III)-acyl product, which has not been previously observed in this reaction. The calculated Gibbs free energy of activation of the oxidative addition reaction is 71 kJ mol(-1), which is in agreement with the experimental value of 82(1) kJ mol(-1). The DFT-calculated oxidative addition corresponds to an associative S(N)2 nucleophilic attack by the rhodium metal centre on the methyl iodide, which is in agreement with calculated and experimental (in brackets) activation parameters of the reaction, 27 (38.8) kJ mol(-1) for ΔH((≠)) and -147 (-146) J K(-1) mol(-1) for ΔS((≠)). PMID:21761056

  17. Complete active space second order perturbation theory (CASPT2) study of N(2D) + H2O reaction paths on D1 and D0 potential energy surfaces: Direct and roaming pathways

    NASA Astrophysics Data System (ADS)

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-10-01

    We report reaction paths starting from N(2D) + H2O for doublet spin states, D0 and D1. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H2ON → H-O(H)N → H-HON → NO(2Π) + H2, (2) cis-HNOH → HNO-H → H-HNO → NO + H2, (3) H2NO → H-HNO → HNO-H → trans-HNOH, are confirmed on the D0 surface.

  18. In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways.

    PubMed

    Dey, Swati; North, Justin A; Sriram, Jaya; Evans, Bradley S; Tabita, F Robert

    2015-12-25

    All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO2-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO2 fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions.

  19. Single-walled carbon nanotubes as nano-electrode and nano-reactor to control the pathways of a redox reaction.

    PubMed

    McSweeney, Robert L; Chamberlain, Thomas W; Davies, E Stephen; Khlobystov, Andrei N

    2014-11-28

    Single-walled carbon nanotubes have been demonstrated as effective nanoscale containers for a redox active organometallic complex Cp(Me)Mn(CO)3, acting simultaneously as nano-electrode and nano-reactor. Extreme spatial confinement of the redox reaction within the nanotubes changes its pathway compared to bulk solution due to stabilisation of a reactive intermediate.

  20. Activation of Aryl Halides by Nickel(I) Pincer Complexes: Reaction Pathways of Stoichiometric and Catalytic Dehalogenations.

    PubMed

    Rettenmeier, Christoph A; Wenz, Jan; Wadepohl, Hubert; Gade, Lutz H

    2016-08-15

    Homolytic C-X bond cleavage of organohalides by the T-shaped nickel(I) complexes [LigNi(I)] 1 bearing the iso-PyrrMeBox ligand had been found previously to be the crucial activation step in the asymmetric hydrodehalogenation of geminal dihalides. Here, this mechanistic investigation is extended to aryl halides, which allowed a systematic study of the activation process by a combination of experimental data and density functional theory modeling. While the activation of both aryl chlorides and geminal dichlorides appears to proceed via an analogous transition state, the generation of a highly stabile nickel(II)aryl species in the reaction of the aryl chlorides for the former represents a major difference in the reactive behavior. This difference was found to have a crucial impact on the activity of these nickel pincer systems as catalysts in the dehalogenation of aryl chlorides compared to geminal dichlorides and highlights the importance of the regulatory pathways controlling the nickel(I) concentration throughout the catalysis. These results along with the identification and characterization of novel nickel(II)aryl species are presented. PMID:27483018

  1. Transition-metal free reactions of boronic acids: cascade addition - ring-opening of furans towards functionalized γ-ketoaldehydes.

    PubMed

    Roscales, S; Csákÿ, A G

    2016-02-18

    We describe the first ring-opening of furfuryl alcohols with boronic acids to afford functionalized γ-ketoaldehydes. The transformation builds a new C-C bond at the original C-4 of the starting furan, and tolerates ring-substitution at C-3 and C-4 positions. The reaction takes place under metal-free conditions by promotion with tartaric acid.

  2. Mechanistic investigations of CO-photoextrusion and oxidative addition reactions of early transition-metal carbonyls: (η(5)-C5H5)M(CO)4 (M = V, Nb, Ta).

    PubMed

    Su, Shih-Hao; Su, Ming-Der

    2016-06-28

    The mechanisms for the photochemical Si-H bond activation reaction are studied theoretically using a model system of the group 5 organometallic compounds, η(5)-CpM(CO)4 (M = V, Nb, and Ta), with the M06-2X method and the Def2-SVPD basis set. Three types of reaction pathways that lead to final insertion products are identified. The structures of the intersystem crossings, which play a central role in these photo-activation reactions, are determined. The intermediates and transitional structures in either the singlet or triplet states are also calculated to provide a mechanistic explanation of the reaction pathways. All of the potential energy surfaces for the group 5 η(5)-CpM(CO)4 complexes are quite similar. In particular, the theoretical evidence suggests that after irradiation using light, η(5)-CpM(CO)4 quickly loses one CO ligand to yield two tricarbonyls, in either the singlet or the triplet states. The triplet tricarbonyl 16-electron intermediates, ([η(5)-CpM(CO)3](3)), play a key role in the formation of the final oxidative addition product, η(5)-CpM(CO)3(H)(SiMe3). However, the singlet counterparts, ([η(5)-CpM(CO)3](1)), play no role in the formation of the final product molecule, but their singlet metal centers interact weakly with solvent molecules ((Me3)SiH) to produce alkyl-solvated organometallic complexes, which are observable experimentally. This theoretical evidence is in accordance with the available experimental observations.

  3. Synchronized electrical stimulation of the rat medial forebrain bundle and perforant pathway generates an additive BOLD response in the nucleus accumbens and prefrontal cortex.

    PubMed

    Krautwald, Karla; Min, Hoon-Ki; Lee, Kendall H; Angenstein, Frank

    2013-08-15

    To study how a synchronized activation of two independent pathways affects the fMRI response in a common targeted brain region, blood oxygen dependent (BOLD) signals were measured during electrical stimulation of the right medial forebrain bundle (MFB), the right perforant pathway (PP) and concurrent stimulation of the two fiber systems. Repetitive electrical stimulations of the MFB triggered significant positive BOLD responses in the nucleus accumbens (NAcc), septum, anterior cingulate cortex/medial prefrontal cortex (ACC/mPFC), ventral tegmental area/substantia nigra (VTA/SN), right entorhinal cortex (EC) and colliculus superior, which, in general, declined during later stimulation trains. At the same time, negative BOLD responses were observed in the striatum. Thus, the same stimulus caused region-specific hemodynamic responses. An identical electrical stimulation of the PP generated positive BOLD responses in the right dentate gyrus/hippocampus proper/subiculum (DG/HC), the right entorhinal cortex and the left entorhinal cortex, which remained almost stable during consecutive stimulation trains. Co-stimulation of the two fiber systems resulted in an additive activation pattern, i.e., the BOLD responses were stronger during the stimulation of the two pathways than during the stimulation of only one pathway. However, during the simultaneous stimulation of the two pathways, the development of the BOLD responses to consecutive trains changed. The BOLD responses in regions that were predominantly activated by MFB stimulation (i.e., NAcc, septum and ACC/mPFC) did not decline as fast as during pure MFB stimulation, thus an additive BOLD response was only observed during later trains. In contrast, in the brain regions that were predominantly activated by PP stimulation (i.e., right EC, DG/HC), co-stimulation of the MFB only resulted in an additive effect during early trains but not later trains. Consequently, the development of the BOLD responses during consecutive

  4. Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric water and in the absence of light: Identification of intermediates and reaction pathways.

    PubMed

    Santos, Patrícia S M; Domingues, M Rosário M; Duarte, Armando C

    2016-07-01

    A previous work showed that the night period is important for the occurrence of Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric waters, which originate new chromophoric compounds apparently more complex than the precursors, although the chemical transformations involved in the process are still unknown. In this work were identified by gas chromatography-mass spectrometry (GC-MS) and by electrospray mass spectrometry (ESI-MS) the organic intermediate compounds formed during the Fenton-like oxidation of three aromatic acids from biomass burning (benzoic, 4-hydroxybenzoic and 3,5-dihydroxybenzoic acids), the same compounds evaluated in the previous study, in water and in the absence of light, which in turns allows to disclose the chemical reaction pathways involved. The oxidation intermediate compounds found for benzoic acid were 2-hydroxybenzoic, 3-hydroxybenzoic, 4-hydroxybenzoic, 2,3-dihydroxybenzoic, 2,5-dihydroxybenzoic, 2,6-dihydroxybenzoic and 3,4-dihydroxybenzoic acids. The oxidation intermediates for 4-hydroxybenzoic acid were 3,4-hydroxybenzoic acid and hydroquinone, while for 3,5-dihydroxybenzoic acid were 2,4,6-trihydroxybenzoic and 3,4,5-trihydroxybenzoic acids, and tetrahydroxybenzene. The results suggested that the hydroxylation of the three small aromatic acids is the main step of Fenton-like oxidation in atmospheric waters during the night, and that the occurrence of decarboxylation is also an important step during the oxidation of the 4-dihydroxybenzoic and 3,5-dihydroxybenzoic acids. In addition, it is important to highlight that the compounds produced are also small aromatic compounds with potential adverse effects on the environment, besides becoming available for further chemical reactions in atmospheric waters.

  5. Visible-Light-Promoted Dual C-C Bond Formations of Alkynoates via a Domino Radical Addition/Cyclization Reaction: A Synthesis of Coumarins.

    PubMed

    Feng, Shangbiao; Xie, Xingang; Zhang, Weiwei; Liu, Lin; Zhong, Zhuliang; Xu, Dengyu; She, Xuegong

    2016-08-01

    A visible-light-promoted, mild, and direct difunctionalization of alkynoates has been accomplished. This procedure provides a new strategy toward synthesis of the coumarin core structure by photoredox-mediated oxidation to generate the α-oxo radical, which supervenes a domino radical addition/cyclization reaction in moderate to good yields with high regioselectivity at ambient temperature.

  6. LDA-mediated selective addition reaction of vinylidenecyclopropanes with aldehydes, ketones, and enones: facile synthesis of vinylcyclopropenes, allenols, and 1,3-enynes.

    PubMed

    Lu, Jian-Mei; Shi, Min

    2008-05-15

    Highly selective addition reaction of vinylidenecyclopropanes 1 was realized by treatment with LDA in THF and quenching with aldehydes, ketones, and enones. A number of vinylcyclopropenes, allenols, and 1,3-enynes were obtained selectively in moderate to good yields depending on the nature of different electrophiles.

  7. H-atom addition and abstraction reactions in mixed CO, H2CO and CH3OH ices - an extended view on complex organic molecule formation

    NASA Astrophysics Data System (ADS)

    Chuang, K.-J.; Fedoseev, G.; Ioppolo, S.; van Dishoeck, E. F.; Linnartz, H.

    2016-01-01

    Complex organic molecules (COMs) have been observed not only in the hot cores surrounding low- and high-mass protostars, but also in cold dark clouds. Therefore, it is interesting to understand how such species can be formed without the presence of embedded energy sources. We present new laboratory experiments on the low-temperature solid state formation of three complex molecules - methyl formate (HC(O)OCH3), glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - through recombination of free radicals formed via H-atom addition and abstraction reactions at different stages in the CO→H2CO→CH3OH hydrogenation network at 15 K. The experiments extend previous CO hydrogenation studies and aim at resembling the physical-chemical conditions typical of the CO freeze-out stage in dark molecular clouds, when H2CO and CH3OH form by recombination of accreting CO molecules and H-atoms on ice grains. We confirm that H2CO, once formed through CO hydrogenation, not only yields CH3OH through ongoing H-atom addition reactions, but is also subject to H-atom-induced abstraction reactions, yielding CO again. In a similar way, H2CO is also formed in abstraction reactions involving CH3OH. The dominant methanol H-atom abstraction product is expected to be CH2OH, while H-atom additions to H2CO should at least partially proceed through CH3O intermediate radicals. The occurrence of H-atom abstraction reactions in ice mantles leads to more reactive intermediates (HCO, CH3O and CH2OH) than previously thought, when assuming sequential H-atom addition reactions only. This enhances the probability to form COMs through radical-radical recombination without the need of UV photolysis or cosmic rays as external triggers.

  8. Involvement of mitogen-activated protein kinase and NF-κB signaling pathways in perfluorooctane sulfonic acid-induced inflammatory reaction in BV2 microglial cells.

    PubMed

    Zhu, Jingying; Qian, Wenyi; Wang, Yixin; Gao, Rong; Wang, Jun; Xiao, Hang

    2015-12-01

    Microglial activation is closely related to the pathogenesis of neurodegenerative diseases by producing proinflammatory cytokines. Perfluorooctane sulfonic acid (PFOS), known as an emerging persistent organic pollutant, is reported to disturb human immune homeostasis; however, whether it affects cytokine production or the immune response in the central nervous system remains unclear. The present study was aimed to explore whether PFOS contributed to inflammatory action and to investigate the corresponding mechanisms in BV2 microglia. PFOS-mediated morphologic changes, cytokine responses and signaling events were examined by light microscopy, real-time polymerase chain reaction, enzyme-linked immunosorbent assay and Western blot assays. Our results indicated that PFOS increased BV2 cells activation and simultaneously increased tumor necrosis factor alpha and interleukin-6 expression. In addition, the c-Jun N-terminal protein kinase inhibitor (SP600125), as well as ERK1/2 blocker (PD98059), transcriptionally at least, displayed anti-inflammatory properties on PFOS-elicited cytokine responses. Moreover, the inflammatory transcription factor NF-κB was specifically activated by PFOS as well. These results, taken together, suggested that PFOS exerts its functional effects on the response of microglial cell activation via, in part, the c-Jun N-terminal protein kinase, ERK and NF-κB signaling pathways with its subsequent influence on proinflammatory action.

  9. An Experiment To Demonstrate How a Catalyst Affects the Rate of a Reaction.

    ERIC Educational Resources Information Center

    Copper, Christine L.; Koubeck, Edward

    1999-01-01

    Describes a chemistry experiment that allows students to calculate rates of reaction, orders of reaction, and activation energies. The activity demonstrates that to increase a reaction's rate, a catalyst need only provide any additional pathway for the reaction, not necessarily a pathway having lower activation energy. (WRM)

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

    PubMed Central

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

    2014-01-01

    Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenyl­alanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully understand the function of the acyl-group binding pocket in substrate specificity. PMID:24699651

  11. Comments on the linear free-energy correlation between O/sub 3/ and OH addition reactions reported in Rate Constants for the Gas-Phase Reactions of O/sub 3/ with a Series of Carbonyls at 296 K

    SciTech Connect

    Gaffney, J.S.; Levine, S.Z.

    1982-01-01

    Recently, Atkinson et al. reported measurements on the reaction of ozone with a series of carbonyls. In that study a correlation between ozone addition and hydroxyl-radical addition reactions was employed to predict OH addition coefficients for acrolein and crotonaldehyde of approximately 2 x 10/sup -12/ and 5 x 10/sup -12/ cm/sup 3/ molecule/sup -1/ s/sup -1/, respectively. These estimates, as pointed out by the authors, are in disagreement (factor of 2 to 3 lower) with the rate coefficients previously predicted by ourselves for the same OH addition reactions using linear correlations with both ionization potentials and O(/sup 3/P) rate data. It was also suggested in that paper that this discrepancy was probably due to the likelihood that O(/sup 3/P) atoms react significantly with carbonyls via an abstraction mechanism, that is, O(/sup 3/P) rate data could not be appropriately correlated with OH addition reaction data. We believe that another, more probable, explanation exists for the above-mentioned discrepancy in rate constant estimates, and that this explanation involves the manner in which the correlation method is handled. Because this method of evaluating rate constants represents a potentially important predictive tool for chemical modelers, we feel it is necessary to reconcile the apparent disagreement in the OH-acrolein and OH-crotonaldehyde addition reaction coefficients estimated from O/sub 3/ correlations as compared to ionization potential and O(/sup 3/P) correlations. In doing so, we will also demonstrate the necessity of employing linear correlations in a consistent manner.

  12. Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766

    PubMed Central

    2013-01-01

    The accuracy of high-fidelity DNA polymerases such as DNA polymerase I (Klenow fragment) is governed by conformational changes early in the reaction pathway that serve as fidelity checkpoints, identifying inappropriate template–nucleotide pairings. The fingers-closing transition (detected by a fluorescence resonance energy transfer-based assay) is the unique outcome of binding a correct incoming nucleotide, both complementary to the templating base and with a deoxyribose (rather than ribose) sugar structure. Complexes with mispaired dNTPs or complementary rNTPs are arrested at an earlier stage, corresponding to a partially closed fingers conformation, in which weak binding of DNA and nucleotide promote dissociation and resampling of the substrate pool. A 2-aminopurine fluorescence probe on the DNA template provides further information about the steps preceding fingers closing. A characteristic 2-aminopurine signal is observed on binding a complementary nucleotide, regardless of whether the sugar is deoxyribose or ribose. However, mispaired dNTPs show entirely different behavior. Thus, a fidelity checkpoint ahead of fingers closing is responsible for distinguishing complementary from noncomplementary nucleotides and routing them toward different outcomes. The E710A mutator polymerase has a defect in the early fidelity checkpoint such that some complementary dNTPs are treated as if they were mispaired. In the Y766A mutant, the early checkpoint functions normally, but some correctly paired dNTPs do not efficiently undergo fingers closing. Thus, both mutator alleles cause a blurring of the distinction between correct and incorrect base pairs and result in a larger fraction of errors passing through the prechemistry fidelity checkpoints. PMID:23937394

  13. Fucose, mannose, and β-N-acetylglucosamine glycopolymers initiate the mouse sperm acrosome reaction through convergent signaling pathways.

    PubMed

    Wu, Linghui; Sampson, Nicole S

    2014-02-21

    The sperm acrosome reaction (AR), an essential exocytosis step in mammalian fertilization, is mediated by a species-specific interaction of sperm surface molecules with glycans on the egg. Previous studies indicate that a subset of terminal carbohydrates on the mouse egg zona pellucida (ZP) trigger the AR by cross-linking or aggregating receptors on the sperm membrane. However, the exact role of those carbohydrates in AR has not been identified and the mechanism underlying the AR still needs further investigation. To study this process, a series of glycopolymers was synthesized. The glycopolymers are composed of a multivalent scaffold (norbornene), a functional ligand (previously identified ZP terminal monosaccharides), and a linker connecting the ligand and the scaffold. The polymers were tested for their ability to initiate AR and through which signaling pathways AR induction occurred. Our data demonstrate that mannose, fucose, and β-N-acetylglucosamine 10-mers and 100-mers initiate AR in a dose-dependent manner, and the 100-mers are more potent on a per monomer basis than the 10-mers. Although nearly equipotent in inducing the AR at the optimal concentrations, their AR activation kinetics are not identical. Similar to mouse ZP3, all 100-mer-activated AR are sensitive to guanine-binding regulatory proteins (G-proteins), tyrosine kinase, protein kinase A, protein kinase C, and Ca(2+)-related antagonists. Thus, the chemotypes of synthetic glycopolymers imitate the physiologic AR-activation agents and provide evidence that occupation of one of at least three different receptor binding sites is sufficient to initiate the AR.

  14. The Wnt and Delta-Notch signalling pathways interact to direct pair-rule gene expression via caudal during segment addition in the spider Parasteatoda tepidariorum.

    PubMed

    Schönauer, Anna; Paese, Christian L B; Hilbrant, Maarten; Leite, Daniel J; Schwager, Evelyn E; Feitosa, Natália Martins; Eibner, Cornelius; Damen, Wim G M; McGregor, Alistair P

    2016-07-01

    In short-germ arthropods, posterior segments are added sequentially from a segment addition zone (SAZ) during embryogenesis. Studies in spiders such as Parasteatoda tepidariorum have provided insights into the gene regulatory network (GRN) underlying segment addition, and revealed that Wnt8 is required for dynamic Delta (Dl) expression associated with the formation of new segments. However, it remains unclear how these pathways interact during SAZ formation and segment addition. Here, we show that Delta-Notch signalling is required for Wnt8 expression in posterior SAZ cells, but represses the expression of this Wnt gene in anterior SAZ cells. We also found that these two signalling pathways are required for the expression of the spider orthologues of even-skipped (eve) and runt-1 (run-1), at least in part via caudal (cad). Moreover, it appears that dynamic expression of eve in this spider does not require a feedback loop with run-1, as is found in the pair-rule circuit of the beetle Tribolium Taken together, our results suggest that the development of posterior segments in Parasteatoda is directed by dynamic interactions between Wnt8 and Delta-Notch signalling that are read out by cad, which is necessary but probably not sufficient to regulate the expression of eve and run-1 Our study therefore provides new insights towards better understanding the evolution and developmental regulation of segmentation in other arthropods, including insects. PMID:27287802

  15. The Wnt and Delta-Notch signalling pathways interact to direct pair-rule gene expression via caudal during segment addition in the spider Parasteatoda tepidariorum.

    PubMed

    Schönauer, Anna; Paese, Christian L B; Hilbrant, Maarten; Leite, Daniel J; Schwager, Evelyn E; Feitosa, Natália Martins; Eibner, Cornelius; Damen, Wim G M; McGregor, Alistair P

    2016-07-01

    In short-germ arthropods, posterior segments are added sequentially from a segment addition zone (SAZ) during embryogenesis. Studies in spiders such as Parasteatoda tepidariorum have provided insights into the gene regulatory network (GRN) underlying segment addition, and revealed that Wnt8 is required for dynamic Delta (Dl) expression associated with the formation of new segments. However, it remains unclear how these pathways interact during SAZ formation and segment addition. Here, we show that Delta-Notch signalling is required for Wnt8 expression in posterior SAZ cells, but represses the expression of this Wnt gene in anterior SAZ cells. We also found that these two signalling pathways are required for the expression of the spider orthologues of even-skipped (eve) and runt-1 (run-1), at least in part via caudal (cad). Moreover, it appears that dynamic expression of eve in this spider does not require a feedback loop with run-1, as is found in the pair-rule circuit of the beetle Tribolium Taken together, our results suggest that the development of posterior segments in Parasteatoda is directed by dynamic interactions between Wnt8 and Delta-Notch signalling that are read out by cad, which is necessary but probably not sufficient to regulate the expression of eve and run-1 Our study therefore provides new insights towards better understanding the evolution and developmental regulation of segmentation in other arthropods, including insects.

  16. An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways.

    PubMed Central

    Zhou, G P; Deng, M H

    1984-01-01

    An extension has been made to the Chou's graphic rules in order to cover those enzyme-catalysed reaction systems in which there are two or more parallel reaction routes between any two enzyme species. PMID:6477507

  17. Asymmetric Catalytic Enantio- and Diastereoselective Boron Conjugate Addition Reactions of α-Functionalized α,β-Unsaturated Carbonyl Substrates.

    PubMed

    Xie, Jian-Bo; Lin, Siqi; Qiao, Shuo; Li, Guigen

    2016-08-01

    An efficient catalytic system has been established for the asymmetric boron conjugate addition of B2pin2 onto α-functionalized (involving C, N, O, and Cl) α,β-unsaturated carbonyls under mild, neutral conditions involving Cu[(S)-(R)-ppfa]Cl, AgNTf2, and alcohols. The dual additives of AgNTf2 and alcohols were found to play crucial roles for achieving high catalytic activity and enantio- and diastereoselectivity (up to 98% ee and 70:1 dr).

  18. Formation of quaternary stereogenic centers by copper-catalyzed asymmetric conjugate addition reactions of alkenylaluminums to trisubstituted enones.

    PubMed

    Müller, Daniel; Alexakis, Alexandre

    2013-11-01

    Alkenylaluminums undergo asymmetric copper-catalyzed conjugate addition (ACA) to β-substituted enones allowing the formation of stereogenic all-carbon quaternary centers. Phosphinamine-copper complexes proved to be particularly active and selective compared with phosphoramidite ligands. After extensive optimization, high enantioselectivities (up to 96% ee) were obtained for the addition of alkenylalanes to β-substituted enones. Two strategies for the generation of the requisite alkenylaluminums were explored allowing for the introduction of aryl- and alkyl-substituted alkenyl nucleophiles. Moreover, alkyl-substituted phosphinamine (SimplePhos) ligands were identified for the first time as highly efficient ligands for the Cu-catalyzed ACA.

  19. Experimental and theoretical studies of the products of addition-elimination reactions between benzil dihydrazone and three isomeric chlorobenzaldehydes.

    PubMed

    Liu, Yun-Na; Cheng, Shuang-Shuang; Wang, Chao; Xing, Dian-Xiang; Liu, Yun; Tan, Xue-Jie

    2015-07-01

    A series of mono- and di-Schiff bases formed between benzil dihydrazone {BDH; systematic name: (1Z)-[(2E)-2-hydrazinylidene-1,2-diphenylethylidene]hydrazine} and three isomeric chlorobenzaldehydes were designed and synthesized to be used as model compounds to help to explain the reaction mechanisms for the formation of Schiff bases. These compounds are 1-(2-chlorobenzylidene)-2-{2-[2-(2-chlorobenzylidene)hydrazin-1-ylidene]-1,2-diphenylethylidene}hydrazine (BDHOCB), and the 3-chloro (BDHMCB) and 4-chloro (BDHPCB) analogues, all having the formula C28H20Cl2N4. Surprisingly, only di-Schiff bases were obtained; our attempts to push the reaction in favour of the mono-Schiff bases all failed. Density functional theory (DFT) calculations were performed to explain the trend in the experimental results. In the case of the systems studied, the type of Schiff base produced exhibits a clear dependence on the HOMO-LUMO energy gaps (ΔE(HOMO-LUMO)), i.e. the product is mainly governed by its stability. The compounds were characterized by single-crystal X-ray diffractometry, elemental analysis, melting point, (1)H NMR and (13)C NMR spectroscopy. The structural features of the three new Schiff bases are similar. For instance, they have the same chemical formula, all the molecules have a symmetrical double helix structure, with each Ph-C=N-N=C-Ph arm exhibiting an anti conformation, and their supramolecular interactions include intermolecular π-π and weak C-H...π stacking interactions. The crystal systems are different, however, viz. triclinic (space group P1¯) for BDHPCB, monoclinic (space group P2(1)/n) for BDHOCB and orthorhombic (space group Pnna) for BDHMCB.

  20. Probing the Reaction Pathway of Dehydrogenation of the LiNH2 + LiH Mixture Using In Situ 1H NMR Spectroscopy

    SciTech Connect

    Hu, Jian Zhi; Kwak, Ja Hun; Yang, Zhenguo; osborn, william; Markmaitree, Tippawan; Shaw, Leonard D.

    2008-06-15

    Using variable temperature in situ 1H NMR spectroscopy on a mixture of LiNH2 + LiH that was mechanically activated using high energy ball milling, the dehydrogenation of the LiNH2 + LiH to Li2NH + H2 was investigated. The analysis indicates NH3 release at a temperature as low as 300C and rapid reaction between NH3 and LiH at ~ 1500C. The transition from NH3 release to H2 appearance accompanied by disappearance of NH3 confirms unambiguously the two-step elementary reaction pathway proposed by other workers.

  1. Synthesis of Bridged Heterocycles via Sequential 1,4- and 1,2-Addition Reactions to α,β-Unsaturated N-Acyliminium Ions: Mechanistic and Computational Studies.

    PubMed

    Yazici, Arife; Wille, Uta; Pyne, Stephen G

    2016-02-19

    Novel tricyclic bridged heterocyclic systems can be readily prepared from sequential 1,4- and 1,2-addition reactions of allyl and 3-substituted allylsilanes to indolizidine and quinolizidine α,β-unsaturated N-acyliminium ions. These reactions involve a novel N-assisted, transannular 1,5-hydride shift. Such a mechanism was supported by examining the reaction of a dideuterated indolizidine, α,β-unsaturated N-acyliminium ion precursor, which provided specifically dideuterated tricyclic bridged heterocyclic products, and from computational studies. In contrast, the corresponding pyrrolo[1,2-a]azepine system did not provide the corresponding tricyclic bridged heterocyclic product and gave only a bis-allyl adduct, while more substituted versions gave novel furo[3,2-d]pyrrolo[1,2-a]azepine products. Such heterocyclic systems would be expected to be useful scaffolds for the preparation of libraries of novel compounds for new drug discovery programs. PMID:26816207

  2. Synthesis of Bridged Heterocycles via Sequential 1,4- and 1,2-Addition Reactions to α,β-Unsaturated N-Acyliminium Ions: Mechanistic and Computational Studies.

    PubMed

    Yazici, Arife; Wille, Uta; Pyne, Stephen G

    2016-02-19

    Novel tricyclic bridged heterocyclic systems can be readily prepared from sequential 1,4- and 1,2-addition reactions of allyl and 3-substituted allylsilanes to indolizidine and quinolizidine α,β-unsaturated N-acyliminium ions. These reactions involve a novel N-assisted, transannular 1,5-hydride shift. Such a mechanism was supported by examining the reaction of a dideuterated indolizidine, α,β-unsaturated N-acyliminium ion precursor, which provided specifically dideuterated tricyclic bridged heterocyclic products, and from computational studies. In contrast, the corresponding pyrrolo[1,2-a]azepine system did not provide the corresponding tricyclic bridged heterocyclic product and gave only a bis-allyl adduct, while more substituted versions gave novel furo[3,2-d]pyrrolo[1,2-a]azepine products. Such heterocyclic systems would be expected to be useful scaffolds for the preparation of libraries of novel compounds for new drug discovery programs.

  3. Multifunctional Electrochemical Platforms Based on the Michael Addition/Schiff Base Reaction of Polydopamine Modified Reduced Graphene Oxide: Construction and Application.

    PubMed

    Huang, Na; Zhang, Si; Yang, Liuqing; Liu, Meiling; Li, Haitao; Zhang, Youyu; Yao, Shouzhuo

    2015-08-19

    In this paper, a new strategy for the construction of multifunctional electrochemical detection platforms based on the Michael addition/Schiff base reaction of polydopamine modified reduced graphene oxide was first proposed. Inspired by the mussel adhesion proteins, 3,4-dihydroxyphenylalanine (DA) was selected as a reducing agent to simultaneously reduce graphene oxide and self-polymerize to obtain the polydopamine-reduced graphene oxide (PDA-rGO). The PDA-rGO was then functionalized with thiols and amines by the reaction of thiol/amino groups with quinine groups of PDA-rGO via the Michael addition/Schiff base reaction. Several typical compounds containing thiol and/or amino groups such as 1-[(4-amino)phenylethynyl] ferrocene (Fc-NH2), cysteine (cys), and glucose oxidase (GOx) were selected as the model molecules to anchor on the surface of PDA-rGO using the strategy for construction of multifunctional electrochemical platforms. The experiments revealed that the composite grafted with ferrocene derivative shows excellent catalysis activity toward many electroactive molecules and could be used for individual or simultaneous detection of dopamine hydrochloride (DA) and uric acid (UA), or hydroquinone (HQ) and catechol (CC), while, after grafting of cysteine on PDA-rGO, simultaneous discrimination detection of Pb(2+) and Cd(2+) was realized on the composite modified electrode. In addition, direct electron transfer of GOx can be observed when GOx-PDA-rGO was immobilized on glassy carbon electrode (GCE). When glucose was added into the system, the modified electrode showed excellent electric current response toward glucose. These results inferred that the proposed multifunctional electrochemical platforms could be simply, conveniently, and effectively regulated through changing the anchored recognition or reaction groups. This study would provide a versatile method to design more detection or biosensing platforms through a chemical reaction strategy in the future. PMID

  4. Multifunctional Electrochemical Platforms Based on the Michael Addition/Schiff Base Reaction of Polydopamine Modified Reduced Graphene Oxide: Construction and Application.

    PubMed

    Huang, Na; Zhang, Si; Yang, Liuqing; Liu, Meiling; Li, Haitao; Zhang, Youyu; Yao, Shouzhuo

    2015-08-19

    In this paper, a new strategy for the construction of multifunctional electrochemical detection platforms based on the Michael addition/Schiff base reaction of polydopamine modified reduced graphene oxide was first proposed. Inspired by the mussel adhesion proteins, 3,4-dihydroxyphenylalanine (DA) was selected as a reducing agent to simultaneously reduce graphene oxide and self-polymerize to obtain the polydopamine-reduced graphene oxide (PDA-rGO). The PDA-rGO was then functionalized with thiols and amines by the reaction of thiol/amino groups with quinine groups of PDA-rGO via the Michael addition/Schiff base reaction. Several typical compounds containing thiol and/or amino groups such as 1-[(4-amino)phenylethynyl] ferrocene (Fc-NH2), cysteine (cys), and glucose oxidase (GOx) were selected as the model molecules to anchor on the surface of PDA-rGO using the strategy for construction of multifunctional electrochemical platforms. The experiments revealed that the composite grafted with ferrocene derivative shows excellent catalysis activity toward many electroactive molecules and could be used for individual or simultaneous detection of dopamine hydrochloride (DA) and uric acid (UA), or hydroquinone (HQ) and catechol (CC), while, after grafting of cysteine on PDA-rGO, simultaneous discrimination detection of Pb(2+) and Cd(2+) was realized on the composite modified electrode. In addition, direct electron transfer of GOx can be observed when GOx-PDA-rGO was immobilized on glassy carbon electrode (GCE). When glucose was added into the system, the modified electrode showed excellent electric current response toward glucose. These results inferred that the proposed multifunctional electrochemical platforms could be simply, conveniently, and effectively regulated through changing the anchored recognition or reaction groups. This study would provide a versatile method to design more detection or biosensing platforms through a chemical reaction strategy in the future.

  5. Unconventional Bifunctional Lewis-Brønsted Acid Activation Mode in Bicyclic Guanidine-Catalyzed Conjugate Addition Reactions.

    PubMed

    Cho, Bokun; Wong, Ming Wah

    2015-08-18

    DFT calculations have demonstrated that the unconventional bifunctional Brønsted-Lewis acid activation mode is generally applicable to a range of nucleophilic conjugate additions catalyzed by bicyclic guanidine catalysts. It competes readily with the conventional bifunctional Brønsted acid mode of activation. The optimal pro-nucleophiles for this unconventional bifunctional activation are acidic substrates with low pKa, while the best electrophiles are flexible 1,4-diamide and 1,4-diester conjugated systems.

  6. Thermochemical treatment of sewage sludge ash with sodium salt additives for phosphorus fertilizer production--Analysis of underlying chemical reactions.

    PubMed

    Stemann, Jan; Peplinski, Burkhard; Adam, Christian

    2015-11-01

    Stocks of high grade phosphate rock are becoming scarce, and there is growing concern about potentially harmful impurities in conventional phosphorus fertilizers. Sewage sludge ash is a promising secondary phosphorus source. However, to remove heavy metals and convert the phosphorus contained in sewage sludge ash into mineral phases available to plants, an after-treatment is required. Laboratory-scale calcination experiments of sewage sludge ash blended with sodium salts using dried sewage sludge as a reducing agent were carried out at 1000°C. Thus, the Ca3(PO4)2 or whitlockite component of raw sewage sludge ash, which is not readily plant available, was converted to CaNaPO4 (buchwaldite). Consequently, nearly complete phosphorus solubility in ammonium citrate (a well-established indicator for plant availability) was achieved. Moreover, it was shown that Na2CO3 may be replaced by moderately priced Na2SO4. However, molar ratios of Na/P>2 were required to achieve >80% phosphorus solubility. Such over-stoichiometric Na consumption is largely caused by side reactions with the SiO2 component of the sewage sludge ash - an explanation for which clear evidence is provided for the first time. PMID:26219587

  7. Thermochemical treatment of sewage sludge ash with sodium salt additives for phosphorus fertilizer production--Analysis of underlying chemical reactions.

    PubMed

    Stemann, Jan; Peplinski, Burkhard; Adam, Christian

    2015-11-01

    Stocks of high grade phosphate rock are becoming scarce, and there is growing concern about potentially harmful impurities in conventional phosphorus fertilizers. Sewage sludge ash is a promising secondary phosphorus source. However, to remove heavy metals and convert the phosphorus contained in sewage sludge ash into mineral phases available to plants, an after-treatment is required. Laboratory-scale calcination experiments of sewage sludge ash blended with sodium salts using dried sewage sludge as a reducing agent were carried out at 1000°C. Thus, the Ca3(PO4)2 or whitlockite component of raw sewage sludge ash, which is not readily plant available, was converted to CaNaPO4 (buchwaldite). Consequently, nearly complete phosphorus solubility in ammonium citrate (a well-established indicator for plant availability) was achieved. Moreover, it was shown that Na2CO3 may be replaced by moderately priced Na2SO4. However, molar ratios of Na/P>2 were required to achieve >80% phosphorus solubility. Such over-stoichiometric Na consumption is largely caused by side reactions with the SiO2 component of the sewage sludge ash - an explanation for which clear evidence is provided for the first time.

  8. Tandem Michael addition-ring transformation reactions of 3-hydroxyoxindoles/3-aminooxindoles with olefinic azlactones: direct access to structurally diverse spirocyclic oxindoles.

    PubMed

    Cui, Bao-Dong; Zuo, Jian; Zhao, Jian-Qiang; Zhou, Ming-Qiang; Wu, Zhi-Jun; Zhang, Xiao-Mei; Yuan, Wei-Cheng

    2014-06-01

    An efficient method for the direct construction of two classes of spirocyclic oxindoles by the reactions of 3-hydroxyoxindoles/3-aminooxindoles and (Z)-olefinic azlactones through a tandem Michael addition-ring transformation process has been developed. With DBU as the catalyst, a range of spiro-butyrolactoneoxindoles and spiro-butyrolactamoxindoles, containing an oxygen or a nitrogen heteroatom, respectively, in the spiro stereocenter, were smoothly obtained with good to excellent diastereoselectivities in high yields.

  9. Reaction Pathways and Excited States in H2O2+OH → HO2+H2O : A New ab initio Investigation

    SciTech Connect

    Ginovska, Bojana; Camaioni, Donald M.; Dupuis, Michel

    2007-08-28

    The mechanism of the hydrogen abstraction reaction H2O2+OH→ HO2+H2O in gas phase was studied, using DFT (MPW1K) level of theory. We located 2 pathways for the reaction, both going through the same intermediate complex OH-H2O2, but via two distinct transition state structures that differ by the orientation of the hydroxyl hydrogen relative to the incipient hydroperoxy hydrogen. In one case, these hydrogens are on same side of the plane made by the 3 oxygen atoms and in the other these hydrogens are on opposite sides of the plane. The first two excited states were calculated for selected points of both pathways using time-dependent DFT, multiconfigurational quasi-degenerate-perturbation theory (MCQDPT2/ CASSCF) and equation of motion coupled cluster singles, doubles model (EOM-CCSD) EOMCCSD energies and completely renormalized EOM-CCSD(T)(IA) correction. An avoided crossing between the two excited states was found on both reaction pathways, on the product side of the barrier to H-transfer on the ground state surface, near the transition states. Further more, we report on the calculation of the rate of the reaction in the gas phase for temperatures in the range of 250-500 K, and suggest that the strong temperature dependence of the rate at high temperatures is due to reaction on the low-lying excited state surface over a barrier that is much larger than on the ground state surface. This work was supported in part by the Office of Basic Energy Sciences of the Department of Energy (DOE), Chemical Sciences program (BG and MD) and in part by the U.S. Department of Energy’s Office of Biological and Environmental Research, Environmental Management Science Program (BG and DMC). The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute.

  10. Evidence for the formation of an enamine species during aldol and Michael-type addition reactions promiscuously catalyzed by 4-oxalocrotonate tautomerase.

    PubMed

    Poddar, Harshwardhan; Rahimi, Mehran; Geertsema, Edzard M; Thunnissen, Andy-Mark W H; Poelarends, Gerrit J

    2015-03-23

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which has a catalytic N-terminal proline residue (Pro1), can promiscuously catalyze various carbon-carbon bond-forming reactions, including aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde, and Michael-type addition of acetaldehyde to a wide variety of nitroalkenes to yield valuable γ-nitroaldehydes. To gain insight into how 4-OT catalyzes these unnatural reactions, we carried out exchange studies in D2 O, and X-ray crystallography studies. The former established that H-D exchange within acetaldehyde is catalyzed by 4-OT and that the Pro1 residue is crucial for this activity. The latter showed that Pro1 of 4-OT had reacted with acetaldehyde to give an enamine species. These results provide evidence of the mechanism of the 4-OT-catalyzed aldol and Michael-type addition reactions in which acetaldehyde is activated for nucleophilic addition by Pro1-dependent formation of an enamine intermediate.

  11. From enantiopure hydroxyaldehydes to complex heterocyclic scaffolds: development of domino Petasis/Diels-Alder and cross-metathesis/Michael addition reactions.

    PubMed

    Cannillo, Alexandre; Norsikian, Stéphanie; Tran Huu Dau, Marie-Elise; Retailleau, Pascal; Iorga, Bogdan I; Beau, Jean-Marie

    2014-09-15

    One-step assembly of hexahydroisoindole scaffolds by a sequence that combines the Petasis (borono-Mannich) and Diels-Alder reactions is described. The unique selectivity observed experimentally was confirmed by quantum calculations. The current method is applicable to a broad range of substrates, including free sugars, and holds significant potential to efficiently and stereoselectively build new heterocyclic structures. This easy and fast entry to functionalized polycyclic compounds can be pursued by further transformations, for example, additional ring closure by a cross-metathesis/Michael addition domino sequence.

  12. Evaluation of gold nanoparticles as the additive in real-time polymerase chain reaction with SYBR Green I dye

    NASA Astrophysics Data System (ADS)

    Yang, Wenchao; Mi, Lijuan; Cao, Xueyan; Zhang, Xiaodong; Fan, Chunhai; Hu, Jun

    2008-06-01

    Gold nanoparticles (AuNPs) have been proven to be able to improve the specificity or increase the efficiency of a polymerase chain reaction (PCR) when a suitable amount of AuNPs was used. However, there is still a lack of systematic evaluation of AuNPs in real-time PCR. In this study, DNA degradation and the fluorescence quenching effect of AuNPs were first tested in real-time PCR. Then two different kinds of Taq DNA polymerase, native and recombinant Taq polymerase, were employed to evaluate the AuNPs' effect on the threshold cycle (CT) values, standard curves and melting curves in real-time PCR. Different ratios of the amount of native Taq DNA polymerase to the amount of AuNPs were also tested. It was found that AuNPs could be applied in real-time PCR with correlation coefficient R2>0.989. The combination of 2.09 nM AuNPs with 3.75 U of native Taq DNA polymerase could make the amplification curves shift to the left and enhance the efficiency of the real-time PCR (0.628 39 without AuNPs compared with 0.717 89 with 2.09 nM AuNPs), thus enabling faster detection in comparison with those of control samples. However, no improvement ability of AuNPs was found in real-time PCR based on recombinant rTaq DNA polymerase. Besides, the results suggest that a complex interaction exists between AuNPs and native Taq DNA polymerase.

  13. Effects of N{sub 2}O gas addition on the properties of ZnO films grown by catalytic reaction-assisted chemical vapor deposition

    SciTech Connect

    Yasui, Kanji Morioka, Makoto; Kanauchi, Shingo; Ohashi, Yuki; Kato, Takahiro; Tamayama, Yasuhiro

    2015-11-15

    The influence of N{sub 2}O gas addition on the properties of zinc oxide (ZnO) films grown on a-plane (11–20) sapphire (a-Al{sub 2}O{sub 3}) substrates was investigated, using a chemical vapor deposition method based on the reaction between dimethylzinc and high-temperature H{sub 2}O produced by a catalytic H{sub 2}-O{sub 2} reaction on platinum (Pt) nanoparticles. The addition of N{sub 2}O was found to increase the size of the crystalline facets and to improve the crystal orientation along the c-axis. The electron mobility at 290 K was also increased to 234 cm{sup 2}/Vs following the addition of N{sub 2}O gas at a pressure of 3.2 × 10{sup −3 }Pa. In addition, the minimum full width at half maximum of the most intense photoluminescence peak derived from neutral donor bound excitons at 10 K decreased to 0.6 meV by the addition of N{sub 2}O gas at a pressure of 3.1 × 10{sup −2 }Pa.

  14. Quantum-chemical ab initio investigation of the two-step charge transfer process of hydrogen reaction: approach of reaction pathways via hydrogen intermediate on Cu(100)

    NASA Astrophysics Data System (ADS)

    Kuznetsov, An. M.; Lorenz, W.

    1994-08-01

    Local reaction events in the course of the electrochemical two-step hydrogen evolution reaction have been investigated by means of quantum-chemical all-electron ab initio calculations on interfacial supermolecular cluster models including a hydrated hydrogen intermediate on Cu(100). Expanding on preceding study to larger hydration clusters, an approach to relevant reaction path characteristics has been pursued for two processes: (i) the transfer of hydrated hydronium ion into a chemisorbed hydrogen intermediate: (ii) the reaction of hydronium ion with the intermediate to molecular hydrogen. Computations were carried out on RHF level, using contracted (12,8,4)/[8,6,2,] and/or 6-31G * or G ** pol-O bases for the metal and adsorbate part, respectively. Destruction of the hydronium configuration in process (i) has been confirmed. Electronic partial charge transfer dut to chemical bond conversions in both steps (i) and (ii) has been displayed along relevant cuts of adiabatic potential surfaces, proving significantly different amounts of charge transfer in both steps, λ 1 > 1, λ 2≡(2-λ 1) < 1. In advance of consideration of macroscopic double layer effects, first insight has been gained into coupled nuclear motions and into the origin of reaction barriers

  15. Addition-fragmentation reaction of thionoesters compounds in free-radical polymerisation (methyl, cyanomethyl and styryl): a theoretical interpretation

    NASA Astrophysics Data System (ADS)

    Hannachi, Douniazed; Ouddai, Nadia; Arotçaréna, Michel; Chermette, Henry

    2015-07-01

    A joint experimental and theoretical study has been carried out on reversible addition-fragmentation chain transfer polymerisation (RAFT). We have performed density functional theory calculations at the (Perdew-Burke-Ernzerhof) PBE/triple zeta plus polarisation level to analyse the RAFT mechanisms corresponding to these compounds. Global and local reactivity indices have been calculated to investigate the effect of the addition of methyl, cyanomethyl and styryl radicals on the double bond C=S of thionoester compounds producing an adduct radical. This mechanism is shown to be difficult when the cyanomethyl is used contrarily to the methyl and styryl radicals, in agreement with experimental results. The activation barrier of fragmentation of adduct radicals does not correlate well with the length of fragmented bond (O-Cα). The bond topological analysis of radical adduct predicts that the distance between the oxygen and a critical point (O-CP) in the fragment bond is a good parameter to estimate the activation energy of the fragmentation mechanism. It is shown that the nature of the free radicals is more selective than that of the thionoester compounds. With an overall large agreement with experiments, these theoretical results afford an explanation of the efficiency for the RAFT mechanism.

  16. Dual electron transfer pathways from the excited C60 radical anion: enhanced reactivities due to the photoexcitation of reaction intermediates.

    PubMed

    Fujitsuka, Mamoru; Ohsaka, Tatsuya; Majima, Tetsuro

    2015-12-14

    In the present study, electron transfer (ET) processes from excited radical anions have been investigated using dyad molecules including C60. The deactivation process of excited C60˙(-), including the internal conversion from the D1 to the D0 state and the cooling process of the vibrationally hot ground state (D), was observed spectroscopically for the first time. These processes could be unambiguously distinguished by the observation of the stimulated emission from the D1 state. The intramolecular ET processes from the excited C60˙(-) were confirmed by the transient absorption spectra. Clearly, both D1 and D states acted as precursors for the ET, i.e., dual ET pathways were confirmed. The driving force dependence of the ET rates was well characterized by the Marcus theory, which revealed that the forward ET processes are located at the top region of the Marcus parabola. In addition, the ET from the excited imide radical anion to C60 and that from the ground state C60˙(-) to imide were examined. The ET rate from the excited imide radical anion and that from ground state C60˙(-) did not follow the Marcus parabola estimated for the ET from the excited C60˙(-). The observed difference can be attributed to the difference in the energy required to form the reduced spacer (Δ) in the superexchange mechanism. Because the Δ value tends to become smaller for ET processes from excited radical ions, fast and efficient ET processes are expected from these states as demonstrated in the present study.

  17. Interfacial Reactions of Zn-Al Alloys with Na Addition on Cu Substrate During Spreading Test and After Aging Treatments

    NASA Astrophysics Data System (ADS)

    Gancarz, Tomasz; Pstruś, Janusz; Berent, Katarzyna

    2016-08-01

    Spreading tests for Cu substrate with Zn-Al eutectic-based alloys with 0.2, 0.5, and 1.0 wt.% of Na were studied using the sessile drop method in the presence of QJ201 flux. Spreading tests were performed for 1, 3, 8, 15, 30, and 60 min of contact, at the temperatures of 475, 500, 525, and 550 °C. After cleaning the flux residue from solidified samples, the spreading area of Zn-Al + Na on Cu was determined in accordance with ISO 9455-10:2013-03. Selected, solidified solder-substrate couples were cross-sectioned and subjected to scanning electron microscopy of the interfacial microstructure. The experiment was designed to demonstrate the effect of Na addition on the kinetics of formation and growth of CuZn, Cu5Zn8, and CuZn4 phases, which were identified using x-ray diffraction and energy-dispersive spectroscopy analysis. The addition of Na to eutectic Zn-Al caused the spreading area to decrease and the thickness of intermetallic compound layers at the interface to reduce. Samples after the spreading test at 500 °C for 1 min were subjected to aging for 1, 10, and 30 days at 120,170, and 250 °C. The greater thicknesses of IMC layers were obtained for a temperature of 250 °C. With increasing Na content in Zn-Al + Na alloys, the thickness reduced, which correlates to the highest value of activation energy for Zn-Al with 1% Na.

  18. Interfacial Reactions of Zn-Al Alloys with Na Addition on Cu Substrate During Spreading Test and After Aging Treatments

    NASA Astrophysics Data System (ADS)

    Gancarz, Tomasz; Pstruś, Janusz; Berent, Katarzyna

    2016-04-01

    Spreading tests for Cu substrate with Zn-Al eutectic-based alloys with 0.2, 0.5, and 1.0 wt.% of Na were studied using the sessile drop method in the presence of QJ201 flux. Spreading tests were performed for 1, 3, 8, 15, 30, and 60 min of contact, at the temperatures of 475, 500, 525, and 550 °C. After cleaning the flux residue from solidified samples, the spreading area of Zn-Al + Na on Cu was determined in accordance with ISO 9455-10:2013-03. Selected, solidified solder-substrate couples were cross-sectioned and subjected to scanning electron microscopy of the interfacial microstructure. The experiment was designed to demonstrate the effect of Na addition on the kinetics of formation and growth of CuZn, Cu5Zn8, and CuZn4 phases, which were identified using x-ray diffraction and energy-dispersive spectroscopy analysis. The addition of Na to eutectic Zn-Al caused the spreading area to decrease and the thickness of intermetallic compound layers at the interface to reduce. Samples after the spreading test at 500 °C for 1 min were subjected to aging for 1, 10, and 30 days at 120,170, and 250 °C. The greater thicknesses of IMC layers were obtained for a temperature of 250 °C. With increasing Na content in Zn-Al + Na alloys, the thickness reduced, which correlates to the highest value of activation energy for Zn-Al with 1% Na.

  19. Effect of Compound Chuanxiong Capsule on Inflammatory Reaction and PI3K/Akt/NF-κB Signaling Pathway in Atherosclerosis.

    PubMed

    Kang, Qunfu; Liu, Weihong; Liu, Hongxu; Zhou, Mingxue

    2015-01-01

    Compound Chuanxiong Capsule (CCC), a Chinese herbal compound, can exhibit antiatherosclerotic effect; however, its mechanism is still unclear. This study is designed to study the mechanism of CCC on atherosclerosis in the ApoE-knockout (ApoE(-/-)) mice fed with a high-fat diet. After 6 weeks of high-fat feeding, 40 ApoE(-/-) mice were randomized (n = 10) and treated with lipitor, high-dose or low-dose CCC, or distilled water (ApoE(-/-) group) for 7 weeks. The blood lipids in serum and the plaque areas of the mice were measured and the mRNA expressions of phosphatidylinositol-3-kinases (PI3K), Akt, nuclear factor-kappa B (NF-κB), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) of the aortae were determined. The data showed that CCC can significantly decrease the levels of blood lipids, atherosclerosis index, and plaque areas and increase collagen proportion in plaques as compared with the untreated mice (p < 0.05, p < 0.01). In addition, CCC can significantly reduce the mRNA expressions of PI3K, Akt, NF-κB, IL-6, and TNF-α in the mice fed with a high-fat diet (p < 0.001). Thus, we concluded that CCC can inhibit inflammatory reaction in the ApoE(-/-) mice fed with a high-fat diet. This mechanism may be attributed to regulating PI3K/Akt/NF-κB signaling pathway. PMID:26539229

  20. Effect of Compound Chuanxiong Capsule on Inflammatory Reaction and PI3K/Akt/NF-κB Signaling Pathway in Atherosclerosis

    PubMed Central

    Kang, Qunfu; Liu, Weihong; Liu, Hongxu; Zhou, Mingxue

    2015-01-01

    Compound Chuanxiong Capsule (CCC), a Chinese herbal compound, can exhibit antiatherosclerotic effect; however, its mechanism is still unclear. This study is designed to study the mechanism of CCC on atherosclerosis in the ApoE-knockout (ApoE−/−) mice fed with a high-fat diet. After 6 weeks of high-fat feeding, 40 ApoE−/− mice were randomized (n = 10) and treated with lipitor, high-dose or low-dose CCC, or distilled water (ApoE−/− group) for 7 weeks. The blood lipids in serum and the plaque areas of the mice were measured and the mRNA expressions of phosphatidylinositol-3-kinases (PI3K), Akt, nuclear factor-kappa B (NF-κB), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) of the aortae were determined. The data showed that CCC can significantly decrease the levels of blood lipids, atherosclerosis index, and plaque areas and increase collagen proportion in plaques as compared with the untreated mice (p < 0.05, p < 0.01). In addition, CCC can significantly reduce the mRNA expressions of PI3K, Akt, NF-κB, IL-6, and TNF-α in the mice fed with a high-fat diet (p < 0.001). Thus, we concluded that CCC can inhibit inflammatory reaction in the ApoE−/− mice fed with a high-fat diet. This mechanism may be attributed to regulating PI3K/Akt/NF-κB signaling pathway. PMID:26539229

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

    SciTech Connect

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

    2015-02-21

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

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

    PubMed

    Kaur, Ramanpreet; Vikas

    2015-02-21

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

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

    PubMed

    Kaur, Ramanpreet; Vikas

    2015-02-21

    2-Aminopropionitrile (APN), a probable candidate as a chiral astrophysical molecule, is a precursor to amino-acid alanine. Stereochemical pathways in 2-APN are explored using Global Reaction Route Mapping (GRRM) method employing high-level quantum-mechanical computations. Besides predicting the conventional mechanism for chiral inversion that proceeds through an achiral intermediate, a counterintuitive flipping mechanism is revealed for 2-APN through chiral intermediates explored using the GRRM. The feasibility of the proposed stereochemical pathways, in terms of the Gibbs free-energy change, is analyzed at the temperature conditions akin to the interstellar medium. Notably, the stereoinversion in 2-APN is observed to be more feasible than the dissociation of 2-APN and intermediates involved along the stereochemical pathways, and the flipping barrier is observed to be as low as 3.68 kJ/mol along one of the pathways. The pathways proposed for the inversion of chirality in 2-APN may provide significant insight into the extraterrestrial origin of life. PMID:25702015

  4. Reaction pathways of dimethyl phthalate degradation in TiO2-UV-O2 and TiO2-UV-Fe(VI) systems.

    PubMed

    Yuan, Bao-ling; Li, Xiang-zhong; Graham, Nigel

    2008-05-01

    The photocatalytic degradation of dimethyl phthalate (DMP) in aqueous TiO2 suspension under UV illumination has been investigated using oxygen (O2) and ferrate (Fe(VI)) as electron acceptors. The experiments demonstrated that Fe(VI) was a more effective electron acceptor than O2 for scavenging the conduction band electrons from the surface of the catalyst. Some major intermediate products from DMP degradation were identified by HPLC and GC/MS analyses. The analytical results identified dimethyl 3-hydroxyphthalate and dimethyl 2-hydroxyphthalate as the two main intermediate products from the DMP degradation in the TiO2-UV-O2 system, while in contrast phthalic acid was found to be the main intermediate product in the TiO2-UV-Fe(VI) system. These findings indicate that DMP degradation in the TiO2-UV-O2 and TiO2-UV-Fe(VI) systems followed different reaction pathways. An electron spin resonance analysis confirmed that hydroxyl radicals existed in the TiO2-UV-O2 reaction system and an unknown radical species (most likely an iron-oxo species) is suspected to exist in the TiO2-UV-Fe(VI) reaction system. Two pathway schemes of DMP degradation in the TiO2-UV-O2 and TiO2-UV-Fe(VI) reaction systems are proposed. It is believed that the radicals formed in the TiO2-UV-O2 reaction system preferably attack the aromatic ring of the DMP, while in contrast the radicals formed in the TiO2-UV-Fe(VI) reaction systems attack the alkyl chain of DMP.

  5. Novel glycol chitosan-based polymeric gene carrier synthesized by a Michael addition reaction with low molecular weight polyethylenimine.

    PubMed

    Lee, Young Hwa; Park, Hae In; Choi, Joon Sig

    2016-02-10

    A glycol chitosan-based polymer that spontaneously assembles with plasmid DNA into nanorods was evaluated as a non-viral vector for gene delivery. Glycol chitosan-methyl acrylate-polyethylenimine (GMP) was synthesized by grafting polyethylenimine onto glycol chitosan via amidation after Michael addition using methyl acrylate. Gel retardation and PicoGreen assay experiments showed complete complex formation with plasmid DNA. GMP/pDNA complexes were characterized using biophysical techniques and were found to be positively charged rod-shape structures with widths in the nanometer scale and lengths in the micrometer scale. Transfection efficiency and cytotoxicity of GMP polymer was evaluated in human epithelial ovary carcinoma (HeLa) cells, human embryonic kidney 293 (HEK293) cells, and human hepatocellular liver carcinoma (HepG2) cells, in comparison to high molecular weight polyethylenimine, a commonly used transfection reagent. Intracellular polymer uptake was compared and confirmed by confocal microscopy. The results demonstrate that GMP, a hybrid polymer of glycol chitosan grafted with branched polyethylenimine, may serve as a promising vehicle for efficient gene delivery.

  6. Reaction of homopiperazine with endogenous formaldehyde: a carbon hydrogen addition metabolite/product identified in rat urine and blood.

    PubMed

    Martin, Scott; Lenz, Eva M; Temesi, Dave; Wild, Martin; Clench, Malcolm R

    2012-08-01

    Drug reactivity and bioactivation are of major concern to the development of potential drug candidates in the pharmaceutical industry (Chem Res Toxicol 17:3-16, 2004; Chem Res Toxicol 19:889-893, 2006). Identifying potentially problematic compounds as soon as possible in the discovery process is of great importance, so often early in vitro screening is used to speed up attrition. Identification of reactive moieties is relatively straightforward with appropriate in vitro trapping experiments; however, on occasion unexpected reactive intermediates can be found later during more detailed in vivo studies. Here, we present one such example involving a series of compounds from an early drug discovery campaign. These compounds were found to react with endogenous formaldehyde from a rat in vivo study, resulting in the formation of novel +13-Da bridged homopiperazine products (equivalent to the addition of one carbon and one hydrogen atom), which were detected in urine and blood. The identification of these +13-Da products and their origin and mechanism of formation are described in detail through analyses of a representative homopiperazine compound [N-(3-(3-fluorophenyl)-1,2,4-thiadiazol-5-yl)-4-(4-isopropyl-1,4-diaze-pane-2-carbonyl)piperazine-1-carboxamide (AZX)] by liquid chromatography-UV-mass spectrometry, (1)H NMR, and chemical tests. PMID:22550270

  7. Use of ion-molecule reactions and methanol addition to improve arsenic determination in high chlorine food samples by DRC-ICP-MS.

    PubMed

    Guo, Wei; Hu, Shenghong; Li, Xiaofang; Zhao, Jian; Jin, Shesheng; Liu, Wenjuan; Zhang, Hongfei

    2011-05-15

    Direct determination of trace arsenic in high chlorine food samples by ICP-MS is complicated by the presence of ArCl(+) interferences, and the high first ionization energy of As (9.81 eV) also results in low analytical sensitivity in ICP-MS. In this work, two strategies based on ion-molecule reactions were successfully used to eliminate ArCl spectral interference in a dynamic reaction cell (DRC). The interference ion ((40)Ar(35)Cl(+)) was directly removed by the reaction with methane gas, and the background signal was reduced by up to 100-fold at m/z 75. Alternatively, by using molecule oxygen as the reaction gas, (75)As(+) was effectively converted to (75)As(16)O(+) that could be detected at m/z 91 where the background is low. The poor signal intensity of As or AsO was improved 3-4 times by addition of 4% methanol in the analyzed solutions. The limit of quantitation (LOQ) for (75)As (CH(4)-DRC method) and (75)As(16)O (O(2)-DRC method) was 0.8 and 0.3 ng g(-1) and the analytical results of seaweed and yellow croaker standard reference materials were in good agreement with the certified values. As the routine arsenic monitoring method in our laboratory, it was applied to the accuracy determination of 119 high chlorine food samples from eight different markets of Beijing.

  8. Expanding Mg-Zn hybrid chemistry: inorganic salt effects in addition reactions of organozinc reagents to trifluoroacetophenone and the implications for a synergistic lithium-magnesium-zinc activation.

    PubMed

    Armstrong, David R; Clegg, William; García-Álvarez, Pablo; Kennedy, Alan R; McCall, Matthew D; Russo, Luca; Hevia, Eva

    2011-07-18

    Numerous organic transformations rely on organozinc compounds made through salt-metathesis (exchange) reactions from organolithium or Grignard reagents with a suitable zinc precursor. By combining X-ray crystallography, NMR spectroscopy and DFT calculations, this study sheds new light on the constitution of the organometallic species involved in this important synthetic tool. Investigations into the metathesis reactions of equimolar amounts of Grignard reagents (RMgX) and ZnCl(2) in THF led to the isolation of novel magnesium-zinc hybrids, [{(thf)(2)Mg(μ-Cl)(3)ZnR}(2)] (R=Et, tBu, nBu or o-OMe-C(6)H(4)), which exhibit an unprecedented structural motif in mixed magnesium-zinc chemistry. Furthermore, theoretical modelling of the reaction of EtMgCl with ZnCl(2) reveals that formation of the mixed-metal compound is thermodynamically preferred to that of the expected homometallic products, RZnCl and MgCl(2). This study also assesses the alkylating ability of hybrid 3 towards the sensitive ketone trifluoroacetophenone, revealing a dramatic increase in the chemoselectivity of the reaction when LiCl is introduced as an additive. This observation, combined with recent related breakthroughs in synthesis, points towards the existence of a trilateral Li/Mg/Zn synergistic effect. PMID:21656589

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

    PubMed

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

    2015-08-28

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

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

    DOE PAGES

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

    2015-07-16

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

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

    SciTech Connect

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

    2015-07-16

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

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

    PubMed

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

    2015-08-28

    The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions. PMID:26204935

  13. Bis(trifluoromethyl)methylene Addition to Vinyl-Terminated SAMs: A Gas-Phase C–C Bond-Forming Reaction on a Surface

    PubMed Central

    2014-01-01

    Vinyl-terminated self-assembled monolayers (SAMs) on silicon oxide substrates were chemically modified by the addition of a bis(trifluoromethyl)methylene group in a rare gas-phase C–C bond-forming reaction to directly generate films carrying terminal CF3 groups. The vinyl-terminated films were treated with hexafluoroacetone azine (HFAA) for modification. The films were characterized with ellipsometry, contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). In this study, we find that for optimized conditions clean reactions occur on a surface between SAMs with terminal olefins and HFAA, and the product is consistent with bis(trifluoromethyl)cyclopropanation formation after nitrogen extrusion. PMID:24806554

  14. Pathways for the OH + Cl2 → HOCl + Cl and HOCl + Cl → HCl + ClO Reactions.

    PubMed

    Wang, Hongyan; Qiu, Yudong; Czakó, Gábor; Schaefer, Henry F

    2015-07-16

    High level coupled-cluster theory, with spin-orbit coupling evaluated via the Breit-Pauli operator in the interacting-states approach, is used to investigate the OH radical reaction with Cl2 and the subsequent reaction HOCl + Cl. The entrance complex, transition state, and exit complex for both reactions have been determined using the CCSD(T) method with correlation consistent basis sets up to cc-pV6Z. Also reported are CCSDT computations. The OH + Cl2 reaction is predicted to be endothermic by 2.2 kcal/mol, compared to the best experiments, 2.0 kcal/mol. The above theoretical results include zero-point vibrational energy corrections and spin-orbit contributions. The activation energy (Ea) of the OH + Cl2 reaction predicted here, 2.3 kcal/mol, could be as much as 1 kcal/mol too high, but it falls among the four experimental Ea values, which span the range 1.1-2.5 kcal/mol. The exothermicity of the second reaction HOCl + Cl → HCl + ClO is 8.4 kcal/mol, compared to experiment 8.7 kcal/mol. The activation energy for latter reaction is unknown experimentally, but predicted here to be large, 11.5 kcal/mol. There are currently no experiments relevant to the theoretical entrance and exit complexes predicted here. PMID:25965106

  15. Transmetalation from B to Rh in the course of the catalytic asymmetric 1,4-addition reaction of phenylboronic acid to enones: a computational comparison of diphosphane and diene ligands.

    PubMed

    Li, You-Gui; He, Gang; Qin, Hua-Li; Kantchev, Eric Assen B

    2015-02-14

    Transmetalation is a key elementary reaction of many important catalytic reactions. Among these, 1,4-addition of arylboronic acids to organic acceptors such as α,β-unsaturated ketones has emerged as one of the most important methods for asymmetric C-C bond formation. A key intermediate for the B-to-Rh transfer arising from quaternization on a boronic acid by a Rh-bound hydroxide (the active catalyst) has been proposed. Herein, DFT calculations (IEFPCM/PBE0/DGDZVP level of theory) establish the viability of this proposal, and characterize the associated pathways. The delivery of phenylboronic acid in the orientation suited for the B-to-Rh transfer from the very beginning is energetically preferable, and occurs with expulsion of Rh-coordinated water molecules. For the bulkier binap ligand, the barriers are higher (particularly for the phenylboronic acid activation step) due to a less favourable entropy term to the free energy, in accordance with the experimentally observed slower transmetalation rate. PMID:25422851

  16. Transmetalation from B to Rh in the course of the catalytic asymmetric 1,4-addition reaction of phenylboronic acid to enones: a computational comparison of diphosphane and diene ligands.

    PubMed

    Li, You-Gui; He, Gang; Qin, Hua-Li; Kantchev, Eric Assen B

    2015-02-14

    Transmetalation is a key elementary reaction of many important catalytic reactions. Among these, 1,4-addition of arylboronic acids to organic acceptors such as α,β-unsaturated ketones has emerged as one of the most important methods for asymmetric C-C bond formation. A key intermediate for the B-to-Rh transfer arising from quaternization on a boronic acid by a Rh-bound hydroxide (the active catalyst) has been proposed. Herein, DFT calculations (IEFPCM/PBE0/DGDZVP level of theory) establish the viability of this proposal, and characterize the associated pathways. The delivery of phenylboronic acid in the orientation suited for the B-to-Rh transfer from the very beginning is energetically preferable, and occurs with expulsion of Rh-coordinated water molecules. For the bulkier binap ligand, the barriers are higher (particularly for the phenylboronic acid activation step) due to a less favourable entropy term to the free energy, in accordance with the experimentally observed slower transmetalation rate.

  17. Shedding new light on ZnCl2-mediated addition reactions of Grignard reagents to ketones: structural authentication of key intermediates and diffusion-ordered NMR studies.

    PubMed

    Armstrong, David R; Clegg, William; García-Alvarez, Pablo; McCall, Matthew D; Nuttall, Lorraine; Kennedy, Alan R; Russo, Luca; Hevia, Eva

    2011-04-11

    Building on recent advances in synthesis showing that the addition of inorganic salts to Grignard reagents can greatly enhance their performance in alkylation reactions to ketones, this study explores the reactions of EtMgCl with benzophenone in the presence of stoichiometric or catalytic amounts of ZnCl(2) with the aim of furthering the understanding of the role and constitution of the organometallic species involved in these transformations. Investigations into the metathesis reactions of three molar equivalents of EtMgCl with ZnCl(2) led to the isolation and characterisation (X-ray crystallography and (1)H and (13)C NMR spectroscopy) of novel magnesium "zinc-rich" zincate [{(THF)(6)Mg(2)Cl(3)}(+){Zn(2)Et(5)}(-)] (1), whose complicated constitution in THF solutions was assessed by variable-temperature (1)H DOSY NMR studies. Compound 1 reacted with one equivalent of benzophenone to yield magnesium magnesiate [{(THF)(6)Mg(2)Cl(3)}(+){Mg(2)(OC(Et)Ph(2))(2)Cl(3)(THF)}(-)] (3), whose structure was determined by X-ray crystallography. (1)H NMR monitoring of this reaction showed two equivalents of ZnEt(2) formed as a co-product, which together with the "magnesium only constitution" of 3 provides experimental insights into how zinc can be efficiently recycled in these reactions, and therefore used catalytically. The chemoselectivity of this reaction can be rationalised in terms of the synergic effect of magnesium and zinc and contrasts with the results obtained when benzophenone was allowed to react with EtMgCl in the absence of ZnCl(2), where the reduction of the ketone takes place preferentially. The reduction product [{(THF)(5)Mg(3)Cl(4){OC(H)Ph(CF(3))}(2)] (4) obtained from the reaction of EtMgCl with 2,2,2-trifluoroacetophenone was established by X-ray crystallography and multinuclear ((1)H, (13)C and (19)F) NMR spectroscopy. Compounds 3 and 4 exhibit new structural motifs in magnesium chemistry having MgCl(2) integrated within their constitution, which highlights

  18. Reaction pathways by quantum Monte Carlo: Insight on the torsion barrier of 1,3-butadiene, and the conrotatory ring opening of cyclobutene

    PubMed Central

    Barborini, Matteo; Guidoni, Leonardo

    2014-01-01

    Quantum Monte Carlo (QMC) methods are used to investigate the intramolecular reaction pathways of 1,3-butadiene. The ground state geometries of the three conformers s-trans, s-cis, and gauche, as well as the cyclobutene structure are fully optimised at the variational Monte Carlo (VMC) level, obtaining an excellent agreement with the experimental results and other quantum chemistry high level calculations. Transition state geometries are also estimated at the VMC level for the s-trans to gauche torsion barrier of 1,3-butadiene and for the conrotatory ring opening of cyclobutene to the gauche-1,3-butadiene conformer. The energies of the conformers and the reaction barriers are calculated at both variational and diffusional Monte Carlo levels providing a precise picture of the potential energy surface of 1,3-butadiene and supporting one of the two model profiles recently obtained by Raman spectroscopy [Boopalachandran et al., J. Phys. Chem. A 115, 8920 (2011)]. Considering the good scaling of QMC techniques with the system’s size, our results also demonstrate how variational Monte Carlo calculations can be applied in the future to properly investigate the reaction pathways of large and correlated molecular systems. PMID:23249005

  19. Synthesis of new lipid-inspired ionic liquids by thiol-ene chemistry: profound solvent effect on reaction pathway.

    PubMed

    Mirjafari, Arsalan; O'Brien, Richard A; West, Kevin N; Davis, James H

    2014-06-16

    The synthesis of a series of new lipid-inspired ionic liquids through thiol-ene "click" reaction with a single-step process. This synthesis offers considerable promise as an efficient and orthogonal method to construct structurally diverse imidazolium-type ionic liquids with linear and branched cationic tails, as well as versatility in the placement of the sulfur heteroatom. Profound solvent effect in this ene reaction regioselectivity has been observed.

  20. Ambiphilic properties of SF5CF2CF2Br derived perfluorinated radical in addition reactions across carbon-carbon double bonds.

    PubMed

    Dudziński, Piotr; Matsnev, Andrej V; Thrasher, Joseph S; Haufe, Günter

    2015-03-01

    The extraordinary properties of the pentafluorosulfanyl (SF5) group attract attention of organic chemists. While numerous SF5-substituted compounds have been synthesized, the direct introduction of SF5(CF2)n moieties has remained almost unexplored. Our investigations revealed the ambiphilic character of the SF5CF2CF2 radical. Addition reactions to electron-rich or electron-deficient alkenes profit either from its electrophilic or nucleophilic properties. Thus, the readily available SF5CF2CF2Br proved to be a promising and versatile building block for the introduction of this perfluorinated moiety.

  1. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.

    1992-03-06

    The objective of this research was to investigate the reaction mechanism of higher alcohol and aldehyde synthesis from syngas and the role of additives in the synthesis. An in situ IR reaction system and probe molecule technique were developed to study adsorbed species, active sites, and reaction pathway during reaction. The catalysts used for this study included silica-supported Rh, Ru, and Ni. (VC)

  2. A chemical bonding model for photo-induced defects in hydrogenated amorphous silicon (a-Si:H): Intrinsic and extrinsic reaction pathways

    SciTech Connect

    Lucovsky, G.; Yang, H.

    1997-07-01

    In device grade a-Si:H photo- or light-induced defect generation is an intrinsic effect for impurity concentrations of oxygen and nitrogen below about 10{sup 19} to 10{sup 20} cm{sup {minus}3}; however, at higher concentrations it increases with increasing impurity content. Charged defect configurations are identified by empirical chemistry and are studied by ab initio calculations. This paper addresses: (1) the chemical stability of charged defects; (2) the reaction pathways for defect metastability; and (3) the transition between extrinsic and intrinsic behavior.

  3. Role of added chloride ions in alteration of reaction pathway in the oxidation of cyclic ketones by dichloroisocyanuric acid—A kinetic study

    NASA Astrophysics Data System (ADS)

    Lakshman Kumar, Y.; Venkata Nadh, R.; Radhakrishnamurti, P. S.

    2015-03-01

    Effect of added chloride ions on kinetics and pathway of reaction between cyclic ketones (five to eight membered rings) and dichloroisocyanuric acid (DCICA) was studied in aqueous acetic acid—perchloric acid medium. Formation of aliphatic dicarboxylic acids as the end products demonstrates the ring cleavage oxidation. Positive effect of acid and negative effect of dielectric constant on the reaction rate reveals a interaction between positive ion (oxidant in the form of H2OCl+) and dipolar substrate molecule. Zero and first orders by oxidant in absence and presence of added chloride ions illustrates the participation of substrate as enolic form of ketone and protonated ketone, respectively, in the rate determining steps. The observed order of reactivity of cyclic ketones (cyclohexanone > cyclooctanone > cyclopentanone > cycloheptanone) was explained on the bases of ring strain, change of hybridization and conformational considerations. The envisaged plausible mechanism based on order of reactants in presence and absence of added chloride ions was substantiated by the order of Arrhenius parameters.

  4. Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization.

    PubMed

    Wang, Yanli; Schlick, Tamar

    2008-10-01

    The nucleotidyl-transfer reaction coupled with the conformational transitions in DNA polymerases is critical for maintaining the fidelity and efficiency of DNA synthesis. We examine here the possible reaction pathways of a Y-family DNA polymerase, Sulfolobus solfataricus DNA polymerase IV (Dpo4), for the correct insertion of dCTP opposite 8-oxoguanine using the quantum mechanics/molecular mechanics (QM/MM) approach, both from a chemistry-competent state and a crystal closed state. The latter examination is important for understanding pre-chemistry barriers to interpret the entire enzyme mechanism, since the crystal closed state is not an ideal state for initiating the chemical reaction. The most favorable reaction path involves initial deprotonation of O3'H via two bridging water molecules to O1A, overcoming an overall potential energy barrier of approximately 20.0 kcal/mol. The proton on O1A-P(alpha) then migrates to the gamma-phosphate oxygen of the incoming nucleotide as O3' attacks P(alpha), and the P(alpha)-O3A bond breaks. The other possible pathway in which the O3'H proton is transferred directly to O1A on P(alpha) has an overall energy barrier of 25.0 kcal/mol. In both reaction paths, the rate-limiting step is the initial deprotonation, and the trigonal-bipyramidal configuration for P(alpha) occurs during the concerted bond formation (O3'-P(alpha)) and breaking (P(alpha)-O3A), indicating the associative nature of the chemical reaction. In contrast, the Dpo4/DNA complex with an imperfect active-site geometry corresponding to the crystal state must overcome a much higher activation energy barrier (29.0 kcal/mol) to achieve a tightly organized site due to hindered O3'H deprotonation stemming from larger distances and distorted conformation of the proton acceptors. This significant difference demonstrates that the pre-chemistry reorganization in Dpo4 costs approximately 4.0 to 9.0 kcal/mol depending on the primer terminus environment. Compared to the higher

  5. Effects of Interface Coating and Nitride Enhancing Additive on Properties of Hi-Nicalon SiC Fiber Reinforced Reaction-Bonded Silicon Nitride Composites

    NASA Technical Reports Server (NTRS)

    Bhatt, Ramakrishana T.; Hull, David R.; Eldridge, Jeffrey I.; Babuder, Raymond

    2000-01-01

    Strong and tough Hi-Nicalon SiC fiber reinforced reaction-bonded silicon nitride matrix composites (SiC/ RBSN) have been fabricated by the fiber lay-up approach. Commercially available uncoated and PBN, PBN/Si-rich PBN, and BN/SiC coated SiC Hi-Nicalon fiber tows were used as reinforcement. The composites contained approximately 24 vol % of aligned 14 micron diameter SiC fibers in a porous RBSN matrix. Both one- and two-dimensional composites were characterized. The effects of interface coating composition, and the nitridation enhancing additive, NiO, on the room temperature physical, tensile, and interfacial shear strength properties of SiC/RBSN matrix composites were evaluated. Results indicate that for all three coated fibers, the thickness of the coatings decreased from the outer periphery to the interior of the tows, and that from 10 to 30 percent of the fibers were not covered with the interface coating. In the uncoated regions, chemical reaction between the NiO additive and the SiC fiber occurs causing degradation of tensile properties of the composites. Among the three interface coating combinations investigated, the BN/SiC coated Hi-Nicalon SiC fiber reinforced RBSN matrix composite showed the least amount of uncoated regions and reasonably uniform interface coating thickness. The matrix cracking stress in SiC/RBSN composites was predicted using a fracture mechanics based crack bridging model.

  6. Ge/Si and 87Sr/86Sr tracers of weathering reactions and hydrologic pathways in a tropical granitoid system

    USGS Publications Warehouse

    Derry, L.A.; Pett-Ridge, J. C.; Kurtz, A.C.; Troester, J.W.

    2006-01-01

    Ge/Si and 87Sr/86Sr data from primary and secondary minerals, soil waters, and stream waters in a tropical granitoid catchment quantitatively reflect mineral alteration reactions that occur at different levels within the bedrock-saprolite-soil zone. Near the bedrock-saprolite interface, plagioclase to kaolinite reaction yields low Ge/Si and 87Sr/86Sr. Higher in the regolith column, biotite weathering and kaolinite dissolution drive Ge/Si and 87Sr/86Sr to high values. Data from streams at base flow sample the bedrock-saprolite interface zone, while at high discharge solutes are derived from upper saprolite-soil zone. Coupled Ge/Si and 87Sr/86Sr can be effective tools for quantifying the importance of specific weathering reactions, and for geochemical hydrograph separation. ?? 2005 Elsevier B.V. All rights reserved.

  7. Elucidating the Reaction Pathways in the Synthesis of Organolead Trihalide Perovskite for High-Performance Solar Cells

    PubMed Central

    Wang, Baohua; Young Wong, King; Xiao, Xudong; Chen, Tao

    2015-01-01

    The past two years have witnessed unprecedentedly rapid development of organic–inorganic halide perovskite–based solar cells. The solution–processability and high efficiency make this technology extraordinarily attractive. The intensive investigations have accumulated rich experiences in the perovskite fabrication; while the mechanism of the chemical synthesis still remains unresolved. Here, we set up the chemical equation of the synthesis and elucidate the reactions from both thermodynamic and kinetic perspectives. Our study shows that gaseous products thermodynamically favour the reaction, while the activation energy and “collision” probability synergistically determine the reaction rate. These understandings enable us to finely tune the crystal size for high-quality perovskite film, leading to a record fill factor among similar device structures in the literature. This investigation provides a general strategy to explore the mechanism of perovskite synthesis and benefits the fabrication of high–efficiency perovskite photoactive layer. PMID:26020476

  8. Protective Effects of Maillard Reaction Products of Whey Protein Concentrate against Oxidative Stress through an Nrf2-Dependent Pathway in HepG2 Cells.

    PubMed

    Pyo, Min Cheol; Yang, Sung-Yong; Chun, Su-Hyun; Oh, Nam Su; Lee, Kwang-Won

    2016-09-01

    Whey protein concentrate (WPC), which contains α-lactalbumin and β-lactoglobulin, is utilized widely in the food industry. The Maillard reaction is a complex reaction that produces Maillard reaction products (MRPs), which are associated with the formation of antioxidant compounds. In this study, the hepatoprotection activity of MRPs of WPC against oxidative stress through the nuclear factor-E2-related factor 2 (Nrf2)-dependent antioxidant pathway in HepG2 cells was examined. Glucose-whey protein concentrate conjugate (Glc-WPC) was obtained from Maillard reaction between WPC and glucose. The fluorescence intensity of Glc-WPC increased after 7 d compared to native WPC, and resulted in loss of 48% of the free amino groups of WPC. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of Glc-WPC showed the presence of a high-molecular-weight portion. Treatment of HepG2 cells with Glc-WPC increased cell viability in the presence of oxidative stress, inhibited the generation of intracellular reactive oxygen species by tert-butyl hydroperoxide (t-BHP), and increased the glutathione level. Nrf2 translocation and Nrf2, reduced nicotinamide adenine dinucleotide phosphate (NAD(P)H)-quinone oxidoreductase 1 (NOQ1), heme oxygenase-1 (HO-1), glutamate-L-cysteine ligase (GCL)M and GCLC mRNA levels were increased by Glc-WPC. Also, Glc-WPC increased the phosphorylation of extracellular signal-regulated kinase (ERK) 1/2 and c-Jun N-terminal kinase (JNK). The results of this study demonstrate that Glc-WPC activates the Nrf2-dependent pathway through the phosphorylation of ERK1/2 and JNK in HepG2 cells, and induces production of antioxidant enzymes and phase II enzymes. PMID:27320783

  9. Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

    PubMed

    Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

    2016-02-11

    The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br. PMID:26766412

  10. Atmospheric chemistry of CF3O2: a theoretical study on mechanisms and pathways of the CF3O2 + IO reaction.

    PubMed

    Li, Hongwei; Tang, Yizhen; Wang, Rongshun

    2013-04-28

    The mechanisms and reaction pathways for the CF3O2 + IO reaction have been investigated by quantum chemistry methods. It has been found that the title reaction takes place on both the singlet and triplet potential energy surfaces (PES). On the singlet PES, the most important products include CF3OOOI, CF3OOIO, CF3OIO2, and CF2O + FIO2, while other products such as CF2O + FOIO, CF2O + FOOI, CF3OOI + O((3)P), CF3OI + O2 ((1)Δ and (3)Σ), and CF3O + OIO are negligible due to high barriers or unstable formations. On the triplet PES, CF3O + OIO is the dominant product with a lower barrier. As for FIO2 and it isomers, the most stable one is FIO2. TDDFT (Time Dependent Density Functional Theory) calculation indicates that CF3OOOI, CF3OOIO and CF3OIO2 undergo photolysis easily under sunlight. Moreover, a minor contribution relative to hydrogen is found in the CX3O2 + IO (X = H and F) reactions.

  11. Complete active space second order perturbation theory (CASPT2) study of N({sup 2}D) + H{sub 2}O reaction paths on D{sub 1} and D{sub 0} potential energy surfaces: Direct and roaming pathways

    SciTech Connect

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-10-21

    We report reaction paths starting from N({sup 2}D) + H{sub 2}O for doublet spin states, D{sub 0} and D{sub 1}. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H{sub 2}ON → H–O(H)N → H–HON → NO({sup 2}Π) + H{sub 2}, (2) cis-HNOH → HNO–H → H–HNO → NO + H{sub 2}, (3) H{sub 2}NO → H–HNO → HNO–H → trans-HNOH, are confirmed on the D{sub 0} surface.

  12. A crossed molecular beam and ab initio investigation of the exclusive methyl loss pathway in the gas phase reaction of boron monoxide (BO; X2Σ+) with dimethylacetylene (CH3CCCH3; X1A(1g)).

    PubMed

    Kaiser, Ralf I; Maity, Surajit; Dangi, Beni B; Su, Yuan-Siang; Sun, B J; Chang, Agnes H H

    2014-01-21

    The crossed molecular beam reaction of boron monoxide ((11)BO; X(2)Σ(+)) with dimethylacetylene (CH3CCCH3; X(1)A(1g)) was investigated at a collision energy of 23.9 ± 1.5 kJ mol(-1). The scattering dynamics were suggested to be indirect (complex forming reaction) and were initiated by the addition of (11)BO(X(2)Σ(+)) with the radical center located at the boron atom to the π electron density at the acetylenic carbon-carbon triple bond without entrance barrier leading to cis-trans(11)BOC4H6 doublet radical intermediates. cis-(11)BOC4H6 underwent cis-trans isomerization followed by unimolecular decomposition via a methyl group (CH3) loss forming 1-propynyl boron monoxide (CH3CC(11)BO) in an overall exoergic reaction (experimental: -91 ± 22 kJ mol(-1); theoretical: -105 ± 9 kJ mol(-1); NIST: -104 ± 12 kJ mol(-1)) via a tight exit transition state; trans-(11)BOC4H6 was found to lose a methyl group instantaneously. Neither atomic nor molecular hydrogen loss pathways were detectable. The experimental finding of an exclusive methyl loss pathway gains full support from our computational study predicting a methyl group versus atomic hydrogen loss branching ratio of 99.99% to 0.01% forming 1-propynyl boron monoxide (CH3CC(11)BO) and 1-methyl-propadienyl boron monoxide (CH3((11)BO)CCCH2), respectively. PMID:24281672

  13. A crossed molecular beam and ab initio investigation of the exclusive methyl loss pathway in the gas phase reaction of boron monoxide (BO; X2Σ+) with dimethylacetylene (CH3CCCH3; X1A(1g)).

    PubMed

    Kaiser, Ralf I; Maity, Surajit; Dangi, Beni B; Su, Yuan-Siang; Sun, B J; Chang, Agnes H H

    2014-01-21

    The crossed molecular beam reaction of boron monoxide ((11)BO; X(2)Σ(+)) with dimethylacetylene (CH3CCCH3; X(1)A(1g)) was investigated at a collision energy of 23.9 ± 1.5 kJ mol(-1). The scattering dynamics were suggested to be indirect (complex forming reaction) and were initiated by the addition of (11)BO(X(2)Σ(+)) with the radical center located at the boron atom to the π electron density at the acetylenic carbon-carbon triple bond without entrance barrier leading to cis-trans(11)BOC4H6 doublet radical intermediates. cis-(11)BOC4H6 underwent cis-trans isomerization followed by unimolecular decomposition via a methyl group (CH3) loss forming 1-propynyl boron monoxide (CH3CC(11)BO) in an overall exoergic reaction (experimental: -91 ± 22 kJ mol(-1); theoretical: -105 ± 9 kJ mol(-1); NIST: -104 ± 12 kJ mol(-1)) via a tight exit transition state; trans-(11)BOC4H6 was found to lose a methyl group instantaneously. Neither atomic nor molecular hydrogen loss pathways were detectable. The experimental finding of an exclusive methyl loss pathway gains full support from our computational study predicting a methyl group versus atomic hydrogen loss branching ratio of 99.99% to 0.01% forming 1-propynyl boron monoxide (CH3CC(11)BO) and 1-methyl-propadienyl boron monoxide (CH3((11)BO)CCCH2), respectively.

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

    PubMed

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

    2014-09-30

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

  15. The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site

    PubMed Central

    Evans, Christopher D.; Smith, Paul J.; Manning, Troy D.; Miedziak, Peter J.; Brett, Gemma L.; Armstrong, Robert D.; Bartley, Jonathan K.; Taylor, Stuart H.; Rosseinsky, Matthew J.; Hutchings, Graham J.

    2016-01-01

    Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology. PMID:27074316

  16. The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site.

    PubMed

    Evans, Christopher D; Kondrat, Simon A; Smith, Paul J; Manning, Troy D; Miedziak, Peter J; Brett, Gemma L; Armstrong, Robert D; Bartley, Jonathan K; Taylor, Stuart H; Rosseinsky, Matthew J; Hutchings, Graham J

    2016-07-01

    Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology. PMID:27074316

  17. Anion radical [2 + 2] cycloaddition as a mechanistic probe: stoichiometry- and concentration-dependent partitioning of electron-transfer and alkylation pathways in the reaction of the Gilman reagent Me2CuLi.LiI with bis(enones).

    PubMed

    Yang, Jingkui; Cauble, David F; Berro, Adam J; Bauld, Nathan L; Krische, Michael J

    2004-11-12

    Exposure of easily reduced aromatic bis(enones) 1a-1e to the methyl Gilman reagent Me(2)CuLi.LiI at 0 degrees C in tetrahydrofuran solvent provides the products of tandem conjugate addition-Michael cyclization, 2a-2e, along with the products of [2 + 2] cycloaddition, 3a-3e. Complete partitioning of the Gilman alkylation and [2 + 2] cycloaddition pathways may be achieved by adjusting the loading of the Gilman reagent, the rate of addition of the Gilman reagent, and the concentration of the reaction mixture. The Gilman alkylation manifold is favored by the rapid addition of excess Gilman reagent at higher substrate concentrations, while the [2 + 2] cycloaddition manifold is favored by slow addition of the same Gilman reagent at lower concentrations and loadings. Notably, [2 + 2] cycloaddition to form 3a-3e is catalytic in Gilman reagent. Kinetic data reveal that the ratio of 2a and 3a changes such that the cycloaddition pathway becomes dominant upon increased consumption of Gilman reagent. These data suggest a concentration-dependent speciation of the Gilman reagent and differential reactivity of the aggregates present at higher and lower concentrations. While the species present at higher concentration induce Gilman alkylation en route to products 2a-2e, the species present at lower concentration provide products of catalytic [2 + 2] cycloaddition, 3a-3e. Moreover, upon electrochemical reduction of the bis(enones) 1a-1e, or chemically induced single-electron transfer from arene anion radicals, the very same [2 + 2] cycloadducts 3a-3e are formed. The collective data suggest that [2 + 2] cycloadducts 3a-3e arising under Gilman conditions may be products of anion radical chain cyclobutanation that derive via electron transfer (ET) from the Me(2)CuLi.LiI aggregate(s) present at low concentration. These observations provide a link between the Gilman alkylation reaction and related ET chemistry and suggest these reaction paths are mechanistically distinct. This analysis

  18. Mixtures of l-Amino Acids as Reaction Medium for Formation of Iron Nanoparticles: The Order of Addition into a Ferrous Salt Solution Matters

    PubMed Central

    Šišková, Karolína M.; Machala, Libor; Tuček, Jiři; Kašlík, Josef; Mojzeš, Peter; Zbořil, Radek

    2013-01-01

    Owing to Mössbauer spectroscopy, an advanced characterization technique for iron-containing materials, the present study reveals previously unknown possibilities using l-amino acids for the generation of magnetic particles. Based on our results, a simple choice of the order of l-amino acids addition into a reaction mixture containing ferrous ions leads to either superparamagnetic ferric oxide/oxyhydroxide particles, or magnetically strong Fe0-Fe2O3/FeOOH core-shell particles after chemical reduction. Conversely, when ferric salts are employed with the addition of selected l-amino acids, only Fe0-Fe2O3/FeOOH core-shell particles are observed, regardless of the addition order. We explain this phenomenon by a specific transient/intermediate complex formation between Fe2+ and l-glutamic acid. This type of complexation prevents ferrous ions from spontaneous oxidation in solutions with full air access. Moreover, due to surface-enhanced Raman scattering spectroscopy we show that the functional groups of l-amino acids are not destroyed during the borohydride-induced reduction. These functionalities can be further exploited for (i) attachment of l-amino acids to the as-prepared magnetic particles, and (ii) for targeted bio- and/or environmental applications where the surface chemistry needs to be tailored and directed toward biocompatible species. PMID:24071943

  19. Detection of OXA-48-type carbapenemase-producing Enterobacteriaceae in diagnostic laboratories can be enhanced by addition of bicarbonates to cultivation media or reaction buffers.

    PubMed

    Studentova, Vendula; Papagiannitsis, Costas C; Izdebski, Radoslaw; Pfeifer, Yvonne; Chudackova, Eva; Bergerova, Tamara; Gniadkowski, Marek; Hrabak, Jaroslav

    2015-03-01

    Carbapenemase-mediated resistance to carbapenems in Enterobacteriaceae has become the main challenge in the treatment and prevention of infections recently. The partially unnoticed spread of OXA-48-type carbapenemase producers is usually assigned to low minimum inhibitory concentrations (MICs) of carbapenems that OXA-48-producing isolates often display. Therefore, there is an urgent need of specific and sensitive methods for isolation and detection of OXA-48 producers in clinical microbiology diagnostics. The influence of bicarbonates on carbapenem MICs against carbapenemase-producing Enterobacteriaceae was tested. We also checked whether the addition of bicarbonates to liquid media supplemented with meropenem may facilitate the selective enrichment of various carbapenemase producers in cultures. Furthermore, the sensitivity of carbapenemase confirmation by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) and spectrophotometric hydrolysis assays upon the addition of NH4HCO3 was examined. The addition of NaHCO3 significantly increased MICs of ertapenem and meropenem for OXA-48 producers. Furthermore, liquid media supplemented with NaHCO3 and meropenem were reliable for the selective enrichment of carbapenemase producers. The presence of NH4HCO3 in buffers used in the spectrophotometric and MALDI-TOF MS carbapenemase detection increased the sensitivity of that assay. Our results demonstrate that bicarbonates in media or reaction buffers can enhance the sensitivity of screening methods and diagnostic tests for carbapenemase producers.

  20. A general mechanism for the copper- and silver-catalyzed olefin aziridination reactions: concomitant involvement of the singlet and triplet pathways.

    PubMed

    Maestre, Lourdes; Sameera, W M C; Díaz-Requejo, M Mar; Maseras, Feliu; Pérez, Pedro J

    2013-01-30

    The olefin aziridination reactions catalyzed by copper and silver complexes bearing hydrotris(pyrazolyl)borate (Tp(x)) ligands have been investigated from a mechanistic point of view. Several mechanistic probe reactions were carried out, specifically competition experiments with p-substituted styrenes, stereospecificity of olefins, effects of the radical inhibitors, and use of a radical clock. Data from these experiments seem to be contradictory, as they do not fully support the previously reported concerted or stepwise mechanisms. But theoretical calculations have provided the reaction profiles for both the silver and copper systems with different olefins to satisfy all experimental data. A mechanistic proposal has been made on the basis of the information that we collected from experimental and theoretical studies. In all cases, the reaction starts with the formation of a metal-nitrene species that holds some radical character, and therefore the aziridination reaction proceeds through the radical mechanism. The silver-based systems however hold a minimum energy crossing point (MECP) between the triplet and closed-shell singlet surfaces, which induce the direct formation of the aziridines, and stereochemistry of the olefin is retained. In the case of copper, a radical intermediate is formed, and this intermediate constitutes the starting point for competition steps involving ring-closure (through a MECP between the open-shell singlet and triplet surfaces) or carbon-carbon bond rotation, and explains the loss of stereochemistry with a given substrate. Overall, all the initially contradictory experimental data fit in a mechanistic proposal that involves both the singlet and the triplet pathways.