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Sample records for additional reaction pathways

  1. On the relative preference of enamine/iminium pathways in an organocatalytic Michael addition reaction.

    PubMed

    Patil, Mahendra P; Sunoj, Raghavan B

    2009-05-04

    The mechanism of the organocatalyzed Michael addition between propanal and methyl vinyl ketone is investigated using the density functional and ab intio methods. Different modes of substrate activation offered by a secondary amine (pyrrolidine) organocatalyst are reported. The electrophilic activation of enone (P-I) through the formation of an iminium ion, and nucleophilic activation of propanal (P-II) in the form of enamine have been examined by identifying the corresponding transition states. The kinetic preference for the formation of key intermediates is established in an effort to identify the competing pathways associated with the title reaction. A comparison of barriers associated with different pathways as well as intermediate formation allows us to provide a suitable mechanistic rationale for Michael addition reactions catalyzed by a secondary amine. The overall barriers for the C-C bond formation pathways involving enol or iminium intermediates are identified as higher than the enamine pathway. Additionally, the generation of iminium is found to be less favored as compared to enamine formation. The effect of co-catalyst/protic solvent on the energetics of the overall reaction is also studied using the cluster continuum approach. Significant reduction in the activation energies for each step of the reaction is predicted for the solvent-assisted models. The co-catalyst assisted addition of propanal-enamine to methyl vinyl ketone is identified as the most preferred pathway (P-IV) for the Michael addition reaction. The results are in concurrence with the available experimental reports on the rate acceleration by the use of a co-catalyst in this reaction.

  2. 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…

  3. Investigation of the O+allyl addition/elimination reaction pathways from the OCH2CHCH2 radical intermediate

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

    These experiments study the preparation of and product channels resulting from OCH2CHCH2, 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-OCH2CHCH2 radicals; these undergo a facile ring opening to the OCH2CHCH2 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 OCH2CHCH2 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 C3H4O (acrolein)+H, C2H4+HCO (formyl radical), and H2CO (formaldehyde)+C2H3. A small signal from C2H2O (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, C2H5+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 each of these product channels

  4. Adverse reactions to drug additives.

    PubMed

    Simon, R A

    1984-10-01

    There is a long list of additives used by the pharmaceutical industry. Most of the agents used have not been implicated in hypersensitivity reactions. Among those that have, only reactions to parabens and sulfites have been well established. Parabens have been shown to be responsible for rare immunoglobulin E-mediated reactions that occur after the use of local anesthetics. Sulfites, which are present in many drugs, including agents commonly used to treat asthma, have been shown to provoke severe asthmatic attacks in sensitive individuals. Recent studies indicate that additives do not play a significant role in "hyperactivity." The role of additives in urticaria is not well established and therefore the incidence of adverse reactions in this patient population is simply not known. In double-blind, placebo-controlled studies, reactions to tartrazine or additives other than sulfites, if they occur at all, are indeed quite rare for the asthmatic population, even for the aspirin-sensitive subpopulation.

  5. 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.

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

    SciTech Connect

    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 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.

  7. 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; ...

    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

  8. 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.

  9. Fundamental reaction pathways during coprocessing

    SciTech Connect

    Stock, L.M.; Gatsis, J.G. . Dept. of Chemistry)

    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.

  10. 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

  11. 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.

  12. Reaction pathway for alkane dehydrocyclization

    SciTech Connect

    Shi, Buchang; Davis, B.H.

    1996-08-01

    Naphtha reforming to produce high octane gasoline is an important process. Many reaction mechanisms are involved in this process. For example, the study of the fundamentals of this process led to the concept of bi- or poly-functional catalysis. The results of this study provide additional mechanistic information about the dehydrocyclization of an n-alkane to produce aromatics. The reaction coordinate diagram advanced to account for the observation of irreversible adsorption should be modified to account for the present results. 32 refs., 1 fig.

  13. Multistage reaction pathways in detonating RDX

    NASA Astrophysics Data System (ADS)

    Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2017-01-01

    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 cystal. Rapid production of N2 and H2O 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 N2 and H2O productions.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Explorations into Chemical Reactions and Biochemical Pathways.

    PubMed

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered.

  4. Aldol reactions in multicomponent reaction based domino pathways: a multipurpose enabling tool in heterocyclic chemistry.

    PubMed

    Xu, Zhigang; De Moliner, Fabio; Cappelli, Alexandra P; Hulme, Christopher

    2013-06-07

    The aldol reaction has been evaluated in combination with the Ugi multicomponent reaction to assemble richly decorated mono- and polycyclic systems via expeditious cascade pathways. A small collection of pyrrolinones was generated thereof, and the scarcely accessible pyridoquinoxalinedione scaffold was also prepared by designing an additional nucleophilic substitution step in this domino sequence requiring minimal operational effort.

  5. 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.

  6. 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.

  7. 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

  8. 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

    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 different time

  9. 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.

  10. Illuminating the Reaction Pathways of Viromimetic Assembly

    PubMed Central

    2017-01-01

    The coassembly of well-defined biological nanostructures relies on a delicate balance between attractive and repulsive interactions between biomolecular building blocks. Viral capsids are a prototypical example, where coat proteins exhibit not only self-interactions but also interact with the cargo they encapsulate. In nature, the balance between antagonistic and synergistic interactions has evolved to avoid kinetic trapping and polymorphism. To date, it has remained a major challenge to experimentally disentangle the complex kinetic reaction pathways that underlie successful coassembly of biomolecular building blocks in a noninvasive approach with high temporal resolution. Here we show how macromolecular force sensors, acting as a genome proxy, allow us to probe the pathways through which a viromimetic protein forms capsids. We uncover the complex multistage process of capsid assembly, which involves recruitment and complexation, followed by allosteric growth of the proteinaceous coat. Under certain conditions, the single-genome particles condense into capsids containing multiple copies of the template. Finally, we derive a theoretical model that quantitatively describes the kinetics of recruitment and growth. These results shed new light on the origins of the pathway complexity in biomolecular coassembly.

  11. Analysis on relationship between extreme pathways and correlated reaction sets

    PubMed Central

    Xi, Yanping; Chen, Yi-Ping Phoebe; Cao, Ming; Wang, Weirong; Wang, Fei

    2009-01-01

    Background Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotypes, network-based pathways, such as extreme pathways and elementary flux modes, are defined. However, as the scale of metabolic network rises, the number of extreme pathways and elementary flux modes increases exponentially. Uniform random sampling solves this problem to some extent to study the contents of the available phenotypes. After uniform random sampling, correlated reaction sets can be identified by the dependencies between reactions derived from sample phenotypes. In this paper, we study the relationship between extreme pathways and correlated reaction sets. Results Correlated reaction sets are identified for E. coli core, red blood cell and Saccharomyces cerevisiae metabolic networks respectively. All extreme pathways are enumerated for the former two metabolic networks. As for Saccharomyces cerevisiae metabolic network, because of the large scale, we get a set of extreme pathways by sampling the whole extreme pathway space. In most cases, an extreme pathway covers a correlated reaction set in an 'all or none' manner, which means either all reactions in a correlated reaction set or none is used by some extreme pathway. In rare cases, besides the 'all or none' manner, a correlated reaction set may be fully covered by combination of a few extreme pathways with related function, which may bring redundancy and flexibility to improve the survivability of a cell. In a word, extreme pathways show strong complementary relationship on usage of reactions in the same correlated reaction set. Conclusion Both extreme pathways and correlated reaction sets are derived from the topology information of metabolic networks. The strong relationship between correlated reaction sets and extreme pathways suggests a possible mechanism: as a controllable unit, an

  12. 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

    2014-11-07

    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.

  13. CHLORINATION OF AMINO ACIDS: REACTION PATHWAYS AND REACTION RATES.

    PubMed

    How, Zuo Tong; Linge, Kathryn; Busetti, Francesco; Joll, Cynthia A

    2017-03-15

    Chlorination of amino acids can result in the formation of organic monochloramines or organic dichloramines, depending on the chlorine to amino acid ratio (Cl:AA). After formation, organic chloramines degrade into aldehydes, nitriles and N-chloraldimines. In this paper, the formation of organic chloramines from chlorination of lysine, tyrosine and valine were investigated. Chlorination of tyrosine and lysine demonstrated that the presence of a reactive secondary group can increase the Cl:AA ratio required for the formation of N,N-dichloramines, and potentially alter the reaction pathways between chlorine and amino acids, resulting in the formation of unexpected by-products. In a detailed investigation, we report rate constants for all reactions in the chlorination of valine, for the first time, using experimental results and modelling. At Cl:AA = 2.8, the chlorine was found to first react quickly with valine (5.4x104 M-1 s-1) to form N-monochlorovaline, with a slower subsequent reaction with N-monochlorovaline to form N,N-dichlorovaline (4.9x102 M-1 s-1), although some N-monochlorovaline degraded into isobutyraldehyde (1.0x10-4 s-1). The N,N-dichlorovaline then competitively degraded into isobutyronitrile (1.3x10-4 s-1) and N-chloroisobutyraldimine (1.2x10-4 s-1). In conventional drinking water disinfection, N-chloroisobutyraldimine can potentially be formed in concentrations higher than its odour threshold concentration, resulting in aesthetic challenges and an unknown health risk.

  14. 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)

  15. 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.

  16. Aligning Metabolic Pathways Exploiting Binary Relation of Reactions

    PubMed Central

    Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

    2016-01-01

    Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways. PMID:27936108

  17. 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.

  18. 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.

  19. 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.

  20. 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

    ... unfarmed land in other countries into cropland for energy grass-based renewable fuel production... AGENCY 40 CFR Part 80 RIN 2060-AR85 Regulation of Fuels and Fuel Additives: Additional Qualifying Renewable Fuel Pathways Under the Renewable Fuel Standard Program; Final Rule Approving Renewable...

  1. Reaction pathways and possible path bifurcation for the Schmidt reaction.

    PubMed

    Katori, Tetsuji; Itoh, Shuhei; Sato, Makoto; Yamataka, Hiroshi

    2010-03-17

    The N(2) liberation from iminodiazonium ion (2-X) is a key step of the Schmidt rearrangement of ketones. Molecular orbital calculations showed that two concurrent reaction channels, syn-benzyl fragmentation and anti-Me rearrangement, exist for syn-2, whereas anti-2-X proceeds via a single TS. Substituent effect analyses of the reactions of syn-2-X gave concave-upward plots, typical for a concurrent reaction mechanism. On the other hand, the reactions of anti-2-X gave linear Hammett plots, indicative of a single reaction mechanism for all anti-2-X. IRC calculations, however, revealed that the TS led to either an anti-benzyl rearrangement or an anti-benzyl fragmentation product depending on the substituent. Thus, the change of the mechanism (identity of the product) could not be detected by the Hammett plots. Ab initio dynamics simulations for anti-2-X were found to follow the IRC path for X = p-NO(2), giving the rearrangement product, and almost so for X = p-MeO, giving the fragmentation products. However, in borderline cases where X is less donating than p-MeO and less withdrawing than p-NO(2), the trajectories did not follow the minimum energy path on the potential energy surface but gave both rearrangement and fragmentation products directly from the single TS. This is a novel example of path bifurcation for a closed shell anionic reaction. It was concluded that a reactivity-selectivity argument based on the traditional TS theory might not always be applicable even to a well-known textbook organic reaction.

  2. 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%.

  3. 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.

  4. 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.

  5. Aldol Reactions in MCR-Based Domino Pathways: a Multipurpose Enabling Tool in Heterocyclic Chemistry

    PubMed Central

    Xu, Zhigang; De Moliner, Fabio; Cappelli, Alexandra P.

    2013-01-01

    The aldol reaction has been evaluated in combination with the Ugi multicomponent reaction to assemble richly decorated mono- and polycyclic systems via expeditious cascade pathways. A small collection of pyrrolinones was generated thereof, and the scarcely accessible pyridoquinoxalinedione scaffold was also prepared by designing an additional nucleophilic substitution step in this domino sequence requiring minimal operational effort. PMID:23718233

  6. From formamide to purine: an energetically viable mechanistic reaction pathway.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-02-28

    A step-by-step mechanistic pathway following the transformation of formamide to purine through a five-membered ring intermediate has been explored by density functional theory computations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest reaction pathway. All necessary reactants are generated from a single starting compound, formamide, through energetically viable reactions. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-membered ring-closure, and deamination. On the basis of the study of noncatalytic pathways, catalytic water has been found to provide energetically viable step-by-step mechanistic pathways. Among these reaction steps, five-member ring-closure is the rate-determining step. The energy barrier (ca. 42 kcal/mol) of this rate-control step is somewhat lower than the rate-determining step (ca. 44 kcal/mol) for a pyrimidine-based pathway reported previously. The mechanistic pathway reported herein is less energetically demanding than for previously proposed routes to adenine.

  7. 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.

  8. 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

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

    PubMed

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

    2010-09-03

    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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

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

    DOE PAGES

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; ...

    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

  15. 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.

  16. Dynamic biochemical reaction process analysis and pathway modification predictions.

    PubMed

    Conejeros, R; Vassiliadis, V S

    2000-05-05

    Recently, the area of model predictive modification of biochemical pathways has received attention with the aim to increase the productivity of microbial systems. In this study, we present a generalization of previous work, where, using a sensitivity study over the fermentation as a dynamic system, the optimal selection of reaction steps for modification (amplification or attenuation) is determined. The influence of metabolites in the activity of enzymes has also been considered (through activation or inhibition). We further introduce a new concept in the dynamic modeling of biochemical reaction systems including a generalized continuous superstructure in which two artificial multiplicative terms are included to account for: (a) enzyme overexpression or underexpression (attenuation or amplification) for the whole enzyme pool; and (b) modification of the apparent order of a kinetic expression with respect to the concentration of a metabolite or any subset of metabolites participating in the pathway. This new formulation allows the prediction of the sensitivity of the pathway performance index (objective function) with respect to the concentration of the enzyme, as well as the interaction of the enzyme with other metabolites. Using this framework, a case study for the production of penicillin V is analyzed, obtaining the most sensitive reaction steps (or bottlenecks) and the most significant regulations of the system, due to the effect of concentration of intracellular metabolites on the activity of each enzyme.

  17. Understanding reaction mechanisms in organic chemistry from catastrophe theory: ozone addition on benzene.

    PubMed

    Ndassa, Ibrahim Mbouombouo; Silvi, Bernard; Volatron, François

    2010-12-16

    The potential energy profiles of the endo and exo additions of ozone on benzene have been theoretically investigated within the framework provided by the electron localization function (ELF). This has been done by carrying out hybrid Hartree-Fock DFT B3LYP calculation followed by a bonding evolution theory (BET) analysis. For both approaches, the reaction is exothermic by ~98 kJ mol(-1). However, the activation energy is calculated to 10 kJ mol(-1) lower in the endo channel than in the exo one; therefore the formation of the endo C(6)H(6)O(3) adduct is kinetically favored. Six structural stability domains are identified along both reaction pathways as well as the bifurcation catastrophes responsible for the changes in the topology of the system. This provides a chemical description of the reaction mechanism in terms of heterolytic synchronous bond formation.

  18. Phosphite radicals and their reactions. Examples of redox, substitution, and addition reactions. [Gamma rays and electrons

    SciTech Connect

    Schaefer, K.; Asmus, K.D.

    1980-08-21

    Phosphite radicals HPO/sub 3/- and PO/sub 3//sup 2/-, which exist in an acid-base equilibrium with pK = 5.75, are shown to take part in various types of reactions. In the absence of scavengers, they disappear mainly by second-order disproportionation and combination; a first-order contribution to the decay is also indicated. HPO/sub 3/- and PO/sub 3//sup 2/- are good reductants toward electron acceptors such as tetranitromethane. In this reaction phosphate and C(NO/sub 2/)/sub 3/- are formed. Phosphite radicals can, however, also act as good oxidants, e.g., toward thiols and thiolate ions. These reactions lead to the formation of RS. radicals which were identified either directly, as in the case of penicillamine, through the optical absorption of PenS. or more indirectly through equilibration of RS. with RS- to the optically absorbing RSSR-. disulfide radical anion. A homolytic substitution reaction (S/sub H/2) occurs in the reaction of the phosphite radicals with aliphatic disulfides, yielding RS. radicals and phosphate thioester RSPO/sub 3//sup 2/-. Lipoic acid, as an example of a cyclic disulfide, is reduced to the corresponding RSSR-. radical anion and also undergoes the S/sub H/2 reaction with about equal probability. An addition reaction is observed between phosphite radicals and molecular oxygen. The resulting peroxo phosphate radicals establish an acid-base equilibrium HPO/sub 5//sup -/. reversible PO/sub 5//sup 2 -/. + H+ with a pK = 3.4. Absolute rate constants were determined for all reactions discussed.

  19. 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.

  20. Kinetics of Hydrogen Abstraction and Addition Reactions of 3-Hexene by ȮH Radicals.

    PubMed

    Yang, Feiyu; Deng, Fuquan; Pan, Youshun; Zhang, Yingjia; Tang, Chenglong; Huang, Zuohua

    2017-03-09

    Rate coefficients of H atom abstraction and H atom addition reactions of 3-hexene by the hydroxyl radicals were determined using both conventional transition-state theory and canonical variational transition-state theory, with the potential energy surface (PES) evaluated at the CCSD(T)/CBS//BHandHLYP/6-311G(d,p) level and quantum mechanical effect corrected by the compounded methods including one-dimensional Wigner method, multidimensional zero-curvature tunneling method, and small-curvature tunneling method. Results reveal that accounting for approximate 70% of the overall H atom abstractions occur in the allylic site via both direct and indirect channels. The indirect channel containing two van der Waals prereactive complexes exhibits two times larger rate coefficient relative to the direct one. The OH addition reaction also contains two van der Waals complexes, and its submerged barrier results in a negative temperature coefficient behavior at low temperatures. In contrast, The OH addition pathway dominates only at temperatures below 450 K whereas the H atom abstraction reactions dominate overwhelmingly at temperature over 1000 K. All of the rate coefficients calculated with an uncertainty of a factor of 5 were fitted in a quasi-Arrhenius formula. Analyses on the PES, minimum reaction path and activation free Gibbs energy were also performed in this study.

  1. Chemical and mathematical modeling of asphaltene reaction pathways

    SciTech Connect

    Salvage, P.E.

    1986-01-01

    Precipitated asphaltene was subjected to pyrolysis and hydropyrolysis, both neat and in solvents, and catalytic hydroprocessing. A solvent extraction procedure defined gas, maltene, asphaltene, and coke product fractions. The apparent first order rate constant for asphaltene conversion at 400/sup 0/C was relatively insensitive to the particular reaction scheme. The yield of gases likewise showed little variation and was always less than 10%. On the other hand, the maltene and coke yields were about 20% and 60%, respectively, from neat pyrolysis, and about 60% and less than 5%, respectively, from catalytic reactions. The temporal variations of the product fractions allowed discernment of asphaltene reaction pathways. The primary reaction of asphaltene was to residual asphaltene, maltenes, and gases. The residual asphaltene reacted thermally to coke and catalytically to maltenes at the expense of coke. Secondary degradation of these primary products led to lighter compounds. Reaction mechanism for pyrolysis of asphaltene model compounds and alkylaromstics were determined. The model compound kinetics results were combined with a stochastic description of asphaltene structure in a mathematical model of asphaltene pyrolysis. Individual molecular product were assigned to either the gas, maltene, asphaltene, or coke product fractions, and summation of the weights of each constituted the model's predictions. The temporal variation of the product fractions from simulated asphaltene pyrolysis compared favorably with experimental results.

  2. HIGH TEMPERATURE POLYMERS FROM 1,3-DIPOLAR ADDITION REACTIONS.

    DTIC Science & Technology

    indazole with nitrobenzene as the reaction solvent has...phenylhydrazide chloride has been prepared. The reaction of this compound with ethynyl benzene in the presence of triethylamine yields 1,1’,5,5’- tetraphenyl-3,3...corresponding heterocycles. The polymerization reaction of 4,4’ oxydi benzoylphenyl- hydrazide chloride with p-diethynyl benzene afforded poly (1,1’,5,5’-tetraphenyl-3,3’- (oxydi-p-phenylene) -dipyrazole).

  3. Membrane fission reactions of the mammalian ESCRT pathway.

    PubMed

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

    2013-01-01

    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 complexes. 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.

  4. 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

  5. Roaming dynamics in ion-molecule reactions: phase space reaction pathways and geometrical interpretation.

    PubMed

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

    2014-04-07

    A model Hamiltonian for the reaction CH4(+) -> CH3(+) + 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.

  6. HIGH TEMPERATURE POLYMERS FROM 1,3-DIPOLAR ADDITION REACTIONS.

    DTIC Science & Technology

    reaction of benzoylphenylhydrazide chloride and m-divinylbenzene in the presence of triethylamine was prepared. The polymerization reaction of p...phenylene-3,3’-disydnone with p-benzoquinone afforded poly(2,4,6,8-tetrahydro-4,8-dioxo-2,6-p-phenylenepyrazolo (3,4-f) indazole ) which had good thermal...stability and an inherent viscosity of 0.6. The polymerization reaction of terephthaloyl phenylhydrazide chloride with m-divinylbenzene gave poly(1,1

  7. Acid-base bifunctional catalytic surfaces for nucleophilic addition reactions.

    PubMed

    Motokura, Ken; Tada, Mizuki; Iwasawa, Yasuhiro

    2008-09-01

    This article illustrates the modification of oxide surfaces with organic amine functional groups to create acid-base bifunctional catalysts, summarizing our previous reports and also presenting new data. Immobilization of organic amines as bases on inorganic solid-acid surfaces afforded highly active acid-base bifunctional catalysts, which enabled various organic transformations including C--C coupling reactions, though these reactions did not proceed with either the homogeneous amine precursors or the acidic supports alone. Spectroscopic characterization, such as by solid-state MAS NMR and FTIR, revealed not only the interactions between acidic and basic sites but also bifunctional catalytic reaction mechanisms.

  8. Phytosphingosine degradation pathway includes fatty acid α-oxidation reactions in the endoplasmic reticulum.

    PubMed

    Kitamura, Takuya; Seki, Naoya; Kihara, Akio

    2017-03-28

    Although normal fatty acids (FAs) are degraded via β-oxidation, unusual FAs such as 2-hydroxy (2-OH) FAs and 3-methyl-branched FAs are degraded via α-oxidation. Phytosphingosine (PHS) is one of the long-chain bases (the sphingolipid components) and exists in specific tissues, including the epidermis and small intestine in mammals. In the degradation pathway, PHS is converted to 2-OH palmitic acid and then to pentadecanoic acid (C15:0-COOH) via FA α-oxidation. However, the detailed reactions and genes involved in the α-oxidation reactions of the PHS degradation pathway have yet to be determined. In the present study, we reveal the entire PHS degradation pathway: PHS is converted to C15:0-COOH via six reactions [phosphorylation, cleavage, oxidation, CoA addition, cleavage (C1 removal), and oxidation], in which the last three reactions correspond to the α-oxidation. The aldehyde dehydrogenase ALDH3A2 catalyzes both the first and second oxidation reactions (fatty aldehydes to FAs). In Aldh3a2-deficient cells, the unmetabolized fatty aldehydes are reduced to fatty alcohols and are incorporated into ether-linked glycerolipids. We also identify HACL2 (2-hydroxyacyl-CoA lyase 2) [previous name, ILVBL; ilvB (bacterial acetolactate synthase)-like] as the major 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the FA α-oxidation of the PHS degradation pathway. HACL2 is localized in the endoplasmic reticulum. Thus, in addition to the already-known FA α-oxidation in the peroxisomes, we have revealed the existence of FA α-oxidation in the endoplasmic reticulum in mammals.

  9. 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

  10. Reaction Pathway for Cocaine Hydrolase-Catalyzed Hydrolysis of (+)-Cocaine

    PubMed Central

    Yao, Yuan; Liu, Junjun; Zheng, Fang; Zhan, Chang-Guo

    2017-01-01

    A recently designed and discovered cocaine hydrolase (CocH), engineered from human butyrylcholinesterase (BChE), has been proven promising as a novel enzyme therapy for treatment of cocaine overdose and addiction because it is highly efficient in catalyzing hydrolysis of naturally occurring (−)-cocaine. It has been known that the CocH also has a high catalytic efficiency against (+)-cocaine, a synthetic enantiomer of cocaine. Reaction pathway and the corresponding free energy profile for the CocH-catalyzed hydrolysis of (+)-cocaine have been determined, in the present study, by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Acordingt to the QM/MM-FE results, the catalytic hydrolysis process is initiated by the nucleophilic attack on carbonyl carbon of (−)-cocaine benzoyl ester via hydroxyl oxygen of S198 side chain, and the second reaction step (i.e. dissociation of benzoyl ester) is rate-determining. This finding for CocH-catalyzed hydrolysis of (+)-cocaine is remarkably different from that for the (+)-cocaine hydrolysis catalyzed by bacterial cocaine esterase in which the first reaction step of the deacylation is associated with the highest free energy barrier (~17.9 kcal/mol). The overall free energy barrier (~16.0 kcal/mol) calculated for the acylation stage of CocH-catalyzed hydrolysis of (+)-cocaine is in good agreement with the experimental free energy barrier of ~14.5 kcal/mol derivated from the experimental kinetic data.

  11. Thermochemistry for silicic acid formation reaction: Prediction of new reaction pathway

    NASA Astrophysics Data System (ADS)

    Mondal, Bhaskar; Ghosh, Deepanwita; Das, Abhijit K.

    2009-08-01

    Reaction between SiO 2 and water has been studied extensively using ab initio methods. The mechanism for formation of metasilicic acid SiO(OH) 2 and orthosilicic acid Si(OH) 4 has been explored and a new pathway for formation of Si(OH) 4 is predicted. Heats of reaction ( ΔrH298∘) and heats of formation ( ΔfH298∘) at 298 K for the related reactions and species calculated at two different theoretical levels G3B3 and G3MP2B3 agree well with the literature values. It is found that when SiO 2 reacts simultaneously with two water molecules, the thermodynamic as well as kinetic feasibility of the process is much greater than that when SiO 2 reacts with one molecule of water.

  12. 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.

  13. [Salidroside biosynthesis pathway: the initial reaction and glycosylation of tyrosol].

    PubMed

    Ma, Lanqing; Liu, Chunmei; Yu, Hansong; Zhang, Jixing; Gao, Dongyao; Li, Yanfang; Wang, Younian

    2012-03-01

    Salidroside, the 8-O-beta-D-glucoside of tyrosol, is a novel adaptogenic drug extracted from the medicinal plant Rhodiola sachalinensis A. Bor. Due to the scarcity of R. sachalinensis and its low yield of salidroside, there is great interest in enhancing the production of salidroside by biotechnological process. Glucosylation of tyrosol is thought to be the final step in salidroside biosynthesis. In our related works, three UGT clones were isolated from the roots and the cultured cells. Our intention was to combine the catalytic specificity of these UGTs in vitro in order to change the level of salidroside in vivo by over-expression of the above UGTs. However, as the aglycone substrate of salidroside, the biosynthetic pathway of tyrosol and its regulation are less well understood. The results of related studies revealed that there are two different possibilities for the tyrosol biosynthetic pathway. One possibility is that tyrosol is produced from a p-coumaric acid precursor, which is derived mainly from phenylalanine. The second possibility is that the precursor of tyrosol might be tyramine, which is synthesized from tyrosine. Our previous work demonstrated that over-expression of the endogenous phenylalanine ammonia-lyase gene (PALrs1) and accumulation of p-coumaric acid did not facilitate tyrosol biosynthesis. In contrast, the data presented in our recent work provide in vitro and in vivo evidence that the tyrosine decarboxylase (RsTyrDC) is most likely to have an important function in the initial reaction of the salidroside biosynthesis pathway in R. Sachalinensis.

  14. 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.

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

    PubMed

    Dibble, T S

    2001-05-09

    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.

  16. Why Are Addition Reactions to N2 Thermodynamically Unfavorable?

    PubMed

    Borden, Weston Thatcher

    2017-02-09

    Thermochemical data are used to show that, of the 89.9 kcal/mol difference between the endothermicity of H2 addition to N2 (ΔH = 47.9 kcal/mol) and the exothermicity of H2 addition to acetylene (ΔH = -42.0 kcal/mol), less than half is due to a stronger π bond in N2 than in acetylene. The other major contributor to the difference of 89.9 kcal/mol between the enthalpies of hydrogenation of N2 and acetylene is that the pair of N-H bonds that are created in the addition of H2 to N2 are significantly weaker than the pair of C-H bonds that are created in the addition of H2 to acetylene. The reasons for this large difference between the strengths of the N-H bonds in E-HN═NH and the C-H bonds in H2C═CH2 are analyzed and discussed.

  17. 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

    2013-09-06

    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.

  18. 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.

  19. 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

  20. 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.

  1. Kinetic Data and Quantum Chemical Calculation Studies on the Stepwise vs. Concerted Pathways for Reaction of Chlorosulfonyl Isocyanate Reactions with Monofluoroalkenes

    DTIC Science & Technology

    2013-01-17

    synthetic utility of CSI reactions with unreactive hydrocarbon and monofluoroalkenes is enhanced by running the reactions at a lower temperature where...public release; distribution unlimited. Free Energy vs. Reaction Coordinate Diagram Solid line: Pathways available to hydrocarbon alkenes with CSI...stepwise vs. concerted pathways for reaction of chlorosulfonyl isocyanate reactions with monofluoroalkenes 5a. CONTRACT NUMBER In-House 5b. GRANT

  2. [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.

  3. 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

    2010-09-07

    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.

  4. 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.

  5. 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.

  6. Automatic Reaction Pathway Search via Combined Molecular Dynamics and Coordinate Driving Method.

    PubMed

    Yang, Manyi; Zou, Jingxiang; Wang, Guoqiang; Li, Shuhua

    2017-02-16

    We proposed and implemented a combined molecular dynamics and coordinate driving (MD/CD) method for automatically searching multistep reaction pathways of chemical reactions. In this approach, the molecular dynamic (MD) method at the molecular mechanics (MM) or semiempirical quantum mechanical (QM) level is employed to explore the conformational space of the minimum structures, and the modified coordinate driving (CD) method is used to build reaction pathways for representative conformers. The MD/CD method is first applied to two model reactions (the Claisen rearrangement and the intermolecular aldol reaction). By comparing the obtained results with those of the existing methods, we found that the MD/CD method has a comparable performance in searching low-energy reaction pathways. Then, the MD/CD method is further applied to investigate two reactions: the electrocyclic reaction of benzocyclobutene-7-carboxaldehyde and the intramolecular Diels-Alder reaction of ketothioester with 11 effectively rotatable single bonds. For the first reaction, our results can correctly account for its torquoselectivity. For the second one, our method predicts eight reaction channels, leading to eight different stereo- and regioselective products. The MD/CD method is expected to become an efficient and cost-effective theoretical tool for automatically searching low-energy reaction pathways for relatively complex chemical reactions.

  7. 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

  8. New Pathways and Time-resolved Vibrational Dynamics of Surface Reactions

    NASA Astrophysics Data System (ADS)

    Wolf, Martin

    2000-03-01

    We discuss recent results of femtosecond laser-induced reactions and time-resolved vibrational spectroscopy at metal surfaces which provide detailed insights into the microscopic reaction mechanism and the rate of energy flow between the adsorbate and the underlying substrate. We demonstrate that fs laser excitation allows to access new reaction pathways which cannot be induced with conventional thermal activation: Heating of a Ru(001) surface on which CO and atomic oxygen are co-adsorbed leads exclusively to desorption of CO. In contrast, excitation with intense fs laser pulses enables also the formation of CO_2, in addition to CO desorption. Thus a new reaction path is opened upon fs laser excitation. Time-resolved two-pulse-correlation and isotope substitution experiments as well as density functional calculations reveal that this novel reaction pathway is initiated by laser heated hot substrate electrons which populate an antibonding unoccupied state of the O-Ru bond. The vibrationally activated oxygen reacts with co-adsorbed CO on an ultrashort time scale. On the other hand, desorption of CO molecules is caused by coupling of the adsorbate to the phonon bath of the substrate, which occurs much slower than the hot electron driven CO2 formation. Thus under fs excitation the process of CO desorption is outpaced, but prevails for conventional thermal heating due to a lower activation energy. In a further set of experiments the technique of fs infrared-visible sum-frequency generation (SFG) has been used as a time-resolved molecule specific 'probe' to analyze the transient changes of the CO stretching mode on Ru(001) after excitation with an intense fs 'pump' pulse. At low CO coverages the broadband infrared laser pulses also allow to excite the overtones of the CO stretch.

  9. 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

  10. Inert gas sparge leads to alternate reaction pathway.

    PubMed

    Franchini, M K; Carstensen, J T

    2000-06-01

    The effect of sparging with an inert gas (argon) was evaluated during the investigation of the solution kinetics of an oxidation-prone amphiphilic drug containing a sulphide moiety. Samples stored with an air headspace in pH7 and 8 phosphate buffers at elevated temperatures and in the absence of light degraded to two main products, a sulphoxide and a cinnamic acid analogue. Initially, this appeared to be a sequential mechanism which could be blocked by removing oxygen. Instead, argon-sparge forced the direct degradation to the cinnamate, which was evidenced by the formation of a strong odour of sulphide. In addition, argon-sparged samples remained colourless, while those sparged with oxygen or stored with an air headspace turned yellow and had negligible odour. The half-lives for samples stored in pH 8 buffers at 93 degrees C at an initial drug concentration of 25 mg mL(-1) were 128 days (argon sparged), 86 days (air headspace), and 65 days (oxygen sparged). The results indicated that for the drug under study, sparging with an inert gas affected the mechanism as well as the rate of the reaction at elevated temperatures.

  11. Catalytic Direct-type 1,4-Addition Reactions of Alkylazaarenes.

    PubMed

    Suzuki, Hirotsugu; Igarashi, Ryo; Yamashita, Yasuhiro; Kobayashi, Shū

    2017-04-10

    1,4-addition reactions of alkylazaarenes catalyzed by strong Brønsted bases have been developed for the first time. The desired reactions with α,β-unsaturated amides proceeded under mild reaction conditions to give the 1,4-adducts in high yields. Both ortho- and para-substituted azaarenes afforded the desired adducts in high yields. Regioselective reactions of di- or trimethylpyridine were found to be possible depending on the acidity of the α-hydrogen atoms. Furthermore, a candidate of allosteric protein kinase modulators was synthesized in two steps. An asymmetric variant of this reaction was also found to be feasible.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  14. 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.

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

    PubMed

    Yang, Juan; Saggiomo, Vittorio; Velders, Aldrik H; Cohen Stuart, Martien A; Kamperman, Marleen

    2016-01-01

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

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

    PubMed Central

    Yang, Juan; Saggiomo, Vittorio; Velders, Aldrik H.; Cohen Stuart, Martien A.; Kamperman, Marleen

    2016-01-01

    Catechol chemistry is used as a crosslinking tool abundantly in both natural organisms (e.g. mussels, sandcastle worms) and synthetic systems to achieve the desired mechanical properties. Despite this abundance and success, the crosslinking chemistry is still poorly understood. In this study, to simplify the system, yet to capture the essential chemistry, model compounds 4-methyl catechol and propylamine are used. The reaction of 4-methyl catechol (2 mM) with propylamine (6 mM) is carried out in the presence of NaIO4 (2 mM) in 10 mM Na2CO3 aqueous solution. A variety of spectroscopic/spectrometric and chromatographic methods such as 1H NMR, LC-MS, and UV-VIS are used to track the reaction and identify the products/intermediates. It is found that the crosslinking chemistry of a catechol and an amine is both fast and complicated. Within five minutes, more than 60 products are formed. These products encompass 19 different masses ranging from molecular weight of 179 to 704. By combining time-dependent data, it is inferred that the dominant reaction pathways: the majority is formed via aryloxyl-phenol coupling and Michael-type addition, whereas a small fraction of products is formed via Schiff base reactions. PMID:27930671

  17. Flash Vacuum Pyrolysis of Lignin Model Compounds: Reaction Pathways of Aromatic Methoxy Groups

    SciTech Connect

    Britt, P.F.; Buchanan, A.C., III; Martineau, D.R.

    1999-03-21

    Currently, there is interest in utilizing lignin, a major constituent of biomass, as a renewable source of chemicals and fuels. High yields of liquid products can be obtained from the flash or fast pyrolysis of biomass, but the reaction pathways that lead to product formation are not understood. To provide insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds at 500 C. This presentation will focus on the FVP of {beta}-ether linkages containing aromatic methoxy groups and the reaction pathways of methoxy-substituted phenoxy radicals.

  18. Covert attention regulates saccadic reaction time by routing between different visual-oculomotor pathways.

    PubMed

    Guan, Shaobo; Liu, Yu; Xia, Ruobing; Zhang, Mingsha

    2012-03-01

    Covert attention modulates saccadic performance, e.g., the abrupt onset of a task-irrelevant visual stimulus grabs attention as measured by a decrease in saccadic reaction time (SRT). The attentional advantage bestowed by the task-irrelevant stimulus is short-lived: SRT is actually longer ~200 ms after the onset of a stimulus than it is when no stimulus appears, known as inhibition of return. The mechanism by which attention modulates saccadic reaction is not well-understood. Here, we propose two possible mechanisms: by selective routing of the visuomotor signal through different pathways (routing hypothesis) or by general modulation of the speed of visuomotor transformation (shifting hypothesis). To test them, we designed a cue gap paradigm in which a 100-ms gap was introduced between the fixation point disappearance and the target appearance to the conventional cued visual reaction time paradigm. The cue manipulated the location of covert attention, and the gap interval resulted in a bimodal distribution of SRT, with an early mode (express saccade) and a late mode (regular saccade). The routing hypothesis predicts changes in the proportion of express saccades vs. regular saccades, whereas the shifting hypothesis predicts a shift of SRT distribution. The addition of the cue had no effect on mean reaction time of express and regular saccades, but it changed the relative proportion of two modes. These results demonstrate that the covert attention modification of the mean SRT is largely attributed to selective routing between visuomotor pathways rather than general modulation of the speed of visuomotor transformation.

  19. Electron-induced hydration of an alkene: alternative reaction pathways.

    PubMed

    Warneke, Jonas; Wang, Ziyan; Swiderek, Petra; Bredehöft, Jan Hendrik

    2015-03-27

    Electron-induced reactions in condensed mixtures of ethylene and water lead to the synthesis of ethanol, as shown by post-irradiation thermal desorption spectrometry (TDS). Interestingly, this synthesis is not only induced by soft electron impact ionization similar to a previously observed electron-induced hydroamination but also, at low electron energy, by electron attachment to ethylene and a subsequent acid/base reaction with water.

  20. 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.

  1. 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

    2014-05-02

    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.

  2. 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.

  3. 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.

  4. Nitro-fatty acid reaction with glutathione and cysteine. Kinetic analysis of thiol alkylation by a Michael addition reaction.

    PubMed

    Baker, Laura M S; Baker, Paul R S; Golin-Bisello, Franca; Schopfer, Francisco J; Fink, Mitchell; Woodcock, Steven R; Branchaud, Bruce P; Radi, Rafael; Freeman, Bruce A

    2007-10-19

    Fatty acid nitration by nitric oxide-derived species yields electrophilic products that adduct protein thiols, inducing changes in protein function and distribution. Nitro-fatty acid adducts of protein and reduced glutathione (GSH) are detected in healthy human blood. Kinetic and mass spectrometric analyses reveal that nitroalkene derivatives of oleic acid (OA-NO2) and linoleic acid (LNO2) rapidly react with GSH and Cys via Michael addition reaction. Rates of OA-NO2 and LNO2 reaction with GSH, determined via stopped flow spectrophotometry, displayed second-order rate constants of 183 M(-1)S(-1) and 355 M(-1)S(-1), respectively, at pH 7.4 and 37 degrees C. These reaction rates are significantly greater than those for GSH reaction with hydrogen peroxide and non-nitrated electrophilic fatty acids including 8-iso-prostaglandin A2 and 15-deoxy-Delta(12,14)-prostaglandin J2. Increasing reaction pH from 7.4 to 8.9 enhanced apparent second-order rate constants for the thiol reaction with OA-NO2 and LNO2, showing dependence on the thiolate anion of GSH for reactivity. Rates of nitroalkene reaction with thiols decreased as the pKa of target thiols increased. Increasing concentrations of the detergent octyl-beta-d-glucopyranoside decreased rates of nitroalkene reaction with GSH, indicating that the organization of nitro-fatty acids into micellar or membrane structures can limit Michael reactivity with more polar nucleophilic targets. In aggregate, these results reveal that the reversible adduction of thiols by nitro-fatty acids is a mechanism for reversible post-translational regulation of protein function by nitro-fatty acids.

  5. 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.

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

    PubMed

    Hoffmann, Reinhard W

    2016-02-07

    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.

  9. Comparative Studies of Cathodically-Promoted and Base-Catalyzed Michael Addition Reactions of Levoglucosenone.

    PubMed

    Samet, Alexander V.; Niyazymbetov, Murat E.; Semenov, Victor V.; Laikhter, Andrei L.; Evans, Dennis H.

    1996-12-13

    Regioselective Michael addition of nitro and heterocyclic compounds to levoglucosenone, 1, is effectively catalyzed by amines and also by cathodic electrolysis. In comparison to the base-catalyzed reaction, it was found that under electrochemical conditions the reaction proceeds under milder conditions and with higher yields. Cathodically-initiated Michael addition of thiols to levoglucosenone using small currents produces the previously unknown threo addition product in several instances. The normal erythro isomer, identified as the kinetic product, tends to be formed when large currents are used. In contrast, slow, low current electrolyses promote equilibration of the two forms so that erythro can be converted to threo by the retro reaction and readdition. Addition of 2-naphthalenethiol to (R)-(+)-apoverbenone is also reported.

  10. Reaction pathways during oxidation of cereal β-glucans.

    PubMed

    Mäkelä, Noora; Sontag-Strohm, Tuula; Schiehser, Sonja; Potthast, Antje; Maaheimo, Hannu; Maina, Ndegwa H

    2017-02-10

    Oxidation of cereal β-glucans may affect their stability in food products. Generally, polysaccharides oxidise via different pathways leading to chain cleavage or formation of oxidised groups within the polymer chain. In this study, oxidation pathways of oat and barley β-glucans were assessed with different concentrations of hydrogen peroxide (H2O2) or ascorbic acid (Asc) with ferrous iron (Fe(2+)) as a catalyst. Degradation of β-glucans was evaluated using high performance size exclusion chromatography and formation of carbonyl groups using carbazole-9-carbonyloxyamine labelling. Furthermore, oxidative degradation of glucosyl residues was studied. Based on the results, the oxidation with Asc mainly resulted in glycosidic bond cleavage. With H2O2, both glycosidic bond cleavage and formation of carbonyl groups within the β-glucan chain was found. Moreover, H2O2 oxidation led to production of formic acid, which was proposed to result from Ruff degradation where oxidised glucose (gluconic acid) is decarboxylated to form arabinose.

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

    PubMed

    Perez-Benito, Joaquin F

    2011-09-08

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

  12. Modeling the flux of metabolites in the juvenile hormone biosynthesis pathway using generalized additive models and ordinary differential equations.

    PubMed

    Martínez-Rincón, Raúl O; Rivera-Pérez, Crisalejandra; Diambra, Luis; Noriega, Fernando G

    2017-01-01

    Juvenile hormone (JH) regulates development and reproductive maturation in insects. The corpora allata (CA) from female adult mosquitoes synthesize fluctuating levels of JH, which have been linked to the ovarian development and are influenced by nutritional signals. The rate of JH biosynthesis is controlled by the rate of flux of isoprenoids in the pathway, which is the outcome of a complex interplay of changes in precursor pools and enzyme levels. A comprehensive study of the changes in enzymatic activities and precursor pool sizes have been previously reported for the mosquito Aedes aegypti JH biosynthesis pathway. In the present studies, we used two different quantitative approaches to describe and predict how changes in the individual metabolic reactions in the pathway affect JH synthesis. First, we constructed generalized additive models (GAMs) that described the association between changes in specific metabolite concentrations with changes in enzymatic activities and substrate concentrations. Changes in substrate concentrations explained 50% or more of the model deviances in 7 of the 13 metabolic steps analyzed. Addition of information on enzymatic activities almost always improved the fitness of GAMs built solely based on substrate concentrations. GAMs were validated using experimental data that were not included when the model was built. In addition, a system of ordinary differential equations (ODE) was developed to describe the instantaneous changes in metabolites as a function of the levels of enzymatic catalytic activities. The results demonstrated the ability of the models to predict changes in the flux of metabolites in the JH pathway, and can be used in the future to design and validate experimental manipulations of JH synthesis.

  13. Modeling the flux of metabolites in the juvenile hormone biosynthesis pathway using generalized additive models and ordinary differential equations

    PubMed Central

    Martínez-Rincón, Raúl O.; Rivera-Pérez, Crisalejandra; Diambra, Luis; Noriega, Fernando G.

    2017-01-01

    Juvenile hormone (JH) regulates development and reproductive maturation in insects. The corpora allata (CA) from female adult mosquitoes synthesize fluctuating levels of JH, which have been linked to the ovarian development and are influenced by nutritional signals. The rate of JH biosynthesis is controlled by the rate of flux of isoprenoids in the pathway, which is the outcome of a complex interplay of changes in precursor pools and enzyme levels. A comprehensive study of the changes in enzymatic activities and precursor pool sizes have been previously reported for the mosquito Aedes aegypti JH biosynthesis pathway. In the present studies, we used two different quantitative approaches to describe and predict how changes in the individual metabolic reactions in the pathway affect JH synthesis. First, we constructed generalized additive models (GAMs) that described the association between changes in specific metabolite concentrations with changes in enzymatic activities and substrate concentrations. Changes in substrate concentrations explained 50% or more of the model deviances in 7 of the 13 metabolic steps analyzed. Addition of information on enzymatic activities almost always improved the fitness of GAMs built solely based on substrate concentrations. GAMs were validated using experimental data that were not included when the model was built. In addition, a system of ordinary differential equations (ODE) was developed to describe the instantaneous changes in metabolites as a function of the levels of enzymatic catalytic activities. The results demonstrated the ability of the models to predict changes in the flux of metabolites in the JH pathway, and can be used in the future to design and validate experimental manipulations of JH synthesis. PMID:28158248

  14. Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields.

    PubMed

    Faccioli, P; a Beccara, S

    2016-01-01

    The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up to ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development of this method. Next, we discuss its validation against the results of plain MD protein folding simulations performed by the DE-Shaw group using the Anton supercomputer. Finally, we review a few representative applications of the DRP approach to study reactions which are far too complex and rare to be investigated by plain MD, even on the Anton machine.

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

    PubMed

    Maeda, Satoshi; Morokuma, Keiji

    2011-08-09

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

  16. Chiral N,N'-Dioxide-Organocatalyzed Regio-, Diastereo- and Enantioselective Michael Addition-Alkylation Reaction.

    PubMed

    Feng, Juhua; Yuan, Xiao; Luo, Weiwei; Lin, Lili; Liu, Xiaohua; Feng, Xiaoming

    2016-10-24

    A highly regio-, diastereo- and enantioselective Michael addition-alkylation reaction between α-substituted cyano ketones and (Z)-bromonitrostyrenes has been realized by using a chiral N,N'-dioxide as organocatalyst. A variety of substrates performed well in this reaction, and the corresponding multifunctionalized chiral 2,3-dihydrofurans were obtained in up to 95 % yield with 95:5 dr and 93 % ee.

  17. 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.

  18. 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.

  19. Silica gel-promoted tandem addition-cyclization reactions of 2-alkynylbenzenamines with isothiocyanates.

    PubMed

    Ding, Qiuping; Cao, Banpeng; Zong, Zhenzhen; Peng, Yiyuan

    2010-05-10

    Tandem addition-cyclization reactions of 2-alkynylbenzenamines with isothiocyanates promoted by silica gel are described. This reaction proceeds smoothly at 80 degrees C under metal- and solvent-free conditions, which provides an efficient and practical route for the generation of 2,4-dihydro-1H-benzo[d][1,3]thiazines. The recovered silica gel could be reused for several times.

  20. 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.

  1. 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

  2. [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.

  3. 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.

  4. [Introduction of platelet additive solution in platelet concentrates: towards a decrease of blood transfusion reactions].

    PubMed

    Rebibo, D; Simonet, M; Hauser, L

    2008-11-01

    Platelet concentrates (PC) are used in thrombocytopenia for curative or preventive treatment for hemorrhagic risk. Since five years, additive solutions have been added in PCs for several reasons; one of them is to present an interest in the intolerance in plasma reactions. The literature data have shown that these solutions entail fewer allergic reactions than PCs kept in plasma. This study was reviewed on three years of transfusion in France. The main objective of this study was to see if there was a difference in frequency when these PCs were in solution or not. All adverse reactions in recipients (ARR) occurring among PCs recipients (with and without additive solution) were analysed. The categories of ARR specifically studied were: allergies, febril non haemolytic reactions (FNHR) and the category "unknown". This study shows that there is significantly lower incidence of allergies by introducing solution. For all ARRs, there is also a decrease in their frequency when PCs are in additive solution, it is significant except for the apheresis platelet concentrates. For categories FNHR and "unknown", the results are opposed and/or not significant. This study confirms that introduction of additive solutions in PCs is able to reduce some allergic transfusion reactions.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Enantioselective Synthesis of β-(3-Hydroxypyrazol-1-yl)ketones Using An Organocatalyzed Michael Addition Reaction

    PubMed Central

    Gogoi, Sanjib; Zhao, Cong-Gui; Ding, Derong

    2009-01-01

    β-(3-Hydroxypyrazol-1-yl)ketones have been prepared in high yields and excellent enantioselectivities (94–98% ee) via a Michael addition reaction between 2-pyrazolin-5-ones and aliphatic acyclic α,β-unsaturated ketones using 9-epi-9-amino-9-deoxyquinine as the catalyst. These results account for the first example of an aza-Michael addition of the ambident 2-pyrazolin-5-one anion to a Michael acceptor. PMID:19415906

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

    NASA Astrophysics Data System (ADS)

    Wang, Chao-Hong; Li, Kuan-Ting

    2016-12-01

    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.

  11. Effect of Pd Additions on the Invariant Reactions in the Ag-CuOx System

    SciTech Connect

    Darsell, Jens T.; Weil, K. Scott

    2006-02-01

    Palladium was added as a ternary component to a series of copper oxide-silver alloys in an effort increase the use temperature of these materials for potential ceramic brazing applications. Phase equilibria at low palladium and copper oxide concentrations in the Pd-CuOx-Ag system were determined experimentally using differential scanning calorimetry, microstructural analysis, and X-ray diffraction. Small additions of palladium were generally found to increase the temperature of the eutectic reaction present in the pseudobinary system, but have little effect on a higher temperature monotectic reaction. However once enough palladium was added (~5 mol%) to increase the new eutectic temperature to that of the original pseudobinary monotectic reaction, the pseudoternary monotectic temperature correspondingly began to move upward as well. The addition of palladium also forced the eutectic point to slightly lower silver concentrations, again causing a convergence with the former monotectic line.

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

    PubMed

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

    2015-04-08

    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.

  13. 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.

  14. 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.

  15. 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).

  16. 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.

  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. 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.

  19. 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.

  20. The Paternò-Büchi reaction: importance of triplet states in the excited-state reaction pathway.

    PubMed

    Brogaard, Rasmus Y; Schalk, Oliver; Boguslavskiy, Andrey E; Enright, Gary D; Hopf, Henning; Raev, Vitaly; Tarcoveanu, Eliza; Sølling, Theis I; Stolow, Albert

    2012-06-28

    The Paternò-Büchi (PB) reaction between an excited carbonyl compound and an alkene has been widely studied, but so far little is known about the excited-state dynamics of the reaction. In this investigation, we used a compound in which a formyl and a vinyl group are attached to a [2.2]paracyclophane in order to obtain a model system in pre-reactive conformation for the PB reaction. We studied the excited-state dynamics of the isolated molecule in a molecular beam using femtosecond time-resolved photoelectron spectroscopy and ab initio calculations. The results show that inter-system crossing within two picoseconds competes efficiently with the reaction in the singlet manifold. Thus, the PB reaction in this model system takes place in the triplet state on a time scale of nanoseconds. This result stresses the importance of triplet states in the excited-state pathway of the PB reaction involving aromatic carbonyl compounds, even in situations in which the reacting moieties are in immediate vicinity.

  1. 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.

  2. 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.

  3. Effect of relative humidity and additives on the reaction of sulfur dioxide with calcium hydroxide

    SciTech Connect

    Ruiz-Alsop, R.N.

    1986-01-01

    The objective of this research was to investigate the effect of process variables and additives on the reaction rate of Ca(OH)/sub 2/ with SO/sub 2/ at conditions similar to these encountered in the bag filters used to collect solids following flue gas desulfurization by spray drying. The effect of Ca(OH)/sub 2/ loading, temperature, relative humidity, and inlet SO/sub 2/ concentration were investigated. Of these variables, relative humidity showed the greatest impact on the reaction rate. The effect of small amounts of additives were also investigated. Of the additives tried (buffer acids, organic deliquescents, and inorganic deliquescents) deliquescent salts were the only additives that improved reactivity. A shrinking core model with zero order kinetics in SO/sub 2/ was used to model experimental data. An empirical correlation was included in the model to account for shape and surface roughness of the Ca(OH)/sub 2/ particles. The diffusion coefficient of the SO/sub 2/ through the product layer was found to increase linearly with relative humidity, and the kinetic rate constant increases exponentially with relative humidity. With a few exceptions the model was able to predict the experimental data within the margin of experimental error (+/- 10%). At high relative humidity and/or high SO/sub 2/ concentration, reaction kinetics control the overall reaction rate, while at low relative humidity and/or low SO/sub 2/ concentration, SO/sub 2/ diffusion through the product layer controls the rate. The reaction solids were characterized by scanning electron microscopy, powder x-ray diffraction, Coulter counter size distribution BET (N/sub 2/) surface area, energy dispersive spectrometry, and differential scanning calorimetry.

  4. 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

  5. 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

  6. Nano- and Microgels Through Addition Reactions of Functional Oligomers and Polymers

    NASA Astrophysics Data System (ADS)

    Albrecht, Krystyna; Moeller, Martin; Groll, Juergen

    Nano- and Microgels are predominantly prepared using radical polymerization techniques. This chapter reviews alternative approaches to microgel preparation based on addition reactions of functional oligomers and polymers. This allows preparation of microgels under physiological conditions and in the presence of biologically active molecules without affecting their function. This method is therefore predominantly used to synthesize microgels for biomedical applications. Different crosslinking chemistries that have been used in this context are presented and discussed with regard to reaction conditions and stability of the reaction product. Microgels that have been prepared by these techniques are divided into two groups. Natural polymers used for the preparation of microgels are described first, followed by artificial prepolymers that are suitable for the preparation of microgels. The different preparation methods as well as the resulting microgels and their properties are presented and discussed.

  7. 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

  8. Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach

    PubMed Central

    Çakır, Tunahan

    2015-01-01

    A systems-based investigation of the effect of perturbations on metabolic machinery is crucial to elucidate the mechanism behind perturbations. One way to investigate the perturbation-induced changes within the cell metabolism is to focus on pathway-level effects. In this study, three different perturbation types (genetic, environmental and disease-based) are analyzed to compute a list of reporter pathways, metabolic pathways which are significantly affected from a perturbation. The most common omics data type, transcriptome, is used as an input to the bioinformatic analysis. The pathways are scored by two alternative approaches: by averaging the changes in the expression levels of the genes controlling the associated reactions (reaction-centric), and by averaging the changes in the associated metabolites which were scored based on the associated genes (metabolite-centric). The analysis reveals the superiority of the novel metabolite-centric approach over the commonly used reaction-centric approach since it is based on metabolites which better represent the cross-talk among different pathways, enabling a more global and realistic cataloguing of network-wide perturbation effects. PMID:26411587

  9. A bond, ring and cage resolved Poincaré-Hopf relationship for isomerisation reaction pathways

    NASA Astrophysics Data System (ADS)

    Jenkins, Samantha; Liu, Zeyu; Kirk, Steven R.

    2013-10-01

    We introduce a new tool for reaction pathway analysis based on a chemical bonding density descriptor obtained from the higher resolution Poincaré-Hopf relation. To remove the degeneracy of the Poincaré-Hopf relationship for critical points of the electron density, we introduce the concepts of bonding cardinality and characterise the topology of rings and cages. This allows us to relate the changes in the relative energetic stability along an isomerisation reaction pathway with changes in the topology of the electron density. To demonstrate the utility of this approach, we consider the complete circuit of the reaction pathway connecting the various Möbius and Hückel structures in Au and/or Pd bis-metallated octaphyrins. Where the topological feature 'cages' exist in adjacent topologies, the degeneracy in the Poincaré-Hopf relationship is completely removed even for differences in relative energies of only 0.1 kcal/mol. Metallation of the Möbius and Hückel structures was found to increase the topological complexity and bonding density. Combining Pd and Au nuclei in the octaphyrin complexes reduced the smoothness of the potential energy surface. The presence of long, weak C-H contacts correlates in all cases with the lowest energy enantiomers and the most negative nuclear-independent chemical shift values of the reaction pathways in Au and/or Pd bis-metallated octaphyrins.

  10. 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.

  11. 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

  12. Expanding the scope of Lewis acid catalysis in water: remarkable ligand acceleration of aqueous ytterbium triflate catalyzed Michael addition reactions.

    PubMed

    Ding, Rui; Katebzadeh, Kambiz; Roman, Lisa; Bergquist, Karl-Erik; Lindström, Ulf M

    2006-01-06

    [reaction: see text] Significant rate acceleration of metal-catalyzed Michael addition reactions in water was observed upon addition of small, dibasic ligands. Ytterbium triflate and TMEDA was the most effective combination leading to a nearly 20-fold faster reaction than in the absence of ligand.

  13. High throughput engineering to revitalize a vestigial electron transfer pathway in bacterial photosynthetic reaction centers.

    PubMed

    Faries, Kaitlyn M; Kressel, Lucas L; Wander, Marc J; Holten, Dewey; Laible, Philip D; Kirmaier, Christine; Hanson, Deborah K

    2012-03-09

    Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization.

  14. Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution

    PubMed Central

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

    2015-01-01

    To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data. PMID:25821238

  15. The role of intramolecular hydrogen bonds in nucleophilic addition reactions of ketenaminals

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2012-08-01

    Quantum-chemical calculations of the geometries and electronic structures of molecules of ketenaminals 3-(diaminomethylene)-2,4-pentanedione and dimethyl-2-(diaminomethylene)-malonate and calculations of the structures of intermediates in the reaction of the nucleophilic addition of the ketenaminals to the acetonitrile molecule are performed by B3LYP/6-31+G** method. Two possible scenarios of the process are shown, depending on the mutual orientation of reacting molecules. The nucleophilic addition proceeds in two stages. It is found that the rate-limiting stage of the process is the transfer of the proton of the intramolecular hydrogen bond in a ketenaminal molecule. The experimentally observed faster reaction of pyrimidine formation for the 3-(diaminomethylene)-2,4-pentanedione molecule relative to that for dimethyl-2-(diaminomethylene)-malonate is explained by the hydrogen bond being stronger and the barrier of proton transfer from the aminogroup to the ketogroup oxygen falling upon nucleophilic attack in the former molecule.

  16. 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.

  17. 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.

  18. 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

    2016-04-07

    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.

  19. Michael addition-elimination reactions of chiral enolates with ethyl 3-halopropenoates.

    PubMed

    Esteban, Jorge; Costa, Anna M; Gómez, Alex; Vilarrasa, Jaume

    2008-01-03

    Key dienoic or dienal substructures of cytotoxic macrolides amphidinolide E and dictyostatin have been prepared via a Michael addition (followed by elimination of X-) of chiral enolates on beta-halo derivatives of ethyl acrylate, with full retention of the initial E or Z configuration. Evans oxazolidin-2-ones and our related thiazolidin-2-ones, as well as a fine-tuning of the reaction conditions, have been essential. Many chiral building blocks are accessible from these adducts.

  20. Initiation and Modification of Reaction by Energy Addition: Kinetic and Transport Phenomena

    DTIC Science & Technology

    1993-10-01

    MODIFICATION OF REACTION BY ENERGY ADDITION: KINETIC AND TRANSPORT PHENOMENA by Francis E. Fendell and Mau-Song Chou Center for Propulsion Technology...TA - A2 L AUHOWAC - F49620-90-C-0070 Francis E. Fendell and Mau-Song Chou 7. PEMOS101IG ORGANIZATION NAME(S AND...a gaseous mixture is more pertinent for the supersonic-combustor applications of interest to the Air Force (compare Figs. 1 and 2) (Carrier, Fendell

  1. 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.

  2. 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

  3. Matrix isolation study of the ozonolysis of 1,3- and 1,4-cyclohexadiene: identification of novel reaction pathways.

    PubMed

    Pinelo, Laura; Gudmundsdottir, Anna D; Ault, Bruce S

    2013-05-23

    The ozonolysis reactions of 1,3- and 1,4-cyclohexadiene have been studied using a combination of matrix isolation, infrared spectroscopy, and theoretical calculations. Experimental and theoretical results demonstrate that these reactions predominantly do not follow the long-accepted Criegee mechanism. Rather, the reaction of O3 with 1,4-cyclohexadiene leads to the essentially barrierless formation of benzene, C6H6, and H2O3. These two species are then trapped in the same argon matrix cage and weakly interact to form a molecular complex. There is also evidence for the formation of a small amount of the primary ozonide as a minor product, formed through a transition state that is slightly higher in energy. The reaction of O3 with 1,3-cyclohexadiene follows two pathways, one of which is the Criegee mechanism through a low energy transition state leading to formation of the primary ozonide. In addition, with a similar barrier, ozone abstracts a single hydrogen from C5 while adding to C1, forming a hydroperoxy intermediate. This study presents two of the rare cases in which the Criegee mechanism is not the dominant pathway for the ozonolysis of an alkene as well as the first evidence for dehydrogenation of an alkene by ozone.

  4. 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.

  5. 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.

  6. Electrocatalytic oxygen reduction reaction on perovskite oxides: series versus direct pathway.

    PubMed

    Poux, Tiphaine; Bonnefont, Antoine; Kéranguéven, Gwénaëlle; Tsirlina, Galina A; Savinova, Elena R

    2014-07-21

    The mechanism of the oxygen reduction reaction (ORR) on LaCoO(3) and La(0.8)Sr(0.2)MnO(3) perovskite oxides is studied in 1 M NaOH by using the rotating ring disc electrode (RRDE) method. By combining experimental studies with kinetic modeling, it was demonstrated that on perovskite, as well as on perovskite/carbon electrodes, the ORR follows a series pathway through the intermediate formation of hydrogen peroxide. The escape of this intermediate from the electrode strongly depends on: 1) The loading of perovskite; high loadings lead to an overall 4 e(-) oxygen reduction due to efficient hydrogen peroxide re-adsorption on the active sites and its further reduction. 2) The addition of carbon to the catalytic layer, which affects both the utilization of the perovskite surface and the production of hydrogen peroxide. 3) The type of oxide; La(0.8)Sr(0.2)MnO(3) displays higher (compared to LaCoO(3)) activity in the reduction of oxygen to hydrogen peroxide and in the reduction/oxidation of the latter.

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

    NASA Astrophysics Data System (ADS)

    Elliott, Scott; Cicerone, Ralph J.; Turco, Richard P.; Drdla, Katja; Tabazadeh, Azadeh

    1994-02-01

    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 ClONO2 and N2O5, 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 HOx 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 10-13 cm3 molecule-1 s-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 HOx 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.

  8. 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

  9. 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

  10. Modeling the Catalysis of Anti-Cocaine Catalytic Antibody: Competing Reaction Pathways and Free Energy Barriers

    PubMed Central

    Pan, Yongmei; Gao, Daquan; Zhan, Chang-Guo

    2010-01-01

    The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb 15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of −6.33 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally-derived free energy barrier shift of −5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through non-covalent bonding interactions with the substrates. PMID:18341277

  11. 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.

  12. Phospha-Michael Addition as a New Click Reaction for Protein Functionalization.

    PubMed

    Lee, Yan-Jiun; Kurra, Yadagiri; Liu, Wenshe R

    2016-03-15

    A new type of click reaction between an alkyl phosphine and acrylamide was developed and applied for site-specific protein labeling in vitro and in live cells. Acrylamide is a small electrophilic olefin that readily undergoes phospha-Michael addition with an alkyl phosphine. Our kinetic study indicated a second-order rate constant of 0.07 m(-1)  s(-1) for the reaction between tris(2-carboxyethyl)phosphine and acrylamide at pH 7.4. To demonstrate its application in protein functionalization, we used a dansyl-phosphine conjugate to successfully label proteins that were site-specifically installed with N(ɛ) -acryloyl-l-lysine and employed a biotin-phosphine conjugate to selectively probe human proteins that were metabolically labeled with N-acryloyl-galactosamine.

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

    PubMed

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

    2016-05-04

    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.

  14. Pathways of electrophilic aromatic substitution reactions catalyzed by group 13 trihalides: An ab initio study

    NASA Astrophysics Data System (ADS)

    Volkov, Alexey N.; Timoshkin, Alexey Y.; Suvorov, Andrew V.

    An ab initio study of the two possible pathways of ectrophilic aromatic substitution reaction catalyzed by monomeric and dimeric forms of group 13 metal halides has been performed. Optimized geometries of π, σ-complexes and corresponding transition states have been obtained at second-order Møller-Plesset/ LANL2DZ(d)+ level of theory. It is found that operation of the dimeric pathway is more favorable both thermodynamically and kinetically. Thus, it is expected that catalytical activity of the metal halide will be greatly increased if the stoichiometric ratio 2:1 is employed. Obtained results are in qualitative agreement with available experimental data.

  15. Substitution and addition reactions of •OH with p-substituted-phenols

    NASA Astrophysics Data System (ADS)

    Albarrán, Guadalupe; Galicia-Jiménez, Eduardo; Mendoza, Edith; Schuler, Robert H.

    2017-04-01

    The directing effect of a hydroxyl group on the substitution and addition reactions of •OH to the substituted and free positions in aromatic rings of p-substituted-phenols were studied in aqueous solutions containing either K3Fe(CN)6 as an oxidant of the substituted hydroxycyclohexadienyl radical initially formed or using ascorbic acid. The results showed that the attack of the •OH to the substituted position (ipso position) was followed by elimination of the substituent producing hydroquinone. The addition reaction of the •OH to the free position on the ring produced 4-substituent-catechol and 4-substituent-resorcinol derivatives. Identification and quantification of the radiolytic products were carried out using high performance liquid chromatography. The results of the yields are given for the p-halogen-phenols (p-X-Ph) p-F-Ph, p-Cl-Ph, p-Br-Ph and p-I-Ph. Other compounds, p-nitro-Ph, p-OH-benzoic acid, p-OH-benzonitrile, p-OH-benzaldehyde, p-OH-anisole and p-OH-benzyl alcohol (represented as p-Z-Ph), were only studied using K3Fe(CN)6 as the oxidant. The results show that the p-X-Ph are attacked by the •OH at the ipso position to the halogen in the proportion 1:0.53:0.46:0.11 for F>Cl>Br>I. The •OH attacked at the ipso position to the p-Z-Phs through a substitution reaction, which depended on the substituent group. Thus, the strongly deactivating groups produced less hydroquinone, indicating less substitution reaction than the strongly activating groups.

  16. Reaction pathways of β-D-glucopyranose pyrolysis to syngas in hydrogen plasma: a density functional theory study.

    PubMed

    Huang, Xiaoyuan; Cheng, Dang-guo; Chen, Fengqiu; Zhan, Xiaoli

    2013-09-01

    In this work, density functional theory (DFT) was employed to investigate the reaction pathways of β-D-glucopyranose for better understanding the pyrolysis mechanism of cellulose in hydrogen plasma. Many possible reactions were considered, and the reaction enthalpies and activation energies of these reactions were calculated using density functional theory (DFT) with a Gaussian method of B3LYP and basic set of 6-31G(d,p). A most possible reaction pathway was brought up. According to this reaction pathway, the main products of cellulose pyrolysis in hydrogen plasma would be syngas, and few light hydrocarbons. CO mainly comes from the decomposition of aldehyde group, while H2 mainly comes from dehydrogenation processes. Active H in plasma are found to play a very important role in many reactions, and they can remarkably lower the energies needed for reactions.

  17. 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.

  18. Catalytic wet air oxidation of phenol with functionalized carbon materials as catalysts: reaction mechanism and pathway.

    PubMed

    Wang, Jianbing; Fu, Wantao; He, Xuwen; Yang, Shaoxia; Zhu, Wanpeng

    2014-08-01

    The development of highly active carbon material catalysts in catalytic wet air oxidation (CWAO) has attracted a great deal of attention. In this study different carbon material catalysts (multi-walled carbon nanotubes, carbon fibers and graphite) were developed to enhance the CWAO of phenol in aqueous solution. The functionalized carbon materials exhibited excellent catalytic activity in the CWAO of phenol. After 60 min reaction, the removal of phenol was nearly 100% over the functionalized multi-walled carbon, while it was only 14% over the purified multi-walled carbon under the same reaction conditions. Carboxylic acid groups introduced on the surface of the functionalized carbon materials play an important role in the catalytic activity in CWAO. They can promote the production of free radicals, which act as strong oxidants in CWAO. Based on the analysis of the intermediates produced in the CWAO reactions, a new reaction pathway for the CWAO of phenol was proposed in this study. There are some differences between the proposed reaction pathway and that reported in the literature. First, maleic acid is transformed directly into malonic acid. Second, acetic acid is oxidized into an unknown intermediate, which is then oxidized into CO2 and H2O. Finally, formic acid and oxalic acid can mutually interconvert when conditions are favorable.

  19. 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.

  20. Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention.

    PubMed

    Tuch, David S; Salat, David H; Wisco, Jonathan J; Zaleta, Alexandra K; Hevelone, Nathanael D; Rosas, H Diana

    2005-08-23

    Humans exhibit significant interindividual variability in behavioral reaction time (RT) performance yet the underlying neural mechanisms for this variability remain largely unknown. It has been proposed that interindividual variability in RT performance may be due to differences in white matter (WM) physiological properties, although such a relationship has never been demonstrated in cortical projection or association pathways in healthy young adults. Using diffusion tensor MRI (DTI), we sought to test whether diffusion tensor fractional anisotropy (FA), a measure of the orientational coherence of water self-diffusion, is regionally correlated with RT on a visual self-paced choice RT (CRT) task. CRT was found to be significantly correlated with FA in projection and association pathways supporting visuospatial attention including the right optic radiation, right posterior thalamus, and right medial precuneus WM. Significant correlations were also observed in left superior temporal sulcus WM and the left parietal operculum. The lateralization of the CRT-FA correlation to right visual and parietal WM pathways is consistent with the specialization of right visual and parietal cortices for visuospatial attention. The localization of the CRT-FA correlations to predominantly visual and parietal WM pathways, but not to motor pathways or the corpus callosum indicates that individual differences in visual CRT performance are associated with variations in the WM underlying the visuospatial attention network as opposed to pathways supporting motor movement or interhemispheric transmission.

  1. 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

  2. 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.

  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. 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.

  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. Theoretical Study on Reaction Pathways Leading to CO and CO2 in the Pyrolysis of Resorcinol.

    PubMed

    Furutani, Yuki; Kudo, Shinji; Hayashi, Jun-Ichiro; Norinaga, Koyo

    2017-01-26

    Possible pathways for the pyrolysis of resorcinol with the formation of CO and CO2 as final products were proposed and evaluated using ab initio calculations. Our experimental study revealed that large quantities of CO2 are generated in the pyrolysis of 1,3-dihydroxybenzene (resorcinol), while the pyrolysis of the dihydroxybenzene isomers 1,2-dihydroxybenzene (catechol) and 1,4-dihydroxybenzene (hydroquinone) produces little CO2. The fate of oxygen atoms in catechol and hydroquinone was essentially the formation of CO. In the proposed pathways, the triplet ground state m-benzoquinone was generated initially from simultaneous cleavage of the two O-H bonds in resorcinol. Subsequently, the direct cleavage of a C-C bond of the m-benzoquinone diradical yields 2-oxidanylcyclopenta-2,4-dien-1-yl-methanone, which can be converted via two channels: release of CO from the aldehyde radical group and combination of the ketone radical and carbon atom in the aldehyde radical group to form the 6-oxabicyclo[3.2.0]hepta-2,4-dien-7-one, resulting in the release of CO2. Potential energy surfaces along the proposed reaction pathways were calculated employing the CBS-QB3 method, and the rate constants at the high-pressure limit were also evaluated based on transition-state theory to assess the feasibility of the proposed reaction pathways.

  7. Theoretical study of ignition reactions of linear symmetrical monoethers as potential diesel fuel additives: DFT calculations

    NASA Astrophysics Data System (ADS)

    Marrouni, Karim El; Abou-Rachid, Hakima; Kaliaguine, Serge

    This work investigates the chemical reactivity of four linear symmetrical monoethers with molecular oxygen. Such oxygenated compounds may be considered as potential diesel fuel additives in order to reduce the ignition delay in diesel fuel engines. For this purpose, a kinetic study is proposed to clarify the relation between the molecular structure of the fuel molecule and its ignition properties. To this end, DFT calculations were performed for these reactions using B3LYP/6-311G(d,p) and BH&HLYP/6-311G(d,p) to determine structures, energies, and vibrational frequencies of stationary points as well as activated complexes involved in each gas-phase combustion initiation reaction of the monoethers CH3OCH3, C2H5OC2H5, C3H7OC3H7, or C4H9OC4H9 with molecular oxygen. This theoretical kinetic study was carried out using electronic structure results and the transition state theory, to assess the rate constants for all studied combustion reactions. As it has been shown in our previous work [Abou-Rachid et al., J Mol Struct (Theochem) 2003, 621, 293], the cetane number (CN) of a pure organic molecule depends on the initiation rate of its homogeneous gas-phase reaction with molecular oxygen. Indeed, the calculated initiation rate constants of the H-abstraction process of linear monoethers with O2 show a very good correlation with experimental CN data of these pure compounds at T D 1,000 K. This temperature is representative of the operating conditions of a diesel fuel engine.0

  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. Kinetic Studies on the Reaction of Chlorosulfonyl Isocyanate with Monofluoralkenes: Experimental Evidence for Both Stepwise and Concerted Mechanisms, and a Pre-equilibrium Complex on the Reaction Pathway

    DTIC Science & Technology

    2012-12-14

    lactams that are readily reduced to β-lactams. Substitution of a vinyl hydrogen for a vinyl fluorine changes the dynamics for reaction with CSI so...hydrogen for a vinyl fluorine changes the dynamics for reaction with CSI so that a concerted pathway is favored. Rate constants were measured for...step pathway has not been demonstrated experimentally.3c In a recent paper, we found that substituting a hydrogen for a fluorine on the π-bond of an

  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

    2015-04-07

    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. Hydrothermal reaction kinetics and pathways of phenylalanine alone and in binary mixtures.

    PubMed

    Changi, Shujauddin; Zhu, Minghan; Savage, Phillip E

    2012-09-01

    We examined the behavior of phenylalanine in high-temperature water (HTW) at 220, 250, 280, and 350 °C. Under these conditions, the major product is phenylethylamine. The minor products include styrene and phenylethanol (1-phenylethanol and 2-phenylethanol), which appear at higher temperatures and longer batch holding times. Phenylethylamine forms via decarboxylation of phenylalanine, styrene forms via deamination of phenylethylamine, and phenylethanol forms via hydration of styrene. We quantified the molar yields of each product at the four temperatures, and the carbon recovery was between 80-100 % for most cases. Phenylalanine disappearance follows first-order kinetics with an activation energy of 144 ± 14 kJ mol⁻¹ and a pre-exponential factor of 10(12.4 ± 1.4)  min⁻¹. A kinetics model based on the proposed pathways was consistent with the experimental data. Effects of five different salts (NaCl, NaNO₃, Na₂ SO₄, KCl, K₂ HPO₄) and boric acid (H₃BO₃) on phenylalanine behavior at 250 °C have also been elucidated. These additives increase phenylalanine conversion, but decrease the yield of phenylethylamine presumably by promoting formation of high molecular weight compounds. Lastly, binary mixtures of phenylalanine and ethyl oleate have been studied at 350 °C and three different molar concentration ratios. The presence of phenylalanine enhances the conversion of ethyl oleate and molar yields of fatty acid. Higher concentration of ethyl oleate leads to increased deamination of phenylethylamine and hydration of styrene. Amides are also formed due to the interaction of oleic acid/ethyl oleate and phenylethylamine/ammonia and lead to a decrease in the fatty acid yields. Taken collectively, these results provide new insights into the reactions of algae during its hydrothermal liquefaction to produce crude bio-oil.

  12. 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

  13. 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

  14. The role of noninnocent solvent molecules in organocatalyzed asymmetric Michael addition reactions.

    PubMed

    Patil, Mahendra P; Sunoj, Raghavan B

    2008-01-01

    A proline-catalyzed asymmetric Michael addition between ketones and trans-beta-nitrostyrene was studied by using the density-functional theory with mPW1PW91 and B3LYP functionals. Improved insight into the enantio- and diastereoselective formation of gamma-nitroketones/-aldehydes is obtained through transition-state analysis. Consideration of the activation parameters obtained from gas-phase calculations and continuum solvation models failed to reproduce the reported experimental stereoselectivities for the reaction between cyclohexanone and 3-pentanone with trans-beta-nitrostyrene. The correct diastereo- and enantioselectivites were obtained only upon explicit inclusion of solvent molecules in the diastereomeric transition states that pertain to the C--C bond formation. Among the several transition-state models that were examined, the one that exhibits cooperative hydrogen-bonding interactions with two molecules of methanol could explain the correct stereochemical outcome of the Michael reaction. The change in differential stabilization that arises as a result of electrostatic and hydrogen-bonding interactions in the key transition states is identified as the contributing factor toward obtaining the correct diastereomer. This study establishes the importance of including explicit solvent molecules in situations in which the gas-phase and continuum models are inadequate in obtaining meaningful insight regarding experimental stereoselectivities.

  15. Dextran-based hydrogel formed by thiol-Michael addition reaction for 3D cell encapsulation.

    PubMed

    Liu, Zhen Qi; Wei, Zhao; Zhu, Xv Long; Huang, Guo You; Xu, Feng; Yang, Jian Hai; Osada, Yoshihito; Zrínyi, Miklós; Li, Jian Hui; Chen, Yong Mei

    2015-04-01

    Cell encapsulation in three-dimensional (3D) hydrogels can mimic native cell microenvironment and plays a major role in cell-based transplantation therapies. In this contribution, a novel in situ-forming hydrogel, Dex-l-DTT hydrogel ("l" means "linked-by"), by cross-linking glycidyl methacrylate derivatized dextran (Dex-GMA) and dithiothreitol (DTT) under physiological conditions, has been developed using thiol-Michael addition reaction. The mechanical properties, gelation process and degree of swelling of the hydrogel can be easily adjusted by changing the pH of phosphate buffer saline. The 3D cell encapsulation ability is demonstrated by encapsulating rat bone marrow mesenchymal stem cells (BMSCs) and NIH/3T3 fibroblasts into the in situ-forming hydrogel with maintained high viability. The BMSCs also maintain their differentiation potential after encapsulation. These results demonstrate that the Dex-l-DTT hydrogel holds great potential for biomedical field.

  16. Synthesis and characterization of polyacids from palm acid oil and sunflower oil via addition reaction.

    PubMed

    Zeimaran, Ehsan; Kadir, Mohammed Rafiq Abdul; Nor, Hussin Mohd; Kamarul, Tunku; Djordjevic, Ivan

    2013-12-15

    In this study aliphatic polyacids were synthesized using palm acid oil (PAO) and sunflower oil (SFO) via addition reaction technique. The synthesized materials were characterized using Fourier-transform infra-red (FTIR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) and thermo-gravimetric analysis (TGA). Mixing formic acid and hydrogen peroxide with PAO or SFO at the ratio 3:10:1 produced the lowest iodine value of 10.57 and 9.24 respectively, indicating the increase in epoxidization of both oils. Adding adipic acid to the epoxidized oils at a ratio of 1:10 increases the acid values of SFO and PAO to 11.22 and 6.73 respectively. The existence of multi-acid groups present in synthesized polyacid was confirmed by MALD-ToF-MS. This feature indicates a possible value to the biomaterials development.

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

    PubMed

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

    2016-08-05

    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.

  18. 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

    2014-11-06

    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.

  19. 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.

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

    DOE PAGES

    Rotavera, Brandon; Zádor, Judit; Welz, Oliver; ...

    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

  1. 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.

  2. Activation of methane by FeO+: determining reaction pathways through temperature-dependent kinetics and statistical modeling.

    PubMed

    Ard, Shaun G; Melko, Joshua J; Ushakov, Vladimir G; Johnson, Ryan; Fournier, Joseph A; Shuman, Nicholas S; Guo, Hua; Troe, Jürgen; Viggiano, Albert A

    2014-03-20

    The temperature dependences of the rate constants and product branching ratios for the reactions of FeO(+) with CH4 and CD4 have been measured from 123 to 700 K. The 300 K rate constants are 9.5 × 10(-11) and 5.1 × 10(-11) cm(3) s(-1) for the CH4 and CD4 reactions, respectively. At low temperatures, the Fe(+) + CH3OH/CD3OD product channel dominates, while at higher temperatures, FeOH(+)/FeOD(+) + CH3/CD3 becomes the majority channel. The data were found to connect well with previous experiments at higher translational energies. The kinetics were simulated using a statistical adiabatic channel model (vibrations are adiabatic during approach of the reactants), which reproduced the experimental data of both reactions well over the extended temperature and energy ranges. Stationary point energies along the reaction pathway determined by ab initio calculations seemed to be only approximate and were allowed to vary in the statistical model. The model shows a crossing from the ground-state sextet surface to the excited quartet surface with large efficiency, indicating that both states are involved. The reaction bottleneck for the reaction is found to be the quartet barrier, for CH4 modeled as -22 kJ mol(-1) relative to the sextet reactants. Contrary to previous rationalizations, neither less favorable spin-crossing at increased energies nor the opening of additional reaction channels is needed to explain the temperature dependence of the product branching fractions. It is found that a proper treatment of state-specific rotations is crucial. The modeled energy for the FeOH(+) + CH3 channel (-1 kJ mol(-1)) agrees with the experimental thermochemical value, while the modeled energy of the Fe(+) + CH3OH channel (-10 kJ mol(-1)) corresponds to the quartet iron product, provided that spin-switching near the products is inefficient. Alternative possibilities for spin switching during the reaction are considered. The modeling provides unique insight into the reaction mechanisms

  3. B-H bond activation using an electrophilic metal complex: insights into the reaction pathway.

    PubMed

    Kumar, Rahul; Jagirdar, Balaji R

    2013-01-07

    A highly electrophilic ruthenium center in the [RuCl(dppe)(2)][OTf] complex brings about the activation of the B-H bond in ammonia borane (H(3)N·BH(3), AB) and dimethylamine borane (Me(2)HN·BH(3), DMAB). At room temperature, the reaction between [RuCl(dppe)(2)][OTf] and AB or DMAB results in trans-[RuH(η(2)-H(2))(dppe)(2)][OTf], trans-[RuCl(η(2)-H(2))(dppe)(2)][OTf], and trans-[RuH(Cl)(dppe)(2)], as noted in the NMR spectra. Mixing the ruthenium complex and AB or DMAB at low temperature (198/193 K) followed by NMR spectral measurements as the reaction mixture was warmed up to room temperature allowed the observation of various species formed enroute to the final products that were obtained at room temperature. On the basis of the variable-temperature multinuclear NMR spectroscopic studies of these two reactions, the mechanistic insights for B-H bond activation were obtained. In both cases, the reaction proceeds via an η(1)-B-H moiety bound to the metal center. The detailed mechanistic pathways of these two reactions as studied by NMR spectroscopy are described.

  4. 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

  5. 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.

  6. 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.

  7. 1,4-Addition of TMSCCl₃ to nitroalkenes: efficient reaction conditions and mechanistic understanding.

    PubMed

    Wu, Na; Wahl, Benoit; Woodward, Simon; Lewis, William

    2014-06-16

    Improved synthetic conditions allow preparation of TMSCCl3 in good yield (70%) and excellent purity. Compounds of the type NBu4X [X=Ph3SiF2 (TBAT), F (tetrabutylammonium fluoride, TBAF), OAc, Cl and Br] act as catalytic promoters for 1,4-additions to a range of cyclic and acyclic nitroalkenes, in THF at 0-25 °C, typically in moderate to excellent yields (37-95%). TBAT is the most effective promoter and bromide the least effective. Multinuclear NMR studies ((1)H, (19)F, (13)C and (29)Si) under anaerobic conditions indicate that addition of TMSCCl3 to TBAT (both 0.13 M) at -20 °C, in the absence of nitroalkene, leads immediately to mixtures of Me3SiF, Ph3SiF and NBu4CCl3. The latter is stable to at least 0 °C and does not add nitroalkene from -20 to 0 °C, even after extended periods. Nitroalkene, in the presence of TMSCCl3 (both 0.13 M at -20 °C), when treated with TBAT, leads to immediate formation of the 1,4-addition product, suggesting the reaction proceeds via a transient [Me3Si(alkene)CCl3] species, in which (alkene) indicates an Si⋅⋅⋅O coordinated nitroalkene. The anaerobic catalytic chain is propagated through the kinetic nitronate anion resulting from 1,4 CCl3(-) addition to the nitroalkene. This is demonstrated by the fact that isolated NBu4[CH2=NO2] is an efficient promoter. Use of H2C=CH(CH2)2CH=CHNO2 in air affords radical-derived bicyclic products arising from aerobic oxidation.

  8. 1,4-Addition of TMSCCl3 to Nitroalkenes: Efficient Reaction Conditions and Mechanistic Understanding

    PubMed Central

    Wu, Na; Wahl, Benoit; Woodward, Simon; Lewis, William

    2014-01-01

    Improved synthetic conditions allow preparation of TMSCCl3 in good yield (70 %) and excellent purity. Compounds of the type NBu4X [X=Ph3SiF2 (TBAT), F (tetrabutylammonium fluoride, TBAF), OAc, Cl and Br] act as catalytic promoters for 1,4-additions to a range of cyclic and acyclic nitroalkenes, in THF at 0–25 °C, typically in moderate to excellent yields (37–95 %). TBAT is the most effective promoter and bromide the least effective. Multinuclear NMR studies (1H, 19F, 13C and 29Si) under anaerobic conditions indicate that addition of TMSCCl3 to TBAT (both 0.13 M) at −20 °C, in the absence of nitroalkene, leads immediately to mixtures of Me3SiF, Ph3SiF and NBu4CCl3. The latter is stable to at least 0 °C and does not add nitroalkene from −20 to 0 °C, even after extended periods. Nitroalkene, in the presence of TMSCCl3 (both 0.13 M at −20 °C), when treated with TBAT, leads to immediate formation of the 1,4-addition product, suggesting the reaction proceeds via a transient [Me3Si(alkene)CCl3] species, in which (alkene) indicates an Si⋅⋅⋅O coordinated nitroalkene. The anaerobic catalytic chain is propagated through the kinetic nitronate anion resulting from 1,4 CCl3− addition to the nitroalkene. This is demonstrated by the fact that isolated NBu4[CH2−NO2] is an efficient promoter. Use of H2C−CH(CH2)2CH−CHNO2 in air affords radical-derived bicyclic products arising from aerobic oxidation. PMID:24849249

  9. Detection of additional genes of the patulin biosynthetic pathway in Penicillium griseofulvum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genes in the patulin biosynthetic pathway are likely to be arranged in a cluster as has been found for biosynthetic pathways of other mycotoxins. The mycotoxin patulin, common in apples and apple juice, is most often associated with Penicillium expansum. However, of 15 fungal species capable of sy...

  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. 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

    2015-11-06

    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.

  12. Selectivity descriptors for the Michael addition reaction as obtained from density functional based approaches.

    PubMed

    Madjarova, G; Tadjer, A; Cholakova, Tz P; Dobrev, A A; Mineva, T

    2005-01-20

    Density functional (DF) based numerical approaches for computing orbital and atomic reactivity indices were employed in the study of selectivity descriptors for the 1,4 Michael addition reaction. To this aim, atomic and orbital Fukui indices and atomic softnesses for 2-arylmethylene-1,4-butanolides and N,N-disubstituted phenylacetamides were computed. Further on, these local selectivity descriptors have been rationalized in terms of the Pearson's hard-soft-acid-base principle to explain the observed regioselectivity. It is shown that the methods employed for local (atomic and orbital) reactivity index computations are useful and reliable for prediction of the regioselectivity upon conjugate addition of ambident nucleophiles to 2,3-unsaturated carboxylic esters. All the results reveal similar degree of localization/hardness of the 1,4-butanolides C4 and active alpha-carbon belonging to the N,N-dimethyl-phenylacetamide, while the soft alpha-carbon in LiCH2CN reacts with the soft C2 1,4-butanolide center.

  13. No impact of a phytogenic feed additive on digestion and unspecific immune reaction in piglets.

    PubMed

    Muhl, A; Liebert, F

    2007-10-01

    Two 35 day experiments were conducted to examine the influence of a commercial phytogenic feed additive (PFA) on nutrient digestibility and unspecific immune reaction of piglets in the post-weaning period. The PFA composition was inulin, an essential oil mix (carvacrol and thymol), chestnut meal (tannins), and cellulose powder as carrier substance. In each experiment, immediately after weaning 40 male castrated piglets were divided into four experimental groups (n = 10). Diets were based on wheat, barley, soy bean meal and fishmeal using lysine as the first limiting amino acid. In experiment 1, graded levels of the PFA were supplied (A: control; B: 0.05% PFA; C: 0.1% PFA; D: 0.15% PFA). Experiment 2 utilized equal diets with 0.1% of the PFA, but different lysine supply (A: control; B: 0.1% PFA; C: +0.35% lysine; D: 0.1% PFA + 0.35% lysine). At the end of the experimental period, acute phase proteins (APPs) haptoglobin and C-reactive protein were examined in individual blood plasma samples. Following each growth study, 16 animals (n = 4) were taken for sampling of ileal chyme and assessing of praecaecal digestibility of protein and amino acids. In addition, digesta samples of the duodenum and the total pancreatic tissue were utilized for determining the enzyme activity of alpha-amylase and trypsin. APP, praecaecal digestibility and enzyme activities did not significantly respond to the PFA supplementaion in diets.

  14. 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.

  15. Phosphorylation of the MAPK pathway has an essential role in the acrosome reaction in miniature pig sperm.

    PubMed

    Kawano, N; Ito, J; Kashiwazaki, N; Yoshida, M

    2010-04-01

    In almost all animal species, sperm acrosome reaction (AR) is a crucial step for fertilization. The step is a Ca(2+)-dependent secretory event that must be completed before fertilization. Many researchers have reported that several chemicals (such as ionomycin, thapsigargin and caffeine) artificially induce this step by increasing [Ca(2+)](i). However, little information has been known on events that occur following Ca(2+) induced initiation of the sperm AR. We show here for the first time that phosphorylation of the mitogen-activated protein kinase (MAPK) pathway is required for the AR in miniature pig sperm. Following caffeine treatment artificially inducing the AR in miniature pig sperm, Raf was phosphorylated and then MAP kinase kinase (MEK) and extracellular-signal regulated kinase 1 (ERK1) were also phosphorylated in a time-dependent manner. However, the total ERK1 level did not change during the culture. Pre-treatment of sperm with U0126, a MEK inhibitor, significantly suppressed both the AR and phosphorylation of MEK/ERK1 in a dose-dependent manner. Additionally, pre-incubation of the sperm with seminal vesicle (SV) fluid, which is known to contain a decapacitation factor, suppressed both the AR and MEK/ERK1 phosphorylation. These results suggest that phosphorylation of MAPK pathway plays an important role in the AR in miniature pig sperm. Moreover, the SV fluid may have an inhibitory effect on the AR via the suppression of the MAPK pathway.

  16. 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...

  17. Lewis acid promoted reactions of ethenetricarboxylates with allenes: synthesis of indenes and gamma-lactones via conjugate addition/cyclization reaction.

    PubMed

    Yamazaki, Shoko; Yamamoto, Yuko; Fukushima, Yugo; Takebayashi, Masachika; Ukai, Tetsuma; Mikata, Yuji

    2010-08-06

    Indenes are important core structures in organic chemistry. Few simple arylallenes have been used to construct indene skeletons by Friedel-Crafts reaction. Lewis acid catalyzed reaction of ethenetricarboxylates 1 and arylallenes has been examined in this study. The reaction of arylallenes and ethenetricarboxylate triesters with SnCl(4) gave indene derivatives efficiently, via a conjugate addition/Friedel-Crafts cyclization reaction. On the other hand, the reactions of 1,1-diethyl 2-hydrogen ethenetricarboxylate and arylallenes or alkylallenes with SnCl(4) at -78 degrees C or room temperature and subsequent treatment with Et(3)N gave gamma-lactones. The reactions of triethyl ethenetricarboxylate and 1,1-dialkylallenes with SnCl(4) at room temperature also gave gamma-lactones.

  18. Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways

    NASA Astrophysics Data System (ADS)

    Mathew, Kiran; Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

    2014-02-01

    Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  20. Gas-Phase Oxidation via Ion/Ion Reactions: Pathways and Applications

    NASA Astrophysics Data System (ADS)

    Pilo, Alice L.; Zhao, Feifei; McLuckey, Scott A.

    2017-01-01

    Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O]+ derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O]+, [M-H]+, and [M-H-NH3]+ species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared. Lastly, the highly efficient generation of molecular radical cations via ion/ion reactions with sulfate radical anion is summarized. Activation of the newly generated molecular radical peptide cations results in losses of various neutral side chains, several of which generate dehydroalanine residues that can be used to localize the amino acid from which the dehydroalanine was generated. The chemistries presented herein result in a diverse range of structures that can be used for a variety of applications, including the identification and localization of S-alkyl cysteine residues, the oxidative cleavage of disulfide bonds, and the generation of molecular radical cations from even-electron doubly protonated peptides.

  1. Catalytic asymmetric tandem Friedel-Crafts alkylation/Michael addition reaction for the synthesis of highly functionalized chromans.

    PubMed

    Peng, Jiahuan; Du, Da-Ming

    2013-01-01

    The enantioselective tandem Friedel-Crafts alkylation/Michael addition reaction of indoles with nitroolefin enoates catalyzed by a diphenylamine-linked bis(oxazoline)-Zn(OTf)2 complex was investigated. This tandem reaction afforded functionalized chiral chromans in good yields with moderate to high stereoselectivities (up to 95:5 dr, up to 99% ee).

  2. Interactions of fluoroquinolone antibacterial agents with aqueous chlorine: reaction kinetics, mechanisms, and transformation pathways.

    PubMed

    Dodd, Michael C; Shah, Amisha D; von Gunten, Urs; Huang, Ching-Hua

    2005-09-15

    Kinetics, products, and mechanistic aspects of reactions between free available chlorine (HOCl/OCl-), ciprofloxacin (CF), and enrofloxacin (EF) were extensively investigated to elucidate the behavior of fluoroquinolone antibacterial agents during water chlorination processes. Although the molecular structures of these two substrates differ only with respect to degree of N(4) amine alkylation, CF and EF exhibit markedly different HOCl reaction kinetics and transformation pathways. HOCI reacts very rapidly at CF's secondary N(4) amine, forming a chloramine intermediate that spontaneously decays in aqueous solution by concerted piperazine fragmentation. In contrast, HOCl reacts relatively slowly at EF's tertiary N(4) amine, apparently forming a highly reactive chlorammonium intermediate (R3N-(4)Cl+) that can catalytically halogenate EF or other substrates present in solution. Flumequine, a fluoroquinolone that lacks the characteristic piperazine ring, exhibits no apparent reactivity toward HOCI but appears to undergo facile halodecarboxylation in the presence of R3N(4)-Cl+ species derived from EF. Measured reaction kinetics were validated in real water matrixes by modeling CF and EF losses in the presence of free chlorine residuals. Combined chlorine (CC) kinetics were determined under selected conditions to evaluate the potential significance of reactions with chloramines. CF's rapid kinetics in direct reactions with HOCl, and relatively high reactivity toward CC, indicate that secondary amine-containing fluoroquinolones should be readily transformed during chlorination of real waters, whether applied chlorine doses are present as free or combined residuals. However, EF's slower HOCl reaction kinetics, recalcitrance toward CC, and participation in the catalytic halogenation cycle described herein suggest that tertiary amine-containing fluoroquinolones will be comparatively stable during most full-scale water chlorination processes.

  3. 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

  4. Ruthenium-catalyzed decarbonylative addition reaction of anhydrides with alkynes: a facile synthesis of isocoumarins and α-pyrones.

    PubMed

    Prakash, Rashmi; Shekarrao, Kommuri; Gogoi, Sanjib; Boruah, Romesh C

    2015-06-21

    A novel ruthenium catalyzed straightforward and efficient synthesis of isocoumarin and α-pyrone derivatives has been accomplished by the decarbonylative addition reaction of anhydrides with alkynes under thermal conditions.

  5. 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.

  6. 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.

  7. 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

    2008-10-08

    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.

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  10. Catalytic enantioselective Friedel-Crafts/Michael addition reactions of indoles to ethenetricarboxylates.

    PubMed

    Yamazaki, Shoko; Iwata, Yuko

    2006-01-20

    [reaction: see text] The Friedel-Crafts reaction is an important reaction for the formation of new C-C bonds. Recently, catalytic enantioselective Friedel-Crafts reaction of alkylidene malonates has been reported. However, the substituents in alkylidene malonates are limited. To explore new substituents such as carboxyl and carbonyl groups, catalytic enantioselective Friedel-Crafts reactions of reactive ethenetricarboxylates and acyl-substituted methylenemalonates 1 were investigated. The reaction of 1 with indoles in the presence of catalytic amounts of chiral bisoxazoline copper(II) complex (10%) in THF at room temperature gave alkylated products in high yields and up to 95% ee. The enantioselectivity can be explained by the secondary orbital interaction on approach of indole to the less hindered side of the 1-Cu(II)-ligand complex.

  11. Correlation of Pt-Re Surface Properties with Reaction Pathways for the Aqueous-Phase Reforming of Glycerol

    SciTech Connect

    Zhang, Liang; Karim, Ayman M.; Engelhard, Mark H.; Wei, Zhehao; King, D. L.; Wang, Yong

    2012-01-17

    The surface properties of Pt-Re catalytic nano-particles supported on carbon following exposure to a hydrogen reducing environment and subsequent hydrothermal conditions have been studied using in-situ X-ray photoelectron spectroscopy (XPS) and ammonia temperature programmed desorption (TPD). These properties have been correlated with the catalyst selectivity for the aqueous phase reforming of glycerol. We show that Pt in reduced Pt-Re/C becomes electron deficient, and a fraction of the Re becomes oxidized when the catalyst is subsequently exposed to hydrothermal reaction conditions. Oxidation of Pt-Re generates surface acidity, which drastically affects the reaction pathways. The acid site concentration, but not acid site strength, increases with Re loading. This acidity increase with Re addition favors C-O over C-C cleavage, which results in higher selectivity to liquid products and alkanes at the expense of hydrogen production. We propose a model for the Pt-Re active site and the origin of acidity enhanced by the addition of Re.

  12. 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.

  13. 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.

  14. Synthesis of polyhydroxylated decalins via two consecutive one-pot reactions: 1,4-addition/aldol reaction followed by RCM/syn-dihydroxylation.

    PubMed

    Malik, Michał; Jarosz, Sławomir

    2016-01-01

    Synthesis of novel polyhydroxylated derivatives of decalin is described. The presented methodology consists in a one-pot copper-catalyzed 1,4-addition of vinylmagnesium bromide to sugar-derived cyclohexenone, followed by an aldol reaction with a derivative of but-3-enal. The obtained diene is then subjected to an assisted tandem catalytic sequence: ring-closing metathesis with the subsequent reuse of the Ru-catalyst in the syn-dihydroxylation. The stereochemical outcome of these reactions is discussed.

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Vikas, Kaur, Gurpreet

    2013-12-01

    C6H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C6H is explored to search isomers of C6H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C6H. The reaction route search is performed through global reaction route mapping method, which utilizes an uphill walking technique based on an anharmonic downward distortion following approach to search intermediates and transition states. The computations performed at the CASSCF/aug-cc-pVTZ, CCSD(T)/6-311++G(d,p)//DFT/B3LYP/6-311++G(d,p), and DFT/B3LYP/aug-cc-pVTZ levels of the theory identified 14 isomers (including 8 new isomeric forms of C6H) and 28 transition states. Most of the identified isomers are found to have significant multireference character. The kinetic stability and natural bond orbital analysis of the identified isomers is also investigated. The isomeric forms are further characterized using spectral analysis involving rotational constants, vibrational frequencies, and Raman scattering activities as well as analyzing the effect of isotopic substitution of hydrogen on the spectral features. This study proposes that the linear-C6H can readily isomerize to a six-member ring isomer.

  18. 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

  19. Reaction Dynamics in Astrochemistry: Low-Temperature Pathways to Polycyclic Aromatic Hydrocarbons in the Interstellar Medium

    NASA Astrophysics Data System (ADS)

    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.

  20. 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.

  1. 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.

  2. Unprecedented chemical reactivity of a paramagnetic endohedral metallofullerene La@C(s)-C82 that leads hydrogen addition in the 1,3-dipolar cycloaddition reaction.

    PubMed

    Takano, Yuta; Slanina, Zdenek; Mateos, Jaime; Tsuchiya, Takayoshi; Kurihara, Hiroki; Uhlik, Filip; Herranz, María Ángeles; Martín, Nazario; Nagase, Shigeru; Akasaka, Takeshi

    2014-12-17

    Synthesizing unprecedented diamagnetic adducts of an endohedral metallofullerene was achieved by using 1,3-dipolar cycloaddition reaction of paramagnetic La@C(s)-C82 with a simultaneous hydrogen addition. The selective formation of two main products, La@C(s)-C82HCMe2NMeCHPh (2a and 2b), was first detected by HPLC analysis and MALDI-TOF mass spectrometry. 2a and 2b-O, which was readily formed by the oxidation of 2b, were isolated by multistep HPLC separation and were fully characterized by spectroscopic methods, including 1D and 2D-NMR, UV-vis-NIR measurements and electrochemistry. The hydrogen atom was found to be connected to the fullerene cage directly in the case of 2a, and the redox behavior indicated that the C-H bond can still be readily oxidized. The reaction mechanism and the molecular structures of 2a and 2b were reasonably proposed by the interplay between experimental observations and DFT calculations. The feasible order of the reaction process would involve a 1,3-dipolar cycloaddition followed by the hydrogen addition through a radical pathway. It is concluded that the characteristic electronic properties and molecular structure of La@C(s)-C82 resulted in a site-selective reaction, which afforded a unique chemical derivative of an endohedral metallofullerene in high yields. Derivative 2a constitutes the first endohedral metallofullerene where the direct linking of a hydrogen atom has been structurally proven.

  3. 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)

  4. 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

  5. Pathway and kinetic analysis on the iso-propyl radical + O{sub 2} reaction system

    SciTech Connect

    Bozzelli, J.W.; Pitz, W.J.

    1997-04-07

    We analyze the isopropyl + 02 reaction system using thermochemical Transition State Theory (TST), molecular thermodynamic properties, analysis (quantum RRK) for k(E) and modified strong collision analyze Cyclic transition states for both hydrogen transfer and concerted propylene from isopropylperoxy are calculated using semi-empirical theory in addition to transition states for H02 elimination from hydroperoxy-isopropyl. Computed rate constants are compared to constant measurements of for isopropyl + H02.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Noble metal-free hydrazine fuel cell catalysts: EPOC effect in competing chemical and electrochemical reaction pathways.

    PubMed

    Sanabria-Chinchilla, Jean; Asazawa, Koichiro; Sakamoto, Tomokazu; Yamada, Koji; Tanaka, Hirohisa; Strasser, Peter

    2011-04-13

    We report the discovery of a highly active Ni-Co alloy electrocatalyst for the oxidation of hydrazine (N(2)H(4)) and provide evidence for competing electrochemical (faradaic) and chemical (nonfaradaic) reaction pathways. The electrochemical conversion of hydrazine on catalytic surfaces in fuel cells is of great scientific and technological interest, because it offers multiple redox states, complex reaction pathways, and significantly more favorable energy and power densities compared to hydrogen fuel. Structure-reactivity relations of a Ni(60)Co(40) alloy electrocatalyst are presented with a 6-fold increase in catalytic N(2)H(4) oxidation activity over today's benchmark catalysts. We further study the mechanistic pathways of the catalytic N(2)H(4) conversion as function of the applied electrode potential using differentially pumped electrochemical mass spectrometry (DEMS). At positive overpotentials, N(2)H(4) is electrooxidized into nitrogen consuming hydroxide ions, which is the fuel cell-relevant faradaic reaction pathway. In parallel, N(2)H(4) decomposes chemically into molecular nitrogen and hydrogen over a broad range of electrode potentials. The electroless chemical decomposition rate was controlled by the electrode potential, suggesting a rare example of a liquid-phase electrochemical promotion effect of a chemical catalytic reaction ("EPOC"). The coexisting electrocatalytic (faradaic) and heterogeneous catalytic (electroless, nonfaradaic) reaction pathways have important implications for the efficiency of hydrazine fuel cells.

  11. Visible-Light-Initiated Thiol-Michael Addition Polymerizations with Coumarin-Based Photobase Generators: Another Photoclick Reaction Strategy.

    PubMed

    Zhang, Xinpeng; Xi, Weixian; Wang, Chen; Podgórski, Maciej; Bowman, Christopher N

    2016-02-16

    An efficient visible-light-sensitive photobase generator for thiol-Michael addition reactions was synthesized and evaluated. This highly reactive catalyst was designed by protecting a strong base (tetramethyl guanidine, TMG) with a visible-light-responsive group which was a coumarin derivative. The coumarin-coupled TMG was shown to exhibit extraordinary catalytic activity toward initiation of the thiol-Michael reaction, including thiol-Michael addition-based polymerization, upon visible-light irradiation, leading to a stoichiometric reaction of both thiol and vinyl functional groups. Owing to its features, this visible-light photobase generator enables homogeneous network formation in thiol-Michael polymerizations and also has the potential to be exploited in other visible-light-induced, base-catalyzed thiol-click processes such as thiol-isocynate and thiol-epoxy network-forming reactions.

  12. 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.

  13. 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.

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

    SciTech Connect

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

    2016-02-23

    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). Lastly, the ability to dissociate H2 on Ni/Cu(111) is also an important factor for enhancing the HDO activity over Cu(111).

  15. 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).

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

    DOE PAGES

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

    2016-02-23

    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)more » through an η2(C,O) configuration which led to the HDO of furfural on Ni/Cu(111). Lastly, the ability to dissociate H2 on Ni/Cu(111) is also an important factor for enhancing the HDO activity over Cu(111).« less

  17. Reaction pathways for hydrogen desorption from magnesium hydride/hydroxide composites: bulk and interface effects.

    PubMed

    Leardini, F; Ares, J R; Bodega, J; Fernández, J F; Ferrer, I J; Sánchez, C

    2010-01-21

    This manuscript investigates the thermal desorption behaviour of MgH(2)/Mg(OH)(2) composites by means of thermal desorption spectroscopy. Besides the H(2)O and H(2) desorption events due to Mg(OH)(2) dehydration and MgH(2) decomposition reactions, respectively, two additional H(2) desorption peaks arise at lower temperatures. These peaks are related to solid-state reactions between magnesium hydride and magnesium hydroxide through different channels. The low temperature H(2) peak ( approximately 150 degrees C) is related to reaction between a H atom diffusing from MgH(2) and a surface OH group, whereas the intermediate temperature H(2) peak ( approximately 350 degrees C) is due to an interface reaction between the hydride and the hydroxide. The present work supports the theory that the onset of the H(2) desorption coming from MgH(2) decomposition is controlled by an incubation process, consisting in the formation of catalytically active vacancies at the MgO/Mg(OH)(2) surface by dehydration. Possible ways to improve the H(2) desorption kinetics from MgH(2) are discussed in the light of the results obtained.

  18. Photocatalytic degradation of pesticide methomyl: determination of the reaction pathway and identification of intermediate products.

    PubMed

    Tamimi, M; Qourzal, S; Assabbane, A; Chovelon, J-M; Ferronato, C; Ait-Ichou, Y

    2006-05-01

    The degradation of pesticide methomyl in aqueous solution by UV-irradiation in the presence of TiO2 "Degussa P-25" has been studied. It was found that mineralisation to carbon dioxide, water, sulfate and ammonia took place during the process. The rate of photodecomposition of methomyl was measured using high performance liquid chromatography (HPLC), while its mineralization was followed using ion chromatography (IC), and total organic carbon (TOC) analysis. The identification of reaction intermediate products was carried out using coupled techniques HPLC-MS (electrospray ionization in positive mode) and a degradation pathway was proposed. Under our conditions, complete disappearance of 1.23 x 10(-4) mol l(-1) of pure pesticide occurred within 45 min of illumination and 80% TOC removal occurred in less than 4 h. Three main intermediates were identified resulting from (i) the rupture of the ester bond (or the N-O bond), (ii) the hydroxylation of methyl group borne by the nitrogen atom and (iii) the product resulting from the decarboxylation of the oxidized hydroxylated methyl group (photo-Kolbe reaction). In order to be sure that the photocatalytic results were consistent, hydrolysis and photolysis tests were performed. Photocatalysis proved to be an excellent new advanced oxidation technology (AOT) to eliminate methomyl present in water.

  19. 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.

  20. Excited-state reaction pathways for s-cis buta-1,3-diene

    NASA Astrophysics Data System (ADS)

    Celani, Paolo; Bernardi, Fernando; Olivucci, Massimo; Robb, Michael A.

    1995-04-01

    The topology and energetics of the potential energy surfaces associated with the 2A1 and 1B2 valence excited states of s-cis butadiene have been investigated via ab initio quantum chemical computations at a level of theory which includes dynamic correlation effects and extended basis sets. The results support a photochemical ring-closure mechanism involving 1B2 and 2A1 reaction/relaxation pathways that are disrotatory. The reaction path on the 2A1 surface begins at a 1B2/2A1 conical intersection and the ground state photoproducts are produced via radiationless decay at a second 2A1/1A1 conical intersection which has been documented in a previous publication. A local Cs equilibrium structure on 1B2 potential energy surface has been optimized using the complete active space-self-consistent field and configuration interaction singles methods. The 1B2/2A1 conical intersection is located near this Cs equilibrium structure and offers a rationalization of the experimentally observed femtosecond lifetime of this state. The observed preferential disrotatory stereochemistry appears to be simply determined by a difference in the energy barriers located along the 2A1 disrotatory and conrotatory paths. This finding is in contrast with the generally accepted notion that the stereochemistry is determined by a different rate of internal conversion at a ``disrotatory'' and ``conrotatory'' avoided crossing minima. Indeed, no avoided crossing can be located along the 2A1 paths.

  1. Titanium dioxide-mediated heterogeneous photocatalytic degradation of terbufos: parameter study and reaction pathways.

    PubMed

    Wu, Ren-Jang; Chen, Chiing-Chang; Chen, Ming-Hung; Lu, Chung-Shin

    2009-03-15

    The photocatalytic degradation of terbufos in aqueous suspensions was investigated by using titanium dioxide (TiO(2)) as a photocatalyst. About 99% of terbufos was degraded after UV irradiation for 90 min. Factors such as pH of the system, TiO(2) dosage, and presence of anions were found to influence the degradation rate. Photodegradation of terbufos by TiO(2)/UV exhibited pseudo-first-order reaction kinetics, and a reaction quantum yield of 0.289. The electrical energy consumption per order of magnitude for photocatalytic degradation of terbufos was calculated and showed that a moderated efficiency (E(EO)=71 kWh/(m(3)order)) was obtained in TiO(2)/UV process. To obtain a better understanding of the mechanistic details of this TiO(2)-assisted photodegradation of terbufos with UV irradiation, the intermediates of the processes were separated, identified, and characterized by the solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS) technique. The probable photodegradation pathways were proposed and discussed.

  2. Levofloxacin ozonation in water: rate determining process parameters and reaction pathway elucidation.

    PubMed

    Witte, Bavo De; Langenhove, Herman Van; Hemelsoet, Karen; Demeestere, Kristof; Wispelaere, Patrick De; Van Speybroeck, Veronique; Dewulf, Jo

    2009-07-01

    Ozonation of the quinolone antibiotic levofloxacin was investigated with focus on both the levofloxacin degradation rate and degradation product formation. Degradation was about 2 times faster at pH 10 compared to pH 3 and 7 explained by direct ozonation at the unprotonated N4('), one of the tertiary amines of the piperazinyl substituent. H2O2 concentration (2-100 microM) had only limited effect. Liquid chromatography - high resolution mass spectrometry revealed degradation at the piperazinyl substituent and the quinolone moiety, with the relative importance of both pathways being strongly affected by changes in pH. Levofloxacin N-oxide concentrations reached up to 40% of the initial levofloxacin concentration during ozonation at pH 10. Degradation at the quinolone moiety resulted in isatin and anthranilic acid type metabolites, probably formed through reaction with hydroxyl radicals. Ab initio molecular orbital calculations predicted radical attack mainly at C2 of the quinolone moiety. This is the carbon atom with the largest Fukui function. Reaction with ozone is expected to mainly occur at N(4)('), characterized by the largest negative charge.

  3. 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

  4. 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.

  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. Catalytic asymmetric aldol addition reactions of 3-fluoro-indolinone derived enolates.

    PubMed

    Zhang, Lijun; Zhang, Wenzhong; Mei, Haibo; Han, Jianlin; Soloshonok, Vadim A; Pan, Yi

    2017-01-04

    Reported herein is a Cu(i)/bisoxazoline ligand-catalyzed aldol reaction of unprotected tertiary enolates generated in situ from 3-(1,1-dihydroxy-2,2,2-trifluoroethyl)-substituted derivatives of 3-fluoro-2-oxindoles. A range of α-fluoro-β-aryl/hetaryl/alkyl-β-hydroxy-indolin-2-ones containing C-F quaternary stereogenic centers of high pharmaceutical importance were furnished in good yields and satisfactory diastereo- and enantioselectivities. The reactions were conducted under operationally convenient conditions and displayed wide substrate/functional group generality including unprotected N-H on the tertiary enolates, and aromatic, hetero-aromatic and aliphatic aldehydes.

  7. 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

    2008-10-09

    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

  8. 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.

  9. Effects of additives on the oscillations of the Briggs-Rauscher reaction

    NASA Astrophysics Data System (ADS)

    Cervellati, R.; Furrow, S. D.

    2013-12-01

    Perturbations with chemical species that have dissimilar physico-chemical properties, such as bromide ions, polyphenols or iron complexes, are often used to investigate the detailed molecular mechanism of the Briggs-Rauscher (BR) oscillating reaction. We describe in this review the effects caused by some of these species and present their mechanistic interpretations. Some new original results are also reported.

  10. 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.

  11. Synthesis of polyhydroxylated decalins via two consecutive one-pot reactions: 1,4-addition/aldol reaction followed by RCM/syn-dihydroxylation

    PubMed Central

    2016-01-01

    Synthesis of novel polyhydroxylated derivatives of decalin is described. The presented methodology consists in a one-pot copper-catalyzed 1,4-addition of vinylmagnesium bromide to sugar-derived cyclohexenone, followed by an aldol reaction with a derivative of but-3-enal. The obtained diene is then subjected to an assisted tandem catalytic sequence: ring-closing metathesis with the subsequent reuse of the Ru-catalyst in the syn-dihydroxylation. The stereochemical outcome of these reactions is discussed. PMID:28144329

  12. Co-liquefaction of swine manure and crude glycerol to bio-oil: model compound studies and reaction pathways.

    PubMed

    Ye, Zhangying; Xiu, Shuangning; Shahbazi, Abolghasem; Zhu, Songming

    2012-01-01

    The reaction pathways of co-liquefaction of swine manure and crude glycerol to bio-oil (ester compounds) were investigated. Swine manure was hydrothermal treated (340 °C, 27.5 MPa, 15 min) with a number of model compounds in a high pressure batch reactor under inert atmosphere. The compounds were methanol, pure glycerol, mixture of pure glycerol, pure methanol and H(2)O, and commercial fatty acids (linoleic acid). The chemical composition of the bio-oil was analyzed by GC/MS. Glycerol, methanol and water showed synergistic effects on manure liquefaction, increasing the oil yield as high as 65%. A maximum oil yield of 79.96% was obtained when linoleic acid reacted with swine manure. Based on the results, the reaction pathways were proposed. Esterification reactions occurred not only because the crude glycerol have methanol, but also because methanol can be produced from hydrothermal reactions of glycerol.

  13. Examining the robustness of first-principles calculations for metal hydride reaction thermodynamics by detection of metastable reaction pathways.

    PubMed

    Kim, Ki Chul; Kulkarni, Anant D; Johnson, J Karl; Sholl, David S

    2011-12-28

    First principles calculations have played a useful role in screening mixtures of complex metal hydrides to find systems suitable for H(2) storage applications. Standard methods for this task efficiently identify the lowest energy reaction mechanisms among all possible reactions involving collections of materials for which DFT calculations have been performed. The resulting mechanism can potentially differ from physical reality due to inaccuracies in the DFT functionals used, or due to other approximations made in estimating reaction free energies. We introduce an efficient method to probe the robustness of DFT-based predictions that relies on identifying reactions that are metastable relative to the lowest energy reaction path predicted with DFT. An important conclusion of our calculations is that in many examples DFT cannot unambiguously predict a single reaction mechanism for a well defined metal hydride mixture because two or more mechanisms have reaction energies that differ by a small amount. Our approach is illustrated by analyzing a series of single step reactions identified in our recent work that examined reactions with a large database of solids [Kim et al., Phys. Chem. Chem. Phys. 2011, 13, 7218].

  14. 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.

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

    PubMed

    Kos, Pavlo; Plenio, Herbert

    2015-11-02

    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.

  16. 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.

  17. 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.

  18. Rapid reaction of superoxide with insulin-tyrosyl radicals to generate a hydroperoxide with subsequent glutathione addition.

    PubMed

    Das, Andrew B; Nauser, Thomas; Koppenol, Willem H; Kettle, Anthony J; Winterbourn, Christine C; Nagy, Péter

    2014-05-01

    Tyrosine (Tyr) residues are major sites of radical generation during protein oxidation. We used insulin as a model to study the kinetics, mechanisms, and products of the reactions of radiation-induced or enzyme-generated protein-tyrosyl radicals with superoxide to demonstrate the feasibility of these reactions under oxidative stress conditions. We found that insulin-tyrosyl radicals combined to form dimers, mostly via the tyrosine at position 14 on the α chain (Tyr14). However, in the presence of superoxide, dimerization was largely outcompeted by the reaction of superoxide with insulin-tyrosyl radicals. Using pulse radiolysis, we measured a second-order rate constant for the latter reaction of (6±1) × 10(8) M(-1) s(-1) at pH 7.3, representing the first measured rate constant for a protein-tyrosyl radical with superoxide. Mass-spectrometry-based product analyses revealed the addition of superoxide to the insulin-Tyr14 radical to form the hydroperoxide. Glutathione efficiently reduced the hydroperoxide to the corresponding monoxide and also subsequently underwent Michael addition to the monoxide to give a diglutathionylated protein adduct. Although much slower, conjugation of the backbone amide group can form a bicyclic Tyr-monoxide derivative, allowing the addition of only one glutathione molecule. These findings suggest that Tyr-hydroperoxides should readily form on proteins under oxidative stress conditions where protein radicals and superoxide are both generated and that these should form addition products with thiol compounds such as glutathione.

  19. A Rh(II)-catalyzed multicomponent reaction by trapping an α-amino enol intermediate in a traditional two-component reaction pathway

    PubMed Central

    Liu, Shunying; Yao, Wenfeng; Liu, Yuan; Wei, Qinghua; Chen, Jianghui; Wu, Xiang; Xia, Fei; Hu, Wenhao

    2017-01-01

    Multicomponent reactions (MCRs) represent an ideal organic synthesis tool for the rapid construction of complex molecules due to their step and atom economy. Compared to two-component reactions, the development of new MCRs has been greatly limited during the 170 years since the first MCR was reported. Theoretically, the trapping of an active intermediate generated from two components by a third component could change the traditional two-component reaction pathway, leading to the discovery of MCRs. We report an example of the trapping of α-imino enols generated in situ from 1-sulfonyl-1,2,3-triazoles via α-imino metal carbene species by vinylimine ions using C(2)-substituted indoles and paraformaldehyde as precursors in the presence of a rhodium(II) catalyst. The traditional enol-ketone transformation pathway was suspended by the trapping procedure and efficiently switched to an MCR pathway to produce α-amino-β-indole ketones in moderate to good yields. Unexpectedly, the resulting products and the theoretical density functional theory (DFT) calculation results indicated that the enolic carbon had a stronger nucleophilicity than the well-known traditional enamic carbon in the trapping process. The reaction mechanism was investigated using control experiments and detailed DFT calculations, and the synthetic application of the products was also illustrated. The developed strategy provides a mild and rapid access to α-amino-β-indole ketones and suggests a rationale for the discovery of MCRs by trapping an active intermediate with a third component in a traditional two-component reaction pathway. PMID:28345053

  20. Reaction of Chlorosulfonyl Isocyanate (CSI) with Fluorosubstituted Alkenes: Evidence of a Concerted Pathway for Reaction of CSI with Fluorosubstituted Alkenes (Preprint)

    DTIC Science & Technology

    2010-06-01

    ABSTRACT Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with monofluoroalkenes. A vinyl fluorine atom on...SO2Cl R F O ‡ N SO2Cl F R O Abstract: Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with...monofluoroalkenes. A vinyl fluorine atom on an alkene raises the energy of a step-wise transition state more than the energy of the competing concerted

  1. Rapid-reaction kinetic characterization of the pathway of streptokinase-plasmin catalytic complex formation.

    PubMed

    Verhamme, Ingrid M; Bock, Paul E

    2008-09-19

    Binding of the fibrinolytic proteinase plasmin (Pm) to streptokinase (SK) in a tight stoichiometric complex transforms Pm into a potent proteolytic activator of plasminogen. SK binding to the catalytic domain of Pm, with a dissociation constant of 12 pm, is assisted by SK Lys(414) binding to a Pm kringle, which accounts for a 11-20-fold affinity decrease when Pm lysine binding sites are blocked by 6-aminohexanoic acid (6-AHA) or benzamidine. The pathway of SK.Pm catalytic complex formation was characterized by stopped-flow kinetics of SK and the Lys(414) deletion mutant (SKDeltaK414) binding to Pm labeled at the active site with 5-fluorescein ([5F]FFR-Pm) and the reverse reactions by competitive displacement of [5F]FFR-Pm with active site-blocked Pm. The rate constants for the biexponential fluorescence quenching caused by SK and SKDeltaK414 binding to [5F]FFR-Pm were saturable as a function of SK concentration, reporting encounter complex affinities of 62-110 nm in the absence of lysine analogs and 4900-6500 and 1430-2200 nm in the presence of 6-AHA and benzamidine, respectively. The encounter complex with SKDeltaK414 was approximately 10-fold weaker in the absence of lysine analogs but indistinguishable from that of native SK in the presence of 6-AHA and benzamidine. The studies delineate for the first time the sequence of molecular events in the formation of the SK.Pm catalytic complex and its regulation by kringle ligands. Analysis of the forward and reverse reactions supports a binding mechanism in which SK Lys(414) binding to a Pm kringle accompanies near-diffusion-limited encounter complex formation followed by two slower, tightening conformational changes.

  2. 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.

  3. Additive Manufacturing: Building the Pathway Towards Process and Material Qualification”

    DOE PAGES

    Carpenter, John S.; Beese, Allison M.; Bourell, David L.; ...

    2016-06-14

    The potential benefits of metal additive manufacturing, as compared with more traditional, subtractive-only approaches, has created excitement within design circles seeking to take advantage of the ability to build and repair complex shapes, to integrate or consolidate multiple parts and minimize joining concerns, and to locally tailor material properties to increase functionality. Tempering the excitement of designers, however, has been concerns with the material deposited by the process. It is not enough for a part to ‘look’ right from a geometric perspective. Rather, the metallurgical aspects associated with the material being deposited must ‘look’ and ‘behave’ correctly along with themore » aforementioned geometric accuracy. Finally, without elucidation of the connections between processing, microstructure, properties, and performance from a materials science perspective, metal additive manufacturing will not realize its potential to change the manufacturing world for property and performance-critical engineering applications.« less

  4. Additive Manufacturing: Building the Pathway Towards Process and Material Qualification”

    SciTech Connect

    Carpenter, John S.; Beese, Allison M.; Bourell, David L.; Hamilton, Reginald F.; Herderick, Edward; Mishra, Rajiv S.; Sears, James

    2016-06-14

    The potential benefits of metal additive manufacturing, as compared with more traditional, subtractive-only approaches, has created excitement within design circles seeking to take advantage of the ability to build and repair complex shapes, to integrate or consolidate multiple parts and minimize joining concerns, and to locally tailor material properties to increase functionality. Tempering the excitement of designers, however, has been concerns with the material deposited by the process. It is not enough for a part to ‘look’ right from a geometric perspective. Rather, the metallurgical aspects associated with the material being deposited must ‘look’ and ‘behave’ correctly along with the aforementioned geometric accuracy. Finally, without elucidation of the connections between processing, microstructure, properties, and performance from a materials science perspective, metal additive manufacturing will not realize its potential to change the manufacturing world for property and performance-critical engineering applications.

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

    PubMed

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

    2016-08-26

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

  6. 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.

  7. Reactivity of CHI3 with OH radicals: X-abstraction reaction pathways (X = H, I), atmospheric chemistry, and nuclear safety.

    PubMed

    Sudolská, Mária; Louis, Florent; Cernušák, Ivan

    2014-10-09

    The X-abstraction (X = H, I) pathways in the reaction of CHI3 with OH radical, a possible iodoform removal process relevant to the Earth's atmosphere and conditions prevailing in the case of a nuclear accident, have been studied applying highly correlated ab initio quantum chemistry methods and canonical transition-state theory to obtain reaction energy profiles and rate constants. Geometry optimizations of reactants, products, molecular complexes, and transition states determined at the MP2/cc-pVTZ level of theory have been followed by DK-CCSD(T)/ANO-RCC single-point energy calculations. Further improvement of electronic energies has been achieved by applying spin-orbit coupling, corrections toward full configuration interaction, vibration contributions, and tunneling corrections. Calculated reaction enthalpies at 0 K are -108.2 and -5.1 kJ mol(-1) for the H- and I-abstraction pathways, respectively; the strongly exothermic H-abstraction pathway is energetically favored over the modestly exothermic I-abstraction one. The overall rate constant at 298 K based on our ab initio calculations is 4.90 × 10(-11) cm(3) molecule(-1) s(-1), with the I-abstraction pathway being the major channel over the temperature range of 250-2000 K. The CHI3 atmospheric lifetime with respect to the removal reaction with OH radical is predicted to be about 6 h, very short compared to that of other halomethanes.

  8. Reaction pathways to CuInSe{sub 2} formation from electrodeposited precursors

    SciTech Connect

    Guillen, C.; Herrero, J.

    1995-06-01

    CuInSe{sub 2} thin films have been obtained from different precursors prepared by direct or sequential electrodeposition processes. The nature of the as-deposited layers and the evolution of the films during the heat-treatment in an inert (vacuum) or a reactive (elemental Se vapor) atmosphere have been studied by X-ray diffraction and X-ray photoelectron spectroscopy analysis. The chemistry of the different phase transformations occurring as a function of the annealing temperature has been examined, and possible reaction pathways for the formation of CuInSe{sub 2} are presented. The results show that high crystalline chalcopyrite CuInSe{sub 2} films with the desired composition can be obtained after annealing either direct or sequentially electrodeposited precursors at 400 C. An improvement in film quality can be gained by using an electrodeposited Cu layer as growth surface for the CuInSe{sub 2} formation. If elemental Se is also added during the heat-treatment, then a higher recrystallization of the films is observed.

  9. Reactive and unreactive pathways in a photochemical ring opening reaction from 2D femtosecond stimulated Raman.

    PubMed

    Valley, David T; Hoffman, David P; Mathies, Richard A

    2015-04-14

    Two-dimensional femtosecond stimulated Raman spectroscopy (2D-FSRS) is used to probe the structural evolution of a modified cyclohexadiene as it undergoes a photoinduced ring opening reaction. Analysis of the excited state stimulated Raman vibrational data reveals oscillations of the center frequencies and amplitudes of 21 high frequency modes. These oscillations in vibrational properties are due to anharmonic couplings between the high frequency finger print modes and the impulsively driven low frequency molecular distortions in the excited state. The largest anharmonic couplings, with intrinsic oscillation magnitudes of up to 40 cm(-1), are observed between the 467 cm(-1) C-C bend and the 1333 cm(-1) C-C stretch with the 191 cm(-1) methyl wag, all of which are centered on the reactive cyclohexadiene moiety. Conversely, motions located on the periphery - the 993 cm(-1) phenyl bend, the 1389 cm(-1) methyl bend and 1580 cm(-1) phenyl C-C stretch - are coupled with the 104 cm(-1) asymmetric bend. These couplings reveal two key energetic pathways: one leading to formation of the ring-opened product and the other reversion back to the ground state. This work is also important because it presents a new powerful method for measuring anharmonicities of potential energy surfaces and determining their role in chemical reactivity.

  10. Tautomer-selective derivatives of enolate, ketone and enaminone by addition reaction of picolyl-type anions with nitriles

    NASA Astrophysics Data System (ADS)

    Bai, Jianliang; Wang, Peng; Cao, Wei; Chen, Xia

    2017-01-01

    We describe an efficient for the synthesis of compounds of tautomeric β-pyridyl/quinolyl-enol, -ketone, -enaminone, which were finally characterized by standard methods like NMR, IR or SCXRD. The addition reaction of lithiated intermediates of picoline, 2-ethylpyridine and 2-methylquinoline, respectively, with nitriles followed by acid hydrolysis afforded the corresponding tautomeric compounds of enol, ketone and emaminone. Interestingly, treatment of 2-methylpyridine or 2-ethylpyridine with nitriles, respectively, yielded mostly β-pyridyl ketone and enol tautomers without enaminones, while 2-methylquinoline with nitriles gave β-quinolyl ketone and enaminone tautomers without enols. The reaction of 2-benzylpyridine with nitriles was not available under the same conditions.

  11. A tandem reaction initiated by 1,4-addition of bis(iodozincio)methane for 1,3-diketone formation.

    PubMed

    Sada, Mutsumi; Matsubara, Seijiro

    2010-01-20

    Treatment of an gamma-acyloxy-alpha,beta-unsaturated ketone with bis(iodozincio)methane leads to a novel tandem reaction consisting of three steps: (1) 1,4-addition of the dizinc reagent to the enone, which affords the corresponding zinc enolate of the beta-zinciomethylated ketone; (2) intramolecular nucleophilic attack by the enolate on the ester group; and (3) Grob-type fragmentation of the adduct, accompanied by elimination of the zinc alkoxide of allyl alcohol. The overall reaction gives 1,3-diketones efficiently.

  12. 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).

  13. 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

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

    SciTech Connect

    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.

    2016-06-07

    The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a modeled water molecule. Recently, a computational analysis of this pathway revealed that the solvent-exposed residue of the pathway (Glu282) could form hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implicating that these residues could function in regulating proton transfer. Substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in a 2.5-fold enhancement in H2 production activity, suggesting that Arg286 serves an important role in controlling the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate approximately 5-fold, implying that it either acts as a member of the pathway or influences Glu282 to enable proton transfer. Interestingly, QM/MM and molecular dynamics calculations indicate that Ser320 does not play an electronic or structural role. QM calculations also estimate that including Ser320 in the pathway does not significantly change the barrier to proton movement, providing further support for its role as a member of the proton pathway. While further studies are needed to quantify the role of Ser320, collectively, these data provide evidence that the enzyme scaffold plays a significant role in modulating the activity of the enzyme, demonstrating that the rate of intraprotein proton transfer can be accelerated, particularly in a non-biological context. This work was supported by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science, DE-FC02-07ER64494). In addition, support from the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences (WJS, BGP, SR) is gratefully acknowledged. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of

  15. Influence of different additives on the reaction between hydrated lime and sulfur dioxide

    SciTech Connect

    Cunill, F.; Izquierdo, J.F.; Martinez, J.C.; Tejero, J.; Querol, J. )

    1991-11-01

    Five commercial calcium hydroxides were tested in a fixed-bed reactor for SO{sub 2} removal at bag-filter conditions. Small amounts of different additives (fly ash, NaOH, NaCl and CaCl{sub 2}) were added to the commercial Ca(OH){sub 2} which showed the greatest reactivity respect to SO{sub 2} (by a drying process). Fly ash performance was negative whereas the rest of additives enhanced the desulfurization power of the Ca(OH){sub 2}, specially NaOH (due to its basic and deliquescent character) and CaCl{sub 2} (by its delilquescence). CaCl{sub 2} has been the best additive tested at the used experimental conditions.

  16. 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

  17. 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

  18. From formamide to purine: a self-catalyzed reaction pathway provides a feasible mechanism for the entire process.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-08-15

    A formamide self-catalyzed mechanistic pathway that transforms formamide to purine through a five-membered ring intermediate has been explored by density functional theory calculations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest and lowest energy reaction pathway. All necessary reactants, including catalysts, are generated from a single initial compound, formamide. The most catalytically effective form of formamide is found to be the imidic acid isomer. The catalytic effect of formamide has been found to be much more significant than that of water. The self-catalytic mechanism revealed here provides a pathway with the lowest energy barriers among all reaction routes previously published. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-member ring-closing, and deamination. Overall, a five-membered ring-closing is the rate-determining step in the present catalytic route, which is consistent with our previous mechanistic investigations. The activation energy of this rate-controlling step (ca. 27 kcal/mol) is significantly lower than the rate-determining step (ca. 34 kcal/mol) in the pathway from 4-aminoimidazole-5-carboxamidine described by Schleyer's group (Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 17272-17277) and in the pyrimidine pathway (ca. 44 kcal/mol) reported by Sponer et al. (J. Phys. Chem. A 2012, 116, 720-726). The self-catalyzed mechanistic pathway reported herein is less energetically demanding than previously proposed routes.

  19. Diastereoselective addition of monoorganocuprates to a chiral fumarate: reaction development and synthesis of (-)-dihydroprotolichesterinic acid.

    PubMed

    Hethcox, J Caleb; Shanahan, Charles S; Martin, Stephen F

    2015-09-16

    Recent studies of diastereoselective conjugate additions of monoorganocuprates, Li[RCuI], to chiral γ-alkoxycrotonates and fumarates are disclosed. This methodology was applied to the shortest total synthesis of (-)-dihydroprotolichesterinic acid to date, but several attempts to prepare other succinate-derived natural products, such as pilocarpine and antrodin E, were unsuccessful.

  20. 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…

  1. 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…

  2. Quantifying Fenton reaction pathways driven by self-generated H2O2 on pyrite surfaces

    PubMed Central

    Gil-Lozano, C.; Davila, A. F.; Losa-Adams, E.; Fairén, A. G.; Gago-Duport, L.

    2017-01-01

    Oxidation of pyrite (FeS2) plays a significant role in the redox cycling of iron and sulfur on Earth and is the primary cause of acid mine drainage (AMD). It has been established that this process involves multi-step electron-transfer reactions between surface defects and adsorbed O2 and H2O, releasing sulfoxy species (e.g., S2O32−, SO42−) and ferrous iron (Fe2+) to the solution and also producing intermediate by-products, such as hydrogen peroxide (H2O2) and other reactive oxygen species (ROS), however, our understanding of the kinetics of these transient species is still limited. We investigated the kinetics of H2O2 formation in aqueous suspensions of FeS2 microparticles by monitoring, in real time, the H2O2 and dissolved O2 concentration under oxic and anoxic conditions using amperometric microsensors. Additional spectroscopic and structural analyses were done to track the dependencies between the process of FeS2 dissolution and the degradation of H2O2 through the Fenton reaction. Based on our experimental results, we built a kinetic model which explains the observed trend of H2O2, showing that FeS2 dissolution can act as a natural Fenton reagent, influencing the oxidation of third-party species during the long term evolution of geochemical systems, even in oxygen-limited environments. PMID:28262831

  3. Quantifying Fenton reaction pathways driven by self-generated H2O2 on pyrite surfaces

    NASA Astrophysics Data System (ADS)

    Gil-Lozano, C.; Davila, A. F.; Losa-Adams, E.; Fairén, A. G.; Gago-Duport, L.

    2017-03-01

    Oxidation of pyrite (FeS2) plays a significant role in the redox cycling of iron and sulfur on Earth and is the primary cause of acid mine drainage (AMD). It has been established that this process involves multi-step electron-transfer reactions between surface defects and adsorbed O2 and H2O, releasing sulfoxy species (e.g., S2O32‑, SO42‑) and ferrous iron (Fe2+) to the solution and also producing intermediate by-products, such as hydrogen peroxide (H2O2) and other reactive oxygen species (ROS), however, our understanding of the kinetics of these transient species is still limited. We investigated the kinetics of H2O2 formation in aqueous suspensions of FeS2 microparticles by monitoring, in real time, the H2O2 and dissolved O2 concentration under oxic and anoxic conditions using amperometric microsensors. Additional spectroscopic and structural analyses were done to track the dependencies between the process of FeS2 dissolution and the degradation of H2O2 through the Fenton reaction. Based on our experimental results, we built a kinetic model which explains the observed trend of H2O2, showing that FeS2 dissolution can act as a natural Fenton reagent, influencing the oxidation of third-party species during the long term evolution of geochemical systems, even in oxygen-limited environments.

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

    SciTech Connect

    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 occurred via autunite (Ca(UO2)(PO4)3) precipitation irrespective of the starting forms of calcium and phosphate. At pH 7.5, the uptake mechanism depended on the nature of the calcium and phosphate. 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 pre-formed 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. The solid phase speciation of the uranium was determined using X-ray absorption spectroscopy and laser induced fluorescence spectroscopy. Dissolved uranium, calcium, and phosphate concentrations with saturation index calculations helped identify removal mechanisms and determine thermodynamically favorable solid phases.

  5. 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

  6. DNA-Accelerated Copper Catalysis of Friedel-Crafts Conjugate Addition/Enantioselective Protonation Reactions in Water.

    PubMed

    García-Fernández, Almudena; Megens, Rik P; Villarino, Lara; Roelfes, Gerard

    2016-12-21

    DNA-induced rate acceleration has been identified as one of the key elements for the success of the DNA-based catalysis concept. Here we report on a novel DNA-based catalytic Friedel-Crafts conjugate addition/enantioselective protonation reaction in water, which represents the first example of a reaction that critically depends on the >700- to 990-fold rate acceleration caused by the presence of a DNA scaffold. The DNA-induced rate acceleration observed is the highest reported due to the environment presented by a biomolecular scaffold for any hybrid catalyst, to date. Based on a combination of kinetics and binding studies, it is proposed that the rate acceleration is in part due to the DNA acting as a pseudophase, analogous to micelles, in which all reaction components are concentrated, resulting in a high effective molarity. The involvement of additional second coordination sphere interactions is suggested by the enantioselectivity of the product. The results presented here show convincingly that the DNA-based catalysis concept, thanks to the DNA-accelerating effect, can be an effective approach to achieving a chemically challenging reaction in water.

  7. 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

  8. 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.

  9. 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.

  10. The First Example of Nickel-Catalyzed Silyl-Heck Reactions: Direct Activation of Silyl Triflates Without Iodide Additives

    PubMed Central

    McAtee, Jesse R.; Martin, Sara E. S.; Cinderella, Andrew P.; Reid, William B.; Johnson, Keywan A.

    2014-01-01

    For the first time, nickel-catalyzed silyl-Heck reactions are reported. Using simple phosphine-supported nickel catalysts, direct activation of silyl triflates has been achieved. These results contrast earlier palladium-catalyzed systems, which require iodide additives to activate silyl-triflates. These nickel-based catalysts exhibit good functional group tolerance in the preparation of vinyl silanes, and unlike earlier systems, allows for the incorporation of trialkylsilanes larger than Me3Si. PMID:24914247

  11. Dinuclear oxidative addition reactions using an isostructural series of Ni2, Co2, and Fe2 complexes.

    PubMed

    Behlen, Michael J; Zhou, You-Yun; Steiman, Talia J; Pal, Sudipta; Hartline, Douglas R; Zeller, Matthias; Uyeda, Christopher

    2016-12-20

    A family of low-valent Ni2, Co2, and Fe2 naphthyridine-diimine (NDI) complexes is presented. Ligand-based π* orbitals are sufficiently low-lying to fall within the metal 3d manifold, resulting in electronic structures that are highly delocalized across the conjugated [NDI]M2 system. This feature confers stability to metal-metal interactions during two-electron redox reactions, as demonstrated in a prototypical oxidative addition of allyl chloride.

  12. 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.

  13. 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.

  14. Time-dependent insulin oligomer reaction pathway prior to fibril formation: cooling and seeding.

    PubMed

    Sorci, Mirco; Grassucci, Robert A; Hahn, Ingrid; Frank, Joachim; Belfort, Georges

    2009-10-01

    The difficulty in identifying the toxic agents in all amyloid-related diseases is likely due to the complicated kinetics and thermodynamics of the nucleation process and subsequent fibril formation. The slow progression of these diseases suggests that the formation, incorporation, and/or action of toxic agents are possibly rate limiting. Candidate toxic agents include precursors (some at very low concentrations), also called oligomers and protofibrils, and the fibrils. Here, we investigate the kinetic and thermodynamic behavior of human insulin oligomers (imaged by cryo-EM) under fibril-forming conditions (pH 1.6 and 65 degrees C) by probing the reaction pathway to insulin fibril formation using two different types of experiments-cooling and seeding-and confirm the validity of the nucleation model and its effect on fibril growth. The results from both the cooling and seeding studies confirm the existence of a time-changing oligomer reaction process prior to fibril formation that likely involves a rate-limiting nucleation process followed by structural rearrangements of intermediates (into beta-sheet rich entities) to form oligomers that then form fibrils. The latter structural rearrangement step occurs even in the absence of nuclei (i.e., with added heterologous seeds). Nuclei are formed at the fibrillation conditions (pH 1.6 and 65 degrees C) but are also continuously formed during cooling at pH 1.6 and 25 degrees C. Within the time-scale of the experiments, only after increasing the temperature to 65 degrees C are the trapped insulin nuclei and resultant structures able to induce the structural rearrangement step and overcome the energy barrier to form fibrils. This delay in fibrillation and accumulation of nuclei at low temperature (25 degrees C) result in a decrease in the mean length of the fibers when placed at 65 degrees C. Fits of an empirical model to the data provide quantitative measures of the delay in the lag-time during the nucleation process and

  15. Time-dependent insulin oligomer reaction pathway prior to fibril formation: Cooling and seeding

    PubMed Central

    Sorci, Mirco; Grassucci, Robert A.; Hahn, Ingrid; Frank, Joachim; Belfort, Georges

    2009-01-01

    The difficulty in identifying the toxic agents in all amyloid-related diseases is likely due to the complicated kinetics and thermodynamics of the nucleation process and subsequent fibril formation. The slow progression of these diseases suggests that the formation, incorporation and/or action of toxic agents is possibly rate limiting. Candidate toxic agents include precursors (some at very low concentrations), also called oligomers and protofibrils, and the fibrils. Here, we investigate the kinetic and thermodynamic behavior of human insulin oligomers (imaged by cryo-EM) under fibril forming conditions (pH 1.6 and 65°C) by probing the reaction pathway to insulin fibril formation using two different types of experiments – cooling and seeding – and confirm the validity of the nucleation model and its effect on fibril growth. The results from both the cooling and seeding studies confirm the existence of a time-changing oligomer reaction process prior to fibril formation that likely involves a rate-limiting nucleation process followed by structural rearrangements of intermediates (into β-sheet rich entities) to form oligomers that then form fibrils. The latter structural rearrangement step occurs even in the absence of nuclei (i.e. with added heterologous seeds). Nuclei are formed at the fibrillation conditions (pH 1.6 and 65°C) but are also continuously formed during cooling at pH 1.6 and 25°C. Within the time-scale of the experiments, only after increasing the temperature to 65°C are the trapped insulin nuclei and resultant structures able to induce the structural rearrangement step and overcome the energy barrier to form fibrils. This delay in fibrillation and accumulation of nuclei at low temperature (25°C), result in a decrease in the mean length of the fibers when placed at 65°C. Fits of an empirical model to the data provide quantitative measures of the delay in the lag-time during the nucleation process and subsequent reduction in fibril growth rate

  16. Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions.

    PubMed

    Rokhlenko, Yekaterina; Geacintov, Nicholas E; Shafirovich, Vladimir

    2012-03-14

    The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(•+), its deptotonation product G(-H)(•), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(•-) and SO(4)(•-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ∼20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(•+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(•), which, at best, reacts only slowly with H(2)O and lives for ∼70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(•) can be oxidized further by reaction with CO(3)(•-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.

  17. In Situ-Forming Polyamidoamine Dendrimer Hydrogels with Tunable Properties Prepared via Aza-Michael Addition Reaction.

    PubMed

    Wang, Juan; He, Hongliang; Cooper, Remy C; Yang, Hu

    2017-03-29

    In this work, we describe synthesis and characterization of novel in situ-forming polyamidoamine (PAMAM) dendrimer hydrogels (DHs) with tunable properties prepared via highly efficient aza-Michael addition reaction. PAMAM dendrimer G5 was chosen as the underlying core and functionalized with various degrees of acetylation using acetic anhydride. The nucleophilic amines on the dendrimer surface reacted with α, β-unsaturated ester in acrylate groups of polyethylene glycol diacrylate (PEG-DA, Mn = 575 g/mol) via aza-Michael addition reaction to form dendrimer hydrogels without the use of any catalyst. The solidification time, rheological behavior, network structure, swelling, and degradation properties of the hydrogel were tuned by adjusting the dendrimer surface acetylation degree and dendrimer concentration. The DHs were shown to be highly cytocompatible and support cell adhesion and proliferation. We also prepared an injectable dendrimer hydrogel formulation to deliver the anticancer drug 5-fluorouracil (5-FU) and demonstrated that the injectable formulation efficiently inhibited tumor growth following intratumoral injection. Taken together, this new class of dendrimer hydrogel prepared by aza-Michael addition reaction can serve as a safe tunable platform for drug delivery and tissue engineering.

  18. Core-structure-inspired asymmetric addition reactions: enantioselective synthesis of dihydrobenzoxazinone- and dihydroquinazolinone-based anti-HIV agents.

    PubMed

    Li, Shen; Ma, Jun-An

    2015-11-07

    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.

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

    PubMed

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

    2015-07-14

    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 acridone product of the synthesis are analyzed by common techniques available in most undergraduate chemistry laboratories, such as melting point, TLC, IR spectroscopy, UV-Vis spectroscopy, and fluorescence spectroscopy. Yields for each transformation in the synthesis are generally moderately low to good (20-90%) and nearly all of the students (>90%) who attempted the synthesis were able to produce the final acridone product.

  20. 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

  1. 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

    2016-07-08

    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/.

  2. Effects of protonation and C5 methylation on the electrophilic addition reaction of cytosine: a computational study.

    PubMed

    Jin, Lingxia; Wang, Wenliang; Hu, Daodao; Min, Suotian

    2013-01-10

    The mechanism for the effects of protonation and C5 methylation on the electrophilic addition reaction of Cyt has been explored by means of CBS-QB3 and CBS-QB3/PCM methods. In the gas phase, three paths, two protonated paths (N3 and O2 protonated paths B and C) as well as one neutral path (path A), were mainly discussed, and the calculated results indicate that the reaction of the HSO(3)(-) group with neutral Cyt is unlikely because of its high activation free energy, whereas O2-protonated path (path C) is the most likely to occur. In the aqueous phase, path B is the most feasible mechanism to account for the fact that the activation free energy of path B decreases compared with the corresponding path in the gas phase, whereas those of paths A and C increase. The main striking results are that the HSO(3)(-) group directly interacts with the C5═C6 bond rather than the N3═C4 bond and that the C5 methylation, compared with Cyt, by decreasing values of global electrophilicity index manifests that C5 methylation forms are less electrophilic power as well as by decreasing values of NPA charges on C5 site of the intermediates make the trend of addition reaction weaken, which is in agreement with the experimental observation that the rate of 5-MeCyt reaction is approximately 2 orders of magnitude slower than that of Cyt in the presence of bisulfite. Apart from cis and trans isomers, the rare third isomer where both the CH(3) and SO(3) occupy axial positions has been first found in the reactions of neutral and protonated 5-MeCyt with the HSO(3)(-) group. Furthermore, the transformation of the third isomer from the cis isomer can occur easily.

  3. A DFT study on the reaction pathways for carbon-carbon bond-forming reactions between propargylic alcohols and alkenes or ketones catalyzed by thiolate-bridged diruthenium complexes.

    PubMed

    Sakata, Ken; Miyake, Yoshihiro; Nishibayashi, Yoshiaki

    2009-01-05

    The reaction pathways of two types of the carbon-carbon bond-forming reactions catalyzed by thiolate-bridged diruthenium complexes have been investigated by density-functional-theory calculations. It is clarified that both carbon-carbon bond-forming reactions proceed through a ruthenium-allenylidene complex as a common reactive intermediate. The attack of pi electrons on propene or the vinyl alcohol on the ruthenium-allenylidene complex is the first step of the reaction pathways. The reaction pathways are different after the attack of nucleophiles on the ruthenium-alkynyl complex. In the reaction with propene, the carbon-carbon bond-forming reaction proceeds through a stepwise process, whereas in the reaction with vinyl alcohol, it proceeds through a concerted process. The interactions between the ruthenium-allenylidene complex and propene or vinyl alcohol have been investigated by applying a simple way of looking at orbital interactions.

  4. tRNAHis guanylyltransferase catalyzes a 3′-5′ polymerization reaction that is distinct from G−1 addition

    PubMed Central

    Jackman, Jane E.; Phizicky, Eric M.

    2006-01-01

    Yeast tRNAHis guanylyltransferase, Thg1, is an essential protein that adds a single guanine to the 5′ end (G−1) of tRNAHis. This G−1 residue is required for aminoacylation of tRNAHis by histidyl-tRNA synthetase, both in vitro and in vivo. The guanine nucleotide addition reaction catalyzed by Thg1 extends the polynucleotide chain in the reverse (3′-5′) direction of other known polymerases, albeit by one nucleotide. Here, we show that alteration of the 3′ end of the Thg1 substrate tRNAHis unleashes an unexpected reverse polymerase activity of wild-type Thg1, resulting in the 3′-5′ addition of multiple nucleotides to the tRNA, with efficiency comparable to the G−1 addition reaction. The addition of G−1 forms a mismatched G·A base pair at the 5′ end of tRNAHis, and, with monophosphorylated tRNA substrates, it is absolutely specific for tRNAHis. By contrast, reverse polymerization forms multiple G·C or C·G base pairs, and, with preactivated tRNA species, it can initiate at positions other than −1 and is not specific for tRNAHis. Thus, wild-type Thg1 catalyzes a templated polymerization reaction acting in the reverse direction of that of canonical DNA and RNA polymerases. Surprisingly, Thg1 can also readily use dNTPs for nucleotide addition. These results suggest that 3′-5′ polymerization represents either an uncharacterized role for Thg1 in RNA or DNA repair or metabolism, or it may be a remnant of an earlier catalytic strategy used in nature. PMID:16731615

  5. Phosphoinositide-Dependent Pathways in Mouse Sperm are Regulated by Egg ZP3 and Drive the Acrosome Reaction

    PubMed Central

    Jungnickel, Melissa K.; Sutton, Keith A.; Wang, Yanli; Florman, Harvey M.

    2007-01-01

    Sperm of many animals must complete an exocytotic event, the acrosome reaction, in order to fuse with eggs. In mammals, acrosome reactions are triggered during sperm contact with the egg extracellular matrix, or zona pellucida, by the matrix glycoprotein ZP3. Here, we show that ZP3 stimulates production of phosphatidylinositol-(3,4,5)-triphosphate in sperm membranes. Phosphatidylinositol-3-kinase antagonists that prevent the production of this phosphoinositide blocked acrosome reactions and fertilization in vitro, while generation of this phosphoinositide in the absence of ZP3 triggered acrosome reactions. Downstream effectors of phosphatidylinositol-(3,4,5)-triphosphate in sperm include the protein kinases, Akt and PKCζ. These studies outline a signal transduction pathway that plays an essential role in the early events of mammalian fertilization. PMID:17258189

  6. Ab initio study of CO2 capture mechanisms in aqueous monoethanolamine: reaction pathways for the direct interconversion of carbamate and bicarbonate.

    PubMed

    Matsuzaki, Yoichi; Yamada, Hidetaka; Chowdhury, Firoz A; Higashii, Takayuki; Onoda, Masami

    2013-09-26

    Ab initio molecular orbital calculations combined with the polarizable continuum model (PCM) formalism have been carried out for a comprehensive understanding of the mechanism of carbon dioxide (CO2) absorption by aqueous amine solutions. CO2 is captured by amines to generate carbamates and bicarbonate. We have examined the direct interconversion pathways of these two species (collectively represented by a reversible hydrolysis of carbamate) with the prototypical amine, monoethanolamine (MEA). We evaluate both a concerted and a stepwise mechanism for the neutral hydrolysis of MEA carbamate. Large activation energies (ca. 36 kcal/mol) and lack of increase in catalytic efficiency with the inclusion of additional water molecules are predicted in both the mechanisms. We also examined the mechanism of alkaline hydrolysis of MEA carbamate at high concentrations of amine (high pH). The addition of OH(-) ion to carbamate anion was theoretically not allowed due to the reduction in the nucleophilicity of the former as a result of microsolvation. We propose an alternative pathway for hydrolysis: a proton transfer from protonated MEA to carbamate to generate the carbamic acid that initially undergoes a nucleophilic addition of OH(-) and subsequent low-barrier reactions leading to the formation of bicarbonate and free MEA. On the basis of the calculated activation energies, this pathway would be the most efficient route for the direct interconversion of carbamate and bicarbonate without the intermediacy of the free CO2, while the actual contributions will be dependent on the concentrations of protonated MEA and OH(-) ions.

  7. 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

  8. 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.

  9. 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.

  10. Apparent anti-Woodward-Hoffmann addition to a nickel bis(dithiolene) complex: the reaction mechanism involves reduced, dimetallic intermediates.

    PubMed

    Dang, Li; Shibl, Mohamed F; Yang, Xinzheng; Harrison, Daniel J; Alak, Aiman; Lough, Alan J; Fekl, Ulrich; Brothers, Edward N; Hall, Michael B

    2013-04-01

    Nickel dithiolene complexes have been proposed as electrocatalysts for alkene purification. Recent studies of the ligand-based reactions of Ni(tfd)2 (tfd = S2C2(CF3)2) and its anion [Ni(tfd)2](-) with alkenes (ethylene and 1-hexene) showed that in the absence of the anion, the reaction proceeds most rapidly to form the intraligand adduct, which decomposes by releasing a substituted dihydrodithiin. However, the presence of the anion increases the rate of formation of the stable cis-interligand adduct, and decreases the rate of dihydrodithiin formation and decomposition. In spite of both computational and experimental studies, the mechanism, especially the role of the anion, remained somewhat elusive. We are now providing a combined experimental and computational study that addresses the mechanism and explains the role of the anion. A kinetic study (global analysis) for the reaction of 1-hexene is reported, which supports the following mechanism: (1) reversible intraligand addition, (2) oxidation of the intraligand addition product prior to decomposition, and (3) interligand adduct formation catalyzed by Ni(tfd)2(-). Density functional theory (DFT) calculations were performed on the Ni(tfd)2/Ni(tfd)2(-)/ethylene system to shed light on the selectivity of adduct formation in the absence of anion and on the mechanism in which Ni(tfd)2(-) shifts the reaction from intraligand addition to interligand addition. Computational results show that in the neutral system the free energy of activation for intraligand addition is lower than that for interligand addition, in agreement with the experimental results. The computations predict that the anion enhances the rate of the cis-interligand adduct formation by forming a dimetallic complex with the neutral complex. The [(Ni(tfd)2)2](-) dimetallic complex then coordinates ethylene and isomerizes to form a Ni,S-bound ethylene complex, which then rapidly isomerizes to the stable interligand adduct but not to the intraligand adduct

  11. Evidence that protons can be the active catalysts in Lewis acid mediated hetero-Michael addition reactions.

    PubMed

    Wabnitz, Tobias C; Yu, Jin-Quan; Spencer, Jonathan B

    2004-01-23

    The mechanism of Lewis acid catalysed hetero-Michael addition reactions of weakly basic nucleophiles to alpha,beta-unsaturated ketones was investigated. Protons, rather than metal ions, were identified as the active catalysts. Other mechanisms have been ruled out by analyses of side products and of stoichiometric enone-catalyst mixtures and by the use of radical inhibitors. No evidence for the involvement of pi-olefin-metal complexes or for carbonyl-metal-ion interactions was obtained. The reactions did not proceed in the presence of the non-coordinating base 2,6-di-tert-butylpyridine. An excellent correlation of catalytic activities with cation hydrolysis constants was obtained. Different reactivities of mono- and dicarbonyl substrates have been rationalised. A (1)H NMR probe for the assessment of proton generation was established and Lewis acids have been classified according to their propensity to hydrolyse in organic solvents. Brønsted acid-catalysed conjugate addition reactions of nitrogen, oxygen, sulfur and carbon nucleophiles are developed and implications for asymmetric Lewis acid catalysis are discussed.

  12. 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

  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. The preparation and intra- and intermolecular addition reactions of acyclic N-acylimines: application to the synthesis of (+/-)-sertraline.

    PubMed

    DeNinno, M P; Eller, C; Etienne, J B

    2001-10-19

    Intramolecular endo-cyclization reactions of N-acyliminium ions have seen wide application for the synthesis of heterocyclic compounds. The corresponding exocyclic variant, which would provide 1-aminotetralin derivatives, for example, has little precedent. We have discovered that acyclic N-acylcarbamates can be readily reduced to the corresponding N-acylhemiaminal derivatives in high yield using DIBAL as the reducing agent. These intermediates are remarkably stable and, if desired, can be purified and stored. The acyclic N-acylhemiaminals undergo both intra- and intermolecular nucleophilic addition reactions mediated by strong Lewis acids, such as TiCl(4). Diastereoselectivity, induced either by a substituent on the newly formed ring, or by utilizing a chiral ester on the carbamic acid, was disappointingly low. This methodology was successfully applied to the synthesis of the racemic form of the marketed antidepressant sertraline.

  15. 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.

  16. Cascade intermolecular Michael addition-intramolecular azide/internal alkyne 1,3-dipolar cycloaddition reaction in one pot.

    PubMed

    Arigela, Rajesh K; Mandadapu, Anil K; Sharma, Sudhir K; Kumar, Brijesh; Kundu, Bijoy

    2012-04-06

    A rapid one-pot protocol for the synthesis of indole-based polyheterocycles via a sequential Lewis acid catalyzed intermolecular Michael addition and an intramolecular azide/internal alkyne 1,3-dipolar cycloaddition reaction has been described. The generality of the method has been demonstrated by treating a series of aromatic/aliphatic 2-alkynyl indoles with substituted (E)-1-azido-2-(2-nitrovinyl)benzenes to furnish annulated tetracyclic indolo[2,3-c][1,2,3]triazolo[1,5-a][1]benzazepines in good yields.

  17. Unexpected Formation of Highly Functionalized Dihydropyrans via Addition-Cyclization Reactions Between Dimethyl Oxoglutaconate and α,β-Unsaturated Hydrazones.

    PubMed

    Mullins, Jason E; Etoga, Jean-Louis G; Gajewski, Mariusz; Degraw, Joseph I; Thompson, Charles M

    2009-05-20

    The condensation between dienophiles and α,β-unsaturated hydrazone azadienes was previously reported to afford piperidines. During an attempt to adapt this reaction to the preparation of piperidine-based conformationally-restricted analogs of glutamate, it was discovered that the electrophile, dimethyl oxoglutaconate (DOG) led to highly substituted dihydropyrans in 20-50% yield. The unexpected pyran product likely results from an initial 1,4-addition of the hydrazone to the oxoglutaconate followed by intramolecular cyclization of the resultant enolate oxygen to the α,β-unsaturated iminium ion. Further manipulations afford substituted tetrahydropyran 6-methamino-2,4-dicarboxylic acids.

  18. Unexpected Formation of Highly Functionalized Dihydropyrans via Addition-Cyclization Reactions Between Dimethyl Oxoglutaconate and α,β-Unsaturated Hydrazones

    PubMed Central

    Mullins, Jason E.; Etoga, Jean-Louis G.; Gajewski, Mariusz; DeGraw, Joseph I.; Thompson, Charles M.

    2009-01-01

    The condensation between dienophiles and α,β-unsaturated hydrazone azadienes was previously reported to afford piperidines. During an attempt to adapt this reaction to the preparation of piperidine-based conformationally-restricted analogs of glutamate, it was discovered that the electrophile, dimethyl oxoglutaconate (DOG) led to highly substituted dihydropyrans in 20–50% yield. The unexpected pyran product likely results from an initial 1,4-addition of the hydrazone to the oxoglutaconate followed by intramolecular cyclization of the resultant enolate oxygen to the α,β-unsaturated iminium ion. Further manipulations afford substituted tetrahydropyran 6-methamino-2,4-dicarboxylic acids. PMID:20161237

  19. 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.

  20. 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

  1. A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways

    PubMed Central

    Wallach, Izhar; Jaitly, Navdeep; Lilien, Ryan

    2010-01-01

    Adverse drug reactions (ADR), also known as side-effects, are complex undesired physiologic phenomena observed secondary to the administration of pharmaceuticals. Several phenomena underlie the emergence of each ADR; however, a dominant factor is the drug's ability to modulate one or more biological pathways. Understanding the biological processes behind the occurrence of ADRs would lead to the development of safer and more effective drugs. At present, no method exists to discover these ADR-pathway associations. In this paper we introduce a computational framework for identifying a subset of these associations based on the assumption that drugs capable of modulating the same pathway may induce similar ADRs. Our model exploits multiple information resources. First, we utilize a publicly available dataset pairing drugs with their observed ADRs. Second, we identify putative protein targets for each drug using the protein structure database and in-silico virtual docking. Third, we label each protein target with its known involvement in one or more biological pathways. Finally, the relationships among these information sources are mined using multiple stages of logistic-regression while controlling for over-fitting and multiple-hypothesis testing. As proof-of-concept, we examined a dataset of 506 ADRs, 730 drugs, and 830 human protein targets. Our method yielded 185 ADR-pathway associations of which 45 were selected to undergo a manual literature review. We found 32 associations to be supported by the scientific literature. PMID:20808786

  2. Selectivity in the Addition Reactions of Organometallic Reagents to Aziridine-2-carboxaldehydes: The Effects of Protecting Groups and Substitution Patterns

    PubMed Central

    Kulshrestha, Aman; Schomaker, Jennifer M.; Holmes, Daniel; Staples, Richard J.; Jackson, James E.; Borhan, Babak

    2014-01-01

    Good to excellent stereo-selectivity has been found in the addition reactions of Grignard and organo-zinc reagents to N-protected aziridine-2-carboxaldehydes. Specifically, high syn selectivity was obtained with benzyl-protected cis, tert-butyloxycar-bonyl-protected trans, and tosyl-pro-tected 2,3-disubstituted aziridine-2-car-boxaldehydes. Furthermore, rate and selectivity effects of ring substituents, temperature, solvent, and Lewis acid and base modifiers were studied. The diastereomeric preference of addition is dominated by the substrate aziri-dines’ substitution pattern and especially the electronic character and conformational preferences of the nitrogen protecting groups. To help rationalize the observed stereochemical outcomes, conformational and electronic structural analyses of a series of model systems representing the various substitution patterns have been explored by density functional calculations at the B3LYP/6–31G* level of theory with the SM8 solvation model to account for solvent effects. PMID:21928447

  3. 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…

  4. Facile construction of macroporous hybrid monoliths via thiol-methacrylate Michael addition click reaction for capillary liquid chromatography.

    PubMed

    Lin, Hui; Ou, Junjie; Liu, Zhongshan; Wang, Hongwei; Dong, Jing; Zou, Hanfa

    2015-01-30

    A facile approach based on thiol-methacrylate Michael addition click reaction was developed for construction of porous hybrid monolithic materials. Three hybrid monoliths were prepared via thiol-methacrylate click polymerization by using methacrylate-polyhedral oligomeric silsesquioxane (POSS) (cage mixture, n=8, 10, 12, POSS-MA) and three multi-thiol crosslinkers, 1,6-hexanedithiol (HDT), trimethylolpropane tris(3-mercaptopropionate) (TPTM) and pentaerythritol tetrakis(3-mercaptopropionate) (PTM), respectively, in the presence of porogenic solvents (n-propanol and PEG 200) and a catalyst (dimethylphenylphosphine, DMPP). The obtained monoliths possessed high thermal and chemical stabilities. Besides, they all exhibited high column efficiencies and excellent separation abilities in capillary liquid chromatography (cLC). The highest column efficiency could reach ca. 195,000N/m for butylbenzene on the monolith prepared with POSS-MA and TPTM (monolith POSS-TPTM) in reversed-phase (RP) mode at 0.64mm/s. Good chromatographic performance were all achieved in the separations of polycyclic aromatic hydrocarbons (PAHs), phenols, anilines, EPA 610 as well as bovine serum albumin (BSA) digest. The high column efficiencies in the range of 51,400-117,000N/m (achieved on the monolith POSS-PTM in RP mode) convincingly demonstrated the high separation abilities of these thiol-methacrylate based hybrid monoliths. All the results demonstrated the feasibility of the phosphines catalyzed thiol-methacrylate Michael addition click reaction in fabrication of monolithic columns with high efficiency for cLC applications.

  5. Reactions of carbonyl compounds with α,β-unsaturated nitriles as a convenient pathway to carbo- and heterocycles

    NASA Astrophysics Data System (ADS)

    Sharanin, Yu A.; Goncharenko, M. P.; Litvinov, Victor P.

    1998-05-01

    Published data on the methods for synthesis of carbo- and heterocyclic compounds based on reactions of α,β-unsaturated nitriles with carbonyl compounds and activated phenols are surveyed. It is demonstrated that all these reactions occur via nucleophilic addition of the carbanion generated from a carbonyl compound to the double bond of an unsaturated nitrile (the Michael reaction). The main routes of transformation of the adducts into carbo- and heterocyclic compounds are considered. The methods for regioselective preparation of fused 4H-pyrans or 1,4-dihydropyridines by varying conditions of cyclisation of Michael adducts are discussed. The bibliography includes 249 references.

  6. 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.

  7. 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.

  8. Reaction of benzene with atomic carbon: pathways to fulvenallene and the fulvenallenyl radical in extraterrestrial atmospheres and the interstellar medium.

    PubMed

    da Silva, Gabriel

    2014-06-05

    The reaction of benzene with ground-state atomic carbon, C((3)P), has been investigated using the G3X-K composite quantum chemical method. A suite of novel energetically favorable pathways that lead to previously unconsidered products are identified. Reaction is initiated by barrierless C atom cycloaddition to benzene on the triplet surface, producing a vibrationally excited [C7H6]* adduct that can dissociate to the cycloheptatrienyl radical (+ H) via a relatively loose transition state 4.4 kcal mol(-1) below the reactant energies. This study also identifies that this reaction adduct can isomerize to generate five-membered ring intermediates that can further dissociate to the global C7H5 minima, the fulvenallenyl radical (+ H), or to c-C5H4 and acetylene, with limiting barriers around 20 and 10 kcal mol(-1) below the reactants, respectively. If intersystem crossing to the singlet surface occurs, isomerization pathways that are lower-yet in energy are available leading to the C7H6 minima fulvenallene, with all barriers over 40 kcal mol(-1) below the reactants. From here further barrierless fragmentation to fulvenallenyl + H can proceed at ca. 25 kcal mol(-1) below the reactants. In the reducing atmospheres of planets like Jupiter and satellites like Titan, where benzene and C((3)P) are both expected, it is proposed that fulvenallene and the fulvenallenyl radical would be the dominant products of the C6H6 + C((3)P) reaction. Fulvenallenyl may also be a significant reaction product under collision-free conditions representative of the interstellar medium, although further work is required here to confirm the identity of the C7H5 radical product.

  9. Insertion and abstraction pathways in the reaction O(1D2) + H2-->OH+H.

    PubMed

    Aoiz, F J; Bañares, L; Castillo, J F; Brouard, M; Denzer, W; Vallance, C; Honvault, P; Launay, J M; Dobbyn, A J; Knowles, P J

    2001-02-26

    Rigorous quantum dynamical calculations have been performed on the ground 1 1A' and first excited 1 1A" electronic states of the title reaction, employing the most accurate potential energy surfaces available. Product rovibrational quantum state populations and rotational angular momentum alignment parameters are reported, and are compared with new experimental, and quasiclassical trajectory calculated results. The quantum calculations agree quantitatively with experiment, and reveal unequivocally that the 1 1A" excited state participates in the reaction.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Effect of rare earth metal Ce addition to Sn-Ag solder on interfacial reactions with Cu substrate

    NASA Astrophysics Data System (ADS)

    Yoon, Jeong-Won; Noh, Bo-In; Jung, Seung-Boo

    2014-05-01

    The effect of adding a small amount of rare earth cerium (Ce) element to low Ag containing Sn-1wt%Ag Pb-free solder on its interfacial reactions with Cu substrate was investigated. The growth of intermetallic compounds (IMCs) between three Sn-1Ag-xCe solders with different Ce contents and a Cu substrate was studied and the results were compared to those obtained for the Ce-free Sn-1Ag/Cu systems. In the solid-state reactions of the Sn-1Ag(-xCe)/Cu solder joints, the two IMC layers, Cu6Sn5 and Cu3Sn, grew as aging time increased. Compared to the Sn-1Ag/Cu joint, the growth of the Cu6Sn5 and Cu3Sn layers was depressed for the Ce-containing Sn-1Ag-xCe/Cu joint. The addition of Ce to the Sn-Ag solder reduced the growth of the interfacial Cu-Sn IMCs and prevented the IMCs from spalling from the interface. The evenly-distributed Ce elements in the solder region blocked the diffusion of Sn atoms to the interface and retarded the growth of the interfacial IMC layer.

  15. 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…

  16. Complete diastereodivergence in asymmetric 1,6-addition reactions enabled by minimal modification of a chiral catalyst

    NASA Astrophysics Data System (ADS)

    Uraguchi, Daisuke; Yoshioka, Ken; Ooi, Takashi

    2017-03-01

    Catalytic systems that allow selective generation of any diastereomer of a reaction product bearing multiple stereocentres through minimal modification of a single catalyst scaffold remain elusive, particularly for carbon-carbon bond formations requiring simultaneous control of multiple selectivity factors. Here, we report a catalyst-directed pinpoint inversion of diastereochemical preference in the 1,6-addition of azlactones to δ-aryl dienyl carbonyl compounds with full control over other selectivities preserved. This rigorous diastereodivergence is enabled by the slight structural adjustment of a chiral iminophosphorane catalyst, providing access to all the stereoisomers with high regio-, distereo- and enantioselectivity. The utility of this method is demonstrated in the facile stereodivergent preparation of densely functionalized proline derivatives. The experimental and computational elucidation of the origin of the diastereodivergence is also reported.

  17. Complete diastereodivergence in asymmetric 1,6-addition reactions enabled by minimal modification of a chiral catalyst.

    PubMed

    Uraguchi, Daisuke; Yoshioka, Ken; Ooi, Takashi

    2017-03-20

    Catalytic systems that allow selective generation of any diastereomer of a reaction product bearing multiple stereocentres through minimal modification of a single catalyst scaffold remain elusive, particularly for carbon-carbon bond formations requiring simultaneous control of multiple selectivity factors. Here, we report a catalyst-directed pinpoint inversion of diastereochemical preference in the 1,6-addition of azlactones to δ-aryl dienyl carbonyl compounds with full control over other selectivities preserved. This rigorous diastereodivergence is enabled by the slight structural adjustment of a chiral iminophosphorane catalyst, providing access to all the stereoisomers with high regio-, distereo- and enantioselectivity. The utility of this method is demonstrated in the facile stereodivergent preparation of densely functionalized proline derivatives. The experimental and computational elucidation of the origin of the diastereodivergence is also reported.

  18. Complete diastereodivergence in asymmetric 1,6-addition reactions enabled by minimal modification of a chiral catalyst

    PubMed Central

    Uraguchi, Daisuke; Yoshioka, Ken; Ooi, Takashi

    2017-01-01

    Catalytic systems that allow selective generation of any diastereomer of a reaction product bearing multiple stereocentres through minimal modification of a single catalyst scaffold remain elusive, particularly for carbon–carbon bond formations requiring simultaneous control of multiple selectivity factors. Here, we report a catalyst-directed pinpoint inversion of diastereochemical preference in the 1,6-addition of azlactones to δ-aryl dienyl carbonyl compounds with full control over other selectivities preserved. This rigorous diastereodivergence is enabled by the slight structural adjustment of a chiral iminophosphorane catalyst, providing access to all the stereoisomers with high regio-, distereo- and enantioselectivity. The utility of this method is demonstrated in the facile stereodivergent preparation of densely functionalized proline derivatives. The experimental and computational elucidation of the origin of the diastereodivergence is also reported. PMID:28317928

  19. 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

  20. Selectivity control between Mizoroki-Heck and homo-coupling reactions for synthesising multinuclear metal complexes: unique addition effects of tertiary phosphines and O2.

    PubMed

    Yamazaki, Yasuomi; Ishitani, Osamu

    2017-04-05

    The addition of a tertiary phosphine and O2 to reaction solutions strongly affected the reactivity and selectivity of coupling reactions between transition metal complexes. The Mizoroki-Heck reaction between metal complexes with bromo and those with vinyl groups in the diimine ligand did not proceed using Pd(OAc)2 in the presence of 2-dicyclohexylphosphino-2',6'-dimethoxybiphenyl (Sphos) under Ar but proceeded selectively after injection of air into the reaction vessel. In the absence of the phosphine ligand, on the other hand, not only the Mizoroki-Heck reaction but also a homo-coupling reaction between the metal complexes with the bromo groups proceeded at the same time. Mechanistic investigation showed that nanoparticles of Pd species were produced in the absence of the phosphine ligand and worked as catalysts for both the Mizoroki-Heck and homo-coupling reactions. On the other hand, larger Pd particles, which were produced in the presence of Sphos but after addition of air for oxidising Sphos, selectively catalysed the Mizoroki-Heck reaction. 'Molecular' Pd species that were stabilised in the presence of non-oxidised Sphos could not catalyse both coupling reactions under the reaction conditions. Based on these results, reaction conditions were established for the selective progress of the Mizoroki-Heck and the homo-coupling reactions.

  1. 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.

  2. Photolytic, thermal, addition, and cycloaddition reactions of 2-diazo-5,6- and -3,8-disubstituted acenaphthenones.

    PubMed

    Blair, Patricia A; Chang, Sou-Jen; Shechter, Harold

    2004-10-15

    Preparation and varied thermal and photolytic reactions of 2-diazo-5,6-(disubstituted)acenaphthenones (11a-d) and 2-diazo-3,8-dimethoxyacenaphthenone (12) are reported. Alcohols react thermally and photolytically with 11a-c with losses of N(2) to yield 2-alkoxynaphthenones (24a,band 47a,b) and acenaphthenones (25 and 48a,b). Aniline and diphenylamine are converted by 11a-c at 180 degrees C to acenaph[1,2-b]indoles (29a,b and 53a,b). Thermolyses of 11a-c at approximately 450 degrees C (0.15 mmHg) yield reduction products 25 and 48a,b, respectively. Wolff rearrangements to 1,8-naphthyleneketenes (15a-d) and/or their derivatives are not observed in the above experiments. Oxygen converts 11a-c thermally to acenaphthenequinones (19a-c) and/or 1,8-naphthalic anhydrides. Insertion, addition, substitution, and/or isomerization reactions occur upon irradiation of 2-diazoacenaphthenones in cyclohexane, benzene, and tetrahydrofuran. Photolysis of 11d in benzene in the presence of O(2) yields the insertion-oxidation product 2-hydroxy-5,6-dinitro-2-phenylacenaphthenone (60). Photolyses of 11a-c in nitriles result in N(2) evolution and dipolar cycloaddition to give acenaph[1,2-d]oxazoles (41 and 61a,b). Acetylenes undergo thermal and photolytic cycloaddition/1,5-sigmatropic rearrangement reactions with 11a-d with N(2) retention to give pyrazolo[5,1-a]quinolin-7-ones (69f-j). 2-Diazoacenaphthenones 1a and 11a react thermally and photolytically with electronegatively-substituted olefins with N(2) expulsion to yield (E)- and (Z)-2-oxospiro[acenaphthylene-1(2H),1'cyclopropanes] 73a-c and 74a-c, respectively. The mechanisms of the reactions of 1a, 11a-d, and 12 reported are discussed.

  3. Disproportionation of rosin on an industrial Pd/C catalyst: reaction pathway and kinetic model discrimination.

    PubMed

    Souto, Juan Carlos; Yustos, Pedro; Ladero, Miguel; Garcia-Ochoa, Felix

    2011-02-01

    In this work, a phenomenological study of the isomerisation and disproportionation of rosin acids using an industrial 5% Pd on charcoal catalyst from 200 to 240°C is carried out. Medium composition is determined by elemental microanalysis, GC-MS and GC-FID. Dehydrogenated and hydrogenated acid species molar amounts in the final product show that dehydrogenation is the main reaction. Moreover, both hydrogen and non-hydrogen concentration considering kinetic models are fitted to experimental data using a multivariable non-linear technique. Statistical discrimination among the proposed kinetic models lead to the conclusion hydrogen considering models fit much better to experimental results. The final kinetic model involves first-order isomerisation reactions of neoabietic and palustric acids to abietic acid, first-order dehydrogenation and hydrogenation of this latter acid, and hydrogenation of pimaric acids. Hydrogenation reactions are partial first-order regarding the acid and hydrogen.

  4. 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

  5. Ab initio characterization of (CH3IO3) isomers and the CH3O2 + IO reaction pathways.

    PubMed

    Drougas, Evangelos; Kosmas, Agnie M

    2007-05-03

    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.

  6. 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.

  7. 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

    2014-11-20

    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. 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.

  8. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    NASA Astrophysics Data System (ADS)

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-11-01

    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.

  9. Modeling reaction pathways of low energy particle deposition on thiophene via ab initio calculations

    NASA Astrophysics Data System (ADS)

    Crenshaw, Jasmine D.; Phillpot, Simon R.; Iordanova, Nedialka; Sinnott, Susan B.

    2011-07-01

    Chemical reactions of thiophene with organic molecules are of interest to modify thermally deposited coatings of conductive polymers. Here, energy barriers for reactions involving thiophene and small hydrocarbon radicals are identified. Enthalpies of formation involving reactants are also calculated using the B3LYP, BMK, and B98 hybrid functionals within the G AUSSIAN03 program. Experimental values, G3, and CBS-QB3 calculations are used as standards, due to their accurate thermochemistry parameters. The BMK functional is found to perform best for the selected organic molecules. These results provide insights into the reactivity of several polymerization and deposition processes.

  10. 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.

  11. Cathodic Aromatic C,C Cross-Coupling Reaction via Single Electron Transfer Pathway.

    PubMed

    Qu, Yang; Tateno, Hiroyuki; Matsumura, Yoshimasa; Kashiwagi, Tsuneo; Atobe, Mahito

    2017-03-07

    We have successfully developed a novel cathodic cross-coupling reaction of aryl halides with arenes. Utilization of the cathodic single electron transfer (SET) mechanism for activation of aryl halides enables the cross-coupling reaction to proceed without the need for any transition metal catalysts or single electron donors in a mild condition. The SET from a cathode to an aryl halide initiates a radical chain by giving an anion radical of the aryl halide. The following propagation cycle also consists entirely of anion radical intermediates.

  12. Novel syn intramolecular pathway in base-catalyzed 1,2-elimination reactions of beta-acetoxy esters.

    PubMed

    Mohrig, Jerry R; Carlson, Hans K; Coughlin, Jane M; Hofmeister, Gretchen E; McMartin, Lea A; Rowley, Elizabeth G; Trimmer, Elizabeth E; Wild, Andrew J; Schultz, Steve C

    2007-02-02

    As part of a comprehensive investigation of electronic effects on the stereochemistry of base-catalyzed 1,2-elimination reactions, we observed a new syn intramolecular pathway in the elimination of acetic acid from beta-acetoxy esters and thioesters. 1H and 2H NMR investigation of reactions using stereospecifically labeled tert-butyl (2R*,3R*)-3-acetoxy-2,3-2H2-butanoate (1) and its (2R*,3S*) diastereomer (2) shows that 23 +/- 2% syn elimination occurs. The elimination reactions were catalyzed with KOH or (CH3)4NOH in ethanol/water under rigorously non-ion-pairing conditions. By contrast, the more sterically hindered beta-trimethylacetoxy ester produces only 6 +/- 1% syn elimination. These data strongly support an intramolecular (Ei) syn path for elimination of acetic acid, most likely through the oxyanion produced by nucleophilic attack at the carbonyl carbon of the beta-acetoxy group. The analogous thioesters, S-tert-butyl (2R*,3R*)-3-acetoxy-2,3-2H2-butanethioate (3) and its (2R*,3S*) diastereomer (4), showed 18 +/- 2% syn elimination, whereas the beta-trimethylacetoxy substrate gave 5 +/- 1% syn elimination. The more acidic thioester substrates do not produce an increased amount of syn stereoselectivity even though their elimination reactions are at the E1cb interface.

  13. Global-scale quantification of mineralization pathways in marine sediments: A reaction-transport modeling approach

    NASA Astrophysics Data System (ADS)

    Thullner, Martin; Dale, Andrew W.; Regnier, Pierre

    2009-10-01

    The global-scale quantification of organic carbon (Corg) degradation pathways in marine sediments is difficult to achieve experimentally due to the limited availability of field data. In the present study, a numerical modeling approach is used as an alternative to quantify the major metabolic pathways of Corg oxidation (Cox) and associated fluxes of redox-sensitive species fluxes along a global ocean hypsometry, using the seafloor depth (SFD) as the master variable. The SFD dependency of the model parameters and forcing functions is extracted from existing empirical relationships or from the NOAA World Ocean Atlas. Results are in general agreement with estimates from the literature showing that the relative contribution of aerobic respiration to Cox increases from <10% at shallow SFD to >80% in deep-sea sediments. Sulfate reduction essentially follows an inversed SFD dependency, the other metabolic pathways (denitrification, Mn and Fe reduction) only adding minor contributions to the global-scale mineralization of Corg. The hypsometric analysis allows the establishment of relationships between the individual terminal electron acceptor (TEA) fluxes across the sediment-water interface and their respective contributions to the Corg decomposition process. On a global average, simulation results indicate that sulfate reduction is the dominant metabolic pathway and accounts for approximately 76% of the total Cox, which is higher than reported so far by other authors. The results also demonstrate the importance of bioirrigation for the assessment of global species fluxes. Especially at shallow SFD most of the TEAs enter the sediments via bioirrigation, which complicates the use of concentration profiles for the determination of total TEA fluxes by molecular diffusion. Furthermore, bioirrigation accounts for major losses of reduced species from the sediment to the water column prohibiting their reoxidation inside the sediment. As a result, the total carbon mineralization

  14. 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.

  15. Reaction of antibiotic sulfadiazine with manganese dioxide in aqueous phase: Kinetics, pathways and toxicity assessment.

    PubMed

    Yang, Ji-Feng; Yang, Li-Ming; Ying, Guang-Guo; Liu, Cheng-Bin; Zheng, Li-Ying; Luo, Sheng-Lian

    2017-01-28

    Sulfonamide antibiotics are often detected in terrestrial and aquatic environment, but little is known about abiotic degradation of these antibiotics. In the present study, the degradation of the sulfonamide antibiotic sulfadiazine by a synthesized δ-MnO2 was investigated. The initial reaction rate of sulfadiazine oxidized by manganese dioxide increased as the solution pH decreased by weakening electrostatic attraction between sulfadiazine and MnO2 and enhancing the reduction potential of MnO2. The presence of metal ions (Mn(2+), Na(+) and Ca(2+)), especially Mn(2+), decreased the initial reaction rate by competitively adsorbing and reacting with MnO2. Two different products were identified during the reaction of sulfadiazine with MnO2 and the transformation of parent compound started with the formation of sulfadiazine radicals. Furthermore, toxicity assay results showed that the toxicity of products produced by bacteria decreased with elapse of reaction time. Results from the present study indicate that manganese dioxides in environmental matrix could be helpful in dissipation of sulfadiazine released into the environment.

  16. 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.

  17. Tunneling Effect That Changes the Reaction Pathway from Epoxidation to Hydroxylation in the Oxidation of Cyclohexene by a Compound I Model of Cytochrome P450.

    PubMed

    Gupta, Ranjana; Li, Xiao-Xi; Cho, Kyung-Bin; Guo, Mian; Lee, Yong-Min; Wang, Yong; Fukuzumi, Shunichi; Nam, Wonwoo

    2017-04-06

    The rate constants of the C═C epoxidation and the C-H hydroxylation (i.e., allylic C-H bond activation) in the oxidation of cyclohexene by a high-valent iron(IV)-oxo porphyrin π-cation radical complex, [(TMP(•+))Fe(IV)(O)(Cl)] (1, TMP = meso-tetramesitylporphyrin dianion), were determined at various temperatures by analyzing the overall rate constants and the products obtained in the cyclohexene oxidation by 1, leading us to conclude that reaction pathway changes from the C═C epoxidation to C-H hydroxylation by decreasing reaction temperature. When cyclohexene was replaced by deuterated cyclohexene (cyclohexene-d10), the epoxidation pathway dominated irrespective of the reaction temperature. The temperature dependence of the rate constant of the C-H hydroxylation pathway in the reactions of cyclohexene and cyclohexene-d10 by 1 suggests that there is a significant tunneling effect on the hydrogen atom abstraction of allylic C-H bonds of cyclohexene by 1, leading us to propose that the tunneling effect is a determining factor for the switchover of the reaction pathway from the C═C epoxidation pathway to the C-H hydroxylation pathway by decreasing reaction temperature. By performing density functional theory (DFT) calculations, the reaction energy barriers of the C═C epoxidation and C-H bond activation reactions by 1 were found to be similar, supporting the notion that small environmental changes, such as the reaction temperature, can flip the preference for one reaction to another.

  18. Role of Lewis acid additives in a palladium catalyzed directed C-H functionalization reaction of benzohydroxamic acid to isoxazolone.

    PubMed

    Athira, C; Sunoj, Raghavan B

    2016-12-20

    Metallic salts as well as protic additives are widely employed in transition metal catalyzed C-H bond functionalization reactions to improve the efficiency of catalytic protocols. In one such example, ZnCl2 and pivalic acid are used as additives in a palladium catalyzed synthesis of isoxazolone from a readily available benzohydroxamic acid under one pot conditions. In this article, we present some important mechanistic insights into the role of ZnCl2 and pivalic acid, gained by using density functional theory (M06) computations. Two interesting modes of action of ZnCl2 are identified in various catalytic steps involved in the formation of isoxazolone. The conventional Lewis acid coordination wherein zinc chloride (ZnCl2·(DMA)) binds to the carbonyl group is found to be more favored in the C-H activation step. However, the participation of a hetero-bimetallic Pd-Zn species is preferred in reductive elimination leading to Caryl-N bond formation. Pivalic acid helps in relay proton transfer in C-H bond activation through a cyclometallation deprotonation (CMD) process. The explicit inclusion of ZnCl2 and solvent N,N-dimethyl acetamide (DMA) stabilizes the transition state and also helps reduce the activation barrier for the C-H bond activation step. The electronic communication between the two metal species is playing a crucial role in stabilizing the Caryl-N bond formation transition state through a Pd-Zn hetero-bimetallic interaction.

  19. Sintered-reaction Bonded Silicon Nitride Densified by a Gas Pressure Sintering Process Effects of Rare Earth Oxide Sintering Additives

    SciTech Connect

    Lee, S. H.; Ko, J. W.; Park, Y. J.; Kim, H. D.; Lin, Hua-Tay; Becher, Paul F

    2012-01-01

    Reaction-bonded silicon nitrides containing rare-earth oxide sintering additives were densified by gas pressure sintering. The sintering behavior, microstructure and mechanical properties of the resultant specimens were analyzed. For that purpose, Lu2O3-SiO2 (US), La2O3-MgO (AM) and Y2O3-Al2O3 (YA) additive systems were selected. Among the tested compositions, densification of silicon nitride occurred at the lowest temperature when using the La2O3-MgO system. Since the Lu2O3-SiO2 system has the highest melting temperature, full densification could not be achieved after sintering at 1950oC. However, the system had a reasonably high bending strength of 527 MPa at 1200oC in air and a high fracture toughness of 9.2 MPa m1/2. The Y2O3-Al2O3 system had the highest room temperature bending strength of 1.2 GPa

  20. Hydrogen radical additions to unsaturated hydrocarbons and the reverse beta-scission reactions: modeling of activation energies and pre-exponential factors.

    PubMed

    Sabbe, Maarten K; Reyniers, Marie-Françoise; Waroquier, Michel; Marin, Guy B

    2010-01-18

    The group additivity method for Arrhenius parameters is applied to hydrogen addition to alkenes and alkynes and the reverse beta-scission reactions, an important family of reactions in thermal processes based on radical chemistry. A consistent set of group additive values for 33 groups is derived to calculate the activation energy and pre-exponential factor for a broad range of hydrogen addition reactions. The group additive values are determined from CBS-QB3 ab-initio-calculated rate coefficients. A mean factor of deviation of only two between CBS-QB3 and experimental rate coefficients for seven reactions in the range 300-1000 K is found. Tunneling coefficients for these reactions were found to be significant below 400 K and a correlation accounting for tunneling is presented. Application of the obtained group additive values to predict the kinetics for a set of 11 additions and beta-scissions yields rate coefficients within a factor of 3.5 of the CBS-QB3 results except for two beta-scissions with severe steric effects. The mean factor of deviation with respect to experimental rate coefficients of 2.0 shows that the group additive method with tunneling corrections can accurately predict the kinetics and is at least as accurate as the most commonly used density functional methods. The constructed group additive model can hence be applied to predict the kinetics of hydrogen radical additions for a broad range of unsaturated compounds.

  1. The Coupled Photothermal Reaction and Transport in a Laser Additive Metal Nanolayer Simultaneous Synthesis and Pattering for Flexible Electronics.

    PubMed

    Tsai, Song-Ling; Liu, Yi-Kai; Pan, Heng; Liu, Chien-Hung; Lee, Ming-Tsang

    2016-01-08

    The Laser Direct Synthesis and Patterning (LDSP) technology has advantages in terms of processing time and cost compared to nanomaterials-based laser additive microfabrication processes. In LDSP, a scanning laser on the substrate surface induces chemical reactions in the reactive liquid solution and selectively deposits target material in a preselected pattern on the substrate. In this study, we experimentally investigated the effect of the processing parameters and type and concentration of the additive solvent on the properties and growth rate of the resulting metal film fabricated by this LDSP technology. It was shown that reactive metal ion solutions with substantial viscosity yield metal films with superior physical properties. A numerical analysis was also carried out the first time to investigate the coupled opto-thermo-fluidic transport phenomena and the effects on the metal film growth rate. To complete the simulation, the optical properties of the LDSP deposited metal film with a variety of thicknesses were measured. The characteristics of the temperature field and the thermally induced flow associated with the moving heat source are discussed. It was shown that the processing temperature range of the LDSP is from 330 to 390 K. A semi-empirical model for estimating the metal film growth rate using this process was developed based on these results. From the experimental and numerical results, it is seen that, owing to the increased reflectivity of the silver film as its thickness increases, the growth rate decreases gradually from about 40 nm at initial to 10 nm per laser scan after ten scans. This self-controlling effect of LDSP process controls the thickness and improves the uniformity of the fabricated metal film. The growth rate and resulting thickness of the metal film can also be regulated by adjustment of the processing parameters, and thus can be utilized for controllable additive nano/microfabrication.

  2. The Coupled Photothermal Reaction and Transport in a Laser Additive Metal Nanolayer Simultaneous Synthesis and Pattering for Flexible Electronics

    PubMed Central

    Tsai, Song-Ling; Liu, Yi-Kai; Pan, Heng; Liu, Chien-Hung; Lee, Ming-Tsang

    2016-01-01

    The Laser Direct Synthesis and Patterning (LDSP) technology has advantages in terms of processing time and cost compared to nanomaterials-based laser additive microfabrication processes. In LDSP, a scanning laser on the substrate surface induces chemical reactions in the reactive liquid solution and selectively deposits target material in a preselected pattern on the substrate. In this study, we experimentally investigated the effect of the processing parameters and type and concentration of the additive solvent on the properties and growth rate of the resulting metal film fabricated by this LDSP technology. It was shown that reactive metal ion solutions with substantial viscosity yield metal films with superior physical properties. A numerical analysis was also carried out the first time to investigate the coupled opto-thermo-fluidic transport phenomena and the effects on the metal film growth rate. To complete the simulation, the optical properties of the LDSP deposited metal film with a variety of thicknesses were measured. The characteristics of the temperature field and the thermally induced flow associated with the moving heat source are discussed. It was shown that the processing temperature range of the LDSP is from 330 to 390 K. A semi-empirical model for estimating the metal film growth rate using this process was developed based on these results. From the experimental and numerical results, it is seen that, owing to the increased reflectivity of the silver film as its thickness increases, the growth rate decreases gradually from about 40 nm at initial to 10 nm per laser scan after ten scans. This self-controlling effect of LDSP process controls the thickness and improves the uniformity of the fabricated metal film. The growth rate and resulting thickness of the metal film can also be regulated by adjustment of the processing parameters, and thus can be utilized for controllable additive nano/microfabrication.

  3. 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.

  4. Disclosing Whole Reaction Pathways of Photochromic 3H-Naphthopyrans with Fast Color Fading.

    PubMed

    Brazevic, Sabina; Sliwa, Michel; Kobayashi, Yoichi; Abe, Jiro; Burdzinski, Gotard

    2017-03-02

    Instantaneous coloration with large absorbance and quick color fading in the dark are desired properties for thermally reversible photochromic compounds. In the case of naphthopyran derivatives, which have been employed to commercial ophthalmic lenses, the quick color fading has been recently achieved by suppression of the generation of the transoid-trans (TT) form by steric hindrance of bulky substituents. However, there are still open questions whether the steric hindrance decreases the photochromic reaction efficiency, which is a crucial problem for industrial applications. Herein, we apply a wide range of electronic and vibrational time-resolved spectroscopies and reveal that the photochromic reaction yields of the naphthopyrans with bulky substituents are almost comparable (∼0.7) to that of nonsubstituted naphthopyran. The suppression of the formation of the TT form and the effect of solvent polarity on the photodynamics are systematically investigated. These findings are important for fundamental photochemistry and developing naphthopyran-based optimal photofunctional materials.

  5. 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.

  6. 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.

  7. Structural requirements and reaction pathways in dimethyl ether combustion catalyzed by supported Pt clusters.

    PubMed

    Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

    2007-10-31

    The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These conclusions are consistent with the measured kinetic response of combustion rates to DME, O2, and H2O, with H/D kinetic isotope effects, and with the absence of isotopic scrambling in reactants containing isotopic mixtures of 18O2-16O2 or 12CH3O12CH3-13CH3O13CH3. Turnover rates increased with Pt

  8. Structural Requirements and Reaction Pathways in Dimethyl Ether Combustion Catalyzed by Supported Pt Clusters

    SciTech Connect

    Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

    2007-10-31

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These

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

    SciTech Connect

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

    1999-11-04

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

  10. 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

  11. 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.

  12. Nucleophilic addition to olefins. 19. Abnormally high intrinsic barrier in the reaction of piperidine and morpholine with benzylideneacetylacetone

    SciTech Connect

    Bernasconi, C.F.; Kanavarioti, A.

    1986-11-26

    The title reaction leads to the formation of the zwitterionic Michael adduct T/sup +/-/ (PhCH(R/sub 2/NH/sup +/)C(COCH/sub 3/)/sub 2//sup -/) which is in rapid acid-base equilibrium with its anionic form T/sup -/ (PhCH(R/sub 2/N)C(COCH/sub 3/)/sub 2//sup -/). Rate (K/sub 1/, k/sub -1/) and equilibrium constants (K/sub 1/) for nucleophilic addition and the pK/sub a/ of the T/sup +/-/-adducts were determined in 50% Me/sub 2/SO-50% water at 20/sup 0/C. From an interpolation of the rate constants to K/sub 1/ = 1 an intrinsic rate constant, log k/sub 0/ = 0.3, was determined. This value deviates negatively by approximately 2.5 log units from a correlation of log k/sub 0/ for amine addition to five olefins of the type PhCH=CXY, with log k/sub 0/ for the deprotonation of the corresponding carbon acids CH/sub 2/XY. Two major factors are believed to contribute to this depressed intrinsic rate constant or enhanced intrinsic barrier: (1) steric inhibition of resonance in T/sup +/-/ with the steric effect developing ahead of C-N bond formation (this conclusion is supported by an X-ray crystallographic study of p-methoxybenzylideneacetylacetone which shows that steric hindrance to optimal ..pi..-overlap in the adduct T/sup+/-/ is already present in the substrate); (2) intramolecular hydrogen bonding in T/sup +/-/, which is inferred from abnormally high pK/sub a/ values and whose development lags behind C-N bond formation. These effects are shown to be manifestations of the Principle of Nonperfect Synchronization.

  13. 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.

  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.

  15. Bifunctional Molecular Photoswitches Based on Overcrowded Alkenes for Dynamic Control of Catalytic Activity in Michael Addition Reactions.

    PubMed

    Pizzolato, Stefano F; Collins, Beatrice S L; van Leeuwen, Thomas; Feringa, Ben L

    2016-11-23

    The emerging field of artificial photoswitchable catalysis has recently shown striking examples of functional light-responsive systems allowing for dynamic control of activity and selectivity in organocatalysis and metal-catalysed transformations. While our group has already disclosed systems featuring first generation molecular motors as the switchable central core, a design based on second generation molecular motors is lacking. Here, the syntheses of two bifunctionalised molecular switches based on a photoresponsive tetrasubstituted alkene core are reported. They feature a thiourea substituent as hydrogen-donor moiety in the upper half and a basic dimethylamine group in the lower half. This combination of functional groups offers the possibility for application of these molecules in photoswitchable catalytic processes. The light-responsive central cores were synthesized by a Barton-Kellogg coupling of the prefunctionalized upper and lower halves. Derivatization using Buchwald-Hartwig amination and subsequent introduction of the thiourea substituent afforded the target compounds. Control of catalytic activity in the Michael addition reaction between (E)-3-bromo-β-nitrostyrene and 2,4-pentanedione is achieved upon irradiation of stable-(E) and stable-(Z) isomers of the bifunctional catalyst 1. Both isomers display a decrease in catalytic activity upon irradiation to the metastable state, providing systems with the potential to be applied as ON/OFF catalytic photoswitches.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Spatiotemporal reaction kinetics of an ultrafast photoreaction pathway visualized by time-resolved liquid x-ray diffraction.

    PubMed

    Kim, Tae Kyu; Lorenc, Maciej; Lee, Jae Hyuk; Lo Russo, Manuela; Kim, Joonghan; Cammarata, Marco; Kong, Qingyu; Noel, Sylvie; Plech, Anton; Wulff, Michael; Ihee, Hyotcherl

    2006-06-20

    We have studied the reaction dynamics for HgI(2) in methanol by using time-resolved x-ray diffraction (TRXD). Although numerous time-resolved spectroscopic studies have provided ample information about the early dynamics of HgI(2), a comprehensive reaction mechanism in the solution phase spanning from picoseconds up to microseconds has been lacking. Here we show that TRXD can provide this information directly and quantitatively. Picosecond optical pulses triggered the dissociation of HgI(2), and 100-ps-long x-ray pulses from a synchrotron probed the evolving structures over a wide temporal range. To theoretically explain the diffracted intensities, the structural signal from the solute, the local structure around the solute, and the hydrodynamics of bulk solvents were considered in the analysis. The results in this work demonstrate that the determination of transient states in solution is strongly correlated with solvent energetics, and TRXD can be used as an ultrafast calorimeter. It also is shown that a manifold of structural channels can be resolved at the same time if the measurements are accurate enough and that global analysis is applied. The rate coefficients for the reactions were obtained by fitting our model against the experimental data in one global fit including all q-values and time delays. The comparison between all putative reaction channels confirms that two-body dissociation is the dominant dissociation pathway. After this primary bond breakage, two parallel channels proceed. Transient HgI associates nongeminately with an iodine atom to form HgI(2), and I(2) is formed by nongeminate association of two iodine atoms.

  2. A halogenophilic pathway in the reactions of transition metal carbonyl anions with [(η⁶-iodobenzene)Cr(CO)₃].

    PubMed

    Sazonov, Petr K; Ivushkin, Vasiliy A; Khrustalev, Victor N; Kolotyrkina, Natal'ya G; Beletskaya, Irina P

    2014-09-21

    The paper provides the first example of formal nucleophilic substitution by the halogenophilic pathway in Cr(CO)3 complexes of haloarenes with metal carbonyl anions. All metal carbonyl anions examined attack [(η(6)-iodobenzene)Cr(CO)3] at halogen, which is shown by aryl carbanion scavenging with t-BuOH. The reaction with K[CpFe(CO)2] gives only the dehalogenated arene, but the reaction with K[Cp*Fe(CO)2] (Cp* = η(5)-C5Me5) results in nucleophilic substitution to give [(η(6)-C6H5FeCp*(CO)2)Cr(CO)3]. Reaction with Na[Re(CO)5] quantitatively gives the iodo(acyl)rhenate anion Na[(η(6)-C6H5C(O)ReI(CO)4)Cr(CO)3] and in the case of K[Mn(CO)5] a mixture of σ-aryl complexes [(η(6)-C6H5Mn(CO)5)Cr(CO)3] and K[(η(6)-C6H5Mn(CO)4I)Cr(CO)3]. An analogous rhenium complex Na[(η(6)-C6H5Re(CO)4I)Cr(CO)3] is formed from the initial iodo(acyl)rhenate upon prolonged standing at 20 °C, and its structure (in the form of [NEt4](+) salt) is established by X-ray diffraction analysis. The reaction of [(η(6)-chlorobenzene)Cr(CO)3] with K[CpFe(CO)2], in contrast, proceeds by the common S(N)2Ar mechanism.

  3. 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.

  4. Kinetic and Reaction Pathway Analysis in the Application of Botulinum Toxin A for Wound Healing

    PubMed Central

    Lebeda, Frank J.; Dembek, Zygmunt F.; Adler, Michael

    2012-01-01

    A relatively new approach in the treatment of specific wounds in animal models and in patients with type A botulinum toxin is the focus of this paper. The indications or conditions include traumatic wounds (experimental and clinical), surgical (incision) wounds, and wounds such as fissures and ulcers that are signs/symptoms of disease or other processes. An objective was to conduct systematic literature searches and take note of the reactions involved in the healing process and identify corresponding pharmacokinetic data. From several case reports, we developed a qualitative model of how botulinum toxin disrupts the vicious cycle of muscle spasm, pain, inflammation, decreased blood flow, and ischemia. We transformed this model into a minimal kinetic scheme for healing chronic wounds. The model helped us to estimate the rate of decline of this toxin's therapeutic effect by calculating the rate of recurrence of clinical symptoms after a wound-healing treatment with this neurotoxin. PMID:22174710

  5. Communication: Energetics of reaction pathways for reactions of ethenol with the hydroxyl radical: the importance of internal hydrogen bonding at the transition state.

    PubMed

    Tishchenko, Oksana; Ilieva, Sonia; Truhlar, Donald G

    2010-07-14

    We find high multireference character for abstraction of H from the OH group of ethenol (also called vinyl alcohol); therefore we adopt a multireference approach to calculate barrier heights for the various possible reaction channels of OH+C(2)H(3)OH. The relative barrier heights of ten possible saddle points for reaction of OH with ethenol are predicted by multireference Møller-Plesset perturbation theory with active spaces based on correlated participating orbitals (CPOs) and CPO plus a correlated pi orbital (CPO+pi). Six barrier heights for abstracting H from a C-H bond range from 3.1 to 7.7 kcal/mol, two barrier heights for abstracting H from an O-H bond are both 6.0 kcal/mol, and two barrier heights for OH addition to the double bond are -1.8 and -2.8 kcal/mol. Thus we expect abstraction at high-temperature and addition at low temperature. The factor that determines which H is most favorable to abstract is an internal hydrogen bond that constitutes part of a six-membered ring at one of the abstraction saddle points; the hydrogen bond contributes about 3 kcal/mol stabilization.

  6. CO2-induced degradation of amine-containing adsorbents: reaction products and pathways.

    PubMed

    Sayari, Abdelhamid; Heydari-Gorji, Aliakbar; Yang, Yong

    2012-08-22

    A comprehensive study was conducted to investigate the stability of a wide variety of mesoporous silica-supported amine-containing adsorbents in the presence of carbon dioxide under dry conditions. CO(2)-induced degradation of grafted primary and secondary monoamines (pMono, sMono), diamines with one primary and one secondary amines (Diamine) and triamine with one primary and two secondary amines (TRI) as well as different impregnated polyamines such as branched and linear polyethylenimine (BPEI and LPEI) and polyallylamine (PALL) was investigated using extensive CO(2) adsorption-desorption cycling as well as diffuse reflectance infrared Fourier transform (DRIFT) and (13)C CP MAS NMR measurements. Except for sMono, all other supported amines underwent significant deactivation in the presence of dry CO(2) under mild conditions. In all cases, the decrease in CO(2) uptake was associated with the formation of urea linkages at the expense of amine groups. The urea-containing species were identified, and the deactivation pathways were delineated.

  7. Characterization of metabolic pathway of linoleic acid 9-hydroperoxide in cytosolic fraction of potato tubers and identification of reaction products.

    PubMed

    Kimura, Hideto; Yokota, Kazushige

    2004-01-01

    Potato tubers are shown to contain a unique lipoxygenase pathway to form 9-hydroperoxy-10,12-octadecadienoic acid (9-HPODE) from linoleic acid. Here, we report the metabolic pathway of 9-HPODE in the cytosolic fraction and the characterization of enzymes involved in the conversion of metabolites. The analysis of enzymatic reaction products at pH 5.5 revealed the formation of 9-keto-10,12-octadecadienoic acid, 9-hydroxy-10,12-octadecadienoic acid, 9,10-epoxy-11-hydroxy-12-octadecenoic acid, 9,10,13-trihydroxy-11-octadecenoic acid, and 9,12,13-trihydroxy-10-octadecenoic acid. The cytosolic enzymes were separated by anion-exchange chromatography into two fractions E1 and E2, having molecular masses of 66 and 54 kDa, respectively. The enzyme fraction E1 only produced 9-keto-10,12-octadecadienoic acid, whereas E2 formed other products. The enzyme E1 showed higher reactivity with 13- and 9-hydroperoxide of alpha-linolenic acid than 9-HPODE, but no reaction with hydroxy fatty acids. In contrast, the enzyme E2 showed the highest reactivity with 9-HPODE, followed by hydroperoxides of alpha-linolenic acid and arachidonic acid. We also evaluated the antibacterial activity of hydroxy fatty acids against Erwinia carotovora T-29, a bacterium infecting potato tubers. Growth of the bacteria was suppressed more potently with 9- or 13-hydroxy fatty acids than dihydroxy or trihydroxy fatty acids, suggesting a role for the metabolites in the resistance of bacterial infection.

  8. Pathways of arachidonic acid peroxyl radical reactions and product formation with guanine radicals.

    PubMed

    Crean, Conor; Geacintov, Nicholas E; Shafirovich, Vladimir

    2008-02-01

    Peroxyl radicals were derived from the one-electron oxidation of polyunsaturated fatty acids by sulfate radicals that were generated by the photodissociation of peroxodisulfate anions in air-equilibrated aqueous solutions. Reactions of these peroxyl and neutral guanine radicals, also generated by oxidation with sulfate radicals, were investigated by laser kinetic spectroscopy, and the guanine oxidation products were identified by HPLC and mass spectrometry methods. Sulfate radicals rapidly oxidize arachidonic (ArAc), linoleic (LnAc), and palmitoleic (PmAc) acids with similar rate constants, (2-4) x 10 (9) M (-1) s (-1). The C-centered radicals derived from the oxidation of ArAc and LnAc include nonconjugated Rn(.) ( approximately 80%) and conjugated bis-allylic Rba(.) ( approximately 20%) radicals. The latter were detectable in the absence of oxygen by their prominent, narrow absorption band at 280 nm. The Rn(.) radicals of ArAc (containing three bis-allylic sites) transform to the Rba(.) radicals via an intramolecular H-atom abstraction [rate constant (7.5 +/- 0.7) x 10 (4) s (-1)]. In contrast, the Rn(.) radicals of LnAc that contain only one bis-allylic site do not transform intramolecularly to the Rba(.) radicals. In the case of PmAc, which contains only one double bond, the Rba(.) radicals are not observed. The Rn(.) radicals of PmAc rapidly combine with oxygen with a rate constant of (3.8 +/- 0.4) x 10(9) M(-1) s(-1). The Rba(.) radicals of ArAc are less reactive and react with oxygen with a rate constant of (2.2 +/- 0.2) x 10 (8) M (-1) s (-1). The ArAc peroxyl radicals formed spontaneously eliminate superoxide radical anions [rate constant = (3.4 +/- 0.3) x 10 (4) M (-1) s (-1)]. The stable oxidative lesions derived from the 2',3',5'-tri- O-acetylguanosine or 2',3',5'-tri- O-acetyl-8-oxo-7,8-dihydroguanosine radicals and their subsequent reactions with ArAc peroxyl radicals were also investigated. The major products found were the 2,5-diamino-4 H

  9. 78 FR 36041 - Regulation of Fuels and Fuel Additives: RFS Pathways II and Technical Amendments to the RFS 2...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-14

    ... Renewable Fuel and That are Registered for RIN Generation 3. Changes Applicable to all Biogas Related Pathways for RIN Generation 4. Changes Applicable To Process Electricity Production Requirement for the... feedstock. The first involved food waste or yard waste that was kept separate, from generation,...

  10. 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.

  11. An examination of the reaction pathways for the HOOOBr and HOOBrO complexes formed from the HO{sub 2} + BrO reaction

    SciTech Connect

    Guha, S.; Francisco, J.S.

    1999-10-07

    The geometries, vibrational spectra, and relative energetics of the HBrO{sub 3} isomers (HOOOBr and HOOBrO) and their transition states have been examined by using the quadratic configuration interaction method in conjunction with various basis sets. From the dissociation energies of the HBrO{sub 3} isomers, it is found that the most energetically favorable process during the HO{sub 2} + BrO reaction pathway is the formation of HOOBrO as an intermediate, and its eventual dissociation into HOBr and O{sub 2}, due to the very low energy barrier (2.8 kcal mol{sup {minus}1}) involved. The HOOOBr species, if formed as an intermediate, will be more likely to dissociate into HBr + O{sub 3} rather than HOBr + O{sub 2}, as the energy barrier for the latter process is quite high (26.4 kcal mol{sup {minus}1}) relative to the energy barrier for the HOOOBr {r{underscore}arrow} HBr + O{sub 3} dissociation process.

  12. 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.; ...

    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

  13. Dexmedetomidine attenuates inflammatory reaction in the lung tissues of septic mice by activating cholinergic anti-inflammatory pathway.

    PubMed

    Liu, Zhaoguo; Wang, Yueping; Wang, Yaoqi; Ning, Qiaoqing; Zhang, Yong; Gong, Chunzhi; Zhao, Wenxiang; Jing, Guangjian; Wang, Qianqian

    2016-06-01

    Dexmedetomidine (Dex) is a highly selective α2-adrenergic receptor agonist that is widely used for sedation in intensive care units and in clinical anesthesia. Dex has also been shown to possess anti-inflammatory benefits. However, the underlying mechanism by which Dex relieves the inflammatory reaction in the lung tissues of septic mice has not been fully elucidated. In this study, we aimed to evaluate the protective effects and possible mechanism of Dex on the sepsis-induced lung inflammatory response in mice. Sepsis was induced in mice models through the intraperitoneal injection of lipopolysaccharide (LPS). The preemptive administration of Dex substantially abated sepsis-induced pulmonary edema, pulmonary histopathological changes, and NF-κB p65 activity. The production of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) at both the mRNA and protein levels was also reduced. Moreover, these effects were significantly blocked by the α7 nicotinic acetylcholine receptor (α7nAChR) antagonist α-bungarotoxin (α-Bgt). α-Bgt aggravated pulmonary edema and pulmonary histopathological changes, as well as increased NF-κB p65 activity and TNF-α and IL-6 expression at both the mRNA and protein levels. The overall results demonstrate that Dex inhibits the LPS-induced inflammatory reaction in the lung tissues of septic mice partly through the α7nAChR-dependent cholinergic anti-inflammatory pathway.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  15. Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes.

    PubMed

    Barman, Prasenjit; Faponle, Abayomi S; Vardhaman, Anil Kumar; Angelone, Davide; Löhr, Anna-Maria; Browne, Wesley R; Comba, Peter; Sastri, Chivukula V; de Visser, Sam P

    2016-10-05

    Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes, which nature uses for the oxidation of metabolites and drugs. In biomimicry and bioremediation, an important reaction relates to the detoxification of ClOx(-) in water, which can lead to a mixture of products through bifurcated reactions. Herein we report the first three water-soluble non-heme iron(II) complexes that can generate chlorine dioxide from chlorite at ambient temperature and physiological pH. These complexes are highly active oxygenation oxidants and convert ClO2(-) into either ClO2 or ClO3¯ via high-valent iron(IV)-oxo intermediates. We characterize the short-lived iron(IV)-oxo species and establish rate constants for the bifurcation mechanism leading to ClO2 and ClO3(-) products. We show that the ligand architecture of the metal center plays a dominant role by lowering the reduction potential of the metal center. Our experiments are supported by computational modeling, and a predictive valence bond model highlights the various factors relating to the substrate and oxidant that determine the bifurcation pathway and explains the origins of the product distributions. Our combined kinetic, spectroscopic, and computational studies reveal the key components necessary for the future development of efficient chlorite oxidation catalysts.

  16. The Photoinitiated Reaction Pathway of Full-length Cyanobacteriochrome Tlr0924 Monitored Over 12 Orders of Magnitude*

    PubMed Central

    Hauck, Anna F. E.; Hardman, Samantha J. O.; Kutta, Roger J.; Greetham, Gregory M.; Heyes, Derren J.; Scrutton, Nigel S.

    2014-01-01

    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

  17. 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

  18. 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.

  19. In vitro metabolism studies of nomifensine monooxygenation pathways: metabolite identification, reaction phenotyping, and bioactivation mechanism.

    PubMed

    Yu, Jian; Brown, Dean G; Burdette, Doug

    2010-10-01

    Multiple GSH adducts of the oxidative products of nomifensine (M1-M9) in human hepatocytes and liver microsomes have been identified recently. The current study reports three new types of monooxygenated metabolites of nomifensine identified in human liver microsomes: C-linked hydroxylated metabolites with modifications at the A ring (H1 and H4), an N-hydroxylamine (H6), and nomifensine N-oxides (H7 and H8). GSH conjugate formation in incubates containing cDNA-expressed P450s and GSH suggests that nomifensine GSH-sulfinamides (M1 and M2) are formed through the reaction between GSH and the oxidative product of H6. C-linked GSH conjugates M3, M4, M5, and M6 are probably formed via nomifensine benzoquinone imine intermediates via H4 and/or nomifensine epoxides. C-linked GSH conjugates M7, M8, and M9 are probably formed through similar mechanisms via H1. Nomifensine N-oxides do not form reactive metabolites that react with GSH. In vitro metabolism studies using a panel of cDNA-expressed human P450 and flavin monooxygenase (FMO) isoforms (CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, FMO1, FMO3, and FMO5) indicated that CYP3A4, CYP2C19, and CYP2B6 generate the largest quantities of H1, H4, and H6, respectively. H7 and H8 are formed almost exclusively by FMOs. The contribution of the individual P450s involved in the formation of H1, H4, and H6 in human liver microsomes was confirmed by the inhibition of product formation by monoclonal anti-cytochrome 450 antibodies. These results showed that CYP3A4 and CYP2B6 contributed primarily to the formation of H1 and H6, respectively. CYP2C19 and CYP1A2 seemed to contribute significantly to the formation of H4.

  20. Revisiting the mechanism of dioxygen activation in soluble methane monooxygenase from M. capsulatus (Bath): evidence for a multi-step, proton-dependent reaction pathway.

    PubMed

    Tinberg, Christine E; Lippard, Stephen J

    2009-12-29

    Stopped-flow kinetic investigations of soluble methane monooxygenase (sMMO) from M. capsulatus (Bath) have clarified discrepancies that exist in the literature regarding several aspects of catalysis by this enzyme. The development of thorough kinetic analytical techniques has led to the discovery of two novel oxygenated iron species that accumulate in addition to the well-established intermediates H(peroxo) and Q. The first intermediate, P*, is a precursor to H(peroxo) and was identified when the reaction of reduced MMOH and MMOB with O(2) was carried out in the presence of >or=540 microM methane to suppress the dominating absorbance signal due to Q. The optical properties of P* are similar to those of H(peroxo), with epsilon(420) = 3500 M(-1) cm(-1) and epsilon(720) = 1250 M(-1) cm(-1). These values are suggestive of a peroxo-to-iron(III) charge-transfer transition and resemble those of peroxodiiron(III) intermediates characterized in other carboxylate-bridged diiron proteins and synthetic model complexes. The second identified intermediate, Q*, forms on the pathway of Q decay when reactions are performed in the absence of hydrocarbon substrate. Q* does not react with methane, forms independently of buffer composition, and displays a unique shoulder at 455 nm in its optical spectrum. Studies conducted at different pH values reveal that rate constants corresponding to P* decay/H(peroxo) formation and H(peroxo) decay/Q formation are both significantly retarded at high pH and indicate that both events require proton transfer. The processes exhibit normal kinetic solvent isotope effects (KSIEs) of 2.0 and 1.8, respectively, when the reactions are performed in D(2)O. Mechanisms are proposed to account for the observations of these novel intermediates and the proton dependencies of P* to H(peroxo) and H(peroxo) to Q conversion.

  1. 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

    2015-12-02

    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%.

  2. 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

  3. Squaramide-catalysed asymmetric cascade aza-Michael/Michael addition reaction for the synthesis of chiral trisubstituted pyrrolidines.

    PubMed

    Zhao, Bo-Liang; Lin, Ye; Yan, Hao-Hao; Du, Da-Ming

    2015-12-14

    A bifunctional squaramide catalysed aza-Michael/Michael cascade reaction between nitroalkenes and tosylaminomethyl enones or enoates has been developed. This organocatalytic cascade reaction provides easy access to highly functionalized chiral pyrrolidines with a broad substrate scope, giving the desired products in good yields (up to 99%) with good diastereoselectivities (up to 91 : 9 dr) and excellent enantioselectivities (up to >99% ee) under mild conditions. This protocol provides a straightforward entry to highly functionalized chiral trisubstituted pyrrolidine derivatives from simple starting materials.

  4. Reversal of stereoselectivity in the Cu-catalyzed conjugate addition reaction of dialkylzinc to cyclic enone in the presence of a chiral azolium compound.

    PubMed

    Shibata, Naoatsu; Okamoto, Masaki; Yamamoto, Yuko; Sakaguchi, Satoshi

    2010-08-20

    Reversal of enantioselectivity in a Cu-catalyzed asymmetric conjugate addition reaction of dialkylzinc to cyclic enone with use of the same chiral ligand was successfully achieved. The reaction of 2-cyclohexen-1-one (30) with Et(2)Zn catalyzed by Cu(OTf)(2) in the presence of an azolium salt derived from a chiral beta-amino alcohol gave (S)-3-ethylcyclohexanone (31) in good enantioselectivity. Among a series of chiral azolium compounds examined, the benzimidazolium salt (10) having both a tert-butyl group at the stereogenic center and a benzyl substituent at the azolium ring was found to be the best choice of ligand in the Cu(OTf)(2)-catalyzed reaction. Good enantioselectivity was observed when the reaction was conducted by employing a benzimidazolium derivative rather than an imidazolium derivative. The influence of the substituent at the azolium ring on the stereoselectivity of the reaction was also examined. In addition, from the results of the reaction catalyzed by Cu(OTf)(2) combined with an azolium compound derived from (S)-leucine methyl ester, it was found that the hydroxy side chain in the chiral ligand is probably crucial for the enantiocontrol of the conjugate addition reaction. On the other hand, it was discovered from a screening test of copper species that the reversal of enantioselectivity was realized by allowing 30 to react with Et(2)Zn in the presence of Cu(acac)(2) combined with the same ligand precursor to afford (R)-31 as a major product. The influence of the stereodirecting group at the chiral ligand on the stereoselectivity in the Cu(acac)(2)-catalyzed reaction differed completely from that observed in the Cu(OTf)(2)-catalyzed reaction. Reaction with a cyclic enone consisting of a seven-membered ring such as 2-cyclohepten-1-one (40) resulted in increasing the enantioselectivity of the reaction. Thus, treatment of 40 with Et(2)Zn catalyzed by Cu(OTf)(2) combined with a benzimidazolium salt produced the corresponding (S)-conjugate adduct in a

  5. 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.

  6. The relationship between surface defects and surface reaction pathways on defective molybdenum sulfide(0001) single crystal surfaces

    NASA Astrophysics Data System (ADS)

    Wiegenstein, Christopher G.

    Hydrodesulfurization (HDS), the removal of sulfur from organic compounds, is important in the processing of crude oil. The industrial catalyst used is sulfided molybdenum promoted with Co or Ni supported on alumina. The present investigation examines MoS2 single crystals as model HDS catalysts. MoS2(0001) was chosen because it has the closest structure to the real catalyst, and still can be easily characterized with standard surface science techniques. This study is divided into two main areas of interest. The first area examined methods to create vacancies on the (0001) surface of MoS2, since the MoS2(0001) surface has been found to be relatively un-reactive for HDS. One way to create vacancies is to use hydrogen to remove sulfur from the surface. This would mimic the way defects are created in the real catalyst environment and develop a better understanding of hydrogen and hydrogen sulfide in HDS reactivity. The other method to create vacancies is to bombard the surface with argon ions to physically remove sulfur atoms from the surface, creating defect sites. Due to the limitation of the amount of hydrogen exposure needed to create sufficient vacancies to effect the surface reactivity, ion bombardment was favored to study the effects of sulfur defects on the HDS reactivity. The second part of this study is to determine the effect of site vacancies on the changes in surface reactivity using two probe molecules. Methanethiol was chosen as the first test molecule because it is the simplest organosulfur molecule and would be the easiest to determine the reaction pathways. Methanethiol HDS on both MoS2(0001) and defective MoS2(0001) surfaces show products of hydrogen, methane, ethane, ethylene and methanethiol, desorbing at 125 K and 300 K. Thiophene was chosen because it is the simplest of the aromatic organosulfur compounds. Thiophene only showed HDS reactivity on defective MoS2(0001) surfaces. Thiophene products were hydrogen, methane, ethylene, propadiene, and

  7. 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.

  8. 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.

  9. 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 Central

    Dey, Swati; North, Justin A.; Sriram, Jaya; Evans, Bradley S.; Tabita, F. Robert

    2015-01-01

    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. PMID:26511314

  10. Quantum-Chemical Study of the Discrimination against dNTP in the Nucleotide Addition Reaction in the Active Site of RNA Polymerase II.

    PubMed

    Roßbach, Sven; Ochsenfeld, Christian

    2017-04-11

    Eukaryotic RNA polymerase II catalyzes the transcription of DNA into mRNA very efficiently and with an extremely low error rate with regard to matching base and sugar moiety. Despite its importance, little is known about how it discriminates against 2'-deoxy NTPs during the chemical reaction. To investigate the differences in the addition reactions of ATP and dATP, we used FF-MD and QM/MM calculations within a nudged elastic band approach, which allowed us to find the energetically accessible reaction coordinates. By converging the QM size, we found that 800 QM atoms are necessary to properly describe the active site. We show how the absence of a single hydrogen bond between the enzyme and the NTP 2'-OH group leads to an increase of the reaction barrier by 16 kcal/mol and therefore conclude that Arg446 is the key residue in the discrimination process.

  11. 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.

  12. 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.

  13. Non-innocent additives in a palladium(II)-catalyzed C-H bond activation reaction: insights into multimetallic active catalysts.

    PubMed

    Anand, Megha; Sunoj, Raghavan B; Schaefer, Henry F

    2014-04-16

    The role of a widely employed additive (AgOAc) in a palladium acetate-catalyzed ortho-C-H bond activation reaction has been examined using the M06 density functional theory. A new hetero-bimetallic Pd-(μ-OAc)3-Ag is identified as the most likely active species. This finding could have far-reaching implications with respect to the notion of the active species in palladium catalysis in the presence of other metal salt additives.

  14. An Experimental and Computational Approach to Defining Structure/Reactivity Relationships for Intramolecular Addition Reactions to Bicyclic Epoxonium Ions

    PubMed Central

    Wan, Shuangyi; Gunaydin, Hakan; Houk, K. N.; Floreancig, Paul E.

    2008-01-01

    In this manuscript we report that oxidative cleavage reactions can be used to form oxocarbenium ions that react with pendent epoxides to form bicyclic epoxonium ions as an entry to the formation of cyclic oligoether compounds. Bicyclic epoxonium ion structure was shown to have a dramatic impact on the ratio of exo- to endo-cyclization reactions, with bicyclo[4.1.0] intermediates showing a strong preference for endo-closures and bicyclo[3.1.0] intermediates showing a preference for exo-closures. Computational studies on the structures and energetics of the transition states using the B3LYP/6-31G(d) method provide substantial insight into the origins of this selectivity. PMID:17547399

  15. Hydrogen bonding mediated enantioselective organocatalysis in brine: significant rate acceleration and enhanced stereoselectivity in enantioselective Michael addition reactions of 1,3-dicarbonyls to β-nitroolefins.

    PubMed

    Bae, Han Yong; Some, Surajit; Oh, Joong Suk; Lee, Yong Seop; Song, Choong Eui

    2011-09-14

    Brine provides remarkable rate acceleration and a higher level of stereoselectivity over organic solvents, due to the hydrophobic hydration effect, in the enantioselective Michael addition reactions of 1,3-dicarbonyls to β-nitroolefins using chiral H-donors as organocatalysts.

  16. Reaction pathways determined by mechanical milling process for dehydrogenation/hydrogenation of the LiNH(2)/MgH(2) system.

    PubMed

    Liang, Chu; Liu, Yongfeng; Luo, Kun; Li, Bo; Gao, Mingxia; Pan, Hongge; Wang, Qidong

    2010-01-11

    The dehydrogenation/hydrogenation processes of the LiNH(2)/MgH(2) (1:1) system were systematically investigated with respect to balller milling and the subsequent heating process. The reaction pathways for hydrogen desorption/absorption of the LiNH(2)/MgH(2) (1:1) system were found to depend strongly on the milling duration due to the presence of two competing reactions in different stages (i.e., the reaction between Mg(NH(2))(2) and MgH(2) and that between Mg(NH(2))(2) and LiH), caused by a metathesis reaction between LiNH(2) and MgH(2), which exhibits more the nature of solid-solid reactions. The study provides us with a new approach for the design of novel hydrogen storage systems and the improvement of hydrogen-storage performance of the amide/hydride systems.

  17. Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

    PubMed Central

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

    2013-01-01

    Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489

  18. N-Heterocyclic Carbene-Catalyzed Diastereoselective Vinylogous Michael Addition Reaction of γ-Substituted Deconjugated Butenolides.

    PubMed

    Guo, Hao; Xing, Fen; Du, Guang-Fen; Huang, Kuo-Wei; Dai, Bin; He, Lin

    2015-12-18

    An efficient N-heterocyclic carbene (NHC)-catalyzed vinylogous Michael addition of deconjugated butenolides was developed. In the presence of 5 mol % of the NHC catalyst, both γ-alkyl- and aryl-substituted deconjugated butenolides undergo vinylogous Michael addition with various α, β-unsaturated ketones, esters, or nitriles to afford γ,γ-disubstituted butenolides containing adjacent quaternary and tertiary carbon centers in good to excellent yields with excellent diastereoselectivities. In this process, the free carbene is assumed to act as a strong Brønsted base to promote the conjugate addition.

  19. Theoretical Study of Addition Reactions of L4M(M = Rh, Ir) and L2M(M = Pd, Pt) to Li(+)@C60.

    PubMed

    Yang, Ming-Chung; Sharma, Akhilesh K; Sameera, W M C; Morokuma, Keiji; Su, Ming-Der

    2017-04-06

    The addition reaction of M(Cl)(CO)(PPh3)2 (M = Rh, Ir) and M(PPh3)2 (M = Pd, Pt) fragments with X@C60 (X = 0, Li(+)) were characterized by density functional theory (DFT) and the artificial force-induced reaction (AFIR) method. The calculated free energy profiles suggested that the η(2)[6:6]-addition is the most favorable reaction, which is consistent with the experimental observations. In the presence of Li(+) ion, the reaction is highly exothermic, leading to η(2)[6:6] product of L4IrLi(+)@C60. In contrast, an endothermic reaction was observed in the absence of a Li(+) ion. The encapsulated Li(+) ion can enhance the thermodynamic stability of the η(2)[6:6] product. The energy decomposition analysis showed that the interaction between metal fragment and X@C60 fragment is the key for the thermodynamic stability. Among the group IA and IIA metal cations, Be(2+) encapsulation is the best candidate for the development of new fullerene-transition metal complexes, which will be useful for future potential applications such as solar cells, catalysts, and electronic devices.

  20. Radical-chain oxidative addition mechanism for the reaction of an [Re(CO)5]- anion with α-bromostilbene.

    PubMed

    Sazonov, Petr K; Ptushkin, Dmitry S; Khrustalev, Victor N; Kolotyrkina, Natal'ya G; Beletskaya, Irina P

    2013-03-28

    E-α-Bromostilbene spontaneously reacts with Na[Re(CO)(5)] at 22 °C in THF to give Na[ReBr(CO)(4){Z-C(Ph)=CHPh}] and Na[Re(2)(CO)(9){Z-C(Ph)=CHPh}] as the main products. Z-α-Bromostilbene is less reactive, but gives the same products. The reaction is stimulated by visible light or a source of solvated electrons (NaK(2.8)) and can be inhibited by a quinomethide radical trap. With an excess of Na[Re(CO)(5)] one can observe the initial formation of Na[ReBr(CO)(4){Z-C(Ph)=CHPh}] and its complete transformation into Na[Re(2)(CO)(9){Z-C(Ph)=CHPh}]. Treatment of Na[ReBr(CO)(4){Z-C(Ph)=CHPh}] with CO almost quantitatively converts it to [Re(CO)(5){Z-C(Ph)=CHPh}], the structure of which is established by a single-crystal X-ray diffraction study. A radical-chain mechanism is proposed for the reaction comprising the following steps: (a) coupling of a Vin˙ radical with Na[Re(CO)(5)], (b) CO-dissociation from the formed 19-electron radical-anion and (c) bromine atom abstraction by [Re(CO)(4){Z-C(Ph)=CHPh}]˙(-) from α-bromostilbene. The mechanism is confirmed by the formation of the same Na[ReBr(CO)(4){Z-C(Ph)=CHPh}] product in the presence of NaI. When the radical-chain process is inhibited, a slow halogenophilic reaction is observed, mainly giving the Z and E-isomers of the acylrhenate Na[Re(2)(CO)(9){C(O)C(Ph)=CHPh}].

  1. 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.

  2. Energetics of tert-butoxyl addition reaction to norbornadiene: a method for estimating the pi-bond strength of a carbon-carbon double bond.

    PubMed

    Nunes, Paulo M; Estácio, Sílvia G; Lopes, Gustavo T; Agapito, Filipe; Santos, Rui C; Costa Cabral, Benedito J; Borges dos Santos, Rui M; Martinho Simões, José A

    2009-06-11

    The energetics of tert-butoxyl radical addition reaction to norbornadiene was investigated by time-resolved photoacoustic calorimetry (TR-PAC). The result, together with the C-O bond dissociation enthalpy (BDE) in the addition product, allowed us to calculate the pi-bond dissociation enthalpy in norbornadiene. Quantum chemistry (QC) methods were also used to obtain several enthalpies of reaction of the addition of oxygen-centered radicals to alkenes. The pi-bond dissociation enthalpies in these molecules were calculated by a procedure similar to that used in the case of norbornadiene and were compared with the pi-BDE values obtained by the method proposed by Benson. These two different approaches yield similar values for the pi-BDEs in alkenes, indicating that the addition method proposed in the present study is a valid way to derive that quantity. The influence of strain in the pi-BDEs of cyclic alkenes was investigated and allowed us to justify the difference between the pi-BDE in norbornene and norbornadiene. Finally, the thermochemistry of the addition and abstraction reactions involving these two molecules and tert-butoxyl radical was analyzed.

  3. Set-reset flip-flop memory based on enzyme reactions: toward memory systems controlled by biochemical pathways.

    PubMed

    Pita, Marcos; Strack, Guinevere; MacVittie, Kevin; Zhou, Jian; Katz, Evgeny

    2009-12-10

    The enzyme-based set-reset flip-flop memory system was designed with the core part composed of horseradish peroxidase and diaphorase biocatalyzing oxidation and reduction of redox species (2,6-dichloroindophenol or ferrocyanide). The biocatalytic redox reactions were activated by H(2)O(2) and NADH produced in situ by different enzymatic reactions allowing transformation of various biochemical signals (glucose, lactate, d-glucose-6-phosphate, ethanol) into reduced or oxidized states of the redox species. The current redox state of the system, controlled by the set and reset signals, was read out by optical and electrochemical means. The multiwell setup with the flip-flop units separately activated by various set/reset signals allowed encoding of complex information. For illustrative purposes, the words "Clarkson" and then "University" were encoded using ASCII character codes. The present flip-flop system will allow additional functions of enzyme-based biocomputing systems, thus enhancing the performance of multisignal biosensors and actuators controlled by logically processed biochemical signals. The integrated enzyme logic systems and flip-flop memories associated with signal-responsive chemical actuators are envisaged as basic elements of future implantable biomedical devices controlled by immediate physiological conditions.

  4. The Importance of Aromatic Reaction Pathways in Titan Aerosol Formation: Evidence from Laboratory Analogs and Comparisons to Cassini

    NASA Astrophysics Data System (ADS)

    Sebree, J.; Trainer, M. G.; Li, X.; Pinnick, V. T.; Getty, S.; Loeffler, M. J.; Anderson, C. M.; Brinckerhoff, W. B.

    2013-12-01

    The arrival of the Cassini spacecraft in orbit around Saturn has led to the discovery of benzene (C6H6) at ppm levels, as well as large positive ions evocative of polycyclic aromatic hydrocarbons (PAHs) in Titan's atmosphere (Waite et al., Science 316: 870, 2007.) The recent assignment of the band at 3.28 μm as observed by the Visual-Infrared Mapping Spectrometer (VIMS) to gas-phase PAHs provides further evidence that these molecules are prevalent on Titan (Lopez-Puertas et al., ApJ 770: 132, 2013). Taken together these observations suggest that aromatic reaction pathways play an important role in the photochemistry of Titan's atmosphere, in particular in the formation of large organic species. Even at low concentrations, aromatic molecules are sufficiently active in the ultraviolet to substantially contribute to the formation of aerosol particles in Titan's haze (Trainer et al., ApJL 766: L4, 2013). We will present results from a laboratory study of the UV irradiation of ppm-level aromatic precursors, both with and without nitrogen heteroatoms, to understand their influence on the observable characteristics of the resultant aerosol. Spectroscopic measurements of our analog aerosols compare favorably to observations of Titan's haze by VIMS and by the Composite Infrared Spectrometer (CIRS) in the far-infrared. In particular, we will present our best fits to the broad aerosol emission feature centered at approximately 145 cm-1 (Anderson et al. Icarus 212 762, 2011). This is the first time laboratory-produced Titan aerosol analogs have been shown to absorb in this region of the far-IR. From the broadness of this feature, we speculate that the emission is a blended composite of low-energy vibrations of large molecules such as polycyclic aromatic hydrocarbons (PAHs) and their nitrogen containing counterparts polycyclic aromatic nitrogen heterocycles (PANHs). Our results indicate the aerosols formed from PANHs provide the best match in this low frequency region. Using

  5. 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)

  6. New method of DNA isolation from two food additives suitable for authentication in polymerase chain reaction assays.

    PubMed

    Urdiaín, Mercedes; Doménech-Sánchez, Antonio; Albertí, Sebastián; Benedí, V Javier; Rosselló, Josep A

    2005-05-04

    Locust bean gum and guar gum are galactomannans used as additives (E 410 and E 412, respectively) in the food industry as stabilizing agents. Analytical discrimination between the two additives in gums and foods is now feasible by molecular techniques. However, only complex and time-consuming DNA isolation protocols are available to date. We have developed simple improved protocols to obtain enough DNA suitable for PCR amplification from a few milligrams of commercial E 410 and E 412 additives (containing more than 75% polysaccharides). The suspension of additives in water or 10 mM Tris-HCl, pH 8.5, efficiently recovers DNA suitable for authentication in PCR assays. However, the Tris method was much more efficient for the extraction of DNA from E 410 than for E 412 additives. Conversely, the water method was the most suitable for detecting DNA extracted from E 412 or from E 410/E 412 mixtures. Combined with the use of the two specific ribosomal primer pairs previously designed, our methods are well-suited for a fast and simple high-throughput sample treatment of commercial gums for molecular certification.

  7. Excitation energy pathways in the photosynthetic units of reaction center LM- and H-subunit deletion mutants of Rhodospirillum rubrum.

    PubMed

    Amarie, Sergiu; Lupo, Domenico; Lenz, Martin O; Saegesser, Rudolf; Ghosh, Robin; Wachtveitl, Josef

    2010-03-01

    Light-induced reaction dynamics of isolated photosynthetic membranes obtained from wild-type (WT) and reaction center (RC)-subunit deletion strains SPUHK1 (an H-subunit deletion mutant) and SK Delta LM (an (L+M) deletion mutant) of the purple non-sulphur bacterium Rhodospirillum rubrum have been investigated by femtosecond transient absorption spectroscopy. Upon excitation of the spirilloxanthin (Spx) S(2) state at 546 nm, of the bacteriochlorophyll Soret band at 388 nm and probing spectral regions, which are characteristic for carotenoids, similar dynamics in the SPUHK1, SK Delta LM and WT strains could be observed. The excitation of Spx S(2) is followed by the simultaneous population of the lower singlet excited states S(1) and S* which decay with lifetimes of 1.4 and 5 ps, respectively for the mutants, and 1.4 and 4 ps, respectively, for the wild-type. The excitation of the BChl Soret band is followed by relaxation into BChl lower excited states which compete with excitation energy transfer BChl-to-Spx. The deexcitation pathway BChl(Soret) --> Spx(S(2)) --> Spx(S(1)) occurs with the same transition rate for all investigated samples (WT, SPUHK1 and SK Delta LM). The kinetic traces measured for the Spx S(1) --> S(N) transition display similar behaviour for all samples showing a positive signal which increases within the first 400 fs (i.e. the time needed for the excitation energy to reach the Spx S(1) excited state) and decays with a lifetime of about 1.5 ps. This suggests that the Spx excited state dynamics in the investigated complexes do not differ significantly. Moreover, a longer excited state lifetime of BChl for SPUHK1 in comparison to WT was observed, consistent with a photochemical quenching channel present in the presence of RC. For long delay times, photobleaching of the RC special pair and an electrochromic blue shift of the monomeric BChl a can be observed only for the WT but not for the mutants. The close similarity of the excited state decay

  8. Rhodium/chiral diene-catalyzed asymmetric 1,4-addition of arylboronic acids to chromones: a highly enantioselective pathway for accessing chiral flavanones.

    PubMed

    He, Qijie; So, Chau Ming; Bian, Zhaoxiang; Hayashi, Tamio; Wang, Jun

    2015-03-01

    Chromone has been noted to be one of the most challenging substrates in the asymmetric 1,4-addition of α,β-unsaturated carbonyl compounds. By employing the rhodium complex associated with a chiral diene ligand, (R,R)-Ph-bod*, the 1,4-addition of a variety of arylboronic acids was realized to give high yields of the corresponding flavanones with excellent enantioselectivities (≥97% ee, 99% ee for most substrates). Ring-opening side products, which would lead to erosion of product enantioselectivity, were not observed under the stated reaction conditions.

  9. 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

    2016-08-05

    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).

  10. Formation of quaternary stereogenic centers by copper-catalyzed asymmetric conjugate addition reactions of alkenylaluminums to trisubstituted enones.

    PubMed

    Müller, Daniel; Alexakis, Alexandre

    2013-11-04

    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.

  11. 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.

  12. 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.

  13. Adult neuron addition to the zebra finch song motor pathway correlates with the rate and extent of recovery from botox-induced paralysis of the vocal muscles.

    PubMed

    Pytte, Carolyn; Yu, Yi-Lo; Wildstein, Sara; George, Shanu; Kirn, John R

    2011-11-23

    In adult songbirds, neurons are continually incorporated into the telencephalic nucleus HVC (used as a proper name), a premotor region necessary for the production of learned vocalizations. Previous studies have demonstrated that neuron addition to HVC is highest when song is most variable: in juveniles during song learning, in seasonally singing adults during peaks in plasticity that precede the production of new song components, or during seasonal reestablishment of a previously learned song. These findings suggest that neuron addition provides motor flexibility for the transition from a variable song to a target song. Here we test the association between the quality of song structure and HVC neuron addition by experimentally manipulating syringeal muscle control with Botox, which produces a transient partial paralysis. We show that the quality of song structure covaries with new neuron addition to HVC. Both the magnitude of song distortion and the rate of song recovery after syringeal Botox injections were correlated with the number of new neurons incorporated into HVC. We suggest that the quality of song structure is either a cause or consequence of the number of new neurons added to HVC. Birds with naturally high rates of neuron addition may have had the greatest success in recovering song. Alternatively, or in addition, new neuron survival in the song motor pathway may be regulated by the quality of song-generated feedback as song regains its original stereotyped structure. Present results are the first to show a relationship between peripheral muscle control and adult neuron addition to cortical premotor circuits.

  14. 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.

  15. 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.

  16. Deprotonation and reductive addition reactions of hypervalent aluminium dihydride compounds containing substituted pyrrolyl ligands with phenols, ketones, and aldehydes.

    PubMed

    Chen, I-Chun; Ho, Shi-Mau; Chen, Ya-Chi; Lin, Che-Yu; Hu, Ching-Han; Tu, Cheng-Yi; Datta, Amitabha; Huang, Jui-Hsien; Lin, Chia-Her

    2009-10-28

    The reactivities of [C4H2N(CH2NMe2)2]AlH2 (1) with primary and secondary amines, phenols, ketones, and phenyl isothiocyanate were examined. Reactions of 1 with one or two equivalents of 2,6-dichloroaniline in methylene chloride generated [C4H2N(CH2NMe2)2]AlH(NHC6H3-2,6-Cl2) (2) and [C4H2N(CH2NMe2)2]Al(NHC6H3-2,6-Cl2)2 (3), respectively, following hydrogen elimination. Similarly, the reactions of 1 with one or two equivalents of carbazole afforded [C4H2N(CH2NMe2)2]AlH(NC12H8) (4) or [C4H2N(CH2NMe2)2]Al(NC12H8)2 (5) by deprotonating the acidic N-H of carbazole. Reacting 1 with one equivalent of 2,6-diisopropylphenol in diethyl ether formed an aluminium phenoxo compound [C4H2N(CH2NMe2)2]AlH(OC6H3-2,6-iPr2) (6), by deprotonation of phenol as well with the elimination of one equivalent hydrogen. Further reaction of 6 with one equivalent of 2,4,6-trimethylacetophenone in methylene chloride generated [C4H2N(CH2NMe2)2]Al(OC6H3-2,6-iPr2)[OC(=CH2)(C6H2-2,4,6-Me3)] (7) by deprotonating the methyl proton of the acetophenone. Similar deprotonation occurred when 1 reacted with two equivalents of 2,4,6-trimethylacetophenone in methylene chloride to generate [C4H2N(CH2NMe2)2]Al[OC(=CH2)(C6H2-2,4,6-Me3)]2 (8). Compounds [C4H2N(CH2NMe2)2]Al(OCHPh2)2 (9), and [C4H2N(CH2NMe2)2]Al(SCHNPh)2 (10) could also be obtained by reacting 1 with two equivalents of benzophenone and phenyl isothiocyanate, respectively through hydroalumination. The 1H NMR spectra of 10 showed broad signals for the CH2N and NMe2 groups, which represent dynamical fluctuations of the molecules in solution state. The estimated energy barrier (DeltaG(c)(double dagger)) from the coalescence temperature for the fluctuation was estimated at 17.1 Kcal mol(-1). The solid-state structures of compounds 2, 3, 5, 7, 9, and 10 have been determined.

  17. Dipeptide-Based Chiral Tertiary Amine-Catalyzed Asymmetric Conjugate Addition Reactions of 5H-Thiazol/Oxazol-4-Ones.

    PubMed

    Li, Jiangtao; Qiu, Shuai; Ye, Xinyi; Zhu, Bo; Liu, Hongjun; Jiang, Zhiyong

    2016-12-02

    Highly enantio- and chemo-selective 1,4-conjugate addition process of 5H-thiazol-4-ones with maleimides or 1,4-naphthoquinones, and 5H-oxazol-4-ones with maleimides were performed under a dipeptide-based tertiary amine (DP-UAA) catalyst. A series of valuable N,S- and N,O-containing heterocyclic compounds with excellent enantio- and disastereo-selectivities (up to >99% ee, > 20:1 dr) were attained.

  18. Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions.

    PubMed

    Jackson, Paul A; Widen, John C; Harki, Daniel A; Brummond, Kay M

    2017-02-09

    Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogues possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Thermochemical properties, rotation barriers, and group additivity for unsaturated oxygenated hydrocarbons and radicals resulting from reaction of vinyl and phenyl radical systems with O2.

    PubMed

    Sebbarand, Nadia; Bockhorn, Henning; Bozzelli, Joseph W

    2005-03-17

    Oxidation of unsaturated and aromatic hydrocarbons in atmospheric and combustion processes results in formation of linear and cyclic unsaturated, oxygenated-hydrocarbon intermediates. The thermochemical parameters delatafH degrees 298, S degrees 298, and C(p)(f298)(T) for these intermediates are needed to understand their stability and reaction paths in further oxidation. These properties are not available for a majority of these unsaturated oxy-hydrocarbons and their corresponding radicals, even via group additivity methods. Enthalpy, entropy, and heat capacity of a series of 40 oxygenated and non-oxygenated molecules, or radicals corresponding to hydrogen atom loss from the parent stable molecules are determined in this study. Enthalpy (delatafH degrees 298 in kcal mol(-1)) is derived from the density function calculations at the B3LYP/6-311g(d,p) calculated enthalpy of reaction (delatafH degrees rxn,298) and by use of isodesmic (work) reactions. Estimation of error in enthalpy delatafH degrees 298, from use of computational chemistry coupled with work reactions analysis, is presented using comparisons between the calculated and literature enthalpies of reaction. Entropies (S degrees 298) and heat capacities (C(p)(f298)(T)) were calculated using the B3LYP/6-311G(d,p) determined frequencies and geometries. Potential barriers for internal rotors in each molecule were determined and used (in place of torsion frequencies) to calculate contributions to S and C(p)(T) from the hindered rotors. Twenty-six groups for use in group additivity (GA) are also developed.

  5. 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.

  6. Lewis Acid Induced Toggle from Ir(II) to Ir(IV) Pathways in Photocatalytic Reactions: Synthesis of Thiomorpholines and Thiazepanes from Aldehydes and SLAP Reagents

    PubMed Central

    2016-01-01

    Redox neutral photocatalytic transformations often require careful pairing of the substrates and photoredox catalysts in order to achieve a catalytic cycle. This can limit the range of viable transformations, as we recently observed in attempting to extend the scope of the photocatalytic synthesis of N-heterocycles using silicon amine protocol (SLAP) reagents to include starting materials that require higher oxidation potentials. We now report that the inclusion of Lewis acids in photocatalytic reactions of organosilanes allows access to a distinct reaction pathway featuring an Ir(III)*/Ir(IV) couple instead of the previously employed Ir(III)*/Ir(II) pathway, enabling the transformation of aromatic and aliphatic aldehydes to thiomorpholines and thiazepanes. The role of the Lewis acid in accepting an electron—either directly or via coordination to an imine—can be extended to other classes of photocatalysts and transformations, including oxidative cyclizations. The combination of light induced reactions and Lewis acids therefore promises access to new pathways and transformations that are not viable using the photocatalysts alone. PMID:28149955

  7. 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.

  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.

  9. Reinvestigation of the Unimolecular Reactions of CHF2CHF2: Identification of the 1,1-HF Elimination Component from Addition of :CFCHF2 to trans-2-Butene.

    PubMed

    Smith, Caleb A; Heard, George L; Setser, D W; Holmes, Bert E

    2016-12-01

    The recombination of ·CHF2 radicals in a room-temperature bath gas was used to generate CHF2CHF2* (where * indicates vibrational excitation) molecules with 96 kcal mol(-1) of vibrational energy. The CHF2CHF2* molecules decompose by four-centered 1,2-HF elimination and by three-centered 1,1-HF elimination reactions to give HF and either CHF═CF2 or :CFCHF2, respectively. The 1,1-HF component was identified by trapping the :CFCHF2 carbene with trans-2-butene that forms 1-fluoro-1-difluoromethyl-2,3-dimethylcyclopropane. The total rate constant for the decomposition of CHF2CHF2* was 6.0 × 10(5) s(-1), and the rate constant for the 1,1-HF pathway forming the carbene, as measured by the 1-fluoro-1-difluoromethyl-2,3-dimethylcyclopropane yield, was 1.4 × 10(5) s(-1). On the basis of matching the experimental rate constants to calculated statistical rate constants, the threshold energies for the four-centered and three-centered reactions are 78 and ≤85 kcal mol(-1), respectively.

  10. Reactions of Anilines and Benzamides with a Fourteen-Electron Iridium(I) Bis(Phosphinite) Complex: N-H Oxidative Addition versus Lewis Base Coordination

    PubMed Central

    Sykes, Alison Cartwright; White, Peter

    2008-01-01

    Anilines react with (POCOP)Ir(C6H5)(H), 12, (POCOP = 2,6-(OPtBu2)2C6H3) to yield equilibrium mixtures of 12, the Ir(I) σ-complexes (POCOP)Ir(NH2Ar), 13, and the Ir(III) oxidative addition adducts (POCOP)Ir(H)(NHAr), 14. Quantitative studies of these equilibria for a series of anilines were carried out. Anilines possessing electron-withdrawing groups favor the Ir(III) oxidative addition adduct over the Ir(I) sigma complex. Low temperature studies using p-chloroaniline show that the Ir(I) σ-complex is the kinetic product of reaction and is likely the precursor to the Ir(III) oxidative addition adduct. Reductive elimination of complexes 14 in the presence of ethylene led to the corresponding anilines and the ethylene complex (POCOP)Ir(C2H4). Kinetic analysis of these reactions for 14e,f,g bearing electron-withdrawing aryl groups (Ar- = p-CF3C6H4-, C6F5-, 3,5-bis(CF3)C6H3-) shows the rate is independent of ethylene concentration. The ΔG‡ values for these reductive eliminations fall in the range of 21–22 kcal/mol. X-Ray analysis establishes 14f (Ar- = C6F5-) as a square pyramidal complex with the hydride occupying the apical site. Reaction of 12 with benzamides 21a,b yields quantitatively the Ir(III) oxidative addition adducts, (POCOP)Ir(H)(NHC(O)Ar), 22. X-Ray analysis of 22b (Ar- = C6F5-) shows significant interaction of the carbonyl oxygen with Ir in the site trans to hydride. The barrier to reductive elimination of 22a, 29 kcal/mol, is substantially higher than for complexes 14e,f,g. PMID:19079781

  11. Atomic layer deposition of Al2O3 on H-passivated Si. I. Initial surface reaction pathways with H/Si(100)-2×1

    NASA Astrophysics Data System (ADS)

    Halls, Mathew D.; Raghavachari, Krishnan

    2003-06-01

    Aluminum oxide (Al2O3) grown by atomic layer deposition (ALD) is currently under investigation for use as a high-κ gate dielectric alternative to SiO2. Cluster calculations employing hybrid density functional theory have been carried out to examine the chemical reaction pathways between the ALD precursors, trimethylaluminum (TMA) and H2O, with the H/Si(100)-2×1 surface. Results obtained using Si9H14 and Si15H20, dimer and double dimer clusters to represent the surface active site are in good agreement, providing a consistent view of reaction energetics on the H/Si(100)-2×1 surface. The adsorption energies for TMA and H2O on the surface are calculated to be 0.02 and 0.15 eV, respectively. For the reaction between H2O and the H/Si(100)-2×1 surface, hydroxylation of the surface accompanied by loss of H2 was found to be the preferred pathway having an activation energy and overall reaction enthalpy of 1.60 eV and -0.75 eV, both of which are ⩾0.70 eV lower than the corresponding values for the possible H/D exchange reaction. TMA exposure of the H/Si(100)-2×1 surface favors the deposition of -Al(CH3)2 with loss of CH4, having a barrier height of 1.30 eV and reaction enthalpy of -0.31 eV, which are 0.10 and 0.40 eV lower than the surface methylation pathway (H/CH3 exchange) and 2.64 and 0.45 eV lower in energy than the H2 loss reaction, that results in the deposition of -CH2-Al(CH3)2 to the surface. Therefore, the dominant reactions identified in this work are those with direct implication in the Al2O3 ALD growth mechanism, leading to the formation of Si-O and Si-Al species on the H/Si(100)-2×1 surface.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. X-Ray absorption in homogeneous catalysis research: the iron-catalyzed Michael addition reaction by XAS, RIXS and multi-dimensional spectroscopy.

    PubMed

    Bauer, Matthias; Gastl, Christoph

    2010-06-07

    A survey over X-ray absorption methods in homogeneous catalysis research is given with the example of the iron-catalyzed Michael addition reaction. A thorough investigation of the catalytic cycle was possible by combination of conventional X-ray absorption spectroscopy (XAS), resonant inelastic X-ray scattering (RIXS) and multi-dimensional spectroscopy. The catalytically active compound formed in the first step of the Michael reaction of methyl vinyl ketone with 2-oxocyclopentanecarboxylate (1) could be elucidated in situ by RIXS spectroscopy, and the reduced catalytic activity of FeCl(3) x 6 H(2)O (2) compared to Fe(ClO(4))(3) x 9 H(2)O (3) could be further explained by the formation of a [Fe(III)Cl(4)(-)](3)[Fe(III)(1-H)(2)(H(2)O)(2)(+)][H(+)](2) complex. Chloride was identified as catalyst poison with a combined XAS-UV/vis study, which revealed that Cl(-) binds quantitatively to the available iron centers that are deactivated by formation of [FeCl(4)(-)]. Operando studies in the course of the reaction of methyl vinyl ketone with 1 by combined XAS-Raman spectroscopy allowed the exclusion of changes in the oxidation state and the octahedral geometry at the iron site; a reaction order of two with respect to methyl vinyl ketone and a rate constant of k = 1.413 min(-2) were determined by analysis of the C=C and C=O vibration band. Finally, a dedicated experimental set-up for three-dimensional spectroscopic studies (XAS, UV/vis and Raman) of homogeneous catalytic reactions under laboratory conditions, which emerged from the discussed investigations, is presented.

  17. TSG-6 secreted by mesenchymal stem cells suppresses immune reactions influenced by BMP-2 through p38 and MEK mitogen-activated protein kinase pathway.

    PubMed

    Um, Soyoun; Kim, Hui Young; Lee, Joo-Hee; Song, In-Seok; Seo, Byoung Moo

    2017-02-28

    Bone morphogenetic protein 2 (BMP-2) has a critical function in bone and cartilage development and in repairing damaged organs and tissue. However, clinical use of BMP-2 at doses of 0.5-1 mg/ml for orthopedics has been associated with severe postoperative swelling requiring emergency surgical intervention. We determined whether a high concentration of BMP-2 induces inflammatory responses in macrophages and the suppression of osteogenesis in hMSCs. We obtained human periodontal ligament stem cells and bone marrow stem cells from the maxilla, i.e., human mesenchymal stem cells (hMSCs), from the periodontal ligament of extracted third molar teeth and from the bone marrow of the maxilla, respectively. Osteogenic differentiation was measured by alkaline phosphatase activity and alizarin red S staining. Proteins were assessed by flow cytometry, enzyme-linked immunosorbent assay, Western blot and immunocytochemistry. Changes of gene expression were measured by reverse transcription plus the polymerase chain reaction (RT-PCR) and real-time PCR. A high BMP-2 concentration inhibited the early stages of osteogenesis in hMSCs. Co-culturing THP-1 cells (human monocytic cells) with hMSCs reduced the late stages of osteogenesis compared with those seen in hMSCs alone. In addition, high-dose BMP-2 induced the expression of inflammatory cytokines in THP-1 cells and the expression of the anti-inflammatory cytokine tumor-necrosis-factor-α-inducible gene 6 protein (TSG-6) in hMSCs. Consistent with the anti-inflammatory effects of hMSCs when co-cultured with THP-1 cells, interleukin-1β expression was downregulated by TSG-6 treatment of THP-1 cells. Our findings suggest that a high BMP-2 concentration triggers inflammation that causes inflammatory cytokine release from THP-1 cells, leading to the suppression of osteogenesis, whereas TSG-6 secreted by hMSCs suppresses inflammatory reactions through p38 and ERK in the mitogen-activated protein kinase pathway.

  18. The influence of an additional load on time and force changes in the ground reaction force during the countermovement vertical jump.

    PubMed

    Vaverka, Frantisek; Jakubsova, Zlatava; Jandacka, Daniel; Zahradnik, David; Farana, Roman; Uchytil, Jaroslav; Supej, Matej; Vodicar, Janez

    2013-01-01

    The aim of this study was to determine how an additional load influences the force-vs-time relationship of the countermovement vertical jump (CMVJ). The participants that took part in the experiment were 18 male university students who played sport recreationally, including regular games of volleyball. They were asked to perform a CMVJ without involving the arms under four conditions: without and with additional loads of 10%, 20%, and 30% of their body weight (BW). The vertical component of the ground reaction force (GRF) was measured by a force plate. The GRF was used to calculate the durations of the preparatory, braking, and acceleration phases, the total duration of the jump, force impulses during the braking and acceleration phases, average forces during the braking and acceleration phases, and the maximum force of impact at landing. Results were evaluated using repeated-measures ANOVA. Increasing the additional load prolonged both the braking and acceleration phases of the jump, with statistically significant changes in the duration of the acceleration phase found for an additional load of 20% BW. The magnitude of the force systematically and significantly increased with the additional load. The force impulse during the acceleration phase did not differ significantly between jumps performed with loads of 20% and 30% BW. The results suggest that the optimal additional load for developing explosive strength in vertical jumping ranges from 20% to 30% of BW, with this value varying between individual subjects.

  19. 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

  20. 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.

  1. 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.

  2. 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.; ...

    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

  3. Enhanced luminescence properties of CaTiO(3):Pr(3+) phosphor with addition of SiO(2) by solid-state reaction.

    PubMed

    Chen, Rui; Chen, Donghua

    2014-06-05

    Red phosphors CaTiO3:Pr(3+) with addition of SiO2 were prepared by solid-state reaction technique (SS). The effect of SiO2 on the crystalline phase, surface morphology and luminescence properties of CaTiO3:Pr(3+) was studied by X-ray diffractometer, transmission electron microscope, brightness meter and photoluminescence spectrometer, respectively. The results indicated that the content of SiO2 has influence on luminescence intensity, initial brightness and persistent time of samples. The red phosphor CaTi0.5Si0.5O3:Pr(3+) exhibited the optimal luminescence properties.

  4. 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

    2015-03-06

    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.

  5. Competitive reaction pathways for o-anilide aryl radicals: 1,5- or 1,6-hydrogen transfer versus nucleophilic coupling reactions. A novel rearrangement to afford an amidyl radical.

    PubMed

    Rey, Valentina; Pierini, Adriana B; Peñéñory, Alicia B

    2009-02-06

    The photoinduced reactions of o-iodoanilides (o-IC6H4N(Me)COR, 4a-d) with sulfur nucleophiles such as thiourea anion (1, -SCNH(NH2)), thioacetate anion (2, MeCOS-), and sulfide anion (3, S(2-)) follow different reaction channels, giving the sulfides by a radical nucleophilic substitution or the dehalogenated products by hydrogen atom transfer pathways. After an initial photoinduced electron transfer (PET) from 1 to iodide 4, the o-amide aryl radicals 12 are generated. These aryl radicals 12 afford alternative reaction pathways depending on the structure of the alpha-carbonyl moiety: (a) 12b (R = Me) adds to 1 to render the methylthio-substituted compounds by quenching the thiolate anion intermediate with MeI after irradiation; (b) 12c (R = -CH2Ph) follows a 1,5-hydrogen transfer to give a stabilized alpha-carbonyl radical (17); and (c) 12d (R = t-Bu) affords 1,6-hydrogen transfer, followed by a 1,4-aryl migration to render an amidyl radical (20), which is reduced to the N-benzyl-N,2-dimethylpropanamide (10). Together with this last rearranged product, the ipso substitution derivative was also observed. Similar results were obtained in the PET reactions of 4d (R = t-Bu) with anions 2 and 3 under entrainment conditions with the enolate anion from cyclohexenone (5) or the tert-butoxide anion (6). From this novel rearrangement, and only under reductive conditions by PET reaction with anion 5, iodide 4d (R = t-Bu) affords quantitatively the propanamide 10. The energetic of the intramolecular rearrangements followed by radicals 12b-d were rationalized by B3LYP/6-31+G* calculations.

  6. Selectivity Guidelines and a Reductive Elimination-Based Model for Predicting the Stereochemical Course of Conjugate Addition Reactions of Organocuprates to γ-Alkoxy-α,β-Enoates

    PubMed Central

    Kireev, Artem S.; Manpadi, Madhuri; Kornienko, Alexander

    2008-01-01

    Current models used to predict the stereochemical outcome of organocopper conjugate addition processes focus on the nucleophilic addition step as stereochemistry-determining. Recent kinetic, NMR, kinetic isotope effect and theoretical density functional studies strongly support the proposal that stereochemical preferences in these processes are dictated by the reductive elimination step, transforming CuIII to CuI intermediates. A new model that considers various steric and stereoelectronic factors involved in the transition state of the reductive elimination step is proposed and then used to interpret the results of systematic studies of arylcuprate conjugate addition reactions with cis and trans γ-alkoxy-α,β-enoates. The results give rise to the following selectivity guidelines for this process. To achieve high anti-addition diastereoselectivities the use of trans esters with a bulky non-alkoxy substituent at the γ-position is recommended. While stereoelectronics disfavor syn-addition, a judicious choice of properly sized γ-substituents may lead to the predominant formation of syn-products, especially with cis enoates. However, high syn-selelectivities may be achieved by using γ-amino-α,β-enoates. PMID:16555814

  7. Selectivity guidelines and a reductive elimination-based model for predicting the stereochemical course of conjugate addition reactions of organocuprates to gamma-alkoxy-alpha,beta-enoates.

    PubMed

    Kireev, Artem S; Manpadi, Madhuri; Kornienko, Alexander

    2006-03-31

    Current models used to predict the stereochemical outcome of organocopper conjugate addition processes focus on the nucleophilic addition step as stereochemistry-determining. Recent kinetic, NMR, kinetic isotope effect, and theoretical density functional studies strongly support the proposal that stereochemical preferences in these processes are dictated by the reductive elimination step, transforming Cu(III) to Cu(I) intermediates. A new model that considers various steric and stereoelectronic factors involved in the transition state of the reductive elimination step is proposed and then used to interpret the results of systematic studies of arylcuprate conjugate addition reactions with cis and trans gamma-alkoxy-alpha,beta-enoates. The results give rise to the following selectivity guidelines for this process. To achieve high anti-addition diastereoselectivities the use of trans esters with a bulky nonalkoxy substituent at the gamma-position is recommended. While stereoelectronics disfavor syn-addition, a judicious choice of properly sized gamma-substituents may lead to the predominant formation of syn-products, especially with cis enoates. However, high syn-selectivities may be achieved by using gamma-amino-alpha,beta-enoates.

  8. Free radical reaction pathway, thermochemistry of peracetic acid homolysis, and its application for phenol degradation: spectroscopic study and quantum chemistry calculations.

    PubMed

    Rokhina, Ekaterina V; Makarova, Katerina; Golovina, Elena A; Van As, Henk; Virkutyte, Jurate

    2010-09-01

    The homolysis of peracetic acid (PAA) as a relevant source of free radicals (e.g., *OH) was studied in detail. Radicals formed as a result of chain radical reactions were detected with electron spin resonance and nuclear magnetic resonance spin trapping techniques and subsequently identified by means of the simulation-based fitting approach. The reaction mechanism, where a hydroxyl radical was a primary product of O-O bond rupture of PAA, was established with a complete assessment of relevant reaction thermochemistry. Total energy analysis of the reaction pathway was performed by electronic structure calculations (ab initio and semiempirical methods) at different levels and basis sets [e.g., HF/6-311G(d), B3LYP/6-31G(d)]. Furthermore, the heterogeneous MnO2/PAA system was tested for the elimination of a model aromatic compound, phenol from aqueous solution. An artificial neural network (ANN) was designed to associate the removal efficiency of phenol with relevant process parameters such as concentrations of both the catalyst and PAA and the reaction time. Results were used to train and test ANN to identify an optimized network structure, which represented the correlations between the operational parameters and removal efficiency of phenol.

  9. Organocatalytic Enantioselective Synthesis of Tetrahydrofluoren-9-ones via Vinylogous Michael Addition/Henry Reaction Cascade of 1,3-Indandione-Derived Pronucleophiles.

    PubMed

    Möhlmann, Lennart; Chang, Geng-Hua; Madhusudhan Reddy, G; Lee, Chia-Jui; Lin, Wenwei

    2016-02-19

    An unprecedented organocatalytic enantioselective vinylogous Michael addition/Henry cyclization cascade is presented for the synthesis of highly substituted tetrahydrofluoren-9-ones 3 employing novel 1,3-indandione-derived pronucleophiles 1a-g and nitroalkenes 2. Following a very simple protocol, a wide range of products were obtained in good to excellent yields and with excellent enantioinduction (43-98% yield, up to 98% ee). The reaction proceeded with excellent diastereocontrol despite the simultaneous generation of four stereogenic centers. Surprisingly, when 2-(1-phenylethylidene)-1H-indandione (1h) was used as a pronucleophile, no cyclization was observed, and only Michael addition adducts 4a-x were furnished in very good yields and excellent enantioselectivities.

  10. Frustrated Lewis Pair-Like Reactivity of Rare-Earth Metal Complexes: 1,4-Addition Reactions and Polymerizations of Conjugated Polar Alkenes.

    PubMed

    Xu, Pengfei; Yao, Yingming; Xu, Xin

    2017-01-26

    Three rare-earth aryloxide ion pairs {[L1REOAr](+) /[B(C6 F5 )4 ](-) ; L1=CH3 C(2,6-iPr2 C6 H3 N)CHC(CH3 )(NCH2 CH2 PPh2 ); RE=Sc, Y, Lu; Ar=2,6-tBu2 C6 H3 } were reported that feature rare-earth/phosphorus (RE/P) combinations exhibiting frustrated Lewis pair (FLP)-like 1,4-addition reactions towards conjugated carbonyl substrates (e.g., enone, ynone, and acrylic substrates). Furthermore, these RE/P complexes were found to be effective catalysts for the polymerization of conjugated polar alkene monomers. Mechanistic studies revealed that the rare-earth metal-catalyzed polymerizations were initiated by new FLP-type 1,4-additions rather than traditional and ubiquitous covalent RE-E (E=H, C, N, etc.) bond insertion or single-electron transfer.

  11. High-pressure vapor-phase hydrodeoxygenation of lignin-derived oxygenates to hydrocarbons by a PtMo bimetallic catalyst: Product selectivity, reaction pathway, and structural characterization

    SciTech Connect

    Yohe, Sara L.; Choudhari, Harshavardhan J.; Mehta, Dhairya D.; Dietrich, Paul J.; Detwiler, Michael D.; Akatay, Cem M.; Stach, Eric A.; Miller, Jeffrey T.; Delgass, W. Nicholas; Agrawal, Rakesh; Ribeiro, Fabio H.

    2016-12-01

    High-pressure, vapor-phase, hydrodeoxygenation (HDO) reactions of dihydroeugenol (2-methoxy-4-propylphenol), as well as other phenolic, lignin-derived compounds, were investigated over a bimetallic platinum and molybdenum catalyst supported on multi-walled carbon nanotubes (5%Pt2.5%Mo/MWCNT). Hydrocarbons were obtained in 100% yield from dihydroeugenol, including 98% yield of the hydrocarbon propylcyclohexane. The final hydrocarbon distribution was shown to be a strong function of hydrogen partial pressure. Kinetic analysis showed three main dihydroeugenol reaction pathways: HDO, hydrogenation, and alkylation. The major pathway occurred via Pt catalyzed hydrogenation of the aromatic ring and methoxy group cleavage to form 4-propylcyclohexanol, then Mo catalyzed removal of the hydroxyl group by dehydration to form propylcyclohexene, followed by hydrogenation of propylcyclohexene on either the Pt or Mo to form the propylcyclohexane. Transalkylation by the methoxy group occurred as a minor side reaction. Catalyst characterization techniques including chemisorption, scanning transmission electron microscopy, X-ray absorption spectroscopy, and X-ray photoelectron spectroscopy were employed to characterize the catalyst structure. Catalyst components identified were Pt particles, bimetallic PtMo particles, a Mo carbide-like phase, and Mo oxide phases.

  12. Reaction pathways by quantum Monte Carlo: insight on the torsion barrier of 1,3-butadiene, and the conrotatory ring opening of cyclobutene.

    PubMed

    Barborini, Matteo; Guidoni, Leonardo

    2012-12-14

    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.

  13. Pathway analysis of super-exchange electronic couplings in electron transfer reactions using a multi-configuration self-consistent field method.

    PubMed

    Nishioka, Hirotaka; Ando, Koji

    2011-04-21

    We present a novel pathway analysis of super-exchange electronic couplings in electron transfer reactions using localized molecular orbitals from multi-configuration self-consistent field (MCSCF) calculations. In our analysis, the electronic coupling and the tunneling pathways can be calculated in terms of the configuration interaction (CI) Hamiltonian matrix obtained from the localized MCSCF wave function. Making use of the occupation restricted multiple active spaces (ORMAS) method can effectively produce the donor, acceptor, and intermediate configuration state functions (CSFs) and CIs among these CSFs. In order to express the electronic coupling as a sum of individual tunneling pathways contributions, we employed two perturbative methods: Löwdin projection-iteration method and higher-order super-exchange method. We applied them to anion couplings of butane-1,4-diyl and pentane-1,5-diyl. The results were (1) the electronic couplings calculated from the two perturbative methods were in reasonable agreement with those from a non-perturbative method (one-half value of the energy difference between the ground and first excited states), (2) the main tunneling pathways consisted of a small number of lower-order super-exchange pathways where bonding, anti-bonding, or extra-valence-shell orbitals were used once or twice, and (3) the interference among a huge number of higher-order super-exchange pathways significantly contributed to the overall electronic coupling, whereas each of them contributed only fractionally. Our method can adequately take into account both effects of non-dynamical electron correlation and orbital relaxation. Comparing with the analyses based on the Koopmans' theorem (ignoring both effects) and the ORMAS-CIs from frozen localized reference orbitals (ignoring the effect of orbital relaxation), we discuss these effects.

  14. Selective Fluorescence Detection of Cysteine over Homocysteine and Glutathione Based on a Cysteine-Triggered Dual Michael Addition/Retro-aza-aldol Cascade Reaction.

    PubMed

    Liu, Yawei; Lv, Xin; Hou, Min; Shi, Yawei; Guo, Wei

    2015-11-17

    In this work, a cysteine (Cys)-triggered dual Michael addition/retro-aza-aldol cascade reaction has been exploited and utilized to construct a fluorescent probe for Cys for the first time. The resulting fluorescent probe 8-alkynylBodipy 1 contains an activated alkynyl unit as Michael receptor and a Bodipy dye as fluorescence reporter and can highly selectively detect Cys over homocysteine (Hcy)/glutathione (GSH) as well as other amino acids with a significant fluorescence off-on response (∼4500-fold) and an ultralow detection limit (0.38 nM). The high selectivity of 1 for Cys could be attributed to a kinetically favored five-membered cyclic intermediate produced by the dual Michael addition of Cys with the activated alkynyl unit of 1. The big fluorescence off-on response is due to the subsequent retro-aza-aldol reaction of the five-membered cyclic intermediate that results in the release of a highly fluorescent 8-methylBodipy dye 2. The probe has been successfully used to detect and image Cys in serum and cells, respectively.

  15. 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 i