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Sample records for enzyme catalyzed reactions

  1. Thermodynamics of Enzyme-Catalyzed Reactions Database

    National Institute of Standards and Technology Data Gateway

    SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

  2. Microorganisms detected by enzyme-catalyzed reaction

    NASA Technical Reports Server (NTRS)

    Vango, S. P.; Weetall, H. H.; Weliky, N.

    1966-01-01

    Enzymes detect the presence of microorganisms in soils. The enzyme lysozymi is used to release the enzyme catalase from the microorganisms in a soil sample. The catalase catalyzes the decomposition of added hydrogen peroxide to produce oxygen which is detected manometrically. The partial pressure of the oxygen serves as an index of the samples bacteria content.

  3. Representing Rate Equations for Enzyme-Catalyzed Reactions

    ERIC Educational Resources Information Center

    Ault, Addison

    2011-01-01

    Rate equations for enzyme-catalyzed reactions are derived and presented in a way that makes it easier for the nonspecialist to see how the rate of an enzyme-catalyzed reaction depends upon kinetic constants and concentrations. This is done with distribution equations that show how the rate of the reaction depends upon the relative quantities of…

  4. Representing Rate Equations for Enzyme-Catalyzed Reactions

    ERIC Educational Resources Information Center

    Ault, Addison

    2011-01-01

    Rate equations for enzyme-catalyzed reactions are derived and presented in a way that makes it easier for the nonspecialist to see how the rate of an enzyme-catalyzed reaction depends upon kinetic constants and concentrations. This is done with distribution equations that show how the rate of the reaction depends upon the relative quantities of

  5. Molecular Mechanism by which One Enzyme Catalyzes Two Reactions

    NASA Astrophysics Data System (ADS)

    Nishimasu, Hiroshi; Fushinobu, Shinya; Wakagi, Takayoshi

    Unlike ordinary enzymes, fructose-1,6-bisphosphate (FBP) aldolase/phosphatase (FBPA/P) catalyzes two distinct reactions : (1) the aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate to FBP, and (2) the dephosphorylation of FBP to fructose-6-phosphate. We solved the crystal structures of FBPA/P in complex with DHAP (its aldolase form) and FBP (its phosphatase form). The crystal structures revealed that FBPA/P exhibits the dual activities through a dramatic conformational change in the active-site architecture. Our findings expand the conventional concept that one enzyme catalyzes one reaction.

  6. Method for predicting enzyme-catalyzed reactions

    DOEpatents

    Hlavacek, William S.; Unkefer, Clifford J.; Mu, Fangping; Unkefer, Pat J.

    2013-03-19

    The reactivity of given metabolites is assessed using selected empirical atomic properties in the potential reaction center. Metabolic reactions are represented as biotransformation rules. These rules are generalized from the patterns in reactions. These patterns are not unique to reactants but are widely distributed among metabolites. Using a metabolite database, potential substructures are identified in the metabolites for a given biotransformation. These substructures are divided into reactants or non-reactants, depending on whether they participate in the biotransformation or not. Each potential substructure is then modeled using descriptors of the topological and electronic properties of atoms in the potential reaction center; molecular properties can also be used. A Support Vector Machine (SVM) or classifier is trained to classify a potential reactant as a true or false reactant using these properties.

  7. Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions

    NASA Astrophysics Data System (ADS)

    Golestanian, Ramin

    2015-09-01

    Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature (London) 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the degree of exothermicity of the catalytic reaction involved. Four mechanisms that can lead to this effect, namely, self-thermophoresis, boost in kinetic energy, stochastic swimming, and collective heating are critically discussed, and it is shown that only the last two can be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.

  8. Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions.

    PubMed

    Golestanian, Ramin

    2015-09-01

    Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel etal., Nature (London) 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the degree of exothermicity of the catalytic reaction involved. Four mechanisms that can lead to this effect, namely, self-thermophoresis, boost in kinetic energy, stochastic swimming, and collective heating are critically discussed, and it is shown that only the last two can be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect. PMID:26382704

  9. Enzyme-Catalyzed Henry Reaction in Choline Chloride-Based Deep Eutectic Solvents.

    PubMed

    Tian, Xuemei; Zhang, Suoqin; Zheng, Liangyu

    2016-01-28

    The enzyme-catalyzed Henry reaction was realized using deep eutectic solvents (DESs) as a reaction medium. The lipase from Aspergillus niger (lipase AS) showed excellent catalytic activity toward the substrates aromatic aldehydes and nitromethane in choline chloride:glycerol at a molar ratio of 1:2. Addition of 30 vol% water to DES further improved the lipase activity and inhibited DES-catalyzed transformation. A final yield of 92.2% for the lipase AS-catalyzed Henry reaction was achieved under optimized reaction conditions in only 4 h. In addition, the lipase AS activity was improved by approximately 3-fold in a DES-water mixture compared with that in pure water, which produced a final yield of only 33.4%. Structural studies with fluorescence spectroscopy showed that the established strong hydrogen bonds between DES and water may be the main driving force that affects the spatial conformation of the enzyme, leading to a change in lipase activity. The methodology was also extended to the aza-Henry reaction, which easily occurred in contrast to that in pure water. The enantioselectivity of both Henry and aza-Henry reactions was not found. However, the results are still remarkable, as we report the first use of DES as a reaction medium in a lipase-catalyzed Henry reaction. PMID:26437947

  10. Mutagenicity screening of reaction products from the enzyme-catalyzed oxidation of phenolic pollutants

    SciTech Connect

    Massey, I.J.; Aitken, M.D.; Ball, L.M.; Heck, P.E. . Dept. of Environmental Sciences and Engineering)

    1994-11-01

    Phenol-oxidizing enzymes such as peroxidases, laccases, and mushroom polyphenol oxidase are capable of catalyzing the oxidation of a wide range of phenolic pollutants. Although the use of these enzymes in waste-treatment applications has been proposed by a number of investigators, little information exists on the toxicological characteristics of the oxidation products. The enzymes chloroperoxidase, horseradish peroxidase, lignin peroxidase, and mushroom polyphenol oxidase were used in this study to catalyze the oxidation of phenol, several mono-substituted phenols, and pentachlorophenol. Seventeen reaction mixtures representing selected combinations of enzyme and parent phenol were subjected to mutagenicity screening using the Ames Salmonella typhimurium plate incorporation assay; five selected mixtures were also incubated with the S9 microsomal preparation to detect the possible presence of promutagens. The majority of reaction mixtures tested were not directly mutagenic, and none of those tested with S9 gave a positive response. Such lack of mutagenicity of enzymatic oxidation products provides encouragement for establishing the feasibility of enzyme-catalyzed oxidation as a waste-treatment process. The only positive responses were obtained with reaction products from the lignin peroxidase-catalyzed oxidation of 2-nitrophenol and 4-nitrophenol. Clear positive responses were observed when strain TA100 was incubated with 2-nitrophenol reaction-product mixtures, and when strain TA98 was incubated with the 4-nitrophenol reaction mixture. Additionally, 2,4-dinitrophenol was identified as a reaction product from 4-nitrophenol, and preliminary evidence indicates that both 2,4- and 2,6-dinitrophenol are produced from the oxidation of 2-nitrophenol. Possible mechanism by which these nitration reactions occur are discussed.

  11. Energy Diagrams for Enzyme-Catalyzed Reactions: Concepts and Misconcepts

    ERIC Educational Resources Information Center

    Aledo, J. Carlos; Lobo, Carolina; del Valle, Alicia Esteban

    2003-01-01

    Despite the utility that energy diagrams have as a teaching and learning tool, a survey of their use, in seven popular Biochemistry textbooks, reveals that there is certain confusion around this topic. In our opinion, this confusion arises from the reluctance of authors to consider and indicate the conditions under which the reaction being

  12. Energy Diagrams for Enzyme-Catalyzed Reactions: Concepts and Misconcepts

    ERIC Educational Resources Information Center

    Aledo, J. Carlos; Lobo, Carolina; del Valle, Alicia Esteban

    2003-01-01

    Despite the utility that energy diagrams have as a teaching and learning tool, a survey of their use, in seven popular Biochemistry textbooks, reveals that there is certain confusion around this topic. In our opinion, this confusion arises from the reluctance of authors to consider and indicate the conditions under which the reaction being…

  13. Water-gas shift reaction catalyzed by redox enzymes on conducting graphite platelets.

    PubMed

    Lazarus, Oliver; Woolerton, Thomas W; Parkin, Alison; Lukey, Michael J; Reisner, Erwin; Seravalli, Javier; Pierce, Elizabeth; Ragsdale, Stephen W; Sargent, Frank; Armstrong, Fraser A

    2009-10-14

    The water-gas shift (WGS) reaction (CO + H(2)O <==> CO(2) + H(2)) is of major industrial significance in the production of H(2) from hydrocarbon sources. High temperatures are required, typically in excess of 200 degrees C, using d-metal catalysts on oxide supports. In our study the WGS process is separated into two half-cell electrochemical reactions (H(+) reduction and CO oxidation), catalyzed by enzymes attached to a conducting particle. The H(+) reduction reaction is catalyzed by a hydrogenase, Hyd-2, from Escherichia coli, and CO oxidation is catalyzed by a carbon monoxide dehydrogenase (CODH I) from Carboxydothermus hydrogenoformans. This results in a highly efficient heterogeneous catalyst with a turnover frequency, at 30 degrees C, of at least 2.5 s(-1) per minimum functional unit (a CODH/Hyd-2 pair) which is comparable to conventional high-temperature catalysts. PMID:19807170

  14. Folylpolyglutamate synthetase: direct evidence for an acyl phosphate intermediate in the enzyme-catalyzed reaction

    SciTech Connect

    Banerjee, R.; McGuire, J.J.; Shane, B.; Coward, J.K.

    1986-05-01

    The nature of the intermediate in the reaction catalyzed by folylpoly-..gamma..-glutamate synthetase (FPGS) has been investigated. Incubation of ..cap alpha..,..gamma..-(/sup 18/O)methotrexate with ATP, glutamate, and FPGS resulted in the formation of (/sup 18/O)phosphate, thus providing strong evidence for the formation of a ..gamma..-glutamyl phosphate during catalysis. The inorganic phosphate formed in the enzyme-catalyzed reaction was separated from other products and substrates by chromatography on DEAE-cellulose, then converted to the trimethyl ester, and analyzed by mass spectroscopy. Stoichiometric formation of (/sup 18/O)phosphate was observed in the case of the E. coli enzyme, isolated from a transformant containing the cloned FPGS-dihydrofolate synthetase (folC) gene. In addition, /sup 31/P-NMR analysis of the phosphate isolated from the reaction using E. coli FPGS showed the expected /sup 18/O-isotopic perturbations due to both singly bonded and doubly bonded P-/sup 18/O species. Similar experiments were carried out with FPGS isolated from hog liver. In this case, the small amounts of pure enzyme available precluded use of the NMR technique. However, mass spectral analysis of the derivatized phosphate product revealed the presence of (/sup 18/O)-trimethyl phosphate, thus indicating that the reaction catalyzed by the mammalian enzyme also proceeds via an acyl phosphate intermediate.

  15. Change in heat capacity accurately predicts vibrational coupling in enzyme catalyzed reactions.

    PubMed

    Arcus, Vickery L; Pudney, Christopher R

    2015-08-01

    The temperature dependence of kinetic isotope effects (KIEs) have been used to infer the vibrational coupling of the protein and or substrate to the reaction coordinate, particularly in enzyme-catalyzed hydrogen transfer reactions. We find that a new model for the temperature dependence of experimentally determined observed rate constants (macromolecular rate theory, MMRT) is able to accurately predict the occurrence of vibrational coupling, even where the temperature dependence of the KIE fails. This model, that incorporates the change in heat capacity for enzyme catalysis, demonstrates remarkable consistency with both experiment and theory and in many respects is more robust than models used at present. PMID:26172507

  16. Isotope Effects as Probes for Enzyme Catalyzed Hydrogen-Transfer Reactions

    PubMed Central

    Roston, Daniel; Islam, Zahidul; Kohen, Amnon

    2015-01-01

    Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studieshas changed our notion of how these enzymes exert their catalytic powers. PMID:23673528

  17. Cysteine oxidation reactions catalyzed by a mononuclear non-heme iron enzyme (OvoA) in ovothiol biosynthesis.

    PubMed

    Song, Heng; Her, Ampon Sae; Raso, Fiona; Zhen, Zhibin; Huo, Yuda; Liu, Pinghua

    2014-04-18

    OvoA in ovothiol biosynthesis is a mononuclear non-heme iron enzyme catalyzing the oxidative coupling between histidine and cysteine. It can also catalyze the oxidative coupling between hercynine and cysteine, yet with a different regio-selectivity. Due to the potential application of this reaction for industrial ergothioneine production, in this study, we systematically characterized OvoA by a combination of three different assays. Our studies revealed that OvoA can also catalyze the oxidation of cysteine to either cysteine sulfinic acid or cystine. Remarkably, these OvoA-catalyzed reactions can be systematically modulated by a slight modification of one of its substrates, histidine. PMID:24684381

  18. Nonequilibrium chemical potentials and free energies for enzyme-catalyzed reactions.

    PubMed

    Keizer, J

    1987-12-01

    Using the statistical theory of nonequilibrium thermodynamics we explore the nature of nonequilibrium corrections to chemical potentials in simple enzyme-catalyzed reactions. The statistical definition of the chemical potential, which pertains to systems that are at stable steady states, is applied to the Michaelis-Menten reaction scheme in a cellular-sized compartment that communicates with outside reservoirs. Calculations based on the kinetic parameters for hexokinase and triose phosphate isomerase show that substantial corrections to the chemical potential of product (the order of 25 mV) are possible if the reaction is sufficiently far from equilibrium. The dependence of the corrections to the chemical potentials on the size of the cellular compartment are explored, and the relevance of the corrections for understanding the thermodynamics of metabolites is discussed. PMID:2450667

  19. Enzyme-catalyzed organic syntheses: transesterification reactions of chlorophyl a, bacteriochlorophyll a, and derivatives with chlorophyllase

    SciTech Connect

    Michalski, T.J.; Hunt, J.E.; Bradshaw, C.; Wagner, A.M.; Norris, J.R.; Katz, J.J.

    1988-08-17

    The green plant enzyme chlorophyllase (EC 3.1.1.14, chlorophyll chlorophyllido-hydroase) has been used for the synthesis of a variety of primary alcohol and diol esters of chlorophyll a, bacteriochlorophyll a, and pyrobacteriochlorophyll a. Green plant chlorophyllase accepts a much larger range of alcohol and chlorophyll substrates than had previously been realized. Thus, chlorophyllide and bacteriochlorophyllide esters of primary alcohols such as retinol and the detergent Triton X-100 and of dihydric alcohols such as ethylene glycol, butanediol, or 2-hydroxyethyl disulfide can readily be obtained by enzyme-assisted transesterification. The diol chlorophyllide esters are valuable intermediates for the synthesis of reaction center special pair models. Chlorophyllase-assisted reactions can be carried out in media containing up to 95% of organic solvents without the concomitant side reactions that important chlorophyll functional groups readily undergo even under mild conditions in conventional chemical synthetic procedures. In competitive chlorophyllase-catalyzed transesterification reactions, long-chain alcohols such as farnesol and retinol vs simple aliphatic alcohols and diols, the enzyme shows a definite preference for the long-chain alcohol. 37 references, 1 figure, 2 tables.

  20. Local Bifurcations of the Enzyme-Catalyzed Reaction Comprising a Branched Network

    NASA Astrophysics Data System (ADS)

    Zhang, Qiuyan; Liu, Lingling; Zhang, Weinian

    2015-06-01

    An enzyme-catalyzed reaction system with four parameters a, b, c, ? is discussed. The system can be reduced to a quartic polynomial differential system with four parameters, which leads to difficulties in the computation of semi-algebraic systems of large degree polynomials. Those systems have to be discussed on subsets of special biological sense, none of which is closed under operations of the polynomial ring. In this paper, we overcome those difficulties to determine the exact number of equilibria and their qualitative properties. Moreover, we obtain parameter conditions for all codimension-1 bifurcations such as saddle-node, transcritical, pitchfork and Hopf bifurcations. We compute varieties of Lyapunov quantities under the limitations of biological requirements and prove that the weak focus is of at most order 2. We further obtain parameter conditions for exact number of limit cycles arising from Hopf bifurcations.

  1. Beta-D-xylosidase from Selenomonas ruminantium: thermodynamics of enzyme-catalyzed and noncatalyzed reactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta-D-xylosidase/alpha-L-arabinofuranosidase from Selenomonas ruminantium (SXA) is the most active enzyme known for catalyzing hydrolysis of 1,4-beta-D-xylooligosaccharides to D-xylose. Temperature dependence for hydrolysis of 4-nitrophenyl-beta-D-xylopyranoside (4NPX), 4-nitrophenyl-alpha-L-arabi...

  2. Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

    SciTech Connect

    Malik, Radhika; Viola, Ronald E.

    2010-10-28

    The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 {angstrom} resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg{sup 2+} and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

  3. Reformulation of the Michaelis-Menten Equation: How Enzyme-Catalyzed Reactions Depend on Gibbs Energy

    ERIC Educational Resources Information Center

    Bozlee, Brian J.

    2007-01-01

    The impact of raising Gibbs energy of the enzyme-substrate complex (G[subscript 3]) and the reformulation of the Michaelis-Menten equation are discussed. The maximum velocity of the reaction (v[subscript m]) and characteristic constant for the enzyme (K[subscript M]) will increase with increase in Gibbs energy, indicating that the rate of reaction

  4. Catalyzed enzyme electrodes

    DOEpatents

    Zawodzinski, Thomas A.; Wilson, Mahlon S.; Rishpon, Judith; Gottesfeld, Shimshon

    1993-01-01

    An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

  5. Reformulation of the Michaelis-Menten Equation: How Enzyme-Catalyzed Reactions Depend on Gibbs Energy

    ERIC Educational Resources Information Center

    Bozlee, Brian J.

    2007-01-01

    The impact of raising Gibbs energy of the enzyme-substrate complex (G[subscript 3]) and the reformulation of the Michaelis-Menten equation are discussed. The maximum velocity of the reaction (v[subscript m]) and characteristic constant for the enzyme (K[subscript M]) will increase with increase in Gibbs energy, indicating that the rate of reaction…

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

    PubMed

    Joseph, Collin; Tseng, Chiao-Yu; Zocchi, Giovanni; Tlusty, Tsvi

    2014-01-01

    The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae). The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient [Formula: see text] for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory. PMID:25000118

  7. Monitoring enzyme-catalyzed reactions in micromachined nanoliter wells using a conventional microscope-based microarray reader

    NASA Astrophysics Data System (ADS)

    van den Doel, L. Richard; Moerman, R.; van Dedem, G. W. K.; Young, Ian T.; van Vliet, Lucas J.

    2002-06-01

    Yeast-Saccharomyces cerevisiae - it widely used as a model system for other higher eukaryotes, including man. One of the basic fermentation processes in yeast is the glycolytic pathway, which is the conversion of glucose to ethanol and carbon dioxide. This pathway consists of 12 enzyme-catalyzed reactions. With the approach of microarray technology we want to explore the metabolic regulation of this pathway in yeast. This paper will focus on the design of a conventional microscope based microarray reader, which is used to monitor these enzymatic reactions in microarrays. These microarrays are fabricated in silicon and have sizes of 300 by 300 micrometers 2. The depth varies from 20 to 50 micrometers . Enzyme activity levels can be derived by monitoring the production or consumption rate of NAD(P)H, which is excited at 360nm and emits around 450nm. This fluorophore is involved in all 12 reactions of the pathway. The microarray reader is equipped with a back-illuminated CCD camera in order to obtain a high quantum efficiency for the lower wavelengths. The dynamic range of our microarray reader varies form 5(mu) Molar to 1mMolar NAD(P)H. With this microarray reader enzyme activity levels down to 0.01 unit per milliliter can be monitored. The acquisition time per well is 0.1s. The total scan cycle time for a 5 X 5 microarray is less than half a minute. The number of cycles for a proper estimation of the enzyme activity is inversely proportional to the enzyme activity: long measurement times are needed to determine low enzyme activity levels.

  8. An "Aufbau" Approach to Understanding How the King-Altman Method of Deriving Rate Equations for Enzyme-Catalyzed Reactions Works

    ERIC Educational Resources Information Center

    Sims, Paul A.

    2009-01-01

    The King-Altman method of deriving rate equations for enzymatic reactions is applied to the derivation of the Michaelis-Menten equation, along with an explanation for how (or why) the King-Altman method works in this case. The slightly more complicated cases of competitive inhibition and a two-substrate enzyme-catalyzed reaction are then treated

  9. Mechanosensitive liposomes as artificial chaperones for shear-driven acceleration of enzyme-catalyzed reaction.

    PubMed

    Natsume, Tomotaka; Yoshimoto, Makoto

    2014-03-12

    Mechanosensitive liposomes were prepared and applied to continuously accelerate the glucose oxidase (GO) reaction in shear flow. The liposome membrane was composed of a ternary lipid mixture containing 20 mol % negatively charged lipid and 30 mol % cholesterol. The liposomes encapsulating GO and catalase were passed through microtubes with inner diameter of 190 or 380 ?m at 25 C to induce the catalytic oxidation of 10 mM glucose with simultaneous decomposition of H2O2 produced. The liposomal GO showed significantly low reactivity in the static liquid system because of the permeation resistance of lipid membranes to glucose. On the other hand, the enzyme activity of liposomal GO observed at the average shear rate of 7.8 10(3) s(-1) was significantly larger than its intrinsic activity free of mass transfer effect in the static liquid system. The structure of liposomes was highly shear-sensitive as elucidated on the basis of shear rate-dependent physical stability of liposomes and membrane permeability to 5(6)-carboxyfluorescein as well as to GO. Thus, the above shear-driven acceleration of GO reaction was indicated to be caused by the free GO molecules released from the structurally altered liposomes at high shear rates. Moreover, the shear-induced denaturation of free GO was completely depressed by the interaction with the sheared liposomes with the chaperone-like function. The shear-sensitive liposomal GO system can be a unique catalyst that continuously accelerates and also decelerates the oxidation reaction depending on the applied shear rate. PMID:24547684

  10. The Effect of Temperature on the Enzyme-Catalyzed Reaction: Insights from Thermodynamics

    ERIC Educational Resources Information Center

    Aledo, Juan Carlos; Jimenez-Riveres, Susana; Tena, Manuel

    2010-01-01

    When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature coefficients…

  11. The Effect of Temperature on the Enzyme-Catalyzed Reaction: Insights from Thermodynamics

    ERIC Educational Resources Information Center

    Aledo, Juan Carlos; Jimenez-Riveres, Susana; Tena, Manuel

    2010-01-01

    When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature coefficients

  12. Kinetic studies on enzyme-catalyzed reactions: oxidation of glucose, decomposition of hydrogen peroxide and their combination.

    PubMed

    Tao, Zhimin; Raffel, Ryan A; Souid, Abdul-Kader; Goodisman, Jerry

    2009-04-01

    The kinetics of the glucose oxidase-catalyzed reaction of glucose with O2, which produces gluconic acid and hydrogen peroxide, and the catalase-assisted breakdown of hydrogen peroxide to generate oxygen, have been measured via the rate of O2 depletion or production. The O2 concentrations in air-saturated phosphate-buffered salt solutions were monitored by measuring the decay of phosphorescence from a Pd phosphor in solution; the decay rate was obtained by fitting the tail of the phosphorescence intensity profile to an exponential. For glucose oxidation in the presence of glucose oxidase, the rate constant determined for the rate-limiting step was k = (3.0 +/- 0.7) x 10(4) M(-1) s(-1) at 37 degrees C. For catalase-catalyzed H2O2 breakdown, the reaction order in [H2O2] was somewhat greater than unity at 37 degrees C and well above unity at 25 degrees C, suggesting different temperature dependences of the rate constants for various steps in the reaction. The two reactions were combined in a single experiment: addition of glucose oxidase to glucose-rich cell-free media caused a rapid drop in [O2], and subsequent addition of catalase caused [O2] to rise and then decrease to zero. The best fit of [O2] to a kinetic model is obtained with the rate constants for glucose oxidation and peroxide decomposition equal to 0.116 s(-1) and 0.090 s(-1) respectively. Cellular respiration in the presence of glucose was found to be three times as rapid as that in glucose-deprived cells. Added NaCN inhibited O2 consumption completely, confirming that oxidation occurred in the cellular mitochondrial respiratory chain. PMID:19348778

  13. Rapid and accurate liquid chromatography and tandem mass spectrometry method for the simultaneous quantification of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes.

    PubMed

    Shi, Rong; Ma, Bingliang; Wu, Jiasheng; Wang, Tianming; Ma, Yueming

    2015-10-01

    The hepatic cytochrome P450 enzymes play a central role in the biotransformation of endogenous and exogenous substances. A sensitive high-throughput liquid chromatography with tandem mass spectrometry assay was developed and validated for the simultaneous quantification of the products of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes. After the substrates were incubated separately, the samples were pooled and analyzed by liquid chromatography with tandem mass spectrometry using an electrospray ionization source in the positive and negative ion modes. The method exhibited linearity over a broad concentration range, insensitivity to matrix effects, and high accuracy, precision, and stability. The novel method was successfully applied to study the kinetics of phenacetin-O deethylation, coumarin-7 hydroxylation, bupropion hydroxylation, taxol-6 hydroxylation, omeprazole-5 hydroxylation, dextromethorphan-O demethylation, tolbutamide-4 hydroxylation, chlorzoxazone-6 hydroxylation, testosterone-6? hydroxylation, and midazolam-1 hydroxylation in rat liver microsomes. PMID:26256777

  14. The application of high-pressure stopped-flow spectroscopy at low temperatures for the study of enzyme catalyzed reactions

    NASA Astrophysics Data System (ADS)

    Balny, Claude

    1986-05-01

    The elucidation of the mechanism of enzyme action generally requires knowledge of the maximum values of the thermodynamic parameters. High hydrostatic pressure associated with temperature variation can lead to such data. In this laboratory, the development of cryoenzymology, which mainly slows down reaction velocity, has permitted a description of catalytic cycles over a single turnover to isolate intermediates in order to analyze single steps. This thermal control of a reaction has opened the way for the investigation of the activation volume ( ?V?) of each step and then to detect their stereochemical changes. This is experimentally attained using a specially designed stopped-flow apparatus interfaced to spectrophotometers working over a wide temperature range (+30 to -30C in hydroorganic media) from 1 to 2000 bar. A description of the apparatus is given together with potential applications.

  15. Strictosidine Synthase: Mechanism of a PictetSpengler Catalyzing Enzyme

    PubMed Central

    Maresh, Justin J.; Giddings, Lesley-Ann; Friedrich, Anne; Loris, Elke A.; Panjikar, Santosh; Trout, Bernhardt L.

    2010-01-01

    The PictetSpengler reaction, which yields either a ?-carboline or a tetrahydroquinoline product from an aromatic amine and an aldehyde, is widely utilized in plant alkaloid biosynthesis. Here we deconvolute the role that the biosynthetic enzyme strictosidine synthase plays in catalyzing the stereoselective synthesis of a ?-carboline product. Notably, the rate-controlling step of the enzyme mechanism, as identified by the appearance of a primary kinetic isotope effect (KIE), is the rearomatization of a positively charged intermediate. The KIE of a nonenzymatic PictetSpengler reaction indicates that rearomatization is also rate-controlling in solution, suggesting that the enzyme does not significantly change the mechanism of the reaction. Additionally, the pH dependence of the solution and enzymatic reactions provides evidence for a sequence of acidbase catalysis steps that catalyze the PictetSpengler reaction. An additional acid-catalyzed step, most likely protonation of a carbinolamine intermediate, is also significantly rate controlling. We propose that this step is efficiently catalyzed by the enzyme. Structural analysis of a bisubstrate inhibitor bound to the enzyme suggests that the active site is exquisitely tuned to correctly orient the iminium intermediate for productive cyclization to form the diastereoselective product. Furthermore, ab initio calculations suggest the structures of possible productive transition states involved in the mechanism. Importantly, these calculations suggest that a spiroindolenine intermediate, often invoked in the PictetSpengler mechanism, does not occur. A detailed mechanism for enzymatic catalysis of the ?-carboline product is proposed from these data. PMID:18081287

  16. Exchange reactions catalyzed by group-transferring enzymes oppose the quantitation and the unravelling of the identify of the pentose pathway.

    PubMed

    Flanigan, I; Collins, J G; Arora, K K; MacLeod, J K; Williams, J F

    1993-04-01

    1. The distributions and rates of transfer of carbon isotopes from a selection of specifically labelled ketosugar-phosphate substrates by exchange reactions catalyzed by the pentose and photosynthetic carbon-reduction-pathway group-transferring enzymes transketolase, transaldolase and aldolase have been measured using 13C-NMR spectroscopy. 2. The rates of these exchange reactions were 5, 4 and 1.5 mumol min-1 mg-1 for transketolase exchange, transaldolase exchange and aldolase exchange, respectively. 3. A comparison of the exchange capacities contributed by the activities of these enzymes in three in vitro liver preparations with the maximum non-oxidative pentose pathway flux rates of the preparations shows that transketolase and aldolase exchanges exceeded flux by 9-19 times in liver cytosol and acetone powder enzyme preparations and by 5 times in hepatocytes. Transaldolase was less effective in the comparison of exchange versus flux rates: transaldolase exchange exceeded flux by 1.6 and 5 in catalysis by liver cytosol and acetone powder preparations, respectively, but was only 0.6 times the flux in hepatocytes. 4. Values of group enzyme exchange and pathway flux rates in the above three preparations are important because of the feature role of liver and of these particular preparations in the establishment, elucidation and measurement of a proposed reaction scheme for the fat-cell-type pentose pathway in biochemistry. 5. It is the claim of this paper that the excess of exchange rate activity (particularly transketolase exchange) over pathway flux will overturn attempts to unravel, using isotopically labelled sugar substrates, the identity, reaction sequence and quantitative contribution of the pentose pathway to glucose metabolism. 6. The transketolase exchange reactions relative to the pentose pathway flux rates in normal, regenerating and foetal liver, Morris hepatomas, mammary carcinoma, melanoma, colonic epithelium, spinach chloroplasts and epididymal fat tissue show that transketolase exchange may exceed flux in these tissues by factors ranging over 5-600 times. 7. The confusion of pentose pathway theory by the effects of transketolase exchange action is illustrated by the 13C-NMR spectrum of the hexose 6-phosphate products of ribose 5-phosphate dissimilation, formed after 30 min of liver enzyme action, and shows 13C-labelling in carbons 1 and 3 of glucose 6-phosphate with ratios which range over 2.1-6.4 rather than the mandatory value of 2 which is imposed by the theoretical mechanism of the pathway. PMID:8477719

  17. On the Temperature Dependence of Enzyme-Catalyzed Rates.

    PubMed

    Arcus, Vickery L; Prentice, Erica J; Hobbs, Joanne K; Mulholland, Adrian J; Van der Kamp, Marc W; Pudney, Christopher R; Parker, Emily J; Schipper, Louis A

    2016-03-29

    One of the critical variables that determine the rate of any reaction is temperature. For biological systems, the effects of temperature are convoluted with myriad (and often opposing) contributions from enzyme catalysis, protein stability, and temperature-dependent regulation, for example. We have coined the phrase "macromolecular rate theory (MMRT)" to describe the temperature dependence of enzyme-catalyzed rates independent of stability or regulatory processes. Central to MMRT is the observation that enzyme-catalyzed reactions occur with significant values of ΔCp(‡) that are in general negative. That is, the heat capacity (Cp) for the enzyme-substrate complex is generally larger than the Cp for the enzyme-transition state complex. Consistent with a classical description of enzyme catalysis, a negative value for ΔCp(‡) is the result of the enzyme binding relatively weakly to the substrate and very tightly to the transition state. This observation of negative ΔCp(‡) has important implications for the temperature dependence of enzyme-catalyzed rates. Here, we lay out the fundamentals of MMRT. We present a number of hypotheses that arise directly from MMRT including a theoretical justification for the large size of enzymes and the basis for their optimum temperatures. We rationalize the behavior of psychrophilic enzymes and describe a "psychrophilic trap" which places limits on the evolution of enzymes in low temperature environments. One of the defining characteristics of biology is catalysis of chemical reactions by enzymes, and enzymes drive much of metabolism. Therefore, we also expect to see characteristics of MMRT at the level of cells, whole organisms, and even ecosystems. PMID:26881922

  18. Efficient antibody-catalyzed oxygenation reaction

    SciTech Connect

    Hsieh, L.C.; Stephans, J.C.; Schultz, P.G. )

    1994-03-09

    Biological oxygen-transfer reactions are essential for the biosynthesis of steroids and neurotransmitters, the degradation of endogenous substances, and the detoxification of xenobiotics. The monooxygenase enzymes responsible for these transformations require biological cofactors such as flavin, heme and non-heme iron, copper, or pterin and typically utilize NADPH for cofactor regeneration. We now report an antibody-catalyzed sulfide oxygenation reaction mediated by the chemical cofactor sodium periodate, with turnover numbers similar to those of the corresponding enzymatic reactions. Sodium periodate NaIO[sub 4]O was chosen as the oxidant, since sulfoxide formation occurs under mild aqueous conditions with minimal overoxidation to the sulfone. Furthermore, compared to the flavin and heme cofactors required by the monooxygenase enzymes, NaIO[sub 4] is very inexpensive, obviating the need for cofactor recycling. Overall, these results raise the possibility of using antibodies as catalysts for regio- and stereoselective sulfide oxidations. 18 refs., 1 fig.

  19. A Lipoxygenase from Red Alga Pyropia haitanensis, a Unique Enzyme Catalyzing the Free Radical Reactions of Polyunsaturated Fatty Acids with Triple Ethylenic Bonds

    PubMed Central

    Zhu, Zhujun; Qian, Feijian; Yang, Rui; Chen, Juanjuan; Luo, Qijun; Chen, Haimin; Yan, Xiaojun

    2015-01-01

    Lipoxygenases (LOXs) are key enzymes to regulate the production of hormones and defensive metabolites in plants, animals and algae. In this research, a full length LOX gene has been cloned and expressed from the red alga Pyropia haitanensis (Bangiales, Rhodophyta) gametophyte (PhLOX2). Subsequent phylogenetic analysis showed that such LOX enzymes are separated at the early stage of evolution, establishing an independent branch. The LOX activity was investigated at the optimal pH of 8.0. It appears that PhLOX2 is a multifunctional enzyme featuring both lipoxygenase and hydroperoxidase activities. Additionally, PhLOX2 exhibits remarkable substrate and position flexibility, and it can catalyze an array of chemical reactions involving various polyunsaturated fatty acids, ranging from C18 to C22. As a matter of fact, mono-hydroperoxy, di-hydroperoxy and hydroxyl products have been obtained from such transformations, and eicosapentaenoic acid seem to be the most preferred substrate. It was found that at least triple ethylenic bonds are required for PhLOX2 to function as a LOX, and the resulting hydroxy products should be originated from the PhLOX2 mediated reduction of mono-hydroperoxides, in which the hydrogen abstraction occurs on the carbon atom between the second and third double bond. Most of the di-hydroperoxides observed seem to be missing their mono-position precursors. The substrate and position flexibility, as well as the function versatility of PhLOXs represent the ancient enzymatic pathway for organisms to control intracellular oxylipins. PMID:25658744

  20. Enzyme-catalyzed protein crosslinking.

    PubMed

    Heck, Tobias; Faccio, Greta; Richter, Michael; Thny-Meyer, Linda

    2013-01-01

    The process of protein crosslinking comprises the chemical, enzymatic, or chemoenzymatic formation of new covalent bonds between polypeptides. This allows (1) the site-directed coupling of proteins with distinct properties and (2) the de novo assembly of polymeric protein networks. Transferases, hydrolases, and oxidoreductases can be employed as catalysts for the synthesis of crosslinked proteins, thereby complementing chemical crosslinking strategies. Here, we review enzymatic approaches that are used for protein crosslinking at the industrial level or have shown promising potential in investigations on the lab-scale. We illustrate the underlying mechanisms of crosslink formation and point out the roles of the enzymes in their natural environments. Additionally, we discuss advantages and drawbacks of the enzyme-based crosslinking strategies and their potential for different applications. PMID:23179622

  1. Mushroom tyrosinase: A model system to combine experimental investigation of enzyme-catalyzed reactions, data handling using R, and enzyme-inhibitor structural studies.

    PubMed

    Nairn, Robert; Cresswell, Will; Nairn, Jacqueline

    2015-01-01

    The activity of mushroom tyrosinase can be measured by monitoring the conversion of phenolic compounds into quinone derivatives using spectrophotometry. This article describes a series of experiments which characterize the functional properties of tyrosinase, the analysis of the resulting data using R to determine the kinetic parameters, and the exploration of the structural properties of tyrosinase-inhibitor complexes. Tyrosinase assay development and subsequent activity measurements, in the presence of varying pH, substrate concentration and inhibitors, offers the opportunity to learn the enzyme characterization skills relevant to a research laboratory setting. Combining the activity studies with an exploration of the nature of the tyrosinase-inhibitor interactions enables a structural understanding of the experimental observations. PMID:26331629

  2. IONIC LIQUIDS: THE PROSPECTS OF ENZYME-CATALYZED GLYCOSYLATIONS WITHOUT WATER

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reversing the hydrolytic reaction catalyzed by glycosidases has great potential for the enzyme-catalyzed synthesis of new glycoconjugates. Hydrolysis of glycosidic bonds requires water as a co-reactant, and the reverse reaction (referred to as transglycosylation) is therefore favored by low- or non...

  3. Controlling reaction specificity in pyridoxal phosphate enzymes

    PubMed Central

    Toney, Michael D.

    2012-01-01

    Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly ?-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at C? of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. PMID:21664990

  4. Enzyme Reaction Annotation Using Cloud Techniques

    PubMed Central

    Huang, Chuan-Ching

    2013-01-01

    An understanding of the activities of enzymes could help to elucidate the metabolic pathways of thousands of chemical reactions that are catalyzed by enzymes in living systems. Sophisticated applications such as drug design and metabolic reconstruction could be developed using accurate enzyme reaction annotation. Because accurate enzyme reaction annotation methods create potential for enhanced production capacity in these applications, they have received greater attention in the global market. We propose the enzyme reaction prediction (ERP) method as a novel tool to deduce enzyme reactions from domain architecture. We used several frequency relationships between architectures and reactions to enhance the annotation rates for single and multiple catalyzed reactions. The deluge of information which arose from high-throughput techniques in the postgenomic era has improved our understanding of biological data, although it presents obstacles in the data-processing stage. The high computational capacity provided by cloud computing has resulted in an exponential growth in the volume of incoming data. Cloud services also relieve the requirement for large-scale memory space required by this approach to analyze enzyme kinetic data. Our tool is designed as a single execution file; thus, it could be applied to any cloud platform in which multiple queries are supported. PMID:24222895

  5. Site-specific DNA transesterification catalyzed by a restriction enzyme

    PubMed Central

    Sasnauskas, Giedrius; Connolly, Bernard A.; Halford, Stephen E.; Siksnys, Virginijus

    2007-01-01

    Most restriction endonucleases use Mg2+ to hydrolyze phosphodiester bonds at specific DNA sites. We show here that BfiI, a metal-independent restriction enzyme from the phospholipase D superfamily, catalyzes both DNA hydrolysis and transesterification reactions at its recognition site. In the presence of alcohols such as ethanol or glycerol, it attaches the alcohol covalently to the 5? terminus of the cleaved DNA. Under certain conditions, the terminal 3?-OH of one DNA strand can attack the target phosphodiester bond in the other strand to create a DNA hairpin. Transesterification reactions on DNA with phosphorothioate linkages at the target bond proceed with retention of stereoconfiguration at the phosphorus, indicating, uniquely for a restriction enzyme, a two-step mechanism. We propose that BfiI first makes a covalent enzymeDNA intermediate, and then it resolves it by a nucleophilic attack of water or an alcohol, to yield hydrolysis or transesterification products, respectively. PMID:17267608

  6. Cyclization Reaction Catalyzed by Glycogen Debranching Enzyme (EC 2.4.1.25/EC 3.2.1.33) and Its Potential for Cycloamylose Production

    PubMed Central

    Yanase, Michiyo; Takata, Hiroki; Takaha, Takeshi; Kuriki, Takashi; Smith, Steven M.; Okada, Shigetaka

    2002-01-01

    Glycogen debranching enzyme (GDE) has 4-?-glucanotransferase and amylo-1,6-glucosidase activities in the single polypeptide chain. We analyzed the detailed action profile of GDE from Saccharomyces cerevisiae on amylose and tested whether GDE catalyzes cyclization of amylose. GDE treatment resulted in a rapid reduction of absorbance of iodine-amylose complex and the accumulation of a product that was resistant to an exo-amylase (glucoamylase [GA]) but was degraded by an endo-type ?-amylase to glucose and maltose. These results indicated that GDE catalyzed cyclization of amylose to produce cyclic ?-1,4 glucan (cycloamylose). The formation of cycloamylose was confirmed by high-performance anion-exchange chromatography, and the size was shown to range from a degree of polymerization of 11 to a degree of polymerization around 50. The minimum size and the size distribution of cycloamylose were different from those of cycloamylose produced by other 4-?-glucanotransferases. GDE also efficiently produced cycloamylose even from the branched glucan substrate, starch, demonstrating its potential for industrial production of cycloamylose. PMID:12200270

  7. Enzyme-catalyzed degradation of carbon nanomaterials

    NASA Astrophysics Data System (ADS)

    Kotchey, Gregg P.

    Carbon nanotubes and graphene, the nanoscale sp 2 allotropes of carbon, have garnered widespread attention as a result of their remarkable electrical, mechanical, and optical properties and the promise of new technologies that harness these properties. Consequently, these carbon nanomaterials (CNMs) have been employed for diverse applications such as electronics, sensors, composite materials, energy conversion devices, and nanomedicine. The manufacture and eventual disposal of these products may result in the release of CNMs into the environment and subsequent exposure to humans, animals, and vegetation. Given the possible pro-inflammatory and toxic effects of CNMs, much attention has been focused on the distribution, toxicity, and persistence of CNMs both in living systems and the environment. This dissertation will guide the reader though recent studies aimed at elucidating fundamental insight into the persistence of CNMs such as carbon nanotubes (CNTs) and graphene derivatives (i.e., graphene oxide and reduced graphene oxide). In particular, in-testtube oxidation/degradation of CNMs catalyzed by peroxidase enzymes will be examined, and the current understanding of the mechanisms underlying these processes will be discussed. Finally, an outlook of the current field including in vitro and in vivo biodegradation experiments, which have benefits in terms of human health and environmental safety, and future directions that could have implications for nanomedical applications such as imaging and drug delivery will be presented. Armed with an understanding of how and why CNMs undergo enzyme-catalyzed oxidation/biodegradation, researchers can tailor the structure of CNMs to either promote or inhibit these processes. For example, in nanomedical applications such as drug delivery, the incorporation of carboxylate functional groups could facilitate biodegradation of the nanomaterial after delivery of the cargo. Also, the incorporation of CNMs with defect sites in consumer goods could provide a mechanism that promotes the degradation of these materials once these products reach landfills.

  8. Epoxide hydrolase-catalyzed enantioselective conversion of trans-stilbene oxide: Insights into the reaction mechanism from steady-state and pre-steady-state enzyme kinetics.

    PubMed

    Archelas, Alain; Zhao, Wei; Faure, Bruno; Iacazio, Gilles; Kotik, Michael

    2016-02-01

    A detailed kinetic study based on steady-state and pre-steady-state measurements is described for the highly enantioselective epoxide hydrolase Kau2. The enzyme, which is a member of the ?/?-hydrolase fold family, preferentially reacts with the (S,S)-enantiomer of trans-stilbene oxide (TSO) with an E value of ?200. The enzyme follows a classical two-step catalytic mechanism with formation of an alkyl-enzyme intermediate in the first step and hydrolysis of this intermediate in a rate-limiting second step. Tryptophan fluorescence quenching during TSO conversion appears to correlate with alkylation of the enzyme. The steady-state data are consistent with (S,S) and (R,R)-TSO being two competing substrates with marked differences in kcat and KM values. The high enantiopreference of the epoxide hydrolase is best explained by pronounced differences in the second-order alkylation rate constant (k2/KS) and the alkyl-enzyme hydrolysis rate k3 between the (S,S) and (R,R)-enantiomers of TSO. Our data suggest that during conversion of (S,S)-TSO the two active site tyrosines, Tyr(157) and Tyr(259), serve mainly as electrophilic catalysts in the alkylation half-reaction, polarizing the oxirane oxygen of the bound epoxide through hydrogen bond formation, however, without fully donating their hydrogens to the forming alkyl-enzyme intermediate. PMID:26714303

  9. Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines.

    PubMed

    McCarty, Reid M; Krebs, Carsten; Bandarian, Vahe

    2013-01-01

    7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH(4)) to CDG in the third step of the biosynthetic pathway to all 7-deazapurines. Here we present a detailed characterization of QueE from Bacillus subtilis to delineate the mechanism of conversion of CPH(4) to CDG. QueE is a member of the radical S-adenosyl-l-methionine (SAM) superfamily, all of which use a bound [4Fe-4S](+) cluster to catalyze the reductive cleavage of the SAM cofactor to generate methionine and a 5'-deoxyadenosyl radical (5'-dAdo()), which initiates enzymatic transformations requiring hydrogen atom abstraction. The ultraviolet-visible, electron paramagnetic resonance, and Mssbauer spectroscopic features of the homodimeric QueE point to the presence of a single [4Fe-4S] cluster per monomer. Steady-state kinetic experiments indicate a K(m) of 20 7 ?M for CPH(4) and a k(cat) of 5.4 1.2 min(-1) for the overall transformation. The kinetically determined K(app) for SAM is 45 1 ?M. QueE is also magnesium-dependent and exhibits a K(app) for the divalent metal ion of 0.21 0.03 mM. The SAM cofactor supports multiple turnovers, indicating that it is regenerated at the end of each catalytic cycle. The mechanism of rearrangement of QueE was probed with CPH(4) isotopologs containing deuterium at C-6 or the two prochiral positions at C-7. These studies implicate 5'-dAdo() as the initiator of the ring contraction reaction catalyzed by QueE by abstraction of the H atom from C-6 of CPH(4). PMID:23194065

  10. Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines

    PubMed Central

    McCarty, Reid M.; Krebs, Carsten; Bandarian, Vahe

    2013-01-01

    7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to CDG in the third step of the biosynthetic pathway to all 7-deazapurines. Here we present a detailed characterization of QueE from Bacillus subtilis to delineate the mechanism of conversion of CPH4 to CDG. QueE is a member of the radical S-adenosyl-L-methionine (SAM) superfamily, all of which use a bound [4Fe-4S]+ cluster to catalyze the reductive cleavage of SAM cofactor to generate methionine and a 5?-deoxyadenosyl radical (5?-dAdo), which initiates enzymatic transformations requiring H-atom abstraction. The UV-visible, EPR, and Mssbauer spectroscopic features of the homodimeric QueE point to the presence of a single [4Fe-4S] cluster per monomer. Steady-state kinetic experiments indicate a Km of 20 7 ?M for CPH4 and kcat of 5.4 1.2 min-1 for the overall transformation. The kinetically determined Kapp for SAM is 45 1 ?M. QueE is also magnesium-dependent and exhibits a Kapp for the divalent metal ion of 0.21 0.03 mM. The SAM cofactor supports multiple turnovers, indicating that it is regenerated at the end of each catalytic cycle. The mechanism of rearrangement of QueE was probed with CPH4 isotopologs containing deuterium at C-6 or the two prochiral positions at C-7. These studies implicate 5?-dAdo as initiating the ring contraction reaction catalyzed by QueE by abstraction of the H-atom from C-6 of CPH4. PMID:23194065

  11. Hydrogen sensing by enzyme-catalyzed electrochemical detection.

    PubMed

    Lutz, Brent J; Fan, Z Hugh; Burgdorf, Tanja; Friedrich, Bärbel

    2005-08-01

    Hydrogen (H2) is a possible future alternative to current fossil-based transportation fuels; however, its lower explosive limit in air requires a reliable sensor to detect leaks wherever H2 is produced, stored, or used. Most current H2 sensors employ palladium or its alloy as the sensing element, featuring high operating temperature and limited selectivity. In this study, we report using soluble hydrogenase (SH) of aerobic beta-proteobacterium Ralstonia eutropha strain H16 to accomplish ambient, electrochemical detection of H2. Gas samples were collected in a solution containing SH that catalyzed the oxidation of H2. The electrons released during the H2 oxidation reaction were accepted by benzyl viologen (BV2+). The product of the redox reaction, BV+, was then detected using chronoamperometry. Using this sensing scheme, we demonstrate detection of H2 ranging from 1 to 100%. In addition, enzyme kinetics and the effect of oxygen on signal response were studied. Our results indicate that it is feasible to develop a sensor to detect H2 in the atmosphere that is based on enzyme-catalyzed electrochemical detection. PMID:16053311

  12. Unusual Cytochrome P450 Enzymes and Reactions*

    PubMed Central

    Guengerich, F. Peter; Munro, Andrew W.

    2013-01-01

    Cytochrome P450 enzymes primarily catalyze mixed-function oxidation reactions, plus some reductions and rearrangements of oxygenated species, e.g. prostaglandins. Most of these reactions can be rationalized in a paradigm involving Compound I, a high-valent iron-oxygen complex (FeO3+), to explain seemingly unusual reactions, including ring couplings, ring expansion and contraction, and fusion of substrates. Most P450s interact with flavoenzymes or iron-sulfur proteins to receive electrons from NAD(P)H. In some cases, P450s are fused to protein partners. Other P450s catalyze non-redox isomerization reactions. A number of permutations on the P450 theme reveal the diversity of cytochrome P450 form and function. PMID:23632016

  13. Characterising Complex Enzyme Reaction Data

    PubMed Central

    Rahman, Syed Asad; Thornton, Janet M.

    2016-01-01

    The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution. PMID:26840640

  14. Characterising Complex Enzyme Reaction Data.

    PubMed

    Dnerta?, Handan Melike; Martnez Cuesta, Sergio; Rahman, Syed Asad; Thornton, Janet M

    2016-01-01

    The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution. PMID:26840640

  15. Gold(I)-catalyzed enantioselective cycloaddition reactions

    PubMed Central

    2013-01-01

    Summary In recent years there have been extraordinary developments of gold(I)-catalyzed enantioselective processes. This includes progress in the area of cycloaddition reactions, which are of particular interest due to their potential for the rapid construction of optically active cyclic products. In this article we will summarize some of the most remarkable examples, emphasizing reaction mechanisms and key intermediates involved in the processes. PMID:24204438

  16. Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of d-xylose isomerase with bound d-xylulose?

    PubMed Central

    Kovalevsky, Andrey Y.; Katz, Amy K.; Carrell, H. L.; Hanson, Leif; Mustyakimov, Marat; Fisher, S. Zoe; Coates, Leighton; Schoenborn, Benno P.; Bunick, Gerard J.; Glusker, Jenny. P.; Langan, Paul

    2008-01-01

    The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme D-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, D-xylulose, shows, unexpectedly, that O5 of D-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in close proximity to C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism. PMID:18578508

  17. Surface catalyzed mercury transformation reactions

    NASA Astrophysics Data System (ADS)

    Varanasi, Patanjali

    Mercury is a known pollutant that has detrimental effect on human health and environment. The anthropogenic emissions of mercury account for 10 to 30% of worldwide mercury emissions. There is a need to control/reduce anthropogenic mercury emissions. Many mercury control technologies are available but their effectiveness is dependent on the chemical form of mercury, because different chemical forms of mercury have different physical and chemical properties. Mercury leaves the boiler in its elemental form but goes through various transformations in the post-combustion zone. There is a need to understand how fly ash and flue gas composition affect speciation, partitioning, and reactions of mercury under the full range of post-combustion zone conditions. This knowledge can then be used to predict the chemical transformation of mercury (elemental, oxidized or particulate) in the post combustion zone and thus help with the control of mercury emissions from coal-burning power plants. To accomplish this goal present study was conducted using five coal fly ashes. These ashes were characterized and their catalytic activity was compared under selected reaction conditions in a fixed bed reactor. Based on the results from these fly ash experiments, three key components (carbon, iron oxide and calcium oxide) were chosen. These three components were then used to prepare model fly ashes. Silica/alumina was used as a base for these model fly ashes. One, two or three component model fly ashes were then prepared to investigate mercury transformation reactions. The third set of experiments was performed with five different oxidation catalysts to further understand the mercury oxidation process. Based on the results of these three studies the key components were predicted for different fly ash compositions under variety of flue gas conditions. A fixed bed reactor system was used to conduct this study. In all the experiments, the inlet concentration of Hg0(g) was maintained at 35 mug/m 3 using a diffusion tube as the source of Hg0(g). All experiments were conducted using 4% O2 in nitrogen mix as a reaction gas, and other reactants (HCl, H2O and SO2, NO 2, Br2) were added as required. The fixed bed reactor was operated over a temperature range of 200 to 400C. In each experiment, the reactor effluent was analyzed using the modified Ontario-Hydro method. After each experiment, fly ash particles were also analyzed for mercury. The results show that the ability of fly ash to adsorb and/or oxidize mercury is primarily dependent on its carbon, iron and calcium content. There can be either one or more than one key component at a particular temperature and flue gas condition. Surface area played a secondary role in effecting the mercury transformations when compared to the concentration of the key component in the fly ash. Amount carbon and surface area played a key important role in the adsorption of mercury. Increased concentration of gases in the flue gas other than oxygen and nitrogen caused decreased the amount of mercury adsorbed on carbon surface. Mercury adsorption by iron oxide primarily depended on the crystalline structure of iron oxide. alpha-iron oxide had no effect on mercury adsorption or oxidation under most of the flue gas conditions, but gamma-iron oxide adsorbed mercury under most of the flue gas conditions. Bromine is a very good oxidizing agent for mercury. But in the presence of calcium oxide containing fly ashes, all the oxidized mercury would be reduced to elemental form. Among the catalysts, it was observed that presence of free lattice chlorine in the catalyst was very important for the oxidation of mercury. But instead of using the catalyst alone, using it along with carbon may better serve the purpose by providing the adsorption surface for mercury and also some extra surface area for the reaction to occur (especially for fly ashes with low surface area).

  18. Physio-pathological roles of transglutaminase-catalyzed reactions.

    PubMed

    Ricotta, Mariangela; Iannuzzi, Maura; Vivo, Giulia De; Gentile, Vittorio

    2010-05-26

    Transglutaminases (TGs) are a large family of related and ubiquitous enzymes that catalyze post-translational modifications of proteins. The main activity of these enzymes is the cross-linking of a glutaminyl residue of a protein/peptide substrate to a lysyl residue of a protein/peptide co-substrate. In addition to lysyl residues, other second nucleophilic co-substrates may include monoamines or polyamines (to form mono- or bi-substituted /crosslinked adducts) or -OH groups (to form ester linkages). In the absence of co-substrates, the nucleophile may be water, resulting in the net deamidation of the glutaminyl residue. The TG enzymes are also capable of catalyzing other reactions important for cell viability. The distribution and the physiological roles of TG enzymes have been widely studied in numerous cell types and tissues and their roles in several diseases have begun to be identified. "Tissue" TG (TG2), a member of the TG family of enzymes, has definitely been shown to be involved in the molecular mechanisms responsible for a very widespread human pathology: i.e. celiac disease (CD). TG activity has also been hypothesized to be directly involved in the pathogenetic mechanisms responsible for several other human diseases, including neurodegenerative diseases, which are often associated with CD. Neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, supranuclear palsy, Huntington's disease and other recently identified polyglutamine diseases, are characterized, in part, by aberrant cerebral TG activity and by increased cross-linked proteins in affected brains. In this review, we discuss the physio-pathological role of TG-catalyzed reactions, with particular interest in the molecular mechanisms that could involve these enzymes in the physio-pathological processes responsible for human neurodegenerative diseases. PMID:21541002

  19. Direct analysis of enzyme-catalyzed DNA demethylation.

    PubMed

    Karkhanina, Anna A; Mecinovi?, Jasmin; Musheev, Michael U; Krylova, Svetlana M; Petrov, Alexander P; Hewitson, Kirsty S; Flashman, Emily; Schofield, Christopher J; Krylov, Sergey N

    2009-07-15

    N/O-methylation of DNA can be cytotoxic and mutagenic; therefore, enzymes that reverse DNA methylation are essential for organism survival. Several 2-oxoglutarate-dependent oxygenases and methyltransferases that remove a methyl group from a methylated DNA base have been identified. Studies of their kinetics and search for their inhibitors have been retarded by the lack of an approach to directly quantitate DNA substrates and products that differ by a single methyl group. Here, we introduce such an approach, which is based on capillary electrophoresis with laser-induced fluorescence detection. We achieved baseline separation of a fluorescently labeled 15-nucleotide-long single-base methylated DNA substrate from its demethylated product, followed by its quantitative detection. We then used this approach to study the kinetics of AlkB-catalyzed DNA demethylation and screen a number of potential inhibitors of this reaction. Ten new inhibitors, which can be used as templates in developing therapies targeting AlkB-like enzymes, were identified. Our approach will be applicable for in vitro kinetic studies of known DNA demethylating and methylating enzymes and in the discovery of new ones. PMID:19518090

  20. Ir-Catalyzed enantioselective group transfer reactions.

    PubMed

    Schafer, Andrew G; Blakey, Simon B

    2015-10-01

    Recently, several novel iridium complexes have been shown to catalyse group transfer reactions in a highly selective fashion. Rhodium complexes, and in particular dirhodium tetracarboxylate salts, have proven to be a remarkably useful class of catalysts for these reactions through several decades of development. Recent results suggest that iridium may offer opportunities to address challenges in this chemistry and provide complementary reactivity patterns. This tutorial review outlines the recent developments in Ir-catalyzed enantioselective group transfer chemistry with highlights on examples which display this unique reactivity. PMID:26051004

  1. In vivo and in vitro olefin cyclopropanation catalyzed by heme enzymes

    DOEpatents

    Coelho, Pedro S; Brustad, Eric M; Arnold, Frances H; Wang, Zhan; Lewis, Jared C

    2015-03-31

    The present invention provides methods for catalyzing the conversion of an olefin to any compound containing one or more cyclopropane functional groups using heme enzymes. In certain aspects, the present invention provides a method for producing a cyclopropanation product comprising providing an olefinic substrate, a diazo reagent, and a heme enzyme; and admixing the components in a reaction for a time sufficient to produce a cyclopropanation product. In other aspects, the present invention provides heme enzymes including variants and fragments thereof that are capable of carrying out in vivo and in vitro olefin cyclopropanation reactions. Expression vectors and host cells expressing the heme enzymes are also provided by the present invention.

  2. [Synthesis of carbohydrate related compounds by using aldolase catalyzed reaction].

    PubMed

    Kajimoto, T

    2000-01-01

    Enzymes proceed the reaction with high regio- and stereoselectivity under mild conditions, i.e. in an aqueous medium at room temperature. However, enzymatic reactions that catalyze carbon-carbon bond formation have not been utilized in organic synthesis until recently. We had an interest in an aldolase-catalyzed reaction which proceed carbon-carbon bond formation referred to aldol condensation, by which many bioactive compounds have been rationally synthesized. On the other hand, recent biological studies on cell recognition (cell adhesion) have disclosed the important roles of oligosaccharides on cell surfaces, especially which include glucuronic acid, 3-deoxy-D-manno-oct-2-ulosonic acid (KDO), and sialic acid in the structures e.g., sialyl Lewis X and endotoxins, in differentiation, induction, viral and bacterial infections, and immune response. As well as acidic oligosaccharides, basic ones have been utilized as practical medicines in the clinical level, like acarbose that acts as an amylase inhibitor. Based on these background, we embarked the synthesis of carbohydrate related compounds which can control the interaction between carbohydrates and carbohydrate recognition protein by the use of several aldolases. Azasugars, potent inhibitors toward glycosidases, were synthesized using fructose-1,6-diphosphate (FDP)-aldolase and other dihdroxyacetonephosphate (DHAP)-dependent aldolases in the key step. Sialyl Lewis X mimetic, peptidic mimetic of RNA having anti-Vero toxin activity, mycestericin D, and aza-idulonic acid were prepared by taking advantage of L-threonine aldolase catalyzed reaction, which afford beta-hydroxy-alpha-L-amino acids. A precursor of KDO, featured acidic sugar of endotoxins was provided by the reaction catalyzed with kynureninase, which generates beta-anion of L-alanine in its active site during the metabolic reaction from kynurenine to anthranilic acid. PMID:10655781

  3. Metal-Catalyzed Cross-Coupling Reactions for Indoles

    NASA Astrophysics Data System (ADS)

    Li, Jie Jack; Gribble, Gordon W.

    Metal-catalyzed cross-coupling reactions for indoles are reviewed. Palladium-catalyzed cross-coupling reactions are the most widely explored and applied of all metal-catalyzed cross-coupling reactions. Applications of Kumada coupling, Negishi coupling, Suzuki coupling, Stille coupling, Sonogashira reaction, the Heck reaction, carbonylation, and C-N bond formation reactions in indoles are summarized. In addition, other transition metal-catalyzed cross-coupling reactions using copper, rhodium, iron, and nickel in indole synthesis are also discussed.

  4. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes.

    PubMed

    Yao, Jianzhuang; Guo, Haobo; Chaiprasongsuk, Minta; Zhao, Nan; Chen, Feng; Yang, Xiaohan; Guo, Hong

    2015-09-01

    Although one of an enzyme's hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. It is known that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. Here we report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Our results demonstrate that this enzyme may use substrate-assisted catalysis involving the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination. PMID:26244568

  5. A model study of sequential enzyme reactions and electrostatic channeling

    NASA Astrophysics Data System (ADS)

    Eun, Changsun; Kekenes-Huskey, Peter M.; Metzger, Vincent T.; McCammon, J. Andrew

    2014-03-01

    We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems.

  6. Biginelli Reaction Catalyzed by Copper Nanoparticles

    PubMed Central

    Dewan, Manika; Kumar, Ajeet; Saxena, Amit; De, Arnab; Mozumdar, Subho

    2012-01-01

    We recently reported a novel synthesis of copper nanoparticles from copper sulphate utilizing the charge-compensatory effect of ionic liquid [bmim]BF4 and ethylene glycol. The nanoparticles were characterized and found to be stable for one year. Here we hypothesize that the stabilized nanoparticles should be able to catalyze one-pot multicomponent organic reactions. We show that the nanoparticles catalyzed Biginelli reaction at room temperature to give the product 3,4-dihydopyrimidinone (>90% yield in ?15 minutes) from aldehydes, ?-diketoester (ethylacetoacetate) and urea (or thiourea). ). Remarkably, such high yields and rapid kinetics was found to be independent of the electronic density on the reactant aryl-aldehyde. This was probably because even the surface-active particles reacted faster in the presence of ionic liquid as compared to conventional methods. The heterocyclic dihydropyrimidinones (DHPMs) and their derivatives are widely used in natural and synthetic organic chemistry due to their wide spectrum of biological and therapeutic properties (resulting from their antibacterial, antiviral, antitumor and anti-inflammatory activities. Our method has an easy work-up procedure and the nanoparticles could be recycled with minimal loss of efficiency. PMID:22912792

  7. Iridium-Catalyzed Hydrogen Transfer Reactions

    NASA Astrophysics Data System (ADS)

    Saidi, Ourida; Williams, Jonathan M. J.

    This chapter describes the application of iridium complexes to catalytic hydrogen transfer reactions. Transfer hydrogenation reactions provide an alternative to direct hydrogenation for the reduction of a range of substrates. A hydrogen donor, typically an alcohol or formic acid, can be used as the source of hydrogen for the reduction of carbonyl compounds, imines, and alkenes. Heteroaromatic compounds and even carbon dioxide have also been reduced by transfer hydrogenation reactions. In the reverse process, the oxidation of alcohols to carbonyl compounds can be achieved by iridium-catalyzed hydrogen transfer reactions, where a ketone or alkene is used as a suitable hydrogen acceptor. The reversible nature of many hydrogen transfer processes has been exploited for the racemization of alcohols, where temporary removal of hydrogen generates an achiral ketone intermediate. In addition, there is a growing body of work where temporary removal of hydrogen provides an opportunity for using alcohols as alkylating agents. In this chemistry, an iridium catalyst "borrows" hydrogen from an alcohol to give an aldehyde or ketone intermediate, which can be transformed into either an imine or alkene under the reaction conditions. Return of the hydrogen from the catalyst provides methodology for the formation of amines or C-C bonds where the only by-product is typically water.

  8. Iodide effects in transition metal catalyzed reactions.

    PubMed

    Maitlis, Peter M; Haynes, Anthony; James, Brian R; Catellani, Marta; Chiusoli, Gian Paolo

    2004-11-01

    The unique properties of I(-) allow it to be involved in several different ways in reactions catalyzed by the late transition metals: in the oxidative addition, the migration, and the coupling/reductive elimination steps, as well as in substrate activation. Most steps are accelerated by I(-)(for example through an increased nucleophilicity of the metal center), but some are retarded, because a coordination site is blocked. The "soft" iodide ligand binds more strongly to soft metals (low oxidation state, electron rich, and polarizable) such as the later and heavier transition metals, than do the other halides, or N- and O-centered ligands. Hence in a catalytic cycle that includes the metal in a formally low oxidation state there will be less tendency for the metal to precipitate (and be removed from the cycle) in the presence of I(-) than most other ligands. Iodide is a good nucleophile and is also easily and reversibly oxidized to I(2). In addition, I(-) can play key roles in purely organic reactions that occur as part of a catalytic cycle. Thus to understand the function of iodide requires careful analysis, since two or sometimes more effects occur in different steps of one single cycle. Each of these topics is illustrated with examples of the influence of iodide from homogeneous catalytic reactions in the literature: methanol carbonylation to acetic acid and related reactions; CO hydrogenation; imine hydrogenation; and C-C and C-N coupling reactions. General features are summarised in the Conclusions. PMID:15510253

  9. Rate equations of solid-catalyzed reactions

    SciTech Connect

    Mezaki, R.; Inoue, H.

    1991-01-01

    Rate Equations of Solid-Catalyzed Reactions, edited by Mezaki and Inoue, contains a comprehensive compilation of kinetic rate expressions for a large number of relevant catalytic reaction systems. Mezaki and Inoue should be commended for their effort. For the practicing catalytic engineer the book should serve as a quick reference guide for assessing the functional dependence of rate on various operating conditions for a catalytic reaction system of interest. Even in this age of computer-aid literature searches this book should reduce the typically large activation barrier and search time associated with locating kinetic rate expressions for a particular reaction system. It is a recommended reference book for all whom are involved in the business of catalytic reactions. However, its format is not amenable for teaching. The book is structured according to the reaction system type. Chapter (1) focuses on synthesis (e.g., of sulfur trioxide, ammonia, methanol), (2) on hydrogenations (e.g., of carbon monoxide, carbon dioxide, ethylene, cyclohexene), (3) on hydrogenolysis (of low molecular weight alkanes such as ethane and/or pentane), (4) on hydrocracking (of higher molecular weight components such as n-hexane and n-dodecane), (5) on dehydrogenation (e.g., of ethanol, ethane, cyclohexane), (6) on complete oxidation (e.g., of hydrogen, carbon monoxide, alkanes, and olefins), (7) on partial oxidation (e.g., of methanol, ethylene, xylenes, and ammonia), (8) on isomerization (e.g., of methane, ethane, and cyclohexane), (10) on decomposition of ammonia and nitric oxide, (11) on dehydration of various alcohols, (12) on cumene cracking, and (13) on other key reactions such as water-gas shift and nitric oxide reduction.

  10. Detoxification of sulfur mustard by enzyme-catalyzed oxidation using chloroperoxidase.

    PubMed

    Popiel, S; Nawa?a, J

    2013-10-10

    One of the most interesting methods for the detoxification of sulfur mustard is enzyme-catalyzed oxidation. This study examined the oxidative destruction of a sulfur mustard by the enzyme chloroperoxidase (EC 1.11.1.10). Chloroperoxidase (CPO) belongs to a group of enzymes that catalyze the oxidation of various organic compounds by peroxide in the presence of a halide ion. The enzymatic oxidation reaction is affected by several factors: pH, presence or absence of chloride ion, temperature, the concentrations of hydrogen peroxide and enzyme and aqueous solubility of the substrate. The optimum reaction conditions were determined by analyzing the effects of all factors, and the following conditions were selected: solvent, Britton-Robinson buffer (pH=3) with tert-butanol (70:30 v/v); CPO concentration, 16U/mL; hydrogen peroxide concentration, 40mmol/L; sodium chloride concentration, 20mmol/L. Under these reaction conditions, the rate constant for the reaction is 0.006s(-1). The Michaelis constant, a measure of the affinity of an enzyme for a particular substrate, is 1.8710(-3)M for this system. The Michaelis constant for enzymes with a high affinity for their substrate is in the range of 10(-5) to 10(-4)M, so this value indicates that CPO does not have a very high affinity for sulfur mustard. PMID:24034427

  11. Enzyme-catalyzed synthesis of heptyl-?-glycosides: effect of water coalescence at high temperature.

    PubMed

    Montiel, Carmina; Bustos-Jaimes, Ismael; Brzana, Eduardo

    2013-09-01

    Alkyl glycosides can be synthesized by glycosidases in organic media with limited amounts of water. These systems, however, limit the solubility of the sugar substrates and decrease reaction yields. Herein we report the enzymatic synthesis of heptyl-?-glycosides in heptanol catalyzed by a hyperthermophilic ?-glycosidase at 90C. Our results indicate that dispersion of water in heptanol changes with time producing coalescence of water at the bottom of the reactor, playing a key role in the reaction yield. Water-soluble substrate, enzyme and products are concentrated in the aqueous phase, according to their partition coefficients, promoting side reactions that inactivate the enzyme. Reaction yield of heptyl-?-glycosides was 35% relative to lactose, at 7% water. The increase in the water phase to 12% diminished the enzyme inactivation and increased the heptyl-?-glycosides yield to 52%. Surface-active compounds, SDS and octyl glucoside, increased water dispersion but were unable to prevent coalescence. PMID:23863873

  12. Activity of formylphosphate in the reaction catalyzed by formyltetrahydrofolate synthetase

    SciTech Connect

    Jahansouz, H.; Kofron, J.L.; Smithers, G.W.; Himes, R.H.; Reed, G.H.

    1986-05-01

    Formylphosphate (FP), a putative enzyme-bound intermediate in the reaction catalyzed by N/sup 10/-formylH/sub 4/folate synthetase, was synthesized from formylfluoride and Pi. Measurement of hydrolysis rates by /sup 31/P NMR showed that FP is very unstable with a half-life of 48 min at 20/sup 0/C and pH 7. At pH 7 hydrolysis occurs with O-P bond cleavage as shown by /sup 18/O incorporation from /sup 18/O-H/sub 2/O into Pi. The substrate activity of FP was tested in the reaction catalyzed by N/sup 10/-formylH/sub 4/folate synthetase isolated from Clostridium cylindrosporum. MgATP + H/sub 4/folate + HCOO/sup -/ in equilibrium MgADP + Pi +N/sup 10/-formylH/sub 4/folate FP supports the reaction in both the forward and reverse directions. Thus, N/sup 10/-formylH/sub 4/folate is produced from H/sub 4/-folate and FP but only if ADP is present, and ATP is produced from FP and ADP but only if H/sub 4/folate is present. The requirements for H/sub 4/folate in the synthesis of ATP from ADP and FP and for ADP in the synthesis of N/sup 10/-formylH/sub 4/folate from FP and H/sub 4/folate, are consistent with past kinetic and isotope exchange studies which showed that the reaction proceeds by a sequential mechanism and that all three substrates must be present for any reaction to occur.

  13. First-principles calculations of Fischer-Tropsch processes catalyzed by nitrogenase enzymes

    NASA Astrophysics Data System (ADS)

    Varley, Joel; Grabow, Lars; Nørskov, Jens

    2012-02-01

    The nitrogenase enzyme system of the bacteria Azotobacter vinelandii, which is used in nature to catalyze ammonia synthesis, has been found recently to catalyze the efficient conversion of carbon monoxide (CO) into hydrocarbons under ambient temperature and pressure [1]. These findings indicate that nitrogenase enzymes could inspire more efficient catalysts for electrochemical CO and CO2 reduction to liquid fuels. The nitrogenase variants, in which vanadium substitutes the molybdenum in the active site of the enzyme, show distinct features in their reaction pathways to hydrocarbon production. To compare and contrast the catalytic properties of these nitrogenase enzymes, we perform first-principles calculations to map out the reaction pathways for both nitrogen fixation and for the reduction of CO to higher-order hydrocarbons. We discuss the trends and differences between the two enzymes and detail the relevant chemical species and rate-limiting steps involved in the reactions. By utilizing this information, we predict the electrochemical conditions necessary for the catalytic reduction of CO into fuels by the nitrogenase active sites, analogous to a Fischer-Tropsch process requiring less extreme conditions. [4pt] [1] Y. Hu, C.C. Lee, M.W. Ribbe, Science 333, 753 (2011)

  14. Probing the Mechanism of 1,4-Conjugate Elimination Reactions Catalyzed by Terpene Synthases

    PubMed Central

    Faraldos, Juan A.; Gonzalez, Veronica; Li, Amang; Yu, Fanglei; Köksal, Mustafa; Christianson, David W.; Allemann, Rudolf K.

    2012-01-01

    The reaction mechanisms of (E)-β-farnesene synthase (EBFS) and isoprene synthase (ISPS), enzymes that catalyze a formal regioespecific 1,4-conjugate elimination of hydrogen-diphosphate from (E, E)-farnesyl and dimethylallyl diphosphate (FDP and DMADP) to generate the semiochemicals (E)-β-farnesene and isoprene, respectively, were probed with substrate analogs and kinetic measurements. The results support stepwise reaction mechanisms through analogous enzyme-bound allylic cationic intermediates. For EBFS, we demonstrate that the elimination reaction can proceed via the enzyme-bound intermediate trans-nerolidyl diphosphate, while for ISPS the intermediacy of 2-methylbut-3-enyl 2-diphosphate can be inferred from the product outcome when deuterated DMADPs are used as substrates. Possible implications derived from the mechanistic details of the EBFS catalyzed reaction for the evolution of sesquiterpene synthases are discussed. PMID:23214943

  15. Recent developments in enzyme promiscuity for carbon-carbon bond-forming reactions.

    PubMed

    Miao, Yufeng; Rahimi, Mehran; Geertsema, Edzard M; Poelarends, Gerrit J

    2015-04-01

    Numerous enzymes have been found to catalyze additional and completely different types of reactions relative to the natural activity they evolved for. This phenomenon, called catalytic promiscuity, has proven to be a fruitful guide for the development of novel biocatalysts for organic synthesis purposes. As such, enzymes have been identified with promiscuous catalytic activity for, one or more, eminent types of carbon-carbon bond-forming reactions like aldol couplings, Michael(-type) additions, Mannich reactions, Henry reactions, and Knoevenagel condensations. This review focuses on enzymes that promiscuously catalyze these reaction types and exhibit high enantioselectivities (in case chiral products are obtained). PMID:25598537

  16. The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path

    NASA Astrophysics Data System (ADS)

    Masterson, Jean E.; Schwartz, Steven D.

    2014-10-01

    Enzymes are the most efficient chemical catalysts known, but the exact nature of chemical barrier crossing in enzymes is not fully understood. Application of transition state theory to enzymatic reactions indicates that the rates of all possible reaction paths, weighted by their relative probabilities, must be considered in order to achieve an accurate calculation of the overall rate. Previous studies in our group have shown a single mechanism for enzymatic barrier passage in human heart lactate dehydrogenase (LDH). To ensure that this result was not due to our methodology insufficiently sampling reactive phase space, we implement high-perturbation transition path sampling in both microcanonical and canonical regimes for the reaction catalyzed by human heart LDH. We find that, although multiple, distinct paths through reactive phase space are possible for this enzymatic reaction, one specific reaction path is dominant. Since the frequency of these paths in a canonical ensemble is inversely proportional to the free energy barriers separating them from other regions of phase space, we conclude that the rarer reaction paths are likely to have a negligible contribution. Furthermore, the non-dominate reaction paths correspond to altered reactive conformations and only occur after multiple steps of high perturbation, suggesting that these paths may be the result of non-biologically significant changes to the structure of the enzymatic active site.

  17. Regio and Stereodivergent Antibiotic Oxidative Carbocyclizations Catalyzed by Rieske Oxygenase-Like Enzymes

    PubMed Central

    Sydor, Paulina K.; Barry, Sarah M.; Odulate, Olanipekun M.; Barona-Gomez, Francisco; Haynes, Stuart W.; Corre, Christophe; Song, Lijiang; Challis, Gregory L.

    2011-01-01

    Oxidative cyclizations, exemplified by the biosynthetic assembly of the penicillin nucleus from a tripeptide precursor, are arguably the most synthetically-powerful implementation of C-H activation reactions in Nature. Here we show that Rieske oxygenase-like enzymes mediate regio and stereodivergent oxidative cyclizations to form 10- and 12-membered carbocyclic rings in the key steps of the biosynthesis of the antibiotics streptorubin B and metacycloprodigiosin, respectively. These reactions represent the first examples of oxidative carbocyclizations catalyzed by non-heme iron-dependent oxidases and define a novel type of catalytic activity for Rieske enzymes. A better understanding of how these enzymes achieve such remarkable regio and stereocontrol in the functionalization of unactivated hydrocarbon chains will greatly facilitate the development of selective manmade C-H activation catalysts. PMID:21505498

  18. Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine

    PubMed Central

    Qiao, Yan; Han, Keli; Zhan, Chang-Guo

    2014-01-01

    As the most active metabolite of heroin, 6-monoacetylmorphine (6-MAM) can penetrate into the brain for the rapid onset of heroin effects. The primary enzymes responsible for the metabolism of 6-MAM to the less potent morphine in humans are acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The detailed reaction pathways for AChE- and BChE-catalyzed hydrolysis of 6-MAM to morphine have been explored, for the first time, in the present study by performing first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the two enzymatic reaction processes follow the similar catalytic reaction mechanism, and the whole catalytic reaction pathway for each enzyme consists of four reaction steps. According to the calculated results, the second reaction step associated with the transition state TS2a/TS2b should be rate-determining for the AChE/BChE-catalyzed hydrolysis, and the free energy barrier calculated for the AChE-catalyzed hydrolysis (18.3 kcal/mol) is 2.5 kcal/mol lower than that for the BChE-catalyzed hydrolysis (20.8 kcal/mol). The free energy barriers calculated for the AChE- and BChE-catalyzed reactions are in good agreement with the experimentally derived activation free energies (17.5 and 20.7 kcal/mol for the AChE- and BChE-catalyzed reactions, respectively). Further structural analysis reveals that the aromatic residues Phe295 and Phe297 in the acyl pocket of AChE (corresponding to Leu286 and Val288 in BChE) contribute to the lower energy of TS2a relative to TS2b. The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse. PMID:24595354

  19. Enzyme-catalyzed synthesis and kinetics of ultrasonic-assisted biodiesel production from waste tallow.

    PubMed

    Adewale, Peter; Dumont, Marie-Jose; Ngadi, Michael

    2015-11-01

    The use of ultrasonic processing was evaluated for its ability to achieve adequate mixing while providing sufficient activation energy for the enzymatic transesterification of waste tallow. The effects of ultrasonic parameters (amplitude, cycle and pulse) and major reaction factors (molar ratio and enzyme concentration) on the reaction kinetics of biodiesel generation from waste tallow bio-catalyzed by immobilized lipase [Candida antarctica lipase B (CALB)] were investigated. Three sets of experiments namely A, B, and C were conducted. In experiment set A, two factors (ultrasonic amplitude and cycle) were investigated at three levels; in experiment set B, two factors (molar ratio and enzyme concentration) were examined at three levels; and in experiment set C, two factors (ultrasonic amplitude and reaction time) were investigated at five levels. A Ping Pong Bi Bi kinetic model approach was employed to study the effect of ultrasonic amplitude on the enzymatic transesterification. Kinetic constants of transesterification reaction were determined at different ultrasonic amplitudes (30%, 35%, 40%, 45%, and 50%) and enzyme concentrations (4, 6, and 8 wt.% of fat) at constant molar ratio (fat:methanol); 1:6, and ultrasonic cycle; 5 Hz. Optimal conditions for ultrasound-assisted biodiesel production from waste tallow were fat:methanol molar ratio, 1:4; catalyst level 6% (w/w of fat); reaction time, 20 min (30 times less than conventional batch processes); ultrasonic amplitude 40% at 5 Hz. The kinetic model results revealed interesting features of ultrasound assisted enzyme-catalyzed transesterification (as compared to conventional system): at ultrasonic amplitude 40%, the reaction activities within the system seemed to be steady after 20 min which means the reaction could proceed with or without ultrasonic mixing. Reversed phase high performance liquid chromatography indicated the biodiesel yield to be 85.60.08%. PMID:26186814

  20. The Biginelli Reaction Is a Urea-Catalyzed Organocatalytic Multicomponent Reaction.

    PubMed

    Puripat, Maneeporn; Ramozzi, Romain; Hatanaka, Miho; Parasuk, Waraporn; Parasuk, Vudhichai; Morokuma, Keiji

    2015-07-17

    The recently developed artificial force induced reaction (AFIR) method was applied to search systematically all possible multicomponent pathways for the Biginelli reaction mechanism. The most favorable pathway starts with the condensation of the urea and benzaldehyde, followed by the addition of ethyl acetoacetate. Remarkably, a second urea molecule catalyzes nearly every step of the reaction. Thus, the Biginelli reaction is a urea-catalyzed multicomponent reaction. The reaction mechanism was found to be identical in both protic and aprotic solvents. PMID:26066623

  1. Hydrolase-catalyzed fast Henry reaction of nitroalkanes and aldehydes in organic media.

    PubMed

    Wang, Jun-Liang; Li, Xia; Xie, Hong-Yan; Liu, Bo-Kai; Lin, Xian-Fu

    2010-02-01

    Nitroalkanes underwent fast additions to a variety of structurally diverse aldehydes under the catalysis of d-aminoacylase in DMSO. The influences of reaction conditions including solvents, temperature, enzyme concentration and molar ratio of substrates were systematically investigated. Seventeen products were obtained in short time with moderate to high yields. It is the first report on hydrolase-catalyzed fast Henry reaction in organic solvent. PMID:19963019

  2. Ultrasound assisted enzyme catalyzed synthesis of glycerol carbonate from glycerol and dimethyl carbonate.

    PubMed

    Waghmare, Govind V; Vetal, Mangesh D; Rathod, Virendra K

    2015-01-01

    The present work illustrates the transesterification of glycerol to glycerol carbonate (GlyC) from dimethyl carbonate (DMC) using commercial immobilized lipase (Novozym 435) under ultrasonic irradiation. The experiments were performed in a batch reactor placed in an ultrasonic water bath using a sequence of experimental protocol to evaluate the effects of temperature, molar ratios of substrates, enzyme loading, duty cycle and ultrasound power on the conversion of glycerol to GlyC. It has been found that ultrasound-assisted lipase-catalyzed transesterification of glycerol would be a potential alternative to conventional alkali-catalyzed method, as high conversion (99.75%) was obtained at mild operating conditions: molar ratio of DMC to glycerol 3:1, catalyst amount of 13% (w/w), lower power input (100W), duty cycle 50% and temperature (60C) in a relatively short reaction time (4h) using Novozym 435 as catalyst. Ultrasound reduces the reaction time up to 4h as compared to conventional stirring method (14h) catalyzed by Novozym 435. The repeated use of the catalyst under the optimum experimental condition resulted in decay in both enzyme activity and product conversion. PMID:25069889

  3. Steroid hydroxylations: A paradigm for cytochrome P450 catalyzed mammalian monooxygenation reactions

    SciTech Connect

    Estabrook, Ronald W. . E-mail: Ronald.estabrook@utsouthwestern.edu

    2005-12-09

    The present article reviews the history of research on the hydroxylation of steroid hormones as catalyzed by enzymes present in mammalian tissues. The report describes how studies of steroid hormone synthesis have played a central role in the discovery of the monooxygenase functions of the cytochrome P450s. Studies of steroid hydroxylation reactions can be credited with showing that: (a) the adrenal mitochondrial enzyme catalyzing the 11{beta}-hydroxylation of deoxycorticosterone was the first mammalian enzyme shown by O{sup 18} studies to be an oxygenase; (b) the adrenal microsomal enzyme catalyzing the 21-hydroxylation of steroids was the first mammalian enzyme to show experimentally the proposed 1:1:1 stoichiometry (substrate:oxygen:reduced pyridine nucleotide) of a monooxygenase reaction; (c) application of the photochemical action spectrum technique for reversal of carbon monoxide inhibition of the 21-hydroxylation of 17{alpha}-OH progesterone was the first demonstration that cytochrome P450 was an oxygenase; (d) spectrophotometric studies of the binding of 17{alpha}-OH progesterone to bovine adrenal microsomal P450 revealed the first step in the cyclic reaction scheme of P450, as it catalyzes the 'activation' of oxygen in a monooxygenase reaction; (e) purified adrenodoxin was shown to function as an electron transport component of the adrenal mitochondrial monooxygenase system required for the activity of the 11{beta}-hydroxylase reaction. Adrenodoxin was the first iron-sulfur protein isolated and purified from mammalian tissues and the first soluble protein identified as a reductase of a P450; (f) fractionation of adrenal mitochondrial P450 and incubation with adrenodoxin and a cytosolic (flavoprotein) fraction were the first demonstration of the reconstitution of a mammalian P450 monooxygenase reaction.

  4. Atom transfer and rearrangement reactions catalyzed by methyltrioxorhenium, MTO

    SciTech Connect

    Jacob, J.

    1999-05-10

    Methyltrioxorhenium (MTO) catalyzes the desulfurization of thiiranes by triphenylphosphine. Enormous enhancement in rate is observed when the catalyst is pretreated with hydrogen sulfide prior to the reaction. Using 2-mercaptomethylthiophenol as a ligand, the author synthesized several model complexes to study the mechanism of this reaction. With suitable model systems, they were able to show that the active catalyst is a Re(V) species. The reactions are highly stereospecific and very tolerant to functional groups. As part of the studies, he synthesized and crystallographically characterized the first examples of neutral terminal and bridging Re(V)sulfidocomplexes. Some of these complexes undergo fast oxygen atom transfer reactions with organic and inorganic oxidants. Studies on these model complexes led them to the discovery that MTO catalyzes the selective oxidation of thiols to disulfides. This report contains the Introduction; ``Chapter 6: Isomerization of Propargylic Alcohols to Enones and Enals Catalyzed by Methylrhenium Trioxide``; and Conclusions.

  5. Recent advances in copper-catalyzed asymmetric coupling reactions

    PubMed Central

    2015-01-01

    Summary Copper-catalyzed (or -mediated) asymmetric coupling reactions have received significant attention over the past few years. Especially the coupling reactions of aryl or alkyl halides with nucleophiles became a very powerful tool for the formation of C–C, C–N, C–O and other carbon–heteroatom bonds as well as for the construction of heteroatom-containing ring systems. This review summarizes the recent progress in copper-catalyzed asymmetric coupling reactions for the formation of C–C and carbon–heteroatom bonds. PMID:26734106

  6. Enzyme catalyzed electricity-driven water softening system.

    PubMed

    Arugula, Mary A; Brastad, Kristen S; Minteer, Shelley D; He, Zhen

    2012-12-10

    Hardness in water, which is caused by divalent cations such as calcium and magnesium ions, presents a major water quality problem. Because hard water must be softened before use in residential applications, there is great interest in the saltless water softening process because, unlike ion exchange softeners, it does not introduce additional ions into water. In this study, a saltless hardness removal driven by bioelectrochemical energy produced through enzymatic oxidation of glucose was proposed and investigated. Glucose dehydrogenase was coated on a carbon electrode to catalyze glucose oxidation in the presence of NAD? as a cofactor/mediator and methylene green as an electrocatalyst. The results showed that electricity generation stimulated hardness removal compared with non-electricity conditions. The enzymatic water softener worked upon a 6h batch operation per day for eight days, and achieved an average hardness removal of 46% at a high initial concentration of 800 mg/L as CaCO?. More hardness was removed at a lower initial concentration. For instance, at 200mg/L as CaCO? the enzymatic water softener removed 76.44.6% of total hardness. The presence of magnesium ions decreased hardness removal because of its larger hydrated radius than calcium ions. The enzymatic water softener removed 70-80% of total hardness from three actual hard water samples. These results demonstrated a proof-of-concept that enzyme catalyzed electricity generation can be used to soften hard water. PMID:23040397

  7. Ligand Intermediates in Metal-Catalyzed Reactions

    SciTech Connect

    Gladysz, John A.

    1999-07-31

    The longest-running goal of this project has been the synthesis, isolation, and physical chemical characterization of homogeneous transition metal complexes containing ligand types believed to be intermediates in the metal-catalyzed conversion of CO/H{sub 2}, CO{sub 2}, CH{sub 4}, and similar raw materials to organic fuels, feedstocks, etc. In the current project period, complexes that contain unusual new types of C{sub x}(carbide) and C{sub x}O{sub y} (carbon oxide) ligands have been emphasized. A new program in homogeneous fluorous phase catalysis has been launched as described in the final report.

  8. Stereochemistry and mechanism of a new single-turnover, half-transamination reaction catalyzed by the tryptophan synthase alpha 2 beta 2 complex

    SciTech Connect

    Miles, E.W.

    1987-01-27

    Tryptophan synthase is a versatile enzyme that catalyzes a wide variety of pyridoxal phosphate dependent reactions that are also catalyzed in model systems. These include beta-replacement, beta-elimination, racemization, and transamination reactions. We now show that the apo-alpha 2 beta 2 complex of tryptophan synthase will bind two unnatural substrates, pyridoxamine phosphate and indole-3-pyruvic acid, and will convert them by a single-turnover, half-transamination reaction to pyridoxal phosphate and L-tryptophan, the natural coenzyme and a natural product, respectively. This enzyme-catalyzed reaction is more rapid and more stereospecific than an analogous model reaction. The pro-S 4'-methylene proton of pyridoxamine phosphate is removed during the reaction, and the product is primarily L-tryptophan. We conclude that pyridoxal phosphate enzymes may be able to catalyze some unnatural reactions involving bound reactants and bound coenzyme since the coenzyme itself has the intrinsic ability to promote a variety of reactions.

  9. In Vitro Analysis of RNA Degradation Catalyzed by Deadenylase Enzymes

    PubMed Central

    Hrit, Joel; Raynard, Nathan; Van Etten, Jamie; Sankar, Kamya; Petterson, Adam; Goldstrohm, Aaron C.

    2014-01-01

    Summary In this chapter, we describe a method for purification and analysis of the enzymatic activity of deadenylase enzymes. Nearly all eukaryotic messenger RNAs are modified at the 3 end by addition of an adenosine polymer: the poly-adenosine tail. The poly(A) tail plays a central role in protein expression and mRNA fate. The poly(A) tail promotes translation of the mRNA. Shortening of the poly(A) tail, referred to as deadenylation, reduces protein synthesis and initiates destruction of the mRNA. A specialized class of exoribonucleases, called deadenylase enzymes, carries out this process. Deadenylases are found throughout eukarya but their functions remain largely unexplored. We present a detailed protocol to analyze deadenylase activity in vitro. First, recombinant deadenylase enzyme is over-expressed and purified from bacteria. Next, labeled RNA substrate is prepared. Deadenylation reactions are performed and reaction products are analyzed by denaturing gel electrophoresis. Reaction rates are then determined quantitatively. Crucial controls and experimental parameters are described along with practical tips that promote success. PMID:24590800

  10. Hydroxyatrazine N-Ethylaminohydrolase (AtzB): an Amidohydrolase Superfamily Enzyme Catalyzing Deamination and Dechlorination?

    PubMed Central

    Seffernick, Jennifer L.; Aleem, Asma; Osborne, Jeffrey P.; Johnson, Gilbert; Sadowsky, Michael J.; Wackett, Lawrence P.

    2007-01-01

    Hydroxyatrazine [2-(N-ethylamino)-4-hydroxy-6-(N-isopropylamino)-1,3,5-triazine] N-ethylaminohydrolase (AtzB) is the sole enzyme known to catalyze the hydrolytic conversion of hydroxyatrazine to N-isopropylammelide. AtzB, therefore, serves as the point of intersection of multiple s-triazine biodegradative pathways and is completely essential for microbial growth on s-triazine herbicides. Here, atzB was cloned from Pseudomonas sp. strain ADP and its product was purified to homogeneity and characterized. AtzB was found to be dimeric, with subunit and holoenzyme molecular masses of 52 kDa and 105 kDa, respectively. The kcat and Km of AtzB with hydroxyatrazine as a substrate were 3 s?1 and 20 ?M, respectively. Purified AtzB had a 1:1 zinc-to-subunit stoichiometry. Sequence analysis revealed that AtzB contained the conserved mononuclear amidohydrolase superfamily active-site residues His74, His76, His245, Glu248, His280, and Asp331. An intensive in vitro investigation into the substrate specificity of AtzB revealed that 20 of the 51 compounds tested were substrates for AtzB; this allowed for the identification of specific substrate structural features required for catalysis. Substrates required a monohydroxylated s-triazine ring with a minimum of one primary or secondary amine substituent and either a chloride or amine leaving group. AtzB catalyzed both deamination and dechlorination reactions with rates within a range of one order of magnitude. This differs from AtzA and TrzN, which do not catalyze deamination reactions, and AtzC, which is not known to catalyze dechlorination reactions. PMID:17660279

  11. Mechanistic Imperatives for Deprotonation of Carbon Catalyzed by Triosephosphate Isomerase: Enzyme-Activation by Phosphite Dianion

    PubMed Central

    Zhai, Xiang; Malabanan, M. Merced; Amyes, Tina L.; Richard, John P.

    2013-01-01

    The mechanistic imperatives for catalysis of deprotonation of ?carbonyl carbon by triosephosphate isomerase (TIM) are discussed. There is a strong imperative to reduce the large thermodynamic barrier for deprotonation of carbon to form an enediolate reaction intermediate; and, a strong imperative for specificity in the expression of the intrinsic phosphodianion binding energy at the transition state for the enzyme-catalyzed reaction. Binding energies of 2 and 6 kcal/mol, respectively, have been determined for formation of phosphite dianion complexes to TIM and to the transition state for TIM-catalyzed deprotonation of the truncated substrate glycolaldehyde [T. L. Amyes, J. P. Richard, Biochemistry 2007, 46, 5841]. We propose that the phosphite dianion binding energy, which is specifically expressed at the transition state complex, is utilized to stabilize a rare catalytically active loop-closed form of TIM. The results of experiments to probe the role of the side chains of Ile172 and Leu232 in activating the loop-closed form of TIM for catalysis of substrate deprotonation are discussed. Evidence is presented that the hydrophobic side chain of Ile172 assists in activating TIM for catalysis of substrate deprotonation through an enhancement of the basicity of the carboxylate side-chain of Glu167. Our experiments link the two imperatives for TIM-catalyzed deprotonation of carbon by providing evidence that the phosphodianion binding energy is utilized to drive an enzyme conformational change, which results in a reduction in the thermodynamic barrier to deprotonation of the carbon acid substrate at TIM compared with the barrier for deprotonation in water. The effects of a P168A mutation on the kinetic parameters for the reactions of whole and truncated substrates are discussed. PMID:24729658

  12. Dinuclear zinc-catalyzed enantioselective Aza-Henry reaction.

    PubMed

    Trost, Barry M; Lupton, David W

    2007-05-10

    The dinuclear zinc catalyst 1a was found to catalyze the addition of nitroalkanes to carbamate-protected imines. This aza-Henry reaction proceeds with high enantioselectivity when various carbamate-protected imines are used. alpha,beta-Unsaturated imines proved to be a particularly useful class of substrate routinely giving the alpha-nitro amine products in high enantiomeric excess. PMID:17439228

  13. Development of a Lewis Base Catalyzed Selenocyclization Reaction

    ERIC Educational Resources Information Center

    Collins, William

    2009-01-01

    The concept of Lewis base activation of selenium Lewis acids has been effectively reduced to practice in the Lewis base catalyzed selenofunctionalization of unactivated olefins. In this reaction, the weakly acidic species, "N"-phenylselenyl succinimide, is cooperatively activated by the addition of a "soft" Lewis base donor (phosphine sulfides,

  14. Cross-ligation and exchange reactions catalyzed by hairpin ribozymes.

    PubMed Central

    Komatsu, Y; Koizumi, M; Sekiguchi, A; Ohtsuka, E

    1993-01-01

    The negative strand of the satellite RNA of tobacco ringspot virus (sTobRV(-)) contains a hairpin catalytic domain that shows self-cleavage and self-ligation activities in the presence of magnesium ions. We describe here that the minimal catalytic domain can catalyze a cross-ligation reaction between two kinds of substrates in trans. The cross-ligated product increased when the reaction temperature was decreased during the reaction from 37 degrees C to 4 degrees C. A two-stranded hairpin ribozyme, divided into two fragments between G45 and U46 in a hairpin loop, showed higher ligation activity than the nondivided ribozyme. The two stranded ribozyme also catalyzed an exchange reaction of the 3'-portion of the cleavage site. Images PMID:8441626

  15. The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture.

    PubMed

    Reyes, Archie C; Zhai, Xiang; Morgan, Kelsey T; Reinhardt, Christopher J; Amyes, Tina L; Richard, John P

    2015-01-28

    The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respective phosphodianion truncated substrates are reported for the following oxydianions: HPO3(2-), FPO3(2-), S2O3(2-), SO4(2-) and HOPO3(2-). Oxydianions bind weakly to these unliganded enzymes and tightly to the transition state complex (ES()), with intrinsic oxydianion Gibbs binding free energies that range from -8.4 kcal/mol for activation of hlGPDH-catalyzed reduction of glycolaldehyde by FPO3(2-) to -3.0 kcal/mol for activation of ScOMPDC-catalyzed decarboxylation of 1-?-d-erythrofuranosyl)orotic acid by HOPO3(2-). Small differences in the specificity of the different oxydianion binding domains are observed. We propose that the large -8.4 kcal/mol and small -3.8 kcal/mol intrinsic oxydianion binding energy for activation of hlGPDH by FPO3(2-) and S2O3(2-), respectively, compared with activation of ScTIM and ScOMPDC reflect stabilizing and destabilizing interactions between the oxydianion -F and -S with the cationic side chain of R269 for hlGPDH. These results are consistent with a cryptic function for the similarly structured oxydianion binding domains of ScTIM, ScOMPDC and hlGPDH. Each enzyme utilizes the interactions with tetrahedral inorganic oxydianions to drive a conformational change that locks the substrate in a caged Michaelis complex that provides optimal stabilization of the different enzymatic transition states. The observation of dianion activation by stabilization of active caged Michaelis complexes may be generalized to the many other enzymes that utilize substrate binding energy to drive changes in enzyme conformation, which induce tight substrate fits. PMID:25555107

  16. Silver and gold-catalyzed multicomponent reactions

    PubMed Central

    Abbiati, Giorgio

    2014-01-01

    Summary Silver and gold salts and complexes mainly act as soft and carbophilic Lewis acids even if their use as σ-activators has been rarely reported. Recently, transformations involving Au(I)/Au(III)-redox catalytic systems have been reported in the literature. In this review we highlight all these aspects of silver and gold-mediated processes and their application in multicomponent reactions. PMID:24605168

  17. Iron-catalyzed synthesis of arylsulfinates through radical coupling reaction.

    PubMed

    Zhang, Weixi; Luo, Meiming

    2016-02-01

    A novel strategy for installation of a sulfonyl fragment into arenes has been accomplished via an iron-catalyzed radical coupling reaction. Arene radicals derived from diaryliodoniums via single electron transfer reaction combine with sulfoxylate anion radicals readily generated from commercially available rongalite (HOCH2SO2Na2H2O) to afford arylsulfinates efficiently at room temperature. In this protocol, a broad range of functional groups are tolerated to give products in good yields. PMID:26781163

  18. Can Chlorine Anion Catalyze the Reaction fo HOCl with HCl?

    NASA Technical Reports Server (NTRS)

    Richardson, S. L.; Francisco, J. S.; Mebel, A. M.; Morokuma, K.

    1997-01-01

    The reaction of HOCl + HCl -> Cl2 + H20 in the presence of Cl has been studied using ab initio methods. This reaction has been shown to have a high activation barrier of 46.5 kcal/mol. The chlorine anion, Cl- is found to catalyze the reaction, viz. two mechanisms. The first involves Cl- interacting through the concerted four-center transition state of the neutral reaction. The other mechanism involves the formation of a HCl-HOCl-Cl- intermediate which dissociates into Cl2 + Cl- + H20. The steps are found to have no barriers. The overall exothermicity is 15.5 kcal/mol.

  19. (Ligand intermediates in metal-catalyzed reactions)

    SciTech Connect

    Not Available

    1992-01-01

    This report consists of sections on sigma bond complexes of alkenes, a new carbon-hydrogen bond activation reaction of alkene complexes, carbon-hydrogen bond migrations in alkylidene complexes, carbon- hydrogen bond migrations in alkyne complexes, synthesis, structure and reactivity of C{sub x} complexes, synthesis and reactivity of alcohol and ether complexes, new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes, pi/sigma equilibria in metal/O=CXX' complexes, and other hydrocarbon ligands; miscellaneous.(WET)

  20. Adenosyl radical: reagent and catalyst in enzyme reactions

    PubMed Central

    Patterson, Dustin P.

    2010-01-01

    Lead in Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors; ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B12, AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosines role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations. In contrast, there has been a recent explosion in the number radical AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions. Although all the radical AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes may be active in aerobic organisms including humans. PMID:20191656

  1. Stau-catalyzed big-bang nucleosynthesis reactions

    SciTech Connect

    Kamimura, Masayasu; Kino, Yasushi; Hiyama, Emiko

    2010-06-01

    We study the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a hypothetical long-lived negatively charged, massive leptonic particle (called X{sup -}) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X{sup -} particle has a lifetime of tau{sub X} > or approx. 10{sup 3} s, it can capture a light element previously synthesized in standard BBN and form a Coulombic bound state and induces various types of reactions in which X{sup -} acts as a catalyst. Some of these X{sup -} catalyzed reactions have significantly large cross sections so that the inclusion of the reactions into the BBN network calculation can markedly change the abundances of some elements. We use a high-accuracy three-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

  2. Enzyme Reactions in Nanoporous, Picoliter Volume Containers

    SciTech Connect

    Siuti, Piro; Retterer, Scott T; Choi, Chang Kyoung; Doktycz, Mitchel John

    2012-01-01

    Advancements in nanoscale fabrication allow creation of small volume reaction containers that can facilitate the screening and characterization of enzymes. A porous, ~19 pL volume vessel has been used in this work to carry out enzyme reactions under varying substrate concentrations. Glucose oxidase and horseradish peroxidase can be contained in these structures and diffusively fed with a solution containing glucose and the fluorogenic substrate Amplex Red through the engineered nanoscale pore structure. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Kinetic characteristics of the enzyme were evaluated and compared with results from conventional scale reactions. These picoliter, nanoporous containers can facilitate quick determination of enzyme kinetics in microfluidic systems without the requirement of surface tethering and can be used for applications in drug discovery, clinical diagnostics and high-throughput screening.

  3. Effectiveness of immobilized lipase Thermomyces lanuginosa in catalyzing interesterification of palm olein in batch reaction.

    PubMed

    Saw, Mei Huey; Siew, Wai Lin

    2014-01-01

    Lipase Thermomyces lanuginosa has shown potential in modifying oils and fats through interesterification. Analyzing the physicochemical properties of the modified oils is important to determine the effectiveness of lipase in catalyzing interesterification. In this study, the effectiveness of the immobilized lipase (Lipozyme(®) TL IM) in catalyzing interesterification of palm olein in pilot-scale batch reactor was determined. The evaluation was done by analyzing the changes of triacylglycerol (TAGs) composition, sn-2 position fatty acids composition and the physical properties of the palm olein after the interesterifications. The pilot-scale batch reaction was conducted for 8 hours with 5 %w/w enzyme dosage based on the results of TAGs composition of the laboratory-scale interesterified products. The pilot-scale results showed that Lipozyme(®) TL IM act as an effective enzyme in converting TAGs, in which 4.5% of trisaturated TAGs (PPP and PPS) were produced in the batch reaction. The formation of these new TAGs had also altered the thermal and physical properties of the palm olein. These interesterified products showed a broad peak and shoulder at high temperature, ranging from 10°C to 40°C, indicating the formation of some new TAGs with high melting points. However, the enzyme did not perform perfectly as a 1,3-specific enzyme in the reaction as a significant reduction of oleic acid and an increment of palmitic acid at the sn-2 position was observed. PMID:24492381

  4. Enzyme Reactions and Acceptability of Plant Foods.

    ERIC Educational Resources Information Center

    Palmer, James K.

    1984-01-01

    Provides an overview of enzyme reactions which contribute to the character and acceptability of plant foods. A detailed discussion of polyphenoloxidase is also provided as an example of an enzyme which can markedly affect the character and acceptability of such foods. (JN)

  5. ENZYME-CATALYZED GEL-FORMATION OF GELATIN AND CHITOSAN. POTENTIAL FOR IN SITU APPLICATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We compared the ability of two enzymes to catalyze the formation of gels from solutions of gelatin and chitosan. A microbial transglutaminase, currently under investigation for food applications, was observed to catalyze the formation of strong and permanent gels from gelatin solutions. Chitosan w...

  6. Investigation of the regiospecificity and stereospecificity of proton transfer in the yeast inorganic pyrophosphatase catalyzed reaction

    SciTech Connect

    Lin, I.; Knight, W.B.; Hsueh, A.; Dunaway-Mariano, D.

    1986-08-12

    The regiospecificity and stereospecificity of proton transfer in the yeast inorganic pyrophosphatase (PPase) catalyzed hydrolysis of P1,P2-bidentate Mg(H/sub 2/O)4(PPi)/sub 2/- were probed with exchange-inert metal complexes of imidodiphosphate (PNP) and thiopyrophosphate (PPS). PPase was unable to catalyze the hydrolysis of Mg(H/sub 2/O)4PNP and P1,P2-bidentate Co(NH/sub 3/)4PNP under conditions that resulted in rapid hydrolysis of the corresponding metal-PPi complexes. PPase was found to catalyze the hydrolysis of Mg(H/sub 2/O)4PPS at 17% the rate of Mg(H/sub 2/O)4PPi hydrolysis. The Km of Mg(H/sub 2/O)4PPS was determined to be 300 microM, which is a value 10-fold greater than that observed for Mg(H/sub 2/O)4PPi. P1,P2-Bidentate Cr(H/sub 2/O)4PPS and Co(NH/sub 3/)4PPS (prepared from PPS) were both found to be substrates for PPase. The enzyme specifically catalyzed the hydrolysis of the Rp enantiomers of these complexes and not the Sp enantiomers. These results are accommodated by a reaction mechanism involving enzyme-mediated proton transfer to the pro-R oxygen atom of the incipient phosphoryl leaving group of the bound P1,P2-bidentate Mg(H/sub 2/O)4PPi2- complex.

  7. Enzyme Substrate Reactions in High Magnetic Fields

    PubMed Central

    Maling, J. E.; Weissbluth, M.; Jacobs, E. E.

    1965-01-01

    The reaction rates of two enzyme substrate systems, ribonuclease-RNA and succinate-cytochrome c reductase, were followed as a function of magnetic field from zero to 48,000 gauss. The reaction rates remained constant to within 10 per cent. PMID:5884011

  8. Hydrogen tunneling in enzyme reactions

    SciTech Connect

    Cha, Y.; Murray, C.J.; Klinman, J.P.

    1989-03-10

    Primary and secondary protium-to-tritium (H/T) and deuterium-to-tritium (D/T) kinetic isotope effects for the catalytic oxidation of benzyl alcohol to benzaldehyde by yeast alcohol dehydrogenase (YADH) at 25 degrees Celsius have been determined. Previous studies showed that this reaction is nearly or fully rate limited by the hydrogen-transfer step. Semiclassical mass considerations that do not include tunneling effects would predict that kH/kT = (kD/kT)3.26, where kH, kD, and kT are the rate constants for the reaction of protium, deuterium, and tritium derivatives, respectively. Significant deviations from this relation have now been observed for both primary and especially secondary effects, such that experimental H/T ratios are much greater than those calculated from the above expression. These deviations also hold in the temperature range from 0 to 40 degrees Celsius. Such deviations were previously predicted to result from a reaction coordinate containing a significant contribution from hydrogen tunneling.

  9. Stereoretentive Copper (II) Catalyzed Ritter Reactions of Secondary Cycloalkanols

    PubMed Central

    Al-huniti, Mohammed H.

    2013-01-01

    A Ritter-like coupling reaction of cyclic alcohols and both aryl and alkyl nitriles to form amides catalyzed by copper (II) triflate is described. These reactions proceed in good yields under mild and often solvent-free conditions. With 2- and 3-substituted cycloalkanols, amide products are formed with near complete retention of configuration. This is likely due to fast nucleophilic capture of a non-planar carbocations (hyperconjomers) stabilized by ring hyperconjugation. A critical aspect of this novel catalytic cycle is the in situ activation of the alcohol substrates by thionyl chloride to form chlorosulfites. PMID:24376393

  10. Substrate activity of synthetic formyl phosphate in the reaction catalyzed by formyltetrahydrofolate synthetase

    SciTech Connect

    Smithers, G.W.; Jahansouz, H.; Kofron, J.L.; Himes, R.H.; Reed, G.H.

    1987-06-30

    Formyl phosphate, a putative enzyme-bound intermediate in the reaction catalyzed by formyltetrahydrofolate synthetase (EC 6.3.4.3), was synthesized from formyl fluoride and inorganic phosphate, and the product was characterized by /sup 31/P, /sup 1/H, and /sup 13/C nuclear magnetic resonance (NMR). Measurement of hydrolysis rates by /sup 31/P NMR indicates that formyl phosphate is particularly labile, with a half-life of 48 min in a buffered neutral solution at 20 /sup 0/C. At pH 7, hydrolysis occurs with P-O bond cleavage, as demonstrated by /sup 18/O incorporation from H/sub 2//sup 18/O into P/sub i/, while at pH 1 and pH 13 hydrolysis occurs with C-O bond cleavage. The substrate activity of formyl phosphate was tested in the reaction catalyzed by formyltetrahydrofolate synthetase isolated from Clostridium cylindrosporum. Formyl phosphate supports the reaction in both the forward and reverse directions. Thus, N/sup 10/-formyltetrahydrofolate is produced from tetrahydrofolate and formyl phosphate in a reaction mixture that contains enzyme, Mg(II), and ADP, and ATP is produced from formyl phosphate and ADP with enzyme, Mg(II), and tetrahydrofolate present. The requirements for ADP and for tetrahydrofolate as cofactors in these reactions are consistent with previous steady-state kinetic and isotope exchange studies, which demonstrated that all substrate subsites must be occupied prior to catalysis. The k/sub cat/ values for both the forward and reverse directions, with formyl phosphate as the substrate, are much lower than those for the normal forward and reverse reactions. Kinetic analysis of the formyl phosphate supported reactions indicates that the low steady-state rates observed for the synthetic intermediate are most likely due to the sequential nature of the normal reaction.

  11. Reversible H atom abstraction catalyzed by the radical S-adenosylmethionine enzyme HydG.

    PubMed

    Duffus, Benjamin R; Ghose, Shourjo; Peters, John W; Broderick, Joan B

    2014-09-24

    The organometallic H-cluster at the active site of [FeFe]-hydrogenases is synthesized by three accessory proteins, two of which are radical S-adenosylmethionine enzymes (HydE, HydG) and one of which is a GTPase (HydF). In this work we probed the specific role of H atom abstraction in HydG-catalyzed carbon monoxide and cyanide production from tyrosine. The isotope distributions of 5'-deoxyadenosine and p-cresol were evaluated using deuterium-labeled tyrosine substrates in H2O and D2O. The observation of multiply deuterated 5'-deoxyadenosine and deuterated S-adenosylmethionine when the reaction is carried out in D2O provides evidence for a 5'-deoxyadenosyl radical-mediated abstraction of a hydrogen atom from a solvent-exchangeable position as a reversible event. PMID:25099480

  12. Novel approach for predicting the joint effects based on the enzyme-catalyzed kinetics.

    PubMed

    Zheng, Min; Yao, Zhifeng; Lin, Zhifen; Fang, Shuxia; Song, Chunlei; Liu, Ying

    2016-04-15

    Organisms are exposed to mixtures of multiple contaminants and it is necessary to build prediction models for the joint effects, considering the high expense and the complexity of the traditional toxicity testing and the flood occurrence of environmental chemical pollutants. In this study, a new method for predicting the joint effects was developed and corresponding prediction models were constructed based on the kinetic models of enzyme-catalyzed reactions. While, we utilized Vibrio fischeri, Escherichia coli and Bacillus subtilis as model organisms and determined the chronic toxicity of the binary mixtures of sulfonamides (SAs) and sulfonamide potentiators (SAPs) (SA+SAP), the mixtures of two kinds of sulfonamides (SA+SA) and the binary mixtures of sulfonamide potentiators (SAPs) and tetracyclines (TCs) (SAP+TC) respectively. Finally, corresponding mixture toxicity data was utilized to fit and verify the prediction models for different joint effects. PMID:26826939

  13. Signal enhancement strategy for a micro-arrayed polydiacetylene (PDA) immunosensor using enzyme-catalyzed precipitation.

    PubMed

    Lee, Jong Uk; Jeong, Ji Hoon; Lee, Doo Sung; Sim, Sang Jun

    2014-11-15

    This paper describes a signal enhancement strategy to improve the sensitivity of an antibody-based immunosensor that uses polydiacetylene (PDA) liposomes to detect a target protein (human immunoglobulin E [hIgE]). To achieve ultrasensitive detection, multiple stimuli applied to PDA immunosensor chips offer a signal enhancement method that combines the primary immune reaction between antigen and antibody with the sandwich method of polyclonal antibody (pAb)-conjugated horseradish peroxidase (HRP). In the second step, fluorescence is enhanced by the mechanical pressure from the precipitate formed by enzyme catalysis. In order to detect hIgE, the surface of immobilized PDA liposomes was conjugated with monoclonal antibodies against hIgE, and fluorescence signals were detected after the antigen-antibody reaction. In this step, hIgE concentrations as low as 10 ng/mL were detected. Fluorescence signals slightly increased when anti-hIgE pAb-HRP was used as an amplifying agent after primary immunoresponse. After secondary immunoresponse, HRP-catalyzed oxidation of 3,3'-diaminobenzidine produced an insoluble precipitate that strongly stimulated PDA liposomes by their weight and pressure, thereby dramatically increasing the fluorescence signal. Thus, PDA liposome immunosensor could detect hIgE concentrations as low as 0.01 ng/mL, representing a 1000-fold increase in sensitivity over the signal generated by the primary immunoresponse. This study indicates that increasing the external mechanical force applied to PDA liposomes by enzyme-catalyzed precipitate formation enhanced the sensitivity of the PDA liposome immunosensor chip. This strategy can be applied to the detection of other biomolecules in experimental or clinical settings where ultrasensitive and highly specific biosensing is required. PMID:24907539

  14. Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution

    PubMed Central

    Renata, Hans; Wang, Z. Jane

    2015-01-01

    High selectivities and exquisite control over reaction outcomes entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature’s known repertoire. We will use this review to outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progressions have been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been discovered and exploited for chemical synthesis, emphasizing reactions that do not have natural counterparts. The new functions have mechanistic parallels to the native reaction mechanisms that often manifest as catalytic promiscuity and the ability to convert from one function to the other with minimal mutation. We present examples of how non-natural activities have been improved by directed evolution, mimicking the process used by nature to create new catalysts. Examples of new enzyme functions include epoxide opening reactions with non-natural nucleophiles catalyzed by a laboratory-evolved halohydrin dehalogenase, cyclopropanation and other carbene transfer reactions catalyzed by cytochrome P450 variants, and non-natural modes of cyclization by a modified terpene synthase. Lastly, we describe discoveries of non-native catalytic functions that may provide future opportunities for expanding the enzyme universe. PMID:25649694

  15. Copper-catalyzed reactions: Research in the gas phase.

    PubMed

    Tsybizova, Alexandra; Roithov, Jana

    2016-01-01

    Electrospray ionization mass spectrometry (ESI-MS) is becoming an important tool for mechanistic studies in organic and organometallic chemistry. It allows investigation of reaction mixtures including monitoring of reactants, products, and intermediates, studying properties of the intermediates and their reactivity. Studying the reactive species in the gas phase can be advantageously combined with theoretical calculations. This review is focused on ESI-MS studies of copper-catalyzed reactions. Possible effects of the electrospray process on the transfer of the copper complexes to the gas phase are discussed. The plethora of mass spectrometric approaches is demonstrated on copper mediated C-H activations, cross coupling reactions, rearrangements, organocuprate chemistry, and other examples. 2015 Wiley Periodicals, Inc. Mass Spec Rev 35: 85-110, 2016. PMID:25975564

  16. Direct evidence for an acyl phosphate intermediate in the folylpoly-. gamma. -glutamate synthetase and dihydrofolate synthetase-catalyzed reactions

    SciTech Connect

    Banerjee, R.

    1987-01-01

    The mechanism of the reactions catalyzed by two enzymes, namely dihydrofolate synthetase (DHFS) and folylpoly-..gamma..-glutamate synthetase (FPGS), has been investigated. The nature of the intermediate in each of the two reactions was monitored simultaneously in the multifunctional enzyme, FPGS/DHFS from E. coli. The latter was isolated from a transformant containing the cloned FPGS/DHFS gene. Incubation of (/sup 18/O)-H/sub 2/Pte and (/sup 17/O)-glutamate with ATP and the enzyme, resulted in the formation of (/sup 18/O)- and (/sup 17/O)-P/sub i/, thus providing strong evidence for the formation of an acyl phosphate species during catalysis of each reaction. The inorganic phosphate formed in the enzyme-catalyzed reaction was purified by chromatography on DEAE-cellulose, then converted to the trimethyl ester and analyzed by mass spectroscopy /sup 17/O NMR and /sup 31/P NMR. Stoichiometric formation of (/sup 17/O)- and (/sup 18/O)-Pi was observed. /sup 31/P NMR analysis showed the expected /sup 18/O-induced isotopic perturbations. The presence of (/sup 17/O)-trimethyl phosphate was revealed by /sup 17/O NMR. The mechanism of the FPGS-catalyzed reaction was also investigated with the antifolate (/sup 18/O)-methotrexate.

  17. Kinetics of Imidazole Catalyzed Ester Hydrolysis: Use of Buffer Dilutions to Determine Spontaneous Rate, Catalyzed Rate, and Reaction Order.

    ERIC Educational Resources Information Center

    Lombardo, Anthony

    1982-01-01

    Described is an advanced undergraduate kinetics experiment using buffer dilutions to determine spontaneous rate, catalyzed rate, and reaction order. The reaction utilized is hydrolysis of p-nitro-phenyl acetate in presence of imidazole, which has been shown to enhance rate of the reaction. (Author/JN)

  18. Kinetic Parameters for the Noncatalyzed and Enzyme-Catalyzed Mutarotation of Glucose Using a Blood Glucometer

    ERIC Educational Resources Information Center

    Hardee, John R.; Delgado, Bryan; Jones, Wray

    2011-01-01

    The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The…

  19. Kinetic Parameters for the Noncatalyzed and Enzyme-Catalyzed Mutarotation of Glucose Using a Blood Glucometer

    ERIC Educational Resources Information Center

    Hardee, John R.; Delgado, Bryan; Jones, Wray

    2011-01-01

    The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The

  20. Investigations of the partial reactions catalyzed by pyruvate phosphate dikinase

    SciTech Connect

    Wang, H.C.; Ciskanik, L.; Dunaway-Mariano, D.; von der Saal, W.; Villafranca, J.J.

    1988-01-26

    The kinetic mechanism of pyruvate phosphate dikinase (PPDK) from Bacteroides symbiosus was investigated with several different kinetic diagnostics. Initial velocity patterns were intersecting for AMP/PPi and ATP/Pi substrate pairs and parallel for all other substrate pairs. PPDK was shown to catalyze (/sup 14/C)pyruvate in equilibrium phosphoenolpyruvate (PEP) exchange in the absence of cosubstrates, (/sup 14/C)AMP in equilibrium ATP exchange in the presence of Pi/PPi but not in their absence, and (/sup 32/P)Pi in equilibrium PPi exchange in the presence of ATP/AMP but not in their absence. The enzyme was also shown, by using (alpha beta-18O, beta, beta-/sup 18/O/sub 2/)ATP and (beta gamma-18O, gamma, gamma, gamma-/sup 18/O/sub 3/)ATP and 31P NMR techniques, to catalyze exchange in ATP between the alpha beta-bridge oxygen and the alpha-P nonbridge oxygen and also between the beta gamma-bridge oxygen and the beta-P nonbridge oxygen. The exchanges were catalyzed by PPDK in the presence of Pi but not in its absence. These results were interpreted to support a bi(ATP,Pi) bi(AMP,PPi) uni(pyruvate) uni(PEP) mechanism. AMP and Pi binding order was examined by carrying out dead-end inhibition studies. The dead-end inhibitor adenosine 5'-monophosphorothioate (AMPS) was found to be competitive vs AMP, noncompetitive vs PPi, and uncompetitive vs PEP. The dead-end inhibitor imidodiphosphate (PNP) was found to be competitive vs PPi, uncompetitive vs AMP, and uncompetitive vs PEP. These results showed that AMP binds before PPi. The ATP and Pi binding order was studied by carrying out inhibition, positional isotope exchange, and alternate substrate studies.

  1. Online Electrospray Ionization Mass Spectrometric Monitoring of Protease-Catalyzed Reactions in Real Time

    NASA Astrophysics Data System (ADS)

    Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Nonami, Hiroshi; Erra-Balsells, Rosa; Hiraoka, Kenzo

    2012-04-01

    Although there are a lot of well established methods for monitoring enzyme-catalyzed reactions, most of them are based on changes in spectroscopic properties during the conversion of substrates to products. However, reactions without optical changes are common, which are inapplicable to these spectroscopic methods. As an alternative technique for enzymologic research, mass spectrometry (MS) is favored due to its specificity, sensitivity, and the ability to obtain stoichiometric information. In this work, probe electrospray ionization (PESI) source coupled with a time of flight mass spectrometer was employed to monitor some typical protease-catalyzed reactions, including pepsinolysis and trypsinolysis of cytochrome c in real time. Due to the high electrical conductivity of each reaction system, corona discharges are likely to occur, which would decrease intensities of mass spectrometric signals. An ultra-fine sampling probe and an auxiliary vapor spray were adopted to prevent corona discharges. Experimental results from peptic and tryptic digestions of cytochrome c showed different and characteristic catalytic pathways. With the data presented in this study, PESI-MS can be considered as a potential tool for real-time monitoring of enzymatic reactions because of its simplicity in instrumental configuration, wide applicability under harsh conditions, and flexibility in combination with other techniques.

  2. Cu-Catalyzed Click Reaction in Carbohydrate Chemistry.

    PubMed

    Tiwari, Vinod K; Mishra, Bhuwan B; Mishra, Kunj B; Mishra, Nidhi; Singh, Anoop S; Chen, Xi

    2016-03-01

    Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC), popularly known as the "click reaction", serves as the most potent and highly dependable tool for facile construction of simple to complex architectures at the molecular level. Click-knitted threads of two exclusively different molecular entities have created some really interesting structures for more than 15 years with a broad spectrum of applicability, including in the fascinating fields of synthetic chemistry, medicinal science, biochemistry, pharmacology, material science, and catalysis. The unique properties of the carbohydrate moiety and the advantages of highly chemo- and regioselective click chemistry, such as mild reaction conditions, efficient performance with a wide range of solvents, and compatibility with different functionalities, together produce miraculous neoglycoconjugates and neoglycopolymers with various synthetic, biological, and pharmaceutical applications. In this review we highlight the successful advancement of Cu(I)-catalyzed click chemistry in glycoscience and its applications as well as future scope in different streams of applied sciences. PMID:26796328

  3. Mechanism of maltal hydration catalyzed by. beta. -amylase: Role of protein structure in controlling the steric outcome of reactions catalyzed by a glycosylase

    SciTech Connect

    Kitahata, Sumio ); Chiba, S. ); Brewer, C.F.; Hehre, E.J. )

    1991-07-09

    Crystalline (monomeric) soybean and (tetrameric) sweet potato {beta}-amylase were shown to catalyze the cis hydration of maltal ({alpha}-D-glucopyranosyl-2-deoxy-D-arabino-hex-1-enitol) to form {beta}-2-deoxymaltose. As reported earlier with the sweet potato enzyme, maltal hydration in D{sub 2}O by soybean {beta}-amylase was found to exhibit an unusually large solvent deuterium kinetic isotope effect (V{sub H}/V{sub D}=6.5), a reaction rate linearly dependent on the mole fraction of deuterium, and 2-deoxy-(2(a)-{sup 2}H)maltose as product. These results indicate (for each {beta}-amylase) that protonation is the rate-limiting step in a reaction involving a nearly symmetric one-proton transition state and that maltal is specifically protonated from above the double bond. That maltal undergoes cis hydration provides evidence in support of a general-acid-catalyzed, carbonium ion mediated reaction. Of fundamental significance is that {beta}-amylase protonates maltal from a direction opposite that assumed for protonating strach, yet creates products of the same anomeric configuration from both. Such stereochemical dichotomy argues for the overriding role of protein structures is dictating the steric outcome of reactions catalyzed by a glycosylase, by limiting the approach and orientation of water or other acceptors to the reaction center.

  4. Mechanistic binding insights for 1-deoxy-d-Xylulose-5-Phosphate synthase, the enzyme catalyzing the first reaction of isoprenoid biosynthesis in the malaria-causing protists, Plasmodium falciparum and Plasmodium vivax.

    PubMed

    Battistini, Matthew R; Shoji, Christopher; Handa, Sumit; Breydo, Leonid; Merkler, David J

    2016-04-01

    We have successfully truncated and recombinantly-expressed 1-deoxy-d-xylulose-5-phosphate synthase (DXS) from both Plasmodium vivax and Plasmodium falciparum. We elucidated the order of substrate binding for both of these ThDP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and d-glyceraldehyde-3-phosphate. These findings are in contrast to other ThDP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful in treatment of malaria. PMID:26699947

  5. Clay-catalyzed reactions of coagulant polymers during water chlorination

    USGS Publications Warehouse

    Lee, J.-F.; Liao, P.-M.; Lee, C.-K.; Chao, H.-P.; Peng, C.-L.; Chiou, C.T.

    2004-01-01

    The influence of suspended clay/solid particles on organic-coagulant reactions during water chlorination was investigated by analyses of total product formation potential (TPFP) and disinfection by-product (DBP) distribution as a function of exchanged clay cation, coagulant organic polymer, and reaction time. Montmorillonite clays appeared to act as a catalytic center where the reaction between adsorbed polymer and disinfectant (chlorine) was mediated closely by the exchanged clay cation. The transition-metal cations in clays catalyzed more effectively than other cations the reactions between a coagulant polymer and chlorine, forming a large number of volatile DBPs. The relative catalytic effects of clays/solids followed the order Ti-Mont > Fe-Mont > Cu-Mont > Mn-Mont > Ca-Mont > Na-Mont > quartz > talc. The effects of coagulant polymers on TPFP follow the order nonionic polymer > anionic polymer > cationic polymer. The catalytic role of the clay cation was further confirmed by the observed inhibition in DBP formation when strong chelating agents (o-phenanthroline and ethylenediamine) were added to the clay suspension. Moreover, in the presence of clays, total DBPs increased appreciably when either the reaction time or the amount of the added clay or coagulant polymer increased. For volatile DBPs, the formation of halogenated methanes was usually time-dependent, with chloroform and dichloromethane showing the greatest dependence. ?? 2003 Elsevier Inc. All rights reserved.

  6. Ab initio study of ice catalyzation of HOCl + HCl reaction

    SciTech Connect

    Zhou, Y.F.; Liu, C.B.

    2000-06-15

    The observations by Farman et al. revealed remarkable depletions in the total atmospheric ozone content in Antarctica. The observed total ozone decreased smoothing during the spring season from about 1975. Satellite observations have proved Antarctic ozone depletions over a very extended region, in general agreement with the local ground-based data of Farman et al. It was suggested that heterogeneous reactions occurring on particles in polar stratospheric clouds (PSCs) play a central role in the depletion of stratospheric ozone. Experiments proved that the reaction of HOCl + HCl was very slow in the gas phase, but on ice surface it was rapid. In this work the ice catalysis of HOCl + HCl reaction was investigated by using ab initio molecular orbital theory. The authors applied the Hartree-Fock self-consistent field and the second-order Moeller-Plesset perturbation theory with the basis sets of 6-31G* to the model system. The complexes and transition state were obtained along the reaction with and without the presence of ice surface. By comparing the results, a possible catalyzation mechanism of ice on the reaction is proposed.

  7. Gold-catalyzed tandem reactions of methylenecyclopropanes and vinylidenecyclopropanes.

    PubMed

    Zhang, Di-Han; Tang, Xiang-Ying; Shi, Min

    2014-03-18

    Gold catalysis is often the key step in the synthesis of natural products, and is a powerful tool for tandem or domino reaction processes. Both gold salts and complexes are among the most powerful soft Lewis acids for electrophilic activation of carbon-carbon multiple bonds toward a variety of nucleophiles. The core of these reactions relies on the interaction between gold catalysts and ?-bonds of alkenes, alkynes, and allenes. Activation of functional groups by gold complexes provides a useful and important method for facilitating many different organic transformations with high atom efficiency. Although they are highly strained, methylenecyclopropanes (MCPs) and vinylidenecyclopropanes (VDCPs) are readily accessible molecules that have served as useful building blocks in organic synthesis. Because of their unique structural and electronic properties, significant developments have been made in the presence of transition metal catalysts such as nickel, rhodium, palladium, and ruthenium during the past decades. However, less attention has been paid to the gold-catalyzed chemistry of MCPs and VDCPs. In this Account, we describe gold-catalyzed chemical transformations of MCPs and VDCPs developed both in our laboratory and by other researchers. Chemists have demonstrated that MCPs and VDCPs have amphiphilic properties. When MCPs or VDCPs are activated by a gold catalyst, subsequent nucleophilic attack by other reagents or ring-opening (ring-expansion) of the cyclopropane moiety will occur. However, the C-C double bonds of MCPs and VDCPs can also serve as nucleophilic reagents while more electrophilic reagents are present and activated by gold catalyst, and then further cascade reactions take place as triggered by the release of ring strain of cyclopropane. Based on this strategy, both our group and others have found some interesting gold-catalyzed transformations in recent years. These transformations of MCPs and VDCPs can produce a variety of polycyclic and heterocyclic structures, containing different sized skeletons. Moreover, we have carried out some isotopic labeling experiments and computational studies for mechanistic investigation. These reactions always give the desired products with high level control of chemo-, regio-, and diastereoselectivities, making them highly valuable for the synthesis of natural products and to the pharmaceutical industry and medicine in general. PMID:24168021

  8. Recent advances in osmium-catalyzed hydrogenation and dehydrogenation reactions.

    PubMed

    Chelucci, Giorgio; Baldino, Salvatore; Baratta, Walter

    2015-02-17

    CONSPECTUS: A current issue in metal-catalyzed reactions is the search for highly efficient transition-metal complexes affording high productivity and selectivity in a variety of processes. Moreover, there is also a great interest in multitasking catalysts that are able to efficiently promote different organic transformations by careful switching of the reaction parameters, such as temperature, solvent, and cocatalyst. In this context, osmium complexes have shown the ability to catalyze efficiently different types of reactions involving hydrogen, proving at the same time high thermal stability and simple synthesis. In the catalytic reduction of C?X (X = O, N) bonds by both hydrogenation (HY) and transfer hydrogenation (TH) reactions, the most interest has been focused on homogeneous systems based on rhodium, iridium, and in particular ruthenium catalysts, which have proved to catalyze chemo- and stereoselective hydrogenations with remarkable efficiency. By contrast, osmium catalysts have received much less attention because they are considered less active on account of their slower ligand exchange kinetics. Thus, this area remained almost neglected until recent studies refuted these prejudices. The aim of this Account is to highlight the impressive developments achieved over the past few years by our and other groups on the design of new classes of osmium complexes and their applications in homogeneous catalytic reactions involving the hydrogenation of carbon-oxygen and carbon-nitrogen bonds by both HY and TH reactions as well as in alcohol deydrogenation (DHY) reactions. The work described in this Account demonstrates that osmium complexes are emerging as powerful catalysts for asymmetric and non-asymmetric syntheses, showing a remarkably high catalytic activity in HY and TH reactions of ketones, aldehydes, imines, and esters as well in DHY reactions of alcohols. Thus, for instance, the introduction of ligands with an NH function, possibly in combination with a pyridine ring, led to a new family of [OsCl2(PP)(NN)] (NN = diamine, 2-aminomethylpyridine; PP = diphosphine) and pincer [OsCl(CNN)(PP)] (HCNN = 6-aryl-2-aminomethylpyridine, 2-aminomethylbenzo[h]quinoline) complexes, which are outstanding catalysts for (asymmetric) HY and TH of carbonyl compounds and DHY of alcohols with turnover numbers and turnover frequencies up to 10(5) and 10(6) h(-1), respectively. In addition, PNN osmium complexes containing the 2-aminomethylpyridine motif have been found to be among the most active catalysts for HY of esters. These complexes have shown catalytic activities that are comparable and in some cases superior to those reported for analogous ruthenium systems. These results give an idea of the potential of Os complexes for the design of new highly productive and robust catalysts for the synthesis of chiral and nonchiral alcohols and amines as well as ketones from alcohols. Thus, we hope that this report will promote increased interest in the chemistry of these metal complexes, opening novel opportunities for new catalytic processes as well as the improvement of existing ones. PMID:25650714

  9. Ultrasound assisted enzyme catalyzed degradation of Cetirizine dihydrochloride.

    PubMed

    Sutar, Rahul S; Rathod, Virendra K

    2015-05-01

    Cetirizine dihydrochloride, a pharmaceutical drug of the class antihistamines is frequently detected in wastewater samples. In the present work, the degradation of Cetirizine dihydrochloride is carried out using a novel technique of laccase enzyme as a catalyst under the influence of ultrasound irradiation. Effect of various process parameters such as enzyme loading, temperature, power, duty cycle, frequency and speed of agitation has been studied along with identification of the degradation intermediates. The maximum degradation of 91% is achieved at optimized experimental parameters such as 0.02% enzyme loading (w/v), 50C temperature, power input of 100 W, 25 kHz frequency and 50% duty cycle with agitation speed of 200 rpm. It is observed that enzymatic degradation of Cetirizine dihydrochloride under the influence of ultrasound irradiation not only enhances the degradation but also reduces the time of degradation as compared to conventional enzymatic degradation technique. PMID:25515235

  10. Acid-catalyzed Heterogeneous Reactions in SOA Formation

    NASA Astrophysics Data System (ADS)

    Ng, N.; Keywood, M.; Varutbangkul, V.; Gao, S.; Loewer, E.; Surratt, J.; Richard, F. C.; John, S. H.

    2003-12-01

    The importance of heterogeneous reactions in secondary organic aerosol (SOA) formation has recently excited a great deal of interest in the aerosol community. Jang and Kamens (2001) showed enhanced aerosol yield from aldehydes, which can be produced by atmospheric photochemical reactions, in the presence of acidic seed. They suggest that the carbonyl functional groups of the aldehydes further react in the aerosol phase via hydration, polymerization, and hemiacetal/acetal formation with alcohols at an accelerated rate in the presence of acid. Jang et al. (2003) demonstrated similar results using a flow reactor and Czoschke et al. (in press) qualitatively showed increased yields for isoprene and alpha-pinene ozonolysis in the presence of acidic seed. While these findings are intriguing and important, the conditions under which the experiments were carried out were atmospherically unrealistic. A series of SOA formation experiments have been carried out in the Caltech Indoor Chamber Facility, which is comprised of dual 28 m3 FEP Teflon chambers, with the flexibility to carry out both dark ozonolysis and photochemical OH oxidation reactions. Cycloheptene and alpha-pinene were oxidized in the presence of neutral seed under dry (<10% RH) and humid (50% RH) conditions and in the presence of acidic seed under humid (50% RH) conditions. The SOA yields for these experiments will be presented, and the extent of the influence of acid-catalyzed reactions on SOA yield will be discussed. Reference List 1. Cocker, D. R. III. and R. C. Flagan and J. H. Seinfeld, State-of-the-art chamber facility for studying atmospheric aerosol chemistry, Environmental Science and Technology, 35, 2594-2601, 2001. 2. Czoschke, N. M., M. Jang, and R. M. Kamens, Effect of acid seed on biogenic sceondary organic aerosol growth, Atmospheric Environment, In press. 3. Jang, M., S. Lee, and R. M. Kamens, Organic aerosol growth by acid-catalyzed heterogeneous reactions of octanal in a flow reactor, Atmospheric Environment, 37, 2125-2138, 2003. 4. Jang, M. S. and R. M Kamens, Atmospheric secondary aerosol formation by heterogeneous reactions of aldehydes in the presence of a sulfuric acid aerosol catalyst. Environmental Science and Technology, 35, 4758-4766,2001.

  11. Functional characterization of enzymes catalyzing ceramide phosphoethanolamine biosynthesis in mice.

    PubMed

    Bickert, Andreas; Ginkel, Christina; Kol, Matthijs; vom Dorp, Katharina; Jastrow, Holger; Degen, Joachim; Jacobs, Ren L; Vance, Dennis E; Winterhager, Elke; Jiang, Xian-Cheng; Drmann, Peter; Somerharju, Pentti; Holthuis, Joost C M; Willecke, Klaus

    2015-04-01

    Besides bulk amounts of SM, mammalian cells produce small quantities of the SM analog ceramide phosphoethanolamine (CPE). Little is known about the biological role of CPE or enzymes responsible for CPE production. Heterologous expression studies revealed that SM synthase (SMS)2 is a bifunctional enzyme producing both SM and CPE, whereas SMS-related protein (SMSr) serves as monofunctional CPE synthase. Acute disruption of SMSr catalytic activity in cultured cells causes a rise in endoplasmic reticulum (ER) ceramides, fragmentation of ER exit sites, and induction of mitochondrial apoptosis. To address the relevance of CPE biosynthesis in vivo, we analyzed the tissue-specific distribution of CPE in mice and generated mouse lines lacking SMSr and SMS2 catalytic activity. We found that CPE levels were >300-fold lower than SM in all tissues examined. Unexpectedly, combined inactivation of SMSr and SMS2 significantly reduced, but did not eliminate, tissue-specific CPE pools and had no obvious impact on mouse development or fertility. While SMSr is widely expressed and serves as the principal CPE synthase in the brain, blocking its catalytic activity did not affect ceramide levels or secretory pathway integrity in the brain or any other tissue. Our data provide a first inventory of CPE species and CPE-biosynthetic enzymes in mammals. PMID:25667419

  12. Nickel-catalyzed alkyl coupling reactions: evaluation of computational methods.

    PubMed

    Pratt, Lawrence M; Voit, Stewart; Okeke, Fabian N; Kambe, Nobuaki

    2011-03-24

    The B3LYP, M06, M06L, M062X, MPW1K, and PBE1PBE DFT methods were evaluated for modeling nickel-catalyzed coupling reactions. The reaction consists of a nucleophilic attack by a carbanion equivalent on the nickel complex, S(N)2 attack by the anionic nickel complex on an alkyl halide, and reductive elimination of the coupled alkane product, regenerating the nickel catalyst. On the basis of CCSD(T)//DFT single-point energies, the B3LYP, M06, and PBE1PBE functionals were judged to generate the best ground state geometries. M06 energies are generally comparable or superior to B3LYP and PBE1PBE energies for transition state calculations. The MP2 and CCSD methods were also evaluated for single-point energies at the M06 geometries. The rate-determining step of this reaction was found to be nucleophilic attack of a L(2)NiR anion on the alkyl halide. PMID:21351749

  13. Potential Energy Surfaces for Reaction Catalyzed by Metalloenzymes from Quantum Chemical Computations

    NASA Astrophysics Data System (ADS)

    Leopoldini, Monica; Marino, Tiziana; Russo, Nino; Toscano, Marirosa

    For several decades quantum mechanical (QM) computational methods have been developed and refined so that it was possible to extend their applicability field enormously. Today, they are used generally to supplement experimental techniques because the theory also affords deeper understanding of molecular processes that cannot be obtained from experiments alone. Due to their favorable scaling when compared to the ab initiomethods, density functional theory (DFT) approach allows the treatment of very large systems such as the biomolecules. Thus, now it is possible, for instance, to study the difficult and critical reactions catalyzed by enzymes in biological systems. Here, a brief account of the studies performed on different metalloenzymes is given, focusing on methods and models used to describe their reaction mechanisms.

  14. Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.

    PubMed

    Renata, Hans; Wang, Z Jane; Arnold, Frances H

    2015-03-01

    High selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature's known repertoire. In this Review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been exploited for chemical synthesis, with an emphasis on reactions that do not have natural counterparts. Non-natural activities can be improved by directed evolution, thus mimicking the process used by nature to create new catalysts. Finally, we describe the discovery of non-native catalytic functions that may provide future opportunities for the expansion of the enzyme universe. PMID:25649694

  15. A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions

    PubMed Central

    Chang, Ivan; Baldi, Pierre

    2013-01-01

    Motivation: Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation–reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus important, current models suffer from limitations to the steady-state domain, lack empirical validation or are too specialized to a single system or set of conditions. Results: To address these limitations, we introduce a novel unifying modeling framework for kinetic descriptions of oxidoreductases. The framework is based on a set of seven elementary reactions that (i) form the basis for 69 pairs of enzyme state transitions for encoding various specific microscopic intra-enzyme reaction networks (micro-models), and (ii) lead to various specific macroscopic steady-state kinetic equations (macro-models) via thermodynamic assumptions. Thus, a synergistic bridge between the micro and macro kinetics can be achieved, enabling us to extract unitary rate constants, simulate reaction variance and validate the micro-models using steady-state empirical data. To help facilitate the application of this framework, we make available RedoxMech: a Mathematica™ software package that automates the generation and customization of micro-models. Availability: The Mathematica™ source code for RedoxMech, the documentation and the experimental datasets are all available from: http://www.igb.uci.edu/tools/sb/metabolic-modeling. Contact: pfbaldi@ics.uci.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23613486

  16. Key enzymes catalyzing glycerol to 1,3-propanediol.

    PubMed

    Jiang, Wei; Wang, Shizhen; Wang, Yuanpeng; Fang, Baishan

    2016-01-01

    Biodiesel can replace petroleum diesel as it is produced from animal fats and vegetable oils, and it produces about 10 % (w/w) glycerol, which is a promising new industrial microbial carbon, as a major by-product. One of the most potential applications of glycerol is its biotransformation to high value chemicals such as 1,3-propanediol (1,3-PD), dihydroxyacetone (DHA), succinic acid, etc., through microbial fermentation. Glycerol dehydratase, 1,3-propanediol dehydrogenase (1,3-propanediol-oxydoreductase), and glycerol dehydrogenase, which were encoded, respectively, by dhaB, dhaT, and dhaD and with DHA kinase are encompassed by the dha regulon, are the three key enzymes in glycerol bioconversion into 1,3-PD and DHA, and these are discussed in this review article. The summary of the main research direction of these three key enzyme and methods of glycerol bioconversion into 1,3-PD and DHA indicates their potential application in future enzymatic research and industrial production, especially in biodiesel industry. PMID:26966462

  17. Enzyme efficiency: An open reaction system perspective.

    PubMed

    Banerjee, Kinshuk; Bhattacharyya, Kamal

    2015-12-21

    A measure of enzyme efficiency is proposed for an open reaction network that, in suitable form, applies to closed systems as well. The idea originates from the description of classical enzyme kinetics in terms of cycles. We derive analytical expressions for the efficiency measure by treating the network not only deterministically but also stochastically. The latter accounts for any significant amount of noise that can be present in biological systems and hence reveals its impact on efficiency. Numerical verification of the results is also performed. It is found that the deterministic equation overestimates the efficiency, the more so for very small system sizes. Roles of various kinetics parameters and system sizes on the efficiency are thoroughly explored and compared with the standard definition k2/KM. Study of substrate fluctuation also indicates an interesting efficiency-accuracy balance. PMID:26696076

  18. Enzyme efficiency: An open reaction system perspective

    NASA Astrophysics Data System (ADS)

    Banerjee, Kinshuk; Bhattacharyya, Kamal

    2015-12-01

    A measure of enzyme efficiency is proposed for an open reaction network that, in suitable form, applies to closed systems as well. The idea originates from the description of classical enzyme kinetics in terms of cycles. We derive analytical expressions for the efficiency measure by treating the network not only deterministically but also stochastically. The latter accounts for any significant amount of noise that can be present in biological systems and hence reveals its impact on efficiency. Numerical verification of the results is also performed. It is found that the deterministic equation overestimates the efficiency, the more so for very small system sizes. Roles of various kinetics parameters and system sizes on the efficiency are thoroughly explored and compared with the standard definition k2/KM. Study of substrate fluctuation also indicates an interesting efficiency-accuracy balance.

  19. Copper-catalyzed cascade reactions of ?,?-unsaturated esters with keto esters

    PubMed Central

    Wang, Chongnian; Li, Zengchang

    2015-01-01

    Summary A copper-catalyzed cascade reaction of ?,?-unsaturated esters with keto esters is reported. It features a copper-catalyzed reductive aldolization followed by a lactonization. This method provides a facile approach to prepare ?-carboxymethyl-?-lactones and ?-carboxymethyl-?-lactones under mild reaction conditions. PMID:25815072

  20. Pd(0)-catalyzed intramolecular ?-arylation of sulfones: domino reactions in the synthesis of functionalized tetrahydroisoquinolines.

    PubMed

    Sol, Daniel; Prez-Janer, Ferran; Mancuso, Raffaella

    2015-03-16

    A new strategy for the synthesis of tetrahydroisoquinolines based on the Pd(0)-catalyzed intramolecular ?-arylation of sulfones is reported. The combination of this Pd-catalyzed reaction with intermolecular Michael and aza-Michael reactions allows the development of two- and three-step domino processes to synthesize diversely functionalized scaffolds from readily available starting materials. PMID:25677083

  1. Model sclerotization studies. 3. Cuticular enzyme catalyzed oxidation of peptidyl model tyrosine and dopa derivatives.

    PubMed

    Sugumaran, M; Ricketts, D

    1995-01-01

    Incubation of N-acetyltyrosine methyl ester with cuticular enzymes, isolated from the wandering stages of Calliphora sp larvae, resulted in the generation of N-acetyldopa methyl ester when the reaction was carried out in the presence of ascorbate which prevented further oxidation of the o-diphenolic product. Enzymatic oxidation of N-acetyldopa methyl ester ultimately generated dehydro N-acetyldopa methyl ester. The identity of enzymatically produced N-acetyldopa methyl ester and dehydro N-acetyldopa methyl ester has been confirmed by comparison of the ultraviolet and infrared spectral and chromatographic properties with those of authentic samples as well as by nuclear magnetic resonance studies. Since N-acetyldopaquinone methyl ester was also converted to dehydro N-acetyldopa methyl ester and tyrosinase was responsible for the oxidation of N-acetyldopa methyl ester, a scheme for the cuticular phenoloxidase catalyzed conversion of N-acetyltyrosine methyl ester to dehydro N-acetyldopa methyl ester involving the intermediary formation of the quinone and the quinone methide is proposed to account for the observed results. The conversion of N-acetyldopa methyl ester to dehydro derivative remarkably resembles the conversion of the sclerotizing precursor, N-acetyldopamine, to dehydro-N-acetyldopamine observed in the insect cuticle. Based on these comparative studies, it is proposed that peptidyl dopa derivatives could also serve as the sclerotizing precursors for the sclerotization of the insect cuticle. PMID:7803812

  2. Multiple hydrogen kinetic isotope effects for enzymes catalyzing exchange with solvent: application to alanine racemase.

    PubMed

    Spies, M Ashley; Toney, Michael D

    2003-05-01

    Alanine racemase catalyzes the pyridoxal phosphate-dependent interconversion of the D- and L-isomers of alanine. Previous studies have shown that the enzyme employs a two-base mechanism in which Lys39 and Tyr265 are the acid/base catalysts. It is thus possible that stereoisomerization of the external aldimine intermediates occurs through a concerted double proton transfer without the existence of a distinct carbanionic intermediate. This possibility was tested by the application of multiple kinetic isotope effect (KIE) methodology to alanine racemase. The mutual dependence of primary substrate and solvent deuterium KIEs has been measured using equilibrium perturbation-type experiments. The conceptually straightforward measurement of the substrate KIE in H(2)O is complemented with a less intuitive protium washout perturbation-type measurement in D(2)O. The primary substrate KIE in the D --> L direction at 25 degrees C is reduced from 1.297 in H(2)O to 1.176 in D(2)O, while in the L --> D direction it is reduced from 1.877 in H(2)O to 1.824 in D(2)O. Similar reductions are also observed at 65 degrees C, the temperature to which the Bacillus stearothermophilus enzyme is adapted. These data strongly support a stepwise racemization of stereoisomeric aldimine intermediates in which a substrate-based carbanion is an obligatory intermediate. The ionizations observed in k(cat)/K(M) pH profiles have been definitively assigned based on the DeltaH(ion) values of the observed pK(a)'s with alanine and on the pH dependence of k(cat)/K(M) for the alternative substrate serine. The acidic pK(a) in the bell-shaped curve is due to the phenolic hydroxyl of Tyr265, which must be unprotonated for reaction with either isomer of alanine. The basic pK(a) is due to the substrate amino group, which must be protonated to react with Tyr265-unprotonated enzyme. A detailed reaction mechanism incorporating these results is proposed. PMID:12718553

  3. Activation Energies for an Enzyme-Catalyzed and Acid-Catalyzed Hydrolysis: An Introductory Interdisciplinary Experiment for Chemists and Biochemists.

    ERIC Educational Resources Information Center

    Adams, K. R.; Meyers, M. B.

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment in which students determine and compare the Arrhenius activation energies (Ea) for the hydrolysis of salicin. This reaction is subject to catalysis both by acid and by the enzyme emulsin (beta-d-glucoside glycohydrolase). (JN)

  4. Gold-catalyzed reactions of 2-alkynyl-phenylamines with alpha,beta-enones.

    PubMed

    Alfonsi, Maria; Arcadi, Antonio; Aschi, Massimiliano; Bianchi, Gabriele; Marinelli, Fabio

    2005-03-18

    [reaction: see text] The gold-catalyzed reaction of 2-alkynyl-phenylamines with alpha,beta-enones represents a new general one-pot entry into C-3-alkyl-indoles by sequential reactions. Gold-catalyzed sequential cyclization/alkylation, N-alkylation/cyclization, or N-alkylation/cyclization/alkylation reactions leading to different indoles can be directed by changing the 2-alkynyl-phenylamine 1/alpha,beta-enone 3 ratio and the reaction temperature. Unusual gold-catalyzed rearrangement reaction of indoles are observed at 140 degrees C. New gold-catalyzed formation of propargyl-alkyl ether under mild conditions and the hydration reaction of N-acetyl-2-ethynyl-phenylamine are reported. PMID:15760214

  5. Entropy is key to the formation of pentacyclic terpenoids by enzyme-catalyzed polycyclization.

    PubMed

    Syrn, Per-Olof; Hammer, Stephan C; Claasen, Birgit; Hauer, Bernhard

    2014-05-01

    Polycyclizations constitute a cornerstone of chemistry and biology. Multicyclic scaffolds are generated by terpene cyclase enzymes in nature through a carbocationic polycyclization cascade of a prefolded polyisoprene backbone, for which electrostatic stabilization of transient carbocationic species is believed to drive catalysis. Computational studies and site-directed mutagenesis were used to assess the contribution of entropy to the polycyclization cascade catalyzed by the triterpene cyclase from A. acidocaldarius. Our results show that entropy contributes significantly to the rate enhancement through the release of water molecules through specific channels. A single rational point mutation that results in the disruption of one of these water channels decreased the entropic contribution to catalysis by 60?kcal?mol(-1) . This work demonstrates that entropy is the key to enzyme-catalyzed polycyclizations, which are highly relevant in biology since 90?% of all natural products contain a cyclic subunit. PMID:24711227

  6. Adrenodoxin supports reactions catalyzed by microsomal steroidogenic cytochrome P450s

    SciTech Connect

    Pechurskaya, Tatiana A. . E-mail: usanov@iboch.bas-net.by

    2007-02-16

    The interaction of adrenodoxin (Adx) and NADPH cytochrome P450 reductase (CPR) with human microsomal steroidogenic cytochrome P450s was studied. It is found that Adx, mitochondrial electron transfer protein, is able to support reactions catalyzed by human microsomal P450s: full length CYP17, truncated CYP17, and truncated CYP21. CPR, but not Adx, supports activity of truncated CYP19. Truncated and the full length CYP17s show distinct preference for electron donor proteins. Truncated CYP17 has higher activity with Adx compared to CPR. The alteration in preference to electron donor does not change product profile for truncated enzymes. The electrostatic contacts play a major role in the interaction of truncated CYP17 with either CPR or Adx. Similarly electrostatic contacts are predominant in the interaction of full length CYP17 with Adx. We speculate that Adx might serve as an alternative electron donor for CYP17 at the conditions of CPR deficiency in human.

  7. Scanning electrochemical impedance microscopy for investigation of glucose oxidase catalyzed reaction.

    PubMed

    Morkvenaite-Vilkonciene, I; Genys, P; Ramanaviciene, A; Ramanavicius, A

    2015-02-01

    In this research biointerface based on immobilized glucose oxidase (GOx) was evaluated by scanning electrochemical impedance microscopy (SEIM), which consisted of merged scanning electrochemical microscopy (SECM) and electrochemical impedance spectroscopy (EIS). The gluconolactone, which is quickly hydrolyzed to gluconic acid, is produced during the enzyme-catalyzed glucose oxidation reaction. Gluconic acid formed above an enzyme-modified not-conducting plastic surface, was evaluated by EIS technique. A two electrode cell consisting of a scanning probe, which was based on 10 ?m diameter ultramicroelectrode and stationary platinum counter/reference electrode was applied for the measurement. Locally measured solution impedance depends on the gluconic acid concentration close to the ultramicroelectrode surface and on the ion diffusion, which is hindered when the electrode is approaching close to the GOx-modified surface. EIS results were evaluated by applying an equivalent circuit consisting of elements representing solution resistance, double-layer capacitance, charge-transfer resistance and Warburg impedance. Solution resistance was calculated and showed to be dependent on the position of ultramicroelectrode. Also it was observed that the thickness of the conducting layer and gluconic acid concentration both are changing in time. The results indicate that here proposed SEIM technique could become a valuable tool for the investigation and characterization of enzyme-modified surfaces of biosensors and biofuel cells. PMID:25620444

  8. Impact of reaction conditions on the laccase-catalyzed conversion of bisphenol A.

    PubMed

    Kim, Young-Jin; Nicell, James A

    2006-08-01

    The oxidative conversion of aqueous BPA catalyzed by laccase from Trametes versicolor was conducted in a closed, temperature-controlled system containing buffer for pH control. The effects of medium pH, buffer concentration, temperature and mediators and the impacts of dissolved wastewater constituents on BPA conversion were investigated. The optimal pH for BPA conversion was approximately 5, with greater than half maximal conversion and good enzyme stability in the range of 4-7. The stability of the enzyme was not impacted by buffer concentration, nor was BPA conversion. Despite the observation that the enzyme tended to be inactivated at elevated temperatures, enhanced conversion of BPA was observed up until a reaction temperature of 45 degrees C. Of the mediators studied, ABTS was most successful at enhancing the conversion of BPA. Dissolved wastewater constituents that were studied included various inorganic salts, organic compounds and heavy metal ions. BPA conversion was inhibited in the presence of anions such as sulfite, thiosulfate, sulfide, nitrite and cyanide. The metal ions Fe(III) and Cu(II) and the halogens chloride and fluoride substantially suppressed BPA conversion, but the presence of selected organic compounds did not significantly reduce the conversion of BPA. PMID:16122923

  9. Nucleophilic addition reactions of free and enzyme-bound deazaflavin.

    PubMed

    Jorns, M S; Hersh, L B

    1976-08-25

    DeazaFMN-containing glycolate oxidase has been prepared and shown to catalyze the stereospecific transfer of the alpha-hydrogen from substrate to enzyme-bound deazaFMN. The reaction of sulfite, cyanide, and hydroxylamine with several deazaflavin-containing enzymes (glycolate oxidase, D-amino acid oxidase, glucose oxidase, N-methylglutamate synthetase) and free deazaFMN has been examined. All the deazaflavin systems tested form reversible 1:1 complexes with sulfite and cyanide. The pH dependence of the reaction of free deazaFMN with cyanide indicates that cyanide anion is the reacting nucleophile. Hydroxylamine complexes are formed with deazaFMN glycolate oxidase and deazaFAD glucose oxidase. The effectiveness of the various nucleophilic reagents in complex formation decreases in the following order: sulfite greater than cyanide greater than hydroxylamine. The relative stability observed for the sulfite and cyanide complexes formed with various deazaflavin systems (glycolate oxidase greater than D-amino acid oxidase greater than free deazaFMN) follows the same trend observed for the stability of the sulfite complexes formed with the corresponding flavin system. A correlation is also observed between the reduction potential (E'o) of the deazaflavin system (glycolate oxidase (- 170 mV) greater than D-amino acid oxidase (-240 mV) greater than free deazaFMN (-178 mV) and the stability of the deazaflavin-nucleophile complexes. The following evidence indicates that deazaflavin systems are generally more susceptible toward nucleophilic attack than corresponding flavin system: (a) with the exception of glucose oxidase, the dissociation constants for the deazaflavin-sulfite complexes are at least 1 order of magnitude less than the corresponding flavin sulfite complexes; (b) the least reactive nucleophile, hydroxylamine, does not form a complex with any of the flavin systems. In the case of cyanide, a complex is formed only with native glycolate oxidase, which is the flavin-containing system most susceptible to attack by the more reactive sulfite. Formation of the various (deaza)flavin-nucleophile complexes is characterized by a bleaching of the longer wavelength absorption band of the chromophore and increases in absorption below the isosbestic point of the reaction in the near-ultraviolet region of the spectrum. These results are consistent with the formation of covalent adducts via attack of the various nucleophiles at position 5 of (deaza)flavin. The reaction with cyanide provides the first example of a reversible addition of carbanion to enzyme-bound (deaza)flavin. PMID:8450

  10. The Biosynthesis of Thiol- and Thioether-containing Cofactors and Secondary Metabolites Catalyzed by Radical S-Adenosylmethionine Enzymes*

    PubMed Central

    Jarrett, Joseph T.

    2015-01-01

    Sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. The biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. Examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links found in peptide natural products. Radical S-adenosyl-l-methionine (SAM) enzymes use an iron-sulfur cluster to catalyze the reduction of SAM to methionine and a highly reactive 5′-deoxyadenosyl radical; this radical can abstract hydrogen atoms at unreactive positions, facilitating the introduction of a variety of functional groups. Radical SAM enzymes that catalyze sulfur insertion reactions contain a second iron-sulfur cluster that facilitates the chemistry, either by donating the cluster's endogenous sulfide or by binding and activating exogenous sulfide or sulfur-containing substrates. The use of radical chemistry involving iron-sulfur clusters is an efficient anaerobic route to the generation of carbon-sulfur bonds in cofactors, secondary metabolites, and other natural products. PMID:25477512

  11. First Novozym 435 lipase-catalyzed Morita-Baylis-Hillman reaction in the presence of amides.

    PubMed

    Tian, Xuemei; Zhang, Suoqin; Zheng, Liangyu

    2016-03-01

    The first Novozym 435 lipase-catalyzed Morita-Baylis-Hillman (MBH) reaction with amides as co-catalyst was realized. Results showed that neither Novozym 435 nor amide can independently catalyze the reaction. This co-catalytic system that used a catalytic amount of Novozym 435 with a corresponding amount of amide was established and optimized. The MBH reaction strongly depended on the structure of aldehyde substrate, amide co-catalyst, and reaction additives. The optimized reaction yield (43.4%) was achieved in the Novozym 435-catalyzed MBH reaction of 2, 4-dinitrobenzaldehyde and cyclohexenone with isonicotinamide as co-catalyst and ?-cyclodextrin as additive only in 2 days. Although enantioselectivity of Novozym 435 was not found, the results were still significant because an MBH reaction using lipase as biocatalyst was realized for the first time. PMID:26827772

  12. Carbon-carbon bond cleavage and formation reactions in drug metabolism and the role of metabolic enzymes.

    PubMed

    Bolleddula, Jayaprakasam; Chowdhury, Swapan K

    2015-11-01

    Elimination of xenobiotics from the human body is often facilitated by a transformation to highly water soluble and more ionizable molecules. In general, oxidation-reduction, hydrolysis, and conjugation reactions are common biotransformation reactions that are catalyzed by various metabolic enzymes including cytochrome P450s (CYPs), non-CYPs, and conjugative enzymes. Although carbon-carbon (C-C) bond formation and cleavage reactions are known to exist in plant secondary metabolism, these reactions are relatively rare in mammalian metabolism and are considered exceptions. However, various reactions such as demethylation, dealkylation, dearylation, reduction of alkyl chain, ring expansion, ring contraction, oxidative elimination of a nitrile through C-C bond cleavage, and dimerization, and glucuronidation through C-C bond formation have been reported for drug molecules. Carbon-carbon bond cleavage reactions for drug molecules are primarily catalyzed by CYP enzymes, dimerization is mediated by peroxidases, and C-glucuronidation is catalyzed by UGT1A9. This review provides an overview of C-C bond cleavage and formation reactions in drug metabolism and the metabolic enzymes associated with these reactions. PMID:26390887

  13. Synthesis of (-)-?9-trans-Tetrahydrocannabinol - Stereocontrol via Mo-catalyzed Asymmetric Allylic Alkylation Reaction

    PubMed Central

    Trost, Barry M.; Dogra, Kalindi

    2008-01-01

    ?9-THC is synthesized in enantiomericaly pure form, where all of the stereochemistry is derived from the molybdenum catalyzed asymmetric alkylation reaction of the extremely sterically congested bis-ortho substituted cinnamyl carbonate in high regio- and enantioselectivity. PMID:17266321

  14. PALLADIUM-CATALYZED OXIDATION OF STYRENE AND ALKENES IN PRESENCE OF IONIC LIQUIDS (WACKER REACTION)

    EPA Science Inventory

    The use of ionic liquids in various synthetic transformations is gaining significance due to the enhanced reaction rates, potential for recycling and compatibility with various organic compounds and organometallic catalysts. Palladium-catalyzed oxidation of styrene and other alk...

  15. Selective production of 1-monocaprin by porcine liver carboxylesterase-catalyzed esterification: Its enzyme kinetics and catalytic performance.

    PubMed

    Park, Kyung-Min; Lee, Jong-Hyuk; Hong, Sung-Chul; Kwon, Chang Woo; Jo, Minje; Choi, Seung Jun; Kim, Keesung; Chang, Pahn-Shick

    2016-01-01

    Porcine liver carboxylesterase (PLE) belongs to carboxylesterase family (EC 3.1.1.1) as a serine-type esterase. The PLE-catalyzed esterification of capric acid with glycerol in reverse micelles was investigated on the catalytic performance and enzyme kinetics. The most suitable structure of reverse micelles was comprised of isooctane (reaction medium) and bis(2-ethylhexyl) sodium sulfosuccinate (AOT, anionic surfactant) with 0.1 of R-value ([water]/[surfactant]) and 3.0 of G/F-value ([glycerol]/[fatty acid]) for the PLE-catalyzed esterification. In the aspect of regio-selectivity, the PLE mainly produced 1-monocaprin without any other products (di- and/or tricaprins of subsequent reactions). Furthermore, the degree of esterification at equilibrium state (after 4h from the initiation) was 62.7% under the optimum conditions at pH 7.0 and 60C. Based on Hanes-Woolf plot, the apparent Km and Vmax values were calculated to be 16.44mM and 38.91?M/min/mg protein, respectively. PMID:26672448

  16. Acid-catalyzed reactions of hexanal on sulfuric acid particles: Identification of reaction products

    NASA Astrophysics Data System (ADS)

    Garland, Rebecca M.; Elrod, Matthew J.; Kincaid, Kristi; Beaver, Melinda R.; Jimenez, Jose L.; Tolbert, Margaret A.

    While it is well established that organics compose a large fraction of the atmospheric aerosol mass, the mechanisms through which organics are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds with carbonyl groups have recently been suggested as important pathways for transfer of volatile organics into acidic aerosols. In the present study, we use the aerodyne aerosol mass spectrometer (AMS) to probe the uptake of gas-phase hexanal into ammonium sulfate and sulfuric acid aerosols. While both deliquesced and dry non-acidic ammonium sulfate aerosols showed no organic uptake, the acidic aerosols took up substantial amounts of organic material when exposed to hexanal vapor. Further, we used 1H-NMR, Fourier transform infrared (FTIR) spectroscopy and GC-MS to identify the products of the acid-catalyzed reaction of hexanal in acidic aerosols. Both aldol condensation and hemiacetal products were identified, with the dominant reaction products dependent upon the initial acid concentration of the aerosol. The aldol condensation product was formed only at initial concentrations of 75-96 wt% sulfuric acid in water. The hemiacetal was produced at all sulfuric acid concentrations studied, 30-96 wt% sulfuric acid in water. Aerosols up to 88.4 wt% organic/11.1 wt% H 2SO 4/0.5 wt% water were produced via these two dimerization reaction pathways. The UV-VIS spectrum of the isolated aldol condensation product, 2-butyl 2-octenal, extends into the visible region, suggesting these reactions may impact aerosol optical properties as well as aerosol composition. In contrast to previous suggestions, no polymerization of hexanal or its products was observed at any sulfuric acid concentration studied, from 30 to 96 wt% in water.

  17. Copper-Catalyzed SN2'-Selective Allylic Substitution Reaction of gem-Diborylalkanes.

    PubMed

    Zhang, Zhen-Qi; Zhang, Ben; Lu, Xi; Liu, Jing-Hui; Lu, Xiao-Yu; Xiao, Bin; Fu, Yao

    2016-03-01

    A Cu/(NHC)-catalyzed SN2'-selective substitution reaction of allylic electrophiles with gem-diborylalkanes is reported. Different substituted gem-diborylalkanes and allylic electrophiles can be employed in this reaction, and various synthetic valuable functional groups can be tolerated. The asymmetric version of this reaction was initially researched with chiral N-heterocyclic carbene (NHC) ligands. PMID:26872072

  18. [The synthesis of P1-[11-(anthracen-9-ylmethoxy)undecyl]-P2(2-Acetamido-2-deoxy-?-D-glucopyranosyl) diphosphate and the study of its acceptor properties in the enzymic reaction catalyzed by D-rhamnosyltransferase from Pseudomonas aeruginosa].

    PubMed

    Vinnikova, A N; Torgov, V I; Utkina, N S; Veselovsky, V V; Druzhinina, T N; Wang, S; Brockhausen; Danilov, L L

    2015-01-01

    P1-[11-(Anthracen-9-ylmethoxy)undecyl]-P2-(2-acetamido-2-deoxy-?-D-glucopyranosyl) diphosphate, a fluorescent derivative of undecyl diphosphate 2-acetamido-2-deoxyglucose, was chemically synthesized. The ability of the compound to serve as acceptor substrate of D-rhamnose residue in the enzymatic reaction catalyzed by D-rhamnosyltransferase from Pseudomonas aeruginosa PAO1 was demonstrated. PMID:26050480

  19. Spatially Organized Enzymes Drive Cofactor-Coupled Cascade Reactions.

    PubMed

    Ngo, Tien Anh; Nakata, Eiji; Saimura, Masayuki; Morii, Takashi

    2016-03-01

    We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes. PMID:26881296

  20. Detergentless microemulsions as media for enzymatic reactions. Cholesterol oxidation catalyzed by cholesterol oxidase.

    PubMed

    Khmelnitsky, Y L; Hilhorst, R; Veeger, C

    1988-09-15

    Catalytic activity and stability of cholesterol oxidase dissolved in ternary systems composed of n-hexane, isopropanol, and water were studied. The dependence of catalytic activity on the composition of the system revealed two maxima, in contrast to the behaviour of previously studied enzymes where a single maximum has been observed. The stability profile of cholesterol oxidase showed a single sharp maximum coinciding with the microemulsion region of the phase diagram. Both catalytic activity and the first-order inactivation rate constant of cholesterol oxidase dissolved in n-hexane/isopropanol/water ternary systems were found to decrease with decreasing temperature. This decrease was more rapid for the inactivation rate constant than for catalytic activity, the activation energies being 200 and 60 kJ.mol-1, respectively. Preparative conversion of cholesterol to cholestenone catalyzed by cholesterol oxidase in n-hexane/isopropanol/water ternary systems was carried out with 100% yield. Decreased temperature and the presence of catalase were required to achieve high degrees of cholesterol conversion. A simple procedure suitable for rapid separation of the reaction product and recovery of the enzyme was developed. PMID:3166425

  1. The reaction mechanism for dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica

    NASA Astrophysics Data System (ADS)

    Yao, Yuan; Li, Ze-Sheng

    2012-01-01

    The fundamental reaction mechanism for the dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica has been studied by density functional theory calculations. The results indicate that the dehydration process undergoes a two-step cis-elimination mechanism, which is different from the previously proposed one. The catalytic roles of both the highly conserved residue His143 and the Schiff base formed between the substrate and Lys170 have also been elucidated. The structural and mechanistic insight presented here may direct the design of type I dehydroquinate dehydratase enzyme inhibitors as non-toxic antimicrobials, anti-fungals, and herbicides.

  2. Identification and characterization of the two-enzyme system catalyzing oxidation of EDTA in the EDTA-degrading bacterial strain DSM 9103.

    PubMed Central

    Witschel, M; Nagel, S; Egli, T

    1997-01-01

    In a gram-negative isolate (DSM 9103) able to grow with EDTA as the sole source of carbon, nitrogen, and energy, the first two steps of the catabolic pathway for EDTA were elucidated. They consisted of the sequential oxidative removal of two acetyl groups, resulting in the formation of glyoxylate. An enzyme complex that catalyzes the removal of two acetyl groups was purified and characterized. In the reaction, ethylenediaminetriacetate (ED3A) was formed as an intermediate and N,N'-ethylenediaminediacetate was the end product. The enzyme complex consisted of two components: component A' (cA'), most likely a monooxygenase, which catalyzes the cleavage of EDTA and ED3A while consuming oxygen and reduced flavin mononucleotide (FMN)-H2, and component B' (cB'), an NADH2:FMN oxidoreductase that provides FMNH2 for cA'. cB' could be replaced by other NADH2:FMN oxidoreductases such as component B of the nitrilotriacetate monooxygenase or the NADH2:FMN oxidoreductase from Photobacterium fischeri. The EDTA-oxidizing enzyme complex accepted EDTA as a substrate only when it was complexed with Mg2+, Zn2+, Mn2+, Co2+, or Cu2+. Moreover, the enzyme complex catalyzed the removal of acetyl groups from several other aminopolycarboxylic acids that possess three or more acetyl groups. PMID:9371437

  3. Unusual Peroxide-Dependent, Heme-Transforming Reaction Catalyzed by HemQ.

    PubMed

    Celis, Arianna I; Streit, Bennett R; Moraski, Garrett C; Kant, Ravi; Lash, Timothy D; Lukat-Rodgers, Gudrun S; Rodgers, Kenton R; DuBois, Jennifer L

    2015-07-01

    A recently proposed pathway for heme b biosynthesis, common to diverse bacteria, has the conversion of two of the four propionates on coproheme III to vinyl groups as its final step. This reaction is catalyzed in a cofactor-independent, H2O2-dependent manner by the enzyme HemQ. Using the HemQ from Staphylococcus aureus (SaHemQ), the initial decarboxylation step was observed to rapidly and obligately yield the three-propionate harderoheme isomer III as the intermediate, while the slower second decarboxylation appeared to control the overall rate. Both synthetic harderoheme isomers III and IV reacted when bound to HemQ, the former more slowly than the latter. While H2O2 is the assumed biological oxidant, either H2O2 or peracetic acid yielded the same intermediates and products, though amounts significantly greater than the expected 2 equiv were required in both cases and peracetic acid reacted faster. The ability of peracetic acid to substitute for H2O2 suggests that, despite the lack of catalytic residues conventionally present in heme peroxidase active sites, reaction pathways involving high-valent iron intermediates cannot be ruled out. PMID:26083961

  4. Role of long-range protein dynamics in different thymidylate synthase catalyzed reactions.

    PubMed

    Abeysinghe, Thelma; Kohen, Amnon

    2015-01-01

    Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 away from the reaction site, plays a key role in the protein's dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-mono-phosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function. PMID:25837629

  5. Probing Nonadiabaticity in the Proton-Coupled Electron Transfer Reaction Catalyzed by Soybean Lipoxygenase

    PubMed Central

    2014-01-01

    Proton-coupled electron transfer (PCET) plays a vital role in many biological and chemical processes. PCET rate constant expressions are available for various well-defined regimes, and determining which expression is appropriate for a given system is essential for reliable modeling. Quantitative diagnostics have been devised to characterize the vibronic nonadiabaticity between the electronproton quantum subsystem and the classical nuclei, as well as the electronproton nonadiabaticity between the electrons and proton(s) within the quantum subsystem. Herein these diagnostics are applied to a model of the active site of the enzyme soybean lipoxygenase, which catalyzes a PCET reaction that exhibits unusually high deuterium kinetic isotope effects at room temperature. Both semiclassical and electronic charge density diagnostics illustrate vibronic and electronproton nonadiabaticity for this PCET reaction, supporting the use of the Golden rule nonadiabatic rate constant expression with a specific form of the vibronic coupling. This type of characterization will be useful for theoretical modeling of a broad range of PCET processes. PMID:25258676

  6. Role of Long-Range Protein Dynamics in Different Thymidylate Synthase Catalyzed Reactions

    PubMed Central

    Abeysinghe, Thelma; Kohen, Amnon

    2015-01-01

    Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 away from the reaction site, plays a key role in the proteins dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-monophosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function. PMID:25837629

  7. Platinum-catalyzed cross-dehydrogenative coupling reaction in the absence of oxidant.

    PubMed

    Shu, Xing-Zhong; Yang, Yan-Fang; Xia, Xiao-Feng; Ji, Ke-Gong; Liu, Xue-Yuan; Liang, Yong-Min

    2010-09-21

    A third strategy for cross-dehydrogenative coupling reaction has been reported via platinum-catalyzed sp(3) C-H and sp(3) C-H coupling reaction in the absence of oxidant. Nitroalkanes as well as dialkyl malonate derivatives, beta-keto esters and malononitrile are active participants in this coupling reaction. Both cyclic and acyclic non-activated simple ketones are good reactants in this reaction. PMID:20664883

  8. Cobalt-catalyzed hydrosilation/hydrogen-transfer cascade reaction: a new route to silyl enol ethers.

    PubMed

    Lyons, Thomas W; Brookhart, Maurice

    2013-07-29

    Capitalizing on cobalt: A new route to silyl enol ethers employing a Co-catalyzed cascade reaction featuring a tandem hydrosilation/hydrogen-transfer reaction is reported. The low catalyst loading, mild reaction conditions, and unique ?(2)-silane resting state showcase the impressive utility of this seldom used transition-metal catalyst in C-H activation reactions (see scheme; VTMS?=?vinyltrimethylsilane; Cp*? = ?1,2,3,4,5-pentamethylcyclopentadiene). PMID:23780615

  9. Metal-catalyzed decaborane-alkyne hydroboration reactions: efficient routes to alkenyldecaboranes.

    PubMed

    Chatterjee, Shahana; Carroll, Patrick J; Sneddon, Larry G

    2010-04-01

    Transition-metal-catalyzed decaborane-alkyne hydroboration reactions have been developed that provide high-yield routes to the previously unknown di- and monoalkenyldecaboranes. These alkenyl derivatives should be easily modified starting materials for many biomedical and/or materials applications. Unusual catalyst product selectivity was observed that suggests quite different mechanistic steps, with the reactions catalyzed by the [RuCl(2)(p-cymene)](2) and [Cp*IrCl(2)](2) complexes giving the beta-E alkenyldecaboranes and the corresponding reactions with the [RuI(2)(p-cymene)](2) complex giving the alpha-alkenyldecaborane isomers. PMID:20222715

  10. C1-symmetric aminosulfoximines in copper-catalyzed asymmetric vinylogous Mukaiyama aldol reactions.

    PubMed

    Frings, Marcus; Atodiresei, Iuliana; Wang, Yutian; Runsink, Jan; Raabe, Gerhard; Bolm, Carsten

    2010-04-19

    Vinylogous Mukaiyama-type aldol reactions have been catalyzed by a combination of Cu(OTf)2 and readily available C1-symmetric aminosulfoximines. After a fine-tuning of the reaction conditions and an optimization of the modularly assembled ligand structure, high stereoselectivities and excellent yields have been achieved in catalyzed reactions involving various electrophile/nucleophile combinations. The relative and absolute configurations of two products were assigned by X-ray single crystal structure analysis and a comparison of calculated and experimental CD spectra. PMID:20229533

  11. A sensitive surface-enhanced Raman scattering enzyme-catalyzed immunoassay of respiratory syncytial virus.

    PubMed

    Zhan, Lei; Zhen, Shu Jun; Wan, Xiao Yan; Gao, Peng Fei; Huang, Cheng Zhi

    2016-02-01

    Respiratory viruses have become a major global health challenge which would benefit from advances in screening methods for early diagnosis. Respiratory syncytial virus (RSV) is one of the most important pathogen causing severe lower respiratory tract infections. Here we present a novel surface-enhanced Raman scattering (SERS) enzyme-catalyzed immunoassay of RSV by employing peroxidase substrate 3, 3'-5, 5'-tetramethylbenzidine (TMB) as Raman molecule. Horseradish peroxidase (HRP) attached to the detection antibody in a novel sandwich immunoassay catalyzes the oxidation of TMB by H2O2 to give a radical cation (TMB(+)), which could be easily adsorbed on the negatively charged surface of silver nanoparticles (AgNPs) through electrostatic interaction, inducing the aggregation of AgNPs and thus giving a strong SERS signal. A linear relationship was obtained between the Raman intensity and the amount of RSV in the range from 0.5 to 20pg/mL, and the minimum detectable concentration of this SERS-based enzyme immunoassay was 0.05pg/mL, which was 20 times lower than that found in the colorimetric method. PMID:26653454

  12. A natural vanishing act: the enzyme-catalyzed degradation of carbon nanomaterials.

    PubMed

    Kotchey, Gregg P; Hasan, Saad A; Kapralov, Alexander A; Ha, Seung Han; Kim, Kang; Shvedova, Anna A; Kagan, Valerian E; Star, Alexander

    2012-10-16

    Over the past three decades, revolutionary research in nanotechnology by the scientific, medical, and engineering communities has yielded a treasure trove of discoveries with diverse applications that promise to benefit humanity. With their unique electronic and mechanical properties, carbon nanomaterials (CNMs) represent a prime example of the promise of nanotechnology with applications in areas that include electronics, fuel cells, composites, and nanomedicine. Because of toxicological issues associated with CNMs, however, their full commercial potential may not be achieved. The ex vitro, in vitro, and in vivo data presented in this Account provide fundamental insights into the biopersistence of CNMs, such as carbon nanotubes and graphene, and their oxidation/biodegradation processes as catalyzed by peroxidase enzymes. We also communicate our current understanding of the mechanism for the enzymatic oxidation and biodegradation. Finally, we outline potential future directions that could enhance our mechanistic understanding of the CNM oxidation and biodegradation and could yield benefits in terms of human health and environmental safety. The conclusions presented in this Account may catalyze a rational rethinking of CNM incorporation in diverse applications. For example, armed with an understanding of how and why CNMs undergo enzyme-catalyzed oxidation and biodegradation, researchers can tailor the structure of CNMs to either promote or inhibit these processes. In nanomedical applications such as drug delivery, the incorporation of carboxylate functional groups could facilitate biodegradation of the nanomaterial after delivery of the cargo. On the other hand, in the construction of aircraft, a CNM composite should be stable to oxidizing conditions in the environment. Therefore, pristine, inert CNMs would be ideal for this application. Finally, the incorporation of CNMs with defect sites in consumer goods could provide a facile mechanism that promotes the degradation of these materials once these products reach landfills. PMID:22824066

  13. A Natural Vanishing Act: The Enzyme-Catalyzed Degradation of Carbon Nanomaterials

    PubMed Central

    Kotchey, Gregg P.; Hasan, Saad A.; Kapralov, Alexander A.; Ha, Seung Han; Kim, Kang; Shvedova, Anna A.; Kagan, Valerian E.; Star, Alexander

    2012-01-01

    CONSPECTUS Over the past three decades, revolutionary research in nanotechnology by the scientific, medical, and engineering communities has yielded a treasure trove of discoveries with diverse applications that promise to benefit humanity. With their unique electronic and mechanical properties, carbon nanomaterials (CNMs) represent a prime example of the promise of nanotechnology with applications in areas that include electronics, fuel cells, composites, and nanomedicine. Because of toxicological issues associated with CNMs, however, their full commercial potential may not be achieved. The ex vitro, in vitro, and in vivo data presented in this Account provide fundamental insights into the biopersistence of CNMs, such as carbon nanotubes and graphene, and their oxidation/biodegradation processes as catalyzed by peroxidase enzymes. We also communicate our current understanding of the mechanism for the enzymatic oxidation/biodegradation. Finally, we outline potential future directions that could enhance our mechanistic understanding of the CNM oxidation/biodegradation and could yield benefits in terms of human health and environmental safety. The conclusions presented in this Account may catalyze a rational rethinking of CNM incorporation in diverse applications. For example, armed with an understanding of how and why CNMs undergo enzyme-catalyzed oxidation/biodegradation, researchers can tailor the structure of CNMs to either promote or inhibit these processes. In nanomedical applications such as drug delivery, the incorporation of carboxylate functional groups could facilitate biodegradation of the nanomaterial after delivery of the cargo. On the other hand, in the construction of aircraft, a CNM composite material should be stable to oxidizing conditions in the environment. Therefore, pristine, inert CNMs would be ideal for this application. Finally, the incorporation of CNMs with defect sites in consumer goods could provide a facile mechanism that promotes the degradation of these materials once these products reach landfills. PMID:22824066

  14. Nickel-Catalyzed Heck-Type Reactions of Benzyl Chlorides and Simple Olefins

    PubMed Central

    Matsubara, Ryosuke; Gutierrez, Alicia C.; Jamison, Timothy F.

    2011-01-01

    Nickel-catalyzed intermolecular benzylation and heterobenzylation of unactivated alkenes to provide functionalized allylbenzene derivatives is described. A wide range of both the benzyl chloride and alkene coupling partners are tolerated. In contrast to analogous palladium-catalyzed variants of this process, all reactions described herein employ electronically unbiased aliphatic olefins (including ethylene), proceed at room temperature and provide 1,1-disubstituted olefins over the more commonly observed 1,2-disubstituted olefins with very high selectivity. PMID:22066899

  15. Organophosphorus-catalyzed diaza-Wittig reaction: application to the synthesis of pyridazines.

    PubMed

    Bel Abed, Hassen; Mammoliti, Oscar; Bande, Omprakash; Van Lommen, Guy; Herdewijn, Piet

    2014-09-28

    The elaboration of the first organophosphorus-catalyzed diaza-Wittig reaction is reported. This catalytic reaction is applied to the synthesis of substituted pyridazine and phthalazine derivatives bearing electron-withdrawing groups with good to excellent yields from substrates containing a diazo functionality as the starting material and a phospholene oxide as the catalyst. PMID:25101802

  16. A deep cavitand catalyzes the Diels-Alder reaction of bound maleimides.

    PubMed

    Hooley, Richard J; Rebek, Julius

    2007-11-21

    A deep cavitand catalyzes Diels-Alder reactions of bound maleimides via activation of the dienophile by interaction with the organized hydrogen bonding network at the cavitand rim. Rapid in-out exchange of reactant and product allows efficient turnover. The increase in steric bulk of the reaction product lessens its binding affinity, reducing (and in some cases completely eliminating) product inhibition. PMID:17971992

  17. 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

  18. Copper-catalyzed arylation of biguanide derivatives via C-N cross-coupling reactions.

    PubMed

    Zhang, Chen; Huang, Bo; Bao, Ai-Qing; Li, Xiao; Guo, Shunna; Zhang, Jin-Quan; Xu, Jun-Zhi; Zhang, Rihao; Cui, Dong-Mei

    2015-12-21

    An efficient copper-catalyzed cross-coupling reaction of biguanide hydrochloride derivatives with both aryl iodides and bromides under mild conditions has been developed. The reaction occurred in good yields and tolerated aryl halides containing functionalities such as nitriles, sulfonamides, ethers, and halogens. Alkyl and cyclic substituted biguanidines were also well tolerated. PMID:26444146

  19. Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of "hunger hormone" ghrelin.

    PubMed

    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

  20. Enantioselective Robinson-type annulation reaction catalyzed by chiral phosphoric acids.

    PubMed

    Akiyama, Takahiko; Katoh, Takuya; Mori, Keiji

    2009-01-01

    Let's resolve our differences: Implementation of an enantioselective Michael addition followed by an intramolecular aldol reaction catalyzed by two phosphoric acids has enabled the synthesis of cyclohexenone derivatives with excellent enantioselectivities. Prominent kinetic resolution was observed in the latter reaction. Ar = aromatic group, X = H, halogen, Y = H, Me, halogen. PMID:19405071

  1. Computational Study of a Model System of Enzyme-Mediated [4+2] Cycloaddition Reaction

    PubMed Central

    2015-01-01

    A possible mechanistic pathway related to an enzyme-catalyzed [4+2] cycloaddition reac-tion was studied by theoretical calculations at density functional (B3LYP, O3LYP, M062X) and semiempirical levels (PM6-DH2, PM6) performed on a model system. The calculations were carried out for the key [4+2] cycloaddition step considering enzyme-catalyzed biosynthesis of Spinosyn A in a model reaction, where a reliable example of a biological Diels-Alder reaction was reported experimentally. In the present study it was demonstrated that the [4+2] cycloaddition reaction may benefit from moving along the energetically balanced reaction coordinate, which enabled the catalytic rate enhancement of the [4+2] cycloaddition pathway involving a single transition state. Modeling of such a system with coordination of three amino acids indicated a reliable decrease of activation energy by ~18.0 kcal/mol as compared to a non-catalytic transformation. PMID:25853669

  2. Stereochemical Course of the Reaction Catalyzed by RimO, a Radical SAM Methylthiotransferase.

    PubMed

    Landgraf, Bradley J; Booker, Squire J

    2016-03-01

    RimO is a member of the growing radical S-adenosylmethionine (SAM) superfamily of enzymes, which use a reduced [4Fe-4S] cluster to effect reductive cleavage of the 5' C-S bond of SAM to form a 5'-deoxyadenosyl 5'-radical (5'-dA(•)) intermediate. RimO uses this potent oxidant to catalyze the attachment of a methylthio group (-SCH3) to C3 of aspartate 89 of protein S12, one of 21 proteins that compose the 30S subunit of the bacterial ribosome. However, the exact mechanism by which this transformation takes place has remained elusive. Herein, we describe the stereochemical course of the RimO reaction. Using peptide mimics of the S12 protein bearing deuterium at the 3 pro-R or 3 pro-S positions of the target aspartyl residue, we show that RimO from Bacteroides thetaiotaomicron (Bt) catalyzes abstraction of the pro-S hydrogen atom, as evidenced by the transfer of deuterium into 5'-deoxyadenosine (5'-dAH). The observed kinetic isotope effect on H atom versus D atom abstraction is ∼1.9, suggesting that this step is at least partially rate determining. We also demonstrate that Bt RimO can utilize the flavodoxin/flavodoxin oxidoreductase/NADPH reducing system from Escherichia coli as a source of requisite electrons. Use of this in vivo reducing system decreases, but does not eliminate, formation of 5'-dAH in excess of methylthiolated product. PMID:26871608

  3. Biosynthesis of isoprenoids in Escherichia coli: stereochemistry of the reaction catalyzed by farnesyl diphosphate synthase.

    PubMed

    Leyes, A E; Baker, J A; Poulter, C D

    1999-10-01

    [formula: see text] Farnesyl diphosphate (FPP) synthase from Escherichia coli catalyzes the condensation of isopentenyl diphosphate (IPP) and geranyl diphosphate (GPP) with selective removal of the pro-R hydrogen at C2 of IPP, the same stereochemistry observed for the pig liver, yeast, and avian enzymes. PMID:10825960

  4. Advances in nickel-catalyzed cycloaddition reactions to construct carbocycles and heterocycles.

    PubMed

    Thakur, Ashish; Louie, Janis

    2015-08-18

    Transition-metal catalysis has revolutionized the field of organic synthesis by facilitating the construction of complex organic molecules in a highly efficient manner. Although these catalysts are typically based on precious metals, researchers have made great strides in discovering new base metal catalysts over the past decade. This Account describes our efforts in this area and details the development of versatile Ni complexes that catalyze a variety of cycloaddition reactions to afford interesting carbocycles and heterocycles. First, we describe our early work in investigating the efficacy of N-heterocyclic carbene (NHC) ligands in Ni-catalyzed cycloaddition reactions with carbon dioxide and isocyanate. The use of sterically hindered, electron donating NHC ligands in these reactions significantly improved the substrate scope as well as reaction conditions in the syntheses of a variety of pyrones and pyridones. The high reactivity and versatility of these unique Ni(NHC) catalytic systems allowed us to develop unprecedented Ni-catalyzed cycloadditions that were unexplored due to the inefficacy of early Ni catalysts to promote hetero-oxidative coupling steps. We describe the development and mechanistic analysis of Ni/NHC catalysts that couple diynes and nitriles to form pyridines. Kinetic studies and stoichiometric reactions confirmed a hetero-oxidative coupling pathway associated with this Ni-catalyzed cycloaddition. We then describe a series of new substrates for Ni-catalyzed cycloaddition reactions such as vinylcyclopropanes, aldehydes, ketones, tropones, 3-azetidinones, and 3-oxetanones. In reactions with vinycyclopropanes and tropones, DFT calculations reveal noteworthy mechanistic steps such as a C-C σ-bond activation and an 8π-insertion of vinylcyclopropane and tropone, respectively. Similarly, the cycloaddition of 3-azetidinones and 3-oxetanones also requires Ni-catalyzed C-C σ-bond activation to form N- and O-containing heterocycles. PMID:26200651

  5. Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: Horseradish peroxidase and dehaloperoxidase.

    PubMed

    Szatkowski, Lukasz; Thompson, Matthew K; Kaminski, Rafal; Franzen, Stefan; Dybala-Defratyka, Agnieszka

    2011-01-01

    The mechanism of the dehalogenation step catalyzed by dehaloperoxidase (DHP) from Amphitrite ornata, an unusual heme-containing protein with a globin fold and peroxidase activity, has remarkable similarity with that of the classical heme peroxidase, horseradish peroxidase (HRP). Based on quantum mechanical/molecular mechanical (QM/MM) modeling and experimentally determined chlorine kinetic isotope effects, we have concluded that two sequential one electron oxidations of the halogenated phenol substrate leads to a cationic intermediate that strongly resembles a Meisenheimer intermediate - a commonly formed reactive complex during nucleophilic aromatic substitution reactions especially in the case of arenes carrying electron withdrawing groups. PMID:20869943

  6. Computational determination of fundamental pathway and activation barriers for acetohydroxyacid synthase-catalyzed condensation reactions of alpha-keto acids.

    PubMed

    Xiong, Ying; Liu, Junjun; Yang, Guang-Fu; Zhan, Chang-Guo

    2010-06-01

    Acetohydroxyacid synthase (AHAS) is the first common enzyme in the biosynthetic pathway leading to the production of various branched-chain amino acids. AHAS is recognized as a promising target for new antituberculosis drugs, antibacterial drugs, and herbicides. Extensive first-principles quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have enabled us, in this study, to uncover the fundamental reaction pathway, determine the activation barriers, and obtain valuable insights concerning the specific roles of key amino acid residues for the common steps of AHAS-catalyzed condensation reactions of alpha-keto acids. The computational results reveal that the rate-determining step of the AHAS-catalyzed reactions is the second reaction step and that the most important amino acid residues involved in the catalysis include Glu144', Gln207', Gly121', and Gly511 that form favorable hydrogen bonds with the reaction center (consisting of atoms from the substrate and cofactor) during the reaction process. In addition, Glu144' also accepts a proton from cofactor thiamin diphosphate (ThDP) through hydrogen bonding during the catalytic reaction. The favorable interactions between the reaction center and protein environment remarkably stabilize the transition state and, thus, lower the activation barrier for the rate-determining reaction step by approximately 20 kcal/mol. The activation barrier calculated for the rate-determining step is in good agreement with the experimental activation barrier. The detailed structural and mechanistic insights should be valuable for rational design of novel, potent AHAS inhibitors that may be used as promising new anti-tuberculosis drugs, antibacterial drugs, and/or herbicides to overcome drug resistance problem. PMID:19554557

  7. Iridium and ruthenium catalyzed syntheses, hydroborations, and metathesis reactions of alkenyl-decaboranes.

    PubMed

    Chatterjee, Shahana; Carroll, Patrick J; Sneddon, Larry G

    2013-08-01

    The selective syntheses of new classes of 6,9-dialkenyl- and 6-alkenyl-decaboranes and 6-alkyl-9-alkenyl-decaboranes have been achieved via iridium and ruthenium catalyzed decaborane and 6-alkyl-decaborane alkyne-hydroborations. Reactions employing [Cp*IrCl2]2 and [RuCl2(p-cymene)]2 precatalysts gave ?-E-alkenyl-decaboranes, while the corresponding reactions with [RuI2(p-cymene)]2 gave the ?-alkenyl-decaborane isomers, with the differences in product selectivity suggesting quite different mechanistic steps for the catalysts. The alkenyl-decaboranes were easily converted to other useful derivatives, including coupled-cage and functionally substituted compounds, via iridium-catalyzed hydroborations and ruthenium-catalyzed homo and cross olefin-metathesis reactions. PMID:23859100

  8. 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.

  9. Theoretical mechanistic study of the TBD-catalyzed intramolecular aldol reaction of ketoaldehydes.

    PubMed

    Hammar, Peter; Ghobril, Cynthia; Antheaume, Cyril; Wagner, Alain; Baati, Rachid; Himo, Fahmi

    2010-07-16

    The intramolecular aldol reaction of acyclic ketoaldehydes catalyzed by 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) is investigated using density functional theory calculations. Compared to the proline-catalyzed aldol reaction, the use of TBD provides a unique and unusual complete switch of product selectivity. Three mechanistic pathways are proposed and evaluated. The calculations provide new insights into the activation mode of bifunctional guanidine catalysts. In the favored mechanism, TBD first catalyzes the enolization of the substrate and then the C-C bond formation through two concerted proton transfers. In addition, the computationally predicted stereochemical outcome of the reaction is in agreement with the experimental findings. PMID:20545376

  10. The Radical S-Adenosyl-L-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds.

    PubMed

    Nakai, Tadashi; Ito, Hiroto; Kobayashi, Kazuo; Takahashi, Yasuhiro; Hori, Hiroshi; Tsubaki, Motonari; Tanizawa, Katsuyuki; Okajima, Toshihide

    2015-04-24

    The bacterial enzyme designated QhpD belongs to the radical S-adenosyl-L-methionine (SAM) superfamily of enzymes and participates in the post-translational processing of quinohemoprotein amine dehydrogenase. QhpD is essential for the formation of intra-protein thioether bonds within the small subunit (maturated QhpC) of quinohemoprotein amine dehydrogenase. We overproduced QhpD from Paracoccus denitrificans as a stable complex with its substrate QhpC, carrying the 28-residue leader peptide that is essential for the complex formation. Absorption and electron paramagnetic resonance spectra together with the analyses of iron and sulfur contents suggested the presence of multiple (likely three) [4Fe-4S] clusters in the purified and reconstituted QhpD. In the presence of a reducing agent (sodium dithionite), QhpD catalyzed the multiple-turnover reaction of reductive cleavage of SAM into methionine and 5'-deoxyadenosine and also the single-turnover reaction of intra-protein sulfur-to-methylene carbon thioether bond formation in QhpC bound to QhpD, producing a multiknotted structure of the polypeptide chain. Homology modeling and mutagenic analysis revealed several conserved residues indispensable for both in vivo and in vitro activities of QhpD. Our findings uncover another challenging reaction catalyzed by a radical SAM enzyme acting on a ribosomally translated protein substrate. PMID:25778402

  11. In-situ nanoelectrospray for high-throughput screening of enzymes and real-time monitoring of reactions.

    PubMed

    Yang, Yuhan; Han, Feifei; Ouyang, Jin; Zhao, Yunling; Han, Juan; Na, Na

    2016-01-01

    The in-situ and high-throughput evaluation of enzymes and real-time monitoring of enzyme catalyzed reactions in liquid phase is quite significant in the catalysis industry. In-situ nanoelectrospray, the direct sampling and ionization method for mass spectrometry, has been applied for high-throughput evaluation of enzymes, as well as the on-line monitoring of reactions. Simply inserting a capillary into a liquid system with high-voltage applied, analytes in liquid reaction system can be directly ionized at the capillary tip with small volume consumption. With no sample pre-treatment or injection procedure, different analytes such as saccharides, amino acids, alkaloids, peptides and proteins can be rapidly and directly extracted from liquid phase and ionized at the capillary tip. Taking irreversible transesterification reaction of vinyl acetate and ethanol as an example, this technique has been used for the high-throughput evaluation of enzymes, fast optimizations, as well as real-time monitoring of reaction catalyzed by different enzymes. In addition, it is even softer than traditional electrospray ionization. The present method can also be used for the monitoring of other homogenous and heterogeneous reactions in liquid phases, which will show potentials in the catalysis industry. PMID:26703263

  12. The methylthiolation reaction mediated by the Radical-SAM enzymes.

    PubMed

    Atta, Mohamed; Arragain, Simon; Fontecave, Marc; Mulliez, Etienne; Hunt, John F; Luff, Jon D; Forouhar, Farhad

    2012-11-01

    Over the past 10 years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. PMID:22178611

  13. Copper(I)-Catalyzed Interrupted Click Reaction: Synthesis of Diverse 5-Hetero-Functionalized Triazoles.

    PubMed

    Wang, Weiguo; Peng, Xianglong; Wei, Fang; Tung, Chen-Ho; Xu, Zhenghu

    2016-01-11

    The 5-heterofunctionalized triazoles are important scaffolds in bioactive compounds, but current click reactions (CuAAC) cannot produce these core structures. A copper(I)-catalyzed interrupted click reaction to access diverse 5-functionalized triazoles is reported. Various 5-amino-, thio-, and selenotriazoles were readily assembled in one step in high yields. The reaction proceeds under mild conditions with complete regioselectivity. It also features a broad substrate scope and good functional group compatibility. PMID:26610884

  14. Ultrasound assisted lipase catalyzed synthesis of cinnamyl acetate via transesterification reaction in a solvent free medium.

    PubMed

    Tomke, Prerana D; Rathod, Virendra K

    2015-11-01

    Cinnamyl acetate is known for its use as flavor and fragrance material in different industries such as food, pharmaceutical, cosmetic etc. This work focuses on ultrasound assisted lipase (Novozym 435) catalyzed synthesis of cinnamyl acetate via transesterification of cinnamyl alcohol and vinyl acetate in non-aqueous, solvent free system. Optimization of various parameters shows that a higher yield of 99.99% can be obtained at cinnamyl alcohol to vinyl acetate ratio of 1:2 with 0.2% of catalyst, at 40C and 150 rpm, with lower ultrasound power input of 50 W (Ultrasound intensity 0.81 W/cm(2)), at 25 kHz frequency, 50% duty cycle. Further, the time required for the maximum conversion is reduced to 20 min as compared to 60 min of conventional process. Similarly, the enzyme can be successfully reused seven times without loss of enzyme activity. Thus, ultrasound helps to enhance the enzyme catalyzed synthesis of flavors. PMID:26186841

  15. Relationship between femtosecond-picosecond dynamics to enzyme catalyzed H-transfer

    PubMed Central

    Cheatum, Christopher M.; Kohen, Amnon

    2015-01-01

    At physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. These conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. Many of these motions have been examined and their role in the enzyme function illuminated, yet most experimental tools applied so far have identified dynamics at time scales of seconds to nanoseconds, which are much slower than the time scale for H-transfer between two heavy atoms. This chemical conversion and other processes involving cleavage of covalent bonds occur on picosecond to femtosecond time scales, where slower processes mask both the kinetics and dynamics. Here we present a combination of kinetic and spectroscopic methods that may enable closer examination of the relationship between enzymatic C-H→C transfer and the dynamics of the active site environment at the chemically relevant time scale. These methods include kinetic isotope effects and their temperature dependence, which are used to study the kinetic nature of the H-transfer, and 2D IR spectroscopy, which is used to study the dynamics of transition-state- and ground-state-analog complexes. The combination of these tools is likely to provide a new approach to examine the protein dynamics that directly influence the chemical conversion catalyzed by enzymes. PMID:23539379

  16. Synthesis of Programmable Reaction-Diffusion Fronts Using DNA Catalyzers

    NASA Astrophysics Data System (ADS)

    Zadorin, Anton S.; Rondelez, Yannick; Galas, Jean-Christophe; Estevez-Torres, André

    2015-02-01

    We introduce a DNA-based reaction-diffusion (RD) system in which reaction and diffusion terms can be precisely and independently controlled. The effective diffusion coefficient of an individual reaction component, as we demonstrate on a traveling wave, can be reduced up to 2.7-fold using a self-assembled hydrodynamic drag. The intrinsic programmability of this RD system allows us to engineer, for the first time, orthogonal autocatalysts that counterpropagate with minimal interaction. Our results are in excellent quantitative agreement with predictions of the Fisher-Kolmogorov-Petrovskii-Piscunov model. These advances open the way for the rational engineering of pattern formation in pure chemical RD systems.

  17. CYP4F Enzymes Are the Major Enzymes in Human Liver Microsomes That Catalyze the O-Demethylation of the Antiparasitic Prodrug DB289 [2,5-Bis(4-amidinophenyl)furan-bis-O-methylamidoxime

    PubMed Central

    Wang, Michael Zhuo; Saulter, Janelle Y.; Usuki, Etsuko; Cheung, Yen-Ling; Hall, Michael; Bridges, Arlene S.; Loewen, Greg; Parkinson, Oliver T.; Stephens, Chad E.; Allen, James L.; Zeldin, Darryl C.; Boykin, David W.; Tidwell, Richard R.; Parkinson, Andrew; Paine, Mary F.; Hall, James Edwin

    2007-01-01

    DB289 [2,5-bis(4-amidinophenyl)furan-bis-O-methylamidoxime] is biotransformed to the potent antiparasitic diamidine DB75 [2,5-bis(4-amidinophenyl) furan] by sequential oxidative O-demethylation and reductive N-dehydroxylation reactions. Previous work demonstrated that the N-dehydroxylation reactions are catalyzed by cytochrome b5/NADH-cytochrome b5 reductase. Enzymes responsible for catalyzing the DB289 O-demethylation pathway have not been identified. We report an in vitro metabolism study to characterize enzymes in human liver microsomes (HLMs) that catalyze the initial O-demethylation of DB289 (M1 formation). Potent inhibition by 1-aminobenzotriazole confirmed that M1 formation is catalyzed by P450 enzymes. M1 formation by HLMs was NADPH-dependent, with a Km and Vmax of 0.5 ?M and 3.8 nmol/min/mg protein, respectively. Initial screening showed that recombinant CYP1A1, CYP1A2, and CYP1B1 were efficient catalysts of M1 formation. However, none of these three enzymes was responsible for M1 formation by HLMs. Further screening showed that recombinant CYP2J2, CYP4F2, and CYP4F3B could also catalyze M1 formation. An antibody against CYP4F2, which inhibited both CYP4F2 and CYP4F3B, inhibited 91% of M1 formation by HLMs. Two inhibitors of P450-mediated arachidonic acid metabolism, HET0016 (N-hydroxy-N?-(4-n-butyl-2-methylphenyl)formamidine) and 17-octadecynoic acid, effectively inhibited M1 formation by HLMs. Inhibition studies with ebastine and antibodies against CYP2J2 suggested that CYP2J2 was not involved in M1 formation by HLMs. Additionally, ketoconazole preferentially inhibited CYP4F2, but not CYP4F3B, and partially inhibited M1 formation by HLMs. We conclude that CYP4F enzymes (e.g., CYP4F2, CYP4F3B) are the major enzymes responsible for M1 formation by HLMs. These findings indicate that, in human liver, members of the CYP4F subfamily biotransform not only endogenous compounds but also xenobiotics. PMID:16997912

  18. Phospholipids chiral at phosphorus. Steric course of the reactions catalyzed by phosphatidylserine synthase from Escherichia coli and yeast

    SciTech Connect

    Raetz, C.R.H.; Carman, G.M.; Dowhan, W.; Jiang, R.T.; Waszkuc, W.; Loffredo, W.; Tsai, M.D.

    1987-06-30

    The steric courses of the reactions catalyzed by phosphatidylserine (PS) synthase from Escherichia coli and yeast were elucidated by the following procedure. R/sub P/ and S/sub P/ isomers of 1,2-dipalmitoyl-sn-glycero-3-(/sup 17/O, /sup 18/O)phosphoethanolamine ((/sup 17/O, /sup 18/O)DPPE) were synthesized and converted to (R/sub P/)- and (S/sub P/)-1,2-dipalmitoyl-sn-glycero-3-(/sup 16/O, /sup 17/O, /sup 18/O)DPPA), respectively, by incubating with phospholipase D. Condensation of (/sup 16/O, /sup 17/O, /sup 18/O)DPPA with cytidine 5'-monophosphomorpholidate in pyridine gave the desired substrate for PS synthase, (/sup 17/O, /sup 18/O)cytidine 5'-diphospho-1,2-dipalmitoyl-sn-glycerol ((/sup 17/O,/sup 18/O)CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of (/sup 17/O, /sup 18/O)CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of (/sup 17/O, /sup 18/O) CDP-DPG with a mixture of L-serine, PS synthase and PS decarboxylase gave (/sup 17/O, /sup 18/O)DPPE. The configuration and isotopic enrichments of the starting (/sup 17/O, /sup 18/O)DPPE and the product were analyzed by /sup 31/P NMR following trimethylsilylation of the DPPE. The results indicate that the reaction of E. coli PS synthase proceeds with retention of configuration at phosphorus, which suggests a two-step mechanism involving a phosphatidyl-enzyme intermediate, while the yeast PS synthase catalyzes the reaction with inversion of configuration, which suggests a single-displacement mechanism. Such results lend strong support to the ping-pong mechanism proposed for the E. coli enzyme and the sequential Bi-Bi mechanism proposed for the yeast enzyme, both based on previous isotopic exchange experiments.

  19. Effects of the donor acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction

    PubMed Central

    Stojkovi?, Vanja; Perissinotti, Laura L.; Willmer, Daniel; Benkovic, Stephen J.

    2015-01-01

    A significant contemporary question in enzymology involves the role of protein dynamics and hydrogen tunneling in enhancing enzyme catalyzed reactions. Here, we report a correlation between the donor-acceptor distance (DAD) distribution and intrinsic kinetic isotope effects (KIEs) for the dihydrofolate reductase (DHFR) catalyzed reaction. This study compares the nature of the hydride transfer step for a series of active-site mutants, where the size of a side chain that modulates the DAD (I14 in E. coli DHFR) is systematically reduced (I14V, I14A, and I14G). The contributions of the DAD and its dynamics to the hydride transfer step were examined by the temperature dependence of intrinsic KIEs, hydride transfer rates, activation parameters, and classical molecular dynamics (MD) simulations. Results are interpreted within the framework of the Marcus-like model where the increase in the temperature dependence of KIEs arises as a direct consequence of the deviation of the DAD from its distribution in the wild type enzyme. Classical MD simulations suggest new populations with larger average DADs, as well as broader distributions, and a reduction in the population of the reactive conformers correlated with the decrease in the size of the hydrophobic residue. The more flexible active site in the mutants required more substantial thermally activated motions for effective H-tunneling, consistent with the hypothesis that the role of the hydrophobic side chain of I14 is to restrict the distribution and dynamics of the DAD and thus assist the hydride transfer. These studies establish relationships between the distribution of DADs, the hydride-transfer rates, and the DADs rearrangement toward tunneling-ready states. This structure-function correlation shall assist in the interpretation of the temperature dependence of KIEs caused by mutants far from the active site in this and other enzymes, and may apply generally to C-H?C transfer reactions. PMID:22171795

  20. Graphene cover-promoted metal-catalyzed reactions

    PubMed Central

    Yao, Yunxi; Fu, Qiang; Zhang, Y. Y.; Weng, Xuefei; Li, Huan; Chen, Mingshu; Jin, Li; Dong, Aiyi; Mu, Rentao; Jiang, Peng; Liu, Li; Bluhm, Hendrik; Liu, Zhi; Zhang, S. B.; Bao, Xinhe

    2014-01-01

    Graphitic overlayers on metals have commonly been considered as inhibitors for surface reactions due to their chemical inertness and physical blockage of surface active sites. In this work, however, we find that surface reactions, for instance, CO adsorption/desorption and CO oxidation, can take place on Pt(111) surface covered by monolayer graphene sheets. Surface science measurements combined with density functional calculations show that the graphene overlayer weakens the strong interaction between CO and Pt and, consequently, facilitates the CO oxidation with lower apparent activation energy. These results suggest that interfaces between graphitic overlayers and metal surfaces act as 2D confined nanoreactors, in which catalytic reactions are promoted. The finding contrasts with the conventional knowledge that graphitic carbon poisons a catalyst surface but opens up an avenue to enhance catalytic performance through coating of metal catalysts with controlled graphitic covers. PMID:25404332

  1. Graphene cover-promoted metal-catalyzed reactions.

    PubMed

    Yao, Yunxi; Fu, Qiang; Zhang, Y Y; Weng, Xuefei; Li, Huan; Chen, Mingshu; Jin, Li; Dong, Aiyi; Mu, Rentao; Jiang, Peng; Liu, Li; Bluhm, Hendrik; Liu, Zhi; Zhang, S B; Bao, Xinhe

    2014-12-01

    Graphitic overlayers on metals have commonly been considered as inhibitors for surface reactions due to their chemical inertness and physical blockage of surface active sites. In this work, however, we find that surface reactions, for instance, CO adsorption/desorption and CO oxidation, can take place on Pt(111) surface covered by monolayer graphene sheets. Surface science measurements combined with density functional calculations show that the graphene overlayer weakens the strong interaction between CO and Pt and, consequently, facilitates the CO oxidation with lower apparent activation energy. These results suggest that interfaces between graphitic overlayers and metal surfaces act as 2D confined nanoreactors, in which catalytic reactions are promoted. The finding contrasts with the conventional knowledge that graphitic carbon poisons a catalyst surface but opens up an avenue to enhance catalytic performance through coating of metal catalysts with controlled graphitic covers. PMID:25404332

  2. Eutectic Salt Catalyzed Environmentally Benign and Highly Efficient Biginelli Reaction

    PubMed Central

    Azizi, Najmadin; Dezfuli, Sahar; Hahsemi, Mohmmad Mahmoodi

    2012-01-01

    A simple deep eutectic solvent based on tin (II) chloride was used as a dual catalyst and environmentally benign reaction medium for an efficient synthesis of 3,4-dihydropyrimidin-2(1H)-one derivatives, from aromatic and aliphatic aldehydes, 1,3-dicarbonyl compounds, and urea in good-to-excellent yields and short reaction time. This simple ammonium deep eutectic solvent, easily synthesized from choline chloride and tin chloride, is relatively inexpensive and recyclable, making it applicable for industrial applications. PMID:22649326

  3. NAD deamidation "a new reaction" by an enzyme from Aspergillus terreus DSM 826.

    PubMed

    Elzainy, Tahany A; Ali, Thanaa H

    2005-02-01

    NAD deamidation is a non-previously recognized reaction. This reaction has been found to be catalyzed by extracts of Aspergillus terreus DSM 826. Conversion of NAD to the biosynthetic intermediate, deamido NAD, by these extracts, at the optimum pH and temperature did not exceed about 55 of the amount of the substrate added. Completion of the reaction was achieved when the extracts were pre-heated at 50 degrees C for 15 min in absence of the substrate. In a very similar manner, the extracts catalyzed hydrolytic cleavage of the amide linkages of different biomolecules such as nicotinamide, nicotinamide riboside, nicotinamide mononucleotide, L-glutamine, L-asparagine and acetamide. Polyacrylamide was also deamidated under the same conditions. In addition, complete dephosphorylation of the dinucleotide molecule was also effected by the same extracts. Separation of the NAD deamidating enzyme from the NAD dephosphorylating enzyme was achieved on using either DEAE - Sephadex A-25 or Sephadex G-200 column chromatography. The obtained phosphohydrolase-free-deamidase showed optimum activity at pH 8 of 0.1 M phosphate buffer and 50 degrees C. It exhibited broad substrate specificity and hyperbolic substrate saturation kinetics. It was isosterically inhibited by the product of its activity and this inhibition was prevented by heating the extracts at 50 degrees C for 15 min. Its activity was not affected in presence of sodium fluoride, partially inhibited in presence of magnesium chloride and was retained in the freezer for some months. PMID:15793621

  4. Ultrasound assisted enzyme catalyzed transesterification of waste cooking oil with dimethyl carbonate.

    PubMed

    Gharat, Nikhil; Rathod, Virendra K

    2013-05-01

    This work reports the production of biodiesel with waste cooking oil and dimethyl carbonate in solvent free system through transesterification by immobilized enzyme (Novozym 435) under the influence of ultrasound irradiation. The experiments were conducted in an ultrasonic water bath under three different conditions i.e. ultrasonic irradiation (UI) without stirring, UI coupled with stirring and only stirring to compare their overall effects on fatty acid methyl esters (FAME) conversion. As compared with the conventional stirring method, where FAME conversion was 38.69% at 4h, the UI without stirring significantly enhanced the conversion of enzymatic transesterification to 57.68% for the same reaction time. However the reaction rate was further increased under the condition of ultrasonication coupled with stirring and resulted into higher conversion of 86.61% for the same reaction time. Effects of reaction parameters, such as temperature, ratio of DMC/oil, speed of agitation and enzyme loading on the conversion were investigated. Furthermore, repeated use of Novozym 435 showed gradual decline in both conversion as well as enzyme activity. PMID:23178034

  5. The methylthiolation reaction mediated by the Radical-SAM enzymes

    PubMed Central

    Atta, Mohamed; Arragain, Simon; Fontecave, Marc; Mulliez, Etienne; Hunt, John F.; Luff, Jon D.; Forouhar, Farhad

    2014-01-01

    Over the past ten years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. PMID:22178611

  6. Textured catalysts, methods of making textured catalysts, and methods of catalyzing reactions conducted in hydrothermal conditions

    DOEpatents

    Werpy, Todd [West Richland, WA; Wang, Yong [Richland, WA

    2003-12-30

    A textured catalyst having a hydrothermally-stable support, a metal oxide and a catalyst component is described. Methods of conducting aqueous phase reactions that are catalyzed by a textured catalyst are also described. The invention also provides methods of making textured catalysts and methods of making chemical products using a textured catalyst.

  7. Synthesis of Terminal Allenes via a Copper-Catalyzed Decarboxylative Coupling Reaction of Alkynyl Carboxylic Acids.

    PubMed

    Lim, Jeongah; Choi, Jinseop; Kim, Han-Sung; Kim, In Seon; Nam, Kye Chun; Kim, Jimin; Lee, Sunwoo

    2016-01-01

    Synthesis of terminal allenes via a copper-catalyzed decarboxylative coupling reaction was developed. Aryl alkynyl carboxylic acid, paraformaldehyde, and dicyclohexylamine were reacted with CuI (20 mol %) in diglyme at 100 C for 2 h to produce the terminal allene in moderate to good yields. The method showed good functional group tolerance. PMID:26618610

  8. Influence of an internal trifluoromethyl group on the rhodium(II)-catalyzed reactions of vinyldiazocarbonyl compounds.

    PubMed

    Nikolaev, Valerij A; Supurgibekov, Murat B; Davies, Huw M L; Sieler, Joachim; Zakharova, Valerija M

    2013-05-01

    Incorporation of a trifluoromethyl group into the structure of 4-(alkoxycarbonyl)vinyldiazocarbonyl compounds greatly decreases the tendency of the carbenoid intermediates formed during Rh(II)-catalyzed reactions to undergo intermolecular processes. Instead, they are prone to experience intramolecular [1,5]- and [1,3]-electrocyclizations to produce reactive cyclopropenes and furans, and these are capable of further transformations. PMID:23614681

  9. Copper-catalyzed domino coupling reaction: an efficient method to synthesize oxindoles.

    PubMed

    Hsieh, Jen-Chieh; Cheng, An-Yi; Fu, Jun-Hao; Kang, Ting-Wei

    2012-08-21

    An efficient and novel procedure for a copper catalyzed domino coupling reaction has been developed, which afforded various oxindoles in good to excellent yields with tolerance of various substituents. In addition, this method could be applied to synthesize horsfiline and coerulescine in few steps with high total yields. PMID:22735645

  10. Acid-catalyzed heterogeneous reaction of 3-methyl-2-buten-1-ol with hydrogen peroxide.

    PubMed

    Liu, Qifan; Wang, Weigang; Ge, Maofa

    2015-05-01

    Acid-catalyzed heterogeneous oxidation with hydrogen peroxide (H2O2) has been suggested to be a potential pathway for secondary organic aerosol (SOA) formation from isoprene and its oxidation products. However, knowledge of the chemical mechanism and kinetics for this process is still incomplete. 3-Methyl-2-buten-1-ol (MBO321), an aliphatic alcohol structurally similar to isoprene, is emitted by pine forests and widely used in the manufacturing industries. Herein the uptake of MBO321 into H2SO4-H2O2 mixed solution was investigated using a flow-tube reactor coupled to a mass spectrometer. The reactive uptake coefficients (?) were acquired for the first time and were found to increase rapidly with increasing acid concentration. Corresponding aqueous-phase reactions were performed to further study the mechanism of this acid-catalyzed reaction. MBO321 could convert to 2-methyl-3-buten-2-ol (MBO232) and yield isoprene in acidic media. Organic hydroperoxides (ROOHs) were found to be generated through the acid-catalyzed route, which could undergo a rearrangement reaction and result in the formation of acetone and acetaldehyde. Organosulfates, which have been proposed to be SOA tracer compounds in the atmosphere, were also produced during the oxidation process. These results suggest that the heterogeneous acid-catalyzed reaction of MBO321 with H2O2 may contribute to SOA mass under certain atmospheric conditions. PMID:25968263

  11. Recent Developments in Pd-Catalyzed Alkene Aminoarylation Reactions for the Synthesis of Nitrogen Heterocycles

    PubMed Central

    Schultz, Danielle M.; Wolfe, John P.

    2012-01-01

    This short review describes new developments in Pd-catalyzed aminoarylation reactions between aryl halides and alkenes bearing pendant nitrogen nucleophiles. These transformations provide a novel and powerful method for accessing numerous 3-, 5-, 6-, and 7-membered nitrogen heterocycles. PMID:23243321

  12. Reaction mechanism of epoxide cycloaddition to CO₂ catalyzed by salen-M (M = Co, Al, Zn).

    PubMed

    Wang, Ting-Ting; Xie, Yong; Deng, Wei-Qiao

    2014-10-01

    We propose a catalytic mechanism for the cycloaddition of epoxide to carbon dioxide catalyzed by salen-M (M = Co, Zn, Al) based on density functional theory calculations. The catalytic reaction follows a single-site mechanism rather than a bimetallic-site mechanism, which includes four steps: epoxide adsorption by salen-M, ring opening of epoxide, CO2 insertion, and intramolecular rearrangement. Our calculation results showed that the highest reaction barrier for salen-Co catalyst is only 9.94 kcal/mol, which is lower than that of salen-Al (14.38 kcal/mol) and salen-Zn (13.05 kcal/mol). The results indicate that the reaction catalyzed by salen-Al, salen-Co, or salen-Zn can occur at room temperature and atmospheric pressure, which is in agreement with experimental results. The mechanism can be used for the design of a novel catalyst for this reaction. PMID:25046346

  13. Palladium-catalyzed coupling reaction of allylic diols and cyclic carbonates

    SciTech Connect

    Suk-Ku Kang; Kyung-Yun Jung; Su-Bum Jang

    1995-12-31

    Pd-catalyzed reaction of organic halides with alkene(Heck-type reaction) is known to be a very convenient method for carbon-carbon bond formation at vinylic positions. Here, the authors report arylation and vinylation of allylic cyclic carbonates and allylic diols. Palladium-catalyzed arylation of allylic cyclic carbonates with iodobenzene afforded phenylsubstituted allylic alcohols via ring opening. However, arylation without ring opening was achieved with diphenyliodonium tetrafluoroborate. The coupling reaction of iodobenzene with allylic diols in the presence of Pd(OAc){sub 2} and nBu{sub 3}P as catalysts afforded the phenyl-substituted allylic diols or phenyl-substituted {alpha}-hydroxy ketones depending on bases used. The mechanism will be discussed. The coupling reaction of hypervalent iodonium salts instead of aryl or vinyl iodide with allylic alcohols provided {beta}-substituted allylic alcohols.

  14. Enantioselective Henry (nitroaldol) reaction catalyzed by axially chiral guanidines.

    PubMed

    Ube, Hitoshi; Terada, Masahiro

    2009-07-15

    The enantioselective activation of nitroalkanes was attempted on the basis of the complexation between chiral guanidinium and nitronate through two hydrogen bonds. The proposed enantioselective activation was applied to the diastereo- and enantioselective Henry (nitroaldol) reaction of nitroalkanes with aldehydes using axially chiral guanidine bases as the catalyst. Optically active nitroaldol products were obtained in acceptable yields with fairly good enantio- and diastereoselectivities at low temperature. PMID:19375310

  15. Recyclable polystyrene-supported siloxane-transfer agent for palladium-catalyzed cross-coupling reactions.

    PubMed

    Nguyen, Minh H; Smith, Amos B

    2014-04-01

    The rational design, synthesis, and validation of a significantly improved insoluble polymer-supported siloxane-transfer agent has been achieved that permits efficient palladium-catalyzed cross-coupling reactions. The cross-linked polystyrene support facilitates product purification with excellent siloxane recycling. Drawbacks of a previous polymer-supported siloxane-transfer agent, relating to reaction efficiency and polymer stability after repeated cycles, have been addressed. PMID:24661113

  16. Copper(I)-catalyzed multicomponent reaction providing a new access to fully substituted thiophene derivatives.

    PubMed

    Jiang, Bo; Tu, Xing-Jun; Wang, Xue; Tu, Shu-Jiang; Li, Guigen

    2014-07-18

    Readily available triethylammonium 1-(2-oxoindolin-3-ylidene)-2-aroylethanethiolates are efficiently converted into a variety of fully substituted thiophene derivatives by copper(I)-catalyzed denitrogenative reactions with terminal alkynes and N-sulfonyl azides. This new reaction simultaneously installs C-N, C-S, and C-C bonds, allowing direct formation of highly functionalized thiophenes with a wide diversity in substituents in a one-pot manner. A plausible mechanism for the domino process is proposed. PMID:24988049

  17. Copper(I)-Catalyzed Multicomponent Reaction Providing a New Access to Fully Substituted Thiophene Derivatives

    PubMed Central

    2015-01-01

    Readily available triethylammonium 1-(2-oxoindolin-3-ylidene)-2-aroylethanethiolates are efficiently converted into a variety of fully substituted thiophene derivatives by copper(I)-catalyzed denitrogenative reactions with terminal alkynes and N-sulfonyl azides. This new reaction simultaneously installs CN, CS, and CC bonds, allowing direct formation of highly functionalized thiophenes with a wide diversity in substituents in a one-pot manner. A plausible mechanism for the domino process is proposed. PMID:24988049

  18. Copper-Catalyzed Reaction of Trifluoromethylketones with Aldehydes via a Copper Difluoroenolate.

    PubMed

    Doi, Ryohei; Ohashi, Masato; Ogoshi, Sensuke

    2016-01-01

    A copper-catalyzed reaction of easily accessible ?,?,?-trifluoromethylketones with various aldehydes affords difluoro-methylene compounds in the presence of diboron and NaOtBu. The key process of the reaction is the formation of a copper difluoroenolate by 1,2-addition of a borylcopper intermediate to ?,?,?-trifluoromethylketones and subsequent ?-fluoride elimination. Mechanistic studies including the isolation and characterization of a possible anionic copper alkoxide intermediate are also described. PMID:26514445

  19. Experimental and theoretical methods in kinetic studies of heterogeneously catalyzed reactions.

    PubMed

    Reyniers, Marie-Franoise; Marin, Guy B

    2014-01-01

    This review aims to illustrate the potential of kinetic analysis in general and microkinetic modeling in particular for rational catalyst design. Both ab initio calculations and experiments providing intrinsic kinetic data allow us to assess the effects of catalytic properties and reaction conditions on the activity and selectivity of the targeted reactions. Three complementary approaches for kinetic analysis of complex reaction networks are illustrated, using select examples of acid zeolite-catalyzed reactions from the authors' recent work. Challenges for future research aimed at defining targets for synthesis strategies that enable us to tune zeolite properties are identified. PMID:24910922

  20. Switching diastereoselectivity in proline-catalyzed aldol reactions.

    PubMed

    Martínez-Castañeda, Ángel; Rodríguez-Solla, Humberto; Concellón, Carmen; del Amo, Vicente

    2012-11-16

    The choice of the anion of an achiral TBD-derived guanidinium salt, used as cocatalyst for proline, allows reacting cycloketones with aromatic aldehydes and preparing either anti- or syn-aldol adducts with very high enantioselectivity. As a proof of principle, we show how the judicious choice of an additive allows individual access to all possible products, thus controlling the stereochemical outcome of the asymmetric aldol reaction. The origin of the syn diastereoselectivity unfolds from an unusual equilibrium process coupled to the enamine-based catalytic cycle standard for proline. PMID:23101761

  1. Enantioselective TADMAP-Catalyzed Carboxyl Migration Reactions for the Synthesis of Stereogenic Quaternary Carbon

    PubMed Central

    Shaw, Scott A.; Aleman, Pedro; Christy, Justin; Kampf, Jeff W.; Va, Porino

    2008-01-01

    The chiral, nucleophilic catalyst TADMAP (1) has been prepared from 3-lithio-4-dimethylamino-pyridine (5) and triphenylacetaldehyde (3), followed by acylation and resolution. TADMAP catalyzes the carboxyl migration of oxazolyl, furanyl, and benzofuranyl enol carbonates with good to excellent levels of enantioselection. The oxazole reactions are especially efficient, and are used to prepare chiral lactams (23) and lactones (30) containing a quaternary asymmetric carbon. TADMAP-catalyzed carboxyl migrations in the indole series are relatively slow and proceed with inconsistent enantioselectivity. Modeling studies (B3LYP/6-31G*) have been used in qualitative correlations of catalyst conformation, reactivity, and enantioselectivity. PMID:16417383

  2. Pd- and Ni-catalyzed cross-coupling reactions in the synthesis of organic electronic materials

    NASA Astrophysics Data System (ADS)

    Xu, Shiqing; Hoo Kim, Eun; Wei, Alexander; Negishi, Ei-ichi

    2014-08-01

    Organic molecules and polymers with extended ?-conjugation are appealing as advanced electronic materials, and have already found practical applications in thin-film transistors, light emitting diodes, and chemical sensors. Transition metal (TM)-catalyzed cross-coupling methodologies have evolved over the past four decades into one of the most powerful and versatile methods for C-C bond formation, enabling the construction of a diverse and sophisticated range of ?-conjugated oligomers and polymers. In this review, we focus our discussion on recent synthetic developments of several important classes of ?-conjugated systems using TM-catalyzed cross-coupling reactions, with a perspective on their utility for organic electronic materials.

  3. Deduction of kinetic mechanism in multisubstrate enzyme reactions from tritium isotope effects. Application to dopamine beta-hydroxylase

    SciTech Connect

    Klinman, J.P.; Humphries, H.; Voet, J.G.

    1980-12-25

    Primary tritium isotope effects have been measured for the hydroxylation of (2-3H) dopamine catalyzed by dopamine beta-hydroxylase. Experimental values vary from 8.8 +/- 1.4 at 0.02 mM oxygen to 4.1 +/- 0.6 at 1.0 mM oxygen. It is shown that the observed dependence of the isotope effect on oxygen concentration provides unequivocal evidence for a kinetically significant dissociation of both dopamine and oxygen from enzyme, ternary complex. This approach, which is applicable to any multisubstrate enzyme characterized by detectable kinetic isotope effects, provides an alternate to classical methods for the elucidation of kinetic order in enzyme-catalyzed reactions.

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

    PubMed

    Hrycay, Eugene G; Bandiera, Stelvio M

    2015-01-01

    This review examines the monooxygenase, peroxidase and peroxygenase properties and reaction mechanisms of cytochrome P450 (CYP) enzymes in bacterial, archaeal and mammalian systems. CYP enzymes catalyze monooxygenation reactions by inserting one oxygen atom from O2 into an enormous number and variety of substrates. The catalytic versatility of CYP stems from its ability to functionalize unactivated carbon-hydrogen (C-H) bonds of substrates through monooxygenation. The oxidative prowess of CYP in catalyzing monooxygenation reactions is attributed primarily to a porphyrin ? radical ferryl intermediate known as Compound I (CpdI) (Por+FeIV=O), or its ferryl radical resonance form (FeIV-O). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex. PMID:26002730

  5. Nickel-Catalyzed Reactions Directed toward the Formation of Heterocycles.

    PubMed

    Kurahashi, Takuya; Matsubara, Seijiro

    2015-06-16

    Heterocycles have garnered significant attention because they are important functional building blocks in various useful molecules, such as pharmaceuticals, agricultural chemicals, pesticides, and materials. Several studies have been conducted regarding the preparation of heterocyclic skeletons with an emphasis on selectivity and efficiency. Three strategies are typically employed to construct cyclic molecules, namely, cyclization, cycloaddition, and ring-size alterations. Although each method has certain advantages, cycloaddition may be superior from the viewpoint of divergence. Specifically, cycloadditions enable the construction of rings from several pieces. However, the construction of heterocycles via cycloadditions is more challenging than the construction of carbocycles. For heterocycle construction, simple pericyclic reactions rarely work smoothly because of the large HOMO-LUMO gap unless well-designed combinations, such as electron-rich dienes and aldehydes, are utilized. Thus, a different approach should be employed to prepare heterocycles via cycloadditions. To this end, the use of metallacycles containing heteroatoms is expected to serve as a promising solution. In this study, we focused on the preparation of heteroatom-containing nickelacycles. Because nickel possesses a relatively high redox potential and an affinity for heteroatoms, several methods were developed to synthesize heteronickelacycles from various starting materials. The prepared nickelacycles were demonstrated to be reasonable intermediates in cycloaddition reactions, which were used to prepare various heterocycles. In this Account, we introduce the following four methods to prepare heterocycles via heteronickelacycles. (1) Direct oxidative insertion of Ni(0) to ?,?-unsaturated enone derivatives: treatment of 3-ethoxycarbonyl-4-phenyl-3-buten-2-one with Ni(0) afforded an oxa-nickelacycle, which reacted with alkynes to give pyrans. (2) Substitution of a part of a cyclic compound with low-valent nickel, accompanied by elimination of small molecules such as CO, CO2, and acetophenone: treatment of phthalic anhydride with Ni(0) in the presence of ZnCl2 afforded the oxanickelacycle, which was formed via decarbonylative insertion of Ni(0) and reacted with alkynes to give isocumarins. (3) Cyclization to a nickelacycle, accompanied by two C-C ?-bond activations: insertion of Ni(0) into an arylnitrile, followed by aryl cyanation of an alkyne, gave alkenylnickel as an intermediate. The alkenylnickel species subsequently underwent an intramolecular nucleophilic attack with an arylcarbonyl group to form a cyclized product with concomitant cleavage of the C-C ?-bond between the carbonyl and aryl groups. (4) Assembly of several components to form a heteroatom-containing nickelacycle via cycloaddition: a new [2 + 2 + 1] cyclization reaction was carried out using an ?,?-unsaturated ester, isocyanate, and alkyne via a nickelacycle. On the basis of these four strategies, we developed new methods to prepare heterocyclic compounds using nickelacycles as the key active species. PMID:25989256

  6. Theoretical study on the Diels-Alder reaction of cyclopentadiene with methacrolein catalyzed by diethylimidazolium cation

    NASA Astrophysics Data System (ADS)

    Sun, Hui; Zhang, Dongju; Ma, Chen; Liu, Chengbu

    The theoretical studies of how room temperature ionic liquids control desired reactions are very scarce in contrast with their increasing applications in many fields as recyclable solvents, catalysts, and reaction mediums. The present work considers the Diels-Alder (D-A) reaction of cyclopentadiene with methacrolein in the presence of diethylimidazolium salts as the first prototype of our systemic studies about important organic synthesis reactions catalyzed by room temperature ionic liquids. We show the mechanism details of the D-A reactions with and without the dialkylimidazolium cation and rationalize the experimental findings based on the results from the quantum chemistry calculations at the AM1, HF/6-31G(d), and B3PW91/6-31G(d,p) levels of theory, respectively. It is found that the diethylimidazolium cation acts as a Lewis acid center to catalyze the D-A reaction, which decreases the barrier and increases the asynchronicity of the D-A reaction, but does not change the potential energy surface profile of the reaction compared to the noncatalyzed process. The present results rationalize the early experimental findings well and provide the first prototype for theoretically understanding the D-A reaction in the presence of dialkylimidazolium salts.

  7. Molecular Epoxidation Reactions Catalyzed by Rhenium, Molybdenum, and Iron Complexes.

    PubMed

    Kück, Jens W; Reich, Robert M; Kühn, Fritz E

    2016-02-01

    Epoxidations are of high relevance in many organic syntheses, both in industry and academia. In this personal account, the development of rhenium, molybdenum, and iron complexes in molecular epoxidation catalysis is presented. Methyltrioxorhenium (MTO) is the benchmark catalyst for these reactions, with a thoroughly investigated mechanism and reactivity profile. More recently, highly active molecular molybdenum and iron catalysts have emerged, challenging the extraordinary role of MTO in epoxidation catalysis with high turnover frequencies (TOFs). This development is highlighted in its use of cheaper, more readily available metals, and the challenges of using base metals in catalysis are discussed. These results show the promise that relatively cheap and abundant metals, such as molybdenum and iron, hold for the future of epoxidation catalysis. PMID:26776087

  8. 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. PMID:11667855

  9. Oxidation reactions catalyzed by manganese peroxidase isoenzymes from Ceriporiopsis subvermispora.

    PubMed

    Urza, U; Fernando Larrondo, L; Lobos, S; Larran, J; Vicua, R

    1995-09-01

    A total of 11 manganese peroxidase isoenzymes (MnP1-MnP11) with isoelectric points (pIs) in the range of 4.58-3.20 were isolated from liquid- and solid-state cultures of the basidiomycete Ceriporiopsis subvermispora. In the presence of hydrogen peroxide, these isoenzymes showed different requirements for Mn(II) in the oxidation of vanillylacetone, o-dianisidine, p-anisidine and ABTS, whereas oxidation of guaiacol by any isoenzyme did not take place when this metal was omitted. Km values for o-dianisidine and p-anisidine in the absence of Mn(II) are in the range of 0.5-1.0 mM and 4.5-42.0 mM, respectively. Oxalate and citrate, but not tartrate, accelerate the oxidation of o-dianisidine, both in the presence and in the absence of Mn(II). MnPs from this fungus are able to oxidize kojic acid without externally added hydrogen peroxide, indicating that they can also act as oxidases. In this reaction, however, the requirement for Mn(II) is absolute. PMID:7672112

  10. Novel method to detect DNA methylation using gold nanoparticles coupled with enzyme-linkage reactions.

    PubMed

    Liu, Tao; Zhao, Jing; Zhang, Dongmei; Li, Genxi

    2010-01-01

    DNA methylation, catalyzed by methylases, plays a critical role in many biological processes, and methylases have been regarded as promising targets for antimicrobial drugs. In this paper, we propose a simple and sensitive colorimetric assay method to detect the activity of methylases so as to monitor DNA methylation using DNA-modified gold nanoparticles (AuNPs) coupled with enzyme-linkage reactions. The duplex DNA molecules modified on the surface of AuNPs are first methylated by DNA adenine methylation (Dam) methyltransferase (MTase) and then cut by methylation-sensitive restriction endonuclease Dpn I. Removal of duplex from the AuNP surfaces by the methylation/cleavage process will destabilize the nanoparticles, resulting in aggregation of AuNPs and a red-to-blue color change. Consequently, the enzyme activity of Dam MTase can be assayed and DNA methylation can be detected. Furthermore, this study may provide a sensitive platform to screen inhibitors for Dam MTase. PMID:19954204

  11. One recognition sequence, seven restriction enzymes, five reaction mechanisms

    PubMed Central

    Gowers, Darren M.; Bellamy, Stuart R.W.; Halford, Stephen E.

    2004-01-01

    The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI, Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence 5?-GGCGCC-3?. Their reactions on plasmids with one or two copies of this sequence revealed five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its recognition sites, but shows full activity only when bound to two sites, which are then cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute requirement for two sites in close physical proximity, which are cleaved concertedly. The range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as is the number of enzymes needing two recognition sites. PMID:15226412

  12. Dual Catalysis: Proton/Metal-Catalyzed Tandem Benzofuran Annulation/Carbene Transfer Reaction.

    PubMed

    Ma, Jun; Chen, Kai; Fu, Hongguang; Zhang, Li; Wu, Wanqing; Jiang, Huanfeng; Zhu, Shifa

    2016-03-18

    An efficient proton/metal-catalyzed tandem benzofuran annulation/carbene transfer reaction for the synthesis of various benzofuryl-substituted cyclopropanes and cycloheptatrienes has been developed. The reaction was proposed to proceed through two key intermediates, o-quinone methide (o-QM) and benzofuryl carbene. The DFT-based computational studies indicated that the reaction was initiated through the dehydration of o-HBA via a Brønsted acid mediated proton shuttle transition state, forming the key intermediate o-QM. PMID:26950391

  13. Organosulfur compounds: electrophilic reagents in transition-metal-catalyzed carbon-carbon bond-forming reactions.

    PubMed

    Dubbaka, Srinivas Reddy; Vogel, Pierre

    2005-12-01

    Transition-metal-catalyzed carbon-carbon bond-forming reactions are among the most powerful methods in organic synthesis and play a crucial role in modern materials science and medicinal chemistry. Recent developments in the area of ligands and additives permit the cross-coupling of a large variety of reactants, including inexpensive and readily available sulfonyl chlorides. Their desulfitative carbon-carbon cross-coupling reactions (Negishi, Stille, carbonylative Stille, Suzuki-Miyaura, and Sonogashira-Hagihara-type cross-couplings and Mizoroki-Heck-type arylations) are reviewed together with carbon-carbon cross-coupling reactions with other organosulfur compounds as electrophilic reagents. PMID:16287179

  14. Pre-Steady-State Kinetic Analysis of Enzyme-monitored Turnover during Cystathionine ?-Synthase-catalyzed H2S-Generation

    PubMed Central

    Singh, Sangita; Ballou, David P.; Banerjee, Ruma

    2010-01-01

    Cystathionine ?-synthase (CBS) catalyzes the first step in the transsulfuration pathway in mammals, i.e., the condensation of serine and homocysteine to produce cystathionine and water. Recently, we have reported a steady-state kinetic analysis of the three hydrogen sulfide (H2S)-generating reactions that are catalyzed by human and yeast CBS (Singh et al (2009) J Biol Chem 284: 22457-66). In the current study, we report a pre-steady-state kinetic analysis of intermediates in the H2S-generating reactions catalyzed by yeast CBS (yCBS). Because yCBS does not have a heme cofactor, in contrast to human CBS, it is easier to observe reaction intermediates with yCBS. The most efficient route for H2S generation by yCBS is the ?-replacement of the cysteine thiol by homocysteine. In this reaction, yCBS first reacts with cysteine to release H2S and forms an aminoacrylate intermediate (kobs=1.61 0.04 mM?1 s?1 at low cysteine and 2.8 0.1 mM?1 s?1 at high cysteine concentrations, at 20 C), which has an absorption maximum at 465 nm. Homocysteine binds to the Eaminoacrylate intermediate with a bimolecular rate constant of 142 mM?1 s?1 and rapidly condenses to form the enzyme-bound external aldimine of cystathionine. The reactions could be partially rate limited by release of the products, cystathionine and H2S. PMID:21141970

  15. Acid-catalyzed transformation of ionophore veterinary antibiotics: reaction mechanism and product implications.

    PubMed

    Sun, Peizhe; Yao, Hong; Minakata, Daisuke; Crittenden, John C; Pavlostathis, Spyros G; Huang, Ching-Hua

    2013-07-01

    Ionophore antibiotics (IPAs) are polyether antimicrobials widely used in the livestock industry and may enter the environment via land application of animal waste and agricultural runoff. Information is scarce regarding potential transformation of IPAs under environmental conditions. This study is among the first to identify the propensity of IPAs to undergo acid-catalyzed transformation in mildly acidic aquatic systems and characterize the reactions in depth. The study focused on the most widely used monensin (MON) and salinomycin (SAL), and also included narasin (NAR) in the investigation. All three IPAs are susceptible to acid-catalyzed transformation. MON reacts much more slowly than SAL and NAR and exhibits a different kinetic behavior that is further evaluated by a reversible reaction kinetic model. Extensive product characterization identifies that the spiro-ketal group of IPAs is the reactive site for the acid-catalyzed hydrolytic transformation, yielding predominantly isomeric and other products. Toxicity evaluation of the transformation products shows that the products retain some antimicrobial properties. The occurrence of IPAs and isomeric transformation products is also observed in poultry litter and agricultural runoff samples. Considering the common presence of mildly acidic environments (pH 4-7) in soils and waters, the acid-catalyzed transformation identified in this study likely plays an important role in the environmental fate of IPAs. PMID:23373828

  16. Enzyme-Catalyzed Synthesis of Unsaturated Aliphatic Polyesters Based on Green Monomers from Renewable Resources

    PubMed Central

    Jiang, Yi; Woortman, Albert J.J.; Alberda van Ekenstein, Gert O.R.; Loos, Katja

    2013-01-01

    Bio-based commercially available succinate, itaconate and 1,4-butanediol are enzymatically co-polymerized in solution via a two-stage method, using Candida antarctica Lipase B (CALB, in immobilized form as Novozyme® 435) as the biocatalyst. The chemical structures of the obtained products, poly(butylene succinate) (PBS) and poly(butylene succinate-co-itaconate) (PBSI), are confirmed by 1H- and 13C-NMR. The effects of the reaction conditions on the CALB-catalyzed synthesis of PBSI are fully investigated, and the optimal polymerization conditions are obtained. With the established method, PBSI with tunable compositions and satisfying reaction yields is produced. The 1H-NMR results confirm that carbon-carbon double bonds are well preserved in PBSI. The differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) results indicate that the amount of itaconate in the co-polyesters has no obvious effects on the glass-transition temperature and the thermal stability of PBS and PBSI, but has significant effects on the melting temperature. PMID:24970176

  17. Enzyme-free electrochemical immunosensor based on host-guest nanonets catalyzing amplification for procalcitonin detection.

    PubMed

    Shen, Wen-Jun; Zhuo, Ying; Chai, Ya-Qin; Yang, Zhe-Han; Han, Jing; Yuan, Ruo

    2015-02-25

    An enzyme-free electrochemical immunosensor based on the host-guest nanonets of N,N-bis(ferrocenoyl)-diaminoethane/?-cyclodextrins/poly(amidoamine) dendrimer-encapsulated Au nanoparticles (Fc-Fc/?-CD/PAMAM-Au) for procalcitonin (PCT) detection has been developed in this study. The signal probe was constructed as follows: amine-terminated ?-CD was adsorbed to PAMAM-Au first, and then the prepared Fc-Fc was recognized by the ?-CD to form stable host-guest nanonets. Next, secondary antibodies (Ab2) were attached into the formed netlike nanostructure of Fc-Fc/?-CD/PAMAM-Au by chemical absorption between PAMAM-Au and -NH2 of ?-CD. Herein, the PAMAM-Au act not only as nanocarriers for anchoring large amounts of the ?-CD and Ab2 but also as nanocatalysts to catalyze the oxidation of ascorbic acid (AA) for signal amplification. Moreover, the Fc-Fc could be stably immobilized by the hydrophobic inner cavity of ?-CD as well as improving solubility by the hydrophilic exterior of ?-CD. With the unique structure of two ferrocene units, Fc-Fc not only affords more electroactive groups to make the electrochemical response more sensitive but also plays a role of combining dispersive ?-CD-functionalized PAMAM-Au to form the netlike nanostructure. Furthermore, Fc-Fc exhibits good catalytic activity for AA oxidation. When the detection solution contained AA, the synergetic catalysis of PAMAM-Au and Fc-Fc to AA oxidation could be obtained, realizing enzyme-free signal amplification. The proposed immunosensor provided a linear range from 1.80 pg/mL to 500 ng/mL for PCT detection and a detection limit of 0.36 pg/mL under optimal experimental conditions. Moreover, the immunosensor has shown potential application in clinical detection of PCT. PMID:25629216

  18. Protease-catalyzed peptide synthesis using inverse substrates: the influence of reaction conditions on the trypsin acyl transfer efficiency.

    PubMed

    Schellenberger, V; Jakubke, H D; Zapevalova, N P; Mitin, Y V

    1991-06-01

    Benzyloxycarbonyl-L-alanine p-guanidinophenyl ester behaves as a trypsin "inverse substrate," i.e., a cationic center is included in the leaving group instead of being in the acyl moiety. Using this substrate as an acyl donor, trypsin catalyzes the synthesis of peptide bonds that cannot be split by this enzyme. An optimal acyl transfer efficiency was achieved between pH 8 and 9 at 30 degrees C.The addition of as much as 50% cosolvent was shown to be of minor influence on the acyl transfer efficiency, whereas the reaction velocity decreases by more than one order of magnitude. The efficiency of H-Leu-NH(2) and H-Val-NH(2) in deacylation is almost the same for "inverse" and normal type substrates. PMID:18600704

  19. 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 ?-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. PMID:25728471

  20. Zinc Enzymes.

    ERIC Educational Resources Information Center

    Bertini, I.; And Others

    1985-01-01

    Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)

  1. Flavohemoglobin denitrosylase catalyzes the reaction of a nitroxyl equivalent with molecular oxygen

    PubMed Central

    Hausladen, Alfred; Gow, Andrew; Stamler, Jonathan S.

    2001-01-01

    We have previously reported that bacterial flavohemoglobin (HMP) catalyzes both a rapid reaction of heme-bound O2 with nitric oxide (NO) to form nitrate [HMP-Fe(II)O2 + NO ? HMP-Fe(III) + NO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\mathrm{_{3}^{-}}}\\end{equation*}\\end{document}] and, under anaerobic conditions, a slower reduction of heme-bound NO to an NO? equivalent (followed by the formation of N2O), thereby protecting against nitrosative stress under both aerobic and anaerobic conditions, and rationalizing our finding that NO is rapidly consumed across a wide range of O2 concentrations. It has been alternatively suggested that HMP activity is inhibited at low pO2 because the enzyme is then in the relatively inactive nitrosyl form [koff/kon for NO (0.000008 ?M) ? koff/kon for O2 (0.012 ?M) and KM for O2 = 30100 ?M]. To resolve this discrepancy, we have directly measured heme-ligand turnover and NADH consumption under various O2/NO concentrations. We find that, at biologically relevant O2 concentrations, HMP preferentially binds NO (not O2), which it then reacts with oxygen to form nitrate (in essence NO? + O2 ? NO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\mathrm{_{3}^{-}}}\\end{equation*}\\end{document}). During steady-state turnover, the enzyme can be found in the ferric (FeIII) state. The formation of a heme-bound nitroxyl equivalent and its subsequent oxidation is a novel enzymatic function, and one that dominates the oxygenase activity under biologically relevant conditions. These data unify the mechanism of HMP/NO interaction with those recently described for the nematode Ascaris and mammalian hemoglobins, and more generally suggest that the peroxidase (FeIII)-like properties of globins have evolved for handling of NO. PMID:11517313

  2. The Structure of SpnF, a Standalone Enzyme that Catalyzes [4+2] Cycloaddition

    PubMed Central

    Fage, Christopher D.; Isiorho, Eta A.; Liu, Yungnan; Wagner, Drew T.; Liu, Hung-wen; Keatinge-Clay, Adrian T.

    2015-01-01

    In the biosynthetic pathway of the spinosyn insecticides, the tailoring enzyme SpnF performs a [4+2]-cycloaddition on a 22-membered macrolactone to forge an embedded cyclohexene ring. To learn more about this reaction, which could potentially proceed through a Diels-Alder mechanism, the 1.50 -resolution crystal structure of SpnF bound to S-adenosylhomocysteine (SAH) was determined. This sets the stage for advanced experimental and computational studies to determine the precise mechanism of SpnF-mediated cyclization. PMID:25730549

  3. Graphene-Catalyzed Direct Friedel-Crafts Alkylation Reactions: Mechanism, Selectivity, and Synthetic Utility.

    PubMed

    Hu, Feng; Patel, Mehulkumar; Luo, Feixiang; Flach, Carol; Mendelsohn, Richard; Garfunkel, Eric; He, Huixin; Szostak, Michal

    2015-11-18

    Transition-metal-catalyzed alkylation reactions of arenes have become a central transformation in organic synthesis. Herein, we report the first general strategy for alkylation of arenes with styrenes and alcohols catalyzed by carbon-based materials, exploiting the unique property of graphenes to produce valuable diarylalkane products in high yields and excellent regioselectivity. The protocol is characterized by a wide substrate scope and excellent functional group tolerance. Notably, this process constitutes the first general application of graphenes to promote direct C-C bond formation utilizing polar functional groups anchored on the GO surface, thus opening the door for an array of functional group alkylations using benign and readily available graphene materials. Mechanistic studies suggest that the reaction proceeds via a tandem catalysis mechanism in which both of the coupling partners are activated by interaction with the GO surface. PMID:26496423

  4. Spatial distance effect of bienzymes on the efficiency of sequential reactions in a microfluidic reactor packed with enzyme-immobilized microbeads.

    PubMed

    Heo, Jinseok

    2014-01-01

    Three different configurations of microfluidic reactors packed with enzyme-bearing microbeads were examined to show that the overall efficiency of coupled enzyme-catalyzed reactions depends on the spatial relationship of two enzymes immobilized on the bead surfaces. The spatial distances of glucose oxidase (GOx) and horseradish peroxidase (HRP) enzymes were controlled by using microbeads as a supporting matrix for immobilizing the two enzymes and packing them in two microfluidic chambers. A microreactor packed with microbeads coimmobilized with the two enzymes showed a better overall reaction efficiency than the other two reactors, where the two enzymes were spatially distant, under a flow condition. These results are ascribed to the reduced diffusional loss of an intermediate product in the bienzyme-coimmobilized microreactor. Furthermore, the inhibition of the GOx enzyme by H2O2, an intermediate product, can be eliminated by quickly converting H2O2 to a final non-inhibiting product in the bienzyme-coimmobilized microreactor. PMID:25312630

  5. A palladium-catalyzed tandem reaction of 2-(2-bromobenzylidene)cyclobutanone with 2-alkynylphenol.

    PubMed

    Pan, Xiaolin; Luo, Yong; Xia, Hong-Guang; Wu, Jie

    2015-11-28

    An efficient approach for the generation of benzo[b]naphtho[2,3-d]oxocin-6-ones through a palladium-catalyzed tandem reaction of 2-alkynylphenol with 2-(2-bromobenzylidene)cyclobutanone is described. This tandem process afforded the fused polycycles easily, with the formation of three bonds with high efficiency, starting from easily available materials. Good functional group tolerance as well as excellent selectivity was displayed. PMID:26414750

  6. Metal-Catalyzed ?-Functionalization of Michael Acceptors through Reductive Radical Addition Reactions.

    PubMed

    Streuff, Jan; Gansuer, 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 ?,?-unsaturated compounds have recently gained substantial attention as a result of their broad applicability in organic synthesis. This Minireview critically discusses the recent landmark achievements in this field in context with earlier reports that laid the foundation for today's developments. PMID:26471460

  7. Enzyme-catalyzed oxidation of 5-hydroxymethylfurfural to furan-2,5-dicarboxylic acid.

    PubMed

    Dijkman, Willem P; Groothuis, Daphne E; Fraaije, Marco W

    2014-06-16

    Furan-2,5-dicarboxylic acid (FDCA) is a biobased platform chemical for the production of polymers. In the past few years, numerous multistep chemical routes have been reported on the synthesis of FDCA by oxidation of 5-hydroxymethylfurfural (HMF). Recently we identified an FAD-dependent enzyme which is active towards HMF and related compounds. This oxidase has the remarkable capability of oxidizing [5-(hydroxymethyl)furan-2-yl]methanol to FDCA, a reaction involving four consecutive oxidations. The oxidase can produce FDCA from HMF with high yield at ambient temperature and pressure. Examination of the underlying mechanism shows that the oxidase acts on alcohol groups only and depends on the hydration of aldehydes for the oxidation reaction required to form FDCA. PMID:24802551

  8. Enzyme homologues have distinct reaction paths through their transition states.

    PubMed

    Zoi, Ioanna; Motley, Matthew W; Antoniou, Dimitri; Schramm, Vern L; Schwartz, Steven D

    2015-03-01

    Recent studies of the bacterial enzymes EcMTAN and VcMTAN showed that they have different binding affinities for the same transition state analogue. This was surprising given the similarity of their active sites. We performed transition path sampling simulations of both enzymes to reveal the atomic details of the catalytic chemical step, which may be the key for explaining the inhibitor affinity differences. Even though all experimental data would suggest the two enzymes are almost identical, subtle dynamic differences manifest in differences of reaction coordinate, transition state structure, and eventually significant differences in inhibitor binding. Unlike EcMTAN, VcMTAN has multiple distinct transition states, which is an indication that multiple sets of coordinated protein motions can reach a transition state. Reaction coordinate information is only accessible from transition path sampling approaches, since all experimental approaches report averages. Detailed knowledge could have a significant impact on pharmaceutical design. PMID:25650981

  9. Enzyme Homologues Have Distinct Reaction Paths through their Transition States

    PubMed Central

    Zoi, Ioanna; Motley, Matthew W.; Antoniou, Dimitri; Schramm, Vern L.; Schwartz, Steven D.

    2015-01-01

    Recent studies of the bacterial enzymes EcMTAN and VcMTAN showed that they have different binding affinities for the same transition state analogue. This was surprising given the similarity of their active sites. We performed Transition Path Sampling simulations of both enzymes to reveal the atomic details of the catalytic chemical step, which may be the key for explaining the inhibitor affinity differences. Even though all experimental data would suggest the two enzymes are almost identical, subtle dynamic differences manifest in differences of reaction coordinate, transition state structure, and eventually significant differences in inhibitor binding. Unlike EcMTAN, VcMTAN has multiple distinct transition states, which is an indication that multiple sets of coordinated protein motions can reach a transition state. Reaction coordinate information is only accessible from transition path sampling approaches, since all experimental approaches report averages. Detailed knowledge could have a significant impact on pharmaceutical design. PMID:25650981

  10. Interfacial mechanisms of heterogeneous Fenton reactions catalyzed by iron-based materials: A review.

    PubMed

    He, Jie; Yang, Xiaofang; Men, Bin; Wang, Dongsheng

    2016-01-01

    The heterogeneous Fenton reaction can generate highly reactive hydroxyl radicals (OH) from reactions between recyclable solid catalysts and H2O2 at acidic or even circumneutral pH. Hence, it can effectively oxidize refractory organics in water or soils and has become a promising environmentally friendly treatment technology. Due to the complex reaction system, the mechanism behind heterogeneous Fenton reactions remains unresolved but fascinating, and is crucial for understanding Fenton chemistry and the development and application of efficient heterogeneous Fenton technologies. Iron-based materials usually possess high catalytic activity, low cost, negligible toxicity and easy recovery, and are a superior type of heterogeneous Fenton catalysts. Therefore, this article reviews the fundamental but important interfacial mechanisms of heterogeneous Fenton reactions catalyzed by iron-based materials. OH, hydroperoxyl radicals/superoxide anions (HO2/O2(-)) and high-valent iron are the three main types of reactive oxygen species (ROS), with different oxidation reactivity and selectivity. Based on the mechanisms of ROS generation, the interfacial mechanisms of heterogeneous Fenton systems can be classified as the homogeneous Fenton mechanism induced by surface-leached iron, the heterogeneous catalysis mechanism, and the heterogeneous reaction-induced homogeneous mechanism. Different heterogeneous Fenton systems catalyzed by characteristic iron-based materials are comprehensively reviewed. Finally, related future research directions are also suggested. PMID:26899649

  11. Coupling reaction of vinyl esters with aldehydes catalyzed by samarium complexes

    SciTech Connect

    Ishii, Yasutaka; Takeno, Mitsuhiro; Sakaguchi, Satoshi; Nishiyama, Yutaka

    1995-12-31

    In recent years, a unique catalysis of samarium(II) complexes such as Cp*{sub 2}Sm(thf){sub 2} is increasing interest in organic synthesis. The authors now find that Sm(II) complexes catalyze a new 1:2 coupling reaction of vinyl esters and aldehydes under mild conditions. For instance, the coupling reaction of vinyl acetate with acetaldehyde under the influence of Cp*{sub 2}Sm(thf){sub 2}(10 mol%) in toluene at room temperature for 3 h afforded a 1:2 coupling product 3a, in 80% yield. From the examination of the reaction of 1a with cyaclohexanecarbaldehyde using several samarium complexes as catalysts, Cp*{sub 2}Sm(thf){sub 2} was found to be the best catalyst. In the coupling of 1a with benzaldehyde, however, SmI{sub 2} was more efficient than CP*{sub 2}Sm(thf){sub 2} to form the corresponding coupling product in almost quantitative yield (>99 %). The reaction of isopropenyl acetate with deutrated acetaldehyde, CD{sub 3}CDO, afforded a coupling product, 5, in which 11 deuteriums are incorporated in the molecule. The authors will present a detailed reaction mechanism in the Cp*{sub 2}Sm(thf){sub 2} - catalyzed coupling reaction of vinyl acetates with aldehydes.

  12. Iron- and bismuth-catalyzed asymmetric Mukaiyama aldol reactions in aqueous media.

    PubMed

    Kitanosono, Taku; Ollevier, Thierry; Kobayashi, Sh?

    2013-12-01

    We have developed asymmetric Mukaiyama aldol reactions of silicon enolates with aldehydes catalyzed by chiral Fe(II) and Bi(III) complexes. Although previous reactions often required relatively harsh conditions, such as strictly anhydrous conditions, very low temperatures (-78 C), etc., the reactions reported herein proceeded in the presence of water at 0 C. To find appropriate chiral water-compatible Lewis acids for the Mukaiyama aldol reaction, many Lewis acids were screened in combination with chiral bipyridine L1, which had previously been found to be a suitable chiral ligand in aqueous media. Three types of chiral catalysts that consisted of a Fe(II) or Bi(III) metal salt, a chiral ligand (L1), and an additive have been discovered and a wide variety of substrates (silicon enolates and aldehydes) reacted to afford the desired aldol products in high yields with high diastereo- and enantioselectivities through an appropriate selection of one of the three catalytic systems. Mechanistic studies elucidated the coordination environments around the Fe(II) and Bi(III) centers and the effect of additives on the chiral catalysis. Notably, both Brnsted acids and bases worked as efficient additives in the Fe(II) -catalyzed reactions. The assumed catalytic cycle and transition states indicated important roles of water in these efficient asymmetric Mukaiyama aldol reactions in aqueous media with the broadly applicable and versatile catalytic systems. PMID:24101589

  13. Elucidating Latent Mechanistic Complexity in Competing Acid-Catalyzed Reactions of Salicylaldehyde-Derived Baylis-Hillman Adducts.

    PubMed

    Olomola, Temitope O; Klein, Rosalyn; Caira, Mino R; Kaye, Perry T

    2016-01-01

    (1)H NMR-based kinetic studies have revealed the latent mechanistic complexity of deceptively simple hydrochloric acid-catalyzed reactions of salicylaldehyde-derived Baylis-Hillman adducts. Reactions conducted at 0 C afforded 2-(chloromethyl)cinnamic acid derivatives as the major products and the corresponding 3-(chloromethyl)coumarin derivatives as the minor products. In reactions conducted in refluxing acetic acid, however, the 3-(chloromethyl)coumarin derivatives are the sole products. Variable-temperature (1)H NMR analysis permitted the determination of the rate constants and kinetic parameters involved in the pseudo-first-order formation of (Z)-2-(chloromethyl)-3-(2-hydroxyphenyl)-2-propenoic acid. The kinetic data clearly preclude the operation of classical kinetic versus thermodynamic control and indicate the operation of three independent reaction pathways. Theoretical studies of these pathways undertaken at the B3LYP/6-31G(d) level permitted rationalization of the experimental data and provided insights into the possible mechanism of the enzymic E-Z isomerization and cyclization of (E)-cinnamic acid analogues to afford coumarins. PMID:26655750

  14. On-line characterization using ultrasound of pectin hydrolysis catalyzed by the enzyme pectinmethylesterase

    NASA Astrophysics Data System (ADS)

    Aparicio, C.; Resa, P.; Sierra, C.; Elvira, L.

    2012-12-01

    The major problem in the fruit juice industry is associated with juice quality deterioration due to the cloud loss of juice concentrates by the enzymatic reaction of pectinmethylesterase enzyme (PME, EC 3.1.1.11). During pectin hydrolysis, pectin and water are transformed into polygalacturonic acid (pectate) and methanol by the action of PME. In this work, a low-intensity ultrasonic technique is used to monitor this enzymatic reaction, with PME both from orange peel and from Aspergillus niger. Changes in sound velocity during pectin hydrolysis (1% concentration of pectin, T = 30°C and pH = 4.5 and 7) with 0.25 ml of enzyme solution (PME) have been measured using a through-transmission technique. Sound velocity decreases as pectin is transformed into pectate and methanol and at the end of the process, the change in sound velocity reaches 0.3 m/s with PME from orange peel and 0.33 m/s with PME from Aspergillus niger.

  15. Beta-lactamase-catalyzed aminolysis of depsipeptides: Proof of the nonexistence of a specific D-phenylalanine/enzyme complex by double-label isotope trapping

    SciTech Connect

    Pazhanisamy, S.; Pratt, R.F. )

    1989-08-22

    The steady-state kinetics of the Enterobacter cloacae P99 beta-lactamase-catalyzed aminolysis of the depsipeptide m-(((phenylacetyl)glycyl)oxy)benzoic acid by D-phenylalanine were consistent with an ordered sequential mechanism with D-phenylalanine binding first. In terms of this mechanism, the kinetics data required that in 20 mM MOPS buffer, pH 7.5, the dissociation constant of the initially formed enzyme/D-phenylalanine complex be around 1.3 mM; at pH 9.0 in 0.1 M carbonate buffer, the complex should be somewhat more stable. Attempts to detect this complex in a binary mixture by spectroscopic methods (fluorescence, circular dichroic, and nuclear magnetic resonance spectra) failed. Kinetic methods were also unsuccessful--the presence of 20 mM D-phenylalanine did not appear to affect beta-lactamase activity nor inhibition of the enzyme by phenylmethanesulfonyl fluoride, phenylboronic acid, or (3-dansylamidophenyl)boronic acid. Equilibrium dialysis experiments appeared to indicate that the dissociation constant of any binary enzyme/D-phenylalanine complex must be somewhat higher than the kinetics allowed (greater than 2 mM). Since the kinetics also required that, at high depsipeptide concentrations, and again with the assumption of the ordered sequential mechanism, the reaction of the enzyme/D-phenylalanine complex to aminolysis products be faster than its reversion to enzyme and D-phenylalanine, a double-label isotope-trapping experiment was performed.

  16. A new family of enzymes catalyzing the first committed step of the methylerythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in bacteria

    PubMed Central

    Sangari, Félix J.; Pérez-Gil, Jordi; Carretero-Paulet, Lorenzo; García-Lobo, Juan M.; Rodríguez-Concepción, Manuel

    2010-01-01

    Isoprenoids are a large family of compounds with essential functions in all domains of life. Most eubacteria synthesize their isoprenoids using the methylerythritol 4-phosphate (MEP) pathway, whereas a minority uses the unrelated mevalonate pathway and only a few have both. Interestingly, Brucella abortus and some other bacteria that only use the MEP pathway lack deoxyxylulose 5-phosphate (DXP) reductoisomerase (DXR), the enzyme catalyzing the NADPH-dependent production of MEP from DXP in the first committed step of the pathway. Fosmidomycin, a specific competitive inhibitor of DXR, inhibited growth of B. abortus cells expressing the Escherichia coli GlpT transporter (required for fosmidomycin uptake), confirming that a DXR-like (DRL) activity exists in these bacteria. The B. abortus DRL protein was found to belong to a family of uncharacterized proteins similar to homoserine dehydrogenase. Subsequent experiments confirmed that DRL and DXR catalyze the same biochemical reaction. DRL homologues shown to complement a DXR-deficient E. coli strain grouped within the same phylogenetic clade. The scattered taxonomic distribution of sequences from the DRL clade and the occurrence of several paralogues in some bacterial strains might be the result of lateral gene transfer and lineage-specific gene duplications and/or losses, similar to that described for typical mevalonate and MEP pathway genes. These results reveal the existence of a novel class of oxidoreductases catalyzing the conversion of DXP into MEP in prokaryotic cells, underscoring the biochemical and genetic plasticity achieved by bacteria to synthesize essential compounds such as isoprenoids. PMID:20660776

  17. Chemo-, Diastereo-, and Enantioselective Iridium-Catalyzed Allylic Intramolecular Dearomatization Reaction of Naphthol Derivatives.

    PubMed

    Cheng, Qiang; Wang, Ye; You, Shu-Li

    2016-03-01

    An iridium-catalyzed intramolecular asymmetric allylic dearomatization reaction of naphthol derivatives is described. Challenges confronted in this reaction include chemoselectivity between carbon and oxygen atoms as nucleophilic centers, diastereoselectivity when contiguous chiral centers are generated, and enantioselective control for constructing an all-carbon quaternary stereocenter. In the presence of an iridium catalyst generated from [{Ir(dbcot)Cl}2 ] (dbcot=dibenzocyclooctatetraene) and a new THQphos (tetrahydroquinolinedinaphthophosphoramidite) ligand, various spironaphthalenones were obtained with up to greater than 95:5 C/O selectivity, greater than 95:5 d.r., and 99?% ee, thus providing a general method for the dearomatization of naphthols. PMID:26848021

  18. Transition-Metal-Catalyzed Laboratory-Scale CarbonCarbon Bond-Forming Reactions of Ethylene

    PubMed Central

    Saini, Vaneet; Stokes, Benjamin J.; Sigman, Matthew S.

    2014-01-01

    Ethylene, the simplest alkene, is the most abundantly synthesized organic molecule by volume. It is readily incorporated into transitionmetalcatalyzed carbon-carbon bond-forming reactions through migratory insertions into alkylmetal intermediates. Because of its D2h symmetry, only one insertion outcome is possible. This limits byproduct formation and greatly simplifies analysis. As described within this Minireview, many carboncarbon bond-forming reactions incorporate a molecule (or more) of ethylene at ambient pressure and temperature. In many cases, a useful substituted alkene is incorporated into the product. PMID:24105881

  19. Transition metal-catalyzed allylic substitution reactions with unactivated allylic substrates.

    PubMed

    Butt, Nicholas A; Zhang, Wanbin

    2015-11-21

    The transition metal-catalyzed allylic substitution of unactivated allylic substrates (allylic alcohols, allylic ethers and allylic amines) is rapidly becoming an important area of research. There are several advantages to using these substrates in allylic substitution reactions: the use of unactivated alcohols minimizes the production of waste by-products and reaction steps; and allylic ethers and allylic amines are useful substrates because of their stability and their presence in numerous biologically active compounds. Research in this field has therefore gained widespread attention for promoting the development of efficient and environmentally benign procedures for the formation of C-C, C-N and C-O bonds. PMID:26293479

  20. Kinetic modeling of lipase-catalyzed esterification reaction between oleic acid and trimethylolpropane: a simplified model for multi-substrate multi-product ping-pong mechanisms.

    PubMed

    Bornadel, Amin; Akerman, Cecilia Orellana; Adlercreutz, Patrick; Hatti-Kaul, Rajni; Borg, Niklas

    2013-01-01

    Kinetic models are among the tools that can be used for optimization of biocatalytic reactions as well as for facilitating process design and upscaling in order to improve productivity and economy of these processes. Mechanism pathways for multi-substrate multi-product enzyme-catalyzed reactions can become very complex and lead to kinetic models comprising several tens of terms. Hence the models comprise too many parameters, which are in general highly correlated and their estimations are often prone to huge errors. In this study, Novozym() 435 catalyzed esterification reaction between oleic acid (OA) and trimethylolpropane (TMP) with continuous removal of side-product (water) was carried out as an example for reactions that follow multi-substrate multi-product ping-pong mechanisms. A kinetic model was developed based on a simplified ping-pong mechanism proposed for the reaction. The model considered both enzymatic and spontaneous reactions involved and also the effect of product removal during the reaction. The kinetic model parameters were estimated using nonlinear curve fitting through unconstrained optimization methodology and the model was verified by using empirical data from different experiments and showed good predictability of the reaction under different conditions. This approach can be applied to similar biocatalytic processes to facilitate their optimization and design. PMID:24013935

  1. Enzymes in Analytical Chemistry.

    ERIC Educational Resources Information Center

    Fishman, Myer M.

    1980-01-01

    Presents tabular information concerning recent research in the field of enzymes in analytic chemistry, with methods, substrate or reaction catalyzed, assay, comments and references listed. The table refers to 128 references. Also listed are 13 general citations. (CS)

  2. Enzyme databases.

    PubMed

    Schomburg, Dietmar; Schomburg, Ida

    2010-01-01

    Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a key role in the regulation of metabolic steps within the cells, as drug targets, and in a wide range of biotechnological applications. With respect to reaction type, they are grouped into six classes, namely oxidoreductases, transferases, hydrolases, lyases, and ligases. EC-Numbers are assigned by the IUBMB. Enzyme functional databases cover a wide range of properties and functions, such as occurrence, kinetics of enzyme-catalyzed reactions, structure, or metabolic function. BRENDA stores a large variety of different data for all classified enzymes whereas KEGG, MEROPS, MetaCyc, REBASE, CAzy, ESTHER, PeroxiBase, and KinBase specialize in either certain aspects of enzyme function or specific enzyme classes, organisms, or metabolic pathways. Databases covering enzyme nomenclature are ExplorEnz, SIB-ENZYME, and IntEnz. PMID:20221916

  3. Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes.

    PubMed

    Wolfenden, Richard

    2011-01-01

    The rates of enzyme reactions fall within a relatively narrow range. To estimate the rate enhancements produced by enzymes, and their expected affinities for transition state analog inhibitors, it is necessary to measure the rates of the corresponding reactions in water in the absence of a catalyst. This review describes the spontaneous cleavages of C-C, C-H, C-N, C-O, P-O, and S-O bonds in biological molecules, as well as the uncatalyzed reactions that correspond to phosphoryl transfer reactions catalyzed by kinases and to peptidyl transfer in the ribosome. The rates of these reactions, some with half-lives in excess of one million years, span an overall range of 10?-fold. Moreover, the slowest reactions tend to be most sensitive to temperature, with rates that increase as much as 10?-fold when the temperature is raised from 25 to 100C. That tendency collapses, by many orders of magnitude, the time that would have been required for chemical evolution on a warm earth. If the catalytic effect of primitive enzymes, like that of modern enzymes and many nonenzymatic catalysts, were mainly to reduce a reaction's enthalpy of activation, then the resulting rate enhancement would have increased automatically as the surroundings cooled. By reducing the time required for early chemical evolution in a warm environment, these findings counter the view that not enough time has passed for terrestrial life to have evolved to its present level of complexity. PMID:21495848

  4. EzCatDB: the enzyme reaction database, 2015 update

    PubMed Central

    Nagano, Nozomi; Nakayama, Naoko; Ikeda, Kazuyoshi; Fukuie, Masaru; Yokota, Kiyonobu; Doi, Takuo; Kato, Tsuyoshi; Tomii, Kentaro

    2015-01-01

    The EzCatDB database (http://ezcatdb.cbrc.jp/EzCatDB/) has emphasized manual classification of enzyme reactions from the viewpoints of enzyme active-site structures and their catalytic mechanisms based on literature information, amino acid sequences of enzymes (UniProtKB) and the corresponding tertiary structures from the Protein Data Bank (PDB). Reaction types such as hydrolysis, transfer, addition, elimination, isomerization, hydride transfer and electron transfer have been included in the reaction classification, RLCP. This database includes information related to ligand molecules on the enzyme structures in the PDB data, classified in terms of cofactors, substrates, products and intermediates, which are also necessary to elucidate the catalytic mechanisms. Recently, the database system was updated. The 3D structures of active sites for each PDB entry can be viewed using Jmol or Rasmol software. Moreover, sequence search systems of two types were developed for the EzCatDB database: EzCat-BLAST and EzCat-FORTE. EzCat-BLAST is suitable for quick searches, adopting the BLAST algorithm, whereas EzCat-FORTE is more suitable for detecting remote homologues, adopting the algorithm for FORTE protein structure prediction software. Another system, EzMetAct, is also available to searching for major active-site structures in EzCatDB, for which PDB-formatted queries can be searched. PMID:25324316

  5. Transition-metal-promoted reactions of boron hydrides. 17. Titanium-catalyzed decaborane-olefin hydroborations.

    PubMed

    Pender, M J; Carroll, P J; Sneddon, L G

    2001-12-12

    The titanium-catalyzed hydroboration reactions of decaborane with a variety of terminal olefins have been found to result in the exclusive, high-yield formation of monosubstituted decaborane 6-R-B(10)H(13) products, arising from anti-Markovnikov addition of the cage B6-H to the olefin. The titanium-catalyzed reactions are slow, often less than one turnover per hour; however, their high selectivities and yields coupled with the fact that they are simple, one-pot reactions give them significant advantages over the previously reported routes to 6-R-B(10)H(13) compounds. The catalyst also has extended activity with reactions carried out for as long as 13 days, showing little decrease in reactivity, thereby allowing for the production of large amounts of 6-R-B(10)H(13). The titanium-catalyzed reactions of decaborane with the nonconjugated diolefins, 1,5-hexadiene and diallylsilane, were found to give, depending upon reaction conditions and stoichiometries, high yields of either alkenyl-substituted 6-(CH(2)=CH(CH(2))(4))-B(10)H(13) (4) and 6-(CH(2)=CHCH(2)SiMe(2)(CH(2))(3))-B(10)H(13) (5) or linked-cage 6,6'-(CH(2))(6)-(B(10)H(13))(2) (6) and Me(2)Si(6-(CH(2))(3)-B(10)H(13))(2) (7) compounds, respectively. The unique tetra-cage product, Si(6-(CH(2))(3)-B(10)H(13))(4) (8), was obtained by the catalyzed reaction of 4 equiv of decaborane with tetraallylsilane. Sequential use of the titanium catalyst and previously reported platinum catalysts (PtBr(2) or H(2)PtCl(6).6H(2)O with an initiator) provides an efficient pathway to asymmetrically substituted 6-R-9-R'-B(10)H(12) species. The structures of compounds 5, 6, and 8, as well as a platinum derivative, (PSH(+))(2)-commo-Pt-[nido-7-Pt-8-(n-C(8)H(17))B(10)H(11)](2)(2-), of 6-(n-octyl)decaborane have been established by single-crystal crystallographic determinations. PMID:11734022

  6. 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. PMID:25997656

  7. Au(I)/Au(III)-catalyzed Sonogashira-type reactions of functionalized terminal alkynes with arylboronic acids under mild conditions

    PubMed Central

    Qian, Deyun

    2011-01-01

    Summary A straightforward, efficient, and reliable redox catalyst system for the Au(I)/Au(III)-catalyzed Sonogashira cross-coupling reaction of functionalized terminal alkynes with arylboronic acids under mild conditions has been developed. PMID:21804876

  8. Copper-catalyzed three-component cascade reaction of alkynes, sulfonyl azides and simple aldehydes/ketones.

    PubMed

    Hu, Yuanyuan; Zhou, Bingwei; Wang, Congyang

    2016-03-21

    A copper-catalyzed dimethylzinc-promoted three-component cascade reaction of alkynes, sulfonyl azides, and simple aldehydes or ketones is described. Polysubstituted olefins were thus constructed expeditiously in a one-pot procedure under mild conditions. PMID:26899625

  9. The phosphorylcholine acceptor in the phosphatidylcholine:ceramide cholinephosphotransferase reaction. Is the enzyme a transferase or a hydrolase?

    PubMed

    Marggraf, W D; Kanfer, J N

    1984-05-11

    The cholinephosphotransferase reaction is shown to be catalyzed by an enzyme which has no hydrolytic activity and which is different from a phospholipase C type activity also present in these plasma membrane preparations. Diacylglycerols and sphingosine, at a concentration above 0.4 mM, are effective inhibitors of sphingomyelin formation in the presence of 0.3 mM free ceramide, the true acceptor in this reaction. Free sphingosine is not an acceptor for the cholinephosphate group, as the anticipated reaction product, sphingosylphosphocholine , could not be detected. Sphingosine inhibition may result from its structural similarity to the natural substrates of the reaction, ceramide and diacylglycerols. From the data obtained with cholesterol, triacylglycerols, acetylated ( triacetyl ) sphingosine and acetylated ceramides used as potential inhibitors of the reaction it is concluded that the free hydroxyl group at C1 of the sphingosine backbone or of the glycerol moiety of diacylglycerols and a non-polar residue consisting of an aliphatic chain were prerequisites for inhibitory activity. These results are discussed in terms of substrate specificity of the enzyme catalyzing the transfer reaction. Some of the factors influencing the regulation of the phosphatidylcholine/sphingomyelin ratio in the plasma membrane were related to the topography of sphingomyelin in the outer half-layer of the plasma membrane. PMID:6324872

  10. Spontaneous high-yield hydrogen production from cellulosic materials and water catalyzed by enzyme cocktail

    SciTech Connect

    Ye, Xinhao; Wang, Yiran; Hopkins, Robert C.; Adams, Michael W. W.; Evans, Barbara R; Mielenz, Jonathan R; Zhang, Y.-H. Percival

    2009-01-01

    Carbon-neutral hydrogen gas is a compelling energy carrier, especially for the transportation section. Low-cost hydrogen can be produced from abundant renewable lignocellulosic biomass through a number of methods employing chemical catalysis, biocatalysis or a combination of both, but these technologies suffer from low hydrogen yields (well below the theoretical yield of 12 H2 per glucose), undesired side-products and/or required severe reaction conditions. Here we present a novel in vitro synthetic biology approach for producing near theoretical hydrogen yields from cellulosic materials (cellodextrins) and water at 32oC and 1 atm. These non-natural catabolic pathways containing up to 14 enzymes and one coenzyme degrade cellodextrins initially to glucose-1-phosphate and eventually to CO2, split water and finally release the chemical energy in the form of hydrogen gas. Up to 11.2 H2 per anhydroglucose was produced in a batch reaction. This spontaneous endothermic reaction is driven by entropy gain, suggesting that the thermal energy is adsorbed for generating more chemical energy (hydrogen gas) than that in cellodextrins, i.e., output/input of chemical energy > 1, with an input of ambient-temperature thermal energy.

  11. Bifunctional-thiourea-catalyzed diastereo- and enantioselective aza-Henry reaction.

    PubMed

    Xu, Xuenong; Furukawa, Tomihiro; Okino, Tomotaka; Miyabe, Hideto; Takemoto, Yoshiji

    2005-12-23

    Bifunctional thiourea 1a catalyzes aza-Henry reaction of nitroalkanes with N-Boc-imines to give syn-beta-nitroamines with good to high diastereo- and enantioselectivity. Apart from the catalyst, the reaction requires no additional reagents such as a Lewis acid or a Lewis base. The N-protecting groups of the imines have a determining effect on the chirality of the products, that is, the reaction of N-Boc-imines gives R adducts as major products, whereas the same reaction of N-phosphonoylimines furnishes the corresponding S adducts. Various types of nitroalkanes bearing aryl, alcohol, ether, and ester groups can be used as nucleophiles, providing access to a wide range of useful chiral building blocks in good yield and high enantiomeric excess. Synthetic versatility of the addition products is demonstrated by the transformation to chiral piperidine derivatives such as CP-99,994. PMID:16187368

  12. Mechanistic Studies of the Radical SAM Enzyme DesII: EPR Characterization of a Radical Intermediate Generated During Its Catalyzed Dehydrogenation of TDP-D-Quinovose

    PubMed Central

    Ruszczycky, Mark W.; Choi, Sei-hyun; Mansoorabadi, Steven O.; Liu, Hung-wen

    2011-01-01

    DesII, a radical SAM enzyme from Streptomyces venezuelae, catalyzes the deamination of TDP-4-amino-4,6- dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose in the desosamine biosynthetic pathway. DesII can also catalyze the dehydrogenation of TDP-D-quinovose to the corresponding 3-keto sugar. Similar to other radical SAM enzymes, DesII catalysis has been proposed to proceed via a radical mechanism. This hypothesis is now confirmed by EPR spectroscopy with the detection of a TDP-D-quinovose radical intermediate having a g-value of 2.0025 with hyperfine coupling to two spin nuclei, each with a splitting constant of 33.6 G. A significant decrease in the EPR linewidth is observed when the radical is generated in reactions conducted in D2O versus H2O. These results are consistent with a C3 ?-hydroxyalkyl radical in which the p-orbital harboring the unpaired electron spin at C3 is periplanar with the CH bonds at both C2 and C4. PMID:21513273

  13. Rh-Catalyzed Intermolecular Reactions of ?-Alkyl-?-Diazo Carbonyl Compounds with Selectivity over ?-Hydride Migration.

    PubMed

    DeAngelis, Andrew; Panish, Robert; Fox, Joseph M

    2016-01-19

    Rh-carbenes derived from ?-diazocarbonyl compounds have found broad utility across a remarkable range of reactivity, including cyclopropanation, cyclopropenation, C-H insertions, heteroatom-hydrogen insertions, and ylide forming reactions. However, in contrast to ?-aryl or ?-vinyl-?-diazocarbonyl compounds, the utility of ?-alkyl-?-diazocarbonyl compounds had been moderated by the propensity of such compounds to undergo intramolecular ?-hydride migration to give alkene products. Especially challenging had been intermolecular reactions involving ?-alkyl-?-diazocarbonyl compounds. This Account discusses the historical context and prior limitations of Rh-catalyzed reactions involving ?-alkyl-?-diazocarbonyl compounds. Early studies demonstrated that ligand and temperature effects could influence chemoselectivity over ?-hydride migration. However, effects were modest and conflicting conclusions had been drawn about the influence of sterically demanding ligands on ?-hydride migration. More recent advances have led to a more detailed understanding of the reaction conditions that can promote intermolecular reactivity in preference to ?-hydride migration. In particular, the use of bulky carboxylate ligands and low reaction temperatures have been key to enabling intermolecular cyclopropenation, cyclopropanation, carbonyl ylide formation/dipolar cycloaddition, indole C-H functionalization, and intramolecular bicyclobutanation with high chemoselectivity over ?-hydride migration. Cyclic ?-diazocarbonyl compounds have been shown to be particularly resilient toward ?-hydride migration and are the first class of compounds that can engage in intermolecular reactivity in the presence of tertiary ?-hydrogens. DFT calculations were used to propose that for cyclic ?-diazocarbonyl compounds, ring constraints relieve steric interaction for intermolecular reactions and thereby accelerate the rate of intermolecular reactivity relative to intramolecular ?-hydride migration. Enantioselective reactions of ?-alkyl-?-diazocarbonyl compounds have been developed using bimetallic N-imido-tert-leucinate-derived complexes. The most effective complexes were found by computation and X-ray crystallography to adopt a "chiral crown" conformation in which all of the imido groups are presented on one face of the paddlewheel complex in a chiral arrangement. Insight from computational studies guided the design and synthesis of a mixed ligand paddlewheel complex, Rh2(S-PTTL)3TPA, the structure of which bears similarity to the chiral crown complex Rh2(S-PTTL)4. Rh2(S-PTTL)3TPA engages substrate classes (aliphatic alkynes, silylacetylenes, ?-olefins) that are especially challenging in intermolecular reactions of ?-alkyl-?-diazoesters and catalyzes enantioselective cyclopropanation, cyclopropenation, and indole C-H functionalization with yields and enantioselectivities that are comparable or superior to Rh2(S-PTTL)4. The work detailed in this Account describes progress toward enabling a more general utility for ?-alkyl-?-diazo compounds in Rh-catalyzed carbene reactions. Further studies on ligand design and synthesis will continue to broaden the scope of their selective reactions. PMID:26689221

  14. Temporal Control of Gelation and Polymerization Fronts Driven by an Autocatalytic Enzyme Reaction.

    PubMed

    Jee, Elizabeth; Bnsgi, Tams; Taylor, Annette F; Pojman, John A

    2016-02-01

    Chemical systems that remain kinetically dormant until activated have numerous applications in materials science. Herein we present a method for the control of gelation that exploits an inbuilt switch: the increase in pH after an induction period in the urease-catalyzed hydrolysis of urea was used to trigger the base-catalyzed Michael addition of a water-soluble trithiol to a polyethylene glycol diacrylate. The time to gelation (minutes to hours) was either preset through the initial concentrations or the reaction was initiated locally by a base, thus resulting in polymerization fronts that converted the mixture from a liquid into a gel (ca. 0.1?mm?min(-1) ). The rate of hydrolytic degradation of the hydrogel depended on the initial concentrations, thus resulting in a gel lifetime of hours to months. In this way, temporal programming of gelation was possible under mild conditions by using the output of an autocatalytic enzyme reaction to drive both the polymerization and subsequent degradation of a hydrogel. PMID:26732469

  15. Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member

    PubMed Central

    Li, Huei-Jiun; Li, Xiaokai; Liu, Nina; Zhang, Huaning; Truglio, James J.; Mishra, Shambhavi; Kisker, Caroline; Garcia-Diaz, Miguel; Tonge, Peter J.

    2014-01-01

    MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate ?-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase, is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in ?-proton acidity. PMID:21830810

  16. Asymmetric 1,3-Dipolar Cycloaddition Reactions Catalyzed by Heterocycle-Based Metal Complexes

    NASA Astrophysics Data System (ADS)

    Suga, Hiroyuki

    Highly enantioselective 1,3-dipolar cycloaddition reactions of several 1,3-dipoles, such as nitrones, nitrile oxides, nitrile imines, diazoalkanes, azomethine imines and carbonyl ylides, catalyzed by heterocyclic supramolecular type of metal complexes consisting of chiral heterocyclic compounds and metal salts were described in terms of their ability of asymmetric induction and enantioface differentiation. The scope and limitations of each cycloaddition reactions were also briefly described. Of the chiral hererocycle-based ligands, chiral bisoxazoline, 2,6-bis(oxazolinyl)pyridine, and related oxazoline ligands are shown to be quite effective in obtaining high levels of asymmtric induction. The combination of the bisoxazoline ligand derived from (1S,2R)-cis-1-amino-2-indanol and metal salts was especially efficient for asymmetric cycloaddition reactions of a number of 1,3-dipoles, such as nitrones, nitrile oxide, nitrile imines, diazoacetates and azomethine imines. The metals utilized for the heterocycle-based complexes show a crucial role for degree of asymmetric induction depending upon the 1,3-dipole used. High levels of enantioselectivity were achieved in 1,3-dipolar cycloaddition reactions of unstable carbonyl ylides with benzyloxyacetaldehyde derivatives, ?-keto esters, 3-(2-alkenoyl)-2-oxazolidinones, and even vinyl ethers, which were catalyzed by Pybox-lanthanoid metal complexes.

  17. Kinetics of acid-catalyzed aldol condensation reactions of aliphatic aldehydes

    NASA Astrophysics Data System (ADS)

    Casale, Mia T.; Richman, Aviva R.; Elrod, Matthew J.; Garland, Rebecca M.; Beaver, Melinda R.; Tolbert, Margaret A.

    Field observations of atmospheric aerosols have established that organic compounds compose a large fraction of the atmospheric aerosol mass. However, the physical/chemical pathway by which organic compounds are incorporated into atmospheric aerosols remains unclear. The potential role of acid-catalyzed reactions of organic compounds on acidic aerosols has been explored as a possible chemical pathway for the incorporation of organic material into aerosols. In the present study, ultraviolet-visible (UV-vis) spectroscopy was used to monitor the kinetics of formation of the products of the acid-catalyzed aldol condensation reaction of a range of aliphatic aldehydes (C 2-C 8). The experiments were carried out at various sulfuric acid concentrations and a range of temperatures in order to estimate the rate constants of such reactions on sulfuric acid aerosols under tropospheric conditions. The rate constants were generally found to decrease as the chain length of the aliphatic aldehyde increased (except for acetaldehyde, which had an unusually small rate constant), increase as a function of sulfuric acid concentration as predicted by excess acidity theory, and showed normal Arrhenius behavior as a function of temperature. While the kinetic data are generally consistent with previous laboratory reports of aldehyde reactivity in various sulfuric acid media, the aldol condensation reactions involving aliphatic aldehydes do not appear fast enough to be responsible for significant transfer of organic material into atmospheric aerosols.

  18. Quantitative characterization of hydroxyl radical generation in a goethite-catalyzed Fenton-like reaction.

    PubMed

    Lin, Zhi-Rong; Zhao, Ling; Dong, Yuan-Hua

    2015-12-01

    In order to find out the truth of influence of solution chemistry on the oxidation efficiency of a goethite-catalyzed Fenton-like reaction, the amount of hydroxyl radicals (OH) was quantified by using coumarin as its trapping agent to produce the only fluorescent derivative 7-hydroxycoumarin (7-HC), because OH was the reactive species responsible for the oxidation activity of Fenton reactions. The concentration of OH achieved maximum at solution pH of 3 and decreased with an increase of solution pH value. However, considerable amount of OH can also generate at near neutral pH (i.e. pH 6 and 7). The concentration of OH was increased both with increasing of goethite and H2O2 dosages, but H2O2 could compete with coumarin to scavenge OH to reduce the formation of 7-HC when the concentration of H2O2 was too high. Anions inhibited OH generation followed an order of H2PO4(-)>SO4(2-)>Cl(-)>NO3(-)>ClO4(-). Higher concentrations of Cl(-) and SO4(2-) resulted in greater inhibition of OH generation. Results of this study demonstrated that the influence of solution chemistry on the oxidation efficiency of the goethite-catalyzed Fenton-like reaction was greatly attributed to the effect of solution chemistry on the amount of OH formed in the process of reaction. PMID:26069944

  19. The Oxidative Fermentation of Ethanol in Gluconacetobacter diazotrophicus Is a Two-Step Pathway Catalyzed by a Single Enzyme: Alcohol-Aldehyde Dehydrogenase (ADHa)

    PubMed Central

    Gmez-Manzo, Sal; Escamilla, Jos E.; Gonzlez-Valdez, Abigail; Lpez-Velzquez, Gabriel; Vanoye-Carlo, Amrica; Marcial-Quino, Jaime; de la Mora-de la Mora, Ignacio; Garcia-Torres, Itzhel; Enrquez-Flores, Sergio; Contreras-Zentella, Martha Lucinda; Arregun-Espinosa, Roberto; Kroneck, Peter M. H.; Sosa-Torres, Martha Elena

    2015-01-01

    Gluconacetobacter diazotrophicus is a N2-fixing bacterium endophyte from sugar cane. The oxidation of ethanol to acetic acid of this organism takes place in the periplasmic space, and this reaction is catalyzed by two membrane-bound enzymes complexes: the alcohol dehydrogenase (ADH) and the aldehyde dehydrogenase (ALDH). We present strong evidence showing that the well-known membrane-bound Alcohol dehydrogenase (ADHa) of Ga. diazotrophicus is indeed a double function enzyme, which is able to use primary alcohols (C2C6) and its respective aldehydes as alternate substrates. Moreover, the enzyme utilizes ethanol as a substrate in a reaction mechanism where this is subjected to a two-step oxidation process to produce acetic acid without releasing the acetaldehyde intermediary to the media. Moreover, we propose a mechanism that, under physiological conditions, might permit a massive conversion of ethanol to acetic acid, as usually occurs in the acetic acid bacteria, but without the transient accumulation of the highly toxic acetaldehyde. PMID:25574602

  20. The oxidative fermentation of ethanol in Gluconacetobacter diazotrophicus is a two-step pathway catalyzed by a single enzyme: alcohol-aldehyde Dehydrogenase (ADHa).

    PubMed

    Gmez-Manzo, Sal; Escamilla, Jos E; Gonzlez-Valdez, Abigail; Lpez-Velzquez, Gabriel; Vanoye-Carlo, Amrica; Marcial-Quino, Jaime; de la Mora-de la Mora, Ignacio; Garcia-Torres, Itzhel; Enrquez-Flores, Sergio; Contreras-Zentella, Martha Lucinda; Arregun-Espinosa, Roberto; Kroneck, Peter M H; Sosa-Torres, Martha Elena

    2015-01-01

    Gluconacetobacter diazotrophicus is a N2-fixing bacterium endophyte from sugar cane. The oxidation of ethanol to acetic acid of this organism takes place in the periplasmic space, and this reaction is catalyzed by two membrane-bound enzymes complexes: the alcohol dehydrogenase (ADH) and the aldehyde dehydrogenase (ALDH). We present strong evidence showing that the well-known membrane-bound Alcohol dehydrogenase (ADHa) of Ga. diazotrophicus is indeed a double function enzyme, which is able to use primary alcohols (C2-C6) and its respective aldehydes as alternate substrates. Moreover, the enzyme utilizes ethanol as a substrate in a reaction mechanism where this is subjected to a two-step oxidation process to produce acetic acid without releasing the acetaldehyde intermediary to the media. Moreover, we propose a mechanism that, under physiological conditions, might permit a massive conversion of ethanol to acetic acid, as usually occurs in the acetic acid bacteria, but without the transient accumulation of the highly toxic acetaldehyde. PMID:25574602

  1. Enzyme Catalysis and the Gibbs Energy

    ERIC Educational Resources Information Center

    Ault, Addison

    2009-01-01

    Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)

  2. Effect of tritium on luminous marine bacteria and enzyme reactions.

    PubMed

    Selivanova, M A; Mogilnaya, O A; Badun, G A; Vydryakova, G A; Kuznetsov, A M; Kudryasheva, N S

    2013-06-01

    The paper studies chronic effect of tritiated water, HTO, (0.0002-200 MBq/L) on bioluminescent assay systems: marine bacteria Photobacterium phosphoreum (intact and lyophilized) and coupled enzyme reactions. Bioluminescence intensity serves as a marker of physiological activity. Linear dependencies of bioluminescent intensity on exposure time or radioactivity were not revealed. Three successive stages in bacterial bioluminescence response to HTO were found: (1) absence of the effect, (2) activation, and (3) inhibition. They were interpreted in terms of reaction of organisms to stress-factor i.e. stress recognition, adaptive response/syndrome, and suppression of physiological function. In enzyme system, in contrast, the kinetic stages mentioned above were not revealed, but the dependence of bioluminescence intensity on HTO specific radioactivity was found. Damage of bacteria cells in HTO (100 MBq/L) was visualized by electron microscopy. Time of bioluminescence inhibition is suggested as a parameter to evaluate the bacterial sensitivity to ionizing radiation. PMID:23410594

  3. Simulating feedback and reversibility in substrate-enzyme reactions

    NASA Astrophysics Data System (ADS)

    van Zwieten, D. A. J.; Rooda, J. E.; Armbruster, D.; Nagy, J. D.

    2011-12-01

    We extend discrete event models (DEM) of substrate-enzyme reactions to include regulatory feedback and reversible reactions. Steady state as well as transient systems are modeled and validated against ordinary differential equation (ODE) models. The approach is exemplified in a model of the first steps of glycolysis with the most common regulatory mechanisms. We find that in glycolysis, feedback and reversibility together act as a significant damper on the stochastic variations of the intermediate products as well as for the stochastic variation of the transit times. This suggests that these feedbacks have evolved to control both the overall rate of, as well as stochastic fluctuations in, glycolysis.

  4. Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

    PubMed

    Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas

    2015-09-15

    Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. PMID:25769515

  5. An Upstream By-product from Ester Activation via NHC-Catalysis Catalyzes Downstream Sulfonyl Migration Reaction.

    PubMed

    Han, Runfeng; He, Liwenze; Liu, Lin; Xie, Xingang; She, Xuegong

    2016-01-01

    A sequential reaction combining N-heterocyclic carbene (NHC) and N-hydroxyphthalimide (NHPI) catalysis allowed for the upstream by-product NHPI, which was generated in the NHC-catalyzed cycloaddition reaction, to act as the catalyst for a downstream nitrogen-to-carbon sulfonyl migration reaction. Enantiomeric excess of the major product in the cycloaddition reaction remained intact in the follow-up sulfonyl migration reaction. PMID:26522328

  6. Cyclic voltammetric simulation for electrochemically mediated enzyme reaction and determination of enzyme kinetic constants.

    PubMed

    Yokoyama, K; Kayanuma, Y

    1998-08-15

    A cyclic voltammetric simulation that can be applied to an electrochemically mediated enzyme reaction involving any substrate and mediator concentrations was developed. Concentration polarization of the substrate in the vicinity of an electrode was considered as well as mediator concentration. Reversible and quasi-reversible electrochemical reactions with one electron followed by an enzyme reaction with two electrons were modeled. The differential equations for the mediator and substrate were solved using digital simulation techniques. The calculated cyclic voltammograms showed prepeaks when there was a low substrate concentration, high mediator concentration, and high enzyme activity. Digital simulation was applied to the determination of the kinetic constants of glucose oxidase (GOx). Cyclic voltammetry was carried out experimentally in a phosphate buffer solution containing GOx, ferrocene derivatives, and glucose. The ratio of the catalytic to the diffusion-controlled current, ik/id, was evaluated. The kcat, KMM, and KMS values were determined from the current values obtained by simulation and by experimentation at various enzyme, mediator, and substrate concentrations. The kcat, KMM, and KMS values for GOx, ferrocenedimethanol, and glucose were 340 s-1, 110 microM, and 30 mM, respectively. PMID:9726163

  7. A specific affinity reagent to distinguish aldehyde dehydrogenases and oxidases. Enzymes catalyzing aldehyde oxidation in an adult moth

    SciTech Connect

    Tasayco, M.L.; Prestwich, G.D. )

    1990-02-25

    Aldehyde dehydrogenase (ALDH) and oxidase (AO) enzymes from the tissue extracts of male and female tobacco budworm moth (Heliothis virescens) were identified after electrophoretic protein separation. AO activity was visualized using formazan- or horseradish peroxidase-mediated staining coupled to the AO-catalyzed oxidation of benzaldehyde. A set of six soluble AO enzymes with isoelectric points from pI 4.6 to 5.3 were detected primarily in the antennal extracts. Partially purified antennal AO enzymes also oxidized both (Z)-9-tetradecenal and (Z)-11-hexadecenal, the two major pheromone components of this moth. ALDH activity was detected using a tritium-labeled affinity reagent based on a known irreversible inhibitor of this enzyme. This labeled vinyl ketone, (3H)(Z)-1,11-hexadecadien-3-one, was synthesized and used to covalently modify the soluble ALDH enzymes from tissue extracts. Molecular subunits of potential ALDH enzymes were visualized in the fluorescence autoradiograms of sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated proteins of the antenna, head, and leg tissues. Covalent modification of these protein subunits decreased specifically in the presence of excess pheromone aldehyde or benzaldehyde. Labeled vinyl ketones are thus novel tools for the identification of molecular subunits of ALDH enzymes.

  8. Recent advancements and challenges of palladiumII-catalyzed oxidation reactions with molecular oxygen as the sole oxidant

    PubMed Central

    Gligorich, Keith M.; Sigman, Matthew S.

    2010-01-01

    During the past 10 years there have been significant advances in PdII-catalyzed oxidation reactions where the use of ligands has led to the development of catalytic systems capable of achieving high turnover numbers, which employ molecular oxygen as the sole stoichiometric oxidant. This Feature article will highlight some of the recent developments in direct molecular oxygen-coupled PdII-catalyzed oxidation reactions with an emphasis on enhanced catalytic systems and new reactions. Additionally, limitations of current catalytic systems, such as ligand oxidation, are presented and their implications for the development of new reactions are discussed. PMID:19662234

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

    PubMed

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

    2011-04-15

    Sequential aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reactions of arylboronic acids to form ?-substituted ketones is described. By using the 1,1'-spirobiindane-7,7'-diol (SPINOL)-based phosphite, an asymmetric version of this type of sequential reaction, with up to 92% ee, was also realized. Our study provided an efficient method to access ?-substituted ketones and might lead to the development of other sequential/tandem reactions with transition metal-catalyzed addition reactions as the key step. PMID:21417359

  10. Cyclones in the Diels-Alder reaction catalyzed by aluminum chloride

    SciTech Connect

    Kiselev, V.D.; Shakirov, I.M.; Konovalov, A.I.

    1986-07-10

    A comparison was made of the kinetic parameters for the uncatalyzed and catalyzed (with aluminum chloride) Diels-Alder reaction between N-arylmaleimides and acrylic, methacrylic, and fumaric esters as dienophiles and phencyclone and tetracyclone as dienes. By thermochemical and spectrophotometric experiments it was shown that the aluminum chloride coordinates with the dienophile in a ratio of 1:1. With a larger concentration of the catalyst coordination also takes place at the carbonyl of the diene. For the complexes of N-arylmaleimides the rate constants for the reaction with free tetracyclone and phencyclone increase by not more than 60 times, those for the esters of the unsaturated acids increase by 300-600 times, whereas those in the reaction with anthracene increase by 10/sup 5/ times. The results are discussed form the standpoint of the change in the energy of the molecular orbitals of the reagents.

  11. Chemiluminescent Reactions Catalyzed by Nanoparticles of Gold, Silver, and Gold/Silver Alloys

    NASA Astrophysics Data System (ADS)

    Abideen, Saqib Ul

    Chemiluminescence (CL) reactions are catalyzed by metals nanoparticles, which display unique catalytic properties due to an increased surface area. The present study describes the catalytic effects of nanoparticles (NP) of silver, gold, and alloys of Au/Ag nanoparticles on the chemiluminescent reaction taking place between luminol and potassium ferricyanide. It was found that silver nanoparticles and alloy nanoparticles enhance the CL process when their sizes remained in the range of 30 nm to 50 nm. The data show that the intensity and rate of chemiluminescence were influenced by the mole fraction of gold and silver in the alloy. Data to this chemiluminescence reaction are modeled by a double exponential curve, which indicates that two competing processes are occurring.

  12. Exploiting Acyl and Enol Azolium Intermediates via NHeterocyclic Carbene Catalyzed Reactions of Alpha-Reducible Aldehydes

    PubMed Central

    Vora, Harit U.; Wheeler, Philip

    2013-01-01

    N-heterocyclic carbenes are well known for their role in catalyzing benzoin and Stetter reactions: the generation of acyl anion equivalents from simple aldehydes to react with a variety of electrophiles. However, when an aldehyde bearing a leaving group or unsaturation adjacent to the acyl anion equivalent is subjected to an NHC, a new avenue of reactivity is unlocked, leading to a number of novel transformations which can generate highly complex products from simple starting materials, many of which are assembled through unconventional bond disconnections. The field of these new reactions - those utilizing ?-reducible aldehydes to access previously unexplored catalytic intermediates has expanded rapidly in the past eight years. This review aims to provide the reader with a historical perspective on the underlying discoveries that led to the current state of the art, a mechanistic description of these reactions, and a summary of the recent advances in this area. PMID:23538785

  13. Solid nanoparticles that catalyze biofuel upgrade reactions at the water/oil interface.

    PubMed

    Crossley, Steven; Faria, Jimmy; Shen, Min; Resasco, Daniel E

    2010-01-01

    A recoverable catalyst that simultaneously stabilizes emulsions would be highly advantageous in streamlining processes such as biomass refining, in which the immiscibility and thermal instability of crude products greatly complicates purification procedures. Here, we report a family of solid catalysts that can stabilize water-oil emulsions and catalyze reactions at the liquid/liquid interface. By depositing palladium onto carbon nanotube-inorganic oxide hybrid nanoparticles, we demonstrate biphasic hydrodeoxygenation and condensation catalysis in three substrate classes of interest in biomass refining. Microscopic characterization of the emulsions supports localization of the hybrid particles at the interface. PMID:20044571

  14. Ultra low momentum neutron catalyzed nuclear reactions on metallic hydride surfaces

    NASA Astrophysics Data System (ADS)

    Widom, A.; Larsen, L.

    2006-04-01

    Ultra low momentum neutron catalyzed nuclear reactions in metallic hydride system surfaces are discussed. Weak interaction catalysis initially occurs when neutrons (along with neutrinos) are produced from the protons that capture “heavy” electrons. Surface electron masses are shifted upwards by localized condensed matter electromagnetic fields. Condensed matter quantum electrodynamic processes may also shift the densities of final states, allowing an appreciable production of extremely low momentum neutrons, which are thereby efficiently absorbed by nearby nuclei. No Coulomb barriers exist for the weak interaction neutron production or other resulting catalytic processes.

  15. Role of Valine 464 in the Flavin Oxidation Reaction Catalyzed by Choline Oxidase

    SciTech Connect

    Finnegan, Steffan; Agniswamy, Johnson; Weber, Irene T.; Gadda, Giovanni

    2010-11-03

    The oxidation of reduced flavin cofactors by oxygen is a very important reaction that is central to the chemical versatility of hundreds of flavoproteins classified as monooxygenases and oxidases. These enzymes are characterized by bimolecular rate constants {ge} 10{sup 5} M{sup -1} s{sup -1} and produce water and hydrogen peroxide, respectively. A hydrophobic cavity close to the reactive flavin C(4a) atom has been previously identified in the 3D structure of monooxygenases but not in flavoprotein oxidases. In the present study, we have investigated by X-ray crystallography, mutagenesis, steady-state, and rapid reaction approaches the role of Val464, which is <6 {angstrom} from the flavin C(4a) atom in choline oxidase. The 3D structure of the Val464Ala enzyme was essentially identical to that of the wild-type enzyme as shown by X-ray crystallography. Time-resolved anaerobic substrate reduction of the enzymes showed that replacement of Val464 with alanine or threonine did not affect the reductive half-reaction. Steady-state and rapid kinetics as well as enzyme-monitored turnovers indicated that the oxidative half-reaction in the Ala464 and Thr464 enzymes was decreased by 50-fold with respect to the wild-type enzyme. We propose that the side chain of Val464 in choline oxidase provides a nonpolar site that is required to guide oxygen in proximity of the C(4a) atom of the flavin, where it will subsequently react via electrostatic catalysis. Visual analysis of available structures suggests that analogous nonpolar sites are likely present in most flavoprotein oxidases. Mechanistic considerations provide rationalization for the differences between sites in monooxygenases and oxidases.

  16. Acyl Enzyme Intermediates in Sortase-Catalyzed Pilus Morphogenesis in Gram-Positive Bacteria?

    PubMed Central

    Guttilla, Irene K.; Gaspar, Andrew H.; Swierczynski, Arlene; Swaminathan, Anu; Dwivedi, Prabhat; Das, Asis; Ton-That, Hung

    2009-01-01

    In gram-positive bacteria, covalently linked pilus polymers are assembled by a specific transpeptidase enzyme called pilus-specific sortase. This sortase is postulated to cleave the LPXTG motif of a pilin precursor between threonine and glycine and to form an acyl enzyme intermediate with the substrate. Pilus polymerization is believed to occur through the resolution of this intermediate upon specific nucleophilic attack by the conserved lysine located within the pilin motif of another pilin monomer, which joins two pilins with an isopeptide bond formed between threonine and lysine. Here, we present evidence for sortase reaction intermediates in Corynebacterium diphtheriae. We show that truncated SrtA mutants that are loosely bound to the cytoplasmic membrane form high-molecular-weight complexes with SpaA polymers secreted into the extracellular milieu. These complexes are not formed with SpaA pilin mutants that have alanine substitutions in place of threonine in the LPXTG motif or lysine in the pilin motif. The same phenotype is observed with alanine substitutions of either the conserved cysteine or histidine residue of SrtA known to be required for catalysis. Remarkably, the assembly of SpaA pili, or the formation of intermediates, is abolished with a SrtA mutant missing the membrane-anchoring domain. We infer that pilus polymerization involves the formation of covalent pilin-sortase intermediates, which occurs within a molecular platform on the exoplasmic face of the cytoplasmic membrane that brings together both sortase and its cognate substrates in close proximity to each other, likely surrounding a secretion apparatus. We present electron microscopic data in support of this picture. PMID:19592583

  17. Reaction Mechanism of the Bicopper Enzyme Peptidylglycine ?-Hydroxylating Monooxygenase*

    PubMed Central

    Abad, Enrique; Rommel, Judith B.; Kstner, Johannes

    2014-01-01

    Peptidylglycine ?-hydroxylating monooxygenase is a noninteracting bicopper enzyme that stereospecifically hydroxylates the terminal glycine of small peptides for its later amidation. Neuroendocrine messengers, such as oxytocin, rely on the biological activity of this enzyme. Each catalytic turnover requires one oxygen molecule, two protons from the solvent, and two electrons. Despite this enzyme having been widely studied, a consensus on the reaction mechanism has not yet been found. Experiments and theoretical studies favor a pro-S abstraction of a hydrogen atom followed by the rebinding of an OH group. However, several hydrogen-abstracting species have been postulated; because two protons are consumed during the reaction, several protonation states are available. An electron transfer between the copper atoms could play a crucial role for the catalysis as well. This leads to six possible abstracting species. In this study, we compare them on equal footing. We perform quantum mechanics/molecular mechanics calculations, considering the glycine hydrogen abstraction. Our results suggest that the most likely mechanism is a protonation of the abstracting species before the hydrogen abstraction and another protonation as well as a reduction before OH rebinding. PMID:24668808

  18. Cure reaction of epoxy resins catalyzed by graphite-based nanofiller

    NASA Astrophysics Data System (ADS)

    Corcione, C. Esposito; Acocella, Maria Rosaria; Giuri, Antonella; Maffezzoli, Alfonso; Guerra, Gaetano

    2015-12-01

    A significant effort was directed to the synthesis of graphene stacks/epoxy nanocomposites and to the analysis of the effect of a graphene precursor on cure reaction of a model epoxy matrix. A comparative thermal analysis of epoxy resins filled with an exfoliated graphite oxide eGO were conducted. The main aim was to understand the molecular origin of the influence of eGO on the Tg of epoxy resins. The higher Tg values previously observed for low curing temperatures, for epoxy resins with graphite-based nanofillers, were easily rationalized by a catalytic activity of graphitic layers on the reaction between the epoxy and amine groups of the resin, which leads to higher crosslinking density in milder conditions. A kinetic analysis of the cure mechanism of the epoxy resin associated to the catalytical activity of the graphite based filler was performed by isothermal DSC measurements. The DSC results showed that the addition of graphite based filler greatly increased the enthalpy of epoxy reaction and the reaction rate, confirming the presence of a catalytic activity of graphitic layers on the crosslinking reaction between the epoxy resin components (epoxide oligomer and di-amine). A kinetic modelling analysis, arising from an auto-catalyzed reaction mechanism, was finally applied to isothermal DSC data, in order to predict the cure mechanism of the epoxy resin in presence of the graphite based nanofiller.

  19. Cobalt- versus ruthenium-catalyzed Alder-ene reaction for the synthesis of credneramide A and B.

    PubMed

    Erver, Florian; Hilt, Gerhard

    2012-06-01

    The first synthesis of the natural products credneramide A and B was accomplished by utilizing Alder-ene reactions between a terminal alkene and an internal alkyne to generate the rather uncommon 1,4-diene substructure of these compounds. Moreover, two different short linear sequences toward these targets are evaluated using either a cobalt-catalyzed Alder-ene reaction of 1-chloropent-1-yne or a ruthenium-catalyzed Alder-ene reaction of 1-trimethylsilyl-1-pentyne with 5-hexenoic acid derivatives in the key step transformation. In addition, saponification of the primary Alder-ene product derived from the cobalt-catalyzed Alder-ene reaction led to credneric acid, the biological precursor of both natural products. PMID:22568728

  20. Non-Precious Metals Catalyze Formal [4 + 2] Cycloaddition Reactions of 1,2-Diazines and Siloxyalkynes under Ambient Conditions

    PubMed Central

    2015-01-01

    Copper(I) and nickel(0) complexes catalyze the formal [4 + 2] cycloaddition reactions of 1,2-diazines and siloxyalkynes, a reaction hitherto best catalyzed by silver salts. These catalysts based on earth abundant metals are not only competent, but the copper catalyst, in particular, promotes cycloadditions of pyrido[2,3-d]pyridazine and pyrido[3,4-d]pyridazine, enabling a new synthesis of quinoline and isoquinoline derivatives, as well as the formal [2 + 2] cycloaddition reaction of cyclohexenone with a siloxyalkyne. PMID:24911346

  1. The radical SAM enzyme AlbA catalyzes thioether bond formation in subtilosin A.

    PubMed

    Flhe, Leif; Knappe, Thomas A; Gattner, Michael J; Schfer, Antje; Burghaus, Olaf; Linne, Uwe; Marahiel, Mohamed A

    2012-04-01

    Subtilosin A is a 35-residue, ribosomally synthesized bacteriocin encoded by the sbo-alb operon of Bacillus subtilis. It is composed of a head-to-tail circular peptide backbone that is additionally restrained by three unusual thioether bonds between three cysteines and the ?-carbon of one threonine and two phenylalanines, respectively. In this study, we demonstrate that these bonds are synthesized by the radical S-adenosylmethionine enzyme AlbA, which is encoded by the sbo-alb operon and comprises two [4Fe-4S] clusters. One [4Fe-4S] cluster is coordinated by the prototypical CXXXCXXC motif and is responsible for the observed S-adenosylmethionine cleavage reaction, whereas the second [4Fe-4S] cluster is required for the generation of all three thioether linkages. On the basis of the obtained results, we propose a new radical mechanism for thioether bond formation. In addition, we show that AlbA-directed substrate transformation is leader-peptide dependent, suggesting that thioether bond formation is the first step during subtilosin A maturation. PMID:22366720

  2. Nickel-Catalyzed Allylic Alkylation with Diarylmethane Pronucleophiles: Reaction Development and Mechanistic Insights.

    PubMed

    Sha, Sheng-Chun; Jiang, Hui; Mao, Jianyou; Bellomo, Ana; Jeong, Soo A; Walsh, Patrick J

    2016-01-01

    Palladium-catalyzed allylic substitution reactions are among the most efficient methods to construct C-C bonds between sp(3) -hybridized carbon atoms. In contrast, much less work has been done with nickel catalysts, perhaps because of the different mechanisms of the allylic substitution reactions. Palladium catalysts generally undergo substitution by a "soft"-nucleophile pathway, wherein the nucleophile attacks the allyl group externally. Nickel catalysts are usually paired with "hard" nucleophiles, which attack the metal before C-C bond formation. Introduced herein is a rare nickel-based catalyst which promotes substitution with diarylmethane pronucleophiles by the soft-nucleophile pathway. Preliminary studies on the asymmetric allylic alkylation are promising. PMID:26756444

  3. Alkali-Stabilized Pt-OHx Species Catalyze Low-Temperature Water-Gas Shift Reactions

    SciTech Connect

    Zhai, Y.; Pierre, D; Si, R; Deng, W; Ferrin, P; Nilekar, A; Peng, G; Herron, J; Bell, D; et. al.

    2010-01-01

    We report that alkali ions (sodium or potassium) added in small amounts activate platinum adsorbed on alumina or silica for the low-temperature water-gas shift (WGS) reaction (H{sub 2}O + CO {yields} H{sub 2} + CO{sub 2}) used for producing H{sub 2}. The alkali ion-associated surface OH groups are activated by CO at low temperatures ({approx}100 C) in the presence of atomically dispersed platinum. Both experimental evidence and density functional theory calculations suggest that a partially oxidized Pt-alkali-O{sub x}(OH){sub y} species is the active site for the low-temperature Pt-catalyzed WGS reaction. These findings are useful for the design of highly active and stable WGS catalysts that contain only trace amounts of a precious metal without the need for a reducible oxide support such as ceria.

  4. Transition metal promoted reactions of boron hydrides. 13. Platinum catalyzed synthesis of 6,9-dialkyldecaboranes

    SciTech Connect

    Mazighi, K.; Carroll, P.J.; Sneddon, L.G. )

    1993-05-12

    Both chloroplatinic acid and platinum bromide have been found to catalyze the reactions of decaborane(14) with terminal olefins, including ethylene, propylene, 1-butene, and 1-pentene, to give the corresponding 6,9-R[sub 2]B[sub 10]H[sub 12] derivatives in high yields. Chemical studies of 6,9-(n-C[sub 5]H[sub 11])[sub 2]B[sub 10]H[sub 12] (1) show that, in contrast to decaborane(14), 1 does not react to form dibase adducts with the Lewis bases Et[sub 3]N, Ph[sub 3]P, Et[sub 2]S, or MeCN. However, 1 undergoes many other reactions, including deprotonation to 6,9-(n-C[sub 5]H[sub 11])[sub 2]B[sub 10]H[sub 11][sup [minus

  5. Secondary sup 15 N isotope effects on the reactions catalyzed by alcohol and formate dehydrogenases

    SciTech Connect

    Rotberg, N.S.; Cleland, W.W. )

    1991-04-23

    Secondary {sup 15}N isotope effects at the N-1 position of 3-acetylpyridine adenine dinucleotide have been determined, by using the internal competition technique, for horse liver alcohol dehydrogenase (LADH) with cyclohexanol as a substrate and yeast formate dehydrogenase (FDH) with formate as a substrate. On the basis of less precise previous measurements of these {sup 15}N isotope effects, the nicotinamide ring of NAD has been suggested to adopt a boat conformation with carbonium ion character at C-4 during hydride transfer. If this mechanism were valid, as N-1 becomes pyramidal an {sup 15}N isotope effect for the reaction catalyzed by LADH was measured. These values suggest that a significant {sup 15}N kinetic isotope effect is not associated with hydride transfer for LADH and FDH. Thus, in contrast with the deformation mechanism previously postulated, the pyridine ring of the nucleotide apparently remains planar during these dehydrogenase reactions.

  6. Gold-Catalyzed Reactions via Cyclopropyl Gold Carbene-like Intermediates

    PubMed Central

    2015-01-01

    Cycloisomerizations of 1,n-enynes catalyzed by gold(I) proceed via electrophilic species with a highly distorted cyclopropyl gold(I) carbene-like structure, which can react with different nucleophiles to form a wide variety of products by attack at the cyclopropane or the carbene carbons. Particularly important are reactions in which the gold(I) carbene reacts with alkenes to form cyclopropanes either intra- or intermolecularly. In the absence of nucleophiles, 1,n-enynes lead to a variety of cycloisomerized products including those resulting from skeletal rearrangements. Reactions proceeding through cyclopropyl gold(I) carbene-like intermediates are ideally suited for the bioinspired synthesis of terpenoid natural products by the selective activation of the alkyne in highly functionalized enynes or polyenynes. PMID:26061916

  7. Surface-catalyzed air oxidation reactions of hydrazines: Tubular reactor studies

    NASA Technical Reports Server (NTRS)

    Kilduff, Jan E.; Davis, Dennis D.; Koontz, Steven L.

    1988-01-01

    The surface-catalyzed air oxidation reactions of hydrazine, monomethylhydrazine, unsymmetrical dimethylhydrazine, symmetrical dimethylhydrazine, trimethylhydrazine and tetramethylhydrazine were investigated in a metal-powder packed turbular flow reactor at 55 plus or minus 3 C. Hydrazine was completely reacted on all surfaces studied. The major products of monomethylhydrazine (MMH) oxidation were methanol, methane and methyldiazene. The di-, tri- and tetra-methyl hydrazines were essentially unreactive under these conditions. The relative catalytic reactivities toward MMH are: Fe greater than Al2O3 greater than Ti greater than Zn greater than 316 SS greater than Cr greater than Ni greater than Al greater than 304L SS. A kinetic scheme and mechanism involving adsorption, oxidative dehydrogenation and reductive elimination reactions on a metal oxide surface are proposed.

  8. An efficient copper-catalyzed cross-coupling reaction of alkyl-triflates with alkyl-Grignard reagents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A highly efficient method for the formation of C-C covalent bonds by cross-coupling reaction between alkyl-triflates and alkyl-Grignard reagents catalyzed by copper catalyst, Li2CuCl4, is described. The reaction works with most primary triflates in diethyl ether at low temperature within 0.5-3 h an...

  9. Rapid Access to Spirocyclized Indolenines via Palladium-Catalyzed Cascade Reactions of Tryptamine Derivatives and Propargyl Carbonate

    PubMed Central

    2015-01-01

    We report the intermolecular palladium-catalyzed reaction of tert-butyl propargyl carbonate with tryptamine derivatives or other indole-containing bis-nucleophiles. The reaction proceeds under mild conditions and with low catalyst loadings to afford novel spiroindolenine products in good to high yields. PMID:24964382

  10. Aryl Ketone Synthesis via Tandem Orthoplatinated Triarylphosphite-Catalyzed Addition Reactions of Arylboronic Acids with Aldehydes Followed by Oxidation

    PubMed Central

    Liao, Yuan-Xi; Hu, Qiao-Sheng

    2010-01-01

    Tandem orthoplatinated triarylphosphite-catalyzed addition reactions of arylboronic acids with aldehydes followed by oxidation to yield aryl ketones is described. 3-Pentanone was identified as a suitable oxidant for the tandem aryl ketone formation reaction. By using microwave energy, aryl ketones were obtained in high yields with the catalyst loading as low as 0.01%. PMID:20849092

  11. TBAI-Catalyzed Reaction between N-Tosylhydrazones and Sulfur: AProcedure toward 1,2,3-Thiadiazole.

    PubMed

    Chen, Jiangfei; Jiang, Yan; Yu, Jin-Tao; Cheng, Jiang

    2016-01-01

    A TBAI-catalyzed reaction between N-tosyl hydrazone and sulfur was developed, leading to 1,2,3-thiadiazoles in moderate to good yields. It represents a facile and practical procedure to access thiadiazole under metal-free conditions. This procedure serves as an improvement for the Hurd-Mori reaction. PMID:26675203

  12. Phosphine-Catalyzed ?,?-Umpolung Domino Reaction of Allenic Esters: Facile Synthesis of Tetrahydrobenzofuranones Bearing a Chiral Tetrasubstituted Stereogenic Carbon Center.

    PubMed

    Takizawa, Shinobu; Kishi, Kenta; Yoshida, Yasushi; Mader, Steffen; Arteaga, Fernando Arteaga; Lee, Shoukou; Hoshino, Manabu; Rueping, Magnus; Fujita, Makoto; Sasai, Hiroaki

    2015-12-14

    An enantio-, diastereo-, regio-, and chemoselective phosphine-catalyzed ?,?-umpolung domino reaction of allenic esters with dienones has been developed for the first time. The designed sequence, involving oxy-Michael and Rauhut-Currier reactions, produced highly functionalized tetrahydrobenzofuranones, bearing a chiral tetrasubstituted stereogenic center, in up to 96?% ee. PMID:26537173

  13. Copper-catalyzed cross-coupling reactions of epoxides with gem-diborylmethane: access to γ-hydroxyl boronic esters.

    PubMed

    Ebrahim-Alkhalil, Ahmed; Zhang, Zhen-Qi; Gong, Tian-Jun; Su, Wei; Lu, Xiao-Yu; Xiao, Bin; Fu, Yao

    2016-04-01

    Herein, we describe a novel copper-catalyzed epoxide opening reaction with gem-diborylmethane. Aliphatic, aromatic epoxides as well as aziridines are converted to the corresponding γ-pinacolboronate alcohols or amines in moderate to excellent yields. This new reaction provides beneficial applications for classic epoxide substrates as well as interesting gem-diborylalkane reagents. PMID:26973991

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

    PubMed

    Ozen, Cihan; Tzn, Nurcan ?

    2012-04-01

    In this study, the mechanism of CuAAC reaction and the structure of copper acetylides have been investigated with quantum mechanical methods, namely B3LYP/6-311+G(d,p). A series of possible copper-acetylide species which contain up to four copper atoms and solvent molecules as ligand has been evaluated and a four-copper containing copper-acetylide, M1A, was proposed more likely to form based on its thermodynamic stability. The reaction has been modeled with a representative simple alkyne and a simple azide to concentrate solely on the electronic effects of the mechanism. Later, the devised mechanism has been applied to a real system, namely to the reaction of 2-azido-1,1,1-trifluoroethane and ethynylbenzene in the presence of copper. The copper catalyst transforms the concerted uncatalyzed reaction to a stepwise process and lowers the activation barrier. The pre-reactive complexation of the negatively charged secondary nitrogen of azide and the positively charged copper of copper-acetylide brings the azide and the alkyne to a suitable geometry for cycloaddition to take place. The calculated activation barrier difference between the catalyzed and the uncatalyzed reactions is consistent with faster and the regioselective synthesis of triazole product. PMID:22306418

  15. Phenylalanine Ammonia-Lyase-Catalyzed Deamination of an Acyclic Amino Acid: Enzyme Mechanistic Studies Aided by a Novel Microreactor Filled with Magnetic Nanoparticles.

    PubMed

    Weiser, Diána; Bencze, László Csaba; Bánóczi, Gergely; Ender, Ferenc; Kiss, Róbert; Kókai, Eszter; Szilágyi, András; Vértessy, Beáta G; Farkas, Ödön; Paizs, Csaba; Poppe, László

    2015-11-01

    Phenylalanine ammonia-lyase (PAL), found in many organisms, catalyzes the deamination of l-phenylalanine (Phe) to (E)-cinnamate by the aid of its MIO prosthetic group. By using PAL immobilized on magnetic nanoparticles and fixed in a microfluidic reactor with an in-line UV detector, we demonstrated that PAL can catalyze ammonia elimination from the acyclic propargylglycine (PG) to yield (E)-pent-2-ene-4-ynoate. This highlights new opportunities to extend MIO enzymes towards acyclic substrates. As PG is acyclic, its deamination cannot involve a Friedel-Crafts-type attack at an aromatic ring. The reversibility of the PAL reaction, demonstrated by the ammonia addition to (E)-pent-2-ene-4-ynoate yielding enantiopure l-PG, contradicts the proposed highly exothermic single-step mechanism. Computations with the QM/MM models of the N-MIO intermediates from L-PG and L-Phe in PAL show similar arrangements within the active site, thus supporting a mechanism via the N-MIO intermediate. PMID:26345352

  16. MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes

    PubMed Central

    Braun, Andreas; Halwachs, Bettina; Geier, Martina; Weinhandl, Katrin; Guggemos, Michael; Marienhagen, Jan; Ruff, Anna J.; Schwaneberg, Ulrich; Rabin, Vincent; Torres Pazmiño, Daniel E.; Thallinger, Gerhard G.; Glieder, Anton

    2012-01-01

    Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL: http://www.MuteinDB.org PMID:22730453

  17. Difructosan anhydrides III preparation from sucrose by coupled enzyme reaction.

    PubMed

    Hang, Hua; Miao, Ming; Li, Yungao; Jiang, Bo; Mu, Wanmeng; Zhang, Tao

    2013-02-15

    Difructosan anhydrides III (DFA III) preparation was usually obtained by inulin hydrolysis with inulin fructotransferase (IFTase). The fructofuranosidic linkages of inulin were the same as fructooligosaccharides (FOS), which was synthesized by sucrose with fructosyltransferase (FTase). FOS was mainly composed of 1-kestose (GF(2)), nystose (GF(3)) and fructofuranosylnystose (GF(4)), and nystose was observed to be the smallest substrate for IFTase to synthesize DFA III. So sucrose, much cheaper than inulin, was considered to produce DFA III by coupled FTase and IFTase reaction. DFA III yield was obtained about 100mg/g (DFA III weight/sucrose weight) through this method. The results demonstrated the high potential of the coupled enzyme reaction as a novel DFA III producing method. PMID:23399196

  18. Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions.

    PubMed

    Kennedy, David C; McKay, Craig S; Legault, Marc C B; Danielson, Dana C; Blake, Jessie A; Pegoraro, Adrian F; Stolow, Albert; Mester, Zoltan; Pezacki, John Paul

    2011-11-01

    Copper toxicity is a critical issue in the development of copper-based catalysts for copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions for applications in living systems. The effects and related toxicity of copper on mammalian cells are dependent on the ligand environment. Copper complexes can be highly toxic, can induce changes in cellular metabolism, and can be rapidly taken up by cells, all of which can affect their ability to function as catalysts for CuAAC in living systems. Herein, we have evaluated the effects of a number of copper complexes that are typically used to catalyze CuAAC reactions on four human cell lines by measuring mitochondrial activity based on the metabolism of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to study toxicity, inductively coupled plasma mass spectrometry to study cellular uptake, and coherent anti-Stokes Raman scattering (CARS) microscopy to study effects on lipid metabolism. We find that ligand environment around copper influences all three parameters. Interestingly, for the Cu(II)-bis-L-histidine complex (Cu(his)(2)), cellular uptake and metabolic changes are observed with no toxicity after 72 h at micromolar concentrations. Furthermore, we show that under conditions where other copper complexes kill human hepatoma cells, Cu(I)-L-histidine is an effective catalyst for CuAAC labeling of live cells following metabolic incorporation of an alkyne-labeled sugar (Ac(4)ManNAl) into glycosylated proteins expressed on the cell surface. This result suggests that Cu(his)(2) or derivatives thereof have potential for in vivo applications where toxicity as well as catalytic activity are critical factors for successful bioconjugation reactions. PMID:21970470

  19. Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models

    NASA Astrophysics Data System (ADS)

    Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

    2010-11-01

    Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtoliters. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small subcellular compartment. This is achieved by applying a mesoscopic version of the quasisteady-state assumption to the exact Fokker-Planck equation associated with the Poisson representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing subcellular volume, decreasing Michaelis-Menten constants, and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.

  20. Enantioselective Diels-Alder reactions of unsaturated beta-ketoesters catalyzed by chiral ruthenium PNNP complexes.

    PubMed

    Schotes, Christoph; Mezzetti, Antonio

    2011-01-01

    We report here dicationic ruthenium PNNP complexes that promote the enantioselective Diels-Alder reaction of alpha-methylene beta-ketoesters with various dienes. Complex [Ru(OEt2)2(PNNP)](PF6)2, formed in situ from [RuCl2,(PNNP)] and (Et3O)PF6 (2 equiv.), catalyzes the Diels-Alder reaction of such unsaturated beta-ketoesters to give novel alkoxycarbonyltetrahydro-1-indanone derivatives (nine examples) with up to 93% ee. The crystal structure of the substrate-catalyst adduct shows that the lower face of the substrate is shielded by a phenyl ring of the PNNP ligand, which accounts for the high enantioselectivity. The attack of the diene from the open re enantioface of the unsaturated beta-ketoester is consistent with the absolute configuration of the product. A useful application of this method is the reaction with Dane's diene to give estrone derivatives with up to 99% ee and an ester-exo:endo ratio of up to 145:1 (after recrystallization). Besides the enantioselective formation of all-carbon quaternary centers, this methodology is notable because unsaturated beta-ketoesters have been rarely used in Diels-Alder reactions. Furthermore, enantiomerically pure estrone derivatives are interesting in view of their potential applications, including the treatment of breast cancer. PMID:21678768

  1. Tyrosinase-catalyzed modification of Bombyx mori silk fibroin: grafting of chitosan under heterogeneous reaction conditions.

    PubMed

    Freddi, Giuliano; Anghileri, Anna; Sampaio, Sandra; Buchert, Johanna; Monti, Patrizia; Taddei, Paola

    2006-09-01

    The capability of mushroom tyrosinase to catalyze the oxidation of tyrosine residues of Bombyx mori silk fibroin was studied under heterogeneous reaction conditions, by using a series of silk substrates differing in surface and bulk morphology and structure, i.e. hydrated and insoluble gels, mechanically generated powder and fibre. Tyrosinase was able to oxidize 10-11% of the tyrosine residues of silk gels. The yield of the reaction was very low for the powder and undetectable for fibres. FT-Raman spectroscopy gave evidence of the oxidation reaction. New bands attributable to vibrations of oxidized tyrosine species (o-quinone) appeared, and the value of the I853/I829 intensity ratio of the tyrosine doublet changed following oxidation of tyrosine. The thermal behaviour of SF substrates was not affected by enzymatic oxidation. o-Quinones formed by tyrosinase onto gels and powder were able to undergo non-enzymatic coupling with chitosan. FT-IR and FT-Raman spectroscopy provided clear evidence of the formation of silk-chitosan bioconjugates under heterogeneous reaction conditions. Chitosan grafting caused a beta-sheet --> random coil conformational transition of silk fibroin and significant changes in the thermal behaviour. Chitosan grafting did not occur, or occurred at an undetectable level on silk fibres. The results reported in this study show the potential of the enzymatically initiated protein-polysaccharide grafting for the production of a new range of bio-based, environmentally friendly polymers. PMID:16621091

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

    PubMed

    Sieffert, Nicolas; Bhl, Michael

    2010-06-16

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

  3. Fenton-Like Reaction Catalyzed by the Rare Earth Inner Transition Metal Cerium

    PubMed Central

    HECKERT, ERIC G.; SEAL, SUDIPTA; SELF, WILLIAM T.

    2011-01-01

    Cerium (Ce) is a rare earth metal that is not known to have any biological role. Cerium oxide materials of several sizes and shapes have been developed in recent years as a scaffold for catalysts. Indeed even cerium oxide nanoparticles themselves have displayed catalytic activities and antioxidant properties in tissue culture and animal models. Because of ceria's ability to cycle between the +3 and +4 states at oxygen vacancy sites, we investigated whether cerium metal would catalyze a Fenton-like reaction with hydrogen peroxide. Indeed, cerium chloride did exhibit radical production in the presence of hydrogen peroxide, as assessed by relaxation of supercoiled plasmid DNA. Radical production in this reaction was also followed by production of radical cation of 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS). Radical scavengers and spin traps were capable of competing with ABTS for radicals produced in this cerium dependent Fenton-like reaction. Electron paramagnetic resonance experiments reveal both hydroxyl radical and superoxide anion in a reaction containing cerium and hydrogen peroxide. Based on these results we propose that cerium is capable of redox-cycling with peroxide to generate damaging oxygen radicals. PMID:18678042

  4. Organo-Iodine(III)-Catalyzed Oxidative Phenol-Arene and Phenol-Phenol Cross-Coupling Reaction.

    PubMed

    Morimoto, Koji; Sakamoto, Kazuma; Ohshika, Takao; Dohi, Toshifumi; Kita, Yasuyuki

    2016-03-01

    The direct oxidative coupling reaction has been an attractive tool for environmentally benign chemistry. Reported herein is that the hypervalent iodine catalyzed oxidative metal-free cross-coupling reaction of phenols can be achieved using Oxone as a terminal oxidant in 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP). This method features a high efficiency and regioselectivity, as well as functional-group tolerance under very mild reaction conditions without using metal catalysts. PMID:26879796

  5. Enzyme-functionalized vascular grafts catalyze in-situ release of nitric oxide from exogenous NO prodrug.

    PubMed

    Wang, Zhihong; Lu, Yaxin; Qin, Kang; Wu, Yifan; Tian, Yingping; Wang, Jianing; Zhang, Jimin; Hou, Jingli; Cui, Yun; Wang, Kai; Shen, Jie; Xu, Qingbo; Kong, Deling; Zhao, Qiang

    2015-07-28

    Nitric oxide (NO) is an important signaling molecule in cardiovascular system, and the sustained release of NO by endothelial cells plays a vital role in maintaining patency and homeostasis. In contrast, lack of endogenous NO in artificial blood vessel is believed to be the main cause of thrombus formation. In this study, enzyme prodrug therapy (EPT) technique was employed to construct a functional vascular graft by immobilization of galactosidase on the graft surface. The enzyme-functionalized grafts exhibited excellent catalytic property in decomposition of the exogenously administrated NO prodrug. Localized and on-demand release of NO was demonstrated by in vitro release assay and fluorescent probe tracing in an ex vivo model. The immobilized enzyme retained catalytic property even after subcutaneous implantation of the grafts for one month. The functional vascular grafts were implanted into the rat abdominal aorta with a 1-month monitoring period. Results showed effective inhibition of thrombus formation in vivo and enhancement of vascular tissue regeneration and remodeling on the grafts. Thus, we create an enzyme-functionalized vascular graft that can catalyze prodrug to release NO locally and sustainably, indicating that this approach may be useful to develop new cell-free vascular grafts for treatment of vascular diseases. PMID:26004323

  6. Evidencing an inner-sphere mechanism for NHC-Au(I)-catalyzed carbene-transfer reactions from ethyl diazoacetate

    PubMed Central

    Fructos, Manuel R; Urbano, Juan

    2015-01-01

    Summary Kinetic experiments based on the measurement of nitrogen evolution in the reaction of ethyl diazoacetate (N2CHCO2Et, EDA) and styrene or methanol catalyzed by the [IPrAu]+ core (IPr = 1,3-bis(diisopropylphenyl)imidazole-2-ylidene) have provided evidence that the transfer of the carbene group CHCO2Et to the substrate (styrene or methanol) takes place in the coordination sphere of Au(I) by means of an inner-sphere mechanism, in contrast to the generally accepted proposal of outer-sphere mechanisms for Au(I)-catalyzed reactions. PMID:26664649

  7. Stereospecific nickel-catalyzed cross-coupling reactions of benzylic ethers and esters.

    PubMed

    Tollefson, Emily J; Hanna, Luke E; Jarvo, Elizabeth R

    2015-08-18

    This Account presents the development of a suite of stereospecific alkyl-alkyl cross-coupling reactions employing nickel catalysts. Our reactions complement related nickel-catalyzed stereoconvergent cross-coupling reactions from a stereochemical and mechanistic perspective. Most reactions of alkyl electrophiles with low-valent nickel complexes proceed through alkyl radicals and thus are stereoablative; the correct enantioselective catalyst can favor the formation of one enantiomer. Our reactions, in contrast, are stereospecific. Enantioenriched ethers and esters are cleanly converted to cross-coupled products with high stereochemical fidelity. While mechanistic details are still to be refined, our results are consistent with a polar, two-electron oxidative addition that avoids the formation of radical intermediates. This reactivity is unusual for a first-row transition metal. The cross-coupling reactions engage a range of benzylic ethers and esters, including methyl ethers, tetrahydropyrans, tetrahydrofurans, esters, and lactones. Coordination of the arene substituent to the nickel catalyst accelerates the reactions. Arenes with low aromatic stabilization energies, such as naphthalene, benzothiophene, and furan, serve as the best ligands and provide the highest reactivity. Traceless directing groups that accelerate reactions of sluggish substrates are described, providing partial compensation for arene coordination. Kumada, Negishi, and Suzuki reactions provide incorporation of a broad range of transmetalating agents. In Kumada coupling reactions, a full complement of Grigard reagents, including methyl, n-alkyl, and aryl Grignard reagents, are employed. In reactions employing methylmagnesium iodide, ligation of the nickel catalyst by rac-BINAP or DPEphos provides the highest yield and stereospecificity. For all other Grignard reagents, Ni(dppe)Cl2 has emerged as the best catalyst. Negishi cross-coupling reactions employing dimethylzinc are reported as a strategy to increase the functional group tolerance of the reaction. We also describe Suzuki reactions using arylboronic esters. These reactions provided the first example in the series of a switch in stereochemical outcome. The reactions maintain stereospecificity, but reactions employing different achiral ligands provide opposite enantiomers of the product. Use of an N-heterocyclic carbene ligand, SIMes, provides inversion, consistent with our prior work in Kumada and Negishi coupling reactions. Use of the electron-rich phosphine PCy3, however, provides retention with stereospecificity, signaling a change in the mechanistic details. Potential applications of the reported cross-coupling reactions include the synthesis of medicinal agents containing the 2-arylalkane and 1,1-diarylalkane moieties, which are pharmacophores in medicinal chemistry. These moieties are found in compounds with activity against a broad range of indications, including cancer, heart disease, diabetes, osteoporosis, smallpox, tuberculosis, and insomnia. We highlight representative examples of bioactive compounds that we have prepared with high enantioselectivity employing our methods, as well as the discovery of a new anti-cancer agent. PMID:26197033

  8. Isolation of bis(copper) key intermediates in Cu-catalyzed azide-alkyne click reaction

    PubMed Central

    Jin, Liqun; Tolentino, Daniel R.; Melaimi, Mohand; Bertrand, Guy

    2015-01-01

    The copper-catalyzed 1,3-dipolar cycloaddition of an azide to a terminal alkyne (CuAAC) is one of the most popular chemical transformations, with applications ranging from material to life sciences. However, despite many mechanistic studies, direct observation of key components of the catalytic cycle is still missing. Initially, mononuclear species were thought to be the active catalysts, but later on, dinuclear complexes came to the front. We report the isolation of both a previously postulated ?,?-bis(copper) acetylide and a hitherto never-mentioned bis(metallated) triazole complex. We also demonstrate that although mono- and bis-copper complexes promote the CuAAC reaction, the dinuclear species are involved in the kinetically favored pathway. PMID:26601202

  9. Isolation of bis(copper) key intermediates in Cu-catalyzed azide-alkyne "click reaction".

    PubMed

    Jin, Liqun; Tolentino, Daniel R; Melaimi, Mohand; Bertrand, Guy

    2015-06-01

    The copper-catalyzed 1,3-dipolar cycloaddition of an azide to a terminal alkyne (CuAAC) is one of the most popular chemical transformations, with applications ranging from material to life sciences. However, despite many mechanistic studies, direct observation of key components of the catalytic cycle is still missing. Initially, mononuclear species were thought to be the active catalysts, but later on, dinuclear complexes came to the front. We report the isolation of both a previously postulated π,σ-bis(copper) acetylide and a hitherto never-mentioned bis(metallated) triazole complex. We also demonstrate that although mono- and bis-copper complexes promote the CuAAC reaction, the dinuclear species are involved in the kinetically favored pathway. PMID:26601202

  10. Transition Metal Catalyzed Reactions of Carbohydrates: a Nonoxidative Approach to Oxygenated Organics

    SciTech Connect

    Andrews, Mark

    1997-01-08

    There is a critical need for new environmentally friendly processes in the United States chemical industry as legislative and economic pressures push the industry to zero-waste and cradle-to-grave responsibility for the products they produce. Carbohydrates represent a plentiful, renewable resource, which for some processes might economically replace fossil feedstocks. While the conversion of biomass to fuels, is still not generally economical, the selective synthesis of a commodity or fine chemical, however, could compete effectively if appropriate catalytic conversion systems can be found. Oxygenated organics, found in a variety of products such as nylon and polyester, are particularly attractive targets. We believe that with concerted research efforts, homogeneous transition metal catalyzed reactions could play a significant role in bringing about this future green chemistry technology.

  11. Palladium-catalyzed reactions in the synthesis of 3- and 4-substituted indoles. 4

    SciTech Connect

    Hegedus, L.S.; Sestrick, M.R.; Michaelson, E.T.; Harrington, P.J. )

    1989-08-18

    4-Bromo-1-tosylindole (1) was converted to tricyclic indole enone 11, a potential intermediate in the synthesis of tetracyclic ergot alkaloids, by a series of palladium-catalyzed processes. Attempts to construct the ergot D ring by the hetero-Diels-Alder reaction of enone 11 and 1-azabutadiene 12 produced not the expected (4 + 2) adduct 13 but the benz(cd)indoline derivative 14 resulting from attack of the aza diene at the indole 2-position. The thermodynamic stability of the naphthol nucleus makes enone 11 generally susceptible to attack at the indole 2-position, as evidenced by the attack of hydride and methyl cuprate nucleophiles at this portion forming indolines 16 and 17, respectively.

  12. Artificial Peroxidase/Oxidase Multiple Enzyme System Based on Supramolecular Hydrogel and Its Application as a Biocatalyst for Cascade Reactions.

    PubMed

    Qu, Rui; Shen, Liangliang; Qu, Aoting; Wang, Ruolin; An, Yingli; Shi, Linqi

    2015-08-01

    Inspired by delicate structures and multiple functions of natural multiple enzyme architectures such as peroxisomes, we constructed an artificial multiple enzyme system by coencapsulation of glucose oxidases (GOx) and artificial peroxidases in a supramolecular hydrogel. The artificial peroxidase was a functional complex micelle, which was prepared by the self-assembly of diblock copolymer and hemin. Compared with catalase or horseradish peroxidase (HRP), the functional micelle exhibited comparable activity and better stability, which provided more advantages in constructing a multienzyme with a proper oxidase. The hydrogel containing the two catalytic centers was further used as a catalyst for green oxidation of glucose, which was a typical cascade reaction. Glucose was oxidized by oxygen (O2) via the GOx-mediated reaction, producing toxic intermediate hydrogen peroxide (H2O2). The produced H2O2 further oxidized peroxidase substrates catalyzed by hemin-micelles. By regulating the diffusion modes of the enzymes and substrates, the artificial multienzyme based on hydrogel could successfully activate the cascade reaction, which the soluble enzyme mixture could not achieve. The hydrogel, just like a protective covering, protected oxidases and micelles from inactivation via toxic intermediates and environmental changes. The artificial multienzyme could efficiently achieve the oxidation task along with effectively eliminating the toxic intermediates. In this way, this system possesses great potentials for glucose detection and green oxidation of a series of substrates related to biological processes. PMID:26173996

  13. Transition-metal-catalyzed carbonylation reactions of olefins and alkynes: a personal account.

    PubMed

    Wu, Xiao-Feng; Fang, Xianjie; Wu, Lipeng; Jackstell, Ralf; Neumann, Helfried; Beller, Matthias

    2014-04-15

    Carbon monoxide was discovered and identified in the 18th century. Since the first applications in industry 80 years ago, academic and industrial laboratories have broadly explored CO's use in chemical reactions. Today organic chemists routinely employ CO in organic chemistry to synthesize all kinds of carbonyl compounds. Despite all these achievements and a century of carbonylation catalysis, many important research questions and challenges remain. Notably, apart from academic developments, industry applies carbonylation reactions with CO on bulk scale. In fact, today the largest applications of homogeneous catalysis (regarding scale) are carbonylation reactions, especially hydroformylations. In addition, the vast majority of acetic acid is produced via carbonylation of methanol (Monsanto or Cativa process). The carbonylation of olefins/alkynes with nucleophiles, such as alcohols and amines, represent another important type of such reactions. In this Account, we discuss our work on various carbonylations of unsaturated compounds and related reactions. Rhodium-catalyzed isomerization and hydroformylation reactions of internal olefins provide straightforward access to higher value aldehydes. Catalytic hydroaminomethylations offer an ideal way to synthesize substituted amines and even heterocycles directly. More recently, our group has also developed so-called alternative metal catalysts based on iridium, ruthenium, and iron. What about the future of carbonylation reactions? CO is already one of the most versatile C1 building blocks for organic synthesis and is widely used in industry. However, because of CO's high toxicity and gaseous nature, organic chemists are often reluctant to apply carbonylations more frequently. In addition, new regulations have recently made the transportation of carbon monoxide more difficult. Hence, researchers will need to develop and more frequently use practical and benign CO-generating reagents. Apart from formates, alcohols, and metal carbonyls, carbon dioxide also offers interesting options. Industrial chemists seek easy to prepare catalysts and patent-free ligands/complexes. In addition, non-noble metal complexes will interest both academic and industrial researchers. The novel Lucite process for methyl methacrylate is an important example of an improved catalyst. This reaction makes use of a specific palladium/bisphosphine catalyst, which led to the successful implementation of the technology. More active and productive catalysts for related carbonylations of less reactive olefins would allow for other large scale applications of this methodology. From an academic point of view, researchers continue to look for selective reactions with more functionalized olefins. Finally, because of the volatility of simple metal carbonyl complexes, carbonylation reactions today remain a domain of homogeneous catalysis. The invention of more stable and recyclable heterogeneous catalysts or metal-free carbonylations (radical carbonylations) will be difficult, but could offer interesting challenges for young chemists. PMID:24564478

  14. Glutathione transferase mimics: micellar catalysis of an enzymic reaction.

    PubMed

    Lindkvist, B; Weinander, R; Engman, L; Koetse, M; Engberts, J B; Morgenstern, R

    1997-04-01

    Substances that mimic the enzyme action of glutathione transferases (which serve in detoxification) are described. These micellar catalysts enhance the reaction rate between thiols and activated halogenated nitroarenes as well as alpha,beta-unsaturated carbonyls. The nucleophilic aromatic substitution reaction is enhanced by the following surfactants in descending order: poly(dimethyldiallylammonium - co - dodecylmethyldiallylammonium) bromide (86/14) >cetyltrimethylammonium bromide>zwittergent 3-16 (n-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulphonate)>zwittergent+ ++ 3-14 (n-tetradecyl-N,N-dimethyl - 3 - ammonio -1 - propanesulphonate) approximately N,N - dimethyl - laurylamine N-oxide>N,N-dimethyloctylamine N-oxide. The most efficient catalyst studied is a polymeric material that incorporates surfactant properties (n-dodecylmethyldiallylammonium bromide) and opens up possibilities for engineering sequences of reactions on a polymeric support. Michael addition to alpha,beta-unsaturated carbonyls is exemplified by a model substance, trans-4-phenylbut-3-en-2-one, and a toxic compound that is formed during oxidative stress, 4-hydroxy-2-undecenal. The latter compound is conjugated with the highest efficiency of those tested. Micellar catalysts can thus be viewed as simple models for the glutathione transferases highlighting the influence of a positive electrostatic field and a non-specific hydrophobic binding site, pertaining to two catalytic aspects, namely thiolate anion stabilization and solvent shielding. PMID:9173899

  15. EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions

    PubMed Central

    Cuesta, Sergio Martinez; Furnham, Nicholas; Holliday, Gemma L.

    2014-01-01

    EC-BLAST is an algorithm for quantitative similarity searches between enzyme reactions at three levels a) bond change, b) reaction centre and c) reaction structure similarity. It exploits the knowledge of bond changes and reaction patterns for all known biochemical reactions derived from atom-atom mapping (AAM) across each reaction. This has the potential to improve the established enzyme classification system, to find novel biochemical transformations, to improve the assignment of enzyme function to sequences, as well as for the re-engineering of enzymes. EC-BLAST URL: http://www.ebi.ac.uk/thornton-srv/software/rbl/ PMID:24412978

  16. Palladium-Based Nanomaterials: A Platform to Produce Reactive Oxygen Species for Catalyzing Oxidation Reactions.

    PubMed

    Long, Ran; Huang, Hao; Li, Yaping; Song, Li; Xiong, Yujie

    2015-11-01

    Oxidation reactions by molecular oxygen (O2 ) over palladium (Pd)-based nanomaterials are a series of processes crucial to the synthesis of fine chemicals. In the past decades, investigations of related catalytic materials have mainly been focused on the synthesis of Pd-based nanomaterials from the angle of tailoring their surface structures, compositions and supporting materials, in efforts to improve their activities in organic reactions. From the perspective of rational materials design, it is imperative to address the fundamental issues associated with catalyst performance, one of which should be oxygen activation by Pd-based nanomaterials. Here, the fundamentals that account for the transformation from O2 to reactive oxygen species over Pd, with a focus on singlet O2 and its analogue, are introduced. Methods for detecting and differentiating species are also presented to facilitate future fundamental research. Key factors for tuning the oxygen activation efficiencies of catalytic materials are then outlined, and recent developments in Pd-catalyzed oxygen-related organic reactions are summarized in alignment with each key factor. To close, we discuss the challenges and opportunities for photocatalysis research at this unique intersection as well as the potential impact on other research fields. PMID:26422795

  17. Analysis of the HindIII-catalyzed reaction by time-resolved crystallography

    SciTech Connect

    Kawamura, Takashi; Kobayashi, Tomoki; Watanabe, Nobuhisa

    2015-02-01

    A time-resolved study using the freeze-trap method elucidates the mechanism of the DNA-cleaving reaction of HindIII. In order to investigate the mechanism of the reaction catalyzed by HindIII, structures of HindIII–DNA complexes with varying durations of soaking time in cryoprotectant buffer containing manganese ions were determined by the freeze-trap method. In the crystal structures of the complexes obtained after soaking for a longer duration, two manganese ions, indicated by relatively higher electron density, are clearly observed at the two metal ion-binding sites in the active site of HindIII. The increase in the electron density of the two metal-ion peaks followed distinct pathways with increasing soaking times, suggesting variation in the binding rate constant for the two metal sites. DNA cleavage is observed when the second manganese ion appears, suggesting that HindIII uses the two-metal-ion mechanism, or alternatively that its reactivity is enhanced by the binding of the second metal ion. In addition, conformational change in a loop near the active site accompanies the catalytic reaction.

  18. Kinetics of Acid-Catalyzed Aldol Condensation Reactions of Aliphatic Aldehydes

    NASA Astrophysics Data System (ADS)

    Elrod, M. J.; Casale, M. T.; Richman, A. R.; Beaver, M. R.; Garland, R. M.; Tolbert, M. A.

    2006-12-01

    While it is well established that organic compounds compose a large fraction of the atmospheric aerosol mass, the mechanisms through which organics are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds with carbonyl groups have recently been suggested as important pathways for transfer of volatile organics into acidic aerosols. In the present study, ultraviolet-visible (UV-Vis) spectroscopy was used to monitor the kinetics of formation of the products of the aldol condensation reaction of a range of aliphatic aldehydes (C2-C8) The experiments were carried out at various sulfuric acid concentrations and a range of temperatures in order to estimate the rate constants of such reactions on sulfuric acid aerosols under tropospheric conditions. The rate constants were generally found to decrease as the chain length of the aliphatic aldehyde increased (except for acetaldehyde, which had an unusually small rate constant), increase as a function of sulfuric acid concentration as predicted by excess acidity theory, and showed normal Arrhenius behavior as a function of temperature.

  19. A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates

    SciTech Connect

    Netzel, D.A.

    1991-04-01

    Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center_dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

  20. A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates

    SciTech Connect

    Netzel, D.A.

    1991-04-01

    Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

  1. Acetyl coenzyme A:salutaridinol-7-O-acetyltransferase from papaver somniferum plant cell cultures. The enzyme catalyzing the formation of thebaine in morphine biosynthesis.

    PubMed

    Lenz, R; Zenk, M H

    1995-12-29

    Acetyl coenzyme A:salutaridinol-7-O-acetyltransferase, a highly substrate-specific enzyme, has been purified nearly 3,000-fold to homogeneity from Papaver somniferum plant cell suspension cultures. Purification was achieved by fractionated ammonium sulfate precipitation, dye-ligand affinity chromatography on matrex red A, gel filtration, ion exchange chromatography on Mono Q and a second dye-ligand affinity chromatography on fractogel TSK AF Blue. The purified enzyme was a single polypeptide with an M(r) = 50,000 displaying an isoelectric point of 4.8, a pH optimum between pH 6 and 9 and a temperature optimum at 47 degrees C. The Km values for the substrate salutaridinol and the co-substrate acetyl co-enzyme A were 7 and 46 microM, respectively. Salutaridinol-7-O-acetyltransferase catalyzes the stoichiometric transfer of the acetyl group from acetyl coenzyme A to the 7-OH group of salutaridinol yielding salutaridinol-7-O-acetate, which is a new intermediate in morphine biosynthesis. Salutaridinol-7-O-acetate undergoes a subsequent spontaneous allylic elimination at pH 8-9, leading to the formation of thebaine (1), the first morphinan alkaloid with the complete pentacyclic ring system, or at pH 7 leading to dibenz[d,f]azonine alkaloids that contain a nine-membered ring. Acetylation and subsequent allylic elimination is a new enzymic mechanism in alkaloid biosynthesis, which in the poppy plant can transform one precursor into alkaloids possessing markedly different ring systems, depending on the reaction pH. PMID:8537369

  2. Iron- and indium-catalyzed reactions toward nitrogen- and oxygen-containing saturated heterocycles.

    PubMed

    Cornil, Johan; Gonnard, Laurine; Bensoussan, Charllie; Serra-Muns, Anna; Gnamm, Christian; Commandeur, Claude; Commandeur, Malgorzata; Reymond, Sbastien; Gurinot, Amandine; Cossy, Janine

    2015-03-17

    A myriad of natural and/or biologically active products include nitrogen- and oxygen-containing saturated heterocycles, which are thus considered as attractive scaffolds in the drug discovery process. As a consequence, a wide range of reactions has been developed for the construction of these frameworks, much effort being specially devoted to the formation of substituted tetrahydropyrans and piperidines. Among the existing methods to form these heterocycles, the metal-catalyzed heterocyclization of amino- or hydroxy-allylic alcohol derivatives has emerged as a powerful and stereoselective strategy that is particularly interesting in terms of both atom-economy and ecocompatibility. For a long time, palladium catalysts have widely dominated this area either in Tsuji-Trost reactions [Pd(0)] or in an electrophilic activation process [Pd(II)]. More recently, gold-catalyzed formation of saturated N- and O-heterocycles has received growing attention because it generally exhibits high efficiency and diastereoselectivity. Despite their demonstrated utility, Pd- and Au-complexes suffer from high costs, toxicity, and limited natural abundance, which can be barriers to their widespread use in industrial processes. Thus, the replacement of precious metals with less expensive and more environmentally benign catalysts has become a challenging issue for organic chemists. In 2010, our group took advantage of the ability of the low-toxicity and inexpensive FeCl3 in activating allylic or benzylic alcohols to develop iron-catalyzed N- and O-heterocylizations. We first focused on N-heterocycles, and a variety of 2,6-disubstituted piperidines as well as pyrrolidines were synthesized in a highly diastereoselective fashion in favor of the cis-compounds. The reaction was further extended to the construction of substituted tetrahydropyrans. Besides triggering the formation of heterocycles, the iron salts were shown to induce a thermodynamic epimerization, which is the key to reach the high diastereoselectivities observed in favor of the most stable cis-isomers. It is worth noting that spiroketals could be prepared by using this method, which was successfully applied to a synthetic approach toward natural products belonging to the bistramide family. We then turned our attention to heterocycles incorporating two heteroatoms such as isoxazolidines. These frameworks can be found in biologically active natural products, and in addition, they can be transformed into 1,3-amino alcohols, which are of importance in organic chemistry. The use of FeCl36H2O allowed the access to a large variety of 3,5-disubstituted isoxazolidines from ?-hydroxylamino allylic alcohol derivatives with good yields and diastereoselectivities in favor of the cis-isomer. Recently, a Lewis acid-catalyzed synthesis of six- and five-membered ring carbonates starting from linear tert-butyl carbonates was reported. In some cases, the mild and chemoselective InCl3 was preferred over FeCl36H2O to avoid side-product formation. The resulting cyclic carbonates were easily transformed into 1,3- or 1,2-diols, and a total synthesis of (3S,5S)-alpinikatin was achieved. PMID:25674664

  3. The Mechanism of the Reaction Catalyzed by Uronate Isomerase Illustrates How an Isomerase May Have Evolved from a Hydrolase within the Amidohydrolase Superfamily

    SciTech Connect

    Nguyen, T.; Fedorov, A; Williams, L; Fedorov, E; Li, Y; Xu, C; Almo, S; Raushel, F

    2009-01-01

    Uronate isomerase (URI) catalyzes the reversible isomerization of d-glucuronate to d-fructuronate and of d-galacturonate to d-tagaturonate. URI is a member of the amidohydrolase superfamily (AHS), a highly divergent group of enzymes that catalyze primarily hydrolytic reactions. The chemical mechanism and active site structure of URI were investigated in an attempt to improve our understanding of how an active site template that apparently evolved to catalyze hydrolytic reactions has been reforged to catalyze an isomerization reaction. The pH-rate profiles for kcat and kcat/Km for URI from Escherichia coli are bell-shaped and indicate that one group must be unprotonated and another residue must be protonated for catalytic activity. Primary isotope effects on the kinetic constants with [2-2H]-d-glucuronate and the effects of changes in solvent viscosity are consistent with product release being the rate-limiting step. The X-ray structure of Bh0493, a URI from Bacillus halodurans, was determined in the presence of the substrate d-glucuronate. The bound complex showed that the mononuclear metal center in the active site is ligated to the C-6 carboxylate and the C-5 hydroxyl group of the substrate. This hydroxyl group is also hydrogen bonded to Asp-355 in the same orientation as the hydroxide or water is bound in those members of the AHS that catalyze hydrolytic reactions. In addition, the C-2 and C-3 hydroxyl groups of the substrate are hydrogen bonded to Arg-357 and the carbonyl group at C-1 is hydrogen bonded to Tyr-50. A chemical mechanism is proposed that utilizes a proton transfer from C-2 of d-glucuronate to C-1 that is initiated by the combined actions of Asp-355 from the end of ?-strand 8 and the C-5 hydroxyl of the substrate that is bound to the metal ion. The formation of the proposed cis-enediol intermediate is further facilitated by the shuttling of the proton between the C-2 and C-1 oxygens by the conserved Tyr-50 and/or Arg-355.

  4. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I.

    PubMed Central

    Matson, S W; Nelson, W C; Morton, B S

    1993-01-01

    DNA helicase I, encoded on the Escherichia coli F plasmid, catalyzes a site- and strand-specific nicking reaction within the F plasmid origin of transfer (oriT) to initiate conjugative DNA strand transfer. The product of the nicking reaction contains a single phosphodiester bond interruption as determined by single-nucleotide resolution mapping of both sides of the nick site. This analysis has demonstrated that the nick is located at precisely the same site previously shown to be nicked in vivo (T. L. Thompson, M. B. Centola, and R. C. Deonier, J. Mol. Biol. 207:505-512, 1989). In addition, studies with two oriT point mutants have confirmed the specificity of the in vitro reaction. Characterization of the nicked DNA product has revealed a modified 5' end and a 3' OH available for extension by E. coli DNA polymerase I. Precipitation of nicked DNA with cold KCl in the presence of sodium dodecyl sulfate suggests the existence of protein covalently attached to the nicked DNA molecule. The covalent nature of this interaction has been directly demonstrated by transfer of radiolabeled phosphate from DNA to protein. On the basis of these results, we propose that helicase I becomes covalently bound to the 5' end of the nicked DNA strand as part of the reaction mechanism for phosphodiester bond cleavage. A model is presented to suggest how helicase I could nick the F plasmid at oriT and subsequently unwind the duplex DNA to provide single-stranded DNA for strand transfer during bacterial conjugation. Images PMID:8386720

  5. Mechanisms by which reactions catalyzed by chloroplast coupling factor 1 are inhibited: ATP synthesis and ATP-H2O oxygen exchange

    SciTech Connect

    Spencer, J.G.; Wimmer, M.J.

    1985-07-16

    The ATP-H2O back-exchange reaction catalyzed by membrane-bound chloroplast coupling factor 1 (CF1) in the light is known to be extensive; each reacting ATP molecule nearly equilibrates its gamma-PO2 oxygens with H2O before it dissociates from the enzyme. Pi, ASi, ADP, and GDP, alternate substrates of photophosphorylation, each inhibit the exchange reaction. At all concentrations of these substrate/inhibitor molecules tested, the high extent of exchange per molecule of ATP that reacts remains the same, while the number of ATP molecules experiencing exchange decreases. Thus, these inhibitors appear to act in a competitive-type manner, decreasing ATP turnover, as opposed to modulating the rate constants responsible for the partitioning of E X ATP during the exchange reaction. This is consistent with the identity of CF1 catalytic sites for ATP-H2O back-exchange and ATP synthesis. The extent of ATP-H2O forward oxygen exchange, which occurs during net ATP synthesis prior to product dissociation, is unaffected by uncouplers, whether catalyzed by native CF1 (ATPase latent) or the dithiothreitol/light-activated ATPase form.

  6. Access to Polyfunctionalized Chiral Piperidines through Enantioselective Addition-Carbocyclization Cascade Reaction Catalyzed by a Rhodium(I)-Diene Complex.

    PubMed

    Serpier, Fabien; Brayer, Jean-Louis; Follas, Benot; Darses, Sylvain

    2015-11-01

    A new addition-carbocyclization cascade reaction initiated by arylboronic acids and catalyzed by a rhodium/chiral diene complex is described. Starting from N-bridged oxoenoate derivatives, highly functionalized piperidines bearing three contiguous stereogenic centers were obtained with excellent enantio- and diastereoselectivities. PMID:26469888

  7. Nafion-catalyzed microwave-assisted Ritter reaction: An atom-economic solvent-free synthesis of amides

    EPA Science Inventory

    An atom-economic solvent-free synthesis of amides by the Ritter reaction of alcohols and nitriles under microwave irradiation is reported. This green protocol is catalyzed by solid supported NafionNR50 with improved efficiency and reduced waste production.

  8. Asymmetric synthesis of cyclopentanes bearing four contiguous stereocenters via an NHC-catalyzed Michael/Michael/esterification domino reaction.

    PubMed

    Shu, Tao; Ni, Qijian; Song, Xiaoxiao; Zhao, Kun; Wu, Tianyu; Puttreddy, Rakesh; Rissanen, Kari; Enders, Dieter

    2016-02-11

    An NHC-catalyzed Michael/Michael/esterification domino reaction via homoenolate/enolate intermediates for the asymmetric synthesis of tetrasubstituted cyclopentanes bearing four contiguous stereocenters is described. A variety of ?,?-unsaturated aldehydes and 2-nitroallylic acetates react well with good domino yields and high stereoselectivities. PMID:26750327

  9. Synthesis of non-proteinogenic phenylalanine derivatives by rhodium-catalyzed [2+2+2] cycloaddition reactions.

    PubMed

    Garcia, Ldia; Pla-Quintana, Anna; Roglans, Anna

    2009-12-01

    Non-proteinogenic phenylalanine derivatives were efficiently prepared by Rh(I)-catalyzed [2+2+2] cycloaddition reactions between enantiopure and racemic propargylglycine amino acids, with different protective groups, and diynes. Diverse substituents, including tags such as dansyl or dabsyl, were introduced onto the aromatic ring of the amino acid derivatives by selecting the most appropriate diyne reacting partners. PMID:19907794

  10. The synthesis of an aryl alkyl ionic liquid and its application in catalyzing Suzuki-Miyaura coupling reaction

    NASA Astrophysics Data System (ADS)

    Chen, Guochang; Ye, Mingfu; Qiao, Hongbin; Qiu, Xiaoning

    2014-08-01

    An aryl alkyl ionic liquids with a tertiary amino group (N(CH3)2) in the cation were synthesized. As a ligand, the synthesized ionic liquids can coordinate with palladium to form N-heterocyclic carbene (NHC)-Pd complex which exhibited high efficiency in catalyzing Suzuki-Miyaura coupling reaction.

  11. Temperature dependence of internal friction in enzyme reactions.

    PubMed

    Rauscher, Anna ; Simon, Zoltn; Szllosi, Gergely J; Grf, Lszl; Dernyi, Imre; Malnasi-Csizmadia, Andras

    2011-08-01

    Our aim was to elucidate the physical background of internal friction of enzyme reactions by investigating the temperature dependence of internal viscosity. By rapid transient kinetic methods, we directly measured the rate constant of trypsin 4 activation, which is an interdomain conformational rearrangement, as a function of temperature and solvent viscosity. We found that the apparent internal viscosity shows an Arrhenius-like temperature dependence, which can be characterized by the activation energy of internal friction. Glycine and alanine mutations were introduced at a single position of the hinge of the interdomain region to evaluate how the flexibility of the hinge affects internal friction. We found that the apparent activation energies of the conformational change and the internal friction are interconvertible parameters depending on the protein flexibility. The more flexible a protein was, the greater proportion of the total activation energy of the reaction was observed as the apparent activation energy of internal friction. Based on the coupling of the internal and external movements of the protein during its conformational change, we constructed a model that quantitatively relates activation energy, internal friction, and protein flexibility. PMID:21555355

  12. Enzyme-catalyzed rearrangement of a diepoxy-germacrane compound into new 7-epi-eudesmane derivatives.

    PubMed

    Garca-Granados, Andrs; Gutirrez, Mara C; Martnez, Antonio; Rivas, Francisco

    2005-01-01

    Two new 7-epi-eudesmane derivatives, together with two new germacrane compounds, have been isolated from the microbial-transformation of a (1alpha,10beta),(4beta,5alpha)-diepoxygermacrane using the hydroxylating fungi Rhizopus nigricans. The rearranged skeleton and the stereochemistry of the chiral centers have been determined by means of their spectral data, and the absolute configuration has been confirmed by single-crystal X-ray analyses. A possible mechanism based on an enzyme-catalyzed isomerization to a 1alpha-hydroxy-(4beta,5alpha)-epoxygermacr-9(E)-ene intermediate and a subsequent cyclization process is proposed in order to explain the formation of the 7-epi-eudesmane compounds. PMID:15624944

  13. Colorimetric assay for heterogeneous-catalyzed lipase activity: enzyme-regulated gold nanoparticle aggregation.

    PubMed

    Zhang, Wei; Tang, Yan; Liu, Jia; Jiang, Ling; Huang, Wei; Huo, Feng-Wei; Tian, Danbi

    2015-01-14

    Lipase is a neglected enzyme in the field of gold nanoparticle-based enzyme assays. This paper reports a novel colorimetric probe to rapidly visualize lipase activities by using Tween 20 functioned GNPs (Tween 20-GNPs) as a reporter. The present strategy hence could overcome the limitations caused by the heterogeneous interface in lipase assay. Catalytic hydrolytic cleavage of the ester bond in Tween 20-GNPs by lipase will trigger the rapid aggregation of GNPs at a high salt solution. The color change from red to purple could be used to sense the activity of lipase. The detection limit (3?) is as low as 2.8 10-2 mg/mL. A preliminary enzyme activity screening was carried out for seven commercially purchased lipase samples. It also has been successfully applied to detecting lipase in fermentation broth of Bacillus subtilis without any pretreatment. PMID:25516269

  14. Mechanistic Studies Lead to Dramatically Improved Reaction Conditions for the Cu-Catalyzed Asymmetric Hydroamination of Olefins.

    PubMed

    Bandar, Jeffrey S; Pirnot, Michael T; Buchwald, Stephen L

    2015-11-25

    Enantioselective copper(I) hydride (CuH)-catalyzed hydroamination has undergone significant development over the past several years. To gain a general understanding of the factors governing these reactions, kinetic and spectroscopic studies were performed on the CuH-catalyzed hydroamination of styrene. Reaction profile analysis, rate order assessment, and Hammett studies indicate that the turnover-limiting step is regeneration of the CuH catalyst by reaction with a silane, with a phosphine-ligated copper(I) benzoate as the catalyst resting state. Spectroscopic, electrospray ionization mass spectrometry, and nonlinear effect studies are consistent with a monomeric active catalyst. With this insight, targeted reagent optimization led to the development of an optimized protocol with an operationally simple setup (ligated copper(II) precatalyst, open to air) and short reaction times (<30 min). This improved protocol is amenable to a diverse range of alkene and alkyne substrate classes. PMID:26522837

  15. Asymmetric Mannich reaction of dicarbonyl compounds with alpha-amido sulfones catalyzed by cinchona alkaloids and synthesis of chiral dihydropyrimidones.

    PubMed

    Lou, Sha; Dai, Peng; Schaus, Scott E

    2007-12-21

    The highly enantioselective cinchona alkaloid-catalyzed Mannich reaction of dicarbonyl compounds with alpha-amido sulfones as acyl imine precursors is described. The reaction requires 10 mol % of the cinchona alkaloid catalyst, which serves as a general base to generate acyl imines in situ, and aqueous Na2CO3 to maintain the concentration of free alkaloid catalyst. The reaction products are obtained in good yields and high enantioselectivities, and in diastereoselectivities that range from 1:1 to >95:5. The cinchonine-catalyzed reactions provide practical access to highly functionalized building blocks which have been employed in the synthesis of chiral dihydropyrimidones, a class of compounds rich in diverse biological activity. Dihydropyrimidone modifications include a highly diastereoselective hydrogenation of the enamide moiety, using an H-Cube flow hydrogenator and a Rh(II)-mediated 1,3-dipolar cycloaddition to afford highly functionalized complex heterocycles. PMID:18047372

  16. The gas phase reaction of singlet dioxygen with water: a water-catalyzed mechanism.

    PubMed

    Xu, Xin; Muller, Richard P; Goddard, William A

    2002-03-19

    Stimulated by the recent surprising results from Wentworth et al. [Wentworth, A. D., Jones, L. H., Wentworth, P., Janda, K. D. & Lerner, R. A. (2000) Proc. Natl. Acad. Sci. USA 97, 10930-10935] that Abs efficiently catalyze the conversion of molecular singlet oxygen ((1)O(2)) plus water to hydrogen peroxide (HOOH), we used quantum chemical methods (B3LYP density functional theory) to delineate the most plausible mechanisms for the observed efficient conversion of water to HOOH. We find two reasonable pathways. In Pathway I, (i) H(2)O catalyzes the reaction of (1)O(2) with a second water to form HOOOH; (ii) two HOOOH form a dimer, which rearranges to form the HOO-HOOO + H(2)O complex; (iii) HOO-HOOO rearranges to HOOH-OOO, which subsequently reacts with H(2)O to form H(2)O(4) + HOOH; and (iv) H(2)O(4) rearranges to the cyclic dimer (HO(2))(2), which in turn forms HOOH plus (1)O(2) or (3)O(2). Pathway II differs in that step ii is replaced with the reaction between HOOOH and (1)O(2), leading to the formation of HOO-HOOO. This then proceeds to similar products. For a system with (18)O H(2)O, Pathway I leads to a 2.2:1 ratio of (16)O:(18)O in the product HOOH, whereas Pathway II leads to 3:1. These ratios are in good agreement with the 2.2:1 ratio observed in isotope experiments by Wentworth et al. These mechanisms lead to two HOOH per initial (1)O(2) or one, depending on whether the product of step iv is (1)O(2) or (3)O(2), in good agreement with the experimental result of 2.0. In addition to the Ab-induced reactions, the hydrogen polyoxides (H(2)O(3) and H(2)O(4)) formed in these mechanisms and their decomposition product polyoxide radicals (HO(2), HO(3)) may play a role in combustion, explosions, atmospheric chemistry, and the radiation chemistry in aqueous systems. PMID:11891316

  17. Mechanism of the Orotidine 5’-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence for Substrate Destabilization†

    PubMed Central

    Chan, Kui K.; Wood, B. McKay; Fedorov, Alexander A.; Fedorov, Elena V.; Imker, Heidi J.; Amyes, Tina L.; Richard, John P.; Almo, Steven C.; Gerlt, John A.

    2009-01-01

    The reaction catalyzed by orotidine 5’-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (kcat/knon, 7.1 × 1016) and proficiency [(kcat/KM)/knon, 4.8 × 1022 M−1] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (≥ 1010). The origin of the “missing” contribution, ≤ 107 (∼1017 total - ≥ 1010), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc Natl Acad Sci U S A 97, 2017−2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of kcat for decarboxylation of FOMP (a more reactive substrate analog) but have little effect on the value of kex for exchange of H6 of FUMP with solvent deuterium; the structures of wild type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis á vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization. PMID:19435314

  18. Understanding the mechanisms of cobalt-catalyzed hydrogenation and dehydrogenation reactions.

    PubMed

    Zhang, Guoqi; Vasudevan, Kalyan V; Scott, Brian L; Hanson, Susan K

    2013-06-12

    Cobalt(II) alkyl complexes of aliphatic PNP pincer ligands have been synthesized and characterized. The cationic cobalt(II) alkyl complex [(PNHP(Cy))Co(CH2SiMe3)]BAr(F)4 (4) (PNHP(Cy) = bis[(2-dicyclohexylphosphino)ethyl]amine) is an active precatalyst for the hydrogenation of olefins and ketones and the acceptorless dehydrogenation of alcohols. To elucidate the possible involvement of the N-H group on the pincer ligand in the catalysis via a metal-ligand cooperative interaction, the reactivities of 4 and [(PNMeP(Cy))Co(CH2SiMe3)]BAr(F)4 (7) were compared. Complex 7 was found to be an active precatalyst for the hydrogenation of olefins. In contrast, no catalytic activity was observed using 7 as a precatalyst for the hydrogenation of acetophenone under mild conditions. For the acceptorless dehydrogenation of 1-phenylethanol, complex 7 displayed similar activity to complex 4, affording acetophenone in high yield. When the acceptorless dehydrogenation of 1-phenylethanol with precatalyst 4 was monitored by NMR spectroscopy, the formation of the cobalt(III) acetylphenyl hydride complex [(PNHP(Cy))Co(III)(?(2)-O,C-C6H4C(O)CH3)(H)]BAr(F)4 (13) was detected. Isolated complex 13 was found to be an effective catalyst for the acceptorless dehydrogenation of alcohols, implicating 13 as a catalyst resting state during the alcohol dehydrogenation reaction. Complex 13 catalyzed the hydrogenation of styrene but showed no catalytic activity for the room temperature hydrogenation of acetophenone. These results support the involvement of metal-ligand cooperativity in the room temperature hydrogenation of ketones but not the hydrogenation of olefins or the acceptorless dehydrogenation of alcohols. Mechanisms consistent with these observations are presented for the cobalt-catalyzed hydrogenation of olefins and ketones and the acceptorless dehydrogenation of alcohols. PMID:23713752

  19. Reaction Pathways and Energetics of Etheric C−O Bond Cleavage Catalyzed by Lanthanide Triflates

    SciTech Connect

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

    2013-07-15

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

  20. Palladium-Catalyzed ?-Arylation of Zinc Enolates of Esters: Reaction Conditions and Substrate Scope

    PubMed Central

    Hama, Takuo; Ge, Shaozhong; Hartwig, John F.

    2013-01-01

    The intermolecular ?-arylation of esters by palladium-catalyzed coupling of aryl bromides with zinc enolates of esters is reported. Reactions of three different types of zinc enolates have been developed. ?-Arylation of esters occurs in high yields with isolated Reformatsky reagents, with Reformatsky reagents generated from ?-bromo esters and activated zinc, and with zinc enolates generated by quenching lithium enolates of esters with zinc chloride. The use of zinc enolates, instead of alkali metal enolates, greatly expands the scope of the arylation of esters. The reactions occur at room temperature or at 70 C with bromoarenes containing cyano, nitro, ester, keto, fluoro, enolizable hydrogen, hydroxyl or amino functionality and with bromopyridines. The scope of esters encompasses acyclic acetates, propionates, and isobutyrates, ?-alkoxyesters, and lactones. The arylation of zinc enolates of esters was conducted with catalysts bearing the hindered pentaphenylferrocenyl di-tert-butylphosphine (Q-phos) or the highly reactive dimeric Pd(I) complex {[P(t-Bu)3]PdBr}2. PMID:23931445

  1. Low temperature iron- and nickel-catalyzed reactions leading to coalbed gas formation

    SciTech Connect

    Medina, J.C.; Butala, S.J.; Bartholomew, C.H.; Lee, M.L.

    2000-02-01

    Hydrocarbon hydrogenolysis and CO{sub 2} hydrogenation in the presence of Fe/SiO{sub 2} and Ni/SiO{sub 2} catalysts were evaluated as potential mechanisms contributing to natural gas formation in coalbeds. The hydrocarbons used as reactants in hydrogenolysis included butane, octane, 1-octene, and 1-dodecene. The reactions carried out in a laboratory batch reactor produced gas that contained methane concentrations greater than 90%, which resembles the composition of natural gas. Reaction temperatures were selected to resemble natural coalbed conditions. Evidence is presented to show that iron and nickel minerals, which can be present in coals at levels of 2,000 and 10 ppm, respectively, can become active under geologic conditions. The oxides (Fe{sub 2}O{sub 3} and NiO) used as precursors of the active catalysts (Fe and Ni metals) were reduced at 200 C under a hydrogen atmosphere. Moessbauer spectroscopy showed that ca. 6% of the iron oxide was converted to the metal; in the case of nickel, oxygen titration showed that the extent of reduction to the metal was ca. 29%. The resultant fractions of the active metals in coals are adequate to catalyze generation of appreciable amounts of methane over geologic time.

  2. Low temperature iron- and nickel-catalyzed reactions leading to coalbed gas formation

    NASA Astrophysics Data System (ADS)

    Medina, Juan Carlos; Butala, Steven J.; Bartholomew, Calvin H.; Lee, Milton L.

    2000-02-01

    Hydrocarbon hydrogenolysis and CO 2 hydrogenation in the presence of Fe/SiO 2 and Ni/SiO 2 catalysts were evaluated as potential mechanisms contributing to natural gas formation in coalbeds. The hydrocarbons used as reactants in hydrogenolysis included butane, octane, 1-octene, and 1-dodecene. The reactions carried out in a laboratory batch reactor produced gas that contained methane concentrations greater than 90%, which resembles the composition of natural gas. Reaction temperatures were selected to resemble natural coalbed conditions. Evidence is presented to show that iron and nickel minerals, which can be present in coals at levels of 2000 and 10 ppm, respectively, can become active under geologic conditions. The oxides (Fe 2O 3 and NiO) used as precursors of the active catalysts (Fe and Ni metals) were reduced at 200C under a hydrogen atmosphere. Mssbauer spectroscopy showed that ca. 6% of the iron oxide was converted to the metal; in the case of nickel, oxygen titration showed that the extent of reduction to the metal was ca. 29%. The resultant fractions of the active metals in coals are adequate to catalyze generation of appreciable amounts of methane over geologic time.

  3. DABCO-catalyzed unusual [4 + 2] cycloaddition reaction: non-substituted allenoate acts as a four-carbon synthon and facile synthesis of spirooxindoles.

    PubMed

    Liu, Yufen; Du, Yanlong; Yu, Aimin; Mu, Haifeng; Meng, Xiangtai

    2016-01-28

    A DABCO-catalyzed domino reaction between methyleneoxindoles and allenoates which enables the direct synthesis of spirooxindoles is reported. This is the first example of a non-substituted allenoate to act as a four-carbon synthon in a tertiary amine-catalyzed reaction. PMID:26677052

  4. An approach to the synthesis of dimeric resveratrol natural products via a palladium-catalyzed domino reaction

    PubMed Central

    Jeffrey, Jenna L.; Sarpong, Richmond

    2009-01-01

    A route for the rapid assembly of the carbon framework of several resveratrol natural products is presented. A palladium-catalyzed domino reaction of bromostilbene derivative 6 and tolane 7, involving two sequential Heck coupling reactions, provides access to the benzofulvene-based core of various resveratrol-derived natural products. The carbon skeleton of pallidol and its congeners is achieved by a Lewis acid-induced Nazarov-type oxidative cyclization of 9. PMID:20161322

  5. Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions.

    PubMed

    Kim, Young-Min; Yamamoto, Eiji; Kang, Min-Sun; Nakai, Hiroyuki; Saburi, Wataru; Okuyama, Masayuki; Mori, Haruhide; Funane, Kazumi; Momma, Mitsuru; Fujimoto, Zui; Kobayashi, Mikihiko; Kim, Doman; Kimura, Atsuo

    2012-09-01

    Bacteroides thetaiotaomicron VPI-5482 harbors a gene encoding a putative cycloisomaltooligosaccharide glucanotransferase (BT3087) belonging to glycoside hydrolase family 66. The goal of the present study was to characterize the catalytic properties of this enzyme. Therefore, we expressed BT3087 (recombinant endo-dextranase from Bacteroides thetaiotaomicron VPI-5482) in Escherichia?coli and determined that recombinant endo-dextranase from Bacteroides thetaiotaomicron VPI-5482 preferentially synthesized isomaltotetraose and isomaltooligosaccharides (degree of polymerization > 4) from dextran. The enzyme also generated large cyclic isomaltooligosaccharides early in the reaction. We conclude that members of the glycoside hydrolase 66 family may be classified into three types: (a) endo-dextranases, (b) dextranases possessing weak cycloisomaltooligosaccharide glucanotransferase activity, and (c) cycloisomaltooligosaccharide glucanotransferases. PMID:22776355

  6. Structural Characterization of a 140 degrees Domain Movement in the Two-Step Reaction Catalyzed by 4-Chlorobenzoate:CoA Ligase

    SciTech Connect

    Reger,A.; Wu, R.; Dunaway-Mariano, D.; Gulick, A.

    2008-01-01

    Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PPi, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140 to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

  7. Structural Characterization of a 140 Degree Domain Movement in the Two-Step Reaction Catalyzed By 4-Chlorobenzoate:CoA Ligase

    SciTech Connect

    Reger, A.S.; Wu, R.; Dunaway-Mariano, D.; Gulick, A.M.

    2009-05-21

    Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PP{sub 1}, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140{sup o} to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue [Wu et al. (2008) Biochemistry 47, 8026-8039]. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

  8. Structural Characterization of a 140 Domain Movement in the Two-Step Reaction Catalyzed by 4-Chlorobenzoate:CoA Ligase#

    PubMed Central

    Reger, Albert S.; Wu, Rui; Dunaway-Mariano, Debra; Gulick, Andrew M.

    2009-01-01

    Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PPi, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by ~140 to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analog, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript (Wu et al.). The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes. PMID:18620418

  9. Lecithin-cholesterol acyltransferase (LCAT) catalyzes transacylation of intact cholesteryl esters. Evidence for the partial reversal of the forward LCAT reaction

    SciTech Connect

    Sorci-Thomas, M.; Babiak, J.; Rudel, L.L. )

    1990-02-15

    Lecithin-cholesterol acyltransferase (LCAT) catalyzes the intravascular synthesis of lipoprotein cholesteryl esters by converting cholesterol and lecithin to cholesteryl ester and lysolecithin. LCAT is unique in that it catalyzes sequential reactions within a single polypeptide sequence. In this report we find that LCAT mediates a partial reverse reaction, the transacylation of lipoprotein cholesteryl oleate, in whole plasma and in a purified, reconstituted system. As a result of the reverse transacylation reaction, a linear accumulation of (3H)cholesterol occurred during incubations of plasma containing high density lipoprotein labeled with (3H)cholesteryl oleate. When high density lipoprotein labeled with cholesteryl (14C)oleate was also included in the incubation the labeled fatty acyl moiety remained in the cholesteryl (14C)oleate pool showing that the formation of labeled cholesterol did not result from hydrolysis of the doubly labeled cholesteryl esters. The rate of release of (3H)cholesterol was only about 10% of the forward rate of esterification of cholesterol using partially purified human LCAT and was approximately 7% in whole monkey plasma. Therefore, net production of cholesterol via the reverse LCAT reaction would not occur. (3H)Cholesterol production from (3H)cholesteryl oleate was almost completely inhibited by a final concentration of 1.4 mM 5,5'-dithiobis(nitrobenzoic acid) during incubation with either purified LCAT or whole plasma. Addition of excess lysolecithin to the incubation system did not result in the formation of (14C)oleate-labeled lecithin, showing that the reverse reaction found here for LCAT was limited to the last step of the reaction. To explain these results we hypothesize that LCAT forms a (14C)oleate enzyme thioester intermediate after its attack on the cholesteryl oleate molecule.

  10. Silylium ion-catalyzed challenging Diels-Alder reactions: the danger of hidden proton catalysis with strong Lewis acids.

    PubMed

    Schmidt, Ruth K; Mther, Kristine; Mck-Lichtenfeld, Christian; Grimme, Stefan; Oestreich, Martin

    2012-03-01

    The pronounced Lewis acidity of tricoordinate silicon cations brings about unusual reactivity in Lewis acid catalysis. The downside of catalysis with strong Lewis acids is, though, that these do have the potential to mediate the formation of protons by various mechanisms, and the thus released Brnsted acid might even outcompete the Lewis acid as the true catalyst. That is an often ignored point. One way of eliminating a hidden proton-catalyzed pathway is to add a proton scavenger. The low-temperature Diels-Alder reactions catalyzed by our ferrocene-stabilized silicon cation are such a case where the possibility of proton catalysis must be meticulously examined. Addition of the common hindered base 2,6-di-tert-butylpyridine resulted, however, in slow decomposition along with formation of the corresponding pyridinium ion. Quantitative deprotonation of the silicon cation was observed with more basic (Mes)(3)P to yield the phosphonium ion. A deuterium-labeling experiment verified that the proton is abstracted from the ferrocene backbone. A reasonable mechanism of the proton formation is proposed on the basis of quantum-chemical calculations. This is, admittedly, a particular case but suggests that the use of proton scavengers must be carefully scrutinized, as proton formation might be provoked rather than prevented. Proton-catalyzed Diels-Alder reactions are not well-documented in the literature, and a representative survey employing TfOH is included here. The outcome of these catalyses is compared with our silylium ion-catalyzed Diels-Alder reactions, thereby clearly corroborating that hidden Brnsted acid catalysis is not operating with our Lewis acid. Several simple-looking but challenging Diels-Alder reactions with exceptionally rare dienophile/enophile combinations are reported. Another indication is obtained from the chemoselectivity of the catalyses. The silylium ion-catalyzed Diels-Alder reaction is general with regard to the oxidation level of the ?,?-unsaturated dienophile (carbonyl and carboxyl), whereas proton catalysis is limited to carbonyl compounds. PMID:22309027

  11. The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?

    NASA Astrophysics Data System (ADS)

    Bothma, Jacques P.; Gilmore, Joel B.; McKenzie, Ross H.

    2010-05-01

    We consider the role of quantum effects in the transfer of hydrogen-like species in enzyme-catalyzed reactions. This review is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects (KIEs) implies that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We review the path integral approach and the Caldeira-Leggett model, which provides a general framework to describe and understand tunneling in a quantum system that interacts with a noisy environment at nonzero temperature. Here the quantum system is the active site of the enzyme, and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature T0, which is determined by the curvature of the potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. We review typical values for the parameters in the Caldeira-Leggett Hamiltonian, including the frequency-dependent friction and noise due to the environment. For physically reasonable parameters, we show that quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of KIEs for two classes of enzymes that have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction and noise due to the environment are weak and only slightly modify the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental fluctuations with frequencies much less than 1000 cm-1 do not have a significant effect on quantum corrections to the reaction rate. This is essentially because the time scales associated with the dynamics of proton transfer are faster than much of the low-frequency noise associated with the protein and solvent.

  12. Nickel-Catalyzed Double Bond Transposition of Alkenyl Boronates for in Situ syn-Selective Allylboration Reactions.

    PubMed

    Weber, Felicia; Ballmann, Monika; Kohlmeyer, Corinna; Hilt, Gerhard

    2016-02-01

    The transposition of a homoallyl pinacol boronic ester was realized by a highly reactive nickel-catalyst system comprising NiCl2(dppp), zinc powder, ZnI2, and Ph2PH. The in situ generated Z-crotyl pinacol boronic esters were reacted with various aldehydes to form syn-homoallylic alcohols in high diastereoselectivities. The present nickel-catalyzed reaction is complementary to the iridium-catalyzed transposition reported by Murakami leading to the corresponding anti-homoallylic alcohols. Also, the multiple transposition of pentenyl pinacol boronic ester was realized. PMID:26771707

  13. Pd(II)-Catalyzed C–H Activation/C–C Cross-Coupling Reactions: Versatility and Practicality

    PubMed Central

    Chen, Xiao; Engle, Keary M.; Wang, Dong-Hui; Yu, Jin-Quan

    2009-01-01

    In the past decade, palladium-catalyzed C–H activation/C–C bond forming reactions have emerged as promising new catalytic transformations; however, development in this field is still at an early stage compared to the state of the art in cross-coupling reactions using aryl and alkyl halides. This Review begins with a brief introduction of four extensively investigated modes of catalysis for forming C–C bonds from C–H bonds: Pd(II)/Pd(0), Pd(II)/Pd(IV), Pd(0)/Pd(II)/Pd(IV) and Pd(0)/Pd(II) catalysis. More detailed discussion is then directed towards the recent development of Pd(II)-catalyzed coupling of C–H bonds with organometallic reagents through a Pd(II)/Pd(0) catalytic cycle. Despite much progress made to date, improving the versatility and practicality of this new reaction remains a tremendous challenge. PMID:19557755

  14. Clustering and Optimal Arrangement of Enzymes in Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

    2013-05-01

    Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

  15. Colorimetric endpoint assay for enzyme-catalyzed iodide ion release for high-throughput screening in microtiter plates.

    PubMed

    Kurtovic, Sanela; Jansson, Ronnie; Mannervik, Bengt

    2007-08-15

    Efforts are being made to engineer enzymes with enhanced activities against haloalkanes, a toxicologically important class of compounds widely used and frequently occurring in the environment. Here we describe a facile, inexpensive, and robust method for the screening of libraries of mutated enzymes with iodoalkane substrates. Iodide formed in the enzymatic reaction is oxidized to iodine, which in the presence of starch gives blue color that can be measured at 610nm or scored with the human eye. The assay can be performed with enzymes in crude cell lysates in 96-wells microtiter plates. Expression clones of several glutathione transferases showed diverse activities with different iodoalkanes, and a mutant library of human glutathione transferase A1-1 expressed variants with enhanced substrate selectivities. PMID:17490601

  16. Rhodium catalyzed chelation-assisted C-H bond functionalization reactions

    PubMed Central

    Colby, Denise A.; Tsai, Andy S.; Bergman, Robert G.; Ellman, Jonathan A.

    2011-01-01

    Conspectus Over the last several decades, researchers have achieved remarkable progress in the field of organometallic chemistry. The development of metal-catalyzed cross-coupling reactions represents a paradigm shift in chemical synthesis, and today synthetic chemists can readily access carbon-carbon and carbon-heteroatom bonds from a vast array of starting compounds. Although we cannot understate the importance of these methods, the required pre-functionalization to carry out these reactions adds cost and reduces the availability of the starting reagents. The use of C-H bond activation in lieu of pre-functionalization has presented a tantalizing alternative to classical cross-coupling reactions. Researchers have met the challenges of selectivity and reactivity associated with the development of C-H bond functionalization reactions with an explosion of creative advances in substrate and catalyst design. Literature reports on selectivity based on steric effects, acidity, and electronic and directing group effects are now numerous. Our group has developed an array of C-H bond functionalization reactions that take advantage of a chelating directing group, and this Account surveys our progress in this area. The use of chelation control in C-H bond functionalization offers several advantages with respect to substrate scope and application to total synthesis. The predictability and decreased dependence on the inherent stereoelectronics of the substrate generally result in selective and high yielding transformations with broad applicability. The nature of the chelating moiety can be chosen to serve as a functional handle in subsequent elaborations. Our work began with the use of Rh(I) catalysts in intramolecular aromatic C-H annulations, which we further developed to include enantioselective transformations. The application of this chemistry to the simple olefinic C-H bonds found in ?,?-unsaturated imines allowed access to highly substituted olefins, pyridines, and piperidines. We observed complementary reactivity with Rh(III) catalysts and developed an oxidative coupling with unactivated alkenes. Further studies on the Rh(III) catalysts led us to develop methods for the coupling of C-H bonds to polarized ? bonds such as those in imines and isocyanates. In several cases the methods that we have developed for chelation-controlled C-H bond functionalization have been applied to the total synthesis of complex molecules such as natural products, highlighting the utility of these methods in organic synthesis. PMID:22148885

  17. Mechanism and stereochemical course at phosphorus of the reaction catalyzed by a bacterial phosphotriesterase

    SciTech Connect

    Lewis, V.E.; Donarski, W.J.; Wild, J.R.; Raushel, F.M.

    1988-03-08

    The reaction mechanism for the phosphotriesterase from Pseudomonas diminuta has been examined. When paraoxon (diethyl 4-nitrophenyl phosphate) is hydrolyzed by this enzyme in oxygen-18-labeled water, the oxygen-18 label is found exclusively in the diethyl phosphate product. The absolute configurations for the (+) and (-) enantiomers of O-ethyl phenylphosphonothioic acid have been determined by X-ray diffraction structural determination of the individual crystalline 1-phenylethylamine salts. The (+) enantiomer of the free acid corresponds to the R/sub P/ configuration. The R/sub P/ enantiomer of O-ethyl phenylphosphonothioic acid has been converted to the S/sub P/ enantiomer of EPN (O-ethyl O-(4-nitrophenyl) phenylphosphonothioate). (S/sub P/)-EPN is hydrolyzed by the phosphotriesterase to the S/sub P/ enantiomer of O-ethyl phenylphosphonothioic acid. The enzymatic reaction therefore proceeds with inversion of configuration. These results have been interpreted as an indication of a single in-line displacement by an activated water molecule directly at the phosphorus center of the phosphotriester substrate. (R/sub P/)-EPN is not hydrolyzed by the enzyme at an appreciable rate.

  18. Study of the oxidative half-reaction catalyzed by a non-heme ferrous catalytic center by means of structural and computational methodologies

    NASA Astrophysics Data System (ADS)

    Cicero, Giancarlo; Carbonera, Chiara; Valegård, Karin; Hajdu, Janos; Andersson, Inger; Ranghino, Graziella

    Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme that catalyzes the expansion of the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporins. In the first half-reaction with dioxygen and 2-oxoglutarate, a reactive iron-oxygen species is produced that can subsequently react with the penicillin substrate to yield the cephalosporin. We describe quantum mechanical calculations of the first part of the reaction based on the high-resolution structures of the active site of DAOCS and its complexes with ligands. These studies are aimed at understanding how the reactive species can be produced and contained in the active site of the enzyme. The results demonstrate the priming of the active site by the co-substrate for oxygen binding and hint to the presence of a stable iron-peroxo intermediate in equilibrium with a more reactive ferryl species and the formation of CO2 as a leaving group by decarboxylation of 2-oxoglutarate. A conclusion from these studies is that substitution of CO2 by the penicillin substrate triggers the oxidation reaction in a booby-trap-like mechanism.

  19. A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase

    SciTech Connect

    Lyubimov, Artem Y.; Chen, Lin; Sampson, Nicole S.; Vrielink, Alice

    2009-11-01

    The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine. Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k{sub cat}. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

  20. Transformation of Fatty Acids Catalyzed by Cytochrome P450 Monooxygenase Enzymes of Candida tropicalis

    PubMed Central

    Eschenfeldt, William H.; Zhang, Yeyan; Samaha, Hend; Stols, Lucy; Eirich, L. Dudley; Wilson, C. Ronald; Donnelly, Mark I.

    2003-01-01

    Candida tropicalis ATCC 20336 can grow on fatty acids or alkanes as its sole source of carbon and energy, but strains blocked in β-oxidation convert these substrates to long-chain α,ω-dicarboxylic acids (diacids), compounds of potential commercial value (Picataggio et al., Biotechnology 10:894-898, 1992). The initial step in the formation of these diacids, which is thought to be rate limiting, is ω-hydroxylation by a cytochrome P450 (CYP) monooxygenase. C. tropicalis ATCC 20336 contains a family of CYP genes, and when ATCC 20336 or its derivatives are exposed to oleic acid (C18:1), two cytochrome P450s, CYP52A13 and CYP52A17, are consistently strongly induced (Craft et al., this issue). To determine the relative activity of each of these enzymes and their contribution to diacid formation, both cytochrome P450s were expressed separately in insect cells in conjunction with the C. tropicalis cytochrome P450 reductase (NCP). Microsomes prepared from these cells were analyzed for their ability to oxidize fatty acids. CYP52A13 preferentially oxidized oleic acid and other unsaturated acids to ω-hydroxy acids. CYP52A17 also oxidized oleic acid efficiently but converted shorter, saturated fatty acids such as myristic acid (C14:0) much more effectively. Both enzymes, in particular CYP52A17, also oxidized ω-hydroxy fatty acids, ultimately generating the α,ω-diacid. Consideration of these different specificities and selectivities will help determine which enzymes to amplify in strains blocked for β-oxidation to enhance the production of dicarboxylic acids. The activity spectrum also identified other potential oxidation targets for commercial development. PMID:14532054

  1. New insights into atrazine degradation by cobalt catalyzed peroxymonosulfate oxidation: kinetics, reaction products and transformation mechanisms.

    PubMed

    Ji, Yuefei; Dong, Changxun; Kong, Deyang; Lu, Junhe

    2015-03-21

    The widespread occurrence of atrazine in waters poses potential risk to ecosystem and human health. In this study, we investigated the underlying mechanisms and transformation pathways of atrazine degradation by cobalt catalyzed peroxymonosulfate (Co(II)/PMS). Co(II)/PMS was found to be more efficient for ATZ elimination in aqueous solution than Fe(II)/PMS process. ATZ oxidation by Co(II)/PMS followed pseudo-first-order kinetics, and the reaction rate constant (k(obs)) increased appreciably with increasing Co(II) concentration. Increasing initial PMS concentration favored the decomposition of ATZ, however, no linear relationship between k(obs) and PMS concentration was observed. Higher efficiency of ATZ oxidation was observed around neutral pH, implying the possibility of applying Co(II)/PMS process under environmental realistic conditions. Natural organic matter (NOM), chloride (Cl(-)) and bicarbonate (HCO3(-)) showed detrimental effects on ATZ degradation, particularly at higher concentrations. Eleven products were identified by applying solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC/MS) techniques. Major transformation pathways of ATZ included dealkylation, dechlorination-hydroxylation, and alkyl chain oxidation. Detailed mechanisms responsible for these transformation pathways were discussed. Our results reveal that Co(II)/PMS process might be an efficient technique for remediation of groundwater contaminated by ATZ and structurally related s-triazine herbicides. PMID:25544494

  2. A novel reactor for determination of kinetics for solid catalyzed gas reactions

    SciTech Connect

    Borman, P.C.; Bos, A.N.R.; Westerterp, K.R. . Dept. of Chemical Engineering)

    1994-05-01

    A novel perfectly mixed laboratory reactor for determining kinetics of heterogeneously catalyzed gas-phase reactions has been developed. Perfect mixing is achieved by circulating the gas in the reactor using an axial flow impeller in a well streamlined enclosure. Pellets are fixed in a rectangular opening in the blades of the impeller. They rotate with the impeller, thus realizing high particle velocities in the reactor. Interparticle mass transfer was studied experimentally by vaporization of naphthalene pellets. The mass-transfer coefficient in the novel reactor was found to depend on the velocity of a particle in the reactor. Mass-transfer coefficients in an internal recycle reactor at equal impeller tip speeds are 4--6 times lower than those in the novel reactor, and conditions can be chosen easily where at higher rotational speeds the mass- and heat-transfer rates are 8--10 times higher than in classical recycle reactors. The recycle flow rate in a recycle reactor was found to depend strongly on the resistance to flow caused by the catalyst bed itself. The novel reactor was tested under reacting conditions using the hydrogenation of ethene.

  3. Effect of carbon on the Ni catalyzed methane cracking reaction: A DFT study

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    To understand the effects of carbon atoms on the Ni catalyzed methane cracking reactions, methane dissociation on clean, surface-carbon-covered, and subsurface-carbon-accumulated Ni(1 1 1) surfaces were investigated using density functional theory (DFT). The results show that the existence of surface and subsurface C atoms destabilized the adsorption of the surface hydrocarbon species when compared to the clean Ni(1 1 1) surface. The projected density state (PDOS) analysis shows that the deposition of C atoms on and into the Ni surface modified the electronic structure of the Ni surface, and thus reduced the catalytic activity of the bonded Ni atoms. Moreover, it was found that the presence carbon atoms increase the CHx (x = 4-1) species activation barriers especially on the surface carbon covered (1/4 ML) Ni(1 1 1) surface, where CHx (x = 4-1) species encounter highest energy barrier for dissociation due to the electronic deactivation induced by Csbnd Ni bonding and the strong repulsive carbon sbnd CHx interaction. The calculations also show that CHx dissociation barriers are not affected by its neighboring C atom at low surface carbon coverage (1/9 ML). This work can be used to estimate more realistic kinetic parameters for this system.

  4. An Improved Method for Studying the Enzyme-Catalyzed Oxidation of Glucose Using Luminescent Probes

    ERIC Educational Resources Information Center

    Bare, William D.; Pham, Chi V.; Cuber, Matthew; Demas, J. N.

    2007-01-01

    A new method is presented for measuring the rate of the oxidation of glucose in the presence of glucose oxidase. The improved method employs luminescence measurements to directly determine the concentration of oxygen in real time, thus obviating complicated reaction schemes employed in previous methods. Our method has been used to determine

  5. Transglycosylation reaction catalyzed by a class V chitinase from cycad, Cycas revoluta: a study involving site-directed mutagenesis, HPLC, and real-time ESI-MS.

    PubMed

    Taira, Toki; Fujiwara, Maho; Dennhart, Nicole; Hayashi, Hiroko; Onaga, Shoko; Ohnuma, Takayuki; Letzel, Thomas; Sakuda, Shohei; Fukamizo, Tamo

    2010-04-01

    Class V chitinase from cycad, Cycas revoluta, (CrChi-A) is the first plant chitinase that has been found to possess transglycosylation activity. To identify the structural determinants that bring about transglycosylation activity, we mutated two aromatic residues, Phe166 and Trp197, which are likely located in the acceptor binding site, and the mutated enzymes (F166A, W197A) were characterized. When the time-courses of the enzymatic reaction toward chitin oligosaccharides were monitored by HPLC, the specific activity was decreased to about 5-10% of that of the wild type and the amounts of transglycosylation products were significantly reduced by the individual mutations. From comparison between the reaction time-courses obtained by HPLC and real-time ESI-MS, we found that the transglycosylation reaction takes place under the conditions used for HPLC but not under the ESI-MS conditions. The higher substrate concentration (5 mM) used for the HPLC determination is likely to bring about chitinase-catalyzed transglycosylation. Kinetic analysis of the time-courses obtained by HPLC indicated that the sugar residue affinity of +1 subsite was strongly reduced in both mutated enzymes, as compared with that of the wild type. The IC(50) value for the inhibitor allosamidin determined by real-time ESI-MS was not significantly affected by the individual mutations, indicating that the state of the allosamidin binding site (from -3 to -1 subsites) was not changed in the mutated enzymes. We concluded that the aromatic side chains of Phe166 and Trp197 in CrChi-A participate in the transglycosylation acceptor binding, thus controlling the transglycosylation activity of the enzyme. PMID:19879383

  6. Purification, Identification, and Cloning of Lysoplasmalogenase, the Enzyme That Catalyzes Hydrolysis of the Vinyl Ether Bond of Lysoplasmalogen*

    PubMed Central

    Wu, Lai-Chu; Pfeiffer, Douglas R.; Calhoon, Elisabeth A.; Madiai, Francesca; Marcucci, Guido; Liu, Shujun; Jurkowitz, Marianne S.

    2011-01-01

    Lysoplasmalogenase (EC 3.3.2.2 and EC 3.3.2.5) is an enzyme that catalyzes hydrolytic cleavage of the vinyl ether bond of lysoplasmalogen, forming fatty aldehyde and glycerophosphoethanolamine or glycerophosphocholine and is specific for the sn-2-deacylated form of plasmalogen. Here we report the purification, characterization, identification, and cloning of lysoplasmalogenase. Rat liver microsomal lysoplasmalogenase was solubilized with octyl glucoside and purified 500-fold to near homogeneity using four chromatography steps. The purified enzyme has apparent Km values of ?50 ?m for both lysoplasmenylcholine and lysoplasmenylethanolamine and apparent Vm values of 24.5 and 17.5 ?mol/min/mg protein for the two substrates, respectively. The pH optimum was 7.0. Lysoplasmalogenase was competitively inhibited by lysophosphatidic acid (Ki ?20 ?m). The predominant band on a gel at ?19 kDa was subjected to trypsinolysis, and the peptides were identified by mass spectrometry as Tmem86b, a protein of unknown function. Transient transfection of human embryonic kidney (HEK) 293T cells showed that TMEM86b cDNA yielded lysoplasmalogenase activity, and Western blot analyses confirmed the synthesis of TMEM86b protein. The protein was localized in the membrane fractions. The TMEM86b gene was also transformed into Escherichia coli, and its expression was verified by Western blot and activity analyses. Tmem86b is a hydrophobic transmembrane protein of the YhhN family. Northern blot analyses demonstrated that liver expressed the highest level of Tmem86b, which agreed with tissue distribution of activity. Overexpression of TMEM86b in HEK 293T cells resulted in decreased levels of plasmalogens, suggesting that the enzyme may be important in regulating plasmalogen levels in animal cells. PMID:21515882

  7. Palladium-Catalyzed Construction of Heteroatom-Containing ?-Conjugated Systems by Intramolecular Oxidative C-H/C-H Coupling Reaction.

    PubMed

    Saito, Kenta; Chikkade, Prasanna Kumara; Kanai, Motomu; Kuninobu, Yoichiro

    2015-06-01

    Synthesis of heteroatom-containing ladder-type ?-conjugated molecules was successfully achieved via a palladium-catalyzed intramolecular oxidative C-H/C-H cross-coupling reaction. This reaction provides a variety of ?-conjugated molecules bearing heteroatoms, such as nitrogen, oxygen, phosphorus, and sulfur atoms, and a carbonyl group. The ?-conjugated molecules were synthesized efficiently, even in gram scale, and larger ?-conjugated molecules were also obtained by a double C-H/C-H cross-coupling reaction and successive oxidative cycloaromatization. PMID:25907683

  8. A coumarin-specific prenyltransferase catalyzes the crucial biosynthetic reaction for furanocoumarin formation in parsley.

    PubMed

    Karamat, Fazeelat; Olry, Alexandre; Munakata, Ryosuke; Koeduka, Takao; Sugiyama, Akifumi; Paris, Cedric; Hehn, Alain; Bourgaud, Frédéric; Yazaki, Kazufumi

    2014-02-01

    Furanocoumarins constitute a sub-family of coumarin compounds with important defense properties against pathogens and insects, as well as allelopathic functions in plants. Furanocoumarins are divided into two sub-groups according to the alignment of the furan ring with the lactone structure: linear psoralen and angular angelicin derivatives. Determination of furanocoumarin type is based on the prenylation position of the common precursor of all furanocoumarins, umbelliferone, at C6 or C8, which gives rise to the psoralen or angelicin derivatives, respectively. Here, we identified a membrane-bound prenyltransferase PcPT from parsley (Petroselinum crispum), and characterized the properties of the gene product. PcPT expression in various parsley tissues is increased by UV irradiation, with a concomitant increase in furanocoumarin production. This enzyme has strict substrate specificity towards umbelliferone and dimethylallyl diphosphate, and a strong preference for the C6 position of the prenylated product (demethylsuberosin), leading to linear furanocoumarins. The C8-prenylated derivative (osthenol) is also formed, but to a much lesser extent. The PcPT protein is targeted to the plastids in planta. Introduction of this PcPT into the coumarin-producing plant Ruta graveolens showed increased consumption of endogenous umbelliferone. Expression of PcPT and a 4-coumaroyl CoA 2'-hydroxylase gene in Nicotiana benthamiana, which does not produce furanocoumarins, resulted in formation of demethylsuberosin, indicating that furanocoumarin production may be reconstructed by a metabolic engineering approach. The results demonstrate that a single prenyltransferase, such as PcPT, opens the pathway to linear furanocoumarins in parsley, but may also catalyze the synthesis of osthenol, the first intermediate committed to the angular furanocoumarin pathway, in other plants. PMID:24354545

  9. Altered (transition) states: Mechanisms of solution and enzyme catalyzed RNA 2?-O-transphosphorylation

    PubMed Central

    Kellerman, Daniel L.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.

    2014-01-01

    Although there have been great strides in defining the mechanisms of RNA strand cleavage by 2?-O-transphosphorylation, long-standing questions remain. How do different catalytic modes such as acid/base and metal ion catalysis influence transition state charge distribution? Does the large rate enhancement characteristic of biological catalysis result in different transition states relative to solution reactions? Answering these questions is important for understanding biological catalysis in general, and revealing principles for designing small molecule inhibitors. Recent application of linear free energy relationships and kinetic isotope effects together with multi-scale computational simulations are providing tentative answers to these questions for this fundamentally important class of phosphoryl transfer reactions. PMID:25023967

  10. Advanced Low Energy Enzyme Catalyzed Solvent for CO{sub 2} Capture

    SciTech Connect

    Zaks, Alex; Reardon, John

    2013-09-30

    A proof-of-concept biocatalyst enhanced solvent process was developed and demonstrated in an integrated bench-scale system using coal post combustion flue gas. The biocatalyst was deployed as a coating on M500X structured packing. Rate enhancement was evaluated using a non-volatile and non- toxic 20 wt% potassium carbonate solution. Greater than 500-fold volumetric scale-up from laboratory to bench scale was demonstrated in this project. Key technical achievements included: 10-fold mass transfer enhancement demonstrated in laboratory testing relative to blank potassium carbonate at 45°C; ~ 7-fold enhancement over blank in bench-scale field testing at National Carbon Capture Center; aerosol emissions were below detection limits (< 0.8 ppm); 90% capture was demonstrated at ~19.5 Nm{sup 3}/hr (dry basis); and ~ 80% CO{sub 2} capture was demonstrated at ~ 30 Nm{sup 3}/hr (dry basis) for more than 2800-hrs on flue gas with minimal detectible decline in activity. The regeneration energy requirement was 3.5 GJ/t CO{sub 2} for this solvent, which was below the target of <2.1 GJ/t CO{sub 2}. Bench unit testing revealed kinetic limitations in the un-catalyzed stripper at around 85°C, but process modeling based on bench unit data showed that equivalent work of less than 300 kWh/t CO{sub 2} including all CO{sub 2} compression can be achieved at lower temperature stripping conditions. Cost analysis showed that 20% potassium carbonate in a basic solvent flow sheet with biocatalyst coated packing has economic performance comparable to the reference NETL Case-12, 30% MEA. A detailed techno-economic analysis indicated that addition of catalyst in the stripper could reduce the cost of capture by ~6% and cost of avoided CO{sub 2} by ~10% below reference NETL Case-12. Based on these results, a directional plan was identified to reduce the cost of CO{sub 2} capture in future work.

  11. An acyl group makes a difference in the reactivity patterns of cytochrome P450 catalyzed N-demethylation of substituted N,N-dimethylbenzamides-high spin selective reactions.

    PubMed

    Wang, Yong; Li, Dongmei; Han, Keli; Shaik, Sason

    2010-03-01

    This paper addresses the experimentally observed mechanistic differences between the cytochrome P450-catalyzed N-demethylation of substituted N,N-dimethylanilines (DMA) and of N,N-dimethylbenzamides (DMBA). The two reactions of these substrates are initiated by C-H activation of the methyl groups on the nitrogen. Thus, the DMA reactions exhibit small deuterium kinetic isotope effects (KIEs), and these KIEs and the corresponding reaction rates exhibit a linear response to the electronic nature of the para substituent. By contrast, the DMBA reactions exhibit large KIEs; the KIEs and reaction rates do not at all respond to the nature of the para substituent. Accordingly, the present paper uses density functional theoretical calculations to address these reactivity patterns in para-substituted DMBA and compare these results to those obtained for the DMA reactions previously (Wang, Y.; Kumar, D.; Yang, C. L.; Han, K. L.; Shaik, S. J. Phys. Chem. B 2007, 111, 7700). The theoretical calculations reproduce the experimental trends of narrow variations in rates and KIEs. It is shown that the above mechanistic differences between the two reaction series of DMA and DMBA are caused by the ability of the para substituent to maintain a conjugation path between the C-H reaction center and the aryl moiety. Furthermore, the computational results show a new feature of reactivity, namely, that the N-demethylation of DMBA proceeds by a spin-selective reaction via the high spin state of the active species of the enzyme. This conclusion is reinforced by the match of the calculated and experimental KIE values. PMID:20146528

  12. Rapid removal of N-linked oligosaccharides using microwave assisted enzyme catalyzed deglycosylation

    NASA Astrophysics Data System (ADS)

    Sandoval, Wendy N.; Arellano, Fred; Arnott, David; Raab, Helga; Vandlen, Richard; Lill, Jennie R.

    2007-01-01

    The removal of N-linked oligosaccharides from glycoproteins is commonly performed during the preparation of samples for mass spectrometry. A reduction in the protein's structural heterogeneity is sometimes essential to obtain a mass for the intact protein. Alternatively, removal of the sugar may be desired to facilitate oligosaccharide analysis. A typical approach to deglycosylation employs overnight digestion with the enzyme peptide N-glycosidase F (PNGase F). We report a method for the accelerated removal of N-linked oligosaccharides using PNGase F assisted by microwave irradiation. Complete deglycosylation was achieved in less than 30 min for most proteins without compromising the integrity of protein samples. This method was tested on a variety of glycoproteins, including antibodies, at the microgram level.

  13. Reaction mechanism of the direct gas phase synthesis of H2O2 catalyzed by Au3

    NASA Astrophysics Data System (ADS)

    Njegic, Bosiljka; Gordon, Mark S.

    2008-09-01

    The gas phase reaction of molecular oxygen and hydrogen catalyzed by a Au3 cluster to yield H2O2 was investigated theoretically using second order Z-averaged perturbation theory, with the final energies obtained with the fully size extensive completely renormalized CR-CC(2,3) coupled cluster theory. The proposed reaction mechanism is initiated by adsorption and activation of O2 on the Au3 cluster. Molecular hydrogen then binds to the Au3O2 global minimum without an energy barrier. The reaction between the activated oxygen and hydrogen molecules proceeds through formation of hydroperoxide (HO2) and a hydrogen atom, which subsequently react to form the product hydrogen peroxide. All reactants, intermediates, and product remain bound to the gold cluster throughout the course of the reaction. The steps in the proposed reaction mechanism have low activation energy barriers below 15kcal/mol. The overall reaction is highly exothermic by 30kcal/mol.

  14. The copper-catalyzed redox reaction between aqueous hydrogen peroxide and hydrazine. 1. New experimental results and observations

    SciTech Connect

    Zhong, Yaping; Lim, Phooi K. )

    1989-10-25

    Important new data are reported which make it possible to deduce the most probable mechanism of the copper-catalyzed redox reaction between aqueous hydrogen peroxide and hydrazine: 2H{sub 2}O{sub 2} + N{sub 2}H{sub 4} {yields} 4H{sub 2}O + N{sub 2}. The reaction is marked by an induction period {tau}{sub e} which varies inversely with the catalyst concentration but essentially independently with the peroxide and hydrazine concentrations. Trace amounts of cerium ion, hydroquinone, quinone, and o-phenylenediamine promote the reaction markedly. Ultrasonication accelerates the reaction, whereas a viscosity increase in the reaction solution has the opposite effect. Maleate ion produces a quantitative increase in nitrogen output above the stoichiometric equivalent of peroxide. The reaction shows no wall effect. The nitrogen and peroxide profiles and the rate are described.

  15. Enzyme-catalyzed hydrolysis of cellulose in ionic liquids: a green approach toward the production of biofuels.

    PubMed

    Bose, Sayantan; Armstrong, Daniel W; Petrich, Jacob W

    2010-06-24

    We investigated the reactivity and stability of a commercial mixture of cellulases in eight ionic liquids by optical and calorimetric techniques. First, hydrolysis by cellulases from Tricoderma reesei in these ionic liquids was benchmarked against that in aqueous buffer. Only 1-methylimidazolium chloride (mim Cl) and tris-(2-hydroxyethyl)methylammonium methylsulfate (HEMA) provided a medium in which hydrolysis could occur. While hydrolysis at 65 degrees C is initially much faster in buffer than in these two liquids, it reaches a plateau after 2 h, whereas the reaction progresses monotonically in the two ionic liquids. This difference in the rate of hydrolysis is largely attributed to two factors: (1) the higher viscosity of the ionic liquids and (2) the enzymes are irreversibly denatured at 50 degrees C in buffer while they are stable to temperatures as high as 115 degrees C in HEMA. We explored whether fluorescence quenching of aromatic amino acids of the enzymes was indeed a signature of protein denaturation, as has been suggested in the literature, and concluded that quenching is not necessarily associated with denaturation. When it does occur, for example, in the presence of ionic liquids formed from imidazolium cations and chloride anions, it arises from the imidazolium rather than the chloride. Finally, we conclude that HEMA is a promising, novel, green medium for performing cellulose hydrolysis reactions to convert biomass into biofuels. Because of the thermal stability it imparts to enzymes, its ability to solubilize biomass, and the fact that it does not quench tryptophyl fluorescence (thus permitting monitoring of the enzymes by fluorescence spectroscopy), HEMA provides an ideal starting point for the design of ionic liquids, not only for the hydrolysis of biomass, but also for use with a wide spectrum of enzymatic reactions. PMID:20509703

  16. Factors that Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase

    PubMed Central

    Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Carrell, Christopher J.; Mathews, F. Scott; Jorns, Marilyn Schuman

    2009-01-01

    NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative 2-electron oxidation of P2C but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single 2-electron oxidation step. Wild-type and mutant enzyme exhibit identical rate constants for P2C oxidation to dihydropicolinate and isomerization of a reduced enzymedihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Picolinate release from Tyr258Phe is 100-fold faster than turnover. The presence of bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10- to 75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate or 1-cyclohexenoate, a 1-deaza P2C analog. The reduced Tyr258Phe1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD. PMID:19702312

  17. Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.

    PubMed

    Kommoju, Phaneeswara-Rao; Bruckner, Robert C; Ferreira, Patricia; Carrell, Christopher J; Mathews, F Scott; Jorns, Marilyn Schuman

    2009-10-13

    NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative two-electron oxidation of P2C, but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single two-electron oxidation step. Wild-type and mutant enzymes exhibit identical rate constants for oxidation of P2C to dihydropicolinate and isomerization of a reduced enzyme.dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Release of picolinate from Tyr258Phe is 100-fold faster than turnover. The presence of a bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10-75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate, or 1-cyclohexenoate, a 1-deaza-P2C analogue. The reduced Tyr258Phe x 1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD. PMID:19702312

  18. Factors That Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase

    SciTech Connect

    Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Carrell, Christopher J.; Mathews, F. Scott; Jorns, Marilyn Schuman

    2009-10-21

    NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an 'aromatic cage' that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative two-electron oxidation of P2C, but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-l-proline) that is aromatized in a single two-electron oxidation step. Wild-type and mutant enzymes exhibit identical rate constants for oxidation of P2C to dihydropicolinate and isomerization of a reduced enzyme-dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Release of picolinate from Tyr258Phe is 100-fold faster than turnover. The presence of a bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10-75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate, or 1-cyclohexenoate, a 1-deaza-P2C analogue. The reduced Tyr258Phe-1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD.

  19. Atomically dispersed Au-(OH)x species bound on titania catalyze the low-temperature water-gas shift reaction.

    PubMed

    Yang, Ming; Allard, Lawrence F; Flytzani-Stephanopoulos, Maria

    2013-03-13

    We report a new method for stabilizing appreciable loadings (~1 wt %) of isolated gold atoms on titania and show that these catalyze the low-temperature water-gas shift reaction. The method combines a typical gold deposition/precipitation method with UV irradiation of the titania support suspended in ethanol. Dissociation of H2O on the thus-created Au-O-TiO(x) sites is facile. At higher gold loadings, nanoparticles are formed, but they were shown to add no further activity to the atomically bound gold on titania. Removal of this "excess" gold by sodium cyanide leaching leaves the activity intact and the atomically dispersed gold still bound on titania. The new materials may catalyze a number of other reactions that require oxidized active metal sites. PMID:23437858

  20. Enzyme-catalyzed synthesis of poly[(R)-(-)-3-hydroxybutyrate]: formation of macroscopic granules in vitro.

    PubMed Central

    Gerngross, T U; Martin, D P

    1995-01-01

    A combined chemical and enzymatic procedure has been developed to synthesize macroscopic poly[(R)-(-)-3-hydroxybutyrate] (PHB) granules in vitro. The granules form in a matter of minutes when purified polyhydroxyalkanoate (PHA) synthase from Alcaligenes eutrophus is exposed to synthetically prepared (R)-3-hydroxybutyryl coenzyme A, thereby establishing the minimal requirements for PHB granule formation. The artificial granules are spherical with diameters of up to 3 microns and significantly larger than their native counterparts (0.5 micron). The isolated PHB was characterized by 1H and 13C NMR, gel-permeation chromatography, and chemical analysis. The in vitro polymerization system yields PHB with a molecular mass > 10 x 10(6) Da, exceeding by an order of magnitude the mass of PHAs typically extracted from microorganisms. We also demonstrate that the molecular mass of the polymer can be controlled by the initial PHA synthase concentration. Preliminary kinetic analysis of de novo granule formation confirms earlier findings of a lag time for the enzyme but suggests the involvement of an additional granule assembly step. Minimal requirements for substrate recognition were investigated. Since substrate analogs lacking the adenosine 3',5'-bisphosphate moiety of (R)-3-hydroxybutyryl coenzyme A were not accepted by the PHA synthase, we provide evidence that this structural element of the substrate is essential for catalysis. Images Fig. 4 PMID:7603982

  1. Enzyme-catalyzed synthesis of poly[(R)-(-)-3-hydroxybutyrate]: Formation of macroscopic granules in vitro

    SciTech Connect

    Gerngross, T.U.; Martin, D.P.

    1995-07-03

    A combined chemical and enzymatic procedure has been developed to synthesize macroscopic poly[(R)-(-)-3-hydroxybutyrate] (PHB) granules in vitro. The granules form in a matter of minutes when purified polyhydroxyalkanoate (PHA) synthase from Alcaligenes eutrophus is exposed to synthetically prepared (R)-3-hydroxybutyryl coenzyme A, thereby establishing the minimal requirements for PHB granule formation. The artificial granules are spherical with diameters of up to 3 {mu}m and significantly larger than their native counterparts (0.5 {mu}m). The isolated PHB was characterized by {sup 1}H and {sup 13}C NMR, gel-permeation chromatography, and chemical analysis. The in vitro polymerization system yields PHB with a molecular mass > 10 x 10{sup 6} Da, exceeding by an order of magnitude the mass of PHAs typically extracted from microorganisms. We also demonstrate that the molecular mass of the polymer can be controlled by the initial PHA synthase concentration. Preliminary kinetic analysis of de novo granule formation confirms earlier findings of a lag time for the enzyme but suggests the involvement of an additional granule assembly step. Minimal requirements for substrate recognition were investigated. Since substrate analogs lacking the adenosine 3{prime}, 5{prime}-bisphosphate moiety of (R)-3-hydroxybutyryl coenzyme A were not accepted by the PHA synthase, we provide evidence that this structural element of the substrate is essential for catalysis. PHAs provide a range of natural, renewable, biodegradable thermoplastics with a broad range of useful material properties. 33 refs., 6 figs., 1 tab.

  2. Unified mechanism of alkali and alkaline earth catalyzed gasification reactions of carbon by CO2 and H2O

    USGS Publications Warehouse

    Chen, S.G.; Yang, R.T.

    1997-01-01

    From molecular orbital calculations, a unified mechanism is proposed for the gasification reactions of graphite by CO2 and H2O, both uncatalyzed and catalyzed by alkali and alkaline earth catalysts. In this mechanism, there are two types of oxygen intermediates that are bonded to the active edge carbon atoms: an in-plane semiquinone type, Cf(O), and an off-plane oxygen bonded to two saturated carbon atoms that are adjacent to the semiquinone species, C(O)Cf(O). The rate-limiting step is the decomposition of these intermediates by breaking the C-C bonds that are connected to Cf(O). A new rate equation is derived for the uncatalyzed reactions, and that for the catalyzed reactions is readily available from the proposed mechanism. The proposed mechanism can account for several unresolved experimental observations: TPD and TK (transient kinetics) desorption results of the catalyzed systems, the similar activation energies for the uncatalyzed and catalyzed reactions, and the relative activities of the alkali and alkaline earth elements. The net charge of the edge carbon active site is substantially changed by gaining electron density from the alkali or alkaline earth element (by forming C-O-M, where M stands for metal). The relative catalytic activities of these elements can be correlated with their abilities of donating electrons and changing the net charge of the edge carbon atom. As shown previously (Chen, S. G.; Yang, R. T. J. Catal. 1993, 141, 102), only clusters of the alkali compounds are active. This derives from the ability of the clusters to dissociate CO2 and H2O to form O atoms and the mobility of the dissociated O atoms facilitated by the clusters.

  3. Supercritical CO2 as a reaction medium for synthesis of capsaicin analogues by lipase-catalyzed transacylation of capsaicin.

    PubMed

    Kobata, Kenji; Kobayashi, Mamiko; Kinpara, Sachiyo; Watanabe, Tatsuo

    2003-09-01

    Capsaicin analogues having different acyl moiety were synthesized by lipase-catalyzed transacylation of capsaicin with a corresponding acyl donor in supercritical CO2 as a reaction medium. Transacylation with methyl tetradecanoate using Novozym 435 as a catalyst gave vanillyl tetradecanamide in a 54% yield at 80 degrees C and 19 MPa over 72 h. Vanillyl (Z)-9-octadecenamide, olvanil, was synthesized from triolein in a 21% yield over 7 d. PMID:14571985

  4. In Vivo and in Vitro Evidence for Biochemical Coupling of Reactions Catalyzed by Lysophosphatidylcholine Acyltransferase and Diacylglycerol Acyltransferase.

    PubMed

    Pan, Xue; Chen, Guanqun; Kazachkov, Michael; Greer, Michael S; Caldo, Kristian Mark P; Zou, Jitao; Weselake, Randall J

    2015-07-17

    Seed oils of flax (Linum usitatissimum L.) and many other plant species contain substantial amounts of polyunsaturated fatty acids (PUFAs). Phosphatidylcholine (PC) is the major site for PUFA synthesis. The exact mechanisms of how these PUFAs are channeled from PC into triacylglycerol (TAG) needs to be further explored. By using in vivo and in vitro approaches, we demonstrated that the PC deacylation reaction catalyzed by the reverse action of acyl-CoA:lysophosphatidylcholine acyltransferase (LPCAT) can transfer PUFAs on PC directly into the acyl-CoA pool, making these PUFAs available for the diacylglycerol acyltransferase (DGAT)-catalyzed reaction for TAG production. Two types of yeast mutants were generated for in vivo and in vitro experiments, respectively. Both mutants provide a null background with no endogenous TAG forming capacity and an extremely low LPCAT activity. In vivo experiments showed that co-expressing flax DGAT1-1 and LPCAT1 in the yeast quintuple mutant significantly increased 18-carbon PUFAs in TAG with a concomitant decrease of 18-carbon PUFAs in phospholipid. We further showed that after incubation of sn-2-[(14)C]acyl-PC, formation of [(14)C]TAG was only possible with yeast microsomes containing both LPCAT1 and DGAT1-1. Moreover, the specific activity of overall LPCAT1 and DGAT1-1 coupling process exhibited a preference for transferring (14)C-labeled linoleoyl or linolenoyl than oleoyl moieties from the sn-2 position of PC to TAG. Together, our data support the hypothesis of biochemical coupling of the LPCAT1-catalyzed reverse reaction with the DGAT1-1-catalyzed reaction for incorporating PUFAs into TAG. This process represents a potential route for enriching TAG in PUFA content during seed development in flax. PMID:26055703

  5. Regio- and stereoselective synthesis of benzothiazolo-pyrimidinones via an NHC-catalyzed Mannich/lactamization domino reaction.

    PubMed

    Ni, Qijian; Song, Xiaoxiao; Xiong, Jiawen; Raabe, Gerhard; Enders, Dieter

    2015-01-25

    An NHC-catalyzed regio- and stereoselective Mannich/lactamization domino reaction of N-(benzothiazolyl)imines with ?-chloroaldehydes has been developed. This new protocol provides a facile approach for the asymmetric synthesis of benzothiazolo-pyrimidinones and a pyrrolo[1,2-a]indolone in moderate to good yields (34-78%) and excellent stereoselectivities (87-99% ee, up to >20?:?1 d.r.). PMID:25476422

  6. Formal [4 + 1] Cycloadditions of ?,?-Diaryl-Substituted ortho-(Alkynyl)styrenes through Gold(I)-Catalyzed Cycloisomerization Reactions.

    PubMed

    Sanjun, Ana M; Virumbrales, Cintia; Garca-Garca, Patricia; Fernndez-Rodrguez, Manuel A; Sanz, Roberto

    2016-03-01

    Gold(I)-catalyzed cycloisomerization of ?,?-diaryl-o-(alkynyl)styrenes at 80 C selectively yields dihydroindeno[2,1-a]indenes in a transformation that encompasses a formal [4 + 1] cycloaddition and takes place through a cascade 5-endo-cyclization-diene activation-iso-Nazarov cyclization. In addition, by performing the reaction at 0 C, the same substrates exclusively give rise to benzofulvene derivatives, which have also been shown to be intermediates in the formation of the tetracyclics. PMID:26883951

  7. Palladium-Catalyzed Nucleophilic Substitution/C-H Activation/Aromatization Cascade Reaction: One Approach To Construct 6-Unsubstituted Phenanthridines.

    PubMed

    Han, Wenyong; Zhou, Xiaojian; Yang, Siyi; Xiang, Guangyan; Cui, Baodong; Chen, Yongzheng

    2015-11-20

    A facile and practical palladium-catalyzed nucleophilic substitution/C-H activation/aromatization cascade reaction has been developed. A range of 6-unsubstituted phenanthridines could be obtained in moderate to good yields (31-85%) with readily prepared N-Ms arylamines and commercially available 2-bromobenzyl bromide derivatives as starting materials. The potential application of the protocol was also demonstrated by the expeditious synthesis of the natural alkaloid trisphaeridine. PMID:26513449

  8. Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

    PubMed Central

    Świderek, Katarzyna; Tuñón, Iñaki; Martí, Sergio; Moliner, Vicent

    2015-01-01

    In the last decade L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed from the 80s that the full catalytic process of LDH starts with the binding of the cofactor and the substrate followed by the enclosure of the active site by a mobile loop of the protein before the reaction to take place. In this paper we show that the chemical step of the LDH catalyzed reaction can proceed within the open loop conformation, and the different reactivity of the different protein conformations would be in agreement with the broad range of rate constants measured in single molecule spectrometry studies. Starting from a recently solved X-ray diffraction structure that presented an open loop conformation in two of the four chains of the tetramer, QM/MM free energy surfaces have been obtained at different levels of theory. Depending on the level of theory used to describe the electronic structure, the free energy barrier for the transformation of pyruvate into lactate with the open conformation of the protein varies between 12.9 and 16.3 kcal/mol, after quantizing the vibrations and adding the contributions of recrossing and tunneling effects. These values are very close to the experimentally deduced one (14.2 kcal·mol−1) and ~2 kcal·mol−1 smaller than the ones obtained with the closed loop conformer. Calculation of primary KIEs and IR spectra in both protein conformations are also consistent with our hypothesis and in agreement with experimental data. Our calculations suggest that the closure of the active site is mainly required for the inverse process; the oxidation of lactate to pyruvate. According to this hypothesis H4 type LDH enzyme molecules, where it has been propose that lactate is transformed into pyruvate, should have a better ability to close the mobile loop than the M4 type LDH molecules. PMID:25705562

  9. Effects of Molecular Oxygen, Solvent, and Light on Iridium-Photoredox/Nickel Dual-Catalyzed Cross-Coupling Reactions.

    PubMed

    Oderinde, Martins S; Varela-Alvarez, Adrian; Aquila, Brian; Robbins, Daniel W; Johannes, Jeffrey W

    2015-08-01

    In order to achieve reproducibility during iridium-photoredox and nickel dual-catalyzed sp(3)-sp(2) carbon-carbon bond-forming reactions, we investigated the role that molecular oxygen (O2), solvent and light-source (CF lamp or blue LED) play in a variety of Ir-photoredox mediated transformations. The presence of O2 was discovered to be important for catalyst activation when air-stable Ni(II) precatalysts were used in DMF under CF lamp irradiation; however, O2 was not required for catalysis when conducted with Ni(COD)2 in the same reaction system. O2 is believed to promote rapid reduction of the Ni(II) precatalyst by Ir(II) to Ni(0). In addition to O2, the effects that solvent and light-source have on the dual-catalyzed decarboxylative cross-coupling reactions will be discussed. These findings have enabled us to develop a more robust dual-catalyzed decarboxylative cross-coupling protocol. PMID:26140623

  10. Aerobic oxidation reactions catalyzed by vanadium complexes of bis(phenolate) ligands.

    PubMed

    Zhang, Guoqi; Scott, Brian L; Wu, Ruilian; Silks, L A Pete; Hanson, Susan K

    2012-07-01

    Vanadium(V) complexes of the tridentate bis(phenolate)pyridine ligand H(2)BPP (H(2)BPP = 2,6-(HOC(6)H(2)-2,4-(t)Bu(2))(2)NC(5)H(3)) and the bis(phenolate)amine ligand H(2)BPA (H(2)BPA = N,N-bis(2-hydroxy-4,5-dimethylbenzyl)propylamine) have been synthesized and characterized. The ability of the complexes to mediate the oxidative C-C bond cleavage of pinacol was tested. Reaction of the complex (BPP)V(V)(O)(O(i)Pr) (4) with pinacol afforded the monomeric vanadium(IV) product (BPP)V(IV)(O)(HO(i)Pr) (6) and acetone. Vanadium(IV) complex 6 was oxidized rapidly by air at room temperature in the presence of NEt(3), yielding the vanadium(V) cis-dioxo complex [(BPP)V(V)(O)(2)]HNEt(3). Complex (BPA)V(V)(O)(O(i)Pr) (5) reacted with pinacol at room temperature, to afford acetone and the vanadium(IV) dimer [(BPA)V(IV)(O)(HO(i)Pr)](2). Complexes 4 and 5 were evaluated as catalysts for the aerobic oxidation of 4-methoxybenzyl alcohol and arylglycerol ?-aryl ether lignin model compounds. Although both 4 and 5 catalyzed the aerobic oxidation of 4-methoxybenzyl alcohol, complex 4 was found to be a more active and robust catalyst for oxidation of the lignin model compounds. The catalytic activities and selectivities of the bis(phenolate) complexes are compared to previously reported catalysts. PMID:22708725

  11. Unification of reaction pathway and kinetic scheme for N2 reduction catalyzed by nitrogenase.

    PubMed

    Lukoyanov, Dmitriy; Yang, Zhi-Yong; Barney, Brett M; Dean, Dennis R; Seefeldt, Lance C; Hoffman, Brian M

    2012-04-10

    Nitrogenase catalyzes the reduction of N(2) and protons to yield two NH(3) and one H(2). Substrate binding occurs at a complex organo-metallocluster called FeMo-cofactor (FeMo-co). Each catalytic cycle involves the sequential delivery of eight electrons/protons to this cluster, and this process has been framed within a kinetic scheme developed by Lowe and Thorneley. Rapid freezing of a modified nitrogenase under turnover conditions using diazene, methyldiazene (HN = N-CH(3)), or hydrazine as substrate recently was shown to trap a common S = intermediate, designated I. It was further concluded that the two N-atoms of N(2) are hydrogenated alternately ("Alternating" (A) pathway). In the present work, Q-band CW EPR and (95)Mo ESEEM spectroscopy reveal such samples also contain a common intermediate with FeMo-co in an integer-spin state having a ground-state "non-Kramers" doublet. This species, designated H, has been characterized by ESEEM spectroscopy using a combination of (14,15)N isotopologs plus (1,2)H isotopologs of methyldiazene. It is concluded that: H has NH(2) bound to FeMo-co and corresponds to the penultimate intermediate of N(2) hydrogenation, the state formed after the accumulation of seven electrons/protons and the release of the first NH(3); I corresponds to the final intermediate in N(2) reduction, the state formed after accumulation of eight electrons/protons, with NH(3) still bound to FeMo-co prior to release and regeneration of resting-state FeMo-co. A proposed unification of the Lowe-Thorneley kinetic model with the "prompt" alternating reaction pathway represents a draft mechanism for N(2) reduction by nitrogenase. PMID:22460797

  12. Can laccases catalyze bond cleavage in lignin?

    PubMed

    Munk, Line; Sitarz, Anna K; Kalyani, Dayanand C; Mikkelsen, J Dalgaard; Meyer, Anne S

    2015-01-01

    Modification of lignin is recognized as an important aspect of the successful refining of lignocellulosic biomass, and enzyme-assisted processing and upcycling of lignin is receiving significant attention in the literature. Laccases (EC 1.10.3.2) are taking the centerstage of this attention, since these enzymes may help degrading lignin, using oxygen as the oxidant. Laccases can catalyze polymerization of lignin, but the question is whether and how laccases can directly catalyze modification of lignin via catalytic bond cleavage. Via a thorough review of the available literature and detailed illustrations of the putative laccase catalyzed reactions, including the possible reactions of the reactive radical intermediates taking place after the initial oxidation of the phenol-hydroxyl groups, we show that i) Laccase activity is able to catalyze bond cleavage in low molecular weight phenolic lignin model compounds; ii) For laccases to catalyze inter-unit bond cleavage in lignin substrates, the presence of a mediator system is required. Clearly, the higher the redox potential of the laccase enzyme, the broader the range of substrates, including o- and p-diphenols, aminophenols, methoxy-substituted phenols, benzenethiols, polyphenols, and polyamines, which may be oxidized. In addition, the currently available analytical methods that can be used to detect enzyme catalyzed changes in lignin are summarized, and an improved nomenclature for unequivocal interpretation of the action of laccases on lignin is proposed. PMID:25560931

  13. Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics.

    PubMed

    Chakravorty, Dhruva K; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2009-11-10

    Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of approximately 8, and dynamical barrier recrossings decrease the rates by a factor of 3-4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen-bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme. PMID:19799395

  14. Evidence of Kinetic Control of Ligand Binding and Staged Product Release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed Reactions

    SciTech Connect

    Jackson, S.; Zhang, F; Chindemi, P; Junop, M; Berti, P

    2009-01-01

    MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k{sub cat}/K{sub M} of 520 M{sup -1} s{sup -1}, was far slower than the normal reaction, and 3 x 10{sup 5}-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new 'staged' MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA {center_dot} ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA {center_dot} UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA.

  15. ESolvent-free, enzyme-catalyzed biodiesel production from mango, neem, and shea oils via response surface methodology.

    PubMed

    Nde, Divine Bup; Astete, Carlos; Boldor, Dorin

    2015-12-01

    Mango, neem and shea kernels produce non-conventional oils whose potentials are not fully exploited. To give an added value to these oils, they were transesterified into biodiesel in a solvent-free system using immobilized enzyme lipozyme from Mucor miehei. The Doehlert experimental design was used to evaluate the methyl ester (ME) yields as influenced by enzyme concentration-EC, temperature-T, added water content-AWC, and reaction time-RT. Biodiesel yields were quantified by (1)H NMR spectroscopy and subsequently modeled by a second order polynomial equation with interactions. Lipozyme enzymes were more tolerant to high temperatures in neem and shea oils reaction media compared to that of mango oil. The optimum reaction conditions EC, T, AWC, and RT assuring near complete conversion were as follows: mango oil 7.25 %, 36.6 °C, 10.9 %, 36.4 h; neem oil EC = 7.19 %, T = 45.7 °C, AWC = 8.43 %, RT = 25.08 h; and shea oil EC = 4.43 %, T = 45.65 °C, AWC = 6.21 % and RT = 25.08 h. Validation experiments of these optimum conditions gave ME yields of 98.1 ± 1.0, 98.5 ± 1.6 and 99.3 ± 0.4 % for mango, neem and shea oils, respectively, which all met ASTM biodiesel standards. PMID:26698315

  16. Bidentate Lewis Acid Catalyzed Domino Diels-Alder Reaction of Phthalazine for the Synthesis of Bridged Oligocyclic Tetrahydronaphthalenes.

    PubMed

    Schweighauser, Luca; Bodoky, Ina; Kessler, Simon N; Häussinger, Daniel; Donsbach, Carsten; Wegner, Hermann A

    2016-03-18

    A domino process consisting of an inverse and a normal electron-demand Diels-Alder reaction is presented for the formation of bridged tri- and tetracyclic 1,2,3,4-tetrahydronaphthalenes catalyzed by a bidentate Lewis acid. The products were synthesized in a one-pot reaction from commercially available starting materials and contain up to six stereogenic centers. The tetrahydronaphthalenes were isolated as single diastereomers and are derivatives of phenylethylamine, which is well-known as a scaffold of amphetamine or dopamine. PMID:26943286

  17. Non-Catalyzed Click Reactions of ADIBO Derivatives with 5-Methyluridine Azides and Conformational Study of the Resulting Triazoles

    PubMed Central

    Smyslova, Petra; Popa, Igor; Lyčka, Antonín; Tejral, Gracian; Hlavac, Jan

    2015-01-01

    Copper-free click reactions between a dibenzoazocine derivative and azides derived from 5-methyluridine were investigated. The non-catalyzed reaction yielded both regioisomers in an approximately equivalent ratio. The NMR spectra of each regioisomer revealed conformational isomery. The ratio of isomers was dependent on the type of regioisomer and the type of solvent. The synthesis of various analogs, a detailed NMR study and computational modeling provided evidence that the isomery was dependent on the interaction of the azocine and pyrimidine parts. PMID:26673606

  18. Re2O7-catalyzed reaction of hemiacetals and aldehydes with O-, S-, and C-nucleophiles

    PubMed Central

    Sittiwong, Wantanee; Richardson, Michael W; Schiaffo, Charles E; Fisher, Thomas J

    2013-01-01

    Summary Re(VII) oxides catalyze the acetalization, monoperoxyacetalization, monothioacetalization and allylation of hemiacetals. The reactions, which take place under mild conditions and at low catalyst loadings, can be conducted using hemiacetals, the corresponding O-silyl ethers, and, in some cases, the acetal dimers. Aldehydes react under similar conditions to furnish good yields of dithioacetals. Reactions of hemiacetals with nitrogen nucleophiles are unsuccessful. 1,2-Dioxolan-3-ols (peroxyhemiacetals) undergo Re(VII)-promoted etherification but not allylation. Hydroperoxyacetals (1-alkoxyhydroperoxides) undergo selective exchange of the alkoxide group in the presence of either Re2O7 or a Brnsted acid. PMID:23946852

  19. Rhodium(II) catalyzed synthesis of macrocycles incorporating oxindole via O-H/N-H insertion reactions.

    PubMed

    Muthusamy, Sengodagounder; Karikalan, Thangaraju

    2014-12-01

    A wide variety of 10- to 29-membered oxaza-macrocycles incorporating an oxindole unit were synthesized in good yield via rhodium(II) acetate dimer catalyzed intramolecular O-H/N-H insertion reactions. Interestingly, synthesis of C2-symmetric macrocycles in moderate yield was also demonstrated via head to tail dimerization involving double intermolecular O-H insertion when the spacer length was decreased. The synthesis of chiral macrocycles was also delineated. This study reveals the effect of spacer length on inter- or intramolecular insertion reactions with the remotely placed hydroxyl/amino group. PMID:25302664

  20. Palladium-catalyzed Heck-type reaction of oximes with allylic alcohols: synthesis of pyridines and azafluorenones.

    PubMed

    Zheng, Meifang; Chen, Pengquan; Wu, Wanqing; Jiang, Huanfeng

    2015-12-15

    We describe herein a palladium-catalyzed Heck-type reaction of O-acetyl ketoximes and allylic alcohols to synthesise pyridines. This protocol allows the robust synthesis of pyridines and azafluorenones in good to excellent yields with tolerance of various functional groups under mild conditions. The reaction is supposed to go through an oxidative addition of oximes to palladium(0) complexes, generating an alkylideneamino-palladium(ii) species, which is utilized as a key intermediate to capture the nonbiased alkenes for carbon-carbon bond formation. PMID:26496814

  1. Characterization of Chemically Modified Enzymes for Bioremediation Reactions

    SciTech Connect

    Davison, Brian H.

    2000-12-31

    Remediation processes frequently involve species possessing limited solubility in water. For this project, we were interested in novel strategies using molecularly modified enzymes with enhanced activity and stability for remediation of recalcitrant compounds in organic solvents. Performance of naturally occurring enzymes is usually quite limited in such organic environments. The primary objective of the work was to gain a fundamental understanding of the molecular and catalytic properties of enzymes that have been chemically modified so that they are catalytically active and chemically stable in organic solvents. The premise was that stabilized and activated enzymes, which can function under harsh chemical conditions, are optimally suited for bioremediation in nonaqueous media where substrates of interest are more soluble and processed with greater efficiency. This unique strategy was examined with respect to the degradation of chlorophenols and PCBs.

  2. Efficient access to substituted silafluorenes by nickel-catalyzed reactions of biphenylenes with Et?SiH?.

    PubMed

    Breunig, Jens Michael; Gupta, Puneet; Das, Animesh; Tussupbayev, Samat; Diefenbach, Martin; Bolte, Michael; Wagner, Matthias; Holthausen, Max C; Lerner, Hans-Wolfram

    2014-11-01

    The reaction of biphenylene (1) with Et2SiH2 in the presence of [Ni(PPhMe2)4] results in the formation of a mixture of 2-diethylhydrosilylbiphenyl [2(Et2HSi)] and 9,9,-diethyl-9-silafluorene (3). Silafluorene 3 was isolated in 37.5% and 2(Et2HSi) in 36.9% yield. The underlying reaction mechanism was elucidated by DFT calculations. 4-Methyl-9,9-diethyl-9-silafluorene (7) was obtained selectively from the [Ni(PPhMe2)4]-catalyzed reaction of Et2SiH2 and 1-methylbiphenylene. By contrast, no selectivity could be found in the Ni-catalyzed reaction between Et2SiH2 and the biphenylene derivative that bears tBu substituents in the 2- and 7-positions. Therefore, two pairs of isomers of tBu-substituted silafluorenes and of the related diethylhydrosilylbiphenyls were formed in this reaction. However, a subsequent dehydrogenation of the diethylhydrosilylbiphenyls with Wilkinson's catalyst yielded a mixture of 2,7-di-tert-butyl-9,9-diethyl-9-silafluorene (8) and 3,6-di-tert-butyl-9,9-diethyl-9-silafluorene (9). Silafluorenes 8 and 9 were separated by column chromatography. PMID:25205601

  3. Controlling thermo-reversibility of gelatin gels through a peroxidase-catalyzed reaction under mild conditions for mammalian cells.

    PubMed

    Sakai, Shinji; Moriyama, Kousuke; Kawakami, Koei

    2011-01-01

    A variety of cross-linking methods is used for obtaining gelatin gels having a tolerance to thermo-reversible gel-sol transition at physiological temperature. In this paper, we investigated the applicability of horseradish peroxidase-catalyzed cross-linking of tyrosine residues originally contained in native gelatin molecules for preparing such gelatin gels. The gelatin gels obtained through exposure to the enzymatic reaction showed a higher resistance to thermo-reversibility at 37°C than gels obtained through a thermally-induced gelation alone. In addition, the resistance property to thermo-reversible gel-sol transition was tunable by controlling enzymatic reaction conditions: higher peroxidase concentration and thermally-induced pre-gelation accomplished by cooling the gelatin solution prior to the enzymatic reaction produced gels with higher resistance to thermo-reversibility. Fibroblast cells enclosed in the gelatin gels obtained through the enzymatic reaction with thermally-induced pre-gelation showed 93% viability. These results demonstrate the feasibility of peroxidase-catalyzed reaction for obtaining gelatin gels having a tolerance to thermo-reversible gel-to-sol transition at physiological temperature toward applications in biomedical and biopharmaceutical fields. PMID:20615328

  4. Reactivity of Cations and Zwitterions Formed in Photochemical and Acid-Catalyzed Reactions from m-Hydroxycycloalkyl-Substituted Phenol Derivatives.

    PubMed

    Cindro, Nikola; Antol, Ivana; Mlinari?-Majerski, Kata; Halasz, Ivan; Wan, Peter; Basari?, Nikola

    2015-12-18

    Three m-substituted phenol derivatives, each with a labile benzylic alcohol group and bearing either protoadamantyl 4, homoadamantyl 5, or a cyclohexyl group 6, were synthesized and their thermal acid-catalyzed and photochemical solvolytic reactivity studied, using preparative irradiations, fluorescence measurements, nanosecond laser flash photolysis, and quantum chemical calculations. The choice of m-hydroxy-substitution was driven by the potential for these phenolic systems to generate m-quinone methides on photolysis, which could ultimately drive the excited-state pathway, as opposed to forming simple benzylic carbocations in the corresponding thermal route. Indeed, thermal acid-catalyzed reactions gave the corresponding cations, which undergo rearrangement and elimination from 4, only elimination from 5, and substitution and elimination from 6. On the other hand, upon photoexcitation of 4-6 to S1 in a polar protic solvent, proton dissociation from the phenol, coupled with elimination of the benzylic OH (as hydroxide ion) gave zwitterions (formal m-quinone methides). The zwitterions exhibit reactivity different from the corresponding cations due to a difference in charge distribution, as shown by DFT calculations. Thus, protoadamantyl zwitterion has a less nonclassical character than the corresponding cation, so it does not undergo 1,2-shift of the carbon atom, as observed in the acid-catalyzed reaction. PMID:26595342

  5. Development of Stereocontrolled Palladium(II)-Catalyzed Domino Heck/Suzuki ?,?-Diarylation Reactions with Chelating Vinyl Ethers and Arylboronic Acids

    PubMed Central

    Trejos, Alejandro; Odell, Luke R; Larhed, Mats

    2012-01-01

    A stereoselective and 1,4-benzoquinone-mediated palladium(II)-catalyzed Heck/Suzuki domino reaction involving metal coordinating cyclic methylamino vinyl ethers and a number of electronically diverse arylboronic acids has been developed and studied. Diastereomeric ratios up to 39:1 and 78 % isolated yields were obtained. The stereoselectivity of the reaction was found to be highly dependent on the nature of the arylboronic acid and the amount of water present in the reaction mixture. Thus, a domino ?,?-diarylationreduction of chelating vinyl ethers can now be accomplished and stereochemically controlled, given that optimized conditions and an appropriate chiral auxiliary are used. To the best of our knowledge, this represents the first example of a stereoselective, oxidative Heck/Suzuki domino reaction in the literature. PMID:24551492

  6. Low-temperature superacid catalysis: Reactions of n-butane catalyzed by iron- and manganese-promoted sulfated zirconia

    SciTech Connect

    Cheung, T.K.; D`Itri, J.L.; Gates, B.C.

    1995-02-01

    Environmental concerns are leading to the replacement of aromatic hydrocarbons in gasoline with high-octane-number branched paraffins and oxygenated compounds such as methyl t-butyl ether, which is produced from methanol and isobutylene. The latter can be formed from n-butane by isomerization followed by dehydrogenation. To meet the need for improved catalysts for isomerization of n-butane and other paraffins, researchers identified solid acids that are noncorrosive and active at low temperatures. Sulfated zirconia catalyzes the isomerization of n-butane even at 25{degrees}C, and the addition of Fe and Mn promoters increases its activity by three orders of magnitude. Little is known about this new catalyst. Here the authors provide evidence of its performance for n-butane conversion, demonstrating that isomerization is accompanied by disproportionation and other, less well understood, acid-catalyzed reactions and undergoes rapid deactivation associated with deposition of carbonaceous material. 10 refs., 3 figs.

  7. Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products

    SciTech Connect

    Achyuthan, Komandoor; Adams, Paul; Simmons, Blake; Singh, Anup

    2011-07-13

    Lignin composition (monolignol types of coniferyl, sinapyl or p-coumaryl alcohol) is causally related to biomass recalcitrance. We describe multiwavelength (220, 228, 240, 250, 260, 290, 295, 300, 310 or 320 nm) absorption spectroscopy of coniferyl alcohol and its laccase- or peroxidase-catalyzed products during real time kinetic, pseudo-kinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 mu L volumes demonstrated assay miniaturization and high throughput screening capabilities. Bathochromic and hypsochromic shifts along with hyperchromicity or hypochromicity accompanied enzymatic oxidations by laccase or peroxidase. The limits of detection and quantitation of coniferyl alcohol averaged 2.4 and 7.1 mu M respectively, with linear trend lines over 3 to 4 orders of magnitude. Coniferyl alcohol oxidation was evident within 10 minutes or with 0.01 mu g/mL laccase and 2 minutes or 0.001 mu g/mL peroxidase. Detection limit improved to 1.0 mu M coniferyl alcohol with Km of 978.7 +/- 150.7 mu M when examined at 260 nm following 30 minutes oxidation with 1.0 mu g/mL laccase. Our assays utilized the intrinsic spectroscopic properties of coniferyl alcohol or its oxidation products for enabling detection, without requiring chemical synthesis or modification of the substrate or product(s). These studies facilitate lignin compositional analyses and augment pretreatment strategies for reducing biomass recalcitrance.

  8. Remarkable Diversity in the Enzymes Catalyzing the Last Step in Synthesis of the Pimelate Moiety of Biotin

    PubMed Central

    Shapiro, Madelyn M.; Chakravartty, Vandana; Cronan, John E.

    2012-01-01

    Biotin synthesis in Escherichia coli requires the functions of the bioH and bioC genes to synthesize the precursor pimelate moiety by use of a modified fatty acid biosynthesis pathway. However, it was previously noted that bioH has been replaced with bioG or bioK within the biotin synthetic gene clusters of other bacteria. We report that each of four BioG proteins from diverse bacteria and two cyanobacterial BioK proteins functionally replace E. coli BioH in vivo. Moreover, purified BioG proteins have esterase activity against pimeloyl-ACP methyl ester, the physiological substrate of BioH. Two of the BioG proteins block biotin synthesis when highly expressed and these toxic proteins were shown to have more promiscuous substrate specificities than the non-toxic BioG proteins. A postulated BioG-BioC fusion protein was shown to functionally replace both the BioH and BioC functions of E. coli. Although the BioH, BioG and BioK esterases catalyze a common reaction, the proteins are evolutionarily distinct. PMID:23152908

  9. Photoelectrochemical biosensor using enzyme-catalyzed in situ propagation of CdS quantum dots on graphene oxide.

    PubMed

    Zeng, Xianxiang; Tu, Wenwen; Li, Jing; Bao, Jianchun; Dai, Zhihui

    2014-09-24

    An innovative photoelectrochemical (PEC) biosensor platform was designed based on the in situ generation of CdS quantum dots (QDs) on graphene oxide (GO) using an enzymatic reaction. Horseradish peroxidase catalyzed the reduction of sodium thiosulfate with hydrogen peroxide to generate H2S, which reacted with Cd(2+) to form CdS QDs. CdS QDs could be photoexcited to generate an elevated photocurrent as a readout signal. This strategy offered a "green" alternative to inconvenient presynthesis procedures for the fabrication of semiconducting nanoparticles. The nanomaterials and assembly procedures were characterized by microscopy and spectroscopy techniques. Combined with immune recognition and on the basis of the PEC activity of CdS QDs on GO, the strategy was successfully applied to a PEC assay to detect carcinoembryonic antigen and displayed a wide linear range from 2.5 ng mL(-1) to 50 ?g mL(-1) and a detection limit of 0.72 ng mL(-1) at a signal-to-noise ratio of 3. The PEC biosensor showed satisfactory performance for clinical sample detection and was convenient for determining high concentrations of solute without dilution. This effort offers a new opportunity for the development of numerous rapid and convenient analytical techniques using the PEC method that may be applied in the design and preparation of various solar-energy-driven applications. PMID:25154012

  10. Sequential Reactions of Surface-Tethered Glycolytic Enzymes

    PubMed Central

    Mukai, Chinatsu; Bergkvist, Magnus; Nelson, Jacquelyn L.; Travis, Alexander J.

    2014-01-01

    SUMMARY The development of complex hybrid organic-inorganic devices faces several challenges, including how they can generate energy. Cells face similar challenges regarding local energy production. Mammalian sperm solve this problem by generating ATP down the flagellar principal piece by means of glycolytic enzymes, several of which are tethered to a cytoskeletal support via germ cell-specific targeting domains. Inspired by this design, we have produced recombinant hexokinase type 1 and glucose-6-phosphate isomerase capable of oriented immobilization on a nickel-nitrilotriacetic acid modified surface. Specific activities of enzymes tethered via this strategy were substantially higher than when randomly adsorbed. Furthermore, these enzymes showed sequential activities when tethered onto the same surface. This is the first demonstration of surface-tethered pathway components showing sequential enzymatic activities, and it provides a first step toward reconstitution of glycolysis on engineered hybrid devices. PMID:19778729

  11. N-Heterocyclic carbene ligands bearing poly(ethylene glycol) chains: effect of the chain length on palladium-catalyzed coupling reactions employing aryl chlorides.

    PubMed

    Fujihara, Tetsuaki; Yoshikawa, Takahiro; Satou, Motoi; Ohta, Hidetoshi; Terao, Jun; Tsuji, Yasushi

    2015-12-21

    N-Heterocyclic carbenes bearing poly(ethylene glycol) chains of different lengths have been designed and employed as ligands in palladium-catalyzed coupling reactions. The catalyst system having longer chains was found to be highly efficient for Suzuki-Miyaura coupling and borylation reactions employing aryl chlorides under mild reaction conditions. PMID:26465096

  12. Reaction of ozone with enzymes of erythrocyte membranes.

    PubMed

    Mudd, J B; Dawson, P J; Adams, J R; Wingo, J; Santrock, J

    1996-11-01

    Ozone is a widespread component of polluted air. It is the cause of many adverse effects on the lung such as decreased athletic performance and exacerbation of asthma. Ozone inactivated acetylcholine esterase (AChE) both in intact washed human erythrocytes and in ghosts prepared from the erythrocytes. This is consistent (a) with the location of AChE on the outer face of the membrane and (b) with the change in structure of AChE when amino acids were oxidized. The glyceraldehyde-3-phosphate dehydrogenase (G3PDH) of intact washed erythrocytes was unaffected by ozone. However, ozone severely inactivated G3PDH of ghosts, much more severely than AChE in ghosts. This result raised questions about the relative permeability of intact erythrocytes and ghosts and also about the inherent susceptibility of the two enzymes. Inhibition of the ozone-treated erythrocyte AChE with the competitive inhibitor trimethyl-(p-aminophenyl) ammonium chloride was measured. The inhibited enzyme had a higher K(M) and slightly lower Vmax than the control. Ozone did not affect the K(M) of the uninhibited enzyme but decreased the K(M) of the inhibited enzyme. Ozone decreased the Vmax of both the inhibited and the uninhibited enzyme. The K(I) was unchanged by the treatment with ozone. This suggested that the active site of the enzyme was not affected by ozone, but other features of the protein were changed by ozone. The effects of products of lipid ozonolysis [hydrogen peroxide, nonanal, and 1-palmitoyl-2-(9-oxononanyl)-sn-3-glycerophosphorylcholine (PN1PC)] were tested on the ghost preparations. The ozonolysis products were tested at concentrations equivalent to calculated amounts that could have been produced by ozone. Hydrogen peroxide had no effect on the G3PDH and AChE. Nonanal slightly increased the permeability of the ghost membrane, as judged by the increase in rate of G3PDH in the absence of Triton X-100, but did not inhibit enzyme activity. PN1PC increased the permeability of the ghosts, as judged by the increase in rate of G3PDH in the absence of Triton X-100. There was also an increase in the activity of G3PDH in the presence of Triton X-100. AChE was not inhibited by ozone in the presence or absence of Triton X-100. PMID:8914845

  13. Target-catalyzed hairpin assembly and intramolecular/intermolecular co-reaction for signal amplified electrochemiluminescent detection of microRNA.

    PubMed

    Yu, Yan-Qing; Wang, Ji-Peng; Zhao, Min; Hong, Lin-Ru; Chai, Ya-Qin; Yuan, Ruo; Zhuo, Ying

    2016-03-15

    Herein, a new electrochemiluminescence (ECL) strategy for enzyme-free microRNA-21 (miR-21) amplified detection was designed based on target-catalyzed hairpin assembly by combining the signal-amplification capability of both intramolecular and intermolecular ECL co-reaction. In this strategy, two hairpin DNA probes of H1 and H2 were designed as capture probes and detection probes, respectively. To be specific, the capture probes of H1 were immobilized on the multilayer interface of AuNPs and thiosemicarbazide (TSC) assembly on the single-walled carbon nanohorns decorated electrode, while the detection probes of H2 was anchored on the nanocarriers of gold nanoparticals functionalized reduced graphene oxide (Au-rGO) which were tagged with the self-enhanced ruthenium complex (PEI-Ru(ΙΙ)) in advance. Based on the target-catalyzed hairpin assembly, target miR-21 could trigger the hybridization of H1 and H2 to further be released for initiating the next hybridization process to capture a large number of H2 bioconjugates on the sensing surface. Herein, the TSC was used not only as a coupling reagent to attach the AuNPs via Au-S and Au-N bonds but also as a novel intermolecular coreactant to enhance the ECL intensity, and the PEI-Ru(ΙΙ) as emitters exhibited enhanced ECL efficiency. Therefore, a strong ECL signal was achieved by the dual amplification strategies of target recycle and the intramolecular/intermolecular co-reaction of PEI-Ru(ΙΙ) and TSC. The designed protocol provided an ultrasensitive ECL detection of miR-21 down to the sub-femtomolar level with a linear response about 6 orders of magnitude (from 1.0 × 10(-16)M to 1.0 × 10(-11)M) with a relatively low detection limit of 0.03 fM (S/N=3). PMID:26453905

  14. An efficient transformation of primary halides into nitriles through palladium-catalyzed hydrogen transfer reaction.

    PubMed

    Zou, Tao; Yu, Xiaoqiang; Feng, Xiujuan; Bao, Ming

    2015-07-01

    Two-step one-pot transformation of primary halides into corresponding nitriles is successfully achieved. Nucleophilic substitution of primary halides with sodium azide and subsequent palladium-catalyzed hydrogen transfer proceeds smoothly in the presence of sterically bulky ligand dicyclohexyl(2',4',6'-triisopropylbiphenyl-2-yl)phosphine (XPhos) in acetone to produce nitriles in satisfactory to good yields. PMID:26050994

  15. Palladium-Catalyzed Double-Suzuki-Miyaura Reactions Using Cyclic Dibenziodoniums: Synthesis of o-Tetraaryls.

    PubMed

    Zhang, Yanxia; Han, Jianwei; Liu, Zhen-Jiang

    2016-02-19

    Palladium-catalyzed double-Suzuki-Miyaura couplings between cyclic dibenziodoniums and arylboronic acids have been developed. As such, a wide range of o-tetraaryls were synthesized in good to excellent yields of 22-94%. Furthermore, tetraphenylene was prepared in 21% isolated yield with 2,2'-biphenyldiboronic acid by using this method. PMID:26608348

  16. ENZYME CATALYZED POLYCONDENSATION REACTIONS FOR THE SYNTHESIS OF AROMATIC POLYCARBONATES AND POLYESTERS. (R825338)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  17. Beta-D-xylosidase from Selenomonas ruminantium: thermodynamics of enzyme-catalyzed and noncatalyzed reactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta-D-xylosidase from Selenomonas ruminantium is the best catalyst known for promoting hydrolysis of 1,4-beta-D-xylooligosaccharides and it has potential utility in industrial saccharification processes. Kinetic parameters, kcat and kcat/Km, are more than 10-fold larger than those reported for the...

  18. BETA-D-XYLOSIDASE FROM SELENOMONAS RUMINANTIUM: THERMODYNAMICS OF ENZYME-CATALYZED AND NONCATALYZED REACTIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta-D-xylosidase from Selenomonas ruminantium has been revealed as the best catalyst known for promoting hydrolysis of 1,4-beta-D-xylooligosaccharides, and it has potential utility in saccharification processes. Kinetic parameters, kcat and kcat/Km, are more than 10-fold larger than those reported...

  19. Optimizing Metalloporphyrin-Catalyzed Reduction Reactions for In Situ Remediation of DOE Contaminants

    SciTech Connect

    Schlautman, Mark A.

    2013-07-14

    Past activities have resulted in a legacy of contaminated soil and groundwater at Department of Energy facilities nationwide. Uranium and chromium are among the most frequently encountered and highest-priority metal and radionuclide contaminants at DOE installations. Abiotic chemical reduction of uranium and chromium at contaminated DOE sites can be beneficial because the reduced metal species are less soluble in water, less mobile in the environment, and less toxic to humans and ecosystems. Although direct biological reduction has been reported for U(VI) and Cr(VI) in laboratory studies and at some field sites, the reactions can sometimes be slow or even inhibited due to unfavorable environmental conditions. One promising approach for the in-situ remediation of DOE contaminants is to develop electron shuttle catalysts that can be delivered precisely to the specific subsurface locations where contaminants reside. Previous research has shown that reduction of oxidized organic and inorganic contaminants often can be catalyzed by electron shuttle systems. Metalloporphyrins and their derivatives are well known electron shuttles for many biogeochemical systems, and thus were selected to study their catalytic capabilities for the reduction of chromium and uranium in the presence of reducing agents. Zero valent iron (ZVI) was chosen as the primary electron donor in most experimental systems. Research proceeded in three phases and the key findings of each phase are reported here. Phase I examined Cr(VI) reduction and utilized micro- and nano-sized ZVI as the electron donors. Electron shuttle catalysts tested were cobalt- and iron-containing metalloporphyrins and Vitamin B12. To aid in the recycle and reuse of the nano-sized ZVI and soluble catalysts, sol-gels and calcium-alginate gel beads were tested as immobilization/support matrices. Although the nano-sized ZVI could be incorporated within the alginate gel beads, preliminary attempts to trap it in sol-gels were not successful. Conversely, the water-soluble catalysts could be trapped within sol-gel matrices but they tended to leach out of the alginate gel beads during use. In general, immobilization of the nano-sized ZVI in gel beads and of the catalysts in sol-gels tended to result in slower rates of Cr(VI) reduction, but these effects could be overcome to some extent by using higher reactant/catalyst concentrations. In addition, the lowering of their effectiveness would likely be offset by the benefits obtained when recycling and reusing the materials because they were immobilized. Addition of the catalytic electron shuttles will be most useful when the micro-sized or nano-sized ZVI becomes less reactive with reaction time. Continued work in Phase II in the area of nano-sized ZVI immobilization led to procedures that were successful in incorporating the iron particles in sol-gel matrices. The water-soluble reductants sodium dithionite and L-ascorbic acid were also tested, but their use appeared to lead to formation of complexes with the uranyl cation which limited their effectiveness. Also, although the sol-gel supported nano-sized ZVI showed some promise at reducing uranium, the fluoride used in the sol-gel synthesis protocol appeared to lead to formation of uranyl-fluoride complexes that were less reactive. Because hexavalent chromium is an anion which does not form complexes with fluoride, it was used to demonstrate the intrinsic reactivity of the sol-gel immobilized nano-sized ZVI. Consistent with our observations in Phase I, the sol-gel matrix once again slowed down the reduction reaction but the expected benefits of recycle/reuse should outweigh this adverse effect. The major emphasis in Phase III of this study was to simultaneously incorporate nano-sized ZVI and water-soluble catalysts in the same sol-gel matrix. The catalysts utilized were cobalt complexes of uroporphyrin and protoporphyrin and Cr(VI) reduction was used to test the efficacy of the combined "catalyst + reductant" sol-gel matrix. When enough catalyst was added to the sol-gels, enhancement of the Cr(VI) reduction reaction was observed. At the lowest levels of catalyst addition, however, the rates of Cr(VI) reduction were similar to those systems which only used sol-gel immobilized nano-sized ZVI without any catalyst present. These findings suggest future areas of research that should be pursued to further optimize abiotic reduction reactions of metals with combined "catalyst + reductant" matrices.

  20. Enzyme catalytic efficiency: a function of bio-nano interface reactions.

    PubMed

    Campbell, Alan S; Dong, Chenbo; Meng, Fanke; Hardinger, Jeremy; Perhinschi, Gabriela; Wu, Nianqiang; Dinu, Cerasela Zoica

    2014-04-23

    Biocatalyst immobilization onto carbon-based nanosupports has been implemented in a variety of applications ranging from biosensing to biotransformation and from decontamination to energy storage. However, retaining enzyme functionality at carbon-based nanosupports was challenged by the non-specific attachment of the enzyme as well as by the enzyme-enzyme interactions at this interface shown to lead to loss of enzyme activity. Herein, we present a systematic study of the interplay reactions that take place upon immobilization of three pure enzymes namely soybean peroxidase, chloroperoxidase, and glucose oxidase at carbon-based nanosupport interfaces. The immobilization conditions involved both single and multipoint single-type enzyme attachment onto single and multi-walled carbon nanotubes and graphene oxide nanomaterials with properties determined by Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray analysis (EDX), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Our analysis showed that the different surface properties of the enzymes as determined by their molecular mapping and size work synergistically with the carbon-based nanosupports physico-chemical properties (i.e., surface chemistry, charge and aspect ratios) to influence enzyme catalytic behavior and activity at nanointerfaces. Knowledge gained from these studies can be used to optimize enzyme-nanosupport symbiotic reactions to provide robust enzyme-based systems with optimum functionality to be used for fermentation, biosensors, or biofuel applications. PMID:24666280

  1. Characterization of a succinyl-CoA radical-cob(II)alamin spin triplet intermediate in the reaction catalyzed by adenosylcobalamin-dependent methylmalonyl-CoA mutase.

    PubMed

    Mansoorabadi, Steven O; Padmakumar, Rugmini; Fazliddinova, Nisso; Vlasie, Monica; Banerjee, Ruma; Reed, George H

    2005-03-01

    The electron paramagnetic resonance (EPR) spectrum of an intermediate freeze trapped during the steady state of the reaction catalyzed by the adenosylcobalamin (AdoCbl)-dependent enzyme, methylmalonyl-CoA mutase, has been studied. The EPR spectrum is that of a hybrid triplet spin system created as a result of strong electron-electron spin coupling between an organic radical and the low-spin Co(2+) in cob(II)alamin. The spectrum was analyzed by simulation to obtain the zero-field splitting (ZFS) parameters and Euler angles relating the radical-to-cobalt interspin vector to the g axis system of the low-spin Co(2+). Labeling of the substrate with (13)C and (2)H was used to probe the identity of the organic radical partner in the triplet spin system. The patterns of inhomogeneous broadening in the EPR signals produced by [2'-(13)C]methylmalonyl-CoA and [2-(13)C]methylmalonyl-CoA as well as line narrowing resulting from deuterium substitution in the substrate were consistent with those expected for a succinyl-CoA radical wherein the unpaired electron was centered on the carbon alpha to the free carboxyate group of the rearranged radical. The interspin distance and the Euler angles were used to position this product radical into the active site of the enzyme. PMID:15736925

  2. Characterization of a Succinyl-CoA RadicalCob(II)alamin Spin Triplet Intermediate in the Reaction Catalyzed by Adenosylcobalamin-Dependent Methylmalonyl-CoA Mutase

    PubMed Central

    Mansoorabadi, Steven O.; Padmakumar, Rugmini; Fazliddinova, Nisso; Vlasie, Monica; Banerjee, Ruma; Reed, George H.

    2011-01-01

    The electron paramagnetic resonance (EPR) spectrum of an intermediate freeze trapped during the steady state of the reaction catalyzed by the adenosylcobalamin (AdoCbl)-dependent enzyme, methylmalonyl-CoA mutase, has been studied. The EPR spectrum is that of a hybrid triplet spin system created as a result of strong electronelectron spin coupling between an organic radical and the low-spin Co2+ in cob(II)alamin. The spectrum was analyzed by simulation to obtain the zero-field splitting (ZFS) parameters and Euler angles relating the radical-to-cobalt interspin vector to the g axis system of the low-spin Co2+. Labeling of the substrate with 13C and 2H was used to probe the identity of the organic radical partner in the triplet spin system. The patterns of inhomogeneous broadening in the EPR signals produced by [2?-13C]methylmalonyl-CoA and [2-13C]methylmalonyl-CoA as well as line narrowing resulting from deuterium substitution in the substrate were consistent with those expected for a succinyl-CoA radical wherein the unpaired electron was centered on the carbon ? to the free carboxyate group of the rearranged radical. The interspin distance and the Euler angles were used to position this product radical into the active site of the enzyme. PMID:15736925

  3. A Novel Glucosylation Reaction on Anthocyanins Catalyzed by Acyl-Glucose–Dependent Glucosyltransferase in the Petals of Carnation and Delphinium[C][W

    PubMed Central

    Matsuba, Yuki; Sasaki, Nobuhiro; Tera, Masayuki; Okamura, Masachika; Abe, Yutaka; Okamoto, Emi; Nakamura, Haruka; Funabashi, Hisakage; Takatsu, Makoto; Saito, Mikako; Matsuoka, Hideaki; Nagasawa, Kazuo; Ozeki, Yoshihiro

    2010-01-01

    Glucosylation of anthocyanin in carnations (Dianthus caryophyllus) and delphiniums (Delphinium grandiflorum) involves novel sugar donors, aromatic acyl-glucoses, in a reaction catalyzed by the enzymes acyl-glucose–dependent anthocyanin 5(7)-O-glucosyltransferase (AA5GT and AA7GT). The AA5GT enzyme was purified from carnation petals, and cDNAs encoding carnation Dc AA5GT and the delphinium homolog Dg AA7GT were isolated. Recombinant Dc AA5GT and Dg AA7GT proteins showed AA5GT and AA7GT activities in vitro. Although expression of Dc AA5GT in developing carnation petals was highest at early stages, AA5GT activity and anthocyanin accumulation continued to increase during later stages. Neither Dc AA5GT expression nor AA5GT activity was observed in the petals of mutant carnations; these petals accumulated anthocyanin lacking the glucosyl moiety at the 5 position. Transient expression of Dc AA5GT in petal cells of mutant carnations is expected to result in the transfer of a glucose moiety to the 5 position of anthocyanin. The amino acid sequences of Dc AA5GT and Dg AA7GT showed high similarity to glycoside hydrolase family 1 proteins, which typically act as β-glycosidases. A phylogenetic analysis of the amino acid sequences suggested that other plant species are likely to have similar acyl-glucose–dependent glucosyltransferases. PMID:20971893

  4. Method of reduction of nitroaromatics by enzymatic reaction with redox enzymes

    DOEpatents

    Shah, Manish M.

    2000-01-01

    A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with redox enzymes, such as Oxyrase (Trademark of Oxyrase, Inc., Mansfield, Ohio).

  5. Method of controlled reduction of nitroaromatics by enzymatic reaction with oxygen sensitive nitroreductase enzymes

    DOEpatents

    Shah, Manish M.; Campbell, James A.

    1998-01-01

    A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with oxygen sensitive nitroreductase enzymes, such as ferredoxin NADP oxidoreductase.

  6. Method of controlled reduction of nitroaromatics by enzymatic reaction with oxygen sensitive nitroreductase enzymes

    DOEpatents

    Shah, M.M.; Campbell, J.A.

    1998-07-07

    A method is described for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with oxygen sensitive nitroreductase enzymes, such as ferredoxin NADP oxidoreductase. 6 figs.

  7. Steady-state kinetics and inhibition studies of the aldol condensation reaction catalyzed by bovine liver and Escherichia coli 2-keto-4-hydroxyglutarate aldolase.

    PubMed

    Grady, S R; Wang, J K; Dekker, E E

    1981-04-28

    Two sensitive assays, one which fluorometrically measures only the L isomer of 2-keto-4-hydroxyglutarate after decarboxylation to L-malate and the other which spectrophotometrically determines both enantiomers by reductive amination with glutamate dehydrogenase, are described. By use of these assays, the steady-state kinetics of the aldol condensation of pyruvate with glyoxylate, as catalyzed by 2-keto-4-hydroxyglutarate aldolase from either bovine liver or Escherichia coli, were studied as was the inhibition of this reaction by glyoxylate and other anions. For the E. coli aldolase, double-reciprocal plots are linear except at high (above 5 mM) glyoxylate concentrations; apparent Km values increase with increasing concentrations of the fixed substrate. The data are consistent with an ordered reaction sequence. Inhibition by halides follows the lyotropic or Hofmeister series. Esters are not good inhibitors; mono-, di-, and tricarboxylic acids are increasingly inhibitory. Of the substrate analogues tested, hydroxypyruvate is the most potent inhibitor. Inhibition studies with citrate, acetaldehyde, and glyoxylate (all competitive inhibitors) suggest there are two domains at the active site-the Schiff base forming lysyl residue which interacts with carbonyl analogues (like acetaldehyde) and a center of positive charge which binds anions (like citrate). In contrast to the bacterial enzyme, liver 2-keto-4-hydroxyglutarate aldolase is inhibited in a competitive manner by much lower concentrations (0.1 mM or even lower) of glyoxylate. Many salts and some carboxylic acids activate the liver enzyme. Similarly, substrate analogues like 2-ketobutyrate and fluoropyruvate are mild activators; no effect is seen with acetaldehyde. Besides glyoxylate, only glyoxal, 2-ketoglutarate, and hydroxypyruvate inhibit the aldol condensation reaction. A uniform value of 1 is found for the number of inhibitor molecules bound per active site of either liver or E. coli 2-keto-4-hydroxyglutarate aldolase. PMID:7016177

  8. Enzyme inhibition studies by integrated Michaelis-Menten equation considering simultaneous presence of two inhibitors when one of them is a reaction product.

    PubMed

    Bezerra, Rui M F; Pinto, Paula A; Fraga, Irene; Dias, Albino A

    2016-03-01

    To determine initial velocities of enzyme catalyzed reactions without theoretical errors it is necessary to consider the use of the integrated Michaelis-Menten equation. When the reaction product is an inhibitor, this approach is particularly important. Nevertheless, kinetic studies usually involved the evaluation of other inhibitors beyond the reaction product. The occurrence of these situations emphasizes the importance of extending the integrated Michaelis-Menten equation, assuming the simultaneous presence of more than one inhibitor because reaction product is always present. This methodology is illustrated with the reaction catalyzed by alkaline phosphatase inhibited by phosphate (reaction product, inhibitor 1) and urea (inhibitor 2). The approach is explained in a step by step manner using an Excel spreadsheet (available as a template in Appendix). Curve fitting by nonlinear regression was performed with the Solver add-in (Microsoft Office Excel). Discrimination of the kinetic models was carried out based on Akaike information criterion. This work presents a methodology that can be used to develop an automated process, to discriminate in real time the inhibition type and kinetic constants as data (product vs. time) are achieved by the spectrophotometer. PMID:26777432

  9. The Mechanism of Iron(II)-Catalyzed Asymmetric Mukaiyama Aldol Reaction in Aqueous Media: Density Functional Theory and Artificial Force-Induced Reaction Study.

    PubMed

    Sameera, W M C; Hatanaka, Miho; Kitanosono, Taku; Kobayashi, Sh?; Morokuma, Keiji

    2015-09-01

    Density functional theory (DFT), combined with the artificial force-induced reaction (AFIR) method, is used to establish the mechanism of the aqueous Mukaiyama aldol reactions catalyzed by a chiral Fe(II) complex. On the bases of the calculations, we identified several thermodynamically stable six- or seven-coordinate complexes in the solution, where the high-spin quintet state is the ground state. Among them, the active intermediates for the selectivity-determining outer-sphere carbon-carbon bond formation are proposed. The multicomponent artificial force-induced reaction (MC-AFIR) method found key transition states for the carbon-carbon bond formation, and explained the enantioselectivity and diastereoselectivity. The overall mechanism consists of the coordination of the aldehyde, carbon-carbon bond formation, the rate-determining proton transfer from water to aldehyde, and dissociation of trimethylsilyl group. The calculated full catalytic cycle is consistent with the experiments. This study provides important mechanistic insights for the transition metal catalyzed Mukaiyama aldol reaction in aqueous media. PMID:26267294

  10. 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. PMID:26511314

  11. Inhibition of peroxidase-catalyzed reactions by arylamines: mechanism for the anti-thyroid action of sulfamethazine.

    PubMed

    Doerge, D R; Decker, C J

    1994-01-01

    Sulfonamide antibiotics, typified by sulfamethazine (SMZ), are widely used in veterinary practice. Sulfonamide residues in milk and meat products are of regulatory concern since SMZ is a thyroid carcinogen in rodents and sulfonamide-induced hypersensitivity reactions, including hypothyroidism, have been reported in humans. SMZ and other primary arylamines inhibited iodination reactions catalyzed by thyroid peroxidase (TPO) and the closely related lactoperoxidase (LPO). Inhibition of LPO-catalyzed triiodide ion formation by SMZ and other primary arylamines was complex as both apparent Km and Vmax values were affected, but consistent with a rapid equilibrium binding mechanism. The apparent Ki for SMZ inhibition of TPO- and LPO-catalyzed iodide ion oxidation was approximately 0.42 and 0.11 mM, respectively. The corresponding Ki values for a series of para-substituted anilines correlated with the ease of one-electron N-oxidation as measured by ionization potentials determined from semiempirical molecular orbital calculations. The aniline derivatives containing electron-donating substituents (e.g., p-CH3, p-OEt, p-Cl) were converted by LPO to colored products characteristic of one-electron oxidation. However, sulfonamides were not consumed in such reactions nor were any N-oxygenated derivatives formed in the absence of ascorbate (e.g., hydroxylamino, nitroso, nitro, azoxy). These observations suggest that the primary mechanism for sulfonamide-induced hypothyroidism is reversible inhibition of TPO-mediated thyroid hormone synthesis and not the formation and covalent binding of reactive N-oxygenated metabolites. These results are consistent with a hormonal mechanism for SMZ-induced thyroid carcinogenesis mediated by thyroid-stimulating hormone (TSH).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8199304

  12. Inhibition of peroxidase-catalyzed reactions by arylamines: mechanism for the anti-thyroid action of sulfamethazine.

    TOXLINE Toxicology Bibliographic Information

    Doerge DR; Decker CJ

    1994-03-01

    Sulfonamide antibiotics, typified by sulfamethazine (SMZ), are widely used in veterinary practice. Sulfonamide residues in milk and meat products are of regulatory concern since SMZ is a thyroid carcinogen in rodents and sulfonamide-induced hypersensitivity reactions, including hypothyroidism, have been reported in humans. SMZ and other primary arylamines inhibited iodination reactions catalyzed by thyroid peroxidase (TPO) and the closely related lactoperoxidase (LPO). Inhibition of LPO-catalyzed triiodide ion formation by SMZ and other primary arylamines was complex as both apparent Km and Vmax values were affected, but consistent with a rapid equilibrium binding mechanism. The apparent Ki for SMZ inhibition of TPO- and LPO-catalyzed iodide ion oxidation was approximately 0.42 and 0.11 mM, respectively. The corresponding Ki values for a series of para-substituted anilines correlated with the ease of one-electron N-oxidation as measured by ionization potentials determined from semiempirical molecular orbital calculations. The aniline derivatives containing electron-donating substituents (e.g., p-CH3, p-OEt, p-Cl) were converted by LPO to colored products characteristic of one-electron oxidation. However, sulfonamides were not consumed in such reactions nor were any N-oxygenated derivatives formed in the absence of ascorbate (e.g., hydroxylamino, nitroso, nitro, azoxy). These observations suggest that the primary mechanism for sulfonamide-induced hypothyroidism is reversible inhibition of TPO-mediated thyroid hormone synthesis and not the formation and covalent binding of reactive N-oxygenated metabolites. These results are consistent with a hormonal mechanism for SMZ-induced thyroid carcinogenesis mediated by thyroid-stimulating hormone (TSH).(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Pyrogallol-to-phloroglucinol conversion and other hydroxyl-transfer reactions catalyzed by cell extracts of Pelobacter acidigallici.

    PubMed Central

    Brune, A; Schink, B

    1990-01-01

    Permeabilized cells and cell extracts of Pelobacter acidigallici catalyzed the conversion of pyrogallol (1,2,3-trihydroxybenzene) to phloroglucinol (1,3,5-trihydroxybenzene) in the presence of 1,2,3,5-tetrahydroxybenzene. Pyrogallol consumption by resting cells stopped after lysis by French press or mild detergent (cetyltrimethylammonium bromide [CTAB]) treatment. Addition of 1,2,3,5-tetrahydroxybenzene to the assay mixture restored pyrogallol consumption and led to stoichiometric phloroglucinol accumulation. The stoichiometry of pyrogallol conversion to phloroglucinol was independent of the amount of tetrahydroxybenzene added. The tetrahydroxybenzene concentration limited the velocity of the transhydroxylation reaction, which reached a maximum at 1.5 mM tetrahydroxybenzene (1 U/mg of protein). Transhydroxylation was shown to be reversible. The equilibrium constant of the reaction was determined, and the free-energy change (delta G degree') of phloroglucinol formation from pyrogallol was calculated to be -15.5 kJ/mol. Permeabilized cells and cell extracts also catalyzed the transfer of hydroxyl moieties between other hydroxylated benzenes. Tetrahydroxybenzene and hydroxyhydroquinone participated as hydroxyl donors and as hydroxyl acceptors in the reaction, whereas pyrogallol, resorcinol, and phloroglucinol were hydroxylated by both donors. A novel mechanism deduced from these data involves intermolecular transfer of the hydroxyl moiety from the cosubstrate (1,2,3,5-tetrahydroxybenzene) to the substrate (pyrogallol), thus forming the product (phloroglucinol) and regenerating the cosubstrate. PMID:2298693

  14. Studies of the Mechanism and Origins of Enantioselectivity for the Chiral Phosphoric Acid-Catalyzed Stereoselective Spiroketalization Reactions.

    PubMed

    Khomutnyk, Yaroslav Ya; Argelles, Alonso J; Winschel, Grace A; Sun, Zhankui; Zimmerman, Paul M; Nagorny, Pavel

    2016-01-13

    Mechanistic and computational studies were conducted to elucidate the mechanism and the origins of enantiocontrol for asymmetric chiral phosphoric acid-catalyzed spiroketalization reactions. These studies were designed to differentiate between the SN1-like, SN2-like, and covalent phosphate intermediate-based mechanisms. The chiral phosphoric acid-catalyzed spiroketalization of deuterium-labeled cyclic enol ethers revealed a highly diastereoselective syn-selective protonation/nucleophile addition, thus ruling out long-lived oxocarbenium intermediates. Hammett analysis of the reaction kinetics revealed positive charge accumulation in the transition state (? = -2.9). A new computational reaction exploration method along with dynamics simulations supported an asynchronous concerted mechanism with a relatively short-lived polar transition state (average lifetime = 519 240 fs), which is consistent with the observed inverse secondary kinetic isotope effect of 0.85. On the basis of these studies, a transition state model explaining the observed stereochemical outcome has been proposed. This model predicts the enantioselective formation of the observed enantiomer of the product with 92% ee, which matches the experimentally observed value. PMID:26641317

  15. Role of MgO and CaO promoters in Ni-catalyzed hydrogenation reactions of CO and carbon

    SciTech Connect

    Haga, Tetsuya; Ozaki, Junichi; Suzuki, Kyosuke; Nishiyama, Yoshiyuki )

    1992-03-01

    The roles of Mg and Ca promoters in Ni-catalyzed hydrogasification of carbon were investigated with emphasis on nickel dispersion and nickel-carbon interactions during gasification. The dispersion of nickel on carbon, which was estimated by means of XRD, H{sub 2}-TPD, and CO methanation test, was (Ni + Mg){much gt}(Ni + Ca)>Ni. The increased dispersions of nickel by the Mg and Ca added were found to result in the enhanced Ni-C interaction, which was monitored through the desorption of CO from oxygen remaining on carbon, and, therefore, in the promotions of Ni-catalyzed lower-temperature gasification at 400-700 C. The Ca promoter was likely to give surface CaO(COO) species upon heating up to 550 C and release CO{sub 2} above {approximately} 650 C. The CO{sub 2} released is efficiently converted by the nickel adjacent to CaO into CO to create Ni-(O)-C species above 700 C, resulting in acceleration of Ni-catalyzed gasification above 700 C. In situ oxygen transfer to Ni/C during reaction is the most important role played by the Ca promoter.

  16. Identification in Haloferax volcanii of Phosphomevalonate Decarboxylase and Isopentenyl Phosphate Kinase as Catalysts of the Terminal Enzyme Reactions in an Archaeal Alternate Mevalonate Pathway

    PubMed Central

    VanNice, John C.; Skaff, D. Andrew; Keightley, Andrew; Addo, James K.; Wyckoff, Gerald J.

    2014-01-01

    Mevalonate (MVA) metabolism provides the isoprenoids used in archaeal lipid biosynthesis. In synthesis of isopentenyl diphosphate, the classical MVA pathway involves decarboxylation of mevalonate diphosphate, while an alternate pathway has been proposed to involve decarboxylation of mevalonate monophosphate. To identify the enzymes responsible for metabolism of mevalonate 5-phosphate to isopentenyl diphosphate in Haloferax volcanii, two open reading frames (HVO_2762 and HVO_1412) were selected for expression and characterization. Characterization of these proteins indicated that one enzyme is an isopentenyl phosphate kinase that forms isopentenyl diphosphate (in a reaction analogous to that of Methanococcus jannaschii MJ0044). The second enzyme exhibits a decarboxylase activity that has never been directly attributed to this protein or any homologous protein. It catalyzes the synthesis of isopentenyl phosphate from mevalonate monophosphate, a reaction that has been proposed but never demonstrated by direct experimental proof, which is provided in this account. This enzyme, phosphomevalonate decarboxylase (PMD), exhibits strong inhibition by 6-fluoromevalonate monophosphate but negligible inhibition by 6-fluoromevalonate diphosphate (a potent inhibitor of the classical mevalonate pathway), reinforcing its selectivity for monophosphorylated ligands. Inhibition by the fluorinated analog also suggests that the PMD utilizes a reaction mechanism similar to that demonstrated for the classical MVA pathway decarboxylase. These observations represent the first experimental demonstration in H. volcanii of both the phosphomevalonate decarboxylase and isopentenyl phosphate kinase reactions that are required for an alternate mevalonate pathway in an archaeon. These results also represent, to our knowledge, the first identification and characterization of any phosphomevalonate decarboxylase. PMID:24375100

  17. Identification in Haloferax volcanii of phosphomevalonate decarboxylase and isopentenyl phosphate kinase as catalysts of the terminal enzyme reactions in an archaeal alternate mevalonate pathway.

    PubMed

    Vannice, John C; Skaff, D Andrew; Keightley, Andrew; Addo, James K; Wyckoff, Gerald J; Miziorko, Henry M

    2014-03-01

    Mevalonate (MVA) metabolism provides the isoprenoids used in archaeal lipid biosynthesis. In synthesis of isopentenyl diphosphate, the classical MVA pathway involves decarboxylation of mevalonate diphosphate, while an alternate pathway has been proposed to involve decarboxylation of mevalonate monophosphate. To identify the enzymes responsible for metabolism of mevalonate 5-phosphate to isopentenyl diphosphate in Haloferax volcanii, two open reading frames (HVO_2762 and HVO_1412) were selected for expression and characterization. Characterization of these proteins indicated that one enzyme is an isopentenyl phosphate kinase that forms isopentenyl diphosphate (in a reaction analogous to that of Methanococcus jannaschii MJ0044). The second enzyme exhibits a decarboxylase activity that has never been directly attributed to this protein or any homologous protein. It catalyzes the synthesis of isopentenyl phosphate from mevalonate monophosphate, a reaction that has been proposed but never demonstrated by direct experimental proof, which is provided in this account. This enzyme, phosphomevalonate decarboxylase (PMD), exhibits strong inhibition by 6-fluoromevalonate monophosphate but negligible inhibition by 6-fluoromevalonate diphosphate (a potent inhibitor of the classical mevalonate pathway), reinforcing its selectivity for monophosphorylated ligands. Inhibition by the fluorinated analog also suggests that the PMD utilizes a reaction mechanism similar to that demonstrated for the classical MVA pathway decarboxylase. These observations represent the first experimental demonstration in H. volcanii of both the phosphomevalonate decarboxylase and isopentenyl phosphate kinase reactions that are required for an alternate mevalonate pathway in an archaeon. These results also represent, to our knowledge, the first identification and characterization of any phosphomevalonate decarboxylase. PMID:24375100

  18. Bulk gold catalyzed oxidation reactions of amines and isocyanides and iron porphyrin catalyzed N-H and O-H bond insertion/cyclization reactions of diamines and aminoalcohols

    SciTech Connect

    Klobukowski, Erik

    2011-12-29

    This work involves two projects. The first project entails the study of bulk gold as a catalyst in oxidation reactions of isocyanides and amines. The main goal of this project was to study the activation and reactions of molecules at metal surfaces in order to assess how organometallic principles for homogeneous processes apply to heterogeneous catalysis. Since previous work had used oxygen as an oxidant in bulk gold catalyzed reactions, the generality of gold catalysis with other oxidants was examined. Amine N-oxides were chosen for study, due to their properties and use in the oxidation of carbonyl ligands in organometallic complexes. When amine N-oxides were used as an oxidant in the reaction of isocyanides with amines, the system was able to produce ureas from a variety of isocyanides, amines, and amine N-oxides. In addition, the rate was found to generally increase as the amine N-oxide concentration increased, and decrease with increased concentrations of the amine. Mechanistic studies revealed that the reaction likely involves transfer of an oxygen atom from the amine N-oxide to the adsorbed isocyanide to generate an isocyanate intermediate. Subsequent nucleophilic attack by the amine yields the urea. This is in contrast to the bulk gold-catalyzed reaction mechanism of isocyanides with amines and oxygen. Formation of urea in this case was proposed to proceed through a diaminocarbene intermediate. Moreover, formation of the proposed isocyanate intermediate is consistent with the reactions of metal carbonyl ligands, which are isoelectronic to isocyanides. Nucleophilic attack at coordinated CO by amine N-oxides produces CO{sub 2} and is analogous to the production of an isocyanate in this gold system. When the bulk gold-catalyzed oxidative dehydrogenation of amines was examined with amine N-oxides, the same products were afforded as when O{sub 2} was used as the oxidant. When the two types of oxidants were directly compared using the same reaction system and conditions, it was found that the oxidative dehydrogenation of dibenzylamine to Nbenzylidenebenzylamine, with N-methylmorpholine N-oxide (NMMO), was nearly quantitative (96%) within 24 h. However, the reaction with oxygen was much slower, with only a 52% yield of imine product over the same time period. Moreover, the rate of reaction was found to be influenced by the nature of the amine N-oxide. For example, the use of the weakly basic pyridine N-oxide (PyNO) led to an imine yield of only 6% after 24 h. A comparison of amine N-oxide and O2 was also examined in the oxidation of PhCH{sub 2}OH to PhCHO catalyzed by bulk gold. In this reaction, a 52% yield of the aldehyde was achieved when NMMO was used, while only a 7% product yield was afforded when O{sub 2} was the oxidant after 48 h. The bulk gold-catalyzed oxidative dehydrogenation of cyclic amines generates amidines, which upon treatment with Aerosil and water were found to undergo hydrolysis to produce lactams. Moreover, 5-, 6-, and 7-membered lactams could be prepared through a one-pot reaction of cyclic amines by treatment with oxygen, water, bulk gold, and Aerosil. This method is much more atom economical than industrial processes, does not require corrosive acids, and does not generate undesired byproducts. Additionally, the gold and Aerosil catalysts can be readily separated from the reaction mixture. The second project involved studying iron(III) tetraphenylporphyrin chloride, Fe(TPP)Cl, as a homogeneous catalyst for the generation of carbenes from diazo reagents and their reaction with heteroatom compounds. Fe(TPP)Cl, efficiently catalyzed the insertion of carbenes derived from methyl 2-phenyldiazoacetates into O-H bonds of aliphatic and aromatic alcohols. Fe(TPP)Cl was also found to be an effective catalyst for tandem N-H and O-H insertion/cyclization reactions when 1,2-diamines and 1,2-alcoholamines were treated with diazo reagents. This approach provides a one-pot process for synthesizing piperazinones and morpholinones and related analogues such as quinoxalinones and benzoxazin-2-ones.

  19. Laccase-catalyzed reactions of 17β-estradiol in the presence of humic acid: Resolved by high-resolution mass spectrometry in combination with (13)C labeling.

    PubMed

    Sun, Kai; Luo, Qi; Gao, Yanzheng; Huang, Qingguo

    2016-02-01

    The widespread presence of estrogens in natural waters poses potential threats to the aquatic organisms and human health. It is known that estrogens undergo enzyme-catalyzed oxidative coupling (ECOC) reactions, which may impact their environmental fate and can be used in wastewater treatment to remove estrogens, but little information is available on how natural organic matter (NOM) may influence 17β-estradiol (E2) transformation in ECOC processes. A series of experiments were conducted to examine the transformation of E2 in aqueous solution containing humic acid (HA) as model NOM by laccase-mediated ECOC reactions. The impact of HA on the reaction behaviors and product distribution is systematically characterized. The presence of HA inhibited the extent of E2 self-coupling in laccase-mediated systems, while promoted cross-coupling between E2 and HA. Reconfiguration of humic molecules was also observed and characterized by changes in absorbance at 275 nm and the ratios between A250 nm/A365 nm. In particular, experiments were conducted with un-labeled E2 mixed with (13)C3-labeled E2 at a set ratio, with the products probed using high-resolution mass spectrometry (HRMS). The high m/z accuracy of HRMS enabled the use of isotope ratio as a tracer to identify possible cross-coupling products between E2 and HA. Such a method combining HRMS and isotope labeling provides a novel means for identification of products in a reaction system involving NOM or other complex matrices. These findings provide a basis for optimization of ECOC reactions for estrogen removal, and also help to understand the environmental transformation of estrogens. PMID:26692517

  20. Two-dimensional reaction free energy surfaces of catalytic reaction: effects of protein conformational dynamics on enzyme catalysis.

    PubMed

    Min, Wei; Xie, X Sunney; Bagchi, Biman

    2008-01-17

    We introduce a two-dimensional (2D) multisurface reaction free energy description of the catalytic cycle that explicitly connects the recently observed multi-time-scale conformational dynamics as well as dispersed enzymatic kinetics to the classical Michaelis-Menten equation. A slow conformational motion on a collective enzyme coordinate Q facilitates the catalytic reaction along the intrinsic reaction coordinate X, providing a dynamic realization of Pauling's well-known idea of transition-state stabilization. The catalytic cycle is modeled as transitions between multiple displaced harmonic wells in the XQ space representing different states of the cycle, which is constructed according to the free energy driving force of the cycle. Subsequent to substrate association with the enzyme, the enzyme-substrate complex under strain exhibits a nonequilibrium relaxation toward a new conformation that lowers the activation energy of the reaction, as first proposed by Haldane. The chemical reaction in X is thus enslaved to the down hill slow motion on the Q surface. One consequence of the present theory is that, in spite of the existence of dispersive kinetics, the Michaelis-Menten expression of the catalysis rate remains valid under certain conditions, as observed in recent single-molecule experiments. This dynamic theory builds the relationship between the protein conformational dynamics and the enzymatic reaction kinetics and offers a unified description of enzyme fluctuation-assisted catalysis. PMID:18085768

  1. Non-Innocent Behavior of Substrate Backbone Esters in Metal-Catalyzed Carbocyclizations and Friedel-Crafts Reactions of Enynes and Arenynes.

    PubMed

    Michelet, Bastien; Thiery, Guillaume; Bour, Christophe; Gandon, Vincent

    2015-11-01

    On the basis of DFT computations and experimental results, we show that the presence of the ester group in the backbone of organic substrates can influence the mechanism of metal-catalyzed carbocyclization reactions. The non-innocent role of the ester functionality in lowering the activation barrier of the key step of the gallium- and indium-catalyzed cycloisomerization of 1,6-enynes is revealed. In the case of the gallium-catalyzed hydroarylation of arenynes, the esters in the tether can deprotonate the Wheland intermediate, thus avoiding more energetically demanding [1,3]- or [1,2]/[1,2]-H shifts. As for the gallium-catalyzed Friedel-Crafts alkylation, an unusual concerted SEAr mechanism involving the esters has been calculated. Lastly, computations evidence that the ester group of methyl propiolates enables a divergent mechanism in the platinum-catalyzed intramolecular hydroarylation. PMID:26448129

  2. Regioselective syntheses of 1,2-benzothiazines by rhodium-catalyzed annulation reactions.

    PubMed

    Cheng, Ying; Bolm, Carsten

    2015-10-12

    Rhodium-catalyzed directed carbene insertions into aromatic C?H bonds of S-aryl sulfoximines lead to intermediates, which upon dehydration provide 1,2-benzothiazines in excellent yields. The domino-type process is regioselective and shows a high functional-group tolerance. It is scalable, and the only by-products are dinitrogen and water. Three illustrative transformations underscore the synthetic value of the products. PMID:25873036

  3. Synthesis of a Biotin-Derived Alkyne for Pd-Catalyzed Coupling Reactions

    PubMed Central

    Corona, Cesear; Bryant, Bj K.; Arterburn, Jeffrey B.

    2008-01-01

    An efficient synthesis of a terminal alkyne derived from d-biotin was developed to provide an alternative for carboxylbased biotinylation. This approach was illustrated by the preparation of alkyne- and alkene-linked phenylalanine derivatives using palladium-catalyzed Sonogashira and Oh methodology. (Strept)avidin binding was observed using soluble and immobilized receptors. These results demonstrate the applicability of carbon-linked biotin derivatives for use in affinity-based purification and bioanalytical applications. PMID:16623575

  4. The heat released in single catalytic events locally enhances enzyme diffusion

    NASA Astrophysics Data System (ADS)

    Tsekouras, Konstantinos; Riedel, Clement; Wilson, Christian; Hamadani, Kambiz; Marqusee, Susan; Presse, Steve; Bustamante, Carlos

    2014-03-01

    Recent experiments have shown that some enzymes catalyzing highly exothermic reactions exhibit increased diffusion with rising substrate concentration. We present a stochastic theory linking increased enzyme diffusion to reaction rate, discuss other possible origins for diffusion coefficient increases and finally provide a mechanistic interpretation showing how the heat released by the reaction perturbs the enzyme.

  5. Rapid-Equilibrium Enzyme Kinetics

    ERIC Educational Resources Information Center

    Alberty, Robert A.

    2008-01-01

    Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics is…

  6. Rapid-Equilibrium Enzyme Kinetics

    ERIC Educational Resources Information Center

    Alberty, Robert A.

    2008-01-01

    Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics is

  7. Initial reaction(s) in biotransformation of CL-20 is catalyzed by salicylate 1-monooxygenase from Pseudomonas sp. strain ATCC 29352.

    PubMed

    Bhushan, Bharat; Halasz, Annamaria; Spain, Jim C; Hawari, Jalal

    2004-07-01

    CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) (C(6)H(6)N(12)O(12)), a future-generation high-energy explosive, is biodegradable by Pseudomonas sp. strain FA1 and Agrobacterium sp. strain JS71; however, the nature of the enzyme(s) involved in the process was not understood. In the present study, salicylate 1-monooxygenase, a flavin adenine dinucleotide (FAD)-containing purified enzyme from Pseudomonas sp. strain ATCC 29352, biotransformed CL-20 at rates of 0.256 +/- 0.011 and 0.043 +/- 0.003 nmol min(-1) mg of protein(-1) under anaerobic and aerobic conditions, respectively. The disappearance of CL-20 was accompanied by the release of nitrite ions. Using liquid chromatography/mass spectrometry in the negative electrospray ionization mode, we detected a metabolite with a deprotonated mass ion [M - H](-) at 345 Da, corresponding to an empirical formula of C(6)H(6)N(10)O(8), produced as a result of two sequential N denitration steps on the CL- 20 molecule. We also detected two isomeric metabolites with [M - H](-) at 381 Da corresponding to an empirical formula of C(6)H(10)N(10)O(10). The latter was a hydrated product of the metabolite C(6)H(6)N(10)O(8) with addition of two H(2)O molecules, as confirmed by tests using (18)O-labeled water. The product stoichiometry showed that each reacted CL-20 molecule produced about 1.7 nitrite ions, 3.2 molecules of nitrous oxide, 1.5 molecules of formic acid, and 0.6 ammonium ion. Diphenyliodonium-mediated inhibition of salicylate 1-monooxygenase and a comparative study between native, deflavo, and reconstituted enzyme(s) showed that FAD site of the enzyme was involved in the biotransformation of CL-20 catalyzed by salicylate 1-monooxygenase. The data suggested that salicylate 1-monooxygenase catalyzed two oxygen-sensitive single-electron transfer steps necessary to release two nitrite ions from CL-20 and that this was followed by the secondary decomposition of this energetic chemical. PMID:15240281

  8. Initial Reaction(s) in Biotransformation of CL-20 Is Catalyzed by Salicylate 1-Monooxygenase from Pseudomonas sp. Strain ATCC 29352

    PubMed Central

    Bhushan, Bharat; Halasz, Annamaria; Spain, Jim C.; Hawari, Jalal

    2004-01-01

    CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) (C6H6N12O12), a future-generation high-energy explosive, is biodegradable by Pseudomonas sp. strain FA1 and Agrobacterium sp. strain JS71; however, the nature of the enzyme(s) involved in the process was not understood. In the present study, salicylate 1-monooxygenase, a flavin adenine dinucleotide (FAD)-containing purified enzyme from Pseudomonas sp. strain ATCC 29352, biotransformed CL-20 at rates of 0.256 ± 0.011 and 0.043 ± 0.003 nmol min−1 mg of protein−1 under anaerobic and aerobic conditions, respectively. The disappearance of CL-20 was accompanied by the release of nitrite ions. Using liquid chromatography/mass spectrometry in the negative electrospray ionization mode, we detected a metabolite with a deprotonated mass ion [M − H]− at 345 Da, corresponding to an empirical formula of C6H6N10O8, produced as a result of two sequential N denitration steps on the CL- 20 molecule. We also detected two isomeric metabolites with [M − H]− at 381 Da corresponding to an empirical formula of C6H10N10O10. The latter was a hydrated product of the metabolite C6H6N10O8 with addition of two H2O molecules, as confirmed by tests using 18O-labeled water. The product stoichiometry showed that each reacted CL-20 molecule produced about 1.7 nitrite ions, 3.2 molecules of nitrous oxide, 1.5 molecules of formic acid, and 0.6 ammonium ion. Diphenyliodonium-mediated inhibition of salicylate 1-monooxygenase and a comparative study between native, deflavo, and reconstituted enzyme(s) showed that FAD site of the enzyme was involved in the biotransformation of CL-20 catalyzed by salicylate 1-monooxygenase. The data suggested that salicylate 1-monooxygenase catalyzed two oxygen-sensitive single-electron transfer steps necessary to release two nitrite ions from CL-20 and that this was followed by the secondary decomposition of this energetic chemical. PMID:15240281

  9. Facile surface PEGylation via tyrosinase-catalyzed oxidative reaction for the preparation of non-fouling surfaces.

    PubMed

    Lee, Yunki; Park, Kyung Min; Bae, Jin Woo; Park, Ki Dong

    2013-02-01

    The control of biological interactions that occur at material-cell/blood interfaces is of great importance to help maximize in vitro and in vivo performance of biomedical devices. PEGylation has been extensively used as an effective surface modification tool that can alter biological responses on device surfaces. Herein, we report a new surface PEGylation method using a tyrosinase-catalyzed oxidative reaction. Tyramine (TA), an enzymatically active phenolic compound, was chemically conjugated to methoxy poly(ethylene glycol) (mPEG). Surface immobilization of mPEG-TA onto various substrates was accomplished simply and rapidly by adding tyrosinase under mild conditions. It was shown that the water contact angles on all surfaces modified with mPEG-TA were decreased, indicating successful introduction of hydrophilic PEG. In addition, the X-ray photoelectron spectroscopy (XPS) spectra demonstrated the differences in the atomic composition on the TiO(2) surface after treatment with mPEG-TA. Non-fouling surfaces prevent non-specific interactions with proteins and cells; consistently, the PEGylated TiO(2) surface clearly showed a decrease in both levels of bovine serum albumin (BSA) adsorption and NIH3T3 cell attachment. Therefore, the facile surface PEGylation using a tyrosinase-catalyzed oxidative reaction should be useful for designing non-fouling surfaces of biomedical devices. PMID:23104029

  10. Acid-catalyzed Reactions in Model Secondary Organic Aerosol (SOA): Insights using Desorption-electrospray Ionization (DESI) Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Fiddler, M. N.; Cooks, R. G.; Shepson, P.

    2008-12-01

    Atmospheric aerosols are presently little understood in terms of their sources, formation, and effect on climate forcing, despite their significant impacts on climate change and respiratory health. Secondary organic aerosols (SOA), which were thought to arise entirely from simple gas-particle partitioning, have recently been found to contain oligomeric species which result from the condensed-phase reactions of volatile organic compounds (VOCs). The non-methane VOC with the greatest emission flux, isoprene, is known to produce aerosols through chemistry involving its oxidation products. We selected one of its major oxidation product, methacrolein, to assess its role in oligomeric SOA formation in response to the acidic conditions found in cloud water. Since it has been found that acidified aerosol produces oligomeric species with greater molecular weight and yield, acid-catalyzed oligomerization is likely a significant process in the formation of SOA. Aqueous solutions of methacrolein were acidified with sulfuric acid, and studied using linear ion trap mass spectrometry (LIT-MS) with a home-built desorption-electrospray ionization (DESI) source. An extremely heterogeneous mixture of products was produced in this system, resulting from hydrolysis, acid- catalyzed oxidation, reduction, and organosulfate formation. Evidence for disproportionation and heterocycle formation are proposed as reaction mechanisms hitherto unrecognized in the production of SOA. The proposed structure and formation mechanism for several species, based upon their MS/MS spectra, will also be presented.

  11. Studies on the oxidation reaction of tyrosine (Tyr) with H 2O 2 catalyzed by horseradish peroxidase (HRP) in alcohol-water medium by spectrofluorimetry and differential spectrophotometry

    NASA Astrophysics Data System (ADS)

    Tang, Bo; Wang, Yan; Liang, Huiling; Chen, Zhenzhen; He, Xiwen; Shen, Hanxi

    2006-03-01

    An oxidation reaction of tyrosine (Tyr) with H 2O 2 catalyzed by horseradish peroxidase (HRP) was studied by spectrofluorimetry and differential spectrophotometry in the alcohol(methanol, ethanol, 1-propanol and isopropanol)-water mutual solubility system. Compared with the enzymatic-catalyzed reaction in the water medium, the fluorescence intensities of the product weakened, even extinguished. Because the addition of alcohols made the conformation of HRP change, the catalytic reaction shifted to the side of polymerization and the polymer (A nH 2, n ? 3) exhibited no fluorescence. The four alcohols cannot deactivate HRP. Moreover isopropanol activated HRP remarkably.

  12. Simulation studies in biochemical signaling and enzyme reactions

    NASA Astrophysics Data System (ADS)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  13. Industrial Enzymes and Biocatalysis

    NASA Astrophysics Data System (ADS)

    McAuliffe, Joseph C.; Aehle, Wolfgang; Whited, Gregory M.; Ward, Donald E.

    All life processes are the result of enzyme activity. In fact, life itself, whether plant or animal, involves a complex network of enzymatic reactions. An enzyme is a protein that is synthesized in a living cell. It catalyzes a thermodynamically possible reaction so that the rate of the reaction is compatible with the numerous biochemical processes essential for the growth and maintenance of a cell. The synthesis of an enzyme thus is under tight metabolic regulations and controls that can be genetically or environmentally manipulated sometimes to cause the overproduction of an enzyme by the cell. An enzyme, like chemical catalysts, in no way modifies the equilibrium constant or the free energy change of a reaction.

  14. Relative Reactivity of Stable Ligated Boranes and a Borohydride Salt in Rhodium(II)-Catalyzed Boron-Hydrogen Insertion Reactions.

    PubMed

    Allen, Thomas H; Curran, Dennis P

    2016-03-01

    Relative reactivities of a series of neutral ligated boranes L-BH3 (where L is NHC, amine, pyridine, or phosphine) and the cyanoborohydride anion have been assessed in Rh(II)-catalyzed B-H insertion reactions with methyl 2-phenyl-2-diazoacetate. Stable α-boryl ester products were isolated by flash chromatography in all cases except for the salt product from cyanoborohydride. All of the substrates were either comparable to or more reactive than 1,4-cyclohexadiene, which is one of the most reactive substrates in C-H insertion reactions. The range of reactivity between the most reactive pyridine-borane and the least reactive phosphine-borane is a factor of approximately 40. PMID:26871613

  15. Coinage metals-catalyzed cascade reactions of aryl alkynylaziridines: silver(I)-single vs gold(I)-double cyclizations.

    PubMed

    Kern, Nicolas; Blanc, Aurlien; Miaskiewicz, Solne; Robinette, Michelle; Weibel, Jean-Marc; Pale, Patrick

    2012-05-01

    Alkynylaziridines carrying an aryl group could be efficiently converted into aminoallenylidene isochromans, isoquinolines, or tetrahydronaphtalenes with silver(I) salts and into 1-azaspiro[4.5]decane derivatives with gold(I) complexes. Mechanistic investigations revealed that both Ag- and Au-catalyzed reactions involved a Friedel-Crafts type intramolecular reaction leading to an allene and that Au also rapidly promoted a second intramolecular cyclization of the aminoallene intermediate to the corresponding spiro derivative. Stereochemical investigations suggested an anti-SN(2)'-type pathway for the first cyclization leading to a stereodefined allene, which could then be cyclized to the corresponding stereodefined spiro product. These results highlight the duality between oxo- or azaphilicity and alkynophilicity of Ag and Au as well as their complementarity in terms of reactivity. PMID:22471846

  16. Pd-catalyzed desymmetric intramolecular O-arylation reaction: enantioselective synthesis of (3,4-dihydro-2H-chromen-3-yl)methanols.

    PubMed

    Yang, Wenqiang; Yan, Jiajie; Long, Yan; Zhang, Shasha; Liu, Jianguang; Zeng, Youlin; Cai, Qian

    2013-12-01

    An enantioselective intramolecular O-arylation was achieved through desymmetrization with Pd-catalyzed coupling reactions. The intramolecular asymmetric aryl C-O coupling reactions of 2-(2-haloaryl)propane-1,3-diols led to the enantioselective formation of chiral (3,4-dihydro-2H-chromen-3-yl)methanols in good yields and high enantiomeric selectivity. PMID:24261632

  17. Efficient synthesis of ?- and ?-carbolines by sequential Pd-catalyzed site-selective C-C and twofold C-N coupling reactions.

    PubMed

    Hung, Tran Quang; Dang, Tuan Thanh; Janke, Julia; Villinger, Alexander; Langer, Peter

    2015-02-01

    Two concise and efficient approaches were developed for the synthesis of ?- and ?-carboline derivatives. The success of the synthesis relies on site-selective Suzuki-Miyaura reactions of 1-chloro-2-bromopyridine or 2,3-dibromopyridine with 2-bromophenylboronic acid and subsequent cyclization with amines which proceeds by twofold Pd-catalyzed C-N coupling reactions. PMID:25464277

  18. Synthesis of indolo[1,2-f]phenanthridines by Pd-catalyzed domino C-N coupling/hydroamination/C-H arylation reactions.

    PubMed

    Ngo, Thang Ngoc; Ehlers, Peter; Dang, Tuan Thanh; Villinger, Alexander; Langer, Peter

    2015-03-21

    A new and convenient method for the synthesis of indolo[1,2-f]phenanthridines via palladium-catalyzed domino C-N coupling/hydroamination/C-H arylation reactions was developed. The reactions allow for the synthesis of various phenanthridines in good yields from easily accessible starting materials using a single palladium catalyst. PMID:25644637

  19. Pd(ii)-catalyzed intramolecular oxidative Heck dearomative reaction: approach to thiazole-fused pyrrolidinones with a C2-azaquarternary center.

    PubMed

    Gao, Shang; Yang, Chi; Huang, Yue; Zhao, Lei; Wu, Xiaoming; Yao, Hequan; Lin, Aijun

    2016-01-21

    A Pd(ii)-catalyzed intramolecular oxidative Heck dearomative reaction for the construction of thiazole-fused pyrrolidinones with a C2-azaquarternary center and C3-exo-double bond has been achieved for the first time. The reaction exhibited good functional group tolerance and gram-scale capacity. PMID:26620717

  20. Synthesis of the copper chelator TGTA and evaluation of its ability to protect biomolecules from copper induced degradation during copper catalyzed azide-alkyne bioconjugation reactions.

    PubMed

    Ekholm, F S; Pynnnen, H; Vilkman, A; Koponen, J; Helin, J; Satomaa, T

    2016-01-21

    One of the most successful bioconjugation strategies to date is the copper(i)-catalyzed cycloaddition reaction (CuAAC), however, the typically applied reaction conditions have been found to degrade sensitive biomolecules. Herein, we present a water soluble copper chelator which can be utilized to protect biomolecules from copper induced degradation. PMID:26647226

  1. Probing the Role of Active Site Residues in NikD, an Unusual Amino Acid Oxidase that Catalyzes an Aromatization Reaction Important in Nikkomycin Biosynthesis

    PubMed Central

    Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Jorns, Marilyn Schuman

    2009-01-01

    NikD catalyzes a remarkable aromatization reaction that converts piperideine-2-carboxylate (P2C) to picolinate, a key component of the nonribosomal peptide in nikkomycin antibiotics. The enzyme exhibits a FAD-Trp355 charge-transfer band at weakly alkaline pH that is abolished upon protonation of an unknown ionizable residue that exhibits a pKa of 7.3. Stopped-flow studies of the reductive half-reaction with wild-type nikD and P2C show that the enzyme oxidizes the enamine tautomer of P2C but do not distinguish among several possible paths for the initial 2-electron oxidation step. Replacement of Glu101 or Asp276 by a neutral residue does not eliminate the ionizable group, although the observed pKa is 1 or 2 pH units higher, respectively, compared with wild-type nikD. Importantly, the mutations cause only a modest decrease (< 5-fold) in the observed rate of oxidation of P2C to dihydropicolinate. The results rule out the only possible candidates for a catalytic base in the initial 2-electron oxidation step. This outcome provides compelling evidence that nikD oxidizes the bond between N(1) and C(6) in the enamine tautomer of P2C, ruling out alternative paths that require an active site base to mediate the oxidation of a carbon-carbon bond. Because the same restraint applies to the second 2-electron oxidation step, the dihydropicolinate intermediate must be converted to an isomer that contains an oxidizable carbon-nitrogen bond. A novel role is proposed for reduced FAD as an acid-base catalyst in the isomerization of dihydropicolinate. PMID:19530706

  2. DFT study on the reaction mechanism of the ring closing enyne metathesis (RCEYM) catalyzed by molybdenum alkylidene complexes.

    PubMed

    Solans-Monfort, Xavier

    2014-03-21

    The ring closing enyne metathesis reaction (RCEYM) catalyzed by molybdenum based monoalkoxy pyrrolyl Schrock type catalysts has been studied by means of DFT (B3LYP-D) calculations. The two potential active alkylidene species as well as the three proposed reaction mechanisms (ene-then-yne, endo-yne-then-ene and exo-yne-then-ene) have been taken into account. Moreover, the influence on the exo- and endo- selectivity of the reactant substituents has also been explored. Results show that, in contrast to what is found for RCEYM processes catalyzed by Ru-based catalysts, the metallacyclobutene is a very short-living reaction intermediate that can be present in two isomeric forms (trigonal bipyramid (TBP) coordination around the metal center and square based pyramid (SPY) coordination). These two isomers are directly involved in the reaction mechanism, and the ring opening takes place from the SPY species. Moreover and regardless of the nature of the reacting metal-alkylidene, the yne-then-ene pathways (endo- or exo-) are computed to present significantly lower energy barriers than the ene-then-yne pathway and thus the latter is computed not to take place. Finally, the exo-/endo- selectivity is predicted to highly depend on the sterics of the two carbon ends of the alkyne fragment. In this way, the carbon bearing the largest group prefers to interact with the carbon end of the metal-alkylidene. This places the bulkiest groups as far away as possible from the metal fragment and overall leads to a generally lower energy barrier for the metallacyclobutene formation, the key step in defining the exo-/endo- selectivity. PMID:24492319

  3. Reaction dynamics and transition-state structures for acetylcholinesterase-catalyzed hydrolysis of aryl esters and anilides

    SciTech Connect

    Acheson, S.A.

    1986-01-01

    The acylation and deacylation stages of acetylcholinesterase-catalyzed hydrolysis of various aryl ester and anilide substrates were investigated. For the natural substrate of acetylcholinesterase (AChE), acetylcholine, diffusion or enzyme conformational processes limit the acylation rate. Several anilides and aryl esters have been synthesized and found to be substrates of AChE. The acylation and deacylation reactivities of o-nitroformanilide, p-methoxyphenyl formate and o-nitrophenyl acetate were characterized by measuring substrate secondary and solvent isotope effects and by determining pL(L = H,D)-rate profiles and Eyring plots. Substrate secondary deuterium kinetic isotope effects are consistent with decreasing nucleophilic interaction at the carbonyl carbon of the scissle bond of the substrate in the rate-determining transition state with increasing V/K. These results lend quantitative support to a model for acylation rate determination involving a virtual transition state that contains contributions from the transition states of sequential physical and chemical steps.

  4. Stereospecific nickel-catalyzed cross-coupling reactions of alkyl ethers: enantioselective synthesis of diarylethanes.

    PubMed

    Taylor, Buck L H; Swift, Elizabeth C; Waetzig, Joshua D; Jarvo, Elizabeth R

    2011-01-26

    Secondary benzylic ethers undergo stereospecific substitution reactions with Grignard reagents in the presence of nickel catalysts. Reactions proceed with inversion of configuration and high stereochemical fidelity. This reaction allows for facile enantioselective synthesis of biologically active diarylethanes from readily available optically enriched carbinols. PMID:21155567

  5. On the radical nature of iron-catalyzed cross-coupling reactions.

    PubMed

    Hedstrm, Anna; Izakian, Zakieh; Vreto, Irma; Wallentin, Carl-Johan; Norrby, Per-Ola

    2015-04-01

    The radical nature of iron-catalyzed cross-coupling between Grignard reagents and alkyl halides has been studied by using a combination of competitive kinetic experiments and DFT calculations. In contrast to the corresponding coupling with aryl halides, which commences through a classical two-electron oxidative addition/reductive elimination sequence, the presented data suggest that alkyl halides react through an atom-transfer-initiated radical pathway. Furthermore, a general iodine-based quenching methodology was developed to enable the determination of highly accurate concentrations of Grignard reagents, a capability that facilitates and increases the information output of kinetic investigations based on these substrates. PMID:25703202

  6. Synthesis of 8-heteroaryl nitroxoline analogues via one-pot sequential Pd-catalyzed coupling reactions.

    PubMed

    Brodnik, Helena; Pogan, Franc; tefane, Bogdan

    2016-02-01

    A series of 8-heteroaryl substituted quinolines were prepared, either by direct C-H arylation of five-membered heteroarenes, or Pd-catalyzed coupling of organoboron reagents with bromoquinolines. The use of (benzo)thiophenyl or (benzo)furanyl boron coupling partners allowed further C-H functionalization on the five-membered heteroaryl ring with aryl bromides in one flask to access a variety of polyconjugated molecular architectures. The developed methodology represents a simple approach towards 8-arylated analogues of the biologically interesting nitroxoline core. PMID:26754567

  7. Redox Reactions of Metalloporphyrins and their Role in Catalyzed Reduction of Carbon Dioxide

    SciTech Connect

    Neta, P.

    2002-09-01

    Pulse radiolysis and laser photolysis are used to study redox processes of metalloporphyrins and related complexes in order to evaluate these light absorbing molecules as sensitizers and intermediates in solar energy conversion schemes. The main thrust of the current studies is to investigate the role of reduced metalloporphyrins as intermediates in the catalyzed reduction of carbon dioxide. Studies involve cobalt and iron porphyrins, phthalocyanines, corroles, and corrins as homogeneous catalysts for reduction of carbon dioxide in solution. The main aim is to understand the mechanisms of these photochemical schemes in order to facilitate their potential utilization.

  8. Regioselective synthesis of multisubstituted isoquinolones and pyridones via Rh(iii)-catalyzed annulation reactions.

    PubMed

    Shi, Liangliang; Yu, Ke; Wang, Baiquan

    2015-11-24

    A mild and efficient Rh(iii)-catalyzed regioselective synthesis of isoquinolones and pyridones has been developed. The protocol uses readily available N-methoxybenzamide or N-methoxymethacrylamide and diazo compounds as starting materials. The process involving tandem C-H activation, cyclization, and condensation steps proceeds under mild conditions, and the corresponding isoquinolone and pyridone derivatives were obtained in good to excellent yields with excellent regioselectivities. The process provides a facile approach for the construction of isoquinolone and pyridone derivatives containing various functional groups. PMID:26463232

  9. L-myo-inosose-1 as a probable intermediate in the reaction catalyzed by myo-inositol oxygenase

    SciTech Connect

    Naber, N.I.; Swan, J.S.; Hamilton, G.A.

    1986-11-04

    In previous investigations, it was necessary to have Fe(II) and cysteine present in order to assay the catalytic activity of purified hog kidney myo-inositol oxygenase. In the present study it was found that, if this purified nonheme iron enzyme is slowly frozen in solution with glutathione and stored at -20 degrees C, it is fully active in the absence of activators if catalase is present to remove adventitious H/sub 2/O/sub 2/. With this simpler assay system it was possible to clarify the effects of several variables on the enzymic reaction. Thus, the maximum velocity is pH-dependent with a maximum around pH 9.5, but the apparent Km for myo-inositol (air atmosphere) remains constant at 5.0 mM throughout a broad pH range. The enzyme is quite specific for its substrate myo-inositol, is very sensitive to oxidants and reductants, but is not affected by a variety of complexing agents, nucleotides, sulfhydryl reagents, etc. In other experiments it was found that L-myo-inosose-1, a potential intermediate in the enzymic reaction, is a potent competitive inhibitor (Ki = 62 microM), while other inososes and a solution thought to contain D-glucodialdehyde, another potential intermediate, are weak inhibitors. Also, both a kinetic deuterium isotope effect (kH/kD = 2.1) and a tritium isotope effect (kH/kT = 7.5) are observed for the enzymic reaction when (1-2H)- and (1-3H)-myo-inositol are used as reactants. These latter results are considered strong evidence that the oxygenase reaction proceeds by a pathway involving L-myo-inosose-1 as an intermediate rather than by an alternative pathway that would have D-glucodialdehyde as the intermediate.

  10. Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes.

    PubMed

    Cheng, Zigang; Sattler, Scott; Maeda, Hiroshi; Sakuragi, Yumiko; Bryant, Donald A; DellaPenna, Dean

    2003-10-01

    Tocopherols are lipid-soluble compounds synthesized only by photosynthetic eukaryotes and oxygenic cyanobacteria. The pathway and enzymes for tocopherol synthesis are homologous in cyanobacteria and plants except for 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ/MSBQ MT), which catalyzes a key methylation step in both tocopherol and plastoquinone (PQ) synthesis. Using a combined genomic, genetic, and biochemical approach, we isolated and characterized the VTE3 (vitamin E defective) locus, which encodes MPBQ/MSBQ MT in Arabidopsis. The phenotypes of vte3 mutants are consistent with the disruption of MPBQ/MSBQ MT activity to varying extents. The ethyl methanesulfonate-derived vte3-1 allele alters tocopherol composition but has little impact on PQ levels, whereas the null vte3-2 allele is deficient in PQ and alpha- and gamma-tocopherols. In vitro enzyme assays confirmed that VTE3 is the plant functional equivalent of the previously characterized MPBQ/MSBQ MT (Sll0418) from Synechocystis sp PCC6803, although the two proteins are highly divergent in primary sequence. Sll0418 orthologs are present in all fully sequenced cyanobacterial genomes, Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana but absent from vascular and nonvascular plant databases. VTE3 orthologs are present in all vascular and nonvascular plant databases and in C. reinhardtii but absent from cyanobacterial genomes. Intriguingly, the only prokaryotic genomes that contain VTE3-like sequences are those of two species of archea, suggesting that, in contrast to all other enzymes of the plant tocopherol pathway, the evolutionary origin of VTE3 may have been archeal rather than cyanobacterial. In vivo analyses of vte3 mutants and the corresponding homozygous Synechocystis sp PCC6803 sll0418::aphII mutant revealed important differences in enzyme redundancy, the regulation of tocopherol synthesis, and the integration of tocopherol and PQ biosynthesis in cyanobacteria and plants. PMID:14508009

  11. Development of asymmetric reactions catalyzed by chiral organotin-alkoxide reagents.

    PubMed

    Yanagisawa, Akira; Yoshida, Kazuhiro

    2013-02-01

    Asymmetric catalysis under almost-neutral reaction conditions is key for the efficient synthesis of optically active polar molecules. We have developed catalytic enantioselective reactions of acyclic or cyclic alkenyl esters by using an (S)-BINOL-derived chiral tin-dibromide reagent that possesses a bulky aryl group at the 3 or 3' position as the chiral pre-catalyst in the presence of a sodium alkoxide and an alcohol, in which a chiral tin alkoxide bromide is generated in situ and recycled with the assistance of an alcohol. In this Personal Account, we describe three types of asymmetric transformation that proceed through a chiral tin enolate: 1) The asymmetric aldol reaction of alkenyl esters or unsaturated lactones with aldehydes or isatins; 2) the asymmetric three-component Mannich-type reaction of alkenyl esters and related cycloaddition reactions; and 3) the asymmetric N-nitroso aldol reaction of unsaturated lactones with nitrosoarenes. PMID:23424074

  12. Pre-steady state transients in the Drosophila alcohol dehydrogenase catalyzed reaction: isotope effects and stereospecificity

    SciTech Connect

    Place, A.R.; Eccleston, J.F.

    1987-05-01

    The alcohol dehydrogenase (ADH) isolated from Drosophila is unique among alcohol metabolizing enzymes by not requiring metals for catalysis, by showing 4-pro-S (B-sided) hydride transfer stereospecificity, and by possessing a greater catalytic turnover rate for secondary alcohols than for primary alcohols. They have extended their studies on the kinetic mechanism for this enzyme by examining the pre-steady state transients of ternary complex interconversion using stopped-flow fluorescence methods. When enzyme and a 30-fold molar excess of NADH is mixed with excess acetadehyde, methyl ethyl ketone (MEK), or cyclohexanone a rapid (> 100 s/sup -1/) transient is observe before the steady-state. The rates are insensitive to isotope substitution. With the substrate MEK, the rate and amplitude suggests a single turnover of the enzyme. Similar pre-steady state transients are observed when enzyme and a 50-fold molar excess of NAD/sup +/ is mixed with ethanol, 2-propanol, and cyclohexanol. The rates show a hyperbolic concentration dependence and a deuterium isotope effect. With d/sub 6/-deuteroethanol the transient no longer occurs in the pre-steady state. When the optical isomers of secondary alcohols are used as substrates, transients are observed only in the R-(-) isomers for all chain lengths. With 2-S(+)-heptanol and 2-S(+)-octanol no transients occur.

  13. Enzyme

    MedlinePLUS

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  14. Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

    PubMed Central

    Náray-Szabó, Gábor; Oláh, Julianna; Krámos, Balázs

    2013-01-01

    Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods. PMID:24970187

  15. Resolution of component proteins in an enzyme complex from Methanosarcina thermophila catalyzing the synthesis or cleavage of acetyl-CoA

    SciTech Connect

    Abbanat, D.R.; Ferry, J.G. )

    1991-04-15

    An enzyme complex was isolated from acetate-grown Methanosarcina thermophila that oxidized CO and catalyzed the synthesis or cleavage of acetyl-CoA. The complex consisted of five subunits ({alpha}1{beta}1{gamma}1{delta}1{epsilon}1) of 89, 71, 60, 58, and 19 kDa. The complex contained nickel, iron, acid-labile sulfide, and cobalt in a corrinoid cofactor. Two components were resolved by anion-exchange chromatography of the complex in the presence of dodecyltrimethylammonium bromide and Triton X-100: a 200-kDa nickel/iron-sulfur protein with the 89-and 19-kDa ({alpha}{sub 2}{epsilon}{sub x}) subunits and a 100-kDa corrinoid/iron-sulfur protein with the 60- and 58-kDa subunits ({gamma}1{delta}1). Both components contained iron-sulfur centers. The nickel/iron-sulfur component oxidized CO and reduced methyl viologen or a ferredoxin isolated from M. thermophila. UV-visible spectroscopy indicated that the reduced corrinoid/iron-sulfur component could be methylated with CH{sub 3}I. The results suggest that the enzyme complex from M. thermophila contained at least two enzyme components, each with a specific function. The properties of the component enzymes support a mechanism proposed for acetyl-CoA synthesis (or cleavage) by the enzyme complex.

  16. Oxygen reduction reaction catalyzed with titanyl phthalocyanines in nonaqueous and aqueous media.

    PubMed

    Demir, Faruk; Erdo?mu?, Ali; Koca, At?f

    2013-10-14

    Electrochemical and in situ spectroelectrochemical behaviors and electrocatalytic reduction of molecular oxygen with titanyl phthalocyanines (TiPc) bearing 3,4-(methylenedioxy)-phenoxy substituents were performed in aprotic solvents. Multi electrons and metal-based and ring-based redox processes of TiPcs indicate their possible electrocatalytic activity toward many target species. Different numbers and positions of the substituents of the complexes affect the peaks' character and assignment of the processes. The presence of O2 in the electrolyte system influences the electrochemical and spectral responses of TiPcs. Electrochemical and in situ spectroelectrochemical analysis indicates interaction of molecular oxygen with TiPcs and these interaction mechanisms depend on both the substituent environments of the complexes and the electrolyte system. Langmuir-Blodgett films of the complexes also catalyze molecular oxygen in aqueous media, which is a desired property for their practical application. PMID:23949120

  17. Platinum-catalyzed domino reaction with benziodoxole reagents for accessing benzene-alkynylated indoles.

    PubMed

    Li, Yifan; Waser, Jerome

    2015-04-27

    Indoles are omnipresent in natural products, bioactive molecules, and organic materials. Consequently, their synthesis or functionalization are important fields of research in organic chemistry. Most works focus on installation or modification of the pyrrole ring. To access benzene-ring-functionalized indoles with an unsubstituted pyrrole ring remains more challenging. Reported herein is a platinum-catalyzed cyclization/alkynylation domino process to selectively obtain C5- or C6-functionalized indoles starting from easily available pyrroles. The work combines, for the first time, a platinum catalyst with ethynylbenziodoxole hypervalent iodine reagents in a domino process for the synthesis of polyfunctionalized arene rings and gives access to important building blocks for the synthesis of bioactive compounds and organic materials. PMID:25759194

  18. Cu-catalyzed synthesis of diaryl thioethers and S-cycles by reaction of aryl iodides with carbon disulfide in the presence of DBU.

    PubMed

    Zhao, Peng; Yin, Hang; Gao, Hongxin; Xi, Chanjuan

    2013-05-17

    Diaryl thioethers and S-cycles were obtained on the basis of the copper-catalyzed reaction of carbon disulfide and aryl iodides in the presence of DBU. This reaction enables the one-pot synthesis of diaryl thioethers by employing cheap, available, and easy-to-handle carbon disulfide with aryl iodides. The reaction was successfully employed in the construction of sulfur-containing cyclic molecules. PMID:23611365

  19. Pd-Catalyzed Three-Component Reaction of 3-(Pinacolatoboryl)ally Acetates, Aldehydes, and Organoboranes: A New Entry to Stereoselective Synthesis of (Z)-anti-Homoallylic Alcohols.

    PubMed

    Horino, Yoshikazu; Aimono, Ataru; Abe, Hitoshi

    2015-06-01

    The Pd-catalyzed three-component reaction of 3-(pinacolatoboryl)allyl acetates, aldehydes, and organoboranes is described. The reaction is initiated by the formation of an allylic gem-palladium/boryl intermediate, which then undergoes allylation of aldehydes by allylboronates followed by a coupling reaction of in situ generated (Z)-vinylpalladium acetates with organoboranes to provide the (Z)-anti-homoallylic alcohols with high levels of diastereoselectivity and alkene stereocontrol. PMID:25997076

  20. Asymmetric direct aldol reactions of acetoacetals catalyzed by a simple chiral primary amine.

    PubMed

    Luo, Sanzhong; Qiao, Yupu; Zhang, Long; Li, Jiuyuan; Li, Xin; Cheng, Jin-Pei

    2009-12-18

    An asymmetric direct aldol reaction of acetoacetals is described. Under the catalysis of a simple chiral primary amine, the direct aldol reactions of acetoacetals occur exclusively on the gamma-position to give vinylogous-type aldol products with high diastereo- and enantioselectivity. PMID:19883088