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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. Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Timescales

    E-print Network

    Paul, Mark

    Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Timescales Debashis Barik-steady-state approximation'' for enzyme-catalyzed reactions provides a useful framework for efficient and accurate stochastic simulations. The method is applied to three examples: a simple enzyme-catalyzed reaction where enzyme

  3. 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.

  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. Monitoring Enzyme-catalyzed Reactions in Micromachined Nanoliter Wells using a Conventional Microscope based

    E-print Network

    van Vliet, Lucas J.

    Monitoring Enzyme-catalyzed Reactions in Micromachined Nanoliter Wells using a Conventional to ethanol and carbon dioxide. This pathway consists of 12 enzyme-catalyzed reactions. With the approach × 300µm2 . The depth varies from 20 to 50µm. Enzyme activity levels can be derived by monitoring

  8. Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions

    E-print Network

    Golestanian, Ramin

    2015-01-01

    Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 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 could be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.

  9. Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions

    E-print Network

    Ramin Golestanian

    2015-08-13

    Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 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 could be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.

  10. 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.

  11. 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.

  12. 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.

  13. 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…

  14. 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

  15. 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.

  16. Starting D-optimal designs for batch kinetics studies of enzyme-catalyzed reactions in the presence of enzyme deactivation.

    PubMed

    Malcata, F X

    1992-09-01

    This paper describes a strategy for the starting experimental design of experiments required by general research in the field of biochemical kinetics. The type of experiments that qualify for this analysis involve batch reactions catalyzed by soluble enzymes where the activity of the enzyme decays with time. Assuming that the catalytic action of the enzyme obeys a Michaelis-Menten rate expression and that the deactivation of the enzyme follows a first-order decay, the present analysis employs the dimensionless, integrated form of the overall rate expression to obtain a criterion (based on the maximization of the determinant of the derivative matrix) that relates the a priori estimates of the parameters with the times at which samples should be withdrawn from the reacting mixture. The analysis indicates that the initial concentration of substrate should be as large as possible, and that the samples should be taken at times corresponding to substrate concentrations of approximately 2/3, 1/4, and I/epsilon of the initial concentration (where epsilon should be as large as possible). PMID:1420847

  17. 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...

  18. 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.

  19. 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

  20. Catalyzed enzyme electrodes

    SciTech Connect

    Zawodzinski, T.A.; Wilson, M.S.; Rishpon, J.; Gottesfeld, S.

    1992-12-31

    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.

  1. Catalyzed enzyme electrodes

    DOEpatents

    Zawodzinski, Thomas A. (Los Alamos, NM); Wilson, Mahlon S. (Los Alamos, NM); Rishpon, Judith (Ramat-Aviv, IL); Gottesfeld, Shimshon (Los Alamos, NM)

    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.

  2. 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.

  3. 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…

  4. Quantitation of low molecular mass substrates and products of enzyme catalyzed reactions using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    PubMed

    Kang, M J; Tholey, A; Heinzle, E

    2000-01-01

    Relative peak-height ratios of products to substrates determined by MALDI-TOFMS allow the quantitative analysis of enzyme catalyzed reactions for screening purposes. Two examples were investigated: the first one was a lipase catalyzed reaction which produces 2-methoxy-N-[(1R)-1-phenylethyl]acetamide (MET) using rac-alpha-phenylethylamine (PEA) as substrate. The second one was the pyruvate decarboxylase catalyzed formation of (1R)-1-hydroxy-1-phenyl-2-propanone (PAC) with benzaldehyde (BzA) as substrate. Here the corresponding oximes were analyzed after derivatization using hydroxylamine. The standard curves (r2 = 0.985 for MET, r2 = 0.991 for PAC) were linear over two orders of magnitude for MET and PAC concentrations. After optimization of the sample preparation an average relative standard deviation of 12.5% was obtained in both cases. PMID:11085406

  5. 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…

  6. Mechanism of enzyme-catalyzed phospho group transfer

    SciTech Connect

    Hansen, D.E.

    1986-01-01

    To understand more fully the mechanism of enzyme-catalyzed phospho group transfer, the stereochemical course at phosphorus of four enzymes has been determined. First, using adenosine (..gamma..-(S)-/sup 16/O, /sup 17/O, /sup 18/O)triphosphate as the substrate, the reaction catalyzed by creatine kinase has been found to proceed with overall inversion of configuration at phosphorus. Second, using adenosine (..beta..-(S)-/sup 16/O, /sup 17/O, /sup 18/O)diphosphate as the substrate, the reaction catalyzed by adenylate kinase has been found also to proceed with overall inversion. Third, the reaction catalyzed by phosphoenolpyruvate carboxylase has been studied using ((S/sub p/)-/sup 16/O, /sup 17/O)thiophospoenolpyruvate as the substrate in H/sub 2/ /sup 18/O. Fourth, using adenosine 5'-O-((..gamma..S/sub p/)-..beta gamma..-/sup 17/O,..gamma..-/sup 17/O,/sup 18/O)(3-thiotriphosphate) as the substrate, the reaction catalyzed by pyruvate carboxylase has been shown to proceed with inversion at phosphorus. This results rules out the chemically and enzymatically precendented composite mechanism that had been proposed for this enzyme and supports a stepwise pathway again involving the intermediacy of carboxyphosphate. The first pair of results supports the growing body of evidence that enzyme-catalyzed phospho group transfer proceeds by an in-line associative mechanism. The second pair of results eliminate mechanistic suggestions of concerted electrocyclic processes in bicarbonate dependent carboxylation reactions.

  7. 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

  8. Part I: RNA hydrolysis catalyzed by imidazole compounds. Part II. Hydrophobic acceleration of reactions and mimics of thiamin-dependent enzymes

    SciTech Connect

    Kool, E.T.

    1988-01-01

    Catalysts modeled after the active site groups of the enzyme Ribonuclease A were synthesized and tested for catalysis of the hydrolysis of poly(rU), using a quantitative assay. The most effective of all the catalysts is N,N{prime}-bis-imidazolylmethane, which gave a four-fold rate enhancement as compared to N-methyl-imidazole. The structure/activity relationships are discussed in light of the ribonuclease mechanism. Also examined were reactions catalyzed by the coenzyme thiamine. In an investigation of the effects of restricting conformational freedom, a thiazolium salt was attached in two positions to {beta}-cyclodextrin. Since the catalyst gave about the same rate for tritium exchange from benzaldehyde as singly-attached catalysts, we surmise that any rate enhancement due to the restriction of bond rotations has been lost by forcing the structure into less productive conformations. The benzoin condensation catalyzed by cyanide was also investigated. The reaction was shown to be faster in water than in most organic solvents. Kinetic salt effects and the effects of added {beta}- and {gamma}-cyclodextrin were measured in water; salting-out ions and {gamma}-cyclodextrin increase the rate, while salting-in ions and {beta}-cyclodextrin decrease it. Negative salt effects were observed in formamide, ethylene glycol, and DMSO. All these media effects are discussed in relation to the compact, hydrophobic transition state for the reaction.

  9. 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

  10. Enzyme-catalyzed protein crosslinking.

    PubMed

    Heck, Tobias; Faccio, Greta; Richter, Michael; Thöny-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

  11. Enzyme reaction annotation using cloud techniques.

    PubMed

    Huang, Chuan-Ching; Lin, Chun-Yuan; Chang, Cheng-Wen; Tang, Chuan Yi

    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

  12. 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

  13. 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 enzyme–DNA intermediate, and then it resolves it by a nucleophilic attack of water or an alcohol, to yield hydrolysis or transesterification products, respectively. PMID:17267608

  14. One-substrate transketolase-catalyzed reaction.

    PubMed

    Bykova, I A; Solovjeva, O N; Meshalkina, L E; Kovina, M V; Kochetov, G A

    2001-01-26

    Apart from catalyzing the common two-substrate reaction with ketose as donor substrate and aldose as acceptor substrate, transketolase is also able to catalyze a one-substrate reaction utilizing only ketose (xylulose 5-phosphate) as substrate. The products of this one-substrate reaction were glyceraldehyde 3-phosphate and erythrulose. No free glycolaldehyde (a product of xylulose 5-phosphate splitting in the transketolase reaction) was revealed. PMID:11162599

  15. Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase

    E-print Network

    Epstein, Irving R.

    Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase David G. Míguez* , Vladimir as catalysts and regulators. We present a reaction­diffusion system catalyzed by the enzyme glucose oxidase previously studied the temporal dynamics of the enzymatic autocatalytic reaction between glucose and ferricya

  16. 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.

  17. 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

  18. 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

  19. 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 Mössbauer 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

  20. The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction 

    E-print Network

    Gourley, David G; Shrive, Annette K; Polikarpov, Igor; Krell, Tino; Coggins, John R; Hawkins, Alastair R; Isaacs, Neil W; Sawyer, Lindsay

    The structures of enzymes catalyzing the reactions in central metabolic pathways are generally well conserved as are their catalytic mechanisms. The two types of 3-dehydroquinate dehydratase (DHQase) are therefore most ...

  1. Palladium-catalyzed oxidative carbonylation reactions.

    PubMed

    Wu, Xiao-Feng; Neumann, Helfried; Beller, Matthias

    2013-02-01

    Palladium-catalyzed coupling reactions have become a powerful tool for advanced organic synthesis. This type of reaction is of significant value for the preparation of pharmaceuticals, agrochemicals, as well as advanced materials. Both, academic as well as industrial laboratories continuously investigate new applications of the different methodologies. Clearly, this area constitutes one of the major topics in homogeneous catalysis and organic synthesis. Among the different palladium-catalyzed coupling reactions, several carbonylations have been developed and widely used in organic syntheses and are even applied in the pharmaceutical industry on ton-scale. Furthermore, methodologies such as the carbonylative Suzuki and Sonogashira reactions allow for the preparation of interesting building blocks, which can be easily refined further on. Although carbonylative coupling reactions of aryl halides have been well established, palladium-catalyzed oxidative carbonylation reactions are also interesting. Compared with the reactions of aryl halides, oxidative carbonylation reactions offer an interesting pathway. The oxidative addition step could be potentially avoided in oxidative reactions, but only few reviews exist in this area. In this Minireview, we summarize the recent development in the oxidative carbonylation reactions. PMID:23307763

  2. 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.

  3. Hydrogen Location in Stages of an Enzyme-Catalyzed Reaction: Time-of-Flight Neutron Structure of D-Xylose Isomerase with Bound D-Xylulose

    SciTech Connect

    Coates, Leighton

    2009-01-01

    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 the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.

  4. 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

  5. A hitherto unknown transketolase-catalyzed reaction.

    PubMed

    Sevostyanova, Irina A; Solovjeva, Olga N; Kochetov, German A

    2004-01-16

    Yeast transketolase, in addition to catalyzing the transferase reaction through utilization of two substrates--the donor substrate (ketose) and the acceptor substrate (aldose)--is also able to catalyze a one-substrate reaction with only aldose (glycolaldehyde) as substrate. The interaction of glycolaldehyde with holotransketolase results in formation of the transketolase reaction intermediate, dihydroxyethyl-thiamin diphosphate. Then the glycolaldehyde residue is transferred from dihydroxyethyl-thiamin diphosphate to free glycolaldehyde. As a result, the one-substrate transketolase reaction product, erythrulose, is formed. The specific activity of transketolase was found to be 0.23 U/mg and the apparent Km for glycolaldehyde was estimated as 140 mM. PMID:14697258

  6. 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

  7. 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 400°C. 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).

  8. [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

  9. 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

  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 1.87×10(-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. 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

  12. Reduction of Intrinsic Kinetic and Thermodynamic Barriers for Enzyme-catalyzed Proton Transfers from

    E-print Network

    Spiteri, Raymond J.

    1 Reduction of Intrinsic Kinetic and Thermodynamic Barriers for Enzyme-catalyzed Proton Transfers. Phone: (902) 494-1974; fax: (902) 494-1355; e-mail: sbearne@dal.ca Running Title: Enzyme-catalyzed Proton Transfers #12;2 Abstract Many enzymes catalyze the heterolytic abstraction of the -proton from

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

    PubMed

    Montiel, Carmina; Bustos-Jaimes, Ismael; Bárzana, 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 90°C. 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

  14. Alternative metals for homogeneous catalyzed hydroformylation reactions.

    PubMed

    Pospech, Jola; Fleischer, Ivana; Franke, Robert; Buchholz, Stefan; Beller, Matthias

    2013-03-01

    Transition-metal-catalyzed hydroformylation reactions constitute one of the most powerful tools for C-C bond formation in organic synthesis and represent an outstanding example of the application of homogeneous catalysis on an industrial scale. This process allows for the straightforward conversion of inexpensive chemical feedstock into broadly applicable aldehydes, which serve as major building blocks for numerous chemical products. These products are highly valuable for the chemical industry and used as plasticizers, detergents, and surfactants on a million ton scale. Moreover, aldehydes serve as versatile chemical intermediates for the production of fine chemicals and pharmaceuticals. Currently, most of the bulk hydroformylation processes rely on rhodium-based catalysts. The increasing demand and resulting high cost of this precious metal has resulted in alternative transition-metal catalysts becoming highly desirable. The following Review summarizes the progress achieved utilizing Ru, Ir, Pd, Pt, and Fe catalysts in hydroformylation reactions. PMID:23436281

  15. Thermodynamic limitations on microbially catalyzed reaction rates

    NASA Astrophysics Data System (ADS)

    LaRowe, Douglas E.; Dale, Andrew W.; Amend, Jan P.; Van Cappellen, Philippe

    2012-08-01

    Quantification of global biogeochemical cycles requires knowledge of the rates at which microorganisms catalyze chemical reactions. In order for models that describe these processes to capture global patterns of change, the underlying formulations in them must account for biogeochemical transformations over seasonal and millennial time scales in environments characterized by different energy levels. Building on existing models, a new thermodynamic limiting function is introduced. With only one adjustable parameter, this function that can be used to model microbial metabolism throughout the range of conditions in which organisms are known to be active. The formulation is based on a comparison of the amount of energy available from any redox reaction to the energy required to maintain a membrane potential, a proxy for the minimum amount of energy required by an active microorganism. This function does not require species- or metabolism-specific parameters, and can be used to model metabolisms that capture any amount of energy. The utility of this new thermodynamic rate limiting term is illustrated by applying it to three low-energy processes: fermentation, methanogenesis and sulfate reduction. The model predicts that the rate of fermentation will be reduced by half once the Gibbs energy of the catalyzed reaction reaches -12 kJ (mol e-)-1, and then slowing exponentially until the energy yield approaches zero. Similarly, the new model predicts that the low energy yield of methanogenesis, -4 to -0.5 kJ (mol e-)-1, for a partial pressure of H2 between 11 and 0.6 Pa decreases the reaction rate by 95-99%. Finally, the new function's utility is illustrated through its ability to accurately model sulfate concentration data in an anoxic marine sediment.

  16. 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.

  17. 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)

  18. ATP-ADP exchange reaction catalyzed by Na+,K+-ATPase: dephosphorylation by ADP of the E1P enzyme form.

    PubMed

    Campos, M; Beaugé, L

    1997-11-18

    We studied the effects of Mg2+ and of ADP and other nucleoside diphosphates on the dephosphorylation of the E1P form of the partially purified pig kidney Na+,K+-ATPase at 20-22 degrees C. We report for the first time the rate of the reversal of ATP phosphorylation. The experiments were done on enzyme subjected to controlled chymotrypsin digestion consisting of a homogenous population of a truncated catalytic subunit. Under this condition the whole cycle is E1 <-- (f1.ATP, b1) --> E1ATP <-- (f2, b2) --> E1P.ADP <-- (fd, bd.ADP) --> E1P-(f3) --> E1. The values of f1, b1, f2, and f3 were independently estimated in the absence of ADP; those of fd, bd, and b2 were obtained from the fit of ADP-dependent dephosphorylation data to the differential equation set. When f2 = 0 or b1 is very large, the model predicts that dephosphorylation by ADP gives a single exponential; in all other cases it predicts a biphasic dephosphorylation in a semilogarithmic plot. The fast phase is governed by b2.ADP and the slow one by b1. This was experimentally verified. Also, ADP stimulates E1P breakdown without release of Pi, thus leading to ATP synthesis. The data indicate that the true substrate for ATP synthesis is free ADP, while Mg2+ inhibits mainly by a reduction in the free [ADP]; in addition, E1P has a very low affinity for MgADP. The nucleotide structure is also very important; all ADP analogues tested were much less effective than ADP due to a reduced affinity for the E1P and a poor capacity to reverse phosphorylation. PMID:9369496

  19. Palladium-Catalyzed Homocoupling Reactions between Two Csp3

    E-print Network

    Zhang, Xumu

    Palladium-Catalyzed Homocoupling Reactions between Two Csp3 -Csp3 Centers Aiwen Lei and Xumu Zhang A novel palladium-catalyzed coupling reaction between two Csp3-Csp3 centers has been investigated. This protocol is initiated by the oxidative addition of an r-halo carbonyl compound to a palladium(0) species

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

    PubMed

    Adewale, Peter; Dumont, Marie-Josée; 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 85.6±0.08%. PMID:26186814

  1. Enzyme-catalyzed Oxidation Facilitates the Return of Fluorescence for Single-Walled Carbon Nanotubes

    PubMed Central

    Chiu, Cheuk Fai; Barth, Brian A.; Kotchey, Gregg P.; Zhao, Yong; Gogick, Kristy A.; Saidi, Wissam A.; Petoud, Stéphane; Star, Alexander

    2013-01-01

    In this work, we studied enzyme-catalyzed oxidation of single-walled carbon nanotubes (SWCNTs) produced by the high-pressure carbon monoxide (HiPco) method. While oxidation via strong acids introduced defects sites on SWCNTs and suppressed their near-infrared (NIR) fluorescence, our results indicated that the fluorescence of SWCNTs was restored upon enzymatic oxidation, which provided new evidence that the reaction catalyzed by horseradish peroxidase (HRP) in the presence of H2O2 is mainly a defect-consuming step. These results were further supported by both UV-vis-NIR and Raman spectroscopy. Therefore, employing acid oxidation followed by HRP-catalyzed enzyme oxidation, shortened (< 300 nm in length) and NIR-fluorescent SWCNTs were produced. In contrast, when treated with myeloperoxidase (MPO), H2O2, and NaCl, the oxidized HiPco SWCNTs underwent complete oxidation (i.e. degradation). The shortened, NIR-fluorescent SWCNTs resulting from HRP-catalyzed oxidation of acid cut HiPco SWCNTs may find applications in cellular NIR imaging and drug delivery systems. PMID:23672715

  2. 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.

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

    E-print Network

    Straube, Arthur V.

    Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate of enzyme-catalyzed reactions which are confined inside a small subcellular compartment. This is achieved of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme

  5. Vanadium-Catalyzed C(sp3 )H Fluorination Reactions

    E-print Network

    Chen, Chuo

    S1 Vanadium-Catalyzed C(sp3 )­H Fluorination Reactions Ji-Bao Xia, Yuyong Ma, and Chuo Chen. Vanadium(III) Oxide (95%) was purchased from Strem Chemicals Inc. Fluorobenzene (99.5%) was purchased from procedure for the V2O3-catalyzed C(sp3 )­H fluorination reaction. To a 4 mL clear vial charged with vanadium

  6. Characterization of an enzyme which catalyzes isomerization and epimerization of D-erythrose 4-phosphate.

    PubMed

    Terada, T; Mukae, H; Ohashi, K; Hosomi, S; Mizoguchi, T; Uehara, K

    1985-04-15

    The enzyme which catalyzes the conversion of D-erythrose 4-phosphate to D-erythrulose 4-phosphate and D-threose 4-phosphate has been purified to homogeneity from a crude extract of beef liver. Analysis of the purified enzyme by Sephadex G-100 gel filtration and sodium dodecyl sulfate/polyacrylamide gel electrophoresis revealed it to be a dimer of relative molecular mass 43 000. From the gas chromatography/mas spectrometry analyses of the enzymatic reaction products, it appeared that about 90% of the total amount of tetrose 4-phosphate was present as D-erythrulose 4-phosphate after equilibration. The purified enzyme, which is tentatively called 'erythrose-4-phosphate isomerase' had no significant isomerase activities on D-glyceraldehyde 3-phosphate, D-ribose 5-phosphate, D-glucose 6-phosphate and D-fructose 6-phosphate, but a strong D-ribulose-5-phosphate 3-epimerase activity was co-purified with the erythrose-4-phosphate isomerase activity through every step in the isolation. Both the erythrose-4-phosphate isomerase and D-ribulose-5-phosphate 3-epimerase activities were inactivated at the same rate at the elevated temperature, and also inhibited to the same extent by various inhibitors. It is likely, that both activities are catalyzed by the single enzyme protein. PMID:3987693

  7. 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 76.4±4.6% 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

  8. 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

  9. 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

  10. 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

  11. 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.

  12. Diamine ligands in copper-catalyzed reactions

    E-print Network

    Surry, David S.

    The utility of copper-mediated cross-coupling reactions has been significantly increased by the development of mild reaction conditions and the ability to employ catalytic amounts of copper. The use of diamine-based ligands ...

  13. 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.

  14. 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)

  15. 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.

  16. Diamine Ligands in Copper-Catalyzed Reactions

    PubMed Central

    Surry, David S.

    2012-01-01

    The utility of copper-mediated cross-coupling reactions has been significantly increased by the development of mild reaction conditions and the ability to employ catalytic amounts of copper. The use of diamine-based ligands has been important in these advances and in this review we discuss these systems, including the choice of reaction conditions and applications in the synthesis of pharmaceuticals, natural products and designed materials. PMID:22384310

  17. 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

  18. 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,…

  19. 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

  20. 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.

  1. Modeling the enzyme kinetic reaction.

    PubMed

    Atangana, Abdon

    2015-09-01

    The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem. PMID:25930963

  2. 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.

  3. 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.

  4. Palladium-catalyzed reaction of allyl halides with a-diazocarbonyl Shufeng Chen and Jianbo Wang*

    E-print Network

    Wang, Jianbo

    Palladium-catalyzed reaction of allyl halides with a-diazocarbonyl compoundsw Shufeng Chen-Allylic palladium complexes are important intermediates in palladium-catalyzed reactions.1 The p-allylic palladium,3-dicarbonyl compounds.2 In connection to our recent interest in the palladium-catalyzed reaction of diazo

  5. 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 ?-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

  6. Removal of benzene from wastewater via Fenton pre-treatment followed by enzyme catalyzed polymerization.

    PubMed

    Saha, Beeta; Taylor, K E; Bewtra, J K; Biswas, N

    2011-01-01

    This study investigated the feasibility of a two-step process for the removal of benzene from buffered synthetic wastewater. Benzene is outside the scope of enzymatic removal. In order to remove it from wastewater using enzyme, its pretreatment by modified Fenton reaction was employed to generate the corresponding phenolic compounds. In the first phase, the optimum pH, H2O2 and Fe2+ concentrations and reaction time for the Fenton reaction were determined to maximize the conversion of benzene to phenolic compounds without causing significant mineralization. The pretreatment process was followed by oxidative polymerization of the phenolic compounds catalyzed by a laccase from Trametes villosa. Factors of interest for the three-hour enzymatic treatment were pH and laccase concentration. Under optimum Fenton reaction conditions, 80% conversion of the initial benzene concentration was achieved, giving a mixture containing oxidative dimerization product (biphenyl) and hydroxylation products (phenol, catechol, resorcinol, benzoquinone and hydroquinone). Enzymatic removal of biphenyl and benzoquinone was not possible but 2.5 U/mL laccase was successful in removal of the rest of the phenolic PMID:21866766

  7. Gold-catalyzed cyclopropanation reactions using a carbenoid precursor toolbox.

    PubMed

    Qian, Deyun; Zhang, Junliang

    2015-02-01

    Homogeneous gold-catalyzed cyclopropanation has emerged as a powerful method in organic synthesis due to its rich chemistry and fascinating reactivity. This thriving strategy is remarkable for its mild conditions, good selectivity, and high efficiency, which provides complementarity and orthogonality to traditional metal-catalyzed cyclopropanation. This review summarizes recent advances in gold-catalyzed cyclopropanation divided by the type of carbenoid precursors. Besides the commonly used diazo compounds, current approaches enable readily available enynes, propargyl esters, cyclopropenes, cycloheptatrienes, alkynes, and sulfonium ylides as safer surrogates in the realm of gold carbenoid chemistry. Meanwhile, these reactions allow for the rapid building of molecular complexity including synthetically useful and intricate cyclic, heterocyclic, and polycyclic skeletons. The combination of the new reactivity of gold complexes with their capability to catalyze cyclopropanations may lead to myriad opportunities for the design of new reactions. Furthermore, the synthetic utilities of such superior methods have also been illustrated by the total syntheses of selected natural and biologically interesting products and the asymmetric formation of challenging target molecules. PMID:25522173

  8. 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.

  9. Enzyme-catalyzed O2 removal system for electrochemical analysis under ambient air: application in an amperometric nitrate biosensor.

    PubMed

    Plumeré, Nicolas; Henig, Jörg; Campbell, Wilbur H

    2012-03-01

    Electroanalytical procedures are often subjected to oxygen interferences. However, achieving anaerobic conditions in field analytical chemistry is difficult. In this work, novel enzymatic systems were designed to maintain oxygen-free solutions in open, small volume electrochemical cells and implemented under field conditions. The oxygen removal system consists of an oxidase enzyme, an oxidase-specific substrate, and catalase for dismutation of hydrogen peroxide generated in the enzyme catalyzed oxygen removal reaction. Using cyclic voltammetry, three oxidase enzyme/substrate combinations with catalase were analyzed: glucose oxidase with glucose, galactose oxidase with galactose, and pyranose 2-oxidase with glucose. Each system completely removed oxygen for 1 h or more in unstirred open vessels. Reagents, catalysts, reaction intermediates, and products involved in the oxygen reduction reaction were not detected electrochemically. To evaluate the oxygen removal systems in a field sensing device, a model nitrate biosensor based on recombinant eukaryotic nitrate reductase was implemented in commercial screen-printed electrochemical cells with 200 ?L volumes. The products of the aldohexose oxidation catalyzed by glucose oxidase and galactose oxidase deactivate nitrate reductase and must be quenched for biosensor applications. For general application, the optimum catalyst is pyranose 2-oxidase since the oxidation product does not interfere with the biorecognition element. PMID:22263529

  10. Detection of the reaction intermediates catalyzed by a copper amine oxidase.

    PubMed

    Kataoka, Misumi; Oya, Hiroko; Tominaga, Ayuko; Otsu, Masayuki; Okajima, Toshihide; Tanizawa, Katsuyuki; Yamaguchi, Hiroshi

    2011-01-01

    To reveal the chemical changes and geometry changes of active-site residues that cooperate with a reaction is important for understanding the functional mechanism of proteins. Consecutive temporal analyses of enzyme structures have been performed during reactions to clarify structure-based reaction mechanisms. Phenylethylamine oxidase from Arthrobacter globiformis (AGAO) contains a copper ion and topaquinone (TPQ(ox)). The catalytic reaction of AGAO catalyzes oxidative deaminations of phenylethylamine and consists of reductive and oxidative half-reactions. In the reduction step, TPQ(ox) reacts with a phenylethylamine (PEA) substrate giving rise to a topasemiquinone (TPQ(sq)) formed Schiff-base and produces phenylacetaldehyde. To elucidate the mechanism of the reductive half-reaction, an attempt was made to trap the reaction intermediates in order to analyze their structures. The reaction proceeded within the crystals when AGAO crystals were soaked in a PEA solution and freeze-trapped in liquid nitrogen. The reaction stage of each crystal was confirmed by single-crystal microspectrometry, before X-ray diffraction measurements were made of four reaction intermediates. The structure at 15 min after the onset of the reaction was analyzed at atomic resolution, and it was shown that TPQ(ox) and some residues in the substrate channel were alternated via catalytic reductive half-reactions. PMID:21169693

  11. Diastereoselective Intermolecular Rhodium-Catalyzed [4 + 2 + 2] Carbocyclization Reactions: Computational and Experimental Evidence for

    E-print Network

    Baik, Mu-Hyun

    Diastereoselective Intermolecular Rhodium-Catalyzed [4 + 2 + 2] Carbocyclization Reactions@indiana.edu (M.-H.B.); paevans@indiana.edu (P.A.E.) Intermolecular rhodium-catalyzed [m + n + o] reactions of 1-directed synthesis.1 We recently reported a diastereoselective intermolecular rhodium-catalyzed [4 + 2 + 2

  12. 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…

  13. 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

  14. Criteria for identifying homogeneous transition metal cluster-catalyzed reactions

    SciTech Connect

    Laine, R.M.

    1980-01-01

    Four criteria were developed for distinguishing homogeneous cluster from mononuclear catalysis. A criterion based on reaction kinetics, which distinguishes catalysis by clusters from catalysis by mononuclear complexes in equilibrium with the clusters, is illustrated with the hydroformylation of 1-pentene by Ru/sub 3/(CO)/sub 12/ clusters in equilibrium with 3Ru(CO)/sub 5/ complexes in the presence of CO. A criterion based on selectivity is illustrated by the water gas shift and deuterium-exchange reactions catalyzed by ruthenium and rhodium carbonyl clusters in methanol and triethylamine; the scope of this criterion is limited to deuterium exchange reactions. A criterion based on mixed-metal catalysis, in which a mixed-metal system has higher catalytic activity than each transition metal cluster alone, is illustrated with hydroformylation of 1-pentene and the water gas shift reaction catalyzed by Ru/sub 3/(CO)/sub 12//Fe/sub 3/(CO)/sub 2/ and Rh/sub 6/(CO)/sub 16//Fe/sub 3/(CO)/sub 12/. A criterion based on changes in asymmetric induction is a special case of the selectivity criterion, in which specific starting metal complexes may produce either of two enantiomers. Catalysis by metal clusters is an analytical tool for modeling heterogeneous catalytic mechanisms.

  15. 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.

  16. Gold-catalyzed cyclization reactions of allenol and alkynol derivatives.

    PubMed

    Alcaide, Benito; Almendros, Pedro

    2014-03-18

    Although gold is chemically inert as a bulk metal, the landmark discovery that gold nanoparticles can be effective catalysts has opened up new and exciting research opportunities in the field. In recent years, there has been growth in the number of reactions catalyzed by gold complexes [gold(I) and gold(III)], usually as homogeneous catalysts, because they are soft Lewis acids. In addition, alkynes and allenes have interesting reactivities and selectivities, notably their ability to produce complex structures in very few steps. In this Account, we describe our work in gold catalysis with a focus on the formation of C-C and C-O bonds using allenes and alkynes as starting materials. Of these, oxa- and carbo-cyclizations are perhaps the best known and most frequently studied. We have divided those contributions into sections arranged according to the nature of the starting material (allene versus alkyne). Gold-catalyzed carbocyclizations in allenyl C2-linked indoles, allenyl-?-lactams, and allenyl sugars follow different mechanistic pathways. The cyclization of indole-tethered allenols results in the efficient synthesis of carbazole derivatives, for example. However, the compound produced from gold-catalyzed 9-endo carbocyclization of (aryloxy)allenyl-tethered 2-azetidinones is in noticeable contrast to the 5-exo hydroalkylation product that results from allenyl sugars. We have illustrated the unusual preference for the 4-exo-dig cyclization in allene chemistry, as well as the rare ?-hydride elimination reaction, in gold catalysis from readily available ?-allenols. We have also observed in ?-allenols that a (methoxymethyl)oxy protecting group not only masks a hydroxyl functionality but also exerts directing effects as a controlling unit in a gold-catalyzed regioselectivity reversal. Our recent work has also led to a combined experimental and computational study on regioselective gold-catalyzed synthetic routes to 1,3-oxazinan-2-ones (kinetically controlled products) and 1,3-oxazin-2-one derivatives (thermodynamically favored) from easily accessible allenic carbamates. In addition, we discuss the direct gold-catalyzed cycloketalization of alkynyldioxolanes, as well as aminoketalization of alkynyloxazolidines. We performed labeling studies and density functional calculations to gain insight into the mechanisms of the bis-heterocyclization reactions. We also describe the controlled gold-catalyzed reactions of primary and secondary propargylic hydroperoxides with a variety of nucleophiles including alcohols and phenols, allowing the direct synthesis of ?-functionalized ketones. Through computations and (18)O-labeling experiments, we discovered various aspects of the controlled reactivity of propargylic hydroperoxides with external nucleophiles under gold catalysis. The mechanism resembles a Meyer-Schuster rearrangement, but notably, the presence and geometry characteristics of the OOH functional group allow a new pathway to happen, which cannot apply to propargylic alcohols. PMID:24428670

  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. Understanding bistability in complex enzyme-driven reaction networks

    E-print Network

    Craciun, Gheorghe

    to variations in enzyme transcription activity (or even to enzyme malformation) when, in fact, those changesUnderstanding bistability in complex enzyme-driven reaction networks Gheorghe Craciun* , Yangzhong for enzyme catalysis of a single overall reaction. We present a theorem that distinguishes between those mass

  19. Critical Review Internal Friction in Enzyme Reactions Anna Rauscher1

    E-print Network

    Derényi, Imre

    Critical Review Internal Friction in Enzyme Reactions Anna Rauscher1 Imre Derenyi2,3 Laszlo Graf1 on the viscosity dependence of enzyme reactions. We also present speculations about the structural background and internal friction are outlined. Alternative concepts regarding the viscosity dependence of enzyme reactions

  20. 4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate

    E-print Network

    Herschlag, Dan

    the stereochemicalcourse of these reactions (for review see Knowles (1980), Eckstein (1985), and Frey (1989)). In addition4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate of Tetrahymena thermophila pre-rRNA catalyzes a guanosine-dependent endonuclease reaction that is analogous

  1. Carboxyphosphonoenolpyruvate phosphonomutase, a novel enzyme catalyzing C-P bond formation.

    PubMed Central

    Hidaka, T; Imai, S; Hara, O; Anzai, H; Murakami, T; Nagaoka, K; Seto, H

    1990-01-01

    An enzyme catalyzing the formation of an unusual C-P bond that is involved in the biosynthesis of the antibiotic bialaphos (BA) was isolated from the cell extract of a mutant (NP71) of Streptomyces hygroscopicus SF1293. This enzyme, carboxyphosphonoenolpyruvate (CPEP) phosphonomutase, was first identified as a protein lacking in a mutant (NP213) defective in one of the steps in the pathway to BA. The first 30 residues of the amino terminus of this protein were identical to those predicted by the nucleotide sequence of the gene that restored BA production to NP213. The substrate of the enzyme, a P-carboxylated derivative of phosphoenolpyruvate named CPEP, was also isolated from the broth filtrate of NP213 as a new biosynthetic intermediate of BA. CPEP phosphonomutase catalyzes the rearrangement of the carboxyphosphono group of CPEP to form the C-P bond of phosphinopyruvate. Images PMID:2160937

  2. Nickel-catalyzed coupling reactions and synthetic studies toward ent-dioxepandehydrothyrsiferol via an epoxide-opening cascade

    E-print Network

    Ng, Sze-Sze

    2008-01-01

    Nickel-Catalyzed Coupling Reactions. Nickel-catalyzed allene--aldehyde coupling and alkene--aldehyde coupling represent two methods of preparing allylic alcohols. Most asymmetric transition metal-catalyzed methods of ...

  3. 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.

  4. 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.

  5. Structure of a Novel Enzyme That Catalyzes Acyl Transfer to Alcohols in Aqueous Conditions

    SciTech Connect

    Mathews, I.; Soltis, M.; Saldajeno, M.; Ganshaw, G.; Sala, R.; Weyler, W.; Cervin, M.A.; Whited, G.; Bott, R.

    2009-06-03

    The unusual architecture of the enzyme (MsAcT) isolated from Mycobacterium smegmatis forms the mechanistic basis for favoring alcoholysis over hydrolysis in water. Unlike hydrolases that perform alcoholysis only under anhydrous conditions, MsAcT demonstrates alcoholysis in substantially aqueous media and, in the presence of hydrogen peroxide, has a perhydrolysis:hydrolysis ratio 50-fold greater than that of the best lipase tested. The crystal structures of the apoenzyme and an inhibitor-bound form have been determined to 1.5 {angstrom} resolution. MsAcT is an octamer in the asymmetric unit and forms a tightly associated aggregate in solution. Relative to other structurally similar monomers, MsAcT contains several insertions that contribute to the oligomerization and greatly restrict the shape of the active site, thereby limiting its accessibility. These properties create an environment by which MsAcT can catalyze transesterification reactions in an aqueous medium and suggests how a serine hydrolase can be engineered to be an efficient acyltransferase.

  6. 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

  7. Fundamentals of heterogeneously catalyzed reactions of environmental importance

    NASA Astrophysics Data System (ADS)

    Deshmukh, Subodh Shrinivas

    Reaction kinetics and spectroscopic characterization are valuable tools for understanding heterogeneously catalyzed chemical reactions. The objective of this work was to apply the tools of catalysis and reaction kinetics to understand the fundamentals of chemical surface phenomena for environmentally important reactions. This thesis presents our work in two areas of catalytic reactions for pollution abatement---"chlorofluorocarbon (CFC) treatment chemistry" and "sulfur-tolerant auto exhaust catalysts." The ozone depletion potential of CFCs has resulted in a great interest in the academic and industrial communities to find replacements for these chemicals. Hydrofluorocarbons (HFCs) are amongst the best "environmentally benign" candidates for CFC replacement. One selective pathway for the synthesis of HFCs is via the hydrodechlorination of CFCs. This route has the added benefit of destroying harmful CFC stockpiles and converting them into more useful chemicals. The work in Chapter 3 shows that parallel hydrogenation pathways starting from a common CF2 species can explain the formation of the products CH2F2 and CH4 for the hydrodechlorination of CF2Cl2 over Pd/AlF3. Transient kinetics experiments using C2H4 as a trapping agent for surface carbenes have provided evidence for the presence of CH2 species on the catalyst surface during this reaction. The absence of either coupling products or trapped products containing F suggests that the rate of hydrogenation of surface CF2 species is faster than that of surface CH2 species. Another important class of CFC reactions is oxide-catalyzed disproportionations to control the number and position of halogen atoms in the CFC/HFC molecule. Chapter 4 combines the use of reaction kinetics tools and spectroscopic characterization techniques to understand the adsorption and reaction of CF3CFCl 2 over gamma-Al2O3. The CF3CFCl 2 reaction over gamma-Al2O3 lead to a modification of the gamma-Al2O3 surface due to fluorination and the modified surface possessed sites that readily catalyzed the disproportionation of CF3CFCl2 at 353 K. FTIR spectroscopy was used to monitor the remarkable transformations taking place on the surface of Al 2O3. The identity and reactivity of surface fluoroacetate intermediates was determined and correlated to the changes in the oxide surface properties. One of the biggest challenges for automotive exhaust catalysts is the deactivation caused by sulfur present in the exhaust gas. There is enormous interest in developing new materials and catalysts that can destroy tailpipe pollutants in the presence of SO2. Work presented in Chapter 5 shows the promise of formulating new molecularly-mixed oxide materials with improved tolerance to sulfur than conventional CeO2. Characterization of the CeO2 and CeO2-ZrO2 mixed oxides after using different sulfur-treatment protocols showed that crystallite growth was the dominant phenomenon, which lead to activity loss in CeO2, on exposure to SO2. The incorporation of ZrO2 into the CeO2 lattice provided stability against sintering and helped maintain the activity of CeO2-ZrO2 over short times on stream.

  8. In situ Regeneration of NADH via Lipoamide Dehydrogenase-catalyzed Electron Transfer Reaction Evidenced by Spectroelectrochemistry

    SciTech Connect

    Tam, Tsz Kin; Chen, Baowei; Lei, Chenghong; Liu, Jun

    2012-08-01

    NAD/NADH is a coenzyme found in all living cells, carrying electrons from one reaction to another. We report on characterizations of in situ regeneration of NADH via lipoamide dehydrogenase (LD)-catalyzed electron transfer reaction to regenerate NADH using UV-vis spectroelectrochemistry. The Michaelis-Menten constant (Km) and maximum velocity (Vmax) of NADH regeneration were measured as 0.80 {+-} 0.15 mM and 1.91 {+-} 0.09 {micro}M s-1 in a 1-mm thin-layer spectroelectrochemical cell using gold gauze as the working electrode at the applied potential -0.75 V (vs. Ag/AgCl). The electrocatalytic reduction of the NAD system was further coupled with the enzymatic conversion of pyruvate to lactate by lactate dehydrogenase to examine the coenzymatic activity of the regenerated NADH. Although the reproducible electrocatalytic reduction of NAD into NADH is known to be difficult compared to the electrocatalytic oxidation of NADH, our spectroelectrochemical results indicate that the in situ regeneration of NADH via LD-catalyzed electron transfer reaction is fast and sustainable and can be potentially applied to many NAD/NADH-dependent enzyme systems.

  9. RNA size is a critical factor for U-containing substrate selectivity and permanent pseudouridylated product release during the RNA:?-synthase reaction catalyzed by box H/ACA sRNP enzyme at high temperature.

    PubMed

    Tillault, Anne-Sophie; Fourmann, Jean-Baptiste; Loegler, Christine; Blaud, Magali; Branlant, Christiane; Charpentier, Bruno

    2015-06-01

    The box H/ACA small ribonucleoprotein particles (H/ACA sRNPs) are RNP enzymes that isomerize uridines (U) into pseudouridines (?) in archaeal RNAs. The RNA component acts as a guide by forming base-pair interactions with the substrate RNA to specify the target nucleotide of the modification to the catalytic subunit Cbf5. Here, we have analyzed association of an H/ACA sRNP enzyme from the hyperthermophilic archaeon Pyrococcus abyssi with synthetic substrate RNAs of different length and with target nucleotide variants, and estimated their turnover at high temperature. In these conditions, we found that a short substrate, which length is restricted to the interaction with RNA guide sequence, has higher turnover rate. However, the longer substrate with additional 5' and 3' sequences non-complementary to the guide RNA is better discriminated by the U to ? conversion allowing the RNP enzyme to distinguish the modified product from the substrate. In addition, we identified that the conserved residue Y179 in the catalytic center of Cbf5 is crucial for substrate selectivity. PMID:25896443

  10. 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

  11. 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)

  12. 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

  13. Atmospheric Environment 40 (2006) 68636878 Acid-catalyzed reactions of hexanal on sulfuric acid particles

    E-print Network

    Elrod, Matthew J.

    2006-01-01

    Atmospheric Environment 40 (2006) 6863­6878 Acid-catalyzed reactions of hexanal on sulfuric acid are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds into acidic aerosols. In the present study, we use the aerodyne aerosol mass spectrometer (AMS) to probe

  14. Exploration Into Copper Catalyzed and Copper-less Click Reactions with Re(CO)3 Complexes

    E-print Network

    Collins, Gary S.

    Exploration Into Copper Catalyzed and Copper-less Click Reactions with Re(CO)3 Complexes Nicholas that combines a alkyne and an oxime to generate a isoxazole cycloaddtion product. Compared to the copper and then proceeding with the typical copper(I) catalyzed "click" reaction procedure, while the other approach involves

  15. 9422 Stratospheric ice catalyzes chlorine reactions 9428 Fusing silk and silica

    E-print Network

    McFadden, Geoff

    deteriorates with age CHEMISTRY Stratospheric ice catalyzes chlorine reactions To explain how ice crystals can9422 Stratospheric ice catalyzes chlorine reactions 9428 Fusing silk and silica 9482 Identifying of hydrochloric acid form a quasiliquid layer on the surface of stratospheric ice crystals. The quasiliquid layer

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

    PubMed

    Syrén, 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

  17. Plant phenylacetaldehyde synthase is a bifunctional homotetrameric enzyme that catalyzes phenylalanine decarboxylation and oxidation.

    PubMed

    Kaminaga, Yasuhisa; Schnepp, Jennifer; Peel, Greg; Kish, Christine M; Ben-Nissan, Gili; Weiss, David; Orlova, Irina; Lavie, Orly; Rhodes, David; Wood, Karl; Porterfield, D Marshall; Cooper, Arthur J L; Schloss, John V; Pichersky, Eran; Vainstein, Alexander; Dudareva, Natalia

    2006-08-18

    We have isolated and characterized Petunia hybrida cv. Mitchell phenylacetaldehyde synthase (PAAS), which catalyzes the formation of phenylacetaldehyde, a constituent of floral scent. PAAS is a cytosolic homotetrameric enzyme that belongs to group II pyridoxal 5'-phosphate-dependent amino-acid decarboxylases and shares extensive amino acid identity (approximately 65%) with plant L-tyrosine/3,4-dihydroxy-L-phenylalanine and L-tryptophan decarboxylases. It displays a strict specificity for phenylalanine with an apparent Km of 1.2 mM. PAAS is a bifunctional enzyme that catalyzes the unprecedented efficient coupling of phenylalanine decarboxylation to oxidation, generating phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in stoichiometric amounts. PMID:16766535

  18. 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

  19. Nickel-catalyzed reductive coupling reactions of 1,6-enynes and the total synthesis of (+)-acutiphycin

    E-print Network

    Moslin, Ryan Thomas McLeod

    2007-01-01

    Nickel-Catalyzed Reductive Coupling Reactions of Aldehydes and Chiral 1,6-Enynes. A study of nickel-catalyzed reductive coupling reactions of aldehydes and chiral 1,6-enynes has provided evidence for stereospecific ligand ...

  20. Dynamic kinetic resolution of secondary alcohols combining enzyme-catalyzed transesterification and zeolite-catalyzed racemization.

    PubMed

    Zhu, Yongzhong; Fow, Kam-Loon; Chuah, Gaik-Khuan; Jaenicke, Stephan

    2007-01-01

    Hydrophobic zeolite beta containing low concentrations of Zr or Al was found to be a good catalyst for the racemization of 1-phenylethanol. The formation of styrene as a side product could be minimized by reducing the metal concentration in the zeolite beta. Combined with an immobilized lipase from Candida antarctica, the dynamic kinetic resolution of 1-phenylethanol to the (R)-phenylethylester can be achieved with high yield and selectivity. The reaction was best conducted in toluene as solvent at 60 degrees C, with higher temperatures leading to a loss in the enantioselectivity of the formed ester. By using high-molecular-weight acyl-transfer reagents, such as vinyl butyrate or vinyl octanoate, a high enantiomeric excess of the product esters of 92 and 98 %, respectively, could be achieved. This is attributed to a steric effect: the bulky ester is less able to enter the pore space of the zeolite catalyst where the active sites for racemization are localized. Close to 100 % conversion of the alcohol was achieved within 2 h. If the more common acyl donor, isopropenyl acetate, was used, the enantiomeric excess (ee) of the formed ester was only 67 %, and the reaction was considerably slower. PMID:17004277

  1. 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 60°C. 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

  2. Triazole-Based Monophosphine Ligands for Palladium-Catalyzed Cross-Coupling Reactions of Aryl Chlorides

    E-print Network

    Zhang, Xumu

    reactions.6 More recently, Beller and co-workers reported the synthesis of ligand 4 for the couplingTriazole-Based Monophosphine Ligands for Palladium-Catalyzed Cross-Coupling Reactions of Aryl excellent yields in the amination reactions and Suzuki-Miyaura coupling reactions of unactivated aryl

  3. Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction

    E-print Network

    Cao, Yang

    1 Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction Yang Cao a) Dept into a product is a common reaction motif in cellular chemical systems. In the three reactions that comprise constituents than to produce a product molecule. This condition makes the reaction set mathematically "stiff

  4. Palladium-Catalyzed Coupling Reactions of Biphenylene with Olefins, Arylboronic Acids, and Ketones Involving

    E-print Network

    Jones, William D.

    Palladium-Catalyzed Coupling Reactions of Biphenylene with Olefins, Arylboronic Acids, and Ketones the catalytic C-C bond activation and functionalization of biphenylene under nickel, palladium, or platinum, palladium-catalyzed cross-coupling of biphenylene with olefins, arylboronic acids, and ketones occurred

  5. Gold(I)-catalyzed enantioselective [32] and [33] cycloaddition reactions of propargyl acetals/ketals

    E-print Network

    Toste, Dean

    Gold(I)-catalyzed enantioselective [3þ2] and [3þ3] cycloaddition reactions of propargyl acetals May 2015 Keywords: Gold Homogeneous catalysis Enantioselective catalysis Cycloaddition Propargyl acetals/ketals a b s t r a c t An asymmetric gold(I)-catalyzed [3þ2] cycloaddition of propargyl acetals

  6. Advances in the Stille reaction and new methods for continuous flow Pd-catalyzed C-N bond forming reactions

    E-print Network

    Naber, John R. (John Robert)

    2010-01-01

    Chapter 1: A highly active catalyst system based upon a biaryl monophosphine ligand, XPhos, for the palladium-catalyzed Stille reaction has been developed. This method allows for the coupling of aryl chlorides with a range ...

  7. Catalysis of a new ribose carbon–insertion reaction by the molybdenum cofactor biosynthetic enzyme MoaA

    PubMed Central

    Mehta, Angad P.; Hanes, Jeremiah W.; Abdelwahed, Sameh H.; Hilmey, David G.; Hänzelmann, Petra; Begley, Tadhg P.

    2013-01-01

    MoaA, a radical S-adenosylmethionine (SAM) enzyme, catalyzes the first step in molybdopterin biosynthesis. This reaction involves a complex rearrangement in which C8 of guanosine triphosphtate is inserted between the C2? and the C3? carbons of the ribose. This study identifies the site of initial hydrogen atom abstraction by the adenosyl radical and advances a mechanistic proposal for this unprecedented reaction. PMID:23286307

  8. STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes.

    PubMed

    Balcão, V M; Malcata, F X

    1993-12-01

    This paper describes a computational algorithm (STADEERS--STAtistical Design of Experiments in Enzyme ReactorS) for the statistical design of biochemical engineering experiments. The type of experiment that qualifies for this package involves a batch reaction catalyzed by a soluble enzyme where the activity of the enzyme decays with time. Assuming that both the catalytic action and the deactivation of the enzyme obey known rate expressions, the present code is helpful in the process of obtaining estimates of the kinetic parameters by providing as output the times at which samples should be withdrawn from the reacting mixture. Starting D-optimal design is used as a basis for the statistical approach. This BASIC code is a powerful tool when fitting a rate expression to data because it increases the effectiveness of experimentation by helping the biochemical kineticist obtain data points with the largest possible informational content. PMID:8143147

  9. 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...

  10. Development of novel transition metal-catalyzed cross-coupling reactions and applications thereof

    E-print Network

    Teverovskiy, Georgiy

    2013-01-01

    Chapter 1 The first example of Pd(0)/(II) catalyzed fluorination of aryl bromides is reported herein. Based on these data, an analogous method was developed for the fluorination of aryl triflates. The reaction proceeds ...

  11. Mechanistic studies on metal-catalyzed carbon-nitrogen bond forming reactions

    E-print Network

    Strieter, Eric R

    2005-01-01

    Mechanistic studies on copper and palladium-catalyzed C-N bond forming reactions are described. To understand the mechanistic details of these processes, several principles of physical organic chemistry have been employed. ...

  12. 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

  13. Efficient Pd-Catalyzed Amination Reactions for Heterocycle Functionalization

    E-print Network

    Henderson, Jaclyn L.

    The Pd-catalyzed amination of unprotected benzo-fused heterocycles is reported, which allows for greater flexibility and efficiency in the modification of this important class of molecules. The generality of these simple ...

  14. Which one is faster? A kinetic investigation of Pd and Ni catalyzed Negishi-type oxidative coupling reactions.

    PubMed

    Xin, Jie; Zhang, Guanghui; Deng, Yi; Zhang, Heng; Lei, Aiwen

    2015-11-18

    The difference between Pd and Ni has been investigated based on the Negishi-type oxidative coupling reactions in which reductive elimination was proved to be the rate determining step. Although DFT calculations illustrate that the Pd catalyzed reaction should be faster than the Ni catalyzed reaction under these conditions, kinetic experiments indicate that the reaction rate of Pd and Ni is dependent on the concentration of the catalyst precursor. The Pd catalyzed reaction is faster than the Ni catalyzed reaction only when the precursor concentration is as low as 1 × 10(-7) M. PMID:26536236

  15. 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

  16. 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

  17. Identification of critical parameters in liquid enzyme-catalyzed biodiesel production.

    PubMed

    Nordblad, Mathias; Silva, Vanessa T L; Nielsen, Per Munk; Woodley, John M

    2014-12-01

    Callera™ Trans L, a liquid formulation of Thermomyces lanuginosus lipase, has recently shown great promise as a cost-efficient catalyst for methanolysis of triglyceride substrates, specifically in the BioFAME process. However, identifying the right combination of temperature and concentrations of catalyst, water and methanol to realize the full potential of the reaction system has remained a challenge. This study presents an investigation of the impact of temperature, enzyme and water concentration on the reaction, as well as the effect of methanol feed rate for the conversion of rapeseed oil in a fed-batch reaction system. It was observed that the reaction can be divided into two distinct parts. The first part of the reaction, during which primarily tri- and diglycerides are converted, proceeded at a high rate and thus required a high rate of methanol supply. The second part of the reaction, where the remaining di- and monoglycerides are converted, proceeded at a much lower rate. Consequently, it is necessary to reduce the methanol feed rate during the latter part of the reaction to avoid inhibition or even inactivation of the enzyme. Since the second part of the reaction occupied most of the 24-h reaction time, it was concluded that this is the part of the process where further development efforts should be targeted. This point was demonstrated by partially substituting the catalyst with a lipase with a different specificity, which enhanced the performance during the second phase of the reaction. PMID:24902824

  18. 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 Å 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

  19. 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

  20. Role of a Guanidinium Cation-Phosphodianion Pair in Stabilizing the Vinyl Carbanion Intermediate of Orotidine 5'-Phosphate Decarboxylase-Catalyzed Reactions.†

    PubMed Central

    Goryanova, Bogdana; Goldman, Lawrence M.; Amyes, Tina L.; Gerlt, John A; Richard, John P.

    2013-01-01

    The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae (OMPDC) catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(?-d-erythrofuranosyl)orotic acid and 1-(?-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, while the 7.2 kcal/mol side-chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex while the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation. PMID:24053466

  1. Recent advances in transition metal-catalyzed N -atom transfer reactions of azides

    PubMed Central

    Driver, Tom G.

    2011-01-01

    Transition metal-catalyzed N-atom transfer reactions of azides provide efficient ways to construct new carbon–nitrogen and sulfur–nitrogen bonds. These reactions are inherently green: no additive besides catalyst is needed to form the nitrenoid reactive intermediate, and the by-product of the reaction is environmentally benign N2 gas. As such, azides can be useful precursors for transition metal-catalyzed N-atom transfer to sulfides, olefins and C–H bonds. These methods offer competitive selectivities and comparable substrate scope as alternative processes to generate metal nitrenoids. PMID:20617243

  2. A practical guide to modelling enzyme-catalysed reactions

    PubMed Central

    Lonsdale, Richard; Harvey, Jeremy N.; Mulholland, Adrian J.

    2012-01-01

    Molecular modelling and simulation methods are increasingly at the forefront of elucidating mechanisms of enzyme-catalysed reactions, and shedding light on the determinants of specificity and efficiency of catalysis. These methods have the potential to assist in drug discovery and the design of novel protein catalysts. This Tutorial Review highlights some of the most widely used modelling methods and some successful applications. Modelling protocols commonly applied in studying enzyme-catalysed reactions are outlined here, and some practical implications are considered, with cytochrome P450 enzymes used as a specific example. PMID:22278388

  3. Odorant Metabolism Catalyzed by Olfactory Mucosal Enzymes Influences Peripheral Olfactory Responses in Rats

    PubMed Central

    Thiebaud, Nicolas; Veloso Da Silva, Stéphanie; Jakob, Ingrid; Sicard, Gilles; Chevalier, Joëlle; Ménétrier, Franck; Berdeaux, Olivier; Artur, Yves; Heydel, Jean-Marie; Le Bon, Anne-Marie

    2013-01-01

    A large set of xenobiotic-metabolizing enzymes (XMEs), such as the cytochrome P450 monooxygenases (CYPs), esterases and transferases, are highly expressed in mammalian olfactory mucosa (OM). These enzymes are known to catalyze the biotransformation of exogenous compounds to facilitate elimination. However, the functions of these enzymes in the olfactory epithelium are not clearly understood. In addition to protecting against inhaled toxic compounds, these enzymes could also metabolize odorant molecules, and thus modify their stimulating properties or inactivate them. In the present study, we investigated the in vitro biotransformation of odorant molecules in the rat OM and assessed the impact of this metabolism on peripheral olfactory responses. Rat OM was found to efficiently metabolize quinoline, coumarin and isoamyl acetate. Quinoline and coumarin are metabolized by CYPs whereas isoamyl acetate is hydrolyzed by carboxylesterases. Electro-olfactogram (EOG) recordings revealed that the hydroxylated metabolites derived from these odorants elicited lower olfactory response amplitudes than the parent molecules. We also observed that glucurono-conjugated derivatives induced no olfactory signal. Furthermore, we demonstrated that the local application of a CYP inhibitor on rat olfactory epithelium increased EOG responses elicited by quinoline and coumarin. Similarly, the application of a carboxylesterase inhibitor increased the EOG response elicited by isoamyl acetate. This increase in EOG amplitude provoked by XME inhibitors is likely due to enhanced olfactory sensory neuron activation in response to odorant accumulation. Taken together, these findings strongly suggest that biotransformation of odorant molecules by enzymes localized to the olfactory mucosa may change the odorant’s stimulating properties and may facilitate the clearance of odorants to avoid receptor saturation. PMID:23555703

  4. 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)

  5. DOI: 10.1002/adsc.200800249 Sequential Copper(I)-Catalyzed Reaction of Amines with

    E-print Network

    Wang, Jianbo

    - lectivity are the major concerns in these metal-cata- lyzed reactions, an emerging area of research/Pauson­Khand reaction,[3] Pd-catalyzed aryl alkylation/cyanation re- action,[4] have been developed. CÀN bond formation 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 2359 FULL PAPERS #12;Results and Discussion o

  6. 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

  7. Cu-catalyzed transannulation reaction of pyridotriazoles: general access to fused polycyclic indolizines.

    PubMed

    Shi, Yi; Gevorgyan, Vladimir

    2015-12-14

    An efficient intramolecular transannulation reaction of pyridotriazoles using internal alkynes en route to various fused polycyclic indolizines has been developed. For the first time it is shown that in addition to the well-established Rh- or Cu-catalyzed carbene mechanism, the transannulation reaction could also follow a Lewis acid-mediated electrophilic pathway. PMID:26456098

  8. 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

  9. Horseradish Peroxidase-Mediated, Iodide-Catalyzed Cascade Reaction for Plasmonic Immunoassays.

    PubMed

    Xianyu, Yunlei; Chen, Yiping; Jiang, Xingyu

    2015-11-01

    This report outlines an enzymatic cascade reaction for signal transduction and amplification for plasmonic immunoassays by using horseradish peroxidase (HRP)-mediated aggregation of gold nanoparticles (AuNPs). HRP-catalyzed oxidation of iodide and iodide-catalyzed oxidation of cysteine is employed to modulate the plasmonic signals of AuNPs. It agrees well with the current immunoassay platforms and allows naked-eye readout with enhanced sensitivity, which holds great promise for applications in resource-constrained settings. PMID:26460152

  10. The Mechanism of the Rhodium(I)-Catalyzed [2 + 2 + 1] Carbocyclization Reaction of Dienes and CO: A

    E-print Network

    Baik, Mu-Hyun

    The Mechanism of the Rhodium(I)-Catalyzed [2 + 2 + 1] Carbocyclization Reaction of Dienes and CO-mail: mbaik@indiana.edu Abstract: The rhodium(I) catalyzed [2 + 2 + 1] carbocyclization of tethered diene rhodium(I)-catalyzed [2 + 2 + 1] carbocyclization. One of the apparent requirements for the [2 + 2 + 1

  11. 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 (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex. PMID:26002730

  12. 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 ?-bond activation and an 8?-insertion of vinylcyclopropane and tropone, respectively. Similarly, the cycloaddition of 3-azetidinones and 3-oxetanones also requires Ni-catalyzed C-C ?-bond activation to form N- and O-containing heterocycles. PMID:26200651

  13. An NADPH and FAD dependent enzyme catalyzes hydroxylation of flavonoids in position 8.

    PubMed

    Halbwirth, Heidrun; Stich, Karl

    2006-06-01

    Yellow flavonols contribute to flower pigmentation in Asteraceae. In contrast to common flavonols, they show additional hydroxyl groups in position 6 and/or 8 of the aromatic A-ring in addition to the basic 5,7-hydroxylation pattern. An enzyme introducing a hydroxyl group in position 8 of flavonols and flavones was demonstrated for the first time with enzyme preparations from petals of Chrysanthemum segetum. Flavanones, dihydroflavonols and glucosylated flavonols and flavones were not accepted as substrates. The enzyme was localized in the microsomal fraction and uses NADPH and FAD as cofactors. Experiments with carbon monoxide/blue light and with antibodies specific for cytochrome P450 reductase did not indicate the involvement of a classical cytochrome P450 dependent monooxygenase in the reaction. Thus, the flavonoid 8-hydroxylase represents a novel type of hydroxylating enzyme in the flavonoid pathway. Apart from flavonoid 8-hydroxylase activity, the presence of all enzymes involved in the formation of flavonoid 7-O-glucosides in C. segetum was demonstrated. The pathway leading to 8-hydroxyflavonoids in C. segetum has been derived from enzyme activities and substrate specificities observed. PMID:16678869

  14. 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.

  15. 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

  16. 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 40°C 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

  17. 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.

  18. Phosphine-catalyzed domino reactions: a route to functionalized bicyclic skeletons.

    PubMed

    Li, Erqing; Huang, You

    2014-03-17

    A novel strategy that involves phosphine-catalyzed sequential [2+3] and [3+2] annulation reactions was developed. In this domino reaction, ?-substituted allenoates were used as novel C4 synthons, and the bicyclic cyclopenta[b]dihydrofuran derivatives were produced in good to excellent diastereoselectivities and yields under mild conditions. Furthermore, preliminary studies on an asymmetric variant of this reaction proceeded with moderate enantioselectivity. PMID:24523030

  19. 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.)

  20. Understanding Lignin-Degrading Reactions of Ligninolytic Enzymes: Binding Affinity and Interactional Profile

    PubMed Central

    Chen, Ming; Zeng, Guangming; Tan, Zhongyang; Jiang, Min; Li, Hui; Liu, Lifeng; Zhu, Yi; Yu, Zhen; Wei, Zhen; Liu, Yuanyuan; Xie, Gengxin

    2011-01-01

    Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity. PMID:21980516

  1. Molybdopterin Biosynthesis: Trapping of Intermediates for the MoaA-Catalyzed Reaction Using 2?-DeoxyGTP and 2?-ChloroGTP as Substrate Analogues.

    PubMed Central

    2015-01-01

    MoaA is a radical S-adenosylmethionine (AdoMet) enzyme that catalyzes a complex rearrangement of guanosine-5'-triphosphate (GTP) in the first step of molybdopterin biosynthesis. In this paper, we provide additional characterization of the MoaA reaction product, describe the use of 2?-chloroGTP to trap the GTP C3? radical, generated by hydrogen atom transfer to the 5?-deoxyadenosyl radical, and the use of 2?-deoxyGTP to block a late step in the reaction sequence. These probes, coupled with the previously reported trapping of an intermediate in which C3? of the ribose is linked to C8 of the purine, allow us to propose a plausible mechanism for the MoaA-catalyzed reaction. PMID:24955657

  2. 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

  3. Efficient chromium(II)-catalyzed cross-coupling reactions between Csp2 centers.

    PubMed

    Steib, Andreas K; Kuzmina, Olesya M; Fernandez, Sarah; Flubacher, Dietmar; Knochel, Paul

    2013-10-16

    Low-toxicity chromium(II) chloride catalyzes at 25 °C within minutes the coupling reactions of various (hetero)arylmagnesium reagents with N-heterocyclic halides, aromatic halogenated ketones or imines, and alkenyl iodides. Remarkably, much lower amounts of homo-coupling side products are obtained compared to related iron, cobalt, or manganese cross-couplings. PMID:24053764

  4. Substituent Effects of Ligands on Asymmetric Induction in a Prototypical Palladium-Catalyzed Allylation Reaction: Making

    E-print Network

    RajanBabu, T. V. "Babu"

    Substituent Effects of Ligands on Asymmetric Induction in a Prototypical Palladium in the palladium-catalyzed asymmetric allylation reaction between 1,3-diphe- nylprop-2-en-1-yl acetate associated with studying the catalytically relevant intermediates.6 In contrast, for the palladium

  5. 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.

  6. 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

  7. The effect of Mg/2+/ and Ca/2+/ on urea-catalyzed phosphorylation reactions

    NASA Technical Reports Server (NTRS)

    Handschuk, G. J.; Lohrmann, R.; Orgel, L. E.

    1973-01-01

    The effect of Mg(2+) and Ca(2+) on phosphorylation reactions catalyzed by urea is investigated, showing that Mg(2+) improves markedly the yield of products containing pyrophosphate bonds. Yields of up to 25% of uridine diphosphate can be obtained with struvite at temperatures as low as 65 C.

  8. Examples of acid-catalyzed mineral dissolution reactions resulting in pH

    E-print Network

    Peters, Catherine A.

    Examples of acid-catalyzed mineral dissolution reactions resulting in pH buffering: The goal, PHREEQC was used to determine pH conditions of the formation over 100 years with injected CO2 in the table below along with the corresponding formation water ionic strength and pH after 100 years. Each

  9. Stereochemistry and Mechanism of Reactions Catalyzed by Tryptophan Synthetase and Its p2 Subunit*

    E-print Network

    Tsai, Ming-Daw

    The synthesis of tryptophan from serine and indole or indoleglycerol phosphate catalyzed by native tryp- tophan no isotope effect was observed in the protonation of C, of tryptophan syn- thesized from indole and serine products. In this paper we report results which clarify various ster- eochemical aspects of these reactions

  10. 2,3-Migration in Rh(II)-Catalyzed Reactions of -Trifluoroacetamido

    E-print Network

    Wang, Jianbo

    2,3-Migration in Rh(II)-Catalyzed Reactions of -Trifluoroacetamido r-Diazocarbonyl Compounds Feng -hydroxy-r-diazo carbonyl compounds with trifluoroacetimidoyl chloride in the presence of DBU. Rh group, 1,2-vinyl, and 1,2-acetylenyl migrations are also observed.2-4 The Rh2(OAc)4-mediated 1,2-acetoxy

  11. 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 10¹?-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 100°C. 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

  12. Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic acid decarboxylase.

    PubMed

    Lin, Fengming; Ferguson, Kyle L; Boyer, David R; Lin, Xiaoxia Nina; Marsh, E Neil G

    2015-04-17

    The decarboxylation of antimicrobial aromatic acids such as phenylacrylic acid (cinnamic acid) and ferulic acid by yeast requires two enzymes described as phenylacrylic acid decarboxylase (PAD1) and ferulic acid decarboxylase (FDC). These enzymes are of interest for various biotechnological applications, such as the production of chemical feedstocks from lignin under mild conditions. However, the specific role of each protein in catalyzing the decarboxylation reaction remains unknown. To examine this, we have overexpressed and purified both PAD1 and FDC from E. coli. We demonstrate that PAD1 is a flavin mononucleotide (FMN)-containing protein. However, it does not function as a decarboxylase. Rather, PAD1 catalyzes the formation of a novel, diffusible cofactor required by FDC for decarboxylase activity. Coexpression of FDC and PAD1 results in the production of FDC with high levels cofactor bound. Holo-FDC catalyzes the decarboxylation of phenylacrylic acid, coumaric acid and ferulic acid with apparent kcat ranging from 1.4-4.6 s(-1). The UV-visible and mass spectra of the cofactor indicate that it appears to be a novel, modified form of reduced FMN; however, its instability precluded determination of its structure. The E. coli enzymes UbiX and UbiD are related by sequence to PAD1 and FDC respectively and are involved in the decarboxylation of 4-hydroxy-3-octaprenylbenzoic acid, an intermediate in ubiquinone biosynthesis. We found that endogenous UbiX can also activate FDC. This implies that the same cofactor is required for decarboxylation of 4-hydroxy-3-polyprenylbenzoic acid by UbiD and suggests a wider role for this cofactor in metabolism. PMID:25647642

  13. 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.

  14. 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.

  15. Rh-Catalyzed Reactions of 3-Diazoindolin-2-imines: Synthesis of Pyridoindoles and Tetrahydrofuropyrroloindoles.

    PubMed

    Wang, Chen; Zhang, Haojie; Lang, Bo; Ren, Anni; Lu, Ping; Wang, Yanguang

    2015-09-18

    The rhodium-catalyzed reactions of 3-diazoindolin-2-imines with furans and dihydrofuran furnished 9H-pyrido[2,3-b]indoles and tetrahydrofuro[3',2':4,5]pyrrolo[2,3-b]indoles, respectively. A cascade reaction mechanism involving an ?-imino rhodium carbene intermediate is proposed. The starting materials are readily available, and the procedure is facile and efficient. PMID:26349028

  16. Development of transitional metal-catalyzed reactions for organic synthesis

    E-print Network

    Rainka, Matthew P. (Matthew Paul)

    2005-01-01

    Chapter 1. A general catalyst system for the synthesis of tetra-ortho-substituted biaryls via the Suzuki-Miyaura cross-coupling reaction is described. It was found that the most efficient catalyst system is based on a ...

  17. Extension and application of the "enzyme test bench" for oxygen consuming enzyme reactions.

    PubMed

    Rachinskiy, Kirill; Kunze, Martin; Graf, Careen; Schultze, Hergen; Boy, Matthias; Büchs, Jochen

    2014-02-01

    Within industrial process development, powerful screening techniques are required to select the optimal biocatalyst regarding such process characteristics as cost effectiveness, turnover number or space time yield. Conventional measurement of the initial enzyme activity, which is the established high throughput screening technique, disregards the long-term stability of an enzyme. A new model based technique called "enzyme test bench" was recently presented before by our group which addresses this issue. It combines the high throughput screening approach with an extensive enzyme characterization, focusing especially on the long-term stability. The technique is based on modeling enzyme activation and deactivation as temperature dependent reactions in accordance with the Arrhenius law. Controlling these reactions by tailor made temperature profiles, the slow long-term deactivation effects are accelerated and characterizing models are parameterized. Thus, the process properties of an enzyme can be predicted and included into the screening procedure. Moreover, the optimum process temperature as function of the envisaged operation time can be found by these means. In this work, the technique is extended to the important class of oxygen consuming reactions. For this aim, a suitable assay and a defined oxygen supply were established. This extended technique was applied to characterize and to optimize a complex, multi-stage laccase-mediator system (LMS). For the variation and optimization of the enzyme to mediator to substrate ratio, experiments in microtiter plates were performed. Predictions from this high throughput characterization were compared to long-term experiments in a RAMOS device (Respiration Activity Monitoring System), a technique for on-line monitoring of the oxygen transfer rate in shake flasks. Within the limits of the model validity, the enzyme test bench predictions are in good agreement with the long-term experiments. PMID:23928872

  18. 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

  19. Big-Bang Nucleosynthesis Reactions Catalyzed by a Long-Lived Negatively Charged Leptonic Particle

    E-print Network

    Masayasu Kamimura; Yasushi Kino; Emiko Hiyama

    2009-06-13

    An accurate quantum three-body calculation is performed for the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a long-lived negatively-charged, massive leptonic particle (called X^-) such as the supersymmetric (SUSY) particle stau. The reactions studied here includes, i) 4He-transfer reactions such as (4He X)+d --> 6Li+X, ii) radiative capture reactions such as (7Be X)+ p --> (8B X) + gamma, iii) three-body breakup reactions such as (7Li X)+ p --> 4He+4He+X, iv) charge-exchange reactions such as (p X)+4He -->(4He X) +p, and v) neutron induced reactions such as (8Be X)+ n -->9Be+X, where (A X) denotes a Coulombic bound state of a nucleus A and X^-. In recent papers it has been claimed that some of the catalyzed BBN reactions have significantly large cross sections so as to markedly change the abundances of some elements, not only giving a solution to the 6Li-7Li problem (calculated underproduction of 6Li by a factor of 1000 and overproduction of 7Li+7Be by a factor of nearly 3) but also imposing strong restrictions on the lifetime and the primordial abundance of X^-. However, most of the calculations of these reaction cross sections in the literature were performed assuming too naive models or approximations that are unsuitable for the complicated low-energy nuclear reactions. We use a high-accuracy few-body calculational method developed by the authors, and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

  20. Chromium-Catalyzed Homoaldol Equivalent Reaction, Indium-Mediated Cycloisomerization, and Palladium-Catalyzed Cross-Coupling Reaction 

    E-print Network

    Kang, Jun

    2011-10-21

    The homoaldol reaction is one of the most powerful methods for the construction of C–C bonds as well as 1,4-oxygenated compounds yet this reaction remains in challenging tasks due to the instability of homoenolates which spontaneously cyclize...

  1. 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

  2. Reaction dynamics of ATP hydrolysis catalyzed by P-glycoprotein.

    PubMed

    Scian, Michele; Acchione, Mauro; Li, Mavis; Atkins, William M

    2014-02-18

    P-glycoprotein (P-gp) is a member of the ABC transporter family that confers drug resistance to many tumors by catalyzing their efflux, and it is a major component of drug-drug interactions. P-gp couples drug efflux with ATP hydrolysis by coordinating conformational changes in the drug binding sites with the hydrolysis of ATP and release of ADP. To understand the relative rates of the chemical step for hydrolysis and the conformational changes that follow it, we exploited isotope exchange methods to determine the extent to which the ATP hydrolysis step is reversible. With ?(18)O4-labeled ATP, no positional isotope exchange is detectable at the bridging ?-phosphorus-O-?-phosphorus bond. Furthermore, the phosphate derived from hydrolysis includes a constant ratio of three (18)O/two (18)O/one (18)O that reflects the isotopic composition of the starting ATP in multiple experiments. Thus, H2O-exchange with HPO4(2-) (Pi) was negligible, suggesting that a [P-gp·ADP·Pi] is not long-lived. This further demonstrates that the hydrolysis is essentially irreversible in the active site. These mechanistic details of ATP hydrolysis are consistent with a very fast conformational change immediately following, or concomitant with, hydrolysis of the ?-phosphate linkage that ensures a high commitment to catalysis in both drug-free and drug-bound states. PMID:24506763

  3. 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 Å-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

  4. 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

  5. Cholesterol glucosylation is catalyzed by transglucosylation reaction of ?-glucosidase 1.

    PubMed

    Akiyama, Hisako; Kobayashi, Susumu; Hirabayashi, Yoshio; Murakami-Murofushi, Kimiko

    2013-11-29

    Cholesteryl glucoside (?-ChlGlc), a monoglucosylated derivative of cholesterol, is involved in the regulation of heat shock responses. ?-ChlGlc, which is rapidly induced in response to heat shock, activates heat shock transcription factor 1 (HSF1) leading to the expression of heat shock protein 70 (HSP70) in human fibroblasts. Identification and biochemical characterization of the enzyme responsible for ?-ChlGlc formation is important for a complete understanding of the molecular mechanisms leading to HSP70-induction following heat shock. Recently, we demonstrated that ?-ChlGlc synthesis is not dependent on UDP-Glucose but glucosylceramide (GlcCer) in animal tissue and human fibroblasts. In this study, we examined the possibility of glucocerebrosidase, a GlcCer-degrading glycosidase, acting as ?-ChlGlc-synthesizing enzyme. Overexpression of ?-glucosidase 1 (GBA1, lysosomal acid ?-glucocerebrosidase) led to an increase in cholesterol glucosylation activity in human fibroblasts. Using a cell line generated from type 2 Gaucher disease patients with severe defects in GBA1 activity, we found that cholesterol glucosylation activity was very low in the cells and the overexpression of GBA1 rescued the activity. In addition, purified recombinant GBA1 exhibits conduritol B-epoxide-sensitive cholesterol glucosylation activity. The optimum pH and temperature for cholesterol glucosylation by GBA1 were at about 5.3 and 43 °C, respectively. Short chain C8:0-GlcCer was the most effective donor for cholesterol glucosylation activity among GlcCer containing saturated fatty acid (C8:0 to C18:0) tested. GlcCer containing mono-unsaturated fatty acid was more preferred substrate for cholesterol glucosylation when compared with GlcCer containing same chain length of saturated fatty acid. These results demonstrate, for the first time, a novel function of GBA1 as a ?-ChlGlc-synthesizing enzyme. Therefore, our results also reveal a new pathway for glycolipid metabolism in mammals. PMID:24211208

  6. 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

  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. Oxidant-Free Au(I)-Catalyzed Halide Exchange and Csp2-O Bond Forming Reactions.

    PubMed

    Serra, Jordi; Whiteoak, Christopher J; Acuña-Parés, Ferran; Font, Marc; Luis, Josep M; Lloret-Fillol, Julio; Ribas, Xavi

    2015-10-21

    Au has been demonstrated to mediate a number of organic transformations through the utilization of its ? Lewis acid character, Au(I)/Au(III) redox properties or a combination of both. As a result of the high oxidation potential of the Au(I)/Au(III) couple, redox catalysis involving Au typically requires the use of a strong external oxidant. This study demonstrates unusual external oxidant-free Au(I)-catalyzed halide exchange (including fluorination) and Csp2-O bond formation reactions utilizing a model aryl halide macrocyclic substrate. Additionally, the halide exchange and Csp2-O coupling reactivity could also be extrapolated to substrates bearing a single chelating group, providing further insight into the reaction mechanism. This work provides the first examples of external oxidant-free Au(I)-catalyzed carbon-heteroatom cross-coupling reactions. PMID:26397959

  9. 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

  10. 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 ½ 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 C–H bonds at both C2 and C4. PMID:21513273

  11. Quantum Transition State Theory for proton transfer reactions in enzymes

    E-print Network

    Jacques P. Bothma; Joel Gilmore; Ross H. McKenzie

    2009-10-07

    We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero 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 $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of kinetic isotope effects for two classes of enzymes which 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 due to the environment is weak and only slightly modifies the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental degrees of freedom with frequencies much less than 1000 cm$^{-1}$ do not have a significant effect on quantum corrections to the reaction rate.

  12. 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.

  13. Synthesis of 2'(3')-O-DL-alanyl hexainosinic acid using T4 RNA ligase: suppression of the enzymic reverse transfer reaction by alkaline phosphatase.

    PubMed Central

    Profy, A T; Lo, K M; Usher, D A

    1983-01-01

    2'(3')-O-DL-Alanyl (Ip)5I was synthesized by a new method. An alanine ortho ester of inosine 5'-phosphate was added to (Ip)4I using the ATP-independent reaction of T4 RNA ligase, and the product was converted smoothly to the desired ester. The enzymic reverse transfer reaction was conveniently suppressed by the dephosphorylation of the adenosine 5'-phosphate coproduct, catalyzed in situ by alkaline phosphatase. PMID:6857753

  14. Synergistic rhodium(II) carboxylate and brønsted acid catalyzed multicomponent reactions of enalcarbenoids: direct synthesis of ?-pyrrolylbenzylamines.

    PubMed

    Dawande, Sudam Ganpat; Kanchupalli, Vinaykumar; Lad, Bapurao Sudam; Rai, Jyoti; Katukojvala, Sreenivas

    2014-07-18

    The design of a synergistic rhodium(II) carboxylate and BINOL phosphoric acid catalyzed efficient multicomponent reaction of enaldiazo compounds, arylamines, and aryl aldehydes leading to the first transition-metal-catalyzed direct synthesis of valuable ?-pyrrolylbenzylamines is disclosed. The reaction is proposed to involve a transient ammonium ylide of a new class of electrophilic rhodium enalcarbenoid, its regioselective Mannich reaction, and a cyclocondensation cascade. The methodology was used in a highly diastereoselective synthesis of a binaphthyl based chiral pyrrole. PMID:24988365

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

    PubMed Central

    Gómez-Manzo, Saúl; Escamilla, José E.; González-Valdez, Abigail; López-Velázquez, Gabriel; Vanoye-Carlo, América; Marcial-Quino, Jaime; de la Mora-de la Mora, Ignacio; Garcia-Torres, Itzhel; Enríquez-Flores, Sergio; Contreras-Zentella, Martha Lucinda; Arreguín-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

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

    PubMed

    Gómez-Manzo, Saúl; Escamilla, José E; González-Valdez, Abigail; López-Velázquez, Gabriel; Vanoye-Carlo, América; Marcial-Quino, Jaime; de la Mora-de la Mora, Ignacio; Garcia-Torres, Itzhel; Enríquez-Flores, Sergio; Contreras-Zentella, Martha Lucinda; Arreguín-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

  17. 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

  18. 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

  19. 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

  20. 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 = 30–100 ?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

  1. 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

  2. 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

  3. Copper-catalyzed selective hydroamination reactions of alkynes

    PubMed Central

    Shi, Shi-Liang; Buchwald, Stephen L.

    2014-01-01

    The development of selective reactions that utilize easily available and abundant precursors for the efficient synthesis of amines is a longstanding goal of chemical research. Despite the centrality of amines in a number of important research areas, including medicinal chemistry, total synthesis and materials science, a general, selective, and step-efficient synthesis of amines is still needed. In this work we describe a set of mild catalytic conditions utilizing a single copper-based catalyst that enables the direct preparation of three distinct and important amine classes (enamines, ?-chiral branched alkylamines, and linear alkylamines) from readily available alkyne starting materials with high levels of chemo-, regio-, and stereoselectivity. This methodology was applied to the asymmetric synthesis of rivastigmine and the formal synthesis of several other pharmaceutical agents, including duloxetine, atomoxetine, fluoxetine, and tolterodine. PMID:25515888

  4. 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.

  5. 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

  6. 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.

  7. Iridium-Catalyzed Intramolecular Asymmetric Allylic Dearomatization Reaction of Pyridines, Pyrazines, Quinolines, and Isoquinolines.

    PubMed

    Yang, Ze-Peng; Wu, Qing-Feng; Shao, Wen; You, Shu-Li

    2015-12-23

    The first Ir-catalyzed intramolecular asymmetric allylic dearomatization reaction of pyridines, pyrazines, quinolines, and isoquinolines has been developed. Enabled by in situ formed chiral Ir-catalyst, the dearomatized products were isolated in high levels of yield (up to 99% yield) and enantioselectivity (up to 99% ee). It is worth noting that the Me-THQphos ligand is much more efficient than other tested ligands for the dearomatization of pyrazines and certain quinolines. Mechanistic studies of the dearomatization reaction were carried out, and the results suggest the feasibility of an alternative process which features the formation of a quinolinium as the key intermediate. The mechanistic findings render this reaction a yet unknown type in the chemistry of Reissert-type reactions. In addition, the utility of this method was showcased by a large-scale reaction and formal synthesis of (+)-gephyrotoxin. PMID:26605697

  8. Synthesis of marine polyacetylenes callyberynes A-C by transition-metal-catalyzed cross-coupling reactions to sp centers.

    PubMed

    López, Susana; Fernandez-Trillo, Francisco; Midón, Pilar; Castedo, Luis; Saa, Carlos

    2006-03-31

    Efficient total syntheses of the sponge-derived hydrocarbon polyacetylenes callyberynes A-C have been achieved using metal-catalyzed cross-coupling reactions of highly unsaturated 1,3-diyne fragments as the key steps, namely: Cadiot-Chodkiewicz reaction under Alami's optimized conditions (sp-sp), sequential Sonogashira reaction of a cis,cis-divinyl dihalide (sp2-sp), and Kumada-Corriu reaction of an unactivated alkyl iodide (sp3-sp). This last approach constitutes the first application of a metal-catalyzed sp3-sp Kumada-Corriu cross-coupling reaction to the synthesis of a natural product. PMID:16555835

  9. Palladium-catalyzed C-N cross-coupling reactions toward the synthesis of drug-like molecules

    E-print Network

    McAvoy, Camille Z

    2012-01-01

    The development of methodologies for C-N bond formation reactions is an important scientific challenge because of many academic and industrial applications. This work will focus particularly on palladium-catalyzed ...

  10. Nickel-catalyzed reductive coupling reactions : application to the total syntheses of pumiliotoxins 209F and 251D

    E-print Network

    Woodin, Katrina Sue

    2007-01-01

    Catalytic Asymmetric Reductive Coupling of 1,3-Enynes and Aromatic Aldehydes Nickel-catalyzed reductive coupling reactions of 1,3-enynes and aromatic aldehydes efficiently afford conjugated dienols in excellent regioselectivity ...

  11. Transition-Metal-Catalyzed Laboratory-Scale Carbon–Carbon 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 transitionmetal–catalyzed 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 carbon–carbon 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

  12. Molybdopterin biosynthesis: Trapping an unusual purine ribose adduct in the MoaA-catalyzed reaction

    PubMed Central

    Mehta, Angad P.; Abdelwahed, Sameh H.; Begley, Tadhg P.

    2013-01-01

    MoaA/MoaC catalyze a remarkable rearrangement reaction in which guanosine-5?-triphosphate (GTP) is converted to cyclicpyranopterin monophosphate (cPMP). In this reaction, the C8 of GTP is inserted between the C2? and the C3? carbons of the GTP ribose. Previous experiments with GTP isotopomers demonstrated that the ribose C3? hydrogen atom is abstracted by the adenosyl radical. This led to a novel mechanistic proposal involving an intermediate with a bond between the C8 of guanine and C3? of the ribose. This paper describes the use of 2?,3?-dideoxyGTP to trap this intermediate. PMID:23848839

  13. Photo-induced excitability in the tris-(bipyridyl)Ru(II)-catalyzed Belousov-Zhabotinsky reaction

    NASA Astrophysics Data System (ADS)

    Kaminaga, Akiko; Mori, Yoshihito; Hanazaki, Ichiro

    1997-11-01

    The tris-(bipyridyl)Ru(II)-catalyzed Belousov-Zhabotinsky reaction in its steady state exhibits an excitable response to a light pulse in the visible region. The threshold light power for the excitability was determined as functions of initial concentrations of BrO 3- and Br - under the flow condition. Excitable response has also been observed to a 'negative' light pulse (a pulsed cut-off of the steady illumination) applied to the steady state under illumination with low light power, while the system is not excitable in the steady state under illumination with high power. The photochemical reaction scheme leading to the observed photo-response is discussed.

  14. 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

  15. Enantioselective 1,2-Difunctionalization of Dienes Enabled by Chiral Palladium Complex-Catalyzed Cascade Arylation/Allylic Alkylation Reaction.

    PubMed

    Wu, Xiang; Lin, Hua-Chen; Li, Ming-Li; Li, Lu-Lu; Han, Zhi-Yong; Gong, Liu-Zhu

    2015-10-28

    A Pd-catalyzed highly enantioselective three-component coupling of 1,3-dienes with aryl iodines and sodium dialkyl malonates has been successfully established by using a H8-BINOL-based phosphoramidite ligand. This reaction proceeded via a Pd-catalyzed cascade arylation and asymmetric allylic alkylation reaction, providing an efficient strategy for the enantioselective 1,2-difunctionalization of 1,3-dienes. PMID:26437362

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

    PubMed Central

    Abad, Enrique; Rommel, Judith B.; Kästner, 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

  17. Cobalt-catalyzed three-component coupling reaction of alkyl halides, 1,3-dienes, and trimethylsilylmethylmagnesium chloride.

    PubMed

    Mizutani, Keiya; Shinokubo, Hiroshi; Oshima, Koichiro

    2003-10-16

    [reaction: see text] A combination of CoCl(2) and 1,6-bis(diphenylphosphino)hexane catalyzes a novel three-component coupling reaction of alkyl bromides, 1,3-dienes, and silylmethylmagnesium chloride, yielding homoallylsilanes in good to excellent yields. The reaction involves a radical species from alkyl halides. PMID:14535753

  18. Development of a One-Pot Tandem Reaction Combining Ruthenium-Catalyzed Alkene Metathesis and Enantioselective Enzymatic

    E-print Network

    Zhao, Huimin

    of chain length (Scheme 1).9 The yields of this one-pot reaction were higher than those obtained whenDevelopment of a One-Pot Tandem Reaction Combining Ruthenium- Catalyzed Alkene Metathesis- thesis with enzymatic epoxidation to provide aryl epoxides. The development of this one-pot reaction

  19. Enhancement of enzyme activity and enantioselectivity by cyclopentyl methyl ether in the transesterification catalyzed by Pseudomonas cepacia lipase co-lyophilized with cyclodextrins.

    PubMed

    Mine, Yurie; Zhang, Lin; Fukunaga, Kimitoshi; Sugimura, Yoshiaki

    2005-03-01

    The solvent effects of cyclopentyl methyl ether (CPME) on the reaction rates and enzyme enantioselectivity in the enantioselective transesterifications of racemic 6-methyl-5-hepten-2-ol (racemic sulcatol: SUL) and racemic 2,2-dimethyl-1,3-dioxolane-4-methanol (racemic solketal: SOL) with a series of enol esters catalyzed by Pseudomonas cepacia lipase co-lyophilized with cyclodextrins (alpha-, beta-, gamma-, partially methylated beta-, and 2,3,6-tri-O-methyl-beta-cyclodextrin: alphaCyD; betaCyD; gammaCyD; Me1.78betaCyD; Me3betaCyD) were investigated and compared with those in diisopropyl ether (IPE). In the case of SUL, enzyme activities of the co-lyophilizate with Me1.78betaCyD in CPME were lower than those in IPE with every acyl source, however, the absolute enantiopreference was shown in the transesterification with vinyl butyrate (VBR) in IPME. When the substrates were SOL and VBR, the enzyme activities in CPME were greatly enhanced as high as 1.6-9.8-fold, while the enantioselectivities in CPME were comparable to those in IPE. PMID:15834802

  20. Nickel-catalyzed Suzuki-Miyaura reactions of unactivated halides with alkyl boranes and planar-chiral borabenzene catalysts for Diels-Alder reactions

    E-print Network

    Lu, Zhe

    2010-01-01

    Part I describes the expansion in scope of a nickel-catalyzed coupling reaction of unactivated alkyl bromides and alkyl boranes to include unactivated alkyl chlorides. The new method is adapted for use outside of a glove ...

  1. Enantioselective nickel-catalyzed reductive coupling reactions of alkynes and aldehydes. Synthesis of amphidinolides T1 and T4 via catalytic, stereoselective macrocyclizations

    E-print Network

    Colby Davie, Elizabeth A. (Elizabeth Anne)

    2005-01-01

    I. Enantioselective Nickel-Catalyzed Reductive Couplings of Alkynes and Aldehydes Allylic alcohol synthesis via a nickel-catalyzed reductive coupling reaction of alkylsubstituted alkynes and aldehydes was studied for ligand ...

  2. 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

  3. Cinchona Alkaloid Catalyzed Sulfa-Michael Addition Reactions Leading to Enantiopure ?-Functionalized Cysteines.

    PubMed

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

    2015-11-01

    Sulfa-Michael additions to ?,?-unsaturated N-acylated oxazolidin-2-ones and related ?,?-unsaturated ?-amino acid derivatives have been enantioselectively catalyzed by Cinchona alkaloids functionalized with a hydrogen bond donating group at the C6' position. The series of Cinchona alkaloids includes known C6' (thio)urea and sulfonamide derivatives and several novel species with a benzimidazole, squaramide or a benzamide group at the C6' position. The sulfonamides were especially suited as bifunctional organocatalysts as they gave the products in very good diastereoselectivity and high enantioselectivity. In particular, the C6' sulfonamides catalyzed the reaction with the ?,?-unsaturated ?-amino acid derivatives to afford the products in a diastereomeric ratio as good as 93:7, with the major isomer being formed in an ee of up to 99%. The products of the organocatalytic sulfa-Michael addition to ?,?-unsaturated ?-amino acid derivatives were subsequently converted in high yields to enantiopure ?-functionalized cysteines suitable for native chemical ligation. PMID:26451627

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Titanocene(III)-Catalyzed Three-Component Reaction of Secondary Amides, Aldehydes, and Electrophilic Alkenes.

    PubMed

    Zheng, Xiao; He, Jiang; Li, Heng-Hui; Wang, Ao; Dai, Xi-Jie; Wang, Ai-E; Huang, Pei-Qiang

    2015-11-01

    An umpolung Mannich-type reaction of secondary amides, aliphatic aldehydes, and electrophilic alkenes has been disclosed. This reaction features the one-pot formation of C?N and C?C bonds by a titanocene-catalyzed radical coupling of the condensation products, from secondary amides and aldehydes, with electrophilic alkenes. N-substituted ?-amido-acid derivatives and ?-amido ketones can be efficiently prepared by the current method. Extension to the reaction between ketoamides and electrophilic alkenes allows rapid assembly of piperidine skeletons with ?-amino quaternary carbon centers. Its synthetic utility has been demonstrated by a facile construction of the tricyclic core of marine alkaloids such as cylindricine?C and polycitorol?A. PMID:26404091

  11. 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

  12. Accelerated Search Kinetics Mediated by Redox Reactions of DNA Repair Enzymes

    E-print Network

    Levine, Alex J.

    Accelerated Search Kinetics Mediated by Redox Reactions of DNA Repair Enzymes Pak-Wing Fok and Tom to explain the localization of base excision repair (BER) enzymes to lesions on DNA. The CT mechanism relies on redox reactions of iron-sulfur cofactors that modify the enzyme's binding affinity. These redox

  13. 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

  14. 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

  15. Evidence that both protium and deuterium undergo significant tunneling in the reaction catalyzed by bovine serum amine oxidase

    SciTech Connect

    Grant, K.L.; Klinman, J.P. )

    1989-08-08

    The magnitudes of primary and secondary H/T and D/T kinetic isotope effects have been measured in the bovine serum amine oxidase catalyzed oxidation of benzylamine from 0 to 45{degree}C. Secondary H/T and D/T kinetic effects are small and in the range anticipated from equilibrium isotope effects; Arrhenius preexponential factors (A{sub H}/A{sub T} and A{sub D}/A{sub T}) determined from the temperature dependence of isotope effects also indicate semiclassical behavior. By contrast, primary H/T and D/T isotope effects, 35.2 {plus minus} 0.8 and 3.07 {plus minus} 0.07, respectively, at 25{degree}C, are larger than semiclassical values and give anomalously low preexponential factor rations, A{sub H}/A{sub T} = 0.12 {plus minus} 0.04 and A{sub D}/A{sub T} = 0.51 {plus minus} 0.10. Stopped-flow studies indicate similar isotope effects on cofactor reduction as seen in the steady state, consistent with a single rate-limiting C-H bond cleavage step for V{sub max}/K{sub m}. The comparison of primary and secondary isotope effects allows the authors to rule out appreciable coupling between the primary and secondary hydrogens at C-1 of the substrate. From the properties of primary isotope effects, they conclude that both protium and deuterium undergo significant tunneling in the course of substrate oxidation. These finding represent the first example of quantum mechanical effects in an enzyme-catalyzed proton abstraction reaction.

  16. COPPER-CATALYZED CROSS-COUPLING REACTIONS: THE FORMATION OF CARBON-CARBON AND CARBON-SULFUR BONDS

    E-print Network

    Venkataraman, Dhandapani "DV"

    COPPER-CATALYZED CROSS-COUPLING REACTIONS: THE FORMATION OF CARBON-CARBON AND CARBON-SULFUR BONDS-COUPLING REACTIONS: THE FORMATION OF CARBON-CARBON AND CARBON-SULFUR BONDS A Dissertation Presented by CRAIG G. BATES: THE FORMATION OF CARBON-CARBON AND CARBON-SULFUR BONDS MAY 2005 CRAIG G BATES, B.S., ROGER WILLIAMS UNIVERISTY

  17. Temperature-Induced Bifurcations in the Cu(II)-Catalyzed and Catalyst-Free Hydrogen Peroxide-Thiosulfate Oscillating Reaction

    E-print Network

    Epstein, Irving R.

    Temperature-Induced Bifurcations in the Cu(II)-Catalyzed and Catalyst-Free Hydrogen Peroxide of thiosulfate ions by hydrogen peroxide in the presence of trace amounts of copper(II) using the reaction be applicable to other pH- oscillatory systems as well. The reaction between hydrogen peroxide and thiosulfate

  18. 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...

  19. TBAI-Catalyzed Reaction between N-Tosylhydrazones and Sulfur: A Procedure 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

  20. 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.

  1. 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

  2. Car--Parrinello Molecular Dynamics Study of Base-Catalyzed Hydrolysis Reactions

    NASA Astrophysics Data System (ADS)

    Alnemrat, Sufian; Vasiliev, Igor; Wang, Haobin

    2011-03-01

    We apply the first principles metadynamics simulation technique implemented in the Car-Parrinello molecular dynamics package to study the base-catalyzed hydrolysis of N-methylacetamide in aqueous solution. Our calculations are carried out in the framework of density functional theory combined with the hybrid BLYP exchange-correlation functional The free energy surfaces and hydrolysis reaction pathways for N-methylacetamide are examined in the presence of a hydroxide ion, and 4, 32, and 64 water molecules. We find that at least 32 water molecules must be explicitly included in metadynamics simulations to accurately describe the mechanism of the hydrolysis reaction of N-Methylacetamide. Our theoretical estimate for the dissociation energy of N-Methylacetamide is in good agreement with the results of previous experimental and theoretical studies. Supported by LANL-NMSU MOU.

  3. Rescue of K12G Triosephosphate Isomerase by Ammonium Cations: The Reaction of an Enzyme in Pieces

    PubMed Central

    Go, Maybelle K.; Amyes, Tina L.; Richard, John P.

    2010-01-01

    The K12G mutation at yeast triosephosphate isomerase (TIM) results in a 5.5 × 105-fold decrease in kcat/Km for isomerization of glyceraldehyde 3-phosphate, and the activity of this mutant can be successfully “rescued” by NH4+ and primary alkylammonium cations. The transition state for the K12G mutant TIM-catalyzed reaction is stabilized by 1.5 kcal/mol by interaction with NH4+. The larger 3.9 kcal/mol stabilization by CH3CH2CH2CH2NH3+ is due to hydrophobic interactions between the mutant enzyme and the butyl side chain of the cation activator. There is no significant transfer of a proton from alkylammonium cations to GAP at the transition state for the K12G mutant TIM-catalyzed reaction, because activation by a series of RNH3+ shows little or no dependence on the pKa of RNH3+. A comparison of kcat/Km = 6.6 × 106 M?1 s?1 for the wildtype TIM-catalyzed isomerization of GAP and the third-order rate constant of 150 M?2 s?1 for activation by NH4+ of the K12G mutant TIM-catalyzed isomerization shows that stabilization of the bound transition state by the effectively intramolecular interaction of the cationic side chain of Lys-12 at wildtype TIM is 6.3 kcal/mol greater than for the corresponding intermolecular interaction of NH4+ at K12G mutant TIM. PMID:20822141

  4. Clustering and optimal arrangement of enzymes in reaction-diffusion systems

    E-print Network

    Alexander Buchner; Filipe Tostevin; Ulrich Gerland

    2013-10-11

    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.

  5. 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.

  6. 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.

  7. Siroheme: A New Prosthetic Group Participating in Six-Electron Reduction Reactions Catalyzed by Both Sulfite and Nitrite Reductases

    PubMed Central

    Murphy, Matthew J.; Siegel, Lewis M.; Tove, Shirley R.; Kamin, Henry

    1974-01-01

    Ferredoxin-nitrite reductase (EC 1.7.7.1) of spinach, an enzyme that catalyzes the six-electron reduction of nitrite to ammonia, contains siroheme, the new type of prosthetic group recently found in several sulfite reductases (both assimilatory and dissimilatory) that can catalyze the reduction of sulfite to sulfide, also a six-electron reduction. The prosthetic group of sulfite reductase had previously been shown to be an iron-tetrahydroporphyrin of the isobacteriochlorin type (adjacent pyrrole rings reduced) with eight carboxylate side chains. This finding suggests that both types of “multi-electron” reduction processes may share common mechanistic features. PMID:4595566

  8. 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

  9. 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

  10. Biocatalytic carbon capture via reversible reaction cycle catalyzed by isocitrate dehydrogenase.

    PubMed

    Xia, Shunxiang; Frigo-Vaz, Benjamin; Zhao, Xueyan; Kim, Jungbae; Wang, Ping

    2014-09-12

    The practice of carbon capture and storage (CCS) requires efficient capture and separation of carbon dioxide from its gaseous mixtures such as flue gas, followed by releasing it as a pure gas which can be subsequently compressed and injected into underground storage sites. This has been mostly achieved via reversible thermochemical reactions which are generally energy-intensive. The current work examines a biocatalytic approach for carbon capture using an NADP(H)-dependent isocitrate dehydrogenase (ICDH) which catalyzes reversibly carboxylation and decarboxylation reactions. Different from chemical carbon capture processes that rely on thermal energy to realize purification of carbon dioxide, the biocatalytic strategy utilizes pH to leverage the reaction equilibrium, thereby realizing energy-efficient carbon capture under ambient conditions. Results showed that over 25 mol of carbon dioxide could be captured and purified from its gas mixture for each gram of ICDH applied for each carboxylation/decarboxylation reaction cycle by varying pH between 6 and 9. This work demonstrates the promising potentials of pH-sensitive biocatalysis as a green-chemistry route for carbon capture. PMID:25152403

  11. Mechanistic insights into a BINOL-derived phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction.

    PubMed

    Overvoorde, Lois M; Grayson, Matthew N; Luo, Yi; Goodman, Jonathan M

    2015-03-01

    The reaction of tryptamine and (2-oxocyclohexyl)acetic acid can be catalyzed by 3,3'-bis(triphenylsilyl)-1,1'-bi-2-naphthol phosphoric acid to give an asymmetric ?-carboline. This reaction was first studied by Holloway et al. ( Org. Lett. 2010 , 12 , 4720 - 4723 ), but their mechanistic work did not explain the high stereoselectivity achieved. This study uses density functional theory and hybrid quantum mechanics/molecular mechanics calculations to investigate this reaction and provide a model to explain its outcome. The step leading to diastereo- and enantioselectivity is an asymmetric Pictet-Spengler reaction involving an N-acyliminium ion bound to the catalyst in a bidentate fashion. This interaction occurs via hydrogen bonds between the two terminal oxygen atoms of the catalyst phosphate group and the hydrogen atoms at N and C2 of the substrate indole group. These bonds hold the transition structure rigidly and thus allow the catalyst triphenylsilyl groups to influence the enantioselectivity. PMID:25654215

  12. 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.

  13. 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

  14. 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

  15. 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

  16. Dynamics of surface catalyzed reactions; the roles of surface defects, surface diffusion, and hot electrons.

    PubMed

    Somorjai, Gabor A; Bratlie, Kaitlin M; Montano, Max O; Park, Jeong Y

    2006-10-12

    The mechanism that controls bond breaking at transition metal surfaces has been studied with sum frequency generation (SFG), scanning tunneling microscopy (STM), and catalytic nanodiodes operating under the high-pressure conditions. The combination of these techniques permits us to understand the role of surface defects, surface diffusion, and hot electrons in dynamics of surface catalyzed reactions. Sum frequency generation vibrational spectroscopy and kinetic measurements were performed under 1.5 Torr of cyclohexene hydrogenation/dehydrogenation in the presence and absence of H(2) and over the temperature range 300-500 K on the Pt(100) and Pt(111) surfaces. The structure specificity of the Pt(100) and Pt(111) surfaces is exhibited by the surface species present during reaction. On Pt(100), pi-allyl c-C6H9, cyclohexyl (C6H11), and 1,4-cyclohexadiene are identified adsorbates, while on the Pt(111) surface, pi-allyl c-C6H9, 1,4-cyclohexadiene, and 1,3-cyclohexadiene are present. A scanning tunneling microscope that can be operated at high pressures and temperatures was used to study the Pt(111) surface during the catalytic hydrogenation/dehydrogenation of cyclohexene and its poisoning with CO. It was found that catalytically active surfaces were always disordered, while ordered surface were always catalytically deactivated. Only in the case of the CO poisoning at 350 K was a surface with a mobile adsorbed monolayer not catalytically active. From these results, a CO-dominated mobile overlayer that prevents reactant adsorption was proposed. By using the catalytic nanodiode, we detected the continuous flow of hot electron currents that is induced by the exothermic catalytic reaction. During the platinum-catalyzed oxidation of carbon monoxide, we monitored the flow of hot electrons over several hours using a metal-semiconductor Schottky diode composed of Pt and TiO2. The thickness of the Pt film used as the catalyst was 5 nm, less than the electron mean free path, resulting in the ballistic transport of hot electrons through the metal. The electron flow was detected as a chemicurrent if the excess electron kinetic energy generated by the exothermic reaction was larger than the effective Schottky barrier formed at the metal-semiconductor interface. The measurement of continuous chemicurrent indicated that chemical energy of exothermic catalytic reaction was directly converted into hot electron flux in the catalytic nanodiode. We found the chemicurrent was well-correlated with the turnover rate of CO oxidation separately measured by gas chromatography. PMID:17020389

  17. 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

  18. Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study.

    PubMed

    Jiang, Yafei; Tan, Hongwei; Zheng, Jimin; Li, Xichen; Chen, Guangju; Jia, Zongchao

    2015-10-14

    Diacylglycerol kinase is an integral membrane protein which catalyzes phosphoryl transfer from ATP to diacylglycerol. As the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. Thus far, its catalytic mechanism remains elusive. Using molecular dynamics and quantum mechanics calculations, we investigated the co-factor and the substrate binding and phosphoryl transfer mechanism. Based on the analysis of density functional theory calculations, we reveal that the phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. Our results further show that the active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes would occur prior to actual phosphoryl transfer. PMID:26352441

  19. 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.

  20. 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

  1. ~ristalsof bovine chyrnotrypsin. Enzymes are proteins specialized to catalyze biological reac-

    E-print Network

    Vallino, Joseph J.

    , but much earlier it was suspected that biological catalysts are involved in the fermentation of sugar of the jack bean. Sumner pre- ' sented evidence that the crystals consist of protein, and he concluded- ever, and it was not until the period 1930 to 1936, during which J. Northrop crystallized the enzymes

  2. Lipoxygenases are nonheme, iron-containing enzymes that catalyze the oxygenation of cer-

    E-print Network

    Ochsner, Kevin

    - tibility gene for peak BMD in mice may have relevance to human osteoporosis. An autoso- mal genome screen to human osteoporosis risk, inhibitors of the enzyme may merit investigation as a treatment for osteoporosis. Such inhibitors have already been developed for other indications (14). References and Notes 1. M

  3. Mathematical Analysis of Activation Thresholds in EnzymeCatalyzed Positive Feedbacks: Application

    E-print Network

    New York at Stoney Brook, State University of

    threshold properties akin to other excitable systems like neuron firing. For those that are amenable. A well­known example is the cascade of kinases that are initiated by the stimulation of G­protein­linked hormone receptors. The controls in these cases, however, are rather different, in that many enzyme

  4. 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

  5. PURIFICATION AND ISOLATION OF THE PHOSPHOGLYCERATE KINASE ENZYME

    E-print Network

    Collins, Gary S.

    PURIFICATION AND ISOLATION OF THE PHOSPHOGLYCERATE KINASE ENZYME IN RICE PLANTS Cynthia Bach (NADH). The enzyme, phosphoglycerate kinase (PGKase), catalyzes the reaction that results to purify the enzyme from developing rice seeds. Isolation of the enzyme was obtained by obtaining a crude

  6. 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.

  7. 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.

  8. 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.

  9. Autocatalysis Before Enzymes: The Emergence of Prebiotic Chain Reactions Nathaniel Virgo, Takashi Ikegami

    E-print Network

    Ikegami, Takashi

    Autocatalysis Before Enzymes: The Emergence of Prebiotic Chain Reactions Nathaniel Virgo, Takashi autocatalytic cycles as a partial answer to this ques- tion, since such reactions exhibit the life-like property reactions. Catalytic effects nevertheless emerge as properties of the reaction network. This suggests

  10. Access to Polyfunctionalized Chiral Piperidines through Enantioselective Addition-Carbocyclization Cascade Reaction Catalyzed by a Rhodium(I)-Diene Complex.

    PubMed

    Serpier, Fabien; Brayer, Jean-Louis; Folléas, Benoît; 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

  11. 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 Nafion®NR50 with improved efficiency and reduced waste production.

  12. Palladium-catalyzed three-component reaction of N-tosyl hydrazones, isonitriles and amines leading to amidines.

    PubMed

    Dai, Qiang; Jiang, Yan; Yu, Jin-Tao; Cheng, Jiang

    2015-12-01

    A palladium-catalyzed three-component reaction between N-tosyl hydrazones, aryl isonitriles and amines was developed, leading to amidines in moderate to good yields. This procedure features the rapid construction of amidine frameworks with high diversity and complexity. Ketenimines serve as intermediates, which encounter nucleophilic attack by amines to produce amidines. PMID:26426254

  13. Ligand-Controlled Access to [4 + 2] and [4 + 3] Cycloadditions in Gold-Catalyzed Reactions of Allene-Dienes

    E-print Network

    Toste, Dean

    the outcome of the catalyzed reaction by variation of the ancillary ligands.1 We were initially attracted and stereoselectivity3 by manipulating the neutral (L) and/or anionic (X)4 ligands. While these ligand effects on catalysis with cationic gold(I) complexes have been demon- strated, examples of ligand variation as a means

  14. A new Ru-catalyzed cascade reaction forming polycyclic cyclohexadienes from 1,6-diynes and alkenes.

    PubMed

    Varela, Jesús A; Rubín, Silvia G; Gonzalez-Rodríguez, Carlos; Castedo, Luis; Saa, Carlos

    2006-07-26

    Functionalized bicyclic 1,3-cyclohexadienes can be easily prepared by a new cascade reaction which involves the Ru-catalyzed addition of acyclic alkenes to 1,6-diynes to give (Z)-hexatrienes, followed by a pure thermal 6e-pi electrocyclization. PMID:16848424

  15. Au-Catalyzed Reaction of Propargylic Sulfides and Dithioacetals Lingling Peng, Xiu Zhang, Shiwei Zhang, and Jianbo Wang*

    E-print Network

    Wang, Jianbo

    Au-Catalyzed Reaction of Propargylic Sulfides and Dithioacetals Lingling Peng, Xiu Zhang, Shiwei Zhang, and Jianbo Wang* Beijing National Laboratory of Molecular Sciences (BNLMS), Green Chemistry) Zhang, L.; Kozmin, S. A. J. Am. Chem. Soc. 2004, 126, 11806. (e) Mamane, V.; Hannen, P.; Fu¨rstner, A

  16. Gold(I)-Catalyzed Intramolecular Acetylenic Schmidt Reaction David J. Gorin, Nicole R. Davis, and F. Dean Toste*

    E-print Network

    Toste, Dean

    Gold(I)-Catalyzed Intramolecular Acetylenic Schmidt Reaction David J. Gorin, Nicole R. Davis, and F 10, 2005; E-mail: fdtoste@berkeley.edu Gold(I) complexes have seen increased utility as catalysts-bonding from gold into an electron-deficient intermediate may play a role in mediating the formation of bicyclo

  17. 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

  18. Palladium(II)-catalyzed Heck reaction of aryl halides and arylboronic acids with olefins under mild conditions

    PubMed Central

    Shaikh, Tanveer Mahamadali

    2013-01-01

    Summary A series of general and selective Pd(II)-catalyzed Heck reactions were investigated under mild reaction conditions. The first protocol has been developed employing an imidazole-based secondary phosphine oxide (SPO) ligated palladium complex (6) as a precatalyst. The catalytic coupling of aryl halides and olefins led to the formation of the corresponding coupled products in excellent yields. A variety of substrates, both electron-rich and electron-poor olefins, were converted smoothly to the targeted products in high yields. Compared with the existing approaches employing SPO–Pd complexes in a Heck reaction, the current strategy features mild reaction conditions and broad substrate scope. Furthermore, we described the coupling of arylboronic acids with olefins, which were catalyzed by Pd(OAc)2 and employed N-bromosuccinimide as an additive under ambient conditions. The resulted biaryls have been obtained in moderate to good yields. PMID:23946858

  19. Configurationally Stable, Enantioenriched Organometallic Nucleophiles in Stereospecific Pd-Catalyzed Cross-Coupling Reactions: An Alternative Approach to Asymmetric Synthesis

    PubMed Central

    Wang, Chao-Yuan; Derosaa, Joseph

    2015-01-01

    Several research groups have recently developed methods to employ configurationally stable, enantioenriched organometallic nucleophiles in stereospecific Pd-catalyzed cross-coupling reactions. By establishing the absolute configuration of a chiral alkyltin or alkylboron nucleophile prior to its use in cross-coupling reactions, new stereogenic centers may be rapidly and reliably generated with preservation of the known initial stereochemistry. While this area of research is still in its infancy, such stereospecific cross-coupling reactions may emerge as simple, general methods to access diverse, optically active products from common enantioenriched organometallic building blocks. This minireview highlights recent progress towards the development of general, stereospecific Pd-catalyzed cross-coupling reactions using configurationally stable organometallic nucleophiles. PMID:26388985

  20. Iron- and indium-catalyzed reactions toward nitrogen- and oxygen-containing saturated heterocycles.

    PubMed

    Cornil, Johan; Gonnard, Laurine; Bensoussan, Charlélie; Serra-Muns, Anna; Gnamm, Christian; Commandeur, Claude; Commandeur, Malgorzata; Reymond, Sébastien; Guérinot, 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 FeCl3·6H2O 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 FeCl3·6H2O 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

  1. 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

  2. Imino-Oxy Acetic Acid Dealkylation as Evidence for an Inner-Sphere Alcohol Intermediate in the Reaction Catalyzed by Peptidylglycine ?-Hydroxylating Monooxygenase (PHM)

    PubMed Central

    McIntyre, Neil R.; Lowe, Edward W.; Merkler, David J.

    2009-01-01

    Peptidylglycine ?-hydroxylating monooxygenase (PHM, EC 1.14.17.3) catalyzes the stereospecific hydroxylation of a glycyl ?-carbon in a reaction that requires O2 and ascorbate. Subsequent dealkylation of the ?-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC 4.3.2.5), yields a bioactive amide and glyoxylate. PHM is a non-coupled, type II dicopper monooxygenase which activates O2 at only a single copper atom, CuM. In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The D(V/K)APPARENT, BIAA decreased from 14.7 ± 1.0 as [O2] ? 0 to 1.0 ± 0.2 as [O2] ? ? suggesting the dissociation rate constant from the PHM·BIAA complex decreases as [O2] increases; thereby, reducing the steady-state concentration of [PHM]free. BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked CuII-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

  3. 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

  4. Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis.

    PubMed

    Samanani, Nailish; Liscombe, David K; Facchini, Peter J

    2004-10-01

    (S)-Norcoclaurine synthase (NCS) (EC 4.2.1.78) catalyzes the condensation of 3,4-dihydroxyphenylethylamine (dopamine) and 4-hydroxyphenylacetaldehyde (4-HPAA) as the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine, sanguinarine, and berberine, in plants. A molecular clone encoding NCS was isolated from a meadow rue (Thalictrum flavum ssp. glaucum) cell suspension culture cDNA library. Heterologous expression of the NCS cDNA, truncated to remove a putative signal peptide, produced a recombinant protein with NCS activity. Recombinant NCS showed sigmoidal saturation kinetics for dopamine (Hill coefficient=1.98), hyperbolic saturation kinetics for 4-HPAA (Km of 700 microm), and pH and temperature optima of 7.0 and 40 degrees C, respectively, all similar to the purified, plant-derived enzyme. NCS exhibits 28-38% identity, and putative structural homology, with the Bet v 1 allergen and pathogenesis-related (PR)10 protein families. NCS also displays 35% identity with the enzyme (HYP1) responsible for hypericin biosynthesis in St John's wort (Hypericum perforatum). The novel catalytic functions of NCS and HYP1 define a new class of plant secondary metabolic enzymes within the Bet v 1 and PR10 protein families. Weaker homology was also detected between NCS and proteins identified in the latex of Papaver somniferum (opium poppy), and in Arabidopsis thaliana. A family of three to five NCS genes is abundantly expressed in the rhizome, followed by petioles and roots of T. flavum. NCS transcripts were localized to the immature endodermis and pericycle in roots, and the protoderm of leaf primordia in rhizomes; thus, the sites of NCS gene expression and berberine accumulation are temporally and spatially separated in roots and rhizomes respectively. PMID:15447655

  5. 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.

  6. Reverse reaction of malic enzyme for HCO3- fixation into pyruvic acid to synthesize L-malic acid with enzymatic coenzyme regeneration.

    PubMed

    Ohno, Yoko; Nakamori, Toshihiko; Zheng, Haitao; Suye, Shin-ichiro

    2008-05-01

    Malic enzyme [L-malate: NAD(P)(+) oxidoreductase (EC 1.1.1.39)] catalyzes the oxidative decarboxylation of L-malic acid to produce pyruvic acid using the oxidized form of NAD(P) (NAD(P)(+)). We used a reverse reaction of the malic enzyme of Pseudomonas diminuta IFO 13182 for HCO(3)(-) fixation into pyruvic acid to produce L-malic acid with coenzyme (NADH) generation. Glucose-6-phosphate dehydrogenase (EC1.1.1.49) of Leuconostoc mesenteroides was suitable for coenzyme regeneration. Optimum conditions for the carboxylation of pyruvic acid were examined, including pyruvic acid, NAD(+), and both malic enzyme and glucose-6-phosphate dehydrogenase concentrations. Under optimal conditions, the ratio of HCO(3)(-) and pyruvic acid to malic acid was about 38% after 24 h of incubation at 30 degrees C, and the concentration of the accumulated L-malic acid in the reaction mixture was 38 mM. The malic enzyme reverse reaction was also carried out by the conjugated redox enzyme reaction with water-soluble polymer-bound NAD(+). PMID:18460807

  7. Purification and identification of a novel primitive secretory enzyme catalyzing the hydrolysis of imidazole-related dipeptides in the jawless vertebrate Lethenteron reissneri.

    PubMed

    Oku, Takahiro; Ando, Seiichi; Hayakawa, Takehiko; Baba, Kyoko; Nishi, Ryuichiro; Shiozaki, Kazuhiro; Yamada, Shoji

    2011-04-01

    Imidazole-related dipeptides, such as carnosine and anserine, occur widely in skeletal muscles of jawed vertebrates. All of the known enzymes that catalyze the hydrolysis of these dipeptides belong to the M20A metallopeptidase subfamily; two secretory enzymes, serum carnosinase (EC 3.4.13.20) and anserinase (EC 3.4.13.5), and one non-secretory enzyme, cytosolic nonspecific dipeptidase (EC 3.4.13.18). Here we report the enzymatic characterization and molecular identification of an unidentified enzyme, which catalyzes the hydrolysis of these dipeptides, from the skeletal muscle of Far Eastern brook lamprey (Lethenteron reissneri). A 60-kDa subunit protein of the enzyme was purified to near homogeneity. We cloned two M20A genes from the skeletal muscle of Far Eastern brook lamprey; one was a secretory-type gene encoding for the 60-kD protein, and another was a non-secretory-type gene presumably encoding for cytosolic nonspecific dipeptidase. Our findings indicate that the purified enzyme is a N-glycosylated secretory M20A dipeptidase distributed specifically in the jawless vertebrate group, and may be derived from a common ancestor gene between serum carnosinase and anserinase. We propose that this dipeptidase is a novel secretory M20A enzyme and is classified as neither serum carnosinase nor anserinase. PMID:21262300

  8. Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides

    NASA Astrophysics Data System (ADS)

    Joshi, Prakash C.; Pitsch, Stefan; Ferris, James P.

    2007-02-01

    The montmorillonite-catalyzed reactions of the 5?-phosphorimidazolides of D, L-adenosine (D, L-ImpA) (Figure 1a. N = A, R = H) and D, L-uridine (Figure 1a., N = U, R = H) yields oligomers that were as long as 7 mers and 6 mers, respectively. The reactions of dilute solutions of D-ImpA and D-ImpU under the same conditions gave oligomers as long as 9 and 8 mers respectively. This demonstrated that oligomer formation is only partially inhibited by incorporation of both the D- and L-enantiomers. The structures of the dimers, trimers and tetramer fractions formed from D, L-ImpA was investigated by selective enzymatic hydrolysis, comparison with authentic samples and mass spectrometry. Homochiral products were present in greater amounts than would be expected if theoretical amounts of each were formed. The ratio of the proportion of homochiral products to that of the amount of each expected for the dimers (cyclic and linear), trimers and tetramers, was 1.3, 1.6, and 2.1, respectively. In the D, L-ImpU reaction homochiral products did not predominate with ratios of dimers (cyclic and linear), trimers and tetramers 0.8, 0.44, and 1.4, respectively. The proportions of cyclic dimers in the dimer fraction were 52 66% with D, L-ImpA and 44 69% with D, L-ImpU. No cyclic dimers were formed in the absence of montmorillonite. The differences in the reaction products of D, L-ImpA and D, L-ImpU are likely to be due to the difference in the orientations of the activated monomers when bound to the catalytic sites on montmorillonite. The consequences of the selectivity of montmorillonite as a prebiotic catalyst are discussed.

  9. 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 ?-oxidation convert these substrates to long-chain ?,?-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 ?-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 ?-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 ?-hydroxy fatty acids, ultimately generating the ?,?-diacid. Consideration of these different specificities and selectivities will help determine which enzymes to amplify in strains blocked for ?-oxidation to enhance the production of dicarboxylic acids. The activity spectrum also identified other potential oxidation targets for commercial development. PMID:14532054

  10. Mechanism of the Orotidine 5?-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence for Substrate Destabilization

    SciTech Connect

    Chan, K.; Wood, M; Fedorov, A; Fedorov, E; Imker, H; Amyes, T; Richard, J; Almo, S; Gerlt, J

    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 x 1016) and proficiency (kcat/KM)/knon, 4.8 x 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. 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 analogue) 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 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.

  11. 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.

  12. 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

  13. 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…

  14. 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

  15. 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

  16. Accelerated search kinetics mediated by redox reactions of DNA repair enzymes

    E-print Network

    Pak-Wing Fok; Tom Chou

    2009-05-20

    A Charge Transport (CT) mechanism has been proposed in several papers (e.g., Yavin, et al. PNAS, v102 3546 (2005)) to explain the localization of Base Excision Repair (BER) enzymes to lesions on DNA. The CT mechanism relies on redox reactions of iron-sulfur cofactors that modify the enzyme's binding affinity. These redox reactions are mediated by the DNA strand and involve the exchange of electrons between BER enzymes along DNA. We propose a mathematical model that incorporates enzyme binding/unbinding, electron transport, and enzyme diffusion along DNA. Analysis of our model within a range of parameter values suggests that the redox reactions can increase desorption of BER enzymes not already bound to their targets, allowing the enzymes to be recycled, thus accelerating the overall search process. This acceleration mechanism is most effective when enzyme copy numbers and enzyme diffusivity along the DNA are small. Under such conditions, we find that CT BER enzymes find their targets more quickly than simple "passive" enzymes that simply attach to the DNA without desorbing.

  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

    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.

  18. 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 3?-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH?? 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?? 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.

  19. 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…

  20. 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.

  1. 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.

  2. Esterification kinetics of triglycerides in n-hexane catalyzed by an immobilized lipase 

    E-print Network

    Gomez Ruiz, Alejandro

    1998-01-01

    The kinetics of enzyme-catalyzed esterification of triglycerides over immobilized lipase in n-hexane was investigated. The reaction kinetics were described in terms of a mechanism developed following the Langmuir-Hinshelwood-Hougen-Watson (LHHW...

  3. Continuous monitoring of enzymatic reactions on surfaces by real-time flow cytometry: sortase a catalyzed protein immobilization as a case study.

    PubMed

    Heck, Tobias; Pham, Phu-Huy; Hammes, Frederik; Thöny-Meyer, Linda; Richter, Michael

    2014-08-20

    Only a few techniques, such as quartz crystal microbalance and surface plasmon resonance spectroscopy, enable the analysis of dynamic processes on solid supports. Here we have developed a straightforward assay based on flow cytometry to continuously follow enzymatic reactions directly on microparticle surfaces. We applied this real-time flow cytometry (RT-FCM) approach to study the covalent immobilization of green-fluorescent protein (GFPuv) on triglycine-modified polystyrene microbeads by the transpeptidase sortase A (SrtA) from Staphylococcus aureus. Though commonly treated as functionally identical catalysts, the SrtA variants SrtA??? and SrtA???, in which the N-terminal amino acid residues 1-59 and 1-25 of the native enzyme are truncated, were shown to perform very differently with regard to this particular immobilization reaction. While SrtA??? efficiently catalyzed the covalent attachment of GFPuv to the surface (as indicated by a linear increase of microbead fluorescence), SrtA??? was essentially inactive. Besides the length of the N-terminal amino acid extension on the SrtA construct, the position of the hexahistidine tag at either the N- or C-terminus affected the efficiency of enzymatic protein immobilization. Apart from three enzyme variants containing the native core structure of SrtA, we also included three recently evolved mutants of SrtA in this comparative study. With these mutants we observed a rapid initial attachment of the GFPuv target protein to the microbeads. However, with proceeding reaction time, cleavage of the covalently immobilized target protein from the surface prevailed over the coupling reaction, consequently causing a decline of microbead fluorescence. In general, the RT-FCM approach used herein represents a powerful analytical tool for qualitative dynamic studies of many heterogeneous enzymatic reactions or other binding events that influence the fluorescence properties of microparticle surfaces. PMID:25075751

  4. Acid-catalyzed conversion of xylose, xylan and straw into furfural by microwave-assisted reaction.

    PubMed

    Yemi?, Oktay; Mazza, Giuseppe

    2011-08-01

    Furfural is a biomass derived-chemical that can be used to replace petrochemicals. In this study, the acid-catalyzed conversion of xylose and xylan to furfural by microwave-assisted reaction was investigated at selected ranges of temperature (140-190°C), time (1-30 min), substrate concentration (1:5-1:200 solid:liquid ratio), and pH (2-0.13). We found that a temperature of 180°C, a solid:liquid ratio of 1:200, a residence time of 20 min, and a pH of 1.12 gave the best furfural yields. The effect of different Brønsted acids on the conversion efficiency of xylose and xylan was also evaluated, with hydrochloric acid being found to be the most effective catalyst. The microwave-assisted process provides highly efficient conversion: furfural yields obtained from wheat straw, triticale straw, and flax shives were 48.4%, 45.7%, and 72.1%, respectively. PMID:21620690

  5. Method of controlled reduction of nitroaromatics by enzymatic reaction with oxygen sensitive nitroreductase enzymes

    DOEpatents

    Shah, Manish M. (Richland, WA); Campbell, James A. (Pasco, WA)

    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 reduction of nitroaromatics by enzymatic reaction with redox enzymes

    DOEpatents

    Shah, Manish M. (Richland, WA)

    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).

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Enantioselective NHC-Catalyzed Redox [4 + 2]-Hetero-Diels-Alder Reactions Using ?,?-Unsaturated Trichloromethyl Ketones as Amide Equivalents.

    PubMed

    Attaba, Nassilia; Taylor, James E; Slawin, Alexandra M Z; Smith, Andrew D

    2015-10-01

    ?,?-Unsaturated trichloromethyl ketones are suitable ?,?-unsaturated amide and ester equivalents in N-heterocyclic carbene (NHC)-catalyzed redox hetero-Diels-Alder reactions with azolium enolates generated from ?-aroyloxyaldehydes. The initially formed syn-dihydropyranone products can be isolated or can undergo ring-opening with benzylamine followed by aminolysis of the resulting CCl3 ketone to form a range of diamides with high diastereo- and enantioselectivity (up to >95:5 dr and >99% ee). PMID:26344498

  12. Metal-Catalyzed Carbon-Carbon Bond Forming Reactions for the Synthesis of Significant Chiral Building Blocks 

    E-print Network

    Bugarin Cervantes, Alejandro

    2011-08-08

    by nucleophilic tertiary amines or phosphines.2 In the seminal report,1 Morita and coworkers reported the first nucleophilic triggered acrylic ?-substitution catalyzed by phosphines. Treatment of acrylonitrile with catalytic amounts of tricyclohexylphosphine... several activated alkenes including alkyl vinyl ketones,5-7 alkyl and aryl acrylates,8-10 acrolien,11,12 allenic esters,13 acrylonitriles,6,14 vinyl sulfones and sulfonates,15,16 as well as vinyl phosphonates17 on reactions with aldehydes at atmospheric...

  13. Preparation of Strontium-and Zinc-Doped LaGaO3 Powders via Precipitation in the Presence of Urea and/or Enzyme Urease

    E-print Network

    Tas, A. Cuneyt

    and/or Enzyme Urease A. Cu¨neyt Tas,*, Peter J. Majewski, and Fritz Aldinger* Max-Planck-Institut fuer the decomposition of urea was catalyzed by the enzyme urease. The calcination behavior of the precursor powders by Mati- jevic,36 ­38 and others.39 ­ 43 Synthesis of ceramics by enzyme- catalyzed reactions, which

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Chiral Phosphine-Silver(I) Complex Catalyzed Enantioselective Interrupted Feist-Bénary Reaction with Ynones: The Aldol-Cycloisomerization Cascade.

    PubMed

    Sinha, Debarshi; Biswas, Arnab; Singh, Vinod K

    2015-07-01

    Silver-catalyzed interrupted Feist-Bénary reaction is described for the efficient enantioselective synthesis of dihydrofuran heterocycles. A new method has been developed for the silver(I)-(R)-BINAP complex mediated aldol-cycloisomerization cascade reaction between ynones and 1,3-diketones to provide functionalized dihydrofurans with moderate to good yields (up to 95%) and good to excellent enantiomeric excess (up to 98%). The presence of an exocyclic double bond and hydroxy group in the dihydrofuran products provides wide scope for further structural manipulation. PMID:26106952

  20. Non-Catalyzed Click Reactions of ADIBO Derivatives with 5-Methyluridine Azides and Conformational Study of the Resulting Triazoles

    PubMed Central

    Smyslova, Petra; Popa, Igor; Ly?ka, 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

  1. 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

  2. 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

  3. 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 = ½ 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

  4. 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

  5. Identification of enzyme responsible for erythritol utilization and reaction product in yeast Lipomyces starkeyi.

    PubMed

    Nishimura, Katsushi; Harada, Teiko; Arita, Yasukazu; Watanabe, Hisayuki; Iwabuki, Hidehiko; Terada, Asako; Naganuma, Takafumi; Uzuka, Yasuyuki

    2006-04-01

    We have identified the enzyme responsible for erythritol utilization and its reaction product in the yeast Lipomyces starkeyi CBS 1807. The enzyme, a polyol dehydrogenase requiring NAD+ as a coenzyme, was induced by erythritol in this yeast. We confirmed that the enzyme product was L-erythrulose by MS, NMR, and polarimeter analyses, meaning that we clarified the first step of erythritol utilization in yeasts for the first time. In the case of the oxidative reaction, D-threitol, (2R,3R)-2,3-butanediol, and erythritol were much better substrates than 21 other polyols tested. These three substrates are tetroses and have an R configuration at C-3, and whose third carbon results in easiest oxidation in this enzyme. The research of the substrate specificity in the reductive reaction demonstrated that L-erythrulose and dihydroxyacetone were better substrates, that D-acetoin was inactive and L-erythrose (aldose) was slightly active. PMID:16716937

  6. 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 ...

  7. Synthesis of Unsymmetrical Diarylureas via Pd-Catalyzed C–N Cross-Coupling Reactions

    E-print Network

    Breitler, Simon

    A facile synthesis of unsymmetrical N,N?-diarylureas is described. The utilization of the Pd-catalyzed arylation of ureas enables the synthesis of an array of diarylureas in good to excellent yields from benzylurea via a ...

  8. Development of copper-catalyzed enantioselective alkene difunctionalization reactions via radical intermediates

    E-print Network

    Zhu, Rong, Ph. D. Massachusetts Institute of Technology

    2015-01-01

    Chapter 1 A mild, versatile, and convenient method for the efficient oxytrifluoromethylation of unactivated alkenes based on a copper-catalyzed ligand-assisted difunctionalization strategy has been developed. This method ...

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

    E-print Network

    Matsubara, Ryosuke

    Nickel-catalyzed intermolecular benzylation and heterobenzylation of unactivated alkenes to provide functionalized allylbenzene derivatives are described. A wide range of both the benzyl chloride and alkene coupling partners ...

  10. 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

  11. Integrated rate equations for irreversible enzyme-catalysed first-order and second-order reactions.

    PubMed Central

    Boeker, E A

    1985-01-01

    Integrated rate equations are presented that describe irreversible enzyme-catalysed first-order and second-order reactions. The equations are independent of the detailed mechanism of the reaction, requiring only that it be hyperbolic and unbranched. The results should be directly applicable in the laboratory. PMID:3977872

  12. 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(??)) 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(??) 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(??) 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 0.03fM (S/N=3). PMID:26453905

  13. Recent advances in "formal" ruthenium-catalyzed [2+2+2] cycloaddition reactions of diynes to alkenes.

    PubMed

    García-Rubín, Silvia; Varela, Jesús A; Castedo, Luis; Saá, Carlos

    2008-01-01

    "Formal" and standard RuII-catalyzed [2+2+2] cycloaddition of 1,6-diynes to alkenes gave bicyclic 1,3-cyclohexadienes in relatively good yields. When terminal 1,6-diynes 1 were used, two isomeric bicyclic 1,3-cyclohexadienes 4 or 6 were obtained, depending on the acyclic or cyclic nature of the alkene partner. When unsymmetrical substituted 1,6-diynes 7 were used, the reaction with acyclic alkenes took place regio- and stereoselectively to afford bicyclic 1,3-cyclohexadienes 8. A cascade process that behaves as a "formal" RuII-catalyzed [2+2+2] cycloaddition explained these results. Initially, a Ru-catalyzed linear coupling of 1,6-diynes 1 and 7 with acyclic alkenes occurs to give open 1,3,5-trienes of type 3, which after a thermal disrotatory 6e(-) pi-electrocyclization led to the final 1,3-cyclohexadienes 4 and 8. When disubstituted 1,6-diyne 10 was used with electron-deficient alkenes, new exo-methylene cyclohexadienes 12 arose from a competitive reaction pathway. PMID:18767111

  14. 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 ?,?-diarylation–reduction 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

  15. Chloroperoxidase-Catalyzed Epoxidation of Cis-?-Methylstyrene: NH-S Hydrogen Bonds and Proximal Helix Dipole Change the Catalytic Mechanism and Significantly Lower the Reaction Barrier.

    PubMed

    Morozov, Alexander N; Pardillo, Armando D; Chatfield, David C

    2015-11-12

    Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH-S) is a conserved feature of heme-thiolate enzymes such as chloroperoxidase (CPO) and cytochrome P450 (P450). In CPO, the effect of NH-S bonds is amplified by the dipole moment of the proximal helix. Our gas-phase DFT studies show that the proximal pocket effect significantly enhances CPO's reactivity toward the epoxidation of olefinic substrates. Comparison of models with and without proximal pocket residues shows that with them, the barrier for C?-O bond formation is lowered by about ?4.6 kcal/mol, while C?-O-C? ring closure becomes barrierless. The dipole moment of the proximal helix was estimated to contribute 1/3 of the decrease, while the rest is attributed to the effect of NH-S bonds. The decrease of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket. The effect is most pronounced on the doublet spin surface and involves a change in the electron-transfer mechanism. A full enzyme QMMM study on the doublet spin surface gives about the same barrier as the gas-phase DFT study. The free-energy barrier was estimated to be in agreement with the experimental results for the CPO-catalyzed epoxidation of styrene. PMID:26452587

  16. Positional assembly of enzymes on bacterial outer membrane vesicles for cascade reactions.

    PubMed

    Park, Miso; Sun, Qing; Liu, Fang; DeLisa, Matthew P; Chen, Wilfred

    2014-01-01

    The systematic organization of enzymes is a key feature for the efficient operation of cascade reactions in nature. Here, we demonstrate a facile method to create nanoscale enzyme cascades by using engineered bacterial outer membrane vesicles (OMVs) that are spheroid nanoparticles (roughly 50 nm in diameter) produced by Gram-negative bacteria during all phases of growth. By taking advantage of the fact that OMVs naturally contain proteins found in the outer cell membrane, we displayed a trivalent protein scaffold containing three divergent cohesin domains for the position-specific presentation of a three-enzyme cascade on OMVs through a truncated ice nucleation protein anchoring motif (INP). The positional assembly of three enzymes for cellulose hydrolysis was demonstrated. The enzyme-decorated OMVs provided synergistic cellulose hydrolysis resulting in 23-fold enhancement in glucose production than free enzymes. PMID:24820175

  17. 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...

  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 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...

  19. 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...

  20. 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

  1. 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.

  2. Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations

    NASA Astrophysics Data System (ADS)

    Kristoffersen, Emil L.; Jørgensen, Line A.; Franch, Oskar; Etzerodt, Michael; Frøhlich, Rikke; Bjergbæk, Lotte; Stougaard, Magnus; Ho, Yi-Ping; Knudsen, Birgitta R.

    2015-05-01

    Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment.Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01474c

  3. Fully diastereoselective synthesis of polysubstituted, functionalized piperidines and decahydroquinolines based on multicomponent reactions catalyzed by cerium(IV) ammonium nitrate.

    PubMed

    Suryavanshi, Padmakar A; Sridharan, Vellaisamy; Maiti, Swarupananda; Menéndez, J Carlos

    2014-07-01

    The cerium(IV) ammonium nitrate (CAN)-catalyzed, three-component reaction between primary amines, ?-dicarbonyl compounds, and ?,?-unsaturated aldehydes in ethanol heated to reflux, constitutes a general, one-pot synthesis of 1,4-dihydropyridines. Their reduction with sodium triacetoxyborohydride furnished piperidine derivatives bearing up to five substituents with full diastereoselectivity in a hitherto inaccessible stereochemical arrangement. The reaction proceeded with no significant loss of enantiomeric purity under mild reduction conditions that are compatible with several functional groups that are normally sensitive to reduction. Octahydroquinolin-5-one derivatives, which were prepared by a modified version of the initial multicomponent reaction, were not suitable substrates for the sodium triacetoxyborohydride mediated reduction, but they were transformed into the corresponding decahydroquinolines, including a precursor of the amphibian alkaloid pumiliotoxin?C, by catalytic hydrogenation under a variety of conditions. PMID:24909665

  4. 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

  5. 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

  6. Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes

    E-print Network

    Minnesota, University of

    1 Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble that enzymes accelerate the rates of chemical reactions has fascinated chemists and biochemists for nearly

  7. Correlations between enzyme histochemical reactions and respective enzyme activities in global ischaemic rat hearts.

    PubMed Central

    Hiltunen, J. K.; Saukko, P.; Hirvonen, J.

    1985-01-01

    NADH-diaphorase, succinate dehydrogenase (SDH), beta-hydroxybutyrate dehydrogenase (beta-HBDH), malate dehydrogenase (MDH) and cytochrome oxidase (CytO) were demonstrated histochemically in isolated perfused rat hearts during global ischaemia from 0 to 12 hours. The corresponding enzyme activities were measured when possible. The histochemically demonstrable activities of NADH-diaphorase and MDH decreased during the first hour of ischaemia. The time course of inactivation of biochemically detectable NADH-ferricyanide oxidoreductase was much the same as that of NADH-diaphorase. Both histochemically and biochemically detectable beta-HBDH gradually decreased by about 6 h of ischaemia. NADH-diaphorase but not MDH itself proved to be the rate-limiting factor when demonstrating MDH histochemically with nitroblue tetrazolium (NBT), whereas in the case of beta-HBDH the situation was probably the reverse. CytO and SDH activities did not change during the experimental period. Histochemistry clearly demonstrated ischaemic cellular injury, even though no significant diagnostic changes of ischaemia were visible by light microscopy. Even though this shows that enzyme-histochemical methods can be sensitive indicators of early ischaemic injury, in practice the time between the onset of injury and death as well as between death and autopsy must be taken into consideration when interpreting the results. PMID:3002415

  8. 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.

  9. Enzyme immunoassay by dynamic enhanced vibrational spectroscopy of the enzyme reaction product

    NASA Astrophysics Data System (ADS)

    Zhao, Haiying; Dou, Xiaoming

    2005-01-01

    This paper reports a kind of application of surface-enhanced Raman scattering (SERS) to immunology. In the proposed system, antibody immobilized on a solid substrate reacts with antigen, which binds with another antibody labeled with peroxidase. If this immunocomplex is subjected to reaction with o-phenylenediamine and hydrogenperoxide at 37°C, azoaniline is generated. This azo compound is adsorbed on a silver colloid and only the azo compound gives a strong surface-enhanced resonance Raman (SERRS) spectrum. A linear relationship was observed between the peak intensity of the N=N stretching band and the concentration of antigen, revealing that one can determine the concentration of antigen by the SERRS measurement of the reaction product.

  10. 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.

  11. 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

  12. 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

  13. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list.

    PubMed

    Kotera, Masaaki; Nishimura, Yosuke; Nakagawa, Zen-ichi; Muto, Ai; Moriya, Yuki; Okamoto, Shinobu; Kawashima, Shuichi; Katayama, Toshiaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2014-12-01

    Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics. PMID:25385078

  14. 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.

  15. Access to Spirocyclized Oxindoles and Indolenines via Palladium-Catalyzed Cascade Reactions of Propargyl Carbonates with 2-Oxotryptamines and Tryptamines.

    PubMed

    Nibbs, Antoinette E; Montgomery, Thomas D; Zhu, Ye; Rawal, Viresh H

    2015-05-15

    Reported here are methods for the direct construction of a range of spirocyclized oxindoles and indolenines in good to excellent yields. Specifically, we report the palladium-catalyzed reactions of oxindoles and indoles, both functioning as bis-nucleophiles, with propargyl carbonates to afford spirocyclic products having an exocyclic double bond on the newly formed ring. The reaction proceeds through a process wherein the first nucleophilic unit on the oxindole or indole reacts with an allenyl-palladium species, formed from oxidative addition of Pd(0) to propargyl carbonates, to generate a ?-allyl palladium intermediate that then reacts further with the second nucleophilic component of the oxindole or indole. The cascade process forges two bonds en route to spirocyclized oxindole and indolenine products. The use of chiral phosphines renders the cyclization sequence enantioselective, providing spirocyclic products with modest to good enantioselectivities. PMID:25876139

  16. Irreducible mass-transport limitations during a heterogeneously catalyzed gas-phase chain reaction: Oxidative coupling of methane

    SciTech Connect

    Couwenberg, P.M.; Chen, Q.; Marin, G.B.

    1996-02-01

    A heterogeneous reactor model was developed describing kinetic experiments on the heterogeneously catalyzed oxidative coupling of methane in a laboratory fixed-bed reactor. The catalyst produces radicals which react further through gas-phase reactions in the pores of the catalyst and in the interstitial phase. The reactor model accounts for the irreducible mass-transport limitations for the reactive radicals, which occur even at conditions where no mass-transport limitations occur for the molecules, both reactants and reaction products. The effects of these irreducible mass-transport limitations on the conversion and selectivity of the process were investigated and were found to be essential for an adequate description of experimental data.

  17. 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)

  18. 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

  19. 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

  20. Asymmetric allylation of ketones and subsequent tandem reactions catalyzed by a novel polymer-supported titanium-BINOLate complex.

    PubMed

    Yadav, Jagjit; Stanton, Gretchen R; Fan, Xinyuan; Robinson, Jerome R; Schelter, Eric J; Walsh, Patrick J; Pericas, Miquel A

    2014-06-01

    By using a novel, simple, and convenient synthetic route, enantiopure 6-ethynyl-BINOL (BINOL = 1,1-binaphthol) was synthesized and anchored to an azidomethylpolystyrene resin through a copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The polystyrene (PS)-supported BINOL ligand was converted into its diisopropoxytitanium derivative in situ and used as a heterogeneous catalyst in the asymmetric allylation of ketones. The catalyst showed good activity and excellent enantioselectivity, typically matching the results obtained in the corresponding homogeneous reaction. The allylation reaction mixture could be submitted to epoxidation by simple treatment with tert-butyl hydroperoxide (TBHP), and the tandem asymmetric allylation epoxidation process led to a highly enantioenriched epoxy alcohol with two adjacent quaternary centers as a single diastereomer. A tandem asymmetric allylation/Pauson-Khand reaction was also performed, involving simple treatment of the allylation reaction mixture with Co2(CO)8/N-methyl morpholine N-oxide. This cascade process resulted in the formation of two diastereomeric tricyclic enones in high yields and enantioselectivities. PMID:24737394

  1. Biodegradation of Chlorinated Solvents: Reactions near DNAPL and Enzyme Function

    SciTech Connect

    McCarty, P. L.; Spormann, Alfred M.; Criddle, Craig, S.

    2003-12-11

    Chlorinated solvents are among the most widespread groundwater contaminants in the country, contamination which is also among the most difficult and expensive for remediation. These solvents are biodegradable in the absence of oxygen, but this biodegradation requires both a food source for the organisms (electron donor) and the presence of chlorinated solvent biodegrading organisms. These two requirements are present naturally at some contamination sites, leading to natural attenuation of the solvents. If one or both requirements are absent, then engineered bioremediation either through addition of an external electron donor or through bioaugmentation with appropriate microorganisms, or both, may be used for site remediation. The most difficult case for cleanup is when a large residual of undissolved chlorinated solvents are present, residing as dense -non-aqueous-phase- liquid ( DNAPL). A major focus of this study was on the potential for biodegradation of the solvents when pre sent as DNAPL where concentrations are very high and potential for toxicity to microorganisms exist. Another focus was on a better understanding of the biological mechanisms involved in chlorinated solvent biodegradation . These studies were directed towards the chlorinated solvents, trichloroethene (TCE), tetrachloroethene or perchloroethene (PCE), and carbon tetrachloride (CT). The potential for biodegradation of TCE and PCE DNAPL was clearly demonstrated in this research. From column soil studies and batch studies we found there to be a clear advantage in focusing efforts at bioremediation near the DNAPL. Here, chlorinated solvent concentrations are the highest, both because of more favorable reaction kinetics and because such high solvent concentrations are toxic to microorganisms, such as methanogens, which compete with dehalogenators for the electron donor. Additionally, biodegradation near a PCE DNAPL results in an enhanced dissolution rate for the chlorinated solvent, by factors of three to five times, leading to a more rapid clean-up of the DNAPL zone. The most favored electron donor to add is one which partitions well with the chlorinated solvent or can be concentrated near it. Unfortunately, an ideal electron donor, such as vegetable oil, is difficult to introduce and mix with DNAPL in the ground, doing this properly remains an engineering challenge. Numerical model studies have indicated that several factors may significantly influence the rate and extent of enhancement, including the inhibitory effects of PCE and cDCE, the level of ED concentration, DNAPL configuration, and competition for ED. Such factors need to be considered when contemplating engineered DNAPL bioremediation. Pseudomonas stuzeri KC is an organism that transforms CT to carbon dioxide and chloride without the formation of the hazardous intermediate, chloroform. This is accomplished by production and secretion of a molecule called PDTC. This study was direct ed towards determining how PDTC works. Cu (II) at a ratio of 1:1 Cu to PDTC was found to result in the most rapid CT transformation, confirming that the PDTC-Cu complex is both a reactant and a catalyst in CT transformation. CT degradation requires that the PDTC be in a reduced form, which is generated by contact with cell components. Fe(II) inhibits CT transformation by PDTC. Studies indicated that this inhibition is enhanced by some compound or factor in the supernatant with molecular weight greater than 10,000 Da. We have made progress in determining what this factor might be, but have not yet been able to identify it. In related studies, we found that CT transformation by another organism, Shewanella oneidensis MR1, also involves an excreted factor, but this factor is different from PDTC and results in chloroform transformation as an intermediate. Our studies have indicated that this factor is similar to vitamin K2, and we have also confirmed that vitamin K2 does transform C T into chloroform.

  2. Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB.

    PubMed

    Ergel, Burçe; Gill, Michelle L; Brown, Lewis; Yu, Bomina; Palmer, Arthur G; Hunt, John F

    2014-10-24

    A central goal of enzymology is to understand the physicochemical mechanisms that enable proteins to catalyze complex chemical reactions with high efficiency. Recent methodological advances enable the contribution of protein dynamics to enzyme efficiency to be explored more deeply. Here, we utilize enzymological and biophysical studies, including NMR measurements of conformational dynamics, to develop a quantitative mechanistic scheme for the DNA repair enzyme AlkB. Like other iron/2-oxoglutarate-dependent dioxygenases, AlkB employs a two-step mechanism in which oxidation of 2-oxoglutarate generates a highly reactive enzyme-bound oxyferryl intermediate that, in the case of AlkB, slowly hydroxylates an alkylated nucleobase. Our results demonstrate that a microsecond-to-millisecond time scale conformational transition facilitates the proper sequential order of substrate binding to AlkB. Mutations altering the dynamics of this transition allow generation of the oxyferryl intermediate but promote its premature quenching by solvent, which uncouples 2-oxoglutarate turnover from nucleobase oxidation. Therefore, efficient catalysis by AlkB depends upon the dynamics of a specific conformational transition, establishing another paradigm for the control of enzyme function by protein dynamics. PMID:25043760

  3. Enzyme-free and sensitive electrochemical determination of the FLT3 gene based on a dual signal amplified strategy: Controlled nanomaterial multilayers and a target-catalyzed hairpin assembly.

    PubMed

    Sun, Yingying; Ren, Qunxiang; Liu, Bo; Qin, Yan; Zhao, Shuang

    2016-04-15

    An isothermal, enzyme-free and sensitive electrochemical DNA sensor was developed for the detection of the FLT3 gene in acute myeloid leukemia (AML). First, aminated multi-walled carbon nanotubes (AMWNTs) and gold nanoparticles (AuNPs) were alternately self-assembled on a gold electrode using a layer-by-layer strategy. Then, the hairpin DNA probe 1 (H1), with a thiol group at the 3' end and a ferrocenyl moiety (Fc) at the 5' end, was immobilized on the AMWNTs/AuNPs multilayer films through Au-S bonding. When the target DNA (TD) appeared, it hybridized with and opened the hairpin structure of H1, and Fc was forced away from the electrode surface, leading to a significant decrease in the current peak of square wave voltammetry. Subsequently, the hairpin DNA probe 2 (H2) bound to H1, freeing the TD to trigger another reaction cycle. The combination of this target-catalyzed hairpin assembly and the LBL assembly of nanomaterials achieved a detection limit of 0.1pM with a wide linear range of 0.1-1000pM. The sensor discriminated between mismatched DNA and the target DNA with high selectivity. This dual signal amplification strategy is relatively simple and inexpensive because it does not need any enzymes or sophisticated equipment and successfully assayed the FLT3 gene from real samples. PMID:26584077

  4. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids.

    PubMed

    Wang, Zhonghua; Yeats, Trevor; Han, Hong; Jetter, Reinhard

    2010-09-24

    The first committed step in triterpenoid biosynthesis is the cyclization of oxidosqualene to polycyclic alcohols or ketones C(30)H(50)O. It is catalyzed by single oxidosqualene cyclase (OSC) enzymes that can carry out varying numbers of carbocation rearrangements and, thus, generate triterpenoids with diverse carbon skeletons. OSCs from diverse plant species have been cloned and characterized, the large majority of them catalyzing relatively few rearrangement steps. It was recently predicted that special OSCs must exist that can form friedelin, the pentacyclic triterpenoid whose formation involves the maximum possible number of rearrangement steps. The goal of the present study, therefore, was to clone a friedelin synthase from Kalanchoe daigremontiana, a plant species known to accumulate this triterpenoid in its leaf surface waxes. Five OSC cDNAs were isolated, encoding proteins with 761-779 amino acids and sharing between 57.4 and 94.3% nucleotide sequence identity. Heterologous expression in yeast and GC-MS analyses showed that one of the OSCs generated the steroid cycloartenol together with minor side products, whereas the other four enzymes produced mixtures of pentacyclic triterpenoids dominated by lupeol (93%), taraxerol (60%), glutinol (66%), and friedelin (71%), respectively. The cycloartenol synthase was found expressed in all leaf tissues, whereas the lupeol, taraxerol, glutinol, and friedelin synthases were expressed only in the epidermis layers lining the upper and lower surfaces of the leaf blade. It is concluded that the function of these enzymes is to form respective triterpenoid aglycones destined to coat the leaf exterior, probably as defense compounds against pathogens or herbivores. PMID:20610397

  5. Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA

    PubMed Central

    Tan, Dazhi; Crabb, Warren M.; Whitman, William B.; Tong, Liang

    2013-01-01

    Dimethyl-sulphoniopropionate (DMSP) is produced in abundance by marine phytoplankton, and the catabolism of this compound is an important source of carbon and reduced sulfur for marine bacteria and other organisms. The enzyme DmdD catalyzes the last step in the methanethiol (MeSH) pathway of DMSP catabolism. DmdD is a member of the crotonase superfamily of enzymes, and it catalyzes both the hydration and the hydrolysis of methylthioacryloyl-CoA (MTA-CoA), converting it to acetaldehyde, CO2, MeSH, and CoA. We report here the crystal structure of Ruegeria pomeroyi DmdD free enzyme at 1.5 Å resolution and the structures of the E121A mutant in complex with MTA-CoA and 3-methylmercaptopropionate-CoA (MMPA-CoA) at 1.8 Å resolution. DmdD is a hexamer, composed of a dimer of trimers where the three monomers of each trimer are related by a crystallographic 3-fold axis. The overall structure of this hexamer is similar to those of canonical crotonases. However, the C-terminal loops of DmdD in one of the trimers assume a different conformation and contribute to CoA binding in the active site of a neighboring monomer of the trimer, while these loops in the second trimer are disordered. MTA-CoA is bound deep in the active site in the first trimer, but shows a 1.5 Å shift in its position in the second trimer. MMPA-CoA has a similar binding mode to MTA-CoA in the first trimer. MMPA-CoA cannot be hydrated and is only hydrolyzed slowly by DmdD. Replacement of the sulfur atom in MMPA-CoA with a methylene group abolishes hydrolysis, suggesting that the unique property of the substrate is a major determinant of the hydrolysis activity of DmdD. PMID:23704947

  6. Cytochrome P450 3A Enzymes Catalyze the O6-Demethylation of Thebaine, a Key Step in Endogenous Mammalian Morphine Biosynthesis.

    PubMed

    Kramlinger, Valerie M; Alvarado Rojas, Mónica; Kanamori, Tatsuyuki; Guengerich, F Peter

    2015-08-14

    Morphine, first characterized in opium from the poppy Papaver somniferum, is one of the strongest known analgesics. Endogenous morphine has been identified in several mammalian cells and tissues. The synthetic pathway of morphine in the opium poppy has been elucidated. The presence of common intermediates in plants and mammals suggests that biosynthesis occurs through similar pathways (beginning with the amino acid L-tyrosine), and the pathway has been completely delineated in plants. Some of the enzymes in the mammalian pathway have been identified and characterized. Two of the latter steps in the morphine biosynthesis pathway are demethylation of thebaine at the O(3)- and the O(6)-positions, the latter of which has been difficult to demonstrate. The plant enzymes responsible for both the O(3)-demethylation and the O(6)-demethylation are members of the Fe(II)/?-ketoglutarate-dependent dioxygenase family. Previous studies showed that human cytochrome P450 (P450) 2D6 can catalyze thebaine O(3)-demethylation. We report that demethylation of thebaine at the O(6)-position is selectively catalyzed by human P450s 3A4 and 3A5, with the latter being more efficient, and rat P450 3A2. Our results do not support O(6)-demethylation of thebaine by an Fe(II)/?-ketoglutarate-dependent dioxygenase. In rat brain microsomes, O(6)-demethylation was inhibited by ketoconazole, but not sulfaphenazole, suggesting that P450 3A enzymes are responsible for this activity in the brain. An alternate pathway to morphine, oripavine O(6)-demethylation, was not detected. The major enzymatic steps in mammalian morphine synthesis have now been identified. PMID:26157146

  7. Co(III)-catalyzed C-H activation/formal SN-type reactions: selective and efficient cyanation, halogenation, and allylation.

    PubMed

    Yu, Da-Gang; Gensch, Tobias; de Azambuja, Francisco; Vásquez-Céspedes, Suhelen; Glorius, Frank

    2014-12-24

    The first cobalt-catalyzed cyanation, halogenation, and allylation via C-H activation have been realized. These formal SN-type reactions generate valuable (hetero)aryl/alkenyl nitriles, iodides, and bromides as well as allylated indoles using a bench-stable Co(III) catalyst. High regio- and mono-selectivity were achieved for these reactions. Additionally, allylation proceeded efficiently with a turnover number of 2200 at room temperature, which is unprecedented for this Co(III) catalyst. Alkenyl substrates and amides have been successfully utilized in Cp*Co(III)-catalyzed C-H activation for the first time. PMID:25472496

  8. The Construction of All-Carbon Quaternary Stereocenters by Use of Pd-Catalyzed Asymmetric Allylic Alkylation Reactions in Total Synthesis

    PubMed Central

    Hong, Allen Y.

    2014-01-01

    All-carbon quaternary stereocenters have posed significant challenges in the synthesis of complex natural products. These important structural motifs have inspired the development of broadly applicable palladium-catalyzed asymmetric allylic alkylation reactions of unstabilized non-biased enolates for the synthesis of enantioenriched ?-quaternary products. This microreview outlines key considerations in the application of palladium-catalyzed asymmetric allylic alkylation reactions and presents recent total syntheses of complex natural products that have employed these powerful transformations for the direct, catalytic, enantioselective construction of all-carbon quaternary stereocenters. PMID:24944521

  9. 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

  10. Investigation at the atomic level of homologous enzymes reveals distinct reaction paths

    NASA Astrophysics Data System (ADS)

    Zoi, Ioanna; Schwartz, Steven D.

    2015-03-01

    Bacterial enzymes Escherichia coli and Vibrio cholerae 5' -Methylthioadenosine nucleosidases (MTANs) have different binding affinities for the same transition state analogue. This was surprising as these enzymes share 60% sequence identity, have almost identical active sites and act under the same mechanism. We performed Transition Path Sampling simulations of both enzymes to reveal the atomic details of the catalytic chemical step, to explain the inhibitor affinity differences. Unlike EcMTAN, VcMTAN has multiple distinct transition states, which is an indication that multiple sets of coordinated protein motions can reach a transition state. We also identified the important residues that participate in each enzyme's reaction coordinate and explained their contribution. Subtle dynamic differences manifest in difference of reaction coordinate and transition state structure and also suggest that MTANs differ from most ribosyl transferases. As experimental approaches report averages regarding reaction coordinate information, this study offers, previously unavailable, detailed knowledge to the explanation of bacterial MTANs catalytic mechanism, and could have a significant impact on pharmaceutical design. We acknowledge the support of the National Institutes of Health through Grant GM068036.

  11. 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

  12. 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.

  13. Accumulation of acyl-enzyme in DD-peptidase-catalysed reactions with analogues of peptide substrates.

    PubMed Central

    Jamin, M; Adam, M; Damblon, C; Christiaens, L; Frère, J M

    1991-01-01

    Thioester substrates can be used to study the hydrolysis and transfer reactions catalysed by beta-lactamases and DD-peptidases. With the latter enzymes, accumulation of the acyl-enzyme can be detected directly. The efficiency of various amines as acceptor substrates was in excellent agreement with previous results obtained with peptide substrates of the DD-peptidases. The results indicated the presence of a specific binding site for the acceptor substrates. Although most of the results agreed well with a simple partition model, more elaborate hypotheses will be needed to account for all the data presented. PMID:1747125

  14. Physiological aspects of free-radical reactions.

    PubMed Central

    Yamazaki, I; Tamura, M; Nakajima, R; Nakamura, M

    1985-01-01

    Enzymes which catalyze the formation of free radicals in vitro will catalyze similar reactions in vivo. We believe that the formation of some kinds of free radicals has definite physiological meanings in metabolism. In this sense, the enzymes forming such free radicals are concluded to be in evolutionally advanced states. Elaborated structure and function of enzymes such as horseradish peroxidase and microsomal flavoproteins support the idea. Deleterious and side reactions caused by free radicals are assumed to be minimized in vivo by localizing the reactions, but this assumption should be verified by future studies. PMID:3007098

  15. Obtaining enzymes in pure form was an essential prerequisite for understanding the

    E-print Network

    Herschlag, Dan

    Obtaining enzymes in pure form was an essential prerequisite for understanding the underlying and affinity tag- ging2. In addition to the most basic task of identifying distinct enzymes that catalyze dis- tinct reactions (an endeavor that continues in the genomic era), enzymes were shown to exhibit high

  16. Evolution of Domain Architectures and Catalytic Functions of Enzymes in Metabolic Systems

    E-print Network

    Yeang, Chen-Hsiang

    Evolution of Domain Architectures and Catalytic Functions of Enzymes in Metabolic Systems Summit architectures and catalytic functions of enzymes constitute the centerpieces of a metabolic network. These types. In contrast, prokaryotic enzymes become more versatile by catalyzing multiple reactions with similar chemical

  17. A Hands-On Classroom Simulation to Demonstrate Concepts in Enzyme Kinetics

    ERIC Educational Resources Information Center

    Junker, Matthew

    2010-01-01

    A classroom exercise is described to introduce enzyme kinetics in an undergraduate biochemistry or chemistry course. The exercise is a simulation in which a student acts as an enzyme that "catalyzes" the unscrewing of a nut from a bolt. With other students assisting, the student enzyme carries out reactions with bolt-nut substrates under different…

  18. Copurification of glucosamine-1-phosphate acetyltransferase and N-acetylglucosamine-1-phosphate uridyltransferase activities of Escherichia coli: characterization of the glmU gene product as a bifunctional enzyme catalyzing two subsequent steps in the pathway for UDP-N-acetylglucosamine synthesis.

    PubMed Central

    Mengin-Lecreulx, D; van Heijenoort, J

    1994-01-01

    The glmU gene product of Escherichia coli was recently identified as the N-acetylglucosamine-1-phosphate uridyltransferase activity which catalyzes the formation of UDP-N-acetylglucosamine, an essential precursor for cell wall peptidoglycan and lipopolysaccharide biosyntheses (D. Mengin-Lecreulx and J. van Heijenoort, J. Bacteriol. 175:6150-6157, 1993). Evidence that the purified GlmU protein is in fact a bifunctional enzyme which also catalyzes acetylation of glucosamine-1-phosphate, the preceding step in the same pathway, is now provided. Kinetic parameters of both reactions were investigated, indicating in particular that the acetyltransferase activity of the enzyme is fivefold higher than its uridyltransferase activity. In contrast to the uridyltransferase activity, which is quite stable and insensitive to thiol reagents, the acetyltransferase activity was rapidly lost when the enzyme was stored in the absence of reducing thiols or acetyl coenzyme A or was treated with thiol-alkylating agents, suggesting the presence of at least one essential cysteine residue in or near the active site. The acetyltransferase activity is greatly inhibited by its reaction product N-acetylglucosamine-1-phosphate and, interestingly, also by UDP-N-acetylmuramic acid, which is one of the first precursors specific for the peptidoglycan pathway. The detection in crude cell extracts of a phosphoglucosamine mutase activity finally confirms that the route from glucosamine-6-phosphate to UDP-N-acetylglucosamine occurs via glucosamine-1-phosphate in bacteria. PMID:8083170

  19. Palladium-catalyzed desulfitative Mizoroki-Heck couplings of sulfonyl chlorides with mono- and disubstituted olefins: rhodium-catalyzed desulfitative heck-type reactions under phosphine- and base-free conditions.

    PubMed

    Dubbaka, Srinivas Reddy; Vogel, Pierre

    2005-04-22

    New conditions have been found for the desulfitative Mizoroki-Heck arylation and trifluoromethylation of mono- and disubustituted olefins with arenesulfonyl and trifluoromethanesulfonyl chlorides. Thus (E)-1,2-disubstituted alkenes with high stereoselectivity and 1,1,2-disubstituted alkenes with 12:1 to 21:1 E/Z steroselectivity can be obtained. Herrmann's palladacycle at 0.1 mol % is sufficient to catalyze these reactions, for which electron-rich or electron-poor sulfonyl chlorides and alkenes are suitable. If phosphine- and base-free conditions are required, 1 mol % [RhCl(C(2)H(4))(2)] catalyzes the desulfitative cross-coupling reactions. Contrary to results reported for [RuCl(2)(PPh(3))(2)]-catalyzed coupling reactions with sulfonyl chlorides, the palladium and rhodium desulfitative Mizoroki-Heck coupling reactions are not inhibited by radical scavenging agents. Possible sulfones arising from the sulfonylation of alkenes at 60 degrees C are not desulfitated at higher temperatures in the presence of the Pd or Rh catalysts. PMID:15593242

  20. Aspergillus parasiticus Cyclase Catalyzes Two Dehydration Steps in Aflatoxin Biosynthesis

    PubMed Central

    Sakuno, Emi; Wen, Ying; Hatabayashi, Hidemi; Arai, Hatsue; Aoki, Chiemi; Yabe, Kimiko; Nakajima, Hiromitsu

    2005-01-01

    In the aflatoxin biosynthetic pathway, 5?-oxoaverantin (OAVN) cyclase, the cytosolic enzyme, catalyzes the reaction from OAVN to (2?S,5?S)-averufin (AVR) (E. Sakuno, K. Yabe, and H. Nakajima, Appl. Environ. Microbiol. 69:6418-6426, 2003). Interestingly, the N-terminal 25-amino-acid sequence of OAVN cyclase completely matched an internal sequence of the versiconal (VHOH) cyclase that was deduced from its gene (vbs). The purified OAVN cyclase also catalyzed the reaction from VHOH to versicolorin B (VB). In a competition experiment using the cytosol fraction of Aspergillus parasiticus, a high concentration of VHOH inhibited the enzyme reaction from OAVN to AVR, and instead VB was newly formed. The recombinant Vbs protein, which was expressed in Pichia pastoris, showed OAVN cyclase activity, as well as VHOH cyclase activity. A mutant of A. parasiticus SYS-4 (= NRRL 2999) with vbs deleted accumulated large amounts of OAVN, 5?-hydroxyaverantin, averantin, AVR, and averufanin in the mycelium. These results indicated that the cyclase encoded by the vbs gene is also involved in the reaction from OAVN to AVR in aflatoxin biosynthesis. Small amounts of VHOH, VB, and aflatoxins also accumulated in the same mutant, and this accumulation may have been due to an unknown enzyme(s) not involved in aflatoxin biosynthesis. This is the first report of one enzyme catalyzing two different reactions in a pathway of secondary metabolism. PMID:15932995

  1. Alkene Cleavage Catalysed by Heme and Nonheme Enzymes: Reaction Mechanisms and Biocatalytic Applications

    PubMed Central

    Mutti, Francesco G.

    2012-01-01

    The oxidative cleavage of alkenes is classically performed by chemical methods, although they display several drawbacks. Ozonolysis requires harsh conditions (?78°C, for a safe process) and reducing reagents in a molar amount, whereas the use of poisonous heavy metals such as Cr, Os, or Ru as catalysts is additionally plagued by low yield and selectivity. Conversely, heme and nonheme enzymes can catalyse the oxidative alkene cleavage at ambient temperature and atmospheric pressure in an aqueous buffer, showing excellent chemo- and regioselectivities in certain cases. This paper focuses on the alkene cleavage catalysed by iron cofactor-dependent enzymes encompassing the reaction mechanisms (in case where it is known) and the application of these enzymes in biocatalysis. PMID:22811656

  2. Heavy atom isotope effects on enzymatic reactions

    NASA Astrophysics Data System (ADS)

    Paneth, Piotr

    1994-05-01

    The theory of isotope effects, which has proved to be extremely useful in providing geometrical details of transition states in a variety of chemical reactions, has recently found an application in studies of enzyme-catalyzed reactions. These reactions are multistep in nature with few steps being partially rate-limiting, thus interpretation of these isotope effects is more complex. The theoretical framework of heavy-atom isotope effects on enzymatic reactions is critically analyzed on the basis of recent results of: carbon kinetic isotope effects on carbonic anhydrase and catalytic antibodies; multiple carbon, deuterium isotope effects on reactions catalyzed by formate decarboxylase; oxygen isotope effects on binding processes in reactions catalyzed by pyruvate kinase; and equilibrium oxygen isotope effect on binding an inhibitor to lactate dehydrogenase. The advantages and disadvantages of reaction complexity in learning details of formal and molecular mechanisms are discussed in the examples of reactions catalyzed by phosphoenolpyruvate carboxylase, orotidine decarboxylase and glutamine synthetase.

  3. Iron-catalyzed Rearrangements and Cycloaddition Reactions of 2H-Chromenes

    PubMed Central

    Luan, Yi; Sun, Huan

    2014-01-01

    Iron(III) salts catalyse the tandem rearrangement/hetero-Diels—Alder reaction of 2H-chromenes to yield tetrahydrochromeno heterocycles. The process can occur as a homodimerization and cycloaddition process using electron rich dienophiles. Deuterium labeling and mechanistic studies revealed a hydride shift and ortho-quinone methide cycloaddition reaction pathway. PMID:22098535

  4. Mechanistic insights into a BINOL-derived phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction

    E-print Network

    Overvoorde, Lois M.; Grayson, Matthew N.; Luo, Yi; Goodman, Jonathan M.

    2015-02-05

    chiral quaternary carbon center via an asymmetric Pictet?Spengler reaction between tryptamine and (2-oxocyclohexyl)acetic acid. The Pictet?Spengler reaction3 was first discovered in 1911 by Ame ? Pictet and Theodor Spengler and has since been used...

  5. Developing five-membered heterocycle substituted phosphinous acids as ligands for palladium-catalyzed Suzuki-Miyaura and Catellani reactions.

    PubMed

    Chang, Ting-Wei; Ho, Pei-Yun; Mao, Kuo-Chung; Hong, Fung-E

    2015-10-21

    A new category of secondary phosphine oxides (SPOs) (5a-5j) with/without benzo-fused five-membered heterocyclic substituents were prepared. These new compounds are air- and moisture-stable ligands and have the advantage of long-term storage. Some of the ligands as well as ligand coordinated palladium complexes (6f' and 6f'') and platinum complexes (7b_trans & 7i_trans) were prepared and their structures were determined using single crystal X-ray diffraction methods. The crystal structure of 6f' revealed the formation of diamond shape di-palladium complexes with a Pd2Cl2 core. As for the structures of 7b_trans & 7i_trans, the processes for the generation of the trans-form of the bis-phosphine ligand coordinated platinum complexes are shown. These SPOs exhibit notable efficiencies in palladium-catalyzed Suzuki-Miyaura reactions. Moreover, organic compounds (9k and 10c) with unexpected conformations were obtained from Heck-type Catellani reactions. Reaction pathways are proposed to accommodate the probable routes for the formation of all organic products. PMID:26370178

  6. Enthalpy and entropy barriers explain the effects of topology on the kinetics of zeolite-catalyzed reactions.

    PubMed

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

    2013-08-26

    The methylation of ethene, propene, and trans-2-butene on zeolites H-ZSM-58 (DDR), H-ZSM-22 (TON), and H-ZSM-5 (MFI) is studied to elucidate the particular influence of topology on the kinetics of zeolite-catalyzed reactions. H-ZSM-58 and H-ZSM-22 are found to display overall lower methylation rates compared to H-ZSM-5 and also different trends in methylation rates with increasing alkene size. These variations may be rationalized based on a decomposition of the free-energy barriers into enthalpic and entropic contributions, which reveals that the lower methylation rates on H-ZSM-58 and H-ZSM-22 have virtually opposite reasons. On H-ZSM-58, the lower methylation rates are caused by higher enthalpy barriers, owing to inefficient stabilization of the reaction intermediates in the large cage-like pores. On the other hand, on H-ZSM-22, the methylation rates mostly suffer from higher entropy barriers, because excessive entropy losses are incurred inside the narrow-channel structure. These results show that the kinetics of crucial elementary steps hinge on the balance between proper stabilization of the reaction intermediates inside the zeolite pores and the resulting entropy losses. These fundamental insights into their inner workings are indispensable for ultimately selecting or designing better zeolite catalysts. PMID:23897717

  7. Concise Enantioselective Synthesis of Oxygenated Steroids via Sequential Copper(II)-Catalyzed Michael Addition/Intramolecular Aldol Cyclization Reactions

    PubMed Central

    Cichowicz, Nathan R.; Kaplan, Will; Khomutnyk, Yaroslav; Bhattarai, Bijay; Sun, Zhankui; Nagorny, Pavel

    2015-01-01

    A new scalable enantioselective approach to functionalized oxygenated steroids is described. This strategy is based on chiral bis(oxazoline) copper(II) complex-catalyzed enantioselective and diastereoselective Michael reactions of cyclic ketoesters and enones to install vicinal quaternary and tertiary stereocenters. In addition, the utility of copper(II) salts as highly active catalysts for the Michael reactions of traditionally unreactive ???-enones and substituted ???-ketoesters that results in unprecedented Michael adducts containing vicinal all-carbon quaternary centers is also demonstrated. The Michael adducts subsequently undergo base-promoted diastereoselective aldol cascade reactions resulting in the natural or unnatural steroid skeletons. The experimental and computational studies suggest that the torsional strain effects arising from the presence of the ?5-unsaturation are key controling elements for the formation of the natural cardenolide scaffold. The described method enables expedient generation of polycyclic molecules including modified steroidal scaffolds as well as challenging-to-synthesize Hajos-Parrish and Wieland-Miescher ketones. PMID:26491886

  8. Concise Enantioselective Synthesis of Oxygenated Steroids via Sequential Copper(II)-Catalyzed Michael Addition/Intramolecular Aldol Cyclization Reactions.

    PubMed

    Cichowicz, Nathan R; Kaplan, Will; Khomutnyk, Yaroslav; Bhattarai, Bijay; Sun, Zhankui; Nagorny, Pavel

    2015-11-18

    A new scalable enantioselective approach to functionalized oxygenated steroids is described. This strategy is based on chiral bis(oxazoline) copper(II) complex-catalyzed enantioselective and diastereoselective Michael reactions of cyclic ketoesters and enones to install vicinal quaternary and tertiary stereocenters. In addition, the utility of copper(II) salts as highly active catalysts for the Michael reactions of traditionally unreactive ?,?'-enones and substituted ?,?'-ketoesters that results in unprecedented Michael adducts containing vicinal all-carbon quaternary centers is also demonstrated. The Michael adducts subsequently undergo base-promoted diastereoselective aldol cascade reactions resulting in the natural or unnatural steroid skeletons. The experimental and computational studies suggest that the torsional strain effects arising from the presence of the ?(5)-unsaturation are key controlling elements for the formation of the natural cardenolide scaffold. The described method enables expedient generation of polycyclic molecules including modified steroidal scaffolds as well as challenging-to-synthesize Hajos-Parrish and Wieland-Miescher ketones. PMID:26491886

  9. Interconversion of ketoprofen recognition in firefly luciferase-catalyzed enantioselective thioesterification reaction using from Pylocoeria miyako (PmL) and Hotaria parvura (HpL) just by mutating two amino acid residues.

    PubMed

    Kato, Dai-ichiro; Hiraishi, Yoshihiro; Maenaka, Mika; Yokoyama, Keisuke; Niwa, Kazuki; Ohmiya, Yoshihiro; Takeo, Masahiro; Negoro, Seiji

    2013-11-01

    We identified the critical amino acid residues for substrate recognition using two firefly luciferases from Pylocoeria miyako (PmL) and Hotaria parvura (HpL), as these two luciferase enzymes exhibit different activities toward ketoprofen. Specifically, PmL can catalyze the apparent enantioselective thioesterification reaction, while HpL cannot. By comparing the amino acid sequences around the active site, we identified two residues (I350 and M397 in PmL and F351 and S398 in HpL) that were different between the two enzymes, and the replacement of these amino acids resulted in changing the ketoprofen recognition pattern. The inactive HpL was converted to the active enzyme toward ketoprofen and vice versa for PmL. These residues also affected the enantioselectivity toward ketoprofen; however, the bioluminescent color was not affected. In addition, using molecular dynamics calculations, the replacement of these two amino acids induced changes in the state of hydrogen bonding between ketoprofen and the S349 side chain through the active site water. As S349 is not considered to influence color tuning, these changes specifically caused the differences in ketoprofen recognition in the enzyme. PMID:23685028

  10. The design, synthesis and validation of recoverable and readily reusable siloxane transfer agents for Pd-catalyzed cross-coupling reactions.

    PubMed

    Martinez-Solorio, Dionicio; Hoye, Adam T; Nguyen, Minh H; Smith, Amos B

    2013-05-17

    The development of competent, recoverable and reusable 1-oxa-2-silacyclopentene (siloxane) transfer agents for Pd-catalyzed cross-coupling reactions (CCRs) of organolithium reagents with aryl and alkenyl iodides has been achieved. Drawbacks of the first-generation siloxane-transfer agent (1), relating to facile recovery for potential recycling, have been addressed. PMID:23627729

  11. Synthesis of Functionalized Chromeno[2,3-b]pyrrol-4(1H)-ones by Silver-Catalyzed Cascade Reactions of Chromones/Thiochromones and Isocyanoacetates.

    PubMed

    Qi, Xueyu; Xiang, Haoyue; Yang, Chunhao

    2015-11-20

    A novel and convenient approach to the synthesis of chromeno[2,3-b]pyrrol-4(1H)-ones has been developed. Furthermore, the method involves a facile silver-catalyzed cascade cyclization reaction including an intramolecular C-O bond formation. The silver salt acts as a key promoter. PMID:26562216

  12. Synthesis of 2-trifluoromethylpyrazolo[5,1-a]isoquinolines via silver triflate-catalyzed or electrophile-mediated one-pot tandem reaction.

    PubMed

    Zhou, Xiaoli; Liu, Meiling; Luo, Puying; Lai, Yingjun; Yang, Tangtao; Ding, Qiuping

    2014-01-01

    An efficient one-pot tandem cyclization/[3 + 2] cycloaddition reaction of N'-(2-alkynylbenzylidene)hydrazides with ethyl 4,4,4-trifluorobut-2-ynoate under silver triflate-catalyzed or electrophile-mediated conditions is described. Various trifluoromethylated pyrazolo[5,1-a]isoquinolines were afforded in moderate to excellent yield by this developed method. PMID:25298796

  13. "N"-Heterocyclic Carbene-Catalyzed Reaction of Chalcone and Cinnamaldehyde to Give 1,3,4-Triphenylcyclopentene Using Organocatalysis to Form a Homoenolate Equivalent

    ERIC Educational Resources Information Center

    Snider, Barry B.

    2015-01-01

    In this experiment, students carry out a modern organocatalytic reaction using IMes·HCl and NaOH to catalyze the formation of 1,3,4-triphenylcyclopentene from cinnamaldehyde and chalcone in water. Deprotonation of IMes·HCl with NaOH forms the "N"-heterocyclic carbene IMes that reacts with cinnamaldehyde to form a homoenolate equivalent…

  14. An Enantioselective Approach to 4-O-Protected-2-cyclopentene-l,4-diol Derivatives via a Rhodium-Catalyzed Redox-Isomerization Reaction.

    PubMed

    Ren, Kai; Zhao, Mengmeng; Hu, Bei; Lu, Bin; Xie, Xiaomin; Ratovelomanana-Vidal, Virginie; Zhang, Zhaoguo

    2015-12-18

    Kinetic resolution of a series of cyclopentene-1,4-diol derivatives has been successfully achieved with enantiomeric excess up to 99.4% and a kf/ks ratio of 55 by a rhodium-catalyzed redox-isomerization reaction in a noncoordinating solvent. PMID:26605977

  15. Lewis acid-catalyzed redox-neutral amination of 2-(3-pyrroline-1-yl)benzaldehydes via intramolecular [1,5]-hydride shift/isomerization reaction

    PubMed Central

    Jiang, Chun-Huan; Lei, Xiantao; Zhen, Le; Du, Hong-Jin; Wen, Xiaoan

    2014-01-01

    Summary Lewis acid-catalyzed redox-neutral amination of 2-(3-pyrroline-1-yl)benzaldehydes via intramolcular [1,5]-hydride shift/isomerization reaction has been realized, using the inherent reducing power of 3-pyrrolines. A series of N-arylpyrrole containing amines are obtained in high yields. PMID:25550755

  16. Gold(I)-Catalyzed Conia-Ene Reaction of -Ketoesters with Alkynes Joshua J. Kennedy-Smith, Steven T. Staben, and F. Dean Toste*

    E-print Network

    Toste, Dean

    Gold(I)-Catalyzed Conia-Ene Reaction of -Ketoesters with Alkynes Joshua J. Kennedy-Smith, Steven T(I) complexes as catalysts. Carbon-carbon bond formation promoted by homogeneous gold catalysts is extremely did not proceed to completion even after a day at room temperature (entry 1). On the other hand, gold

  17. Rapid and Efficient Functionalized Ionic Liquid-Catalyzed Aldol Condensation Reactions Associated with Microwave Irradiation

    PubMed Central

    Wang, Chang; Liu, Jing; Leng, Wenguang; Gao, Yanan

    2014-01-01

    Five quaternary ammonium ionic liquid (IL) and two tetrabutylphosphonium ILs were prepared and characterized. An environmentally benign and convenient functionalized ionic liquid catalytic system was thus explored in the aldol condensation reactions of aromatic aldehydes with acetone. The aldol reactions proceeded more efficiently through microwave-assisted heating than through conventional thermal heating. The yield of products obtained under microwave heating for 30 min was approximately 90%, and the ILs can be recovered and reused at least five times without apparent loss of activity. In addition, this catalytic system can be successfully extended to the Henry reactions. PMID:24445262

  18. Synthesis of 1,4:3,6-dianhydrohexitols diesters from the palladium-catalyzed hydroesterification reaction.

    PubMed

    Pruvost, Romain; Boulanger, Jérôme; Léger, Bastien; Ponchel, Anne; Monflier, Eric; Ibert, Mathias; Mortreux, André; Chenal, Thomas; Sauthier, Mathieu

    2014-11-01

    The hydroesterification of alpha olefins has been used to synthesize diesters from bio-based secondary diols: isosorbide, isomannide, and isoidide. The reaction was promoted by 0.2% palladium catalyst generated in?situ from palladium acetate/triphenylphosphine/para-toluene sulfonic acid. Optimized reaction conditions allowed the selective synthesis of the diesters with high yields and the reaction conditions could be scaled up to the synthesis of hundred grams of diesters from isosorbide and 1-octene with solvent-free conditions. PMID:25209303

  19. Excited State Dynamics Can Be Used to Probe Donor-Acceptor Distances for H-Tunneling Reactions Catalyzed by Flavoproteins

    PubMed Central

    Hardman, Samantha J.O.; Pudney, Christopher R.; Hay, Sam; Scrutton, Nigel S.

    2013-01-01

    In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H4, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H4-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems. PMID:24314085

  20. Horseradish peroxidase-catalyzed polymerization of l-DOPA for mono-/bi-enzyme immobilization and amperometric biosensing of H2O2 and uric acid.

    PubMed

    Dai, Mengzhen; Huang, Ting; Chao, Long; Xie, Qingji; Tan, Yueming; Chen, Chao; Meng, Wenhua

    2016-03-01

    Horseradish peroxidase (HRP)-catalyzed polymerization of l-DOPA (vs. dopamine) in the presence of H2O2 (and uricase (UOx)) was exploited to immobilize mono-/bi-enzymes for hydroquinone-mediated amperometric biosensing of H2O2 and uric acid (UA). The relevant polymeric biocomposites (PBCs) were prepared in phosphate buffer solution containing HRP and l-DOPA (or plus UOx) after adding H2O2. The mono-/bi-enzyme amperometric biosensors were prepared simply by casting some of the PBCs on Au-plated Au (Auplate/Au) electrodes, followed by coating with an outer-layer chitosan (CS) film for each. UV-vis spectrophotometry, scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy were used for film characterization and/or process monitoring. The HRP immobilized by enzyme catalysis well preserved its bioactivity, as confirmed by UV-vis spectrophotometry. Under optimized conditions, the monoenzyme CS/HRP-poly(l-DOPA) (PD)/Auplate/Au electrode potentiostated at -0.1V responded linearly to H2O2 concentration from 0.001 to 1.25mM with a sensitivity of 700?AmM(-1)cm(-2) and a limit of detection (LOD) of 0.1?M, and the bienzyme CS/UOx-HRP-PD/Auplate/Au electrode at -0.1V responded linearly to UA concentration from 0.001 to 0.4mM with a sensitivity of 349?AmM(-1)cm(-2) and a LOD of 0.1?M. The mono-/bi-enzyme biosensors based on biosynthesized PD performed better than many reported analogues and those based on similarly biosynthesized polydopamine. PMID:26717822

  1. Palladium-Catalyzed Carbonylative Annulation Reactions Using Aryl Formate as a CO Source: Synthesis of 2-Substituted Indene-1,3(2H)-dione Derivatives.

    PubMed

    Zhang, Ying; Chen, Jing-Lei; Chen, Zhen-Bang; Zhu, Yong-Ming; Ji, Shun-Jun

    2015-11-01

    An efficient synthesis of 2-substituted indene-1,3(2H)-diones from stable and readily available 1-(2-halophenyl)-1,3-diones by employing phenyl formate as a CO source has been developed. The reaction occurred via palladium-catalyzed intramolecular carbonylative annulation using K3PO4 as a base and DMSO as a solvent at 95 °C. In this protocol, the reaction showed a broad substrate scope with good to excellent yields. PMID:26452462

  2. Wash Bottle Laboratory Exercises: Iodide-Catalyzed H[subscript 2]O[subscript 2] Decomposition Reaction Kinetics Using the Initial Rate Approach

    ERIC Educational Resources Information Center

    Barlag, Rebecca; Nyasulu, Frazier

    2010-01-01

    A wash bottle water displacement scheme is used to determine the kinetics of the iodide-catalyzed H[subscript 2]O[subscript 2] decomposition reaction. The reagents (total volume 5.00 mL) are added to a test tube that is placed in a wash bottle containing water. The mass of the water displaced in [approximately]60 s is measured. The reaction is…

  3. Phosphine-catalyzed cascade [3 + 2] cyclization-allylic alkylation, [2 + 2 + 1] annulation, and [3 + 2] cyclization reactions between allylic carbonates and enones.

    PubMed

    Zhou, Rong; Wang, Jianfang; Song, Haibin; He, Zhengjie

    2011-02-18

    The phosphine-catalyzed annulations between Morita-Baylis-Hillman adduct carbonates and enones are reported. Under the catalysis of PBu(3) (20 mol %), cascade [3 + 2] cyclization-allylic alkylation, [2 + 2 + 1] annulation, and [3 + 2] cyclization reactions chemoselectively occur depending on the substituent variation of both the carbonate and enone. These reactions provide efficient syntheses of highly functionalized cyclopentenes and cyclopentanes. PMID:21235263

  4. Palladium-catalyzed intramolecular asymmetric C-H functionalization/cyclization reaction of metallocenes: an efficient approach toward the synthesis of planar chiral metallocene compounds.

    PubMed

    Deng, Ruixian; Huang, Yunze; Ma, Xinna; Li, Gencheng; Zhu, Rui; Wang, Bin; Kang, Yan-Biao; Gu, Zhenhua

    2014-03-26

    A palladium-catalyzed asymmetric synthesis of planar chiral metallocene compounds is reported. The reaction stereoselectively functionalized one of the ortho C-H bonds of Cp rings by intramolecular cyclization to form indenone derivatives in high yields with excellent enantioselectivity. The mild set of reaction conditions allowed a wide variety of chiral metallocene compounds to be synthesized with broad functional group tolerance. The influences of preinstalled chiralities on the other Cp-ring were also investigated. PMID:24617772

  5. Highly convergent, stereospecific synthesis of 11-cis-retinoids by metal-catalyzed cross-coupling reactions of (Z)-1-alkenylmetals.

    PubMed

    López, Susana; Montenegro, Javier; Saá, Carlos

    2007-12-01

    A stereospecific synthesis of 11-cis-retinoids has as its key step the hitherto unexplored palladium-catalyzed cross-coupling of trans-trienyl electrophiles and (1Z,3E)-penta-1,3-dienyl boronates (a Suzuki-Miyaura reaction) or stannanes (a Stille reaction). This highly convergent approach constitutes the first application of cis-organometallic moieties to the synthesis of 11-cis-retinoids and represents a general, straightforward route to the visual chromophore. PMID:18001096

  6. Regio-, Diastereo-, and Enantioselective Nitroso-Diels-Alder Reaction of 1,3-Diene-1-carbamates Catalyzed by Chiral Phosphoric Acids.

    PubMed

    Pous, Jonathan; Courant, Thibaut; Bernadat, Guillaume; Iorga, Bogdan I; Blanchard, Florent; Masson, Géraldine

    2015-09-23

    Chiral phosphoric acid-catalyzed asymmetric nitroso-Diels-Alder reaction of nitrosoarenes with carbamate-dienes afforded cis-3,6-disubstituted dihydro-1,2-oxazines in high yields with excellent regio-, diastereo-, and enantioselectivities. Interestingly, we observed that the catalyst is able not only to control the enantioselectivity but also to reverse the regioselectivity of the noncatalyzed nitroso-Diels-Alder reaction. The regiochemistry reversal and asynchronous concerted mechanism were confirmed by DFT calculations. PMID:26355670

  7. Polysubstituted 2-Aminopyrrole Synthesis via Gold-Catalyzed Intermolecular Nitrene Transfer from Vinyl Azide to Ynamide: Reaction Scope and Mechanistic Insights.

    PubMed

    Wu, Yufeng; Zhu, Lei; Yu, Yinghua; Luo, Xuesong; Huang, Xueliang

    2015-11-20

    A gold-catalyzed intermolecular reaction of vinyl azides and ynamides is described. This process presents an efficient and mild approach to multisubstituted 2-aminopyrroles in good-to-excellent yields. Control experiments were carried out to distinguish the reactivity between vinyl azides and the corresponding 2H-azirines. A plausible reaction mechanism was also proposed according to previous reports and our preliminary mechanistic studies. PMID:26503292

  8. What are proteins? Proteins are important; e.g. for catalyzing and regulating biochemical reactions,

    E-print Network

    Gerstein, Mark

    (or lack thereof) ·Proteins unfold or denature with increasing temperature or chemical denaturants reactions, transporting molecules, ... ·Linear polymer chain composed of tens (peptides) to thousands interactions, ... ·Unfolding: increase in conformational entropy, electric charge... H (hydrophobic) P (polar

  9. Selective, nickel-catalyzed carbon-carbon bond-forming reactions of alkynes

    E-print Network

    Miller, Karen M. (Karen Marie)

    2005-01-01

    Catalytic addition reactions to alkynes are among the most useful and efficient methods for preparing diverse types of substituted olefins. Controlling both regioselectivity and (EIZ)- selectivity in such transformations ...

  10. A Computational Study of Acid Catalyzed Aerosol Reactions of Atmospherically Relevant Epoxides

    EPA Science Inventory

    Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that ...

  11. Ethenolysis Reactions Catalyzed by Imido Alkylidene Monoaryloxide Monopyrrolide (MAP) Complexes of Molybdenum

    E-print Network

    Müller, Peter

    of Molybdenum Smaranda C. Marinescu, Richard R. Schrock,*, Peter Mu¨ller, and Amir H. Hoveyda Department that ethenolysis reactions that employ molybdenum-based MAP species can be highly efficient at room temperature

  12. Lewis Acid Catalyzed Asymmetric Three-Component Coupling Reaction: Facile Synthesis of ?-Fluoromethylated Tertiary Alcohols.

    PubMed

    Aikawa, Kohsuke; Kondo, Daisuke; Honda, Kazuya; Mikami, Koichi

    2015-12-01

    A chiral dicationic palladium complex is found to be an efficient Lewis acid catalyst for the synthesis of ?-fluoromethyl-substituted tertiary alcohols using a three-component coupling reaction. The reaction transforms three simple and readily available components (terminal alkyne, arene, and fluoromethylpyruvate) to valuable chiral organofluorine compounds. This strategy is completely atom-economical and results in perfect regioselectivities and high enantioselectivities of the corresponding tertiary allylic alcohols in good to excellent yields. PMID:26486488

  13. Recent progress in transition-metal-catalyzed reduction of molecular dinitrogen under ambient reaction conditions.

    PubMed

    Nishibayashi, Yoshiaki

    2015-10-01

    This paper describes our recent progress in catalytic nitrogen fixation by using transition-metal-dinitrogen complexes as catalysts. Two reaction systems for the catalytic transformation of molecular dinitrogen into ammonia and its equivalent such as silylamine under ambient reaction conditions have been achieved by the molybdenum-, iron-, and cobalt-dinitrogen complexes as catalysts. Many new findings presented here may provide new access to the development of economical nitrogen fixation in place of the Haber-Bosch process. PMID:26131967

  14. Large-Scale Refolding and Enzyme Reaction of Human Preproinsulin for Production of Human Insulin.

    PubMed

    Kim, Chang-Kyu; Lee, Seung-Bae; Son, Young-Jin

    2015-10-28

    Human insulin is composed of 21 amino acids of an A-chain and 30 amino acids of a B-chain. This is the protein hormone that has the role of blood sugar control. When the recombinant human proinsulin is expressed in Escherichia coli, a serious problem is the formation of an inclusion body. Therefore, the inclusion body must be denatured and refolded under chaotropic agents and suitable reductants. In this study, H27R-proinsulin was refolded from the denatured form with ?-mercaptoethanol and urea. The refolding reaction was completed after 15 h at 15°C, whereas the reaction at 25°C was faster than that at 15°C. The refolding yield at 15°C was 17% higher than that at 25°C. The refolding reaction could be carried out at a high protein concentration (2 g/l) using direct refolding without sulfonation. The most economical and optimal refolding condition for human preproinsulin was 1.5 g/l protein, 10 mM glycine buffer containing 0.6 M urea, pH 10.6, and 0.3 mM ?-mercaptoethanol at 15°C for 16 h. The maximum refolding yield was 74.8% at 15°C with 1.5 g/l protein. Moreover, the refolded preproinsulin could be converted into normal mature insulin with two enzymes. The average amount of human insulin was 138.2 g from 200 L of fermentation broth after enzyme reaction with H27R-proinsulin. The direct refolding process for H27R-proinsulin was successfully set up without sulfonation. The step yields for refolding and enzyme reaction were comparatively high. Therefore, our refolding process for production of recombinant insulin may be beneficial to the large-scale production of other biologically active proteins. PMID:26139616

  15. Spectrophotometric-dual-enzyme-simultaneous assay in one reaction solution: chemometrics and experimental models.

    PubMed

    Liu, Hongbo; Yang, Xiaolan; Liu, Lin; Dang, Jizheng; Xie, Yanling; Zhang, Yi; Pu, Jun; Long, Gaobo; Li, Yuanli; Yuan, Yonghua; Liao, Juan; Liao, Fei

    2013-02-19

    Spectrophotometric-dual-enzyme-simultaneous assay in one reaction solution (SDESA) is proposed. SDESA requires the following: (a) Enzyme A acts on Substrate A to release Product A bearing the longest difference absorbance peak (?(A)) much larger than that of Product B (?(B)) formed by Enzyme B action on Substrate B; ?(B) is close to the longest isoabsorbance wavelength of Product A and Substrate A (?(0)); (b) absorbance at ?(A) and ?(0) is quantified via swift alternation of detection wavelengths and corrected on the basis of absorbance additivity; (c) inhibition/activation on either enzyme by any substance is eliminated; (d) Enzyme A is quantified via an integration strategy if levels of Substrate A are lower than the Michaelis constant. Chemometrics of SDESA was tested with ?-glutamyltransferase and lactate-dehydrogenase of complicated kinetics. ?-Glutamyltransferase releases p-nitroaniline from ?-glutamyl-p-nitroaniline with ?(0) at 344 nm and ?(A) close to 405 nm, lactate-dehydrogenase consumes reduced nicotinamide dinucleotide bearing ?(B) at 340 nm. Kinetic analysis of reaction curve yielded lactate-dehydrogenase activity free from inhibition by p-nitroaniline; the linear range of initial rates of ?-glutamyltransferase via the integration strategy, and that of lactate-dehydrogenase after interference elimination, was comparable to those by separate assays, respectively; the quantification limit of either enzyme by SDESA at 25-fold higher activity of the other enzyme remained comparable to that by a separate assay. To test potential application, SDESA of alkaline phosphatase (ALP) and ?-D-galactosidase as enzyme-linked-immunoabsorbent assay (ELISA) labels were examined. ALP releases 4-nitro-1-naphthol from 4-nitronaphthyl-1-phosphate with ?(0) at 405 nm and ?(A) at 458 nm, ?-D-galactosidase releases 4-nitrophenol from ?-D-(4-nitrophenyl)-galactoside with ?(B) at 405 nm. No interference from substrates/products made SDESA of ?-galactosidase and ALP simple for ELISA of penicillin G and clenbuterol in one well, and the quantification limit of either hapten was comparable to that via a separate assay. Hence, SDESA is promising. PMID:23305208

  16. Malic enzyme (ME) catalyzes the oxidative decarboxylation of L-malate to pyruvate with the concomitant reduction of the

    E-print Network

    Tong, Liang

    , with fumarate as an activator and ATP as an inhibitor9, which is unique among malic enzymes. The amino acid in most living organisms, from bacteria to humans, and their amino acid sequences are highly conserved acid sequence homology to other proteins, such as the dehydro- genases and the decarboxylases. We

  17. Red Seaweed Enzyme-Catalyzed Bromination of Bromophenol Red: An Inquiry-Based Kinetics Laboratory Experiment for Undergraduates

    ERIC Educational Resources Information Center

    Jittam, Piyachat; Boonsiri, Patcharee; Promptmas, Chamras; Sriwattanarothai, Namkang; Archavarungson, Nattinee; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2009-01-01

    Haloperoxidase enzymes are of interest for basic and applied bioscientists because of their increasing importance in pharmaceutical industry and environmental cleanups. In a guided inquiry-based laboratory experiment for life-science, agricultural science, and health science undergraduates, the bromoperoxidase from a red seaweed was used to…

  18. Controllable cyclization reactions of 2-(2',3'-allenyl)acetylacetates catalyzed by gold and palladium affording substituted cyclopentene and 4,5-dihydrofuran derivatives with distinct selectivity.

    PubMed

    Jiang, Xuefeng; Ma, Xiaojing; Zheng, Zilong; Ma, Shengming

    2008-01-01

    Efficient room-temperature syntheses of cyclopentenes and 4,5-dihydrofurans with different substitution patterns were performed starting from the same materials (i.e., 2-(2',3'-allenyl)acetylacetates). Depending on the choice of metal catalyst, the Au-catalyzed reaction afforded C-attack-5-endo cyclization products 2, whereas the Pd-catalyzed one led to the formation of O-attack-5-exo cyclization products 3. The selectivity may be explained by the steric and electronic effects of the substrates and catalysts. PMID:18680128

  19. Degradation of Anthraquinone Dye Reactive Blue 4 in Pyrite Ash Catalyzed Fenton Reaction

    PubMed Central

    Becelic-Tomin, Milena; Dalmacija, Bozo; Rajic, Ljiljana; Tomasevic, Dragana; Kerkez, Djurdja; Watson, Malcolm; Prica, Miljana

    2014-01-01

    Pyrite ash (PA) is created by burning pyrite in the chemical production of sulphuric acid. The high concentration of iron oxide, mostly hematite, present in pyrite ash, gives the basis for its application as a source of catalytic iron in a modified Fenton process for anthraquinone dye reactive blue 4 (RB4) degradation. The effect of various operating variables such as catalyst and oxidant concentration, initial pH and RB4 concentration on the abatement of total organic carbon, and dye has been assessed in this study. Here we show that degradation of RB4 in the modified Fenton reaction was efficient under the following conditions: pH = 2.5; [PA]0 = 0.2?g?L?1; [H2O2]0 = 5?mM and initial RB4 concentration up to 100?mg?L?1. The pyrite ash Fenton reaction can overcome limitations observed from the classic Fenton reaction, such as the early termination of the Fenton reaction. Metal (Pb, Zn, and Cu) content of the solution after the process suggests that an additional treatment step is necessary to remove the remaining metals from the water. These results provide basic knowledge to better understand the modified, heterogeneous Fenton process and apply the PA Fenton reaction for the treatment of wastewaters which contains anthraquinone dyes. PMID:24526885

  20. An ionic liquid dependent mechanism for base catalyzed ?-elimination reactions from QM/MM simulations.

    PubMed

    Allen, Caley; Sambasivarao, Somisetti V; Acevedo, Orlando

    2013-01-23

    Ionic liquids have been proposed to induce a mechanistic change in the reaction pathway for the fundamentally important base-induced ?-elimination class compared to conventional solvents. The role of the reaction medium in the elimination of 1,1,1-tribromo-2,2-bis(3,4-dimethoxyphenyl)ethane via two bases, piperidine and pyrrolidine, has been computationally investigated using methanol and the ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate [BMIM][BF(4)] and [BMIM][PF(6)], respectively. QM/MM Monte Carlo simulations utilizing free-energy perturbation theory found the ionic liquids did produce a reaction pathway change from an E1cB-like mechanism in methanol to a pure E2 route that is consistent with experimental observations. The origin of the ionic liquid effect has been found as: (1) a combination of favorable electrostatic interactions, for example, bromine-imidazolium ion, and (2) ?-? interactions that enhance the coplanarity between aromatic rings maximizing the electronic effects exerted on the reaction route. Solute-solvent interaction energies have been analyzed and show that liquid clathrate solvation of the transition state is primarily responsible for the observed mechanistic changes. This work provides the first theoretical evidence of an ionic liquid dependent mechanism and elucidates the interplay between sterics and electrostatics crucial to understanding the effect of these unique solvents upon chemical reactions. PMID:23273322

  1. Effect of polyvinylpyrrolidone on mesoporous silica morphology and esterification of lauric acid with 1-butanol catalyzed by immobilized enzyme

    SciTech Connect

    Zhang, Jinyu; Zhou, Guowei Jiang, Bin; Zhao, Minnan; Zhang, Yan

    2014-05-01

    Mesoporous silica materials with a range of morphology evolution, i.e., from curved rod-shaped mesoporous silica to straight rod-shaped mesoporous silica, were successfully prepared using polyvinylpyrrolidone (PVP) and triblock copolymer as dual template. The effects of PVP molecular weight and concentration on mesoporous silica structure parameters were studied. Results showed that surface area and pore volume continuously decreased with increased PVP molecular weight. Mesoporous silica prepared with PVP K30 also possessed larger pore diameter, interplanar spacing (d{sub 100}), and cell parameter (a{sub 0}) than that prepared with PVP K15 and PVP K90. In addition, with increased PVP concentration, d{sub 100} and a{sub 0} continuously decreased. The mechanism of morphology evolution caused by the change in PVP concentration was investigated. The conversion rate of lauric acid with 1-butanol catalyzed by immobilized Porcine pancreatic lipase (PPL) was also evaluated. Results showed that PPL immobilized on amino-functionalized straight rod-shaped mesoporous silica maintained 50% of its esterification conversion rate even after five cycles of use with a maximum conversion rate was about 90.15%. - Graphical abstract: Curved rod-shaped mesoporous silica can be obtained at low and the highest PVP concentration, while straight rod-shaped mesoporous silica can be obtained at higher PVP concentration. - Highlights: • Mesoporous silica with morphology evolution from CRMS to SRMS were prepared. • Effects of PVP molecular weight and concentration on silica morphology were studied. • A possible mechanism for the formation of morphology evolution SiO{sub 2} was proposed. • Esterification of lauric acid with 1-butanol catalyzed by immobilized PPL.

  2. Factors influencing the mechanism of surfactant catalyzed reaction of vitamin C-ferric chloride hexahydrate system

    NASA Astrophysics Data System (ADS)

    Farrukh, Muhammad Akhyar; Kauser, Robina; Adnan, Rohana

    2013-09-01

    The kinetics of vitamin C by ferric chloride hexahydrate has been investigated in the aqueous ethanol solution of basic surfactant viz. octadecylamine (ODA) under pseudo-first order conditions. The critical micelle concentration (CMC) of surfactant was determined by surface tension measurement. The effect of pH (2.5-4.5) and temperature (15-35°C) in the presence and absence of surfactant were investigated. Activation parameters, ? E a, ? H #, ? S #, ? G ?, for the reaction were calculated by using Arrhenius and Eyring plot. Surface excess concentration (?max), minimum area per surfactant molecule ( A min), average area occupied by each molecule of surfactant ( a), surface pressure at the CMC (?max), Gibb's energy of micellization (? G M°), Gibb's energy of adsorption (? G ad°), were calculated. It was found that the reaction in the presence of surfactant showed faster oxidation rate than the aqueous ethanol solution. Reaction mechanism has been deduced in the presence and absence of surfactant.

  3. Chemoselective Boron-Catalyzed Nucleophilic Activation of Carboxylic Acids for Mannich-Type Reactions.

    PubMed

    Morita, Yuya; Yamamoto, Tomohiro; Nagai, Hideoki; Shimizu, Yohei; Kanai, Motomu

    2015-06-10

    The carboxyl group (COOH) is an omnipresent functional group in organic molecules, and its direct catalytic activation represents an attractive synthetic method. Herein, we describe the first example of a direct catalytic nucleophilic activation of carboxylic acids with BH3·SMe2, after which the acids are able to act as carbon nucleophiles, i.e. enolates, in Mannich-type reactions. This reaction proceeds with a mild organic base (DBU) and exhibits high levels of functional group tolerance. The boron catalyst is highly chemoselective toward the COOH group, even in the presence of other carbonyl moieties, such as amides, esters, or ketones. Furthermore, this catalytic method can be extended to highly enantioselective Mannich-type reactions by using a (R)-3,3'-I2-BINOL-substituted boron catalyst. PMID:26011419

  4. A palladium-catalyzed regio- and stereoselective four-component coupling reaction.

    PubMed

    Knapton, Daniel J; Meyer, Tara Y

    2005-02-01

    Pd(PPh(3))(4) catalytically assembles sulfenamide, alkyne, carbon monoxide, and diphenyl diselenide regio- and stereoselectively in a one-pot four-component coupling reaction to yield (Z)-beta-selenyl acrylamides. The reaction proceeds in good to excellent yields (60-95%) and is tolerant of a range of functional groups on both the nitrogen of the sulfenamide and the alkyne. Moderate selectivities ranging from 4:1 to 7:1 beta-selenyl to beta-sulfenyl acrylamide have been observed despite the initial concentration of 2:1 selenium to sulfur in the reaction. The chalcogeno selectivity was found to depend directly on CO pressure; increased pressure decreased selectivity for selenium over sulfur. PMID:15675833

  5. Three-phase slug flow in microchips can provide beneficial reaction conditions for enzyme liquid-liquid reactions

    PubMed Central

    ?ech, Ji?í; P?ibyl, Michal; Šnita, Dalimil

    2013-01-01

    Here, we introduce a solution to low stability of a two-phase slug flow with a chemical reaction occurring at the phase interface in a microfluidic reactor where substantial merging of individual reacting slugs results in the loss of uniformity of the flow. We create a three-phase slug flow by introducing a third fluid phase into the originally two-phase liquid-liquid slug flow, which generates small two-phase liquid slugs separated by gas phase. Introduction of the third phase into our system efficiently prevents merging of slugs and provides beneficial reaction conditions, such as uniform flow pattern along the whole reaction capillary, interfacial area with good reproducibility, and intensive water-oil interface renewal. We tested the three-phase flow on an enzyme hydrolysis of soybean oil and compared the reaction conversion with those from unstable two-phase slug flows. We experimentally confirmed that the three-phase slug flow arrangement provides conversions and pressure drops comparable or even better with two-phase liquid-liquid arrangements. PMID:24404066

  6. Two herbivore-induced cytochrome P450 enzymes CYP79D6 and CYP79D7 catalyze the formation of volatile aldoximes involved in poplar defense.

    PubMed

    Irmisch, Sandra; McCormick, Andrea Clavijo; Boeckler, G Andreas; Schmidt, Axel; Reichelt, Michael; Schneider, Bernd; Block, Katja; Schnitzler, Jörg-Peter; Gershenzon, Jonathan; Unsicker, Sybille B; Köllner, Tobias G

    2013-11-01

    Aldoximes are known as floral and vegetative plant volatiles but also as biosynthetic intermediates for other plant defense compounds. While the cytochrome P450 monooxygenases (CYP) from the CYP79 family forming aldoximes as biosynthetic intermediates have been intensively studied, little is known about the enzymology of volatile aldoxime formation. We characterized two P450 enzymes, CYP79D6v3 and CYP79D7v2, which are involved in herbivore-induced aldoxime formation in western balsam poplar (Populus trichocarpa). Heterologous expression in Saccharomyces cerevisiae revealed that both enzymes produce a mixture of different aldoximes. Knockdown lines of CYP79D6/7 in gray poplar (Populus × canescens) exhibited a decreased emission of aldoximes, nitriles, and alcohols, emphasizing that the CYP79s catalyze the first step in the formation of a complex volatile blend. Aldoxime emission was found to be restricted to herbivore-damaged leaves and is closely correlated with CYP79D6 and CYP79D7 gene expression. The semi-volatile phenylacetaldoxime decreased survival and weight gain of gypsy moth (Lymantria dispar) caterpillars, suggesting that aldoximes may be involved in direct defense. The wide distribution of volatile aldoximes throughout the plant kingdom and the presence of CYP79 genes in all sequenced genomes of angiosperms suggest that volatile formation mediated by CYP79s is a general phenomenon in the plant kingdom. PMID:24220631

  7. Amine-catalyzed direct aldol reactions of hydroxy- and dihydroxyacetone: biomimetic synthesis of carbohydrates.

    PubMed

    Popik, Oskar; Pasternak-Suder, Monika; Le?niak, Katarzyna; Jawiczuk, Magdalena; Górecki, Marcin; Frelek, Jadwiga; Mlynarski, Jacek

    2014-06-20

    This article presents comprehensive studies on the application of primary, secondary, and tertiary amines as efficient organocatalysts for the de novo synthesis of ketoses and deoxyketoses. Mimicking the actions of aldolase enzymes, the synthesis of selected carbohydrates was accomplished in aqueous media by using proline- and serine-based organocatalysts. The presented methodology also provides direct access to unnatural L-carbohydrates from the (S)-glyceraldehyde precursor. Determination of the absolute configuration of all obtained sugars was feasible using a methodology consisting of concerted ECD and VCD spectroscopy. PMID:24837738

  8. Chemical model of reaction cascades induced by activated enzymes or catalysts. Two-step cascades in visual transduction.

    PubMed Central

    Shirane, K; Tokimoto, T; Yamaguchi, Y

    1990-01-01

    A dissipative system is approximated by a nonlinear rate equation: Z congruent to K1Z - K2Z3 (K2 greater than 0), in which the right side is derived from -delta G/delta Z of Taylor's series of the thermodynamic potential given by Gibbs' function G(Tc, Pc) (Z) at about the critical point C(Tc, Pc) of the control variables (parameters) T and P. The stability or instability of the system is treated by the changes in the control parameters. In the case that T not equal to P not equal to 0 in the steady state, Z = 0, and T and P pass the point C, K1 becomes negative. By this change, the G function is convex at Z = 0 and each product is created rapidly with concentration or number of the molecules Z = ([K1]/K2)1/2. This dynamic theory is applied to enzyme cascades. Based on cyclic GMP (cGMP) hypothesis in visual transduction, the cascade hydrolysis of cGMP of vertebrates is analyzed by dividing it into two-step reaction cascades: The initial process is that metarhodopsin II catalyzes the exchange of GDP for GTP by transducin (Gtd) and that GTP-Gtd complex is hydrolyzed to GDP-Gtd complex. In the following cascade cGMP is hydrolyzed with amplification of phosphodiesterase (PDE) activated by the removal of the small inhibitory subunit. The quantity of the hydrolysis of cGMP is estimated as approximately 5 x 10(4-5) molecules per photolyzed rhodopsin semiempirically, and this coincides well with experiments. PMID:2153420

  9. A novel rhodium-catalyzed domino-hydroformylation-reaction for the synthesis of sulphonamides.

    PubMed

    Dong, Kaiwu; Fang, Xianjie; Jackstell, Ralf; Beller, Matthias

    2015-03-25

    An efficient and highly selective method for the synthesis of sulphonamides by a domino hydroformylation-reductive sulphonamidation reaction has been developed. Various olefins and sulphonamides are converted into the desired products in good yields and with excellent selectivities in the presence of a rhodium/Naphos catalyst. PMID:25712242

  10. Inverted supercritical carbon dioxide/aqueous biphasic media for rhodium-catalyzed hydrogenation reactions.

    PubMed

    Burgemeister, Katja; Franciò, Giancarlo; Gego, Volker H; Greiner, Lasse; Hugl, Herbert; Leitner, Walter

    2007-01-01

    An inverted supercritical carbon dioxide (scCO(2))/aqueous biphasic system has been used as reaction media for Rh-catalysed hydrogenation of polar substrates. Chiral and achiral CO(2)-philic catalysts were efficiently immobilised in scCO(2) as the stationary phase, while the polar substrates and products were contained in water as the mobile phase. Notably, product separation and catalyst recycling were conducted without depressurisation of the autoclave. The catalyst phase was reused several times with high conversion and product recovery of more than 85 %. Loss of rhodium and phosphorus by leaching were found to be below the detection limit after the first two cycles in the majority of repetitive experiments. The reaction conditions were optimised with a minimum of experiments by using a simplex algorithm in a sequential optimisation. Total turnover numbers (TTNs) of up to 1600, turnover frequencies (TOFs) of up to 340 h(-1) and ee's up to 99 % were obtained in repetitive batch operations. The scope of the devised catalytic system has been investigated and a semicontinuous reaction setup has been implemented. The chiral ligand (R,S)-3-H(2)F(6)-BINAPHOS allowed highly enantioselective hydrogenation of itaconic acid and methyl-2-acetamidoacrylate combined with a considerable catalyst stability in these reaction media. PMID:17295365

  11. Reaction Mechanism for Light Sensitivity of the Ru(bpy)3 2+-Catalyzed

    E-print Network

    Showalter, Kenneth

    subset of the reaction comprised of bromomalonic acid, sulfuric acid, and Ru(bpy)3 2+ as well as on an inorganic subset comprised of bromate, sulfuric acid, and Ru(bpy)3 2+. Experiments were also carried out in sulfuric acid. They proposed a scheme involving the photochemical production of the autocatalyst HBrO2

  12. From the Design of a Chiral Lewis Acid Catalyst to Metal-Catalyzed Coupling Reactions

    E-print Network

    Fu, Gregory C.

    in chiral Lewis acid catalysis to a project focused on the development of new palladium and nickel catalysts for carbon- carbon bond-forming reactions. I. Design of a Versatile Chiral Lewis Acid Catalyst The origin reported to date, the carbonyl system is activated through a -symmetry interaction between an oxygen lone

  13. RUTHENIUM-CATALYZED TANDEM OLEFIN MIGRATION-ALDOL AND MANNICH-TYPE REACTIONS IN IONIC LIQUID.

    EPA Science Inventory

    In the presence of a catalytic amount of RuCl2(PPh3)3, a cross-coupling of 3-buten-2-ol with aldehydes and imines was developed via a tandem olefin migration--aldol--Mannich reaction in bmim[PF6]. With In(OAc)3 as a co-catalyst, a-vinylbenzyl alcohol and aldehydes underwent sim...

  14. Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation.

    PubMed Central

    Berry, Hugues

    2002-01-01

    Conventional equations for enzyme kinetics are based on mass-action laws, that may fail in low-dimensional and disordered media such as biological membranes. We present Monte Carlo simulations of an isolated Michaelis-Menten enzyme reaction on two-dimensional lattices with varying obstacle densities, as models of biological membranes. The model predicts that, as a result of anomalous diffusion on these low-dimensional media, the kinetics are of the fractal type. Consequently, the conventional equations for enzyme kinetics fail to describe the reaction. In particular, we show that the quasi-stationary-state assumption can hardly be retained in these conditions. Moreover, the fractal characteristics of the kinetics are increasingly pronounced as obstacle density and initial substrate concentration increase. The simulations indicate that these two influences are mainly additive. Finally, the simulations show pronounced S-P segregation over the lattice at obstacle densities compatible with in vivo conditions. This phenomenon could be a source of spatial self organization in biological membranes. PMID:12324410

  15. The Roles of Acids and Bases in Enzyme Catalysis

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2007-01-01

    Many organic reactions are catalyzed by strong acids or bases that protonate or deprotonate neutral reactants leading to reactive cations or anions that proceed to products. In enzyme reactions, only weak acids and bases are available to hydrogen bond to reactants and to transfer protons in response to developing charges. Understanding this…

  16. Glutaraldehyde: behavior in aqueous solution, reaction with proteins, and application to enzyme crosslinking.

    PubMed

    Migneault, Isabelle; Dartiguenave, Catherine; Bertrand, Michel J; Waldron, Karen C

    2004-11-01

    Glutaraldehyde possesses unique characteristics that render it one of the most effective protein crosslinking reagents. It can be present in at least 13 different forms depending on solution conditions such as pH, concentration, temperature, etc. Substantial literature is found concerning the use of glutaraldehyde for protein immobilization, yet there is no agreement about the main reactive species that participates in the crosslinking process because monomeric and polymeric forms are in equilibrium. Glutaraldehyde may react with proteins by several means such as aldol condensation or Michael-type addition, and we show here 8 different reactions for various aqueous forms of this reagent. As a result of these discrepancies and the unique characteristics of each enzyme, crosslinking procedures using glutaraldehyde are largely developed through empirical observation. The choice of the enzyme-glutaraldehyde ratio, as well as their final concentration, is critical because insolubilization of the enzyme must result in minimal distortion of its structure in order to retain catalytic activity. The purpose of this paper is to give an overview of glutaraldehyde as a crosslinking reagent by describing its structure and chemical properties in aqueous solution in an attempt to explain its high reactivity toward proteins, particularly as applied to the production of insoluble enzymes. PMID:15560135

  17. One- and two-dimensional chemical exchange nuclear magnetic resonance studies of the creatine kinase catalyzed reaction

    SciTech Connect

    Gober, J.R.

    1988-01-01

    The equilibrium chemical exchange dynamics of the creatine kinase enzyme system were studied by one- and two-dimensional {sup 31}P NMR techniques. Pseudo-first-order reaction rate constants were measured by the saturation transfer method under an array of experimental conditions of pH and temperature. Quantitative one-dimensional spectra were collected under the same conditions in order to calculate the forward and reverse reaction rates, the K{sub eq}, the hydrogen ion stoichiometry, and the standard thermodynamic functions. The pure absorption mode in four quadrant two-dimensional chemical exchange experiment was employed so that the complete kinetic matrix showing all of the chemical exchange process could be realized.

  18. Reduction of the explosive 2,4,6-trinitrophenylmethylnitramine (tetryl) catalyzed by oxygen sensitive nitro reductase enzymes

    SciTech Connect

    Shah, M.M.; Spain, J.C.

    1995-12-01

    Reduction of nitroaromatic compounds by nitroreductase enzymes generally leads to the formation of the corresponding amines. However, we recently found that the incubation of the explosive 2,4,6-trinitrophenylmethylnitramine (tetryl) with ferredoxin-NADP oxidoreductase, an oxygen sensitive nitroreductase from spinach in the presence of NADPH led to the elimination of the nitramine nitro group from tetryl and the formation of N-methylpicramide (NMP). Other oxygen sensitive nitroreductase enzymes including glutathione reductase, xanthine oxidase, and cytochrome c reductase were also able to release nitrite from tetryl. Nitrite was not eliminated from tetryl by an oxygen insensitive nitrobenzene reductase. For every mole of tetryl reduced, one mole each of nitrite and NMP were produced. The rate of nitrite elimination was inhibited under aerobic conditions. Subsequent oxygen uptake studies suggested that under aerobic conditions, molecular oxygen was reduced by FNR and tetryl served as the redox mediator. Our results suggest that under aerobic conditions; tetryl is reduced to the nitroanion radical by the enzyme and this radical is involved in the reduction of molecular oxygen.

  19. Legume Lectins: I. Immunological Cross-Reactions between the Enzymic Lectin from Mung Beans and other Well Characterized Legume Lectins.

    PubMed

    Hankins, C N; Kindinger, J I; Shannon, L M

    1979-07-01

    A number of well characterized legume lectins including the enzymic lectin from Vigna radiata were examined for immunological relatedness. The immunological cross-reactions observed indicate that most of the legume lectins, including Vigna lectin, are evolutionarily closely related proteins. The possibility that these proteins are homologs with enzymic functions is discussed. PMID:16660894

  20. Ascorbic acid and 4-hexylresorcinol effects on pear PPO and PPO catalyzed browning reaction.

    PubMed

    Arias, E; González, J; Oria, R; Lopez-Buesa, P

    2007-10-01

    The effects of ascorbic acid (AA) and 4-hexylresorcinol (4-HR) on pear polyphenoloxidase (PPO) activity and stability have been investigated in vitro. AA does not interact directly with PPO but prevents browning by reducing oxidized substrates. The 4-HR exerts a dual role on PPO. If no substrates are present, it interacts preferably with the deoxy form of PPO inactivating it. If substrates and 4-HR are both present they compete for the catalytic site. The 4-HR behaves then as a canonical enzyme inhibitor, binding to the met form of PPO. Simultaneous addition of 4-HR and AA has synergistic inhibition or inactivatory effects depending on the presence or the absence of PPO substrates. PMID:17995596

  1. Thiourea-catalyzed Diels–Alder reaction of a naphthoquinone monoketal dienophile

    PubMed Central

    Kramer, Carsten S

    2013-01-01

    Summary A variety of organocatalysts were screened for the catalysis of the naphthoquinone monoketal Diels–Alder reaction. In this study we found that Schreiner's thiourea catalyst 10 and Jacobson's thiourea catalyst 12 facilitate the cycloaddition of the sterically hindered naphthoquinone monoketal dienophile 3 with diene 4. The use of thiourea catalysis allowed for the first time the highly selective synthesis of the exo-product 2a in up to 63% yield. In this reaction a new quaternary center was built. The so formed cycloaddition product 2a represents the ABC tricycle of beticolin 0 (1) and is also a valuable model substrate for the total synthesis of related natural products. PMID:23946836

  2. Chiral Dawson-Type Hybrid Polyoxometalate Catalyzes Enantioselective Diels-Alder Reactions.

    PubMed

    Xuan, Wen-Jing; Botuha, Candice; Hasenknopf, Bernold; Thorimbert, Serge

    2015-11-01

    Can achiral organocatalysts linked to chiral polyanionic metal oxide clusters provide good selectivity in enantioselective C?C bond formations? The answer to this question is investigated by developing a new active hybrid polyoxometalate-based catalyst for asymmetric Diels-Alder reaction. Chirality transfer from the chiral anionic polyoxometalate to the covalently linked achiral imidazolidinone allows Diels-Alder cycloaddition products to be obtained with good yields and high enantioselectivities when using cyclopentadiene and acrylaldehydes as partners. PMID:26406341

  3. H(3)PW(12)O(40)-catalyzed multicomponent reaction for efficient synthesis of highly substituted piperidines.

    PubMed

    Khaksar, Samad; Baghbanian, Seyed Meysam; Barsan, Nastaran

    2014-01-01

    A simple, diastereoselective, inexpensive, and efficient route for the synthesis of highly functionalized piperidines by the condensation of ?-keto-esters, aromatic aldehydes and anilines using H3PW12O40 as a catalyst is described. The catalyst could be easily recovered after completion of the reaction and reused without a considerable change in its activity. Furthermore, in most cases the piperidine precipitates out of solution. PMID:24372051

  4. Activated carbon catalyzes reactions of phenolics during liquid-phase adsorption

    SciTech Connect

    Cooney, D.O.; Xi, Z. . Chemical Engineering Dept.)

    1994-02-01

    Various phenolic compounds in aqueous buffer solutions were contacted batchwise with powdered activated carbon. Relatively slow, but continual, decreases in the solution phenolic concentrations were measured over a period of several weeks. The decreases were due to oxidative coupling reactions of the phenolics which occurred on the carbon surface subsequent to adsorption. The effects of time, pH, dissolved oxygen, and the molecular nature of the phenolic were determined.

  5. Efficient Rhodium-Catalyzed Multicomponent Reaction for the Synthesis of Novel Propargylamines.

    PubMed

    Rubio-Pérez, Laura; Iglesias, Manuel; Munárriz, Julen; Polo, Victor; Pérez-Torrente, Jesús J; Oro, Luis A

    2015-12-01

    [{Rh(?-Cl)(H)2 (IPr)}2 ] (IPr = 1,3-bis-(2,6-diisopropylphenyl)imidazole-2-ylidene) was found to be an efficient catalyst for the synthesis of novel propargylamines by a one-pot three-component reaction between primary arylamines, aliphatic aldehydes, and triisopropylsilylacetylene. This methodology offers an efficient synthetic pathway for the preparation of secondary propargylamines derived from aliphatic aldehydes. The reactivity of [{Rh(?-Cl)(H)2 (IPr)}2 ] with amines and aldehydes was studied, leading to the identification of complexes [RhCl(CO)IPr(MesNH2 )] (MesNH2 = 2,4,6-trimethylaniline) and [RhCl(CO)2 IPr]. The latter shows a very low catalytic activity while the former brought about reaction rates similar to those obtained with [{Rh(?-Cl)(H)2 (IPr)}2 ]. Besides, complex [RhCl(CO)IPr(MesNH2 )] reacts with an excess of amine and aldehyde to give [RhCl(CO)IPr{MesN?CHCH2 CH(CH3 )2 }], which was postulated as the active species. A mechanism that clarifies the scarcely studied catalytic cycle of A3 -coupling reactions is proposed based on reactivity studies and DFT calculations. PMID:26490447

  6. Effect of polyvinylpyrrolidone on mesoporous silica morphology and esterification of lauric acid with 1-butanol catalyzed by immobilized enzyme

    NASA Astrophysics Data System (ADS)

    Zhang, Jinyu; Zhou, Guowei; Jiang, Bin; Zhao, Minnan; Zhang, Yan

    2014-05-01

    Mesoporous silica materials with a range of morphology evolution, i.e., from curved rod-shaped mesoporous silica to straight rod-shaped mesoporous silica, were successfully prepared using polyvinylpyrrolidone (PVP) and triblock copolymer as dual template. The effects of PVP molecular weight and concentration on mesoporous silica structure parameters were studied. Results showed that surface area and pore volume continuously decreased with increased PVP molecular weight. Mesoporous silica prepared with PVP K30 also possessed larger pore diameter, interplanar spacing (d100), and cell parameter (a0) than that prepared with PVP K15 and PVP K90. In addition, with increased PVP concentration, d100 and a0 continuously decreased. The mechanism of morphology evolution caused by the change in PVP concentration was investigated. The conversion rate of lauric acid with 1-butanol catalyzed by immobilized Porcine pancreatic lipase (PPL) was also evaluated. Results showed that PPL immobilized on amino-functionalized straight rod-shaped mesoporous silica maintained 50% of its esterification conversion rate even after five cycles of use with a maximum conversion rate was about 90.15%.

  7. Farnesyl Diphosphate Analogues with ?-Bioorthogonal Azide and Alkyne Functional Groups for PFTase-Catalyzed Ligation Reactions

    PubMed Central

    Labadie, Guillermo R.; Viswanathan, Rajesh; Poulter, C. Dale

    2008-01-01

    Eleven farnesyl diphosphate analogues, which contained ?-azide or alkyne substituents suitable for bioorthogonal Staudinger and Huisgen [3+2] cycloaddition coupling reactions, were synthesized. The analogues were evaluated as substrates for alkylation of peptide co-substrates by yeast protein farnesyl transferase. Five of the diphosphates were good alternative substrates for FPP. Steady-state kinetic constants were measured for the active compounds, and the products were characterized by HPLC and LC-Mass. Two of the analogues gave steady state kinetic parameters (kcat and KM) very similar to those of the natural substrate. PMID:17979291

  8. A Francisella Virulence Factor Catalyzes an Essential Reaction of Biotin Synthesis

    PubMed Central

    Feng, Youjun; Napier, Brooke A.; Manandhar, Miglena; Henke, Sarah K; Weiss, David S.; Cronan, John E.

    2014-01-01

    Summary We recently identified a gene (FTN_0818) required for Francisella virulence that seemed likely involved in biotin metabolism. However, the molecular function of this virulence determinant was unclear. Here we show that this protein named BioJ is the enzyme of the biotin biosynthesis pathway that determines the chain length of the biotin valeryl side chain. Expression of bioJ allows growth of an E. coli bioH strain on biotin-free medium, indicating functional equivalence of BioJ to the paradigm pimeloyl-ACP methyl ester carboxyl-esterase, BioH. BioJ was purified to homogeneity, shown to be monomeric and capable of hydrolysis of its physiological substrate methyl pimeloyl-ACP to pimeloyl-ACP, the precursor required to begin formation of the fused heterocyclic rings of biotin. Phylogenetic analyses confirmed that distinct from BioH, BioJ represents a novel sub-clade of the ?/?-hydrolase family. Structure-guided mapping combined with site-directed mutagenesis revealed that the BioJ catalytic triad consists of Ser151, Asp248 and His278, all of which are essential for activity and virulence. The biotin synthesis pathway was reconstituted in vitro and the physiological role of BioJ directly assayed. To the best of our knowledge, these data represent further evidence linking biotin synthesis to bacterial virulence. PMID:24313380

  9. Iron(II)-dependent dioxygenase and N-formylamide deformylase catalyze the reactions from 5-hydroxy-2-pyridone to maleamate

    PubMed Central

    Yao, Yuxiang; Tang, Hongzhi; Ren, Huixue; Yu, Hao; Wang, Lijuan; Zhang, Wei; Behrman, Edward J.; Xu, Ping

    2013-01-01

    5-Hydroxy-2-pyridone (2,5-DHP) is a central metabolic intermediate in catabolism of many pyridine derivatives, and has been suggested as a potential carcinogen. 2,5-DHP is frequently transformed to N-formylmaleamic acid (NFM) by a 2,5-DHP dioxygenase. Three hypotheses were formerly discussed for conversion of 2,5-DHP to maleamate. Based on enzymatic reactions of dioxygenase (Hpo) and N-formylamide deformylase (Nfo), we demonstrated that the dioxygenase does not catalyze the hydrolysis of NFM but rather that this activity is brought about by a separate deformylase. We report that the deformylase acts both on NFM and its trans-isomer, N-formylfumaramic acid (NFF), but the catalytic efficiency of Nfo for NFM is about 1,400 times greater than that for NFF. In addition, we uncover catalytic and structural characteristics of the new family that the Hpo belongs to, and support a potential 2-His-1-carboxylate motif (HX52HXD) by three-dimensional modeling and site-directed mutagenesis. This study provides a better understanding of 2,5-DHP catabolism. PMID:24241081

  10. Tandem Regioselective Substitution and Palladium-Catalyzed Ring Fusion Reaction for Core-Expanded Boron Dipyrromethenes with Red-Shifted Absorption and Intense Fluorescence.

    PubMed

    Zhou, Xin; Wu, Qinghua; Feng, Yuanmei; Yu, Yang; Yu, Changjiang; Hao, Erhong; Wei, Yun; Mu, Xiaolong; Jiao, Lijuan

    2015-09-01

    A selective method for the core-extension of boron dipyrromethene (BODIPY) with two annulated indole rings with exclusive syn-connectivity is reported. The method is based on a regioselective nucleophilic substitution reaction of 2,3,5,6-tetrabromoBODIPY with aryl amines, followed by palladium-catalyzed intramolecular C-C coupling ring fusion. The unsymmetrical core-expanded BODIPY with annulated indole and benzofuran rings was also synthesized by stepwise and regioselective nucleophilic substitution and palladium-catalyzed intramolecular C-C coupling reaction. The diindole-annulated BODIPY was unambiguously characterized by single-crystal X-ray analysis. The optical properties of the present core-expanded BODIPYs were studied, revealing clearly red-shifted absorption and emission bands and enhanced absorption coefficients upon annulation. PMID:26083775

  11. Computational studies on the regioselectivity of metal-catalyzed synthesis of 1,2,3 triazoles via click reaction: a review.

    PubMed

    Hosseinnejad, Tayebeh; Fattahi, Bahareh; Heravi, Majid M

    2015-10-01

    Recently, the experimental and computational chemists have been attracted widely to the click synthesis of 1,2,3 triazoles and their derivatives, mainly due to the fact that they are interesting from structural and mechanistic points of view. Moreover, catalyzed click have been well established as a successful strategy showing high regioselectivity and high yield for the synthesis of 1,2,3-triazoles. In this review, we try to highlight the recently reported computational assessments on the origins and predection of regioselectivity in the catalyzed click synthesis of triazoles from the mechanistic and thermodynamical points of view. In this light, density functional theory (DFT) calculations on the free energy profiles of azide-alkyne cycloaddition reactions have been underscored. The stereoelectronic features for the role of copper, ruthenium, and iridium as catalyst on regioselectivity of click reactions have also be discussed. Graphical Abstract Computational origins for the regioselective behavior of 1,2,3 triazoles click synthesis. PMID:26385849

  12. Study of fluorescence quenching mechanism between quercetin and tyrosine-H 2O 2-enzyme catalyzed product

    NASA Astrophysics Data System (ADS)

    Zhang, Miao; Lv, Qingluan; Yue, Ningning; Wang, Huaiyou

    2009-04-01

    Because of catalysis of horseradish peroxidase, the tyrosine reacted with H 2O 2 to form the product S which was a strong fluorescence substance. To the product S, the quercetin was acted as a quencher. The fluorescence quenching mechanism was studied by the measurement of fluorescence lifetime and based on the Stern-Volmer plot. The reaction mechanism, which was the static quenching process between quercetin and product S, was studied. The binding constant, K = 4.03 × 10 5 L mol -1 and the number of binding sites n = 1.09, were obtained against this reaction. The thermodynamic parameters were estimated. The data, ? H = -75.68 kJ mol -1, ? S = -147.9 J K -1 mol -1 and ? G = -29.17 kJ mol -1 showed that the reaction was spontaneous and exothermic. What is more, both ? H and ? S were negative values indicated that van der Waals interaction and hydrogen bonding were the predominant intermolecular forces between quercetin and product S.

  13. Studies of the enzymic mechanism of Candida tenuis xylose reductase (AKR 2B5): X-ray structure and catalytic reaction profile for the H113A mutant.

    PubMed

    Kratzer, Regina; Kavanagh, Kathryn L; Wilson, David K; Nidetzky, Bernd

    2004-05-01

    Xylose reductase from the yeast Candida tenuis (CtXR) is a family 2 member of the aldo-keto reductase (AKR) superfamily of proteins and enzymes. Active site His-113 is conserved among AKRs, but a unified mechanism of how it affects catalytic activity is outstanding. We have replaced His-113 by alanine using site-directed mutagenesis, determined a 2.2 A structure of H113A mutant bound to NADP(+), and compared catalytic reaction profiles of NADH-dependent reduction of different aldehydes catalyzed by the wild type and the mutant. Deuterium kinetic isotope effects (KIEs) on k(cat) and k(cat)/K(m xylose) show that, relative to the wild type, the hydride transfer rate constant (k(7) approximately 0.16 s(-1)) has decreased about 1000-fold in H113A whereas xylose binding was not strongly affected. No solvent isotope effect was seen on k(cat) and k(cat)/K(m xylose) for H113A, suggesting that proton transfer has not become rate-limiting as a result of the mutation. The pH profiles of log(k(cat)/K(m xylose)) for the wild type and H113A decreased above apparent pK(a) values of 8.85 and 7.63, respectively. The DeltapK(a) of -1.2 pH units likely reflects a proximally disruptive character of the mutation, affecting the position of Asp-50. A steady-state kinetic analysis for H113A-catalyzed reduction of a homologous series of meta-substituted benzaldehyde derivatives was carried out, and quantitative structure-reactivity correlations were used to factor the observed kinetic substituent effect on k(cat) and k(cat)/K(m aldehyde) into an electronic effect and bonding effects (which are lacking in the wild type). Using the Hammett sigma scale, electronic parameter coefficients (rho) of +0.64 (k(cat)) and +0.78 (k(cat)/K(m aldehyde)) were calculated and clearly differ from rho(k(cat)/K(aldehyde)) and rho(k(cat)) values of +1.67 and approximately 0.0, respectively, for the wild-type enzyme. Hydride transfer rate constants of H113A, calculated from kinetic parameters and KIE data, display a substituent dependence not seen in the corresponding wild-type enzyme rate constants. An enzymic mechanism is proposed in which His-113, through a hydrogen bond from Nepsilon2 to aldehyde O1, assists in catalysis by optimizing the C=O bond charge separation and orbital alignment in the ternary complex. PMID:15109252

  14. The Reaction Kinetics of 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1 Provide an Understanding of the para-Hydroxylation Enzyme Catalytic Cycle*

    PubMed Central

    Sucharitakul, Jeerus; Tongsook, Chanakan; Pakotiprapha, Danaya; van Berkel, Willem J. H.; Chaiyen, Pimchai

    2013-01-01

    3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is an NADH-specific flavoprotein monooxygenase that catalyzes the para-hydroxylation of 3-hydroxybenzoate (3HB) to form 2,5-dihydroxybenzoate (2,5-DHB). Based on results from stopped-flow spectrophotometry, the reduced enzyme-3HB complex reacts with oxygen to form a C4a-peroxy flavin with a rate constant of 1.13 ± 0.01 × 106 m?1 s?1 (pH 8.0, 4 °C). This intermediate is subsequently protonated to form a C4a-hydroperoxyflavin with a rate constant of 96 ± 3 s?1. This step shows a solvent kinetic isotope effect of 1.7. Based on rapid-quench measurements, the hydroxylation occurs with a rate constant of 36 ± 2 s?1. 3HB6H does not exhibit substrate inhibition on the flavin oxidation step, a common characteristic found in most ortho-hydroxylation enzymes. The apparent kcat at saturating concentrations of 3HB, NADH, and oxygen is 6.49 ± 0.02 s?1. Pre-steady state and steady-state kinetic data were used to construct the catalytic cycle of the reaction. The data indicate that the steps of product release (11.7 s?1) and hydroxylation (36 ± 2 s?1) partially control the overall turnover. PMID:24129570

  15. Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).

    PubMed

    Quitterer, Felix; Frank, Annika; Wang, Ke; Rao, Guodong; O'Dowd, Bing; Li, Jikun; Guerra, Francisco; Abdel-Azeim, Safwat; Bacher, Adelbert; Eppinger, Jörg; Oldfield, Eric; Groll, Michael

    2015-06-19

    IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence. PMID:25868383

  16. Remarkable aliphatic hydroxylation by the diiron enzyme toluene 4-monooxygenase in reactions with radical or cation diagnostic probes norcarane, 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane.

    PubMed

    Moe, Luke A; Hu, Zhengbo; Deng, Dayi; Austin, Rachel N; Groves, John T; Fox, Brian G

    2004-12-21

    Toluene 4-monooxygenase (T4MO) catalyzes the hydroxylation of toluene to yield 96% p-cresol. This diiron enzyme complex was used to oxidize norcarane (bicyclo[4.1.0]heptane), 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane, substrate analogues that can undergo diagnostic reactions upon the production of transient radical or cationic intermediates. Norcarane closely matches the shape and volume of the natural substrate toluene. Reaction of isoforms of the hydroxylase component of T4MO (T4moH) with different regiospecificities for toluene hydroxylation (k(cat) approximately 1.9-2.3 s(-)(1) and coupling efficiency approximately 81-96%) revealed similar catalytic parameters for norcarane oxidation (k(cat) approximately 0.3-0.5 s(-)(1) and coupling efficiency approximately 72%). The products included variable amounts of the un-rearranged isomeric norcaranols and cyclohex-2-enyl methanol, a product attributed to rearrangement of a radical oxidation intermediate. A ring-expansion product derived from the norcaranyl C-2 cation, cyclohept-3-enol, was not produced by either the natural enzyme or any of the T4moH isoforms tested. Comparative studies of 1,1-dimethylcyclopropane and 1,1-diethylcyclopropane, diagnostic substrates with differences in size and with approximately 50-fold slower k(cat) values, gave products consistent with both radical rearrangement and cation ring expansion. Examination of the isotopic enrichment of the incorporated O-atoms for all products revealed high-fidelity incorporation of an O-atom from O(2) in the un-rearranged and radical-rearranged products, while the O-atom found in the cation ring-expansion products was predominantly obtained by reaction with H(2)O. The results show a divergence of radical and cation pathways for T4moH-mediated hydroxylation that can be dissected by diagnostic substrate probe rearrangements and by changes in the source of oxygen used for substrate oxygenation. PMID:15595825

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

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

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

  18. One-pot synthesis of benzoxaborole derivatives from the palladium-catalyzed cross-coupling reaction of alkoxydiboron with unprotected o-bromobenzylalcohols.

    PubMed

    Zhu, Jianan; Wei, Ying; Lin, Dongqing; Ou, Changjin; Xie, Linghai; Zhao, Yu; Huang, Wei

    2015-12-14

    Under very mild conditions, functionalized benzoxaborole derivatives were prepared in good to excellent yields via a palladium-catalyzed Miyaura borylation reaction of readily available unprotected o-bromobenzylalcohols, and bis(pinacolato)diboron (B2pin2) without the assistance of an acid. Blue-light-emitting materials based on spiro benzoxaborole building blocks have been obtained with potential applications in organic electronics and biomedicine. PMID:26440765

  19. Escherichia coli DNA helicase I catalyzes a sequence-specific cleavage/ligation reaction at the F plasmid origin of transfer.

    PubMed

    Sherman, J A; Matson, S W

    1994-10-21

    Recent studies have shown that the Escherichia coli F plasmid-encoded traI gene product (TraIp), also known as DNA helicase I, catalyzes the formation of the site- and strand-specific nick that initiates F plasmid DNA transfer. Scission of the phosphodiester bond at the nic site within the origin of transfer (oriT) is accompanied by the covalent attachment of TraIp to the 5'-phosphate of the nicked DNA strand. This mechanism suggests that TraIp may also be capable of catalyzing a DNA ligation reaction using the energy stored in the protein-DNA intermediate. To test this possibility, an in vitro assay was designed that utilized short single-stranded DNA oligonucleotides of different lengths derived from the region within oriT that spanned the nic site. Purified TraIp was capable of efficiently cleaving single-stranded DNA that contained a nic site, and upon cleavage, the protein became covalently linked to the 5'-end of the nic site. When TraIp was incubated with two oligonucleotides of different length that contained the nic site, there was formation of novel recombinant products resulting from a TraIp-catalyzed cleavage/ligation reaction. Furthermore, the cleavage and ligation reactions were both sequence-specific. These data suggest that TraIp plays an important role in the initiation and termination of conjugative DNA transfer. PMID:7929337

  20. RDH13L, an enzyme responsible for the aldehyde-alcohol redox coupling reaction (AL-OL coupling reaction) to supply 11-cis retinal in the carp cone retinoid cycle.

    PubMed

    Sato, Shinya; Miyazono, Sadaharu; Tachibanaki, Shuji; Kawamura, Satoru

    2015-01-30

    Cone photoreceptors require effective pigment regeneration mechanisms to maintain their sensitivity in the light. Our previous studies in carp cones suggested the presence of an unconventional and very effective mechanism to produce 11-cis retinal, the necessary component in pigment regeneration. In this reaction (aldehyde-alcohol redox coupling reaction, AL-OL coupling reaction), formation of 11-cis retinal, i.e. oxidation of 11-cis retinol is coupled to reduction of an aldehyde at a 1:1 molar ratio without exogenous NADP(H) which is usually required in this kind of reaction. Here, we identified carp retinol dehydrogenase 13-like (RDH13L) as an enzyme catalyzing the AL-OL coupling reaction. RDH13L was partially purified from purified carp cones, identified as a candidate protein, and its AL-OL coupling activity was confirmed using recombinant RDH13L. We further examined the substrate specificity, subcellular localization, and expression level of RDH13L. Based on these results, we concluded that RDH13L contributes to a significant part, but not all, of the AL-OL coupling activity in carp cones. RDH13L contained tightly bound NADP(+) which presumably functions as a cofactor in the reaction. Mouse RDH14, a mouse homolog of carp RDH13L, also showed the AL-OL coupling activity. Interestingly, although carp cone membranes, carp RDH13L and mouse RDH14 all showed the coupling activity at 15-37 °C, they also showed a conventional NADP(+)-dependent 11-cis retinol oxidation activity above 25 °C without addition of aldehydes. This dual mechanism of 11-cis retinal synthesis attained by carp RDH13L and mouse RDH14 probably contribute to effective pigment regeneration in cones that function in the light. PMID:25533474

  1. Structure Sensitivity of the Oxygen Evolution Reaction Catalyzed by Cobalt(II,III) Oxide.

    PubMed

    Plaisance, Craig P; van Santen, Rutger A

    2015-11-25

    Quantum chemical calculations and simulated kinetics were used to examine the structure sensitivity of the oxygen evolution reaction on several surface terminations of Co3O4. Active sites consisting of two adjacent Co(IV) cations connected by bridging oxos were identified on both the (001) and (311) surfaces. Formation of the O-O bond proceeds on these sites by nucleophilic attack of water on a bridging oxo. It was found that the relative turnover frequencies for the different sites are highly dependent on the overpotential, with the dual-Co site on the (311) surface being most active at medium overpotentials (0.46-0.77 V), where O-O bond formation by water addition is rate limiting. A similar dual-Co site on the (001) surface is most active at low overpotentials (<0.46 V), where O2 release is rate limiting, and a single-Co site on the (110) surface is most active at overpotentials that are high enough (>0.77 V) to form a significant concentration of highly reactive terminal Co(V)?O species. Two overpotential-dependent Sabatier relationships were identified based on the Brønsted basicity and redox potential of the active site, explaining the change in the active site with overpotential. The (311) dual-Co site that is most active in the medium overpotential range is consistent with recent experimental observations suggesting that a defect site is responsible for the observed oxygen evolution activity and that a modest concentration of superoxo intermediates is present on the surface. Importantly, we find that it is essential to consider the kinetics of the water addition and O2 release steps rather than only the thermodynamics. PMID:26479891

  2. Spectroscopic Analyses on Reaction Intermediates Formed during Chlorination of Alkanes with NaOCl Catalyzed by a Nickel Complex.

    PubMed

    Draksharapu, Apparao; Codolà, Zoel; Gómez, Laura; Lloret-Fillol, Julio; Browne, Wesley R; Costas, Miquel

    2015-11-16

    The spectroscopic, electrochemical, and crystallographic characterization of [((Me,H)PyTACN)Ni(II)(CH3CN)2](OTf)2 (1) ((Me,H)PyTACN = 1-(2-pyridylmethyl)-4,7-dimethyl-1,4,7-triazacyclononane, OTf = CF3SO3) is described together with its reactivity with NaOCl. 1 catalyzes the chlorination of alkanes with NaOCl, producing only a trace amount of oxygenated byproducts. The reaction was monitored spectroscopically and by high resolution electrospray-mass spectrometry (ESI-MS) with the aim to elucidate mechanistic aspects. NaOCl reacts with 1 in acetonitrile to form the transient species [(L)Ni(II)-OCl(S)](+) (A) (L = (Me,H)PyTACN, S = solvent), which was identified by ESI-MS. UV/vis absorption, electron paramagnetic resonance, and resonance Raman spectroscopy indicate that intermediate A decays to the complex [(L)Ni(III)-OH(S)](2+) (B) presumably through homolytic cleavage of the O-Cl bond, which liberates a Cl(•) atom. Hydrolysis of acetonitrile to acetic acid under the applied conditions results in the formation of [(L)Ni(III)-OOCCH3(S)](2+) (C), which undergoes subsequent reduction to [(L)Ni(II)-OOCCH3(S)](2+) (D), presumably via reaction with OCl(-) or ClO2(-). Subsequent addition of NaOCl to [(L)Ni(II)-OOCCH3(S)](+) (D) regenerates [(L)Ni(III)-OH(S)](2+) (B) to a much greater extent and at a faster rate. Addition of acids such as acetic and triflic acid enhances the rate and extent of formation of [(L)Ni(III)-OH(S)](2+) (B) from 1, suggesting that O-Cl homolytic cleavage is accelerated by protonation. Overall, these reactions generate Cl(•) atoms and ClO2 in a catalytic cycle where the nickel center alternates between Ni(II) and Ni(III). Chlorine atoms in turn react with the C-H bonds of alkanes, forming alkyl radicals that are trapped by Cl(•) to form alkyl chlorides. PMID:26540133

  3. Reaction of alpha-tubulin with iodotyrosines catalyzed by tubulin:tyrosine ligase: carboxy-terminal labeling of tubulin with ( sup 125 I)monoiodotyrosine

    SciTech Connect

    Joniau, M.; Coudijzer, K.; De Cuyper, M. )

    1990-02-01

    We have studied the capacity of different iodinated derivatives of phenylalanine and tyrosine to inhibit the incorporation of (3H)tyrosine into tubulin catalyzed by tubulin:tyrosine ligase. In contrast to thyronine and its iodinated derivatives, iodotyrosines were efficient inhibitors. That they also functioned as substrates of the enzyme was shown by the effective incorporation of (125I)mono- and diiodotyrosine into tubulin. The label was shown to be located at the carboxy terminus. Labeling by this method conserves the polymerization capacity of tubulin in contrast with classical radioiodination methods involving oxidation.

  4. Enantioselective Synthesis of 5,7-Bicyclic Ring Systems from Axially Chiral Allenes Using a Rh(I)-Catalyzed Cyclocarbonylation Reaction

    PubMed Central

    Grillet, Francois; Brummond, Kay M.

    2013-01-01

    A transfer of chirality in an intramolecular Rh(I)-catalyzed allenic Pauson-Khand reaction (APKR) to access tetrahydroazulenones, tetrahydrocyclopenta[c]azepinones and dihydrocyclopenta[c]oxepinones enantioselectively (22 – 99% ee) is described. The substitution pattern of the allene affected the transfer of chiral information. Complete transfer of chirality was obtained for all trisubstituted allenes, but loss of chiral information was observed for disubstituted allenes. This work constitutes the first demonstration of a transfer of chiral information from an allene to the 5-position of a cyclopentenone using a cyclocarbonylation reaction. The absolute configuration of the corresponding cyclocarbonylation product was also established, something that is rarely done. PMID:23485149

  5. Green polymer chemistry: enzyme catalysis for polymer functionalization.

    PubMed

    Sen, Sanghamitra; Puskas, Judit E

    2015-01-01

    Enzyme catalyzed reactions are green alternative approaches to functionalize polymers compared to conventional methods. This technique is especially advantageous due to the high selectivity, high efficiency, milder reaction conditions, and recyclability of enzymes. Selected reactions can be conducted under solventless conditions without the application of metal catalysts. Hence this process is becoming more recognized in the arena of biomedical applications, as the toxicity created by solvents and metal catalyst residues can be completely avoided. In this review we will discuss fundamental aspects of chemical reactions biocatalyzed by Candida antarctica lipase B, and their application to create new functionalized polymers, including the regio- and chemoselectivity of the reactions. PMID:26007188

  6. Gold-catalyzed 1,2-acyloxy migration/intramolecular [3+2] 1,3-dipolar cycloaddtion cascade reaction: an efficient strategy for syntheses of medium-sized-ring ethers and amines.

    PubMed

    Zhao, Changgui; Xie, Xingang; Duan, Shuangshuang; Li, Huilin; Fang, Ran; She, Xuegong

    2014-09-26

    A highly efficient strategy for the formation of medium-sized-ring ethers and amines based on a gold-catalyzed cascade reaction, involving enynyl ester isomerization and intramolecular [3+2]?cyclization, has been developed. Various multisubstituted medium-sized-ring unsaturated ethers and amines were obtained through this transformation. This method represents one of the relatively few transition metal catalyzed intramolecular cycloaddition reactions for medium-sized ring synthesis. PMID:25111560

  7. Genetic characterization of genes encoding enzymes catalyzing addition of phospho-ethanolamine to the glycosylphosphatidylinositol anchor in Saccharomyces cerevisiae.

    PubMed

    Toh-e, Akio; Oguchi, Tomoko

    2002-10-01

    MPC1/GPI13/YLL031C, one of the genes involved in the addition of phospho-ethanolamine to the glycosylphosphatidylinositol (GPI) anchor core, is an essential gene. Three available temperature-sensitive mutant alleles, mpc1-3, mpc1-4, and mpc1-5, displayed different phenotypes to each other and, correspondingly, these mutants were found to have different mutations in the MPC1 ORF. Temperature-sensitivity of mpc1-5 mutants was suppressed by 5 mM ZnSO(4) and by 5 mM MnCl(2). Multicopy suppressors were isolated from mpc1-5 mutant. Suppressors commonly effective to mpc1-4 and mpc1-5 mutations are PSD1, encoding phosphatidylserine decarboxylase, and ECM33, which were found to suppress the temperature-sensitive phenotype shown by the fsr2-1 and las21delta mutants, those of which have defects in the GPI anchor synthesis. PSD2, encoding another phosphatidylserine decarboxylase that is localized in Golgi/vacuole, was found to be able to serve as a multicopy suppressor of mpc1 and fsr2-1 mutants but not of the las21 delta mutant. In contrast to psd1delta, psd2delta showed a synthetic growth defect with mpc1 mutants but not with fsr2-1 or las21delta. Furthermore, psd1delta psd2delta mpc1 triple mutants did not form colonies on nutrient medium unless ethanolamine was supplied to the medium, whereas psd1delta psd2 delta fsr2-1 or psd1delta psd2 delta las21delta triple mutants grew on nutrient medium without supplementation of ethanolamine. These observations suggest that Mpc1 preferentially utilizes phosphatidylethanolamine produced by Psd2 that is localized in Golgi/vacuole. fsr2-1 dpl1 Delta psd1delta strains showed slower growth than fsr2-1 dpl1delta psd2 delta, suggesting that Fsr2 enzyme depends more on Dpl1 and Psd1 for production of phosphatidylethanolamine. Las21 did not show preference for the metabolic pathway to produce phosphatidylethanolamine. PMID:12441642

  8. Expanding the substrate scope in palladium-catalyzed C-N and C-C bond-forming reactions

    E-print Network

    Anderson, Kevin William

    2006-01-01

    Chapter 1. The first detailed study of the palladium-catalyzed amination of aryl nonaflates is reported. Use of bulky electron-rich monophosphinobiaryl ligands or BINAP allow for the catalytic amination of electron-rich ...

  9. Quantification of kinetics for enzyme-catalysed reactions: implications for diffusional limitations at the 10 ml scale.

    PubMed

    Matosevic, S; Micheletti, M; Woodley, J M; Lye, G J; Baganz, F

    2008-06-01

    The effects of different reaction scales [100 microl reactions in 96-standard round well (SRW) plates and 10 ml reactions in 24-square well (SW) plates] have been investigated using, as a model, transketolase (TK)-catalysed reaction producing L-erythrulose. Reactions were carried out under non-shaking, shaking and at 10 ml scale stirring conditions to assess the effect of diffusional limitations. Statistical analysis confirmed the significance of the observed difference in reaction rates under given conditions. Only when the laboratory scale system (10 ml) was well mixed did the reaction rate become comparable to that in the microwells, where there is negligible diffusional limitation. These findings have important implications for the scale-up (or scale-down) of enzyme-catalysed reactions. PMID:18224278

  10. Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with ?? Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.

    PubMed

    Harris, Golda G; Lombardi, Patrick M; Pemberton, Travis A; Matsui, Tsutomu; Weiss, Thomas M; Cole, Kathryn E; Köksal, Mustafa; Murphy, Frank V; Vedula, L Sangeetha; Chou, Wayne K W; Cane, David E; Christianson, David W

    2015-12-01

    Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique ?? domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg(2+) for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg(2+) ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of ?36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible ?? domain architectures as frameworks for bifunctional catalysis. PMID:26598179

  11. Visible-light-induced, Ir-catalyzed reactions of N-methyl-N-((trimethylsilyl)methyl)aniline with cyclic ?,?-unsaturated carbonyl compounds

    PubMed Central

    Lenhart, Dominik

    2014-01-01

    Summary N-Methyl-N-((trimethylsilyl)methyl)aniline was employed as reagent in visible-light-induced, iridium-catalyzed addition reactions to cyclic ?,?-unsaturated carbonyl compounds. Typical reaction conditions included the use of one equivalent of the reaction substrate, 1.5 equivalents of the aniline and 2.5 mol % (in MeOH) or 1.0 mol % (in CH2Cl2) [Ir(ppy)2(dtbbpy)]BF4 as the catalyst. Two major reaction products were obtained in combined yields of 30–67%. One product resulted from aminomethyl radical addition, the other product was a tricyclic compound, which is likely formed by attack of the intermediately formed ?-carbonyl radical at the phenyl ring. For five-membered ?,?-unsaturated lactone and lactam substrates, the latter products were the only products isolated. For the six-membered lactones and lactams and for cyclopentenone the simple addition products prevailed. PMID:24778745

  12. The Development of Versatile Methods for Palladium-Catalyzed Coupling Reactions of Aryl Electrophiles Through the Use of P(t-Bu)3 and PCy3 as Ligands

    PubMed Central

    FU, GREGORY C.

    2009-01-01

    CONSPECTUS Metal-catalyzed coupling reactions of aryl electrophiles with organometallics and with olefins serve as unusually effective tools for forming new carbon-carbon bonds. By 1998, researchers had developed catalysts that achieved reactions of aryl iodides, bromides, and triflates. Nevertheless, many noteworthy challenges remained, among them: couplings of aryl iodides, bromides, and triflates under mild conditions (at room temperature, for example); couplings of hindered reaction partners; and, couplings of inexpensive aryl chlorides. This Account highlights some of the progress that has been made over the past decade, largely through the appropriate choice of ligand, in achieving these synthetic objectives. In particular, we have established that palladium in combination with a bulky trialkylphosphine accomplishes a broad spectrum of coupling processes, including Suzuki, Stille, Negishi, and Heck reactions. These methods have been applied in a wide array of settings, such as natural-product synthesis, materials science, and bioorganic chemistry. PMID:18947239

  13. Brønsted acid catalyzed Morita-Baylis-Hillman reaction: a new mechanistic view for thioureas revealed by ESI-MS(/MS) monitoring and DFT calculations.

    PubMed

    Amarante, Giovanni W; Benassi, Mario; Milagre, Humberto M S; Braga, Ataualpa A C; Maseras, Feliu; Eberlin, Marcos N; Coelho, Fernando

    2009-11-16

    A Morita-Baylis-Hillman (MBH) reaction catalyzed by thiourea was monitored by ESI-MS(/MS) and key intermediates were intercepted and characterized. These intermediates suggest that thiourea acts as an organocatalyst in all steps of the MBH reaction cycle, including the rate-limiting proton-transfer step. DFT calculations, performed for a model MBH reaction between formaldehyde and acrolein with trimethylamine as base and in the presence or the absence of thiourea, suggest that thiourea accelerates MBH reactions by decreasing the transition-state (TS) energies through bidentate hydrogen bonding throughout the whole catalytic cycle. In the rate-limiting proton-transfer step, the thiourea acts not as a proton shuttle, but as a Brønsted acid stabilizing the basic oxygen center that is formed in the TS. PMID:19813234

  14. Visible-light-induced, Ir-catalyzed reactions of N-methyl-N-((trimethylsilyl)methyl)aniline with cyclic ?,?-unsaturated carbonyl compounds.

    PubMed

    Lenhart, Dominik; Bach, Thorsten

    2014-01-01

    N-Methyl-N-((trimethylsilyl)methyl)aniline was employed as reagent in visible-light-induced, iridium-catalyzed addition reactions to cyclic ?,?-unsaturated carbonyl compounds. Typical reaction conditions included the use of one equivalent of the reaction substrate, 1.5 equivalents of the aniline and 2.5 mol % (in MeOH) or 1.0 mol % (in CH2Cl2) [Ir(ppy)2(dtbbpy)]BF4 as the catalyst. Two major reaction products were obtained in combined yields of 30-67%. One product resulted from aminomethyl radical addition, the other product was a tricyclic compound, which is likely formed by attack of the intermediately formed ?-carbonyl radical at the phenyl ring. For five-membered ?,?-unsaturated lactone and lactam substrates, the latter products were the only products isolated. For the six-membered lactones and lactams and for cyclopentenone the simple addition products prevailed. PMID:24778745

  15. Nested arithmetic progressions of oscillatory phases in Olsen's enzyme reaction model

    NASA Astrophysics Data System (ADS)

    Gallas, Marcia R.; Gallas, Jason A. C.

    2015-06-01

    We report some regular organizations of stability phases discovered among self-sustained oscillations of a biochemical oscillator. The signature of such organizations is a nested arithmetic progression in the number of spikes of consecutive windows of periodic oscillations. In one of them, there is a main progression of windows whose consecutive number of spikes differs by one unit. Such windows are separated by a secondary progression of smaller windows whose number of spikes differs by two units. Another more complex progression involves a fan-like nested alternation of stability phases whose number of spikes seems to grow indefinitely and to accumulate methodically in cycles. Arithmetic progressions exist abundantly in several control parameter planes and can be observed by tuning just one among several possible rate constants governing the enzyme reaction.

  16. Intramolecular Gold-Catalyzed and NaH-Supported Cyclization Reactions of N-Propargyl Indole Derivatives with Pyrazole and Pyrrole Rings: Synthesis of Pyrazolodiazepinoindole, Pyrazolopyrazinoindole, and Pyrrolopyrazinoindole.

    PubMed

    Basceken, Sinan; Kaya, Serdal; Balci, Metin

    2015-12-18

    Gold-catalyzed and NaH-supported intramolecular cyclization of N-propargyl indole derivatives with pyrazole and pyrrole units attached to indole is described. An efficient route to the synthesis of pyrazolodiazepinoindole, pyrazolopyrazinoindole, and pyrrolopyrazinoindole has been established. First, N-propargyl 2-(1H-pyrazol-5-yl)-1H-indole and 2-(1H-pyrrol-2-yl)-1H-indole were synthesized. Introduction of various substituents into the alkyne functionality was accomplished by Sonogashira cross-coupling reaction. Gold-catalyzed cyclization of pyrazoles having a terminal alkyne afforded the 6-exo-dig cyclization product. However, exclusive formation of 7-endo-dig cyclization products was observed with internal alkynes. On the other hand, cyclization with NaH only resulted in the formation of 6-exo-dig cyclization products regardless of the substitution of the alkyne functionality. Allenic intermediates were postulated for this outcome. PMID:26629889

  17. Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa[W

    PubMed Central

    Wang, Jack P.; Naik, Punith P.; Chen, Hsi-Chuan; Shi, Rui; Lin, Chien-Yuan; Liu, Jie; Shuford, Christopher M.; Li, Quanzi; Sun, Ying-Hsuan; Tunlaya-Anukit, Sermsawat; Williams, Cranos M.; Muddiman, David C.; Ducoste, Joel J.; Sederoff, Ronald R.; Chiang, Vincent L.

    2014-01-01

    We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of the monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, a comprehensive study was performed to obtain the reaction and inhibition kinetic parameters of all 21 enzymes based on functional recombinant proteins. A total of 104 Michaelis-Menten kinetic parameters and 85 inhibition kinetic parameters were derived from these enzymes. Through mass spectrometry, we obtained the absolute quantities of all 21 pathway enzymes in the secondary differentiating xylem. This extensive experimental data set, generated from a single tissue specialized in wood formation, was used to construct the predictive kinetic metabolic-flux model to provide a comprehensive mathematical description of the monolignol biosynthetic pathway. The model was validated using experimental data from transgenic P. trichocarpa plants. The model predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis. This model provides an explanation of the effects of genetic and transgenic perturbations of the monolignol biosynthetic pathway in flowering plants. PMID:24619611

  18. Formal and standard ruthenium-catalyzed [2 + 2 + 2] cycloaddition reaction of 1,6-diynes to alkenes: a mechanistic density functional study.

    PubMed

    Varela, Jesús A; Rubín, Silvia G; Castedo, Luis; Saa, Carlos

    2008-02-15

    "Formal" and standard Ru(II)-catalyzed [2 + 2 + 2] cycloaddition of 1,6-diynes 1 to alkenes gave bicyclic 1,3-cyclohexadienes in relatively good yields. The neutral Ru(II) catalyst was formed in situ by mixing equimolecular amounts of [Cp*Ru(CH3CN)3]PF6 and Et4NCl. Two isomeric bicyclic 1,3-cyclohexadienes 3 and 8 were obtained depending on the cyclic or acyclic nature of the alkene partner. Mechanistic studies on the Ru catalytic cycle revealed a clue for this difference: (a) when acyclic alkenes were used, linear coupling of 1,6-diynes with alkenes was observed giving 1,3,5-trienes 6 as the only initial reaction products, which after a thermal disrotatory 6e-pi electrocyclization led to the final 1,3-cyclohexadienes 3 as probed by NMR studies. This cascade process behaved as a formal Ru-catalyzed [2 + 2 + 2] cycloaddition. (b) With cyclic alkenes, the standard Ru-catalyzed [2 + 2 + 2] cycloaddition occurred, giving the bicyclic 1,3-cyclohexadienes 8 as reaction products. A complete catalytic cycle for the formal and standard Ru-catalyzed [2 + 2 + 2] cycloaddition of acetylene and cyclic and acyclic alkenes with the Cp*RuCl fragment has been proposed and discussed based on DFT/B3LYP calculations. The most likely mechanism for these processes would involve the formation of ruthenacycloheptadiene intermediates XXIII or XXVII depending on the alkene nature. From these complexes, two alternatives could be envisioned: (a) a reductive elimination in the case of cyclic alkenes 7 and (b) a beta-elimination followed by reductive elimination to give 1,3,5-hexatrienes 6 in the case of acyclic alkenes. Final 6e-pi electrocyclization of 6 gave 1,3-cyclohexadienes 3. PMID:18197681

  19. Reactions catalyzed by haloporphyrins

    DOEpatents

    Ellis, P.E. Jr.; Lyons, J.E.

    1996-02-06

    The invention provides novel methods for the oxidation of hydrocarbons with oxygen-containing gas to form hydroxy-group containing compounds and for the decomposition of hydroperoxides to form hydroxy-group containing compounds. The catalysts used in the methods of the invention comprise transition metal complexes of a porphyrin ring having 1 to 12 halogen substituents on the porphyrin ring, at least one of said halogens being in a meso position and/or the catalyst containing no aryl group in a meso position. The catalyst compositions are prepared by halogenating a transition metal complex of a porphyrin. In one embodiment, a complex of a porphyrin with a metal whose porphyrin complexes are not active for oxidation of alkanes is halogenated, thereby to obtain a haloporphyrin complex of that metal, the metal is removed from the haloporphyrin complex to obtain the free base form of the haloporphyrin, and a metal such as iron whose porphyrin complexes are active for oxidation of alkanes and for the decomposition of alkyl hydroperoxides is complexed with the free base to obtain an active catalyst for oxidation of alkanes and decomposition of alkyl hydroperoxides.

  20. Reactions catalyzed by haloporphyrins

    DOEpatents

    Ellis, Jr., Paul E. (Downingtown, PA); Lyons, James E. (Wallingford, PA)

    1996-01-01

    The invention provides novel methods for the oxidation of hydrocarbons with oxygen-containing gas to form hydroxy-group containing compounds and for the decomposition of hydroperoxides to form hydroxygroup containing compounds. The catalysts used in the methods of the invention comprise transition metal complexes of a porphyrin ring having 1 to 12 halogen substituents on the porphyrin ring, at least one of said halogens being in a meso position and/or the catalyst containing no aryl group in a meso position. The catalyst compositions are prepared by halogenating a transition metal complex of a porphyrin. In one embodiment, a complex of a porphyrin with a metal whose porphyrin complexes are not active for oxidation of alkanes is halogenated, thereby to obtain a haloporphyrin complex of that metal, the metal is removed from the haloporphyrin complex to obtain the free base form of the haloporphyrin, and a metal such as iron whose porphyrin complexes are active for oxidation of alkanes and for the decomposition of alkyl hydroperoxides is complexed with the free base to obtain an active catalyst for oxidation of alkanes and decomposition of alkyl hydroperoxides.

  1. Rhenium-Catalyzed Aromatic Propargylation

    E-print Network

    Toste, Dean

    Rhenium-Catalyzed Aromatic Propargylation Joshua J. Kennedy-Smith, Lauren A. Young, and F. Dean propargylation reaction, employing an air- and moisture-tolerant rhenium-oxo complex ((dppm)ReOCl3) as a catalyst. The potential of this rhenium(V)-catalyzed reaction is exemplified by application of the propargylation

  2. Following Solid-Acid-Catalyzed Reactions by MAS NMR Spectroscopy in Liquid Phase -Zeolite-Catalyzed Conversion of Cyclohexanol in Water

    SciTech Connect

    Vjunov, Aleksei; Hu, Mary Y.; Feng, Ju; Camaioni, Donald M.; Mei, Donghai; Hu, Jian Z.; Zhao, Chen; Lercher, Johannes A.

    2014-01-07

    The catalytic conversion of cyclohexanol on zeolite HBEA in hot liquid water leads to dehydration as well as alkylation products. A novel micro autoclave suitable for application in MAS NMR at high temperatures and pressures is developed and successfully applied to obtain new insight into the mechanistic pathway leading to an understanding of the reactions under selected experimental conditions.

  3. Enzymic synthesis of indole-3-acetyl-1-O-beta-d-glucose. I. Partial purification and characterization of the enzyme from Zea mays

    NASA Technical Reports Server (NTRS)

    Leznicki, A. J.; Bandurski, R. S.

    1988-01-01

    The first enzyme-catalyzed reaction leading from indole-3-acetic acid (IAA) to the myo-inositol esters of IAA is the synthesis of indole-3-acetyl-1-O-beta-D-glucose from uridine-5'-diphosphoglucose (UDPG) and IAA. The reaction is catalyzed by the enzyme, UDPG-indol-3-ylacetyl glucosyl transferase (IAA-glucose-synthase). This work reports methods for the assay of the enzyme and for the extraction and partial purification of the enzyme from kernels of Zea mays sweet corn. The enzyme has an apparent molecular weight of 46,500 an isoelectric point of 5.5, and its pH optimum lies between 7.3 and 7.6. The enzyme is stable to storage at zero degrees but loses activity during column chromatographic procedures which can be restored only fractionally by addition of column eluates. The data suggest either multiple unknown cofactors or conformational changes leading to activity loss.

  4. Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: Controlling single E-coli ?-galactosidase enzyme catalysis through the elementary reaction steps

    SciTech Connect

    Das, Biswajit; Gangopadhyay, Gautam; Banerjee, Kinshuk

    2013-12-28

    In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli ?-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises.

  5. Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: controlling single E-coli ?-galactosidase enzyme catalysis through the elementary reaction steps.

    PubMed

    Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

    2013-12-28

    In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli ?-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises. PMID:24387354

  6. Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: Controlling single E-coli ?-galactosidase enzyme catalysis through the elementary reaction stepsa)

    NASA Astrophysics Data System (ADS)

    Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

    2013-12-01

    In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli ?-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises.

  7. Four mechanisms in the reactions of 3-aminopyrrole with 1,3,5-triazines: inverse electron demand Diels-Alder cycloadditions vs S(N)Ar reactions via uncatalyzed and acid-catalyzed pathways.

    PubMed

    De Rosa, Michael; Arnold, David; Hartline, Douglas

    2013-09-01

    Reaction of 3-aminopyrrole with seven 1,3,5-triazines was studied in a one-step reaction (in situ formation of 3-aminopyrrole) and a two-step reaction (using the tetraphenylborate salt and an amine base). An inverse-electron demand Diels-Alder reaction (IEDDA) was observed with R1 = CF3, CO2Et, and H with the formation of 5H-pyrrolo[3,2-d]pyrimidine derivatives. S(N)Ar was observed when 2,4,6-trifluoro- or 2,4,6-trichloro-1,3,5-triazine were used--1,3,5-triazines that had leaving groups. If excess 1,3,5-triazine was present the initial S(N)Ar product reacted further, in the presence of acid and water, with another equivalent of 1,3,5-triazine to give compounds containing three linked heterocyclic rings. No reaction was observed with R1 = C6H5 and OCH3. Four mechanisms are proposed to explain the experimental results: uncatalyzed and acid catalyzed inverse electron demand Diels-Alder cascades leading to cycloaddition, and uncatalyzed and acid-catalyzed S(N)Ar reactions leading, respectively, to single and double substitution products. Acid catalysis was a factor when there was reduced reactivity in either reactant. PMID:23898949

  8. Total synthesis of (+)-asteriscanolide: further exploration of the rhodium(I)-catalyzed [(5+2)+1] reaction of ene-vinylcyclopropanes and CO.

    PubMed

    Liang, Yong; Jiang, Xing; Fu, Xu-Fei; Ye, Siyu; Wang, Tao; Yuan, Jie; Wang, Yuanyuan; Yu, Zhi-Xiang

    2012-03-01

    The total synthesis of (+)-asteriscanolide is reported. The synthetic route features two key reactions: 1) the rhodium(I)-catalyzed [(5+2)+1] cycloaddition of a chiral ene-vinylcyclopropane (ene-VCP) substrate to construct the [6.3.0] carbocyclic core with excellent asymmetric induction, and 2) an alkoxycarbonyl-radical cyclization that builds the bridging butyrolactone ring with high efficiency. Other features of this synthetic route include the catalytic asymmetric alkynylation of an aldehyde to synthesize the chiral ene-VCP substrate, a highly regioselective conversion of the [(5+2)+1] cycloadduct into its enol triflate, and the inversion of the inside-outside tricycle to the outside-outside structure by an ester-reduction/elimination to enol-ether/hydrogenation procedure. In addition, density functional theory (DFT) rationalization of the chiral induction of the [(5+2)+1] reaction and the diastereoselectivity of the radical annulation has been presented. Equally important is that we have also developed other routes to synthesize asteriscanolide using the rhodium(I)-catalyzed [(5+2)+1] cycloaddition as the key step. Even though these routes failed to achieve the total synthesis, these experiments gave further useful information about the scope of the [(5+2)+1] reaction and paved the way for its future application in synthesis. PMID:22223465

  9. Cobalt-catalyzed negishi cross-coupling reactions of (hetero)arylzinc reagents with primary and secondary alkyl bromides and iodides.

    PubMed

    Hammann, Jeffrey M; Haas, Diana; Knochel, Paul

    2015-04-01

    We report a cobalt-catalyzed cross-coupling of di(hetero)arylzinc reagents with primary and secondary alkyl iodides or bromides using THF-soluble CoCl2 ?2?LiCl and TMEDA as a ligand, which leads to the corresponding alkylated products in up to 88?% yield. A range of functional groups (e.g. COOR, CN, CF3 , F) are tolerated in these substitution reactions. Remarkably, we do not observe rearrangement of secondary alkyl iodides to unbranched products. Additionally, the use of cyclic TBS-protected iodohydrins leads to trans-2-arylcyclohexanol derivatives in excellent diastereoselectivities (up to d.r.=99:1). PMID:25694155

  10. Exploiting the gem-Disubstitution Effect in FcPHOX and HetPHOX P,N Ligands: Synthesis and Applications in Pd-Catalyzed Intermolecular Heck Reactions.

    PubMed

    McCartney, Dennis; Nottingham, Chris; Müller-Bunz, Helge; Guiry, Patrick J

    2015-10-16

    The synthesis of a range of novel gem-disubstituted and electronically varied thiophene-oxazoline (HetPHOX) ligands and ferrocene-oxazoline (FcPHOX) ligands and their application in the Pd-catalyzed intermolecular asymmetric Heck reaction (IAH) is described. These investigations show that gem-disubstitution of i-Pr-PHOX-type ligands can lead to effective and cost-efficient alternatives to the corresponding t-Bu-PHOX systems. The Pd complexes of these ligands were very effective in the IAH, providing phenylated products in up to 100% conversion with up to 97% ee. PMID:26327681

  11. Beyond Directed ortho Metalation: Ruthenium-Catalyzed Amide-Directed CAr-OMe Activation/Cross-Coupling Reaction of Naphthamides with Aryl Boronates.

    PubMed

    Zhao, Yigang; Snieckus, Victor

    2015-10-01

    A new and general synthetic methodology for the construction of biaryl, heterobiaryl, and polyaryl molecules by the ruthenium-catalyzed cross-coupling of ortho-methoxy naphthamides with aryl boroneopentylates is described. The isomeric 1-MeO-2-naphthamides and 2-MeO-1-naphthamides furnish an expansive series of arylated naphthamides in excellent yields. Competition experiments showed the higher reactivity of 1-MeO-2-naphthamide over 2-MeO-benzamide. Orthogonality between the C-O activation/cross-coupling and the Suzuki-Miyaura reactions was established. The method provides naphthalenes which are difficult to prepare by directed ortho metalation. PMID:26371873

  12. Water-catalyzed dehalogenation reactions of the isomer of CBr4 and its reaction products and a comparison to analogous reaction of the isomers of di-and trihalomethanes.

    PubMed

    Zhao, Cunyuan; Lin, Xufeng; Kwok, Wai Ming; Guan, Xiangguo; Du, Yong; Wang, Dongqi; Hung, Kam Fa; Phillips, David Lee

    2005-02-01

    A combined experimental and theoretical study of the UV photolysis of a typical tetrahalomethane, CBr4, in water and acetonitrile/water was performed. Ultraviolet photolysis of low concentrations of CBr4 in water mostly leads to the production of four HBr leaving groups and CO2. Picosecond time-resolved resonance Raman (Ps-TR3) experiments and ab initio calculations indicate that water-catalyzed O-H insertion/HBr elimination of the isomer of CBr4 and subsequent reactions of its products lead to the formation of these products. The UV photolyses of di-, tri-, and tetrahalomethanes at low concentrations in water-solvated environments are compared to one another. This comparison enables a general reaction scheme to be deduced that can account for the different products produced by UV photolysis of low concentrations of di-, tri-, and tetrahalomethanes in water. The fate of the (halo)formaldehyde intermediate in the chemical reaction mechanism is the key to determining how many strong acid leaving groups are produced and which carbon atom final product is likely formed by UV photolysis of a polyhalomethane at low concentrations in a water-solvated environment. PMID:15742469

  13. Detection of Covalent and Noncovalent Intermediates in the Polymerization Reaction Catalyzed by a C149S Class III Polyhydroxybutyrate Synthase

    E-print Network

    Li, Ping

    Polyhydroxybutyrate (PHB) synthases catalyze the conversion of 3-hydroxybutyryl coenzyme A (HBCoA) to PHB with a molecular mass of 1.5 MDa. The class III synthase from Allochromatium vinosum is a tetramer of PhaEPhaC (each ...

  14. Direct Synthesis of 5-Aryl Barbituric Acids by Rhodium(II)-Catalyzed Reactions of Arenes with Diazo Compounds**

    PubMed Central

    Best, Daniel; Burns, David J; Lam, Hon Wai

    2015-01-01

    A commercially available rhodium(II) complex catalyzes the direct arylation of 5-diazobarbituric acids with arenes, allowing straightforward access to 5-aryl barbituric acids. Free N—H groups are tolerated on the barbituric acid, with no complications arising from N—H insertion processes. This method was applied to the concise synthesis of a potent matrix metalloproteinase (MMP) inhibitor. PMID:25959544

  15. A DNA enzyme with N-glycosylase activity

    NASA Technical Reports Server (NTRS)

    Sheppard, T. L.; Ordoukhanian, P.; Joyce, G. F.

    2000-01-01

    In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

  16. Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis

    SciTech Connect

    Ramanathan, Arvind; Agarwal, Pratul K

    2011-01-01

    Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.

  17. Mechanistic studies of an unprecedented enzyme-catalysed 1,2-phosphono-migration reaction

    E-print Network

    Chang, Wei-chen

    (S)-2-hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-haem-iron-dependent enzyme1, 2, 3 responsible for the final step in the biosynthesis of the clinically useful antibiotic fosfomycin4. Enzymes ...

  18. The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions

    PubMed Central

    Piedrafita, Gabriel; Keller, Markus A; Ralser, Markus

    2015-01-01

    Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease—age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network. PMID:26378592

  19. The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions.

    PubMed

    Piedrafita, Gabriel; Keller, Markus A; Ralser, Markus

    2015-01-01

    Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease-age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network. PMID:26378592

  20. 2-Oxindole Acts as a Synthon of 2-Aminobenzoyl Anion in the K2CO3-Catalyzed Reaction with Enones: Preparation of 1,4-Diketones Bearing an Amino Group and Their Further Transformations.

    PubMed

    Miao, Chun-Bao; Zeng, Yu-Mei; Shi, Tong; Liu, Rui; Wei, Peng-Fei; Sun, Xiao-Qiang; Yang, Hai-Tao

    2016-01-01

    A convenient approach for the synthesis of 1,4-diketones bearing an amino group has been developed through the K2CO3-catalyzed reaction of 2-oxindoles with enones with the assistance of atmospheric O2 via sequential Michael addition-oxidation-ring-cleavage process. The further intramolecular reaction leads to the formation of benzoazepinone, quinoline, and 3-oxindole derivatives. PMID:26656574