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Sample records for enzyme catalyzed reactions

  1. Thermodynamics of Enzyme-Catalyzed Reactions Database

    National Institute of Standards and Technology Data Gateway

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

  2. Microorganisms detected by enzyme-catalyzed reaction

    NASA Technical Reports Server (NTRS)

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

    1966-01-01

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

  3. Representing Rate Equations for Enzyme-Catalyzed Reactions

    ERIC Educational Resources Information Center

    Ault, Addison

    2011-01-01

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

  4. 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.

  5. Chemical and genomic evolution of enzyme-catalyzed reaction networks.

    PubMed

    Kanehisa, Minoru

    2013-09-01

    There is a tendency that a unit of enzyme genes in an operon-like structure in the prokaryotic genome encodes enzymes that catalyze a series of consecutive reactions in a metabolic pathway. Our recent analysis shows that this and other genomic units correspond to chemical units reflecting chemical logic of organic reactions. From all known metabolic pathways in the KEGG database we identified chemical units, called reaction modules, as the conserved sequences of chemical structure transformation patterns of small molecules. The extracted patterns suggest co-evolution of genomic units and chemical units. While the core of the metabolic network may have evolved with mechanisms involving individual enzymes and reactions, its extension may have been driven by modular units of enzymes and reactions.

  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. Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes.

    PubMed

    Kasparyan, Elena; Richter, Michael; Dresen, Carola; Walter, Lydia S; Fuchs, Georg; Leeper, Finian J; Wacker, Tobias; Andrade, Susana L A; Kolter, Geraldine; Pohl, Martina; Müller, Michael

    2014-12-01

    The intermolecular asymmetric Stetter reaction is an almost unexplored transformation for biocatalysts. Previously reported thiamine diphosphate (ThDP)-dependent PigD from Serratia marcescens is the first enzyme identified to catalyze the Stetter reaction of α,β-unsaturated ketones (Michael acceptor substrates) and α-keto acids. PigD is involved in the biosynthesis of the potent cytotoxic agent prodigiosin. Here, we describe the investigation of two new ThDP-dependent enzymes, SeAAS from Saccharopolyspora erythraea and HapD from Hahella chejuensis. Both show a high degree of homology to the amino acid sequence of PigD (39 and 51 %, respectively). The new enzymes were heterologously overproduced in Escherichia coli, and the yield of soluble protein was enhanced by co-expression of the chaperone genes groEL/ES. SeAAS and HapD catalyze intermolecular Stetter reactions in vitro with high enantioselectivity. The enzymes possess a characteristic substrate range with respect to Michael acceptor substrates. This provides support for a new type of ThDP-dependent enzymatic activity, which is abundant in various species and not restricted to prodigiosin biosynthesis in different strains. Moreover, PigD, SeAAS, and HapD are also able to catalyze asymmetric carbon-carbon bond formation reactions of aldehydes and α-keto acids, resulting in 2-hydroxy ketones.

  8. Pericyclic reactions catalyzed by chorismate-utilizing enzymes

    PubMed Central

    Lamb, Audrey L.

    2011-01-01

    One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure-function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions. Specifically, salicylate synthesis by the two-enzyme pathway in Pseudomonas aeruginosa is examined. The isochorismate-pyruvate lyase is discussed in the context of its homologues, the chorismate mutases, and the isochorismate synthase is compared to its homologues in the MST-family (menaquinone, siderophore or tryptophan biosynthesis) of enzymes. The tentative conclusion is that the activities observed cannot be reconciled by inspection of the active site participants alone. Instead, individual activities must arise from unique dynamic properties of each enzyme that are tuned to promote specific chemistries. PMID:21823653

  9. 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.

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

    PubMed

    Tian, Xuemei; Zhang, Suoqin; Zheng, Liangyu

    2016-01-01

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

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

    ERIC Educational Resources Information Center

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

    2003-01-01

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

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

    PubMed

    Arcus, Vickery L; Pudney, Christopher R

    2015-08-01

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

  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. Cysteine Oxidation Reactions Catalyzed by a Mononuclear Non-heme Iron Enzyme (OvoA) in Ovothiol Biosynthesis

    PubMed Central

    2015-01-01

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

  16. An analytical method for determining relative specificities for sequential reactions catalyzed by the same enzyme: general formulation.

    PubMed

    Mitchell, David Alexander; Carrière, Frédéric; Krieger, Nadia

    2008-04-01

    We present a general formulation of a model that can be used to analyze reaction profiles in systems in which a single enzyme catalyzes several sequential reactions with the same molecular backbone. The analysis of these so-called "repeated-attack systems" allows estimation of the specificities that the enzyme has for the various intermediate substrates that appear in the reaction mixture, relative to the specificity that it has for the initial substrate. Our analytical method has the important advantage that it is not affected by competitive or uncompetitive inhibition, nor by denaturation of the enzyme during the reaction. We carry out case studies in three different systems, the lipase-catalyzed alcoholysis of triacylglycerols, the phytase-catalyzed removal of phosphate groups from phytic acid and the beta-amylase-catalyzed removal of maltose units from maltoheptaose. Our model fits well to all reaction profiles in which the phenomenon of processivity does not occur. It can therefore be used as a general tool for characterizing the relative specificities of "repeated-attack enzymes".

  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. Isopentenyl diphosphate isomerase catalyzed reactions in D2O: product release limits the rate of this sluggish enzyme-catalyzed reaction.

    PubMed

    Jonnalagadda, Venkatadurga; Toth, Krisztina; Richard, John P

    2012-04-18

    The E. coli isopentenyl diphosphate isomerase (IDI) catalyzed reaction of isopentenyl diphosphate (IPP) in D(2)O gives a 66% yield of dimethylallyl diphosphate labeled with deuterium at the (E)-methyl group (d-DMAPP) and a 34% yield of IPP labeled with 1 mol of deuterium at C-2 (d-IPP). This shows that the release to D(2)O of the initial product of the IDI-catalyzed reaction (d-DMAPP) is slower than its conversion to d-IPP. Product dissociation is therefore rate determining for isomerization of IPP with a rate constant k(dis) ≈ k(cat) = 0.08 s(-1). The data provide an estimated rate constant of k(as) = 6 × 10(3) M(-1) s(-1) for binding of DMAPP to E. coli IDI that is similar to rate constants determined for the binding of N-protonated 2-amino ethyl diphosphate intermediate analogs to IDI from yeast [Reardon, J. E.; Abeles, R. H. Biochemistry1986, 25, 5609-5616]. We propose that ligand binding to IDI is relatively slow because there is a significant kinetic barrier to reorganization of the initial encounter complex between enzyme, substrate, and an essential Mg(2+) to form the Michaelis complex where the metal cation bridges the protein and the substrate diphosphate group.

  19. 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.

  20. Haloperoxidase reactions catalyzed by lignin peroxidase, an extracellular enzyme from the basidiomycete Phanerochaete chrysosporium

    SciTech Connect

    Renganathan, V.; Miki, K.; Gold, M.H.

    1987-08-11

    Lignin peroxidase (ligninase, LiP) an H/sub 2/O/sub 2/-dependent lignin-degrading heme enzyme from the basidiomycetous fungus Phanerochaete chrysosporium, catalyzes the oxidation of a variety of lignin model compounds. In this paper the authors examine the haloperoxidase reactions of LiP. In the presence of H/sub 2/O/sub 2/, homogeneous LiP oxidized bromide and iodide but not chloride. Halide oxidation was measured by the halogenation of monochlorodimedone (MCD) and a variety of other aromatic compounds. Bromination of MCD produced monochloromonobromodimedone. The pH optimum for the bromination of MCD was 3.5. Both chloride and fluoride inhibited the bromination reaction. LiP binds halides to produce characteristic optical difference spectra. From these spectra apparent dissociation constants for fluoride and chloride were determined to be 0.3 and 20 mM, respectively. Incubation of LiP with bromide and H/sub 2/O/sub 2/ in the absence of organic substrate led to the bleaching of the heme as measured by a decrease in Soret maximum. LiP brominated a variety of aromatic substrates including 3,4-dimethoxybenzyl alcohol (veratryl alcohol) to produce 6-bromoveratryl alcohol (VII). LiP hydrobrominated cinnamic acid (IV) to produce 2-bromo-3-hydroxy-3-phenylpropionic acid (XII). In an analogous reaction LiP hydrobrominated 1-(4-ethoxy-3-methoxyphenyl)propene (II) to produce 2-bromo-1-(4-ethoxy-3-methoxyphenyl)-1-hydroxypropane (XIII). Finally, with 3,4-dimethoxycinnamic acid as the substrate, three bromination products were identified: trans-2-bromo-1-(3,4-dimethoxyphenyl)ethylene (IX), 2,2-dibromo-1-(3,4-dimethoxyphenyl)-1-hydroxyethane (X), and 2-bromo-3-(3,4-dimethoxyphenyl)-3-hydroxypropionic acid (XI).

  1. 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…

  2. Monte Carlo simulations of single- and multistep enzyme-catalyzed reaction sequences: effects of diffusion, cell size, enzyme fluctuations, colocalization, and segregation.

    PubMed

    Anderson, James B; Anderson, Louise E; Kussmann, Jörg

    2010-07-21

    Following the discovery of slow fluctuations in the catalytic activity of an enzyme in single-molecule experiments, it has been shown that the classical Michaelis-Menten (MM) equation relating the average enzymatic velocity and the substrate concentration may hold even for slowly fluctuating enzymes. In many cases, the average velocity is that given by the MM equation with time-averaged values of the fluctuating rate constants and the effect of enzyme fluctuations is simply averaged out. The situation is quite different for a sequence of reactions. For colocalization of a pair of enzymes in a sequence to be effective in promoting reaction, the second must be active when the first is active or soon after. If the enzymes are slowly varying and only rarely active, the product of the first reaction may diffuse away before the second enzyme is active, and colocalization may have little value. Even for single-step reactions the interplay of reaction and diffusion with enzyme fluctuations leads to added complexities, but for multistep reactions the interplay of reaction and diffusion, cell size, compartmentalization, enzyme fluctuations, colocalization, and segregation is far more complex than for single-step reactions. In this paper, we report the use of stochastic simulations at the level of whole cells to explore, understand, and predict the behavior of single- and multistep enzyme-catalyzed reaction systems exhibiting some of these complexities. Results for single-step reactions confirm several earlier observations by others. The MM relationship, with altered constants, is found to hold for single-step reactions slowed by diffusion. For single-step reactions, the distribution of enzymes in a regular grid is slightly more effective than a random distribution. Fluctuations of enzyme activity, with average activity fixed, have no observed effects for simple single-step reactions slowed by diffusion. Two-step sequential reactions are seen to be slowed by segregation of

  3. 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.

  4. Catalyzed enzyme electrodes

    SciTech Connect

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

    1993-07-13

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

  5. Catalyzed enzyme electrodes

    DOEpatents

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

    1993-01-01

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

  6. Synthesis of 2-monoacylglycerols and structured triacylglycerols rich in polyunsaturated fatty acids by enzyme catalyzed reactions.

    PubMed

    Rodríguez, Alicia; Esteban, Luis; Martín, Lorena; Jiménez, María José; Hita, Estrella; Castillo, Beatriz; González, Pedro A; Robles, Alfonso

    2012-08-10

    This paper studies the synthesis of structured triacylglycerols (STAGs) by a four-step process: (i) obtaining 2-monoacylglycerols (2-MAGs) by alcoholysis of cod liver oil with several alcohols, catalyzed by lipases Novozym 435, from Candida antartica and DF, from Rhizopus oryzae, (ii) purification of 2-MAGs, (iii) formation of STAGs by esterification of 2-MAGs with caprylic acid catalyzed by lipase DF, from R. oryzae, and (iv) purification of these STAGs. For the alcoholysis of cod liver oil, absolute ethanol, ethanol 96% (v/v) and 1-butanol were compared; the conditions with ethanol 96% were then optimized and 2-MAG yields of around 54-57% were attained using Novozym 435. In these 2-MAGs, DHA accounted for 24-31% of total fatty acids. In the operational conditions this lipase maintained a stable level of activity over at least 11 uses. These results were compared with those obtained with lipase DF, which deactivated after only three uses. The alcoholysis of cod liver oil and ethanol 96% catalyzed by Novozym 435 was scaled up by multiplying the reactant amounts 100-fold and maintaining the intensity of treatment constant (IOT=3g lipase h/g oil). In these conditions, the 2-MAG yield attained was about 67%; these 2-MAGs contained 36.6% DHA. The synthesized 2-MAGs were separated and purified from the alcoholysis reaction products by solvent extraction using solvents of low toxicity (ethanol and hexane); 2-MAG recovery yield and purity of the target product were approximately 96.4% and 83.9%, respectively. These 2-MAGs were transformed to STAGs using the optimal conditions obtained in a previous work. After synthesis and purification, 93% pure STAGs were obtained, containing 38% DHA at sn-2 position and 60% caprylic acid (CA) at sn-1,3 positions (of total fatty acids at these positions), i.e. the major TAG is the STAG with the structure CA-DHA-CA. PMID:22759534

  7. Synthesis of 2-monoacylglycerols and structured triacylglycerols rich in polyunsaturated fatty acids by enzyme catalyzed reactions.

    PubMed

    Rodríguez, Alicia; Esteban, Luis; Martín, Lorena; Jiménez, María José; Hita, Estrella; Castillo, Beatriz; González, Pedro A; Robles, Alfonso

    2012-08-10

    This paper studies the synthesis of structured triacylglycerols (STAGs) by a four-step process: (i) obtaining 2-monoacylglycerols (2-MAGs) by alcoholysis of cod liver oil with several alcohols, catalyzed by lipases Novozym 435, from Candida antartica and DF, from Rhizopus oryzae, (ii) purification of 2-MAGs, (iii) formation of STAGs by esterification of 2-MAGs with caprylic acid catalyzed by lipase DF, from R. oryzae, and (iv) purification of these STAGs. For the alcoholysis of cod liver oil, absolute ethanol, ethanol 96% (v/v) and 1-butanol were compared; the conditions with ethanol 96% were then optimized and 2-MAG yields of around 54-57% were attained using Novozym 435. In these 2-MAGs, DHA accounted for 24-31% of total fatty acids. In the operational conditions this lipase maintained a stable level of activity over at least 11 uses. These results were compared with those obtained with lipase DF, which deactivated after only three uses. The alcoholysis of cod liver oil and ethanol 96% catalyzed by Novozym 435 was scaled up by multiplying the reactant amounts 100-fold and maintaining the intensity of treatment constant (IOT=3g lipase h/g oil). In these conditions, the 2-MAG yield attained was about 67%; these 2-MAGs contained 36.6% DHA. The synthesized 2-MAGs were separated and purified from the alcoholysis reaction products by solvent extraction using solvents of low toxicity (ethanol and hexane); 2-MAG recovery yield and purity of the target product were approximately 96.4% and 83.9%, respectively. These 2-MAGs were transformed to STAGs using the optimal conditions obtained in a previous work. After synthesis and purification, 93% pure STAGs were obtained, containing 38% DHA at sn-2 position and 60% caprylic acid (CA) at sn-1,3 positions (of total fatty acids at these positions), i.e. the major TAG is the STAG with the structure CA-DHA-CA.

  8. 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.

  9. 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…

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

    PubMed

    Natsume, Tomotaka; Yoshimoto, Makoto

    2014-03-12

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

  11. The application of transient-state kinetic isotope effects to the resolution of mechanisms of enzyme-catalyzed reactions.

    PubMed

    Fisher, Harvey F

    2013-01-01

    Much of our understanding of the mechanisms of enzyme-catalyzed reactions is based on steady-state kinetic studies. Experimentally, this approach depends solely on the measurement of rates of free product appearance (d[P]/dt), a mechanistically and mathematically complex entity. Despite the ambiguity of this observed parameter, the method's success is due in part to the elaborate rigorously derived algebraic theory on which it is based. Transient-state kinetics, on the other hand, despite its ability to observe the formation of intermediate steps in real time, has contributed relatively little to the subject due in, some measure, to the lack of such a solid mathematical basis. Here we discuss the current state of existing transient-state theory and the difficulties in its realistic application to experimental data. We describe a basic analytic theory of transient-state kinetic isotope effects in the form of three novel fundamental rules. These rules are adequate to define an extended mechanism, locating the isotope-sensitive step and identifying missing steps from experimental data. We demonstrate the application of these rules to resolved component time courses of the phenylalanine dehydrogenase reaction, extending the previously known reaction by one new prehydride transfer step and two new post hydride transfer steps. We conclude with an assessment of future directions in this area. PMID:23857126

  12. 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…

  13. In situ gellable sugar beet pectin via enzyme-catalyzed coupling reaction of feruloyl groups for biomedical applications.

    PubMed

    Takei, Takayuki; Sugihara, Kotaro; Ijima, Hiroyuki; Kawakami, Koei

    2011-11-01

    In situ gellable hydrogels are more attractive in many biomedical and biopharmaceutical applications than pre-formed hydrogels because they can be implanted simply by injection and allow homogeneous incorporation of bioactive materials. In this study, the potential suitability of in situ gellable sugar beet pectin (SBP) for biomedical and biopharmaceutical applications was investigated. SBP aqueous solution gelled within 1 min after addition of appropriate amounts of horseradish peroxidase (HRP) and H₂O₂ via HRP-catalyzed oxidative coupling reaction of feruloyl groups on SBP molecules. The resultant gels gradually degraded under simulated physiological condition. L929 fibroblast cells encapsulated in the gels were scarcely damaged during the gelation process. A subcutaneously injected mixture of SBP, HRP and H₂O₂ solutions successfully gelled, and the gel did not induce necrosis in the surrounding tissue 1 week after implantation. These results demonstrate that the in situ gellable SBP gels are useful for biomedical and biopharmaceutical applications.

  14. Oxygen isotope effects of enzyme-catalyzed organophosphorus hydrolysis reactions: implications for interpretation of dissolved PO4 δ18O values in natural waters

    NASA Astrophysics Data System (ADS)

    Liang, Y.; Blake, R. E.

    2002-12-01

    The geochemical cycling of P in Earth surface environments is controlled largely by biota. It has been recently demonstrated that intracellular cycling of P in microbial cultures and biological turnover of P in natural waters leads to temperature-dependent O isotope equilibrium between dissolved inorganic PO4 (Pi) and ambient water, and that the δ18O of Pi can be a useful tracer of biological reactions and P cycling in aquatic systems/sediments. Oxygen isotope exchange between Pi and water during biological turnover of P is catalyzed by enzymes at low-temperature. Phosphoenzymes play a crucial role in the intracellular functions of all living organisms and also have important extracellular functions in aquatic ecosystems such as regeneration of Pi from organophosphorus compounds (e.g., phosphoesters). Laboratory experiments indicate that extracellular enzyme reactions may result in incomplete Pi turnover and non-equilibrium Pi-water O isotope exchange. Determination of the O isotope effects of phosphoenzyme-catalyzed reactions is fundamental to the understanding of mechanisms of PO4-water O isotope exchange, pathways of biogeochemical P cycling, and interpretation of PO4 δ18O values from natural systems. Here we report on the O isotope fractionation between enzymatically-released Pi and water, in cell-free abiotic systems. Alkaline phosphatase (Apase) is a non-specific phosphohydrolase commonly found in fresh and marine coastal waters that catalyzes the hydrolysis of Pi from phosphomonoesters. We examined the O isotope effects of Apase derived from both microbial and eukaryotic sources and acting on different phosphomonoester substrates (e.g., α-D-Glucose 1-Phosphate, β-Glycerophosphate, AMP) in 18O-labeled waters. Oxygen isotope ratios of Pi released by Apase indicate that only 1 of the 4 O atoms in PO4 is incorporated from water with little or no apparent O isotopic fractionation at the site of incorporation. This observation is consistent with

  15. Abasic and oxidized abasic site reactivity in DNA: enzyme inhibition, cross-linking, and nucleosome catalyzed reactions.

    PubMed

    Greenberg, Marc M

    2014-02-18

    , an enzyme that is irreversibly inactivated, is vitally important in base excision repair and is overproduced in some tumor cells. Nucleosome core particles, the monomeric components that make up chromatin, accentuate the chemical instability of abasic lesions. In experiments using synthetic nucleosome core particles containing abasic sites, the histone proteins catalyze strand cleavage at the sites that incorporate these lesions. Furthermore, in the presence of the C4-AP lesion, strand scission is accompanied by modification of the histone protein. The reactivity of (oxidized) abasic lesions illustrates how seemingly simple nucleic acid modifications can have significant biochemical effects and may provide a chemical basis for the cytotoxicity of the chemotherapeutic agents that produce them. PMID:24369694

  16. 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.

  17. Pd-catalyzed steroid reactions.

    PubMed

    Czajkowska-Szczykowska, Dorota; Morzycki, Jacek W; Wojtkielewicz, Agnieszka

    2015-05-01

    We review the most important achievements of the last decade in the field of steroid synthesis in the presence of palladium catalysts. Various palladium-catalyzed cross-coupling reactions, including Heck, Suzuki, Stille, Sonogashira, Negishi and others, are exemplified with steroid transformations.

  18. Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction.

    PubMed

    Kumar, Praveen; Verma, Anjali; Saini, Adesh Kumar; Chopra, Puneet; Chakraborti, Pradip K; Singh, Yogendra; Chowdhury, Shantanu

    2005-01-01

    The reason for secretion of nucleoside diphosphate kinase (NdK), an enzyme involved in maintaining the cellular pool of nucleoside triphosphates in both prokaryotes and eukaryotes, by Mycobacterium tuberculosis is intriguing. We recently observed that NdK from M.tuberculosis (mNdK) localizes within nuclei of HeLa and COS-1 cells and also nicks chromosomal DNA in situ (A. K. Saini, K. Maithal, P. Chand, S. Chowdhury, R. Vohra, A. Goyal, G. P. Dubey, P. Chopra, R. Chandra, A. K. Tyagi, Y. Singh and V. Tandon (2004) J. Biol. Chem., 279, 50142-50149). In the current study, using a molecular beacon approach, we demonstrate that the mNdK catalyzes the cleavage of single strand DNA. It displays Michaelis-Menten kinetics with a kcat/K(M) of 9.65 (+/-0.88) x 10(6) M(-1) s(-1). High affinity (K(d) approximately K(M) of approximately 66 nM) and sequence-specific binding to the sense strand of the nuclease hypersensitive region in the c-myc promoter was observed. This is the first study demonstrating that the cleavage reaction is also enzyme-catalyzed in addition to the enzymatic kinase activity of multifunctional NdK. Using our approach, we demonstrate that GDP competitively inhibits the nuclease activity with a K(I) of approximately 1.9 mM. Recent evidence implicates mNdK as a potent virulence factor in tuberculosis owing to its DNase-like activity. In this context, our results demonstrate a molecular mechanism that could be the basis for assessing in situ DNA damage by secretory mNdK.

  19. Efficient antibody-catalyzed oxygenation reaction

    SciTech Connect

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

    1994-03-09

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

  20. A lipoxygenase from red alga Pyropia haitanensis, a unique enzyme catalyzing the free radical reactions of polyunsaturated fatty acids with triple ethylenic bonds.

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  2. 4-alkyl-o-quinone/2-hydroxy-p-quinone methide isomerase from the larval hemolymph of Sarcophaga bullata. I. Purification and characterization of enzyme-catalyzed reaction.

    PubMed

    Saul, S J; Sugumaran, M

    1990-10-01

    An enzyme which catalyzes the conversion of certain 4-alkyl-o-benzoquinones to 2-hydroxy-p-quinone methides has been purified to apparent homogeneity from the hemolymph of Sarcophaga bullata by employing conventional protein purification techniques. The purified enzyme migrated with an approximate molecular weight of 98,000 on gel filtration chromatography. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, it migrated as a single band with a molecular weight of 46,000, indicating that it is made up of two identical subunits. It exhibited a pH optimum of 6.0 and readily converted chemically synthesized as well as enzymatically generated quinones derived from N-acetyldopamine, N-beta-alanyldopamine, and 3,4-dihydroxyphenethyl alcohol to highly unstable 2-hydroxy-p-quinone methides. The quinone methides thus formed were rapidly and nonenzymatically hydrated to form side chain hydroxylated o-diphenols as the stable product. In support of this proposition, when the enzyme reaction with N-acetyldopamine quinone was conducted in the presence of 10% methanol, racemic beta-methoxy-N-acetyldopamine was recovered as an additional product. The quinones of N-acetylnorepinephrine, N-beta-alanylnorepinephrine, and 3,4-dihydroxyphenylglycol were also attacked by the isomerase, resulting in the formation of N-acetylarterenone, N-beta-alanylarterenone and 2-hydroxy-3',4'-dihydroxyacetophenone, respectively as the stable products. The isomerase converted the dihydrocaffeiyl methyl amide quinone to its quinone methide analog which rapidly tautomerized to yield caffeiyl methyl amide. The importance of quinone isomerase in insect immunity and sclerotization of insect cuticle is discussed.

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

    PubMed

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

    2016-03-29

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

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

    PubMed

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

    2016-03-29

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

  5. Hydroxylation and dealkylation reactions catalyzed by hemoglobin.

    PubMed

    Mieyal, J J; Starke, D W

    1994-01-01

    Red blood cells contain many enzymes that are akin to those that catalyze xenobiotic metabolism in liver and other tissues. An obvious exception is the cytochrome P-450 system that is found in virtually all other tissues. In vitro studies, however, have shown that hemoglobin can be a broad monooxygenase catalyst, exhibiting the properties of a monooxygenase enzyme. Thus, catalysis by Hb displays typical Michaelis-Menten kinetics, dependence on the native protein, coupling to NADPH-dependent flavoprotein reductases, and inhibition by carbon monoxide. The reconstituted system containing Hb along with P-450 reductase utilizes NADPH and O2 to catalyze typical monooxygenase reactions, including O- and N-demethylations as well as aromatic and aliphatic hydroxylations, and the catalytic cycle appears to mimic the typical P-450 mechanism. Turnover numbers for aniline hydroxylation are similar for Hb and P-450 reconstituted systems, whereas P-450 systems are more effective for other reactions. Catalysis by Hb seems to be restricted to the beta-heme sites of the tetramer, reflecting more facile substrate access. Overall the similarities and differences between Hb and P-450 provide an opportunity to examine the basis for their differential monooxygenase or peroxidase/peroxygenase activities in a comparative manner. Hb may be especially useful in delineating the early events in the respective reaction schemes, because it can be studied in various stable redox/ligand states, including the oxyferrous form. Similar hemoglobin-catalyzed oxidative biotransformations occur within intact erythrocytes, but apparent turnover numbers are much lower than those with the reconstituted Hb system, suggesting different mechanisms of catalysis. Although Hb-mediated oxidase activity in erythrocytes is low relative to other sites of xenobiotic metabolism, it may contribute to in situ activation of xenobiotics leading to oxidative stress, disruption of sulfhydryl homeostasis in the erythrocytes

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

    PubMed

    Nairn, Robert; Cresswell, Will; Nairn, Jacqueline

    2015-01-01

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

  7. 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 α-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 Cα 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

  8. 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.

  9. Gold(I)-catalyzed enantioselective cycloaddition reactions.

    PubMed

    López, Fernando; Mascareñas, José L

    2013-10-30

    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.

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

    PubMed

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

    2013-01-01

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

  11. 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 μM for CPH4 and kcat of 5.4 ± 1.2 min-1 for the overall transformation. The kinetically determined Kapp for SAM is 45 ± 1 μM. 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

  12. 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

  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. Transition-Metal-Catalyzed Bioorthogonal Cycloaddition Reactions.

    PubMed

    Yang, Maiyun; Yang, Yi; Chen, Peng R

    2016-02-01

    In recent years, bioorthogonal reactions have emerged as a powerful toolbox for specific labeling and visualization of biomolecules, even within the highly complex and fragile living systems. Among them, copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction is one of the most widely studied and used biocompatible reactions. The cytotoxicity of Cu(I) ions has been greatly reduced due to the use of Cu(I) ligands, which enabled the CuAAC reaction to proceed on the cell surface, as well as within an intracellular environment. Meanwhile, other transition metals such as ruthenium, rhodium and silver are now under development as alternative sources for catalyzing bioorthogonal cycloadditions. In this review, we summarize the development of CuAAC reaction as a prominent bioorthogonal reaction, discuss various ligands used in reducing Cu(I) toxicity while promoting the reaction rate, and illustrate some of its important biological applications. The development of additional transition metals in catalyzing cycloaddition reactions will also be briefly introduced. PMID:27572985

  15. Gold(I)-catalyzed enantioselective cycloaddition reactions

    PubMed Central

    2013-01-01

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

  16. Characterising Complex Enzyme Reaction Data

    PubMed Central

    Rahman, Syed Asad; Thornton, Janet M.

    2016-01-01

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

  17. Characterising Complex Enzyme Reaction Data.

    PubMed

    Dönertaş, Handan Melike; Martínez Cuesta, Sergio; Rahman, Syed Asad; Thornton, Janet M

    2016-01-01

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

  18. 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

  19. Desaturation reactions catalyzed by soluble methane monooxygenase.

    PubMed

    Jin, Y; Lipscomb, J D

    2001-09-01

    Soluble methane monooxygenase (MMO) is shown to be capable of catalyzing desaturation reactions in addition to the usual hydroxylation and epoxidation reactions. Dehydrogenated products are generated from MMO-catalyzed oxidation of certain substrates including ethylbenzene and cyclohexadienes. In the reaction of ethylbenzene, desaturation of ethyl C-H occurred along with the conventional hydroxvlations of ethyl and phenyl C-Hs. As a result, styrene is formed together with ethylphenols and phenylethanols. Similarly, when 1,3- and 1,4-cyclohexadienes were used as substrates, benzene was detected as a product in addition to the corresponding alcohols and epoxides. In all cases, reaction conditions were found to significantly affect the distribution among the different products. This new activity of MMO is postulated to be associated with the chemical properties of the substrates rather than fundamental changes in the nature of the oxygen and C-H activation chemistries. The formation of the desaturated products is rationalized by formation of a substrate cationic intermediate, possibly via a radical precursor. The cationic species is then proposed to partition between recombination (alcohol formation) and elimination (alkene production) pathways. This novel function of MMO indicates close mechanistic kinship between the hydroxylation and desaturation reactions catalyzed by the nonheme diiron clusters.

  20. A Link between Protein Structure and Enzyme Catalyzed Hydrogen Tunneling

    NASA Astrophysics Data System (ADS)

    Bahnson, Brian J.; Colby, Thomas D.; Chin, Jodie K.; Goldstein, Barry M.; Klinman, Judith P.

    1997-11-01

    We present evidence that the size of an active site side chain may modulate the degree of hydrogen tunneling in an enzyme-catalyzed reaction. Primary and secondary kH/kT and kD/kT kinetic isotope effects have been measured for the oxidation of benzyl alcohol catalyzed by horse liver alcohol dehydrogenase at 25 degrees C. As reported in earlier studies, the relationship between secondary kH/kT and kD/kT isotope effects provides a sensitive probe for deviations from classical behavior. In the present work, catalytic efficiency and the extent of hydrogen tunneling have been correlated for the alcohol dehydrogenase-catalyzed hydride transfer among a group of site-directed mutants at position 203. Val-203 interacts with the opposite face of the cofactor NAD+ from the alcohol substrate. The reduction in size of this residue is correlated with diminished tunneling and a two orders of magnitude decrease in catalytic efficiency. Comparison of the x-ray crystal structures of a ternary complex of a high-tunneling (Phe-93 --> Trp) and a low-tunneling (Val-203 --> Ala) mutant provides a structural basis for the observed effects, demonstrating an increase in the hydrogen transfer distance for the low-tunneling mutant. The Val-203 --> Ala ternary complex crystal structure also shows a hyperclosed interdomain geometry relative to the wild-type and the Phe-93 --> Trp mutant ternary complex structures. This demonstrates a flexibility in interdomain movement that could potentially narrow the distance between the donor and acceptor carbons in the native enzyme and may enhance the role of tunneling in the hydride transfer reaction.

  1. Lipase-catalyzed aza-Michael reaction on acrylate derivatives.

    PubMed

    Steunenberg, Peter; Sijm, Maarten; Zuilhof, Han; Sanders, Johan P M; Scott, Elinor L; Franssen, Maurice C R

    2013-04-19

    A methodology has been developed for an efficient and selective lipase-catalyzed aza-Michael reaction of various amines (primary and secondary) with a series of acrylates and alkylacrylates. Reaction parameters were tuned, and under the optimal conditions it was found that Pseudomonas stutzeri lipase and Chromobacterium viscosum lipase showed the highest selectivity for the aza-Michael addition to substituted alkyl acrylates. For the first time also, some CLEAs were examined that showed a comparable or higher selectivity and yield than the free enzymes and other formulations.

  2. Asymmetric petasis reactions catalyzed by chiral biphenols.

    PubMed

    Lou, Sha; Schaus, Scott E

    2008-06-01

    Chiral biphenols catalyze the enantioselective Petasis reaction of alkenyl boronates, secondary amines, and ethyl glyoxylate. The reaction requires the use of 15 mol % of (S)-VAPOL as the catalyst, alkenyl boronates as nucleophiles, ethyl glyoxylate as the aldehyde component, and 3 A molecular sieves as an additive. The chiral alpha-amino ester products are obtained in good yields (71-92%) and high enantiomeric ratios (89:11-98:2). Mechanistic investigations indicate single ligand exchange of acyclic boronate with VAPOL and tetracoordinate boronate intermediates. PMID:18459782

  3. Metal-Catalyzed Cross-Coupling Reactions for Indoles

    NASA Astrophysics Data System (ADS)

    Li, Jie Jack; Gribble, Gordon W.

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

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

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2011-06-01

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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  7. 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

  8. 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.

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

    DOE PAGES

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

    2015-08-05

    Although one of an enzyme’s hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. We know that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. 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). Finally, our results demonstrate that this enzyme may use substrate-assisted catalysis involvingmore » the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.« less

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

    SciTech Connect

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

    2015-08-05

    Although one of an enzyme’s hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. We know that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. 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). Finally, 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.

  11. An analytical method for determining relative specificities for sequential reactions catalyzed by the same enzyme: application to the hydrolysis of triacylglycerols by lipases.

    PubMed

    Mitchell, David Alexander; Rodriguez, Jorge A; Carrière, Frédéric; Baratti, Jacques; Krieger, Nadia

    2008-02-01

    We propose a model for the sequential hydrolysis of ester bonds of triacylglycerols by lipases and use it as the basis for an analytical method for determining the relative specificity of the lipase for the various substrates with which it can react, when the substrates occur simultaneously in a single reaction system. We then apply the method to our own data and literature data involving the hydrolysis of triacylglycerols by lipases. Our model is able to fit well to most of the reaction profiles, enabling the estimation of relative specificities. We discuss the limitations and potential applications of our method.

  12. Modelling enzyme reaction mechanisms, specificity and catalysis.

    PubMed

    Mulholland, Adrian J

    2005-10-15

    Modern modelling methods can now give uniquely detailed understanding of enzyme-catalyzed reactions, including the analysis of mechanisms and the identification of determinants of specificity and catalytic efficiency. A new field of computational enzymology has emerged that has the potential to contribute significantly to structure-based design and to develop predictive models of drug metabolism and, for example, of the effects of genetic polymorphisms. This review outlines important techniques in this area, including quantum-chemical model studies and combined quantum-mechanics and molecular-mechanics (QM/MM) methods. Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled and the insight they can give.

  13. Volume changes during enzyme reactions: indications of enzyme pulsation during fumarase catalysis.

    PubMed

    Butz, P; Greulich, K O; Ludwig, H

    1988-03-01

    Overall activation volumes for multistep reactions are not usually pressure independent. The present investigation gives a quantitative description of this effect under Theory. Simple relations are obtained which can easily be applied to experimental data and which allow more insight into the dynamics of enzyme reactions. This is demonstrated under Experimental Application for the conversion of fumarate to L-malate catalyzed by the enzyme fumarase. The volume profile of this reaction indicates a pulsation of the enzyme molecule during catalysis. The appendix discusses the question whether Eyring's transition-state theory is an appropriate basis for investigations of this kind. PMID:3365410

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

    SciTech Connect

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

    1986-05-01

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

  15. Enzyme-catalyzed synthesis of heptyl-β-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-β-glycosides in heptanol catalyzed by a hyperthermophilic β-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-β-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-β-glycosides yield to 52%. Surface-active compounds, SDS and octyl glucoside, increased water dispersion but were unable to prevent coalescence.

  16. Enzyme-catalyzed biocathode in a photoelectrochemical biofuel cell

    NASA Astrophysics Data System (ADS)

    Yang, Jing; Hu, Donghua; Zhang, Xiaohuan; Wang, Kunqi; Wang, Bin; Sun, Bo; Qiu, Zhidong

    2014-12-01

    A novel double-enzyme photoelectrochemical biofuel cell (PEBFC) has been developed by taking glucose dehydrogenase (GDH) and horseradish peroxidase (HRP) as the enzyme of the photoanode and biocathode to catalyze the oxidation of glucose and the reduction of oxygen. A H2-mesoporphyrin IX is used as a dye for a TiO2 film electrode to fabricate a photoanode. The horseradish peroxidase (HRP) is immobilized on a glassy carbon (GC) electrode to construct a biocathode which is used to catalyze the reduction of oxygen in the PEBFC for the first time. The biocathode exhibits excellent electrocatalytic activity in the presence of O2. The performances of the PEBFC are obtained by current-voltage and power-voltage curves. The short-circuit current density (Isc), the open-circuit voltage (Voc), maximum power density (Pmax), fill factor (FF) and energy conversion efficiency (η) are 439 μA cm-2, 678 mV, 79 μW cm-2, 0.39 and 0.016%, respectively, and the incident photon-to-collected electron conversion efficiency (IPCE) is 32% at 350 nm. The Isc is higher than that of the PEBFC with Pt cathode, and the Voc is higher than that of the dye-sensitized solar cell or the enzyme-catalyzed biofuel cell operating individually, which demonstrates that the HRP is an efficient catalyst for the biocathode in the PEBFC.

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

    PubMed Central

    Masterson, Jean E.; Schwartz, Steven D.

    2014-01-01

    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. PMID:25368440

  18. Enzyme-catalyzed removal of phenol from refinery wastewater: feasibility studies.

    PubMed

    Ibrahim, M S; Ali, H I; Taylor, K E; Biswas, N; Bewtra, J K

    2001-01-01

    Phenols are present in petroleum refining wastewater. An enzymatic method for removing phenols from industrial aqueous effluent has been developed in the past several years. In this method, a peroxidase enzyme catalyzes the oxidation of phenol by hydrogen peroxide generation of phenoxyl radicals. These radicals diffuse from the active center of the enzyme into solution and react nonenzymatically to eventually form higher oligomers and polymers, which can be removed from wastewater by conventional coagulation and sedimentation or filtration. In this study, Arthromyces ramosus peroxidase (ARP) was applied to treat a petroleum refining wastewater containing 2 mM (188 mg/L) phenol in a batch and continuous-flow system. The latter consisted of a plug-flow reactor (PFR) where the reaction took place between phenol and hydrogen peroxide catalyzed by the enzyme in the presence of polyethylene glycol (PEG). A flocculation tank followed the PFR where alum and sodium hydroxide were added and then the polymers formed were settled in a sedimentation tank and removed from the system. Most (95 to 99%) of the phenol was removed by the same dose of ARP required for the treatment of synthetic wastewater containing an equal amount of phenol. Polyethylene glycol, as an additive, reduced enzyme inactivation and consequently reduced the enzyme dose and the cost of the treatment process. Step feeding of hydrogen peroxide was not effective in reducing the enzyme requirement. A significant removal of chemical oxygen demand was achieved when using PEG to reduce the enzyme dose.

  19. 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.

  20. Insights into the "free state" enzyme reaction kinetics in nanoconfinement.

    PubMed

    Wang, Chen; Ye, De-Kai; Wang, Yun-Yi; Lu, Tao; Xia, Xing-Hua

    2013-04-21

    The investigation of enzyme reaction kinetics in nanoconfined spaces mimicking the conditions in living systems is of great significance. Here, a nanofluidics chip integrated with an electrochemical detector has been designed for studying "free state" enzyme reaction kinetics in nanoconfinement. The nanofluidics chip is fabricated using the UV-ablation technique developed in our group. The enzyme and substrate solutions are simultaneously supplied from two single streams into a nanochannel through a Y-shaped junction. The laminar flow forms in the front of the nanochannel, then the two liquids fully mix at their downstream where a homogeneous enzyme reaction occurs. The "free state" enzyme reaction kinetics in nanoconfinement can thus be investigated in this laminar flow based nanofluidics device. For demonstration, glucose oxidase (GOx) is chosen as the model enzyme, which catalyzes the oxidation of beta-d-glucose. The reaction product hydrogen peroxide (H2O2) can be electrochemically detected by a microelectrode aligning to the end of nanochannel. The steady-state electrochemical current responding to various glucose concentrations is used to evaluate the activity of the "free state" GOx under nanoconfinement conditions. The effect of liquid flow rate, enzyme concentration, and nanoconfinement on reaction kinetics has been studied in detail. Results show that the "free state" GOx activity increases significantly compared to the immobilized enzyme and bath system, and the GOx reaction rate in the nanochannel is two-fold faster than that in bulk solution, demonstrating the importance of "free state" and spatial confinement for the enzyme reaction kinetics. The present approach provides an effective method for exploiting the "free state" enzyme activity in nanospatial confinement.

  1. Recent advances in copper-catalyzed asymmetric coupling reactions

    PubMed Central

    2015-01-01

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

  2. Recent advances in copper-catalyzed asymmetric coupling reactions.

    PubMed

    Zhou, Fengtao; Cai, Qian

    2015-01-01

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

  3. Endo-Selective Pd-Catalyzed Silyl Methyl Heck Reaction

    PubMed Central

    2015-01-01

    A palladium (Pd)-catalyzed endo-selective Heck reaction of iodomethylsilyl ethers of phenols and aliphatic alkenols has been developed. Mechanistic studies reveal that this silyl methyl Heck reaction operates via a hybrid Pd-radical process and that the silicon atom is crucial for the observed endo selectivity. The obtained allylic silyloxycycles were further oxidized into (Z)-alkenyldiols. PMID:25494921

  4. 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%.

  5. 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.

  6. Toward cell circuitry: Topological analysis of enzyme reaction networks via reaction route graphs

    NASA Astrophysics Data System (ADS)

    Datta, Ravindra; Vilekar, Saurabh A.; Fishtik, Ilie; Dittami, James P.

    2008-05-01

    The first step toward developing complete cell circuitry is to build quantitative networks for enzyme reactions. The conventional King-Altman-Hill (KAH) algorithm for topological analysis of enzyme networks, adapted from electrical networks, is based on “Reaction Graphs” that, unlike electrical circuits, are not quantitative, being straightforward renderings of conventional schematics of reaction mechanisms. Therefore, we propose the use of “Reaction Route (RR) Graphs” instead, as a more suitable graph-theoretical representation for topological analysis of enzyme reaction networks. The RR Graphs are drawn such that they are not only useful for visualizing the various reaction routes or pathways, but unlike Reaction Graphs possess network properties consistent with requisite kinetic, mass balance, and thermodynamic constraints. Therefore, they are better than the conventional Reaction Graphs for topological representation and analysis of enzyme reactions, both via the KAH methodology as well as via numerical matrix inversion. The difference between the two is highlighted based on the example of a single enzyme reaction network for the conversion of 7,8-dihydrofolate and NADPH into 5,6,7,8-tetrahydrofolate and NADP +, catalyzed by the enzyme dihydrofolate reductase.

  7. Complex Biotransformations Catalyzed by Radical S-Adenosylmethionine Enzymes*

    PubMed Central

    Zhang, Qi; Liu, Wen

    2011-01-01

    The radical S-adenosylmethionine (AdoMet) superfamily currently comprises thousands of proteins that participate in numerous biochemical processes across all kingdoms of life. These proteins share a common mechanism to generate a powerful 5′-deoxyadenosyl radical, which initiates a highly diverse array of biotransformations. Recent studies are beginning to reveal the role of radical AdoMet proteins in the catalysis of highly complex and chemically unusual transformations, e.g. the ThiC-catalyzed complex rearrangement reaction. The unique features and intriguing chemistries of these proteins thus demonstrate the remarkable versatility and sophistication of radical enzymology. PMID:21771780

  8. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  11. Metal-catalyzed annulation reactions for π-conjugated polycycles.

    PubMed

    Jin, Tienan; Zhao, Jian; Asao, Naoki; Yamamoto, Yoshinori

    2014-03-24

    The progress of the metal-catalyzed annulation reactions toward construction of various π-conjugated polycyclic cores with high conjugation extension is described. This article gives a brief overview of various annulation reactions promoted by metal catalysts including C-H bond functionalization, [2+2+2] cycloaddition, cascade processes, ring closing metathesis, electrophilic aromatization, and various cross-coupling reactions. A variety of conjugated polycycles with planar, bowl-shaped, and helical structures have been constructed in high efficiency and selectivity.

  12. Copper bronze catalyzed Heck reaction in ionic liquids.

    PubMed

    Calò, Vincenzo; Nacci, Angelo; Monopoli, Antonio; Ieva, Eliana; Cioffi, Nicola

    2005-02-17

    Heck reaction of aryl iodides and activated aryl bromides catalyzed by copper bronze in tetrabutylammonium bromide as solvent and tetrabutylammonium acetate as base was developed. The effective catalysts are Cu nanoparticles deriving from the reaction of iodobenzene with copper bronze. These nanoparticles are very stable in tetraalkylammonium salts, are easily recycled, and can be stored for months without a loss of catalytic efficiency. [reaction: see text

  13. Nickel-Catalyzed Coupling Reactions of Alkenes

    PubMed Central

    Ng, Sze-Sze; Ho, Chun-Yu; Schleicher, Kristin D.; Jamison, Timothy F.

    2011-01-01

    Several reactions of simple, unactivated alkenes with electrophiles under nickel(0) catalysis are discussed. The coupling of olefins with aldehydes and silyl triflates provides allylic or homoallylic alcohol derivatives, depending on the supporting ligands and, to a lesser extent, the substrates employed. Reaction of alkenes with isocyanates yields N-alkyl acrylamides. In these methods, alkenes act as the functional equivalents of alkenyl- and allylmetal reagents. PMID:21814295

  14. Cascade reactions catalyzed by metal organic frameworks.

    PubMed

    Dhakshinamoorthy, Amarajothi; Garcia, Hermenegildo

    2014-09-01

    Cascade or tandem reactions where two or more individual reactions are carried out in one pot constitute a clear example of process intensification, targeting the maximization of spatial and temporal productivity with mobilization of minimum resources. In the case of catalytic reactions, cascade processes require bi-/multifunctional catalysts that contain different classes of active sites. Herein, we show that the features and properties of metal-organic frameworks (MOFs) make these solids very appropriate materials for the development of catalysts for cascade reactions. Due to composition and structure, MOFs can incorporate different types of sites at the metal nodes, organic linkers, or at the empty internal pores, allowing the flexible design and synthesis of multifunctional catalysts. After some introductory sections on the relevance of cascade reactions from the point of view of competitiveness, sustainability, and environmental friendliness, the main part of the text provides a comprehensive review of the literature reporting the use of MOFs as heterogeneous catalysts for cascade reactions including those that combine in different ways acid/base, oxidation/reduction, and metal-organic centers. The final section summarizes the current state of the art, indicating that the development of a first commercial synthesis of a high-added-value fine chemical will be a crucial milestone in this area.

  15. 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 CaCO₃. More hardness was removed at a lower initial concentration. For instance, at 200mg/L as CaCO₃ 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

  16. Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions.

    PubMed

    Tanriver, Gamze; Dedeoglu, Burcu; Catak, Saron; Aviyente, Viktorya

    2016-06-21

    Remarkable progress in the area of asymmetric organocatalysis has been achieved in the last decades. Cinchona alkaloids and their derivatives have emerged as powerful organocatalysts owing to their reactivities leading to high enantioselectivities. The widespread usage of cinchona alkaloids has been attributed to their nontoxicity, ease of use, stability, cost effectiveness, recyclability, and practical utilization in industry. The presence of tunable functional groups enables cinchona alkaloids to catalyze a broad range of reactions. Excellent experimental studies have extensively contributed to this field, and highly selective reactions were catalyzed by cinchona alkaloids and their derivatives. Computational modeling has helped elucidate the mechanistic aspects of cinchona alkaloid catalyzed reactions as well as the origins of the selectivity they induce. These studies have complemented experimental work for the design of more efficient catalysts. This Account presents recent computational studies on cinchona alkaloid catalyzed organic reactions and the theoretical rationalizations behind their effectiveness and ability to induce selectivity. Valuable efforts to investigate the mechanisms of reactions catalyzed by cinchona alkaloids and the key aspects of the catalytic activity of cinchona alkaloids in reactions ranging from pharmaceutical to industrial applications are summarized. Quantum mechanics, particularly density functional theory (DFT), and molecular mechanics, including ONIOM, were used to rationalize experimental findings by providing mechanistic insights into reaction mechanisms. B3LYP with modest basis sets has been used in most of the studies; nonetheless, the energetics have been corrected with higher basis sets as well as functionals parametrized to include dispersion M05-2X, M06-2X, and M06-L and functionals with dispersion corrections. Since cinchona alkaloids catalyze reactions by forming complexes with substrates via hydrogen bonds and long

  17. Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions.

    PubMed

    Tanriver, Gamze; Dedeoglu, Burcu; Catak, Saron; Aviyente, Viktorya

    2016-06-21

    Remarkable progress in the area of asymmetric organocatalysis has been achieved in the last decades. Cinchona alkaloids and their derivatives have emerged as powerful organocatalysts owing to their reactivities leading to high enantioselectivities. The widespread usage of cinchona alkaloids has been attributed to their nontoxicity, ease of use, stability, cost effectiveness, recyclability, and practical utilization in industry. The presence of tunable functional groups enables cinchona alkaloids to catalyze a broad range of reactions. Excellent experimental studies have extensively contributed to this field, and highly selective reactions were catalyzed by cinchona alkaloids and their derivatives. Computational modeling has helped elucidate the mechanistic aspects of cinchona alkaloid catalyzed reactions as well as the origins of the selectivity they induce. These studies have complemented experimental work for the design of more efficient catalysts. This Account presents recent computational studies on cinchona alkaloid catalyzed organic reactions and the theoretical rationalizations behind their effectiveness and ability to induce selectivity. Valuable efforts to investigate the mechanisms of reactions catalyzed by cinchona alkaloids and the key aspects of the catalytic activity of cinchona alkaloids in reactions ranging from pharmaceutical to industrial applications are summarized. Quantum mechanics, particularly density functional theory (DFT), and molecular mechanics, including ONIOM, were used to rationalize experimental findings by providing mechanistic insights into reaction mechanisms. B3LYP with modest basis sets has been used in most of the studies; nonetheless, the energetics have been corrected with higher basis sets as well as functionals parametrized to include dispersion M05-2X, M06-2X, and M06-L and functionals with dispersion corrections. Since cinchona alkaloids catalyze reactions by forming complexes with substrates via hydrogen bonds and long

  18. [Enzyme-catalyzed synthesis of ASGPR ligand-targeted modifier in non-aqueous medium].

    PubMed

    Cheng, Yi; Wu, Wei; Zhang, Dong-qing; Mai, Yan-zhen

    2010-09-01

    The asialoglycoprotein receptor (ASGPR) was used to mediate drug carrier for hepatic targeted drug delivery, this article showed the enzyme-catalyzed esterification of galactose and vinyl stearate and a kind of ASGPR ligand-targeted which was used to insert the surface of liposome has been synthesized. The structure of product has been confirmed by TLC, ESI-MS and 1H NMR. The factors of types and quantity of enzyme, organic solvents, molar ratio of substrate, temperature and time of reaction have been studied. Results showed when using acetone as reaction medium, the quantity of Novozym 435 immobilized lipase was 30 mg mL(-1), molar ratio of galactose to vinyl stearate was 1:5, and reacted at 60 degrees C for 12 h, the transformation of vinyl stearate reached more than 70%. This study provides a novel and efficient route to the synthesis of ligand-targeted modifier.

  19. Rubber muscle actuation with pressurized CO2 from enzyme-catalyzed urea hydrolysis

    NASA Astrophysics Data System (ADS)

    Sutter, Thomas M.; Dickerson, Matthew B.; Creasy, Terry S.; Justice, Ryan S.

    2013-09-01

    A biologically inspired pneumatic pressure source was designed and sized to supply high pressure CO2(g) to power a rubber muscle actuator. The enzyme urease served to catalyze the hydrolysis of urea, producing CO2(g) that flowed into the actuator. The actuator’s power envelope was quantified by testing actuator response on a custom-built linear-motion rig. Reaction kinetics and available work density were determined by replacing the actuator with a double-action piston and measuring volumetric gas generation against a fixed pressure on the opposing piston. Under the conditions investigated, urease catalyzed the generation of up to 0.81 MPa (117 psi) of CO2(g) in the reactor headspace within 18 min, and the evolved gas produced a maximum work density of 0.65 J ml-1.

  20. 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,…

  1. Stereoselectivity in (Acyloxy)borane-Catalyzed Mukaiyama Aldol Reactions.

    PubMed

    Lee, Joshua M; Zhang, Xin; Norrby, Per-Ola; Helquist, Paul; Wiest, Olaf

    2016-07-01

    The origin of diastereo- and enantioselectivity in a Lewis acid-catalyzed Mukaiyama aldol reaction is investigated using a combination of dispersion corrected DFT calculations and transition state force fields (TSFF) developed using the quantum guided molecular mechanics (Q2MM) method. The reaction proceeds via a closed transition structure involving a nontraditional hydrogen bond that is 3.3 kJ/mol lower in energy than the corresponding open transition structure. The correct prediction of the diastereoselectivity of a Mukaiyama aldol reaction catalyzed by the conformationally flexible Yamamoto chiral (acyloxy) borane (CAB) requires extensive conformational sampling at the transition structure, which is achieved using a Q2MM-derived TSFF, followed by DFT calculations of the low energy conformational clusters. Finally, a conceptual model for the rationalization of the observed diastereo- and enantioselectivity of the reaction using a closed transition state model is proposed. PMID:27247023

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

    PubMed Central

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

    1993-01-01

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

  3. Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase.

    PubMed

    Quaye, Osbourne; Cowins, Sharonda; Gadda, Giovanni

    2009-06-19

    The FAD-dependent choline oxidase has a flavin cofactor covalently attached to the protein via histidine 99 through an 8alpha-N(3)-histidyl linkage. The enzyme catalyzes the four-electron oxidation of choline to glycine betaine, forming betaine aldehyde as an enzyme-bound intermediate. The variant form of choline oxidase in which the histidine residue has been replaced with asparagine was used to investigate the contribution of the 8alpha-N(3)-histidyl linkage of FAD to the protein toward the reaction catalyzed by the enzyme. Decreases of 10-fold and 30-fold in the k(cat)/K(m) and k(cat) values were observed as compared with wild-type choline oxidase at pH 10 and 25 degrees C, with no significant effect on k(cat)/K(O) using choline as substrate. Both the k(cat)/K(m) and k(cat) values increased with increasing pH to limiting values at high pH consistent with the participation of an unprotonated group in the reductive half-reaction and the overall turnover of the enzyme. The pH independence of both (D)(k(cat)/K(m)) and (D)k(cat), with average values of 9.2 +/- 3.3 and 7.4 +/- 0.5, respectively, is consistent with absence of external forward and reverse commitments to catalysis, and the chemical step of CH bond cleavage being rate-limiting for both the reductive half-reaction and the overall enzyme turnover. The temperature dependence of the (D)k(red) values suggests disruption of the preorganization in the asparagine variant enzyme. Altogether, the data presented in this study are consistent with the FAD-histidyl covalent linkage being important for the optimal positioning of the hydride ion donor and acceptor in the tunneling reaction catalyzed by choline oxidase.

  4. Gold-catalyzed homogeneous oxidative cross-coupling reactions.

    PubMed

    Zhang, Guozhu; Peng, Yu; Cui, Li; Zhang, Liming

    2009-01-01

    Oxidizing gold? A gold(I)/gold(III) catalytic cycle is essential for the first oxidative cross-coupling reaction in gold catalysis. By using Selectfluor for gold(I) oxidation, this chemistry reveals the synthetic potential of incorporating gold(I)/gold(III) catalytic cycles into contemporary gold chemistry and promises a new area of gold research by merging powerful gold catalysis and oxidative metal-catalyzed cross-coupling reactions.

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

    PubMed

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

    2016-01-13

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

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

    PubMed

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

    2016-01-13

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

  7. Silver and gold-catalyzed multicomponent reactions

    PubMed Central

    Abbiati, Giorgio

    2014-01-01

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

  8. 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.

  9. Enzyme catalysis in organic solvents: influence of water content, solvent composition and temperature on Candida rugosa lipase catalyzed transesterification.

    PubMed

    Herbst, Daniela; Peper, Stephanie; Niemeyer, Bernd

    2012-12-31

    In the present study the influence of water content, solvent composition and reaction temperature on the transesterification of 1-phenylpropan-2-ol catalyzed by Candida rugosa lipase was examined. Reactions were carried out in different mixtures of hexane and tetrahydrofurane. The studies showed that an increasing water content of the organic solvent results in an increasing enzyme activity and a decreasing enantiomeric excess. Furthermore, a significant influence of the solvent hydrophilicity both on the enzyme activity and on the enantiomeric excess was found. An increase in solvent hydrophilicity leads to a decrease of enzyme activity and an increase of the enantiomeric excess. This indicates that the enzyme becomes more selective with decreasing flexibility. Similar effects were found by variation of the reaction temperature. Taken together, the decrease in conversion and the increase in selectivity with increasing solvent hydrophilicity are induced by the different water contents on the enzyme surface and not by the solvent itself.

  10. 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.

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

    PubMed Central

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

    2007-01-01

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

  12. Enzyme-catalyzed synthesis of saccharide acrylate monomers from nonedible biomass.

    PubMed

    Kloosterman, Wouter M J; Brouwer, Sander G M; Loos, Katja

    2014-08-01

    Various cellulase preparations were found to catalyze the transglycosidation between cotton linters and 2-hydroxyethyl acrylate. The conversion and enzyme activity were found to be optimal in reaction mixtures that contained 5 vol % of the acrylate. The structures of the products were revealed by using TLC and (1) H and (13) C NMR spectroscopy. The enzyme-catalyzed reaction resulted in two products. The minor product originated from transglycosidation to hemicellulose and was found to be 2-(β-xylosyloxy)-ethyl acrylate. The major product was identified as 2-(β-glucosyloxy)-ethyl acrylate and the yield of the product was 5 wt % based on the amount of consumed cellulose. Glycosidation products with oligosaccharide moieties could not be detected in the reaction mixture. This result can be explained by the hydrolytic activities of the used cellulase preparation. Cellulase from Trichoderma reesei was found to possess, in addition to endoglucanase activity, cellobiosidase and β-glucosidase activities. Five other cellulase preparations from different origins were tested as well for catalysis of oligosaccharide acrylate synthesis. For most cellulase preparations the major transglycosidation product appeared to be 2-(β-glucosyloxy)-ethyl acrylate. Nevertheless, the endo-β-(1,4)-glucanase from Trichoderma longibrachiatum was found to catalyze the synthesis of 2-(β-cellobiosyloxy)-ethyl acrylate. Unlike the other cellulase preparations, endo-β-(1,4)-glucanase from T. longibrachiatum showed no detectable β-glucosidase activity and therefore oligosaccharide acrylate monomers were not further hydrolyzed into the monosaccharide acrylate 2-(β-glucosyloxy)-ethyl acrylate. PMID:24866837

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

    PubMed

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

    2014-04-01

    The mechanistic imperatives for catalysis of deprotonation of α-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.

  14. Differential Quantum Tunneling Contributions in Nitroalkane Oxidase Catalyzed and the Uncatalyzed Proton Transfer Reaction

    SciTech Connect

    Major , D.; Heroux , A; Orville , A; Valley , M; Fitzpatrick , P; Gao , J

    2009-01-01

    The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.

  15. Lipase-catalyzed process in an anhydrous medium with enzyme reutilization to produce biodiesel with low acid value.

    PubMed

    Azócar, Laura; Ciudad, Gustavo; Heipieper, Hermann J; Muñoz, Robinson; Navia, Rodrigo

    2011-12-01

    One major problem in the lipase-catalyzed production of biodiesel or fatty acid methyl esters (FAME) is the high acidity of the product, mainly caused by water presence, which produces parallel hydrolysis and esterification reactions instead of transesterification to FAME. Therefore, the use of reaction medium in absence of water (anhydrous medium) was investigated in a lipase-catalyzed process to improve FAME yield and final product quality. FAME production catalyzed by Novozym 435 was carried out using waste frying oil (WFO) as raw material, methanol as acyl acceptor, and 3Å molecular sieves to extract the water. The anhydrous conditions allowed the esterification of free fatty acids (FFA) from feedstock at the initial reaction time. However, after the initial esterification process, water absence avoided the consecutives reactions of hydrolysis and esterification, producing FAME mainly by transesterification. Using this anhydrous medium, a decreasing in both the acid value and the diglycerides content in the product were observed, simultaneously improving FAME yield. Enzyme reuse in the anhydrous medium was also studied. The use of the moderate polar solvent tert-butanol as a co-solvent led to a stable catalysis using Novozym 435 even after 17 successive cycles of FAME production under anhydrous conditions. These results indicate that a lipase-catalyzed process in an anhydrous medium coupled with enzyme reuse would be suitable for biodiesel production, promoting the use of oils of different origin as raw materials.

  16. Transition-metal-catalyzed C-S bond coupling reaction.

    PubMed

    Lee, Chin-Fa; Liu, Yi-Chen; Badsara, Satpal Singh

    2014-03-01

    Sulfur-containing molecules such as thioethers are commonly found in chemical biology, organic synthesis, and materials chemistry. While many reliable methods have been developed for preparing these compounds, harsh reaction conditions are usually required in the traditional methods. The transition metals have been applied in this field, and the palladium-catalyzed coupling of thiols with aryl halides and pseudo halides is one of the most important methods in the synthesis of thioethers. Other metals have also been used for the same purpose. Here, we summarize recent efforts in metal-catalyzed C-S bond cross-coupling reactions, focusing especially on the coupling of thiols with aryl- and vinyl halides based on different metals.

  17. 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.

  18. Bi(OTf)3-Catalyzed Multicomponent α-Amidoalkylation Reactions.

    PubMed

    Schneider, Angelika E; Manolikakes, Georg

    2015-06-19

    A bismuth(III) triflate catalyzed three-component synthesis of α-substituted amides starting from amides, aldehydes, and (hetero)arenes is reported. The reaction has a broad substrate scope, encompassing formaldehyde as well as aryl and alkyl aldehydes. Low catalyst loadings are required, and water is formed as the only side product. The scope and limitation of this method will be discussed. PMID:25996906

  19. 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)

  20. Enzyme-Catalyzed Regioselective Modification of Starch Nanoparticles

    SciTech Connect

    Chakraborty, Soma; Sahoo, Bishwabhusan; Teraoka, Iwao; Miller, Lisa M.; Gross, Richard A.

    2004-12-13

    The selective esterification of starch nanoparticles was performed using as catalyst Candida antartica Lipase B (CAL-B) in its immobilized (Novozym 435) and free (SP-525) forms. The starch nanoparticles were made accessible for acylation reactions by formation of Aerosol-OT (AOT, bis(2-ethylhexyl)sodium sulfosuccinate) stabilized microemulsions. Starch nanoparticles in microemulsions were reacted with vinyl stearate, ε-caprolactone, and maleic anhydride at 40 °C for 48 h to give starch esters with degrees of substitution (DS) of 0.8, 0.6, and 0.4, respectively. Substitution occurred regioselectively at the C-6 position of the glucose repeat units. Infrared microspectroscopy (IRMS) revealed that AOT-coated starch nanoparticles diffuse into the outer 50 μm shell of catalyst beads. Thus, even though CAL-B is immobilized within a macroporous resin, CAL-B is sufficiently accessible to the starch nanoparticles. When free CAL-B was incorporated along with starch within AOT-coated reversed micelles, CAL-B was also active and catalyzed the acylation with vinyl stearate (24 h, 40 °C) to give DS = 0.5. After removal of surfactant from the modified starch nanoparticles, they were dispersed in DMSO or water and were shown to retain their nanodimensions.

  1. Pd-catalyzed cross-coupling reactions of alkyl halides.

    PubMed

    Kambe, Nobuaki; Iwasaki, Takanori; Terao, Jun

    2011-10-01

    Cross-coupling reactions have become indispensable tools for creating carbon-carbon (or heteroatom) bonds in organic synthesis. Like in other important transition metal catalyzed reactions, such as metathesis, addition, and polymerization, unsaturated compounds are usually employed as substrates for cross-coupling reactions. However during the past decade, a great deal of effort has been devoted to the use of alkyl halides as saturated compounds in cross-coupling reactions, which has resulted in significant progress in this undeveloped area by introducing new effective ligands. Many useful catalytic systems are now available for synthetic transformations based on C(sp(3))-C(sp(3)), C(sp(3))-C(sp(2)) and C(sp(3))-C(sp) bond formation as complementary methods to conventional C(sp(2))-C(sp(2)), C(sp(2))-C(sp) and C(sp)-C(sp) coupling. This tutorial review summarizes recent advances in cross-coupling reactions of alkyl halides and pseudohalides catalyzed by a palladium complex.

  2. 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.

  3. 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

  4. Hydrogen Tunneling in Enzyme Reactions

    NASA Astrophysics Data System (ADS)

    Cha, Yuan; Murray, Christopher J.; Klinman, Judith P.

    1989-03-01

    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.

  5. Hydrogen tunneling in enzyme reactions.

    PubMed

    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.

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

    SciTech Connect

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

    1987-06-30

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

  7. Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes.

    PubMed

    Renata, Hans; Lewis, Russell D; Sweredoski, Michael J; Moradian, Annie; Hess, Sonja; Wang, Z Jane; Arnold, Frances H

    2016-09-28

    Following the recent discovery that heme proteins can catalyze the cyclopropanation of styrenyl olefins with high efficiency and selectivity, interest in developing new enzymes for a variety of non-natural carbene transfer reactions has burgeoned. The fact that diazo compounds and other carbene precursors are known mechanism-based inhibitors of P450s, however, led us to investigate if they also interfere with this new enzyme function. We present evidence for two inactivation pathways that are operative during cytochrome P450-catalyzed cyclopropanation. Using a combination of UV-vis, mass spectrometry, and proteomic analyses, we show that the heme cofactor and several nucleophilic side chains undergo covalent modification by ethyl diazoacetate (EDA). Substitution of two of the affected residues with less-nucleophilic amino acids led to a more than twofold improvement in cyclopropanation performance (total TTN). Elucidating the inactivation pathways of heme protein-based carbene transfer catalysts should aid in the optimization of this new biocatalytic function. PMID:27573353

  8. Solvent effects in acid-catalyzed biomass conversion reactions.

    PubMed

    Mellmer, Max A; Sener, Canan; Gallo, Jean Marcel R; Luterbacher, Jeremy S; Alonso, David Martin; Dumesic, James A

    2014-10-27

    Reaction kinetics were studied to quantify the effects of polar aprotic organic solvents on the acid-catalyzed conversion of xylose into furfural. A solvent of particular importance is γ-valerolactone (GVL), which leads to significant increases in reaction rates compared to water in addition to increased product selectivity. GVL has similar effects on the kinetics for the dehydration of 1,2-propanediol to propanal and for the hydrolysis of cellobiose to glucose. Based on results obtained for homogeneous Brønsted acid catalysts that span a range of pKa values, we suggest that an aprotic organic solvent affects the reaction kinetics by changing the stabilization of the acidic proton relative to the protonated transition state. This same behavior is displayed by strong solid Brønsted acid catalysts, such as H-mordenite and H-beta. PMID:25214063

  9. 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-β-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 β-hydride elimination reaction, in gold catalysis from readily available α-allenols. We have also observed in γ-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

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

    PubMed Central

    Renata, Hans; Wang, Z. Jane

    2015-01-01

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

  11. 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)

  12. Synthesis of hindered biphenyls by sequential non-transition metal-catalyzed reaction/palladium-catalyzed cross-couplings.

    PubMed

    He, Ping; Dong, Cheng-Guo; Hu, Qiao-Sheng

    2008-03-17

    The sequential reaction of 1,2-dihalobenzenes with aryl lithiums followed by palladium-catalyzed cross-coupling reactions with Grignard reagents and arylboronic acids is described. This sequential reaction provides a convenient and expeditious access to tri-ortho substituted biaryl derivatives.

  13. Ultrasound assisted enzyme catalyzed hydrolysis of waste cooking oil under solvent free condition.

    PubMed

    Waghmare, Govind V; Rathod, Virendra K

    2016-09-01

    The present work demonstrates the hydrolysis of waste cooking oil (WCO) under solvent free condition using commercial available immobilized lipase (Novozyme 435) under the influence of ultrasound irradiation. The process parameters were optimized using a sequence of experimental protocol to evaluate the effects of temperature, molar ratios of substrates, enzyme loading, duty cycle and ultrasound intensity. It has been observed that ultrasound-assisted lipase-catalyzed hydrolysis of WCO would be a promising alternative for conventional methods. A maximum conversion of 75.19% was obtained at mild operating parameters: molar ratio of oil to water (buffer pH 7) 3:1, catalyst loading of 1.25% (w/w), lower ultrasound power 100W (ultrasound intensity - 7356.68Wm(-2)), duty cycle 50% and temperature (50°C) in a relatively short reaction time (2h). The activation energy and thermodynamic study shows that the hydrolysis reaction is more feasible when ultrasound is combined with mechanical agitation as compared with the ultrasound alone and simple conventional stirring technique. Application of ultrasound considerably reduced the reaction time as compared to conventional reaction. The successive use of the catalyst for repetitive cycles under the optimum experimental conditions resulted in a loss of enzymatic activity and also minimized the product conversion. PMID:27150746

  14. Ultrasound assisted enzyme catalyzed hydrolysis of waste cooking oil under solvent free condition.

    PubMed

    Waghmare, Govind V; Rathod, Virendra K

    2016-09-01

    The present work demonstrates the hydrolysis of waste cooking oil (WCO) under solvent free condition using commercial available immobilized lipase (Novozyme 435) under the influence of ultrasound irradiation. The process parameters were optimized using a sequence of experimental protocol to evaluate the effects of temperature, molar ratios of substrates, enzyme loading, duty cycle and ultrasound intensity. It has been observed that ultrasound-assisted lipase-catalyzed hydrolysis of WCO would be a promising alternative for conventional methods. A maximum conversion of 75.19% was obtained at mild operating parameters: molar ratio of oil to water (buffer pH 7) 3:1, catalyst loading of 1.25% (w/w), lower ultrasound power 100W (ultrasound intensity - 7356.68Wm(-2)), duty cycle 50% and temperature (50°C) in a relatively short reaction time (2h). The activation energy and thermodynamic study shows that the hydrolysis reaction is more feasible when ultrasound is combined with mechanical agitation as compared with the ultrasound alone and simple conventional stirring technique. Application of ultrasound considerably reduced the reaction time as compared to conventional reaction. The successive use of the catalyst for repetitive cycles under the optimum experimental conditions resulted in a loss of enzymatic activity and also minimized the product conversion.

  15. 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.

  16. Effect of enzyme impurities on phenol removal by the method of polymerization and precipitation catalyzed by Coprinus cinereus peroxidase.

    PubMed

    Masuda, M; Sakurai, A; Sakakibara, M

    2001-11-01

    The removal of phenol by peroxidase-catalyzed polymerization was examined using the Coprinus cinereus peroxidases at different levels of impurity with respect to contamination. The phenol removal efficiency was improved by lowering the peroxidase purity. Acidic and high molecular weight proteins present as impurities in the peroxidase solution had some positive effect on the phenol-polymerizing reaction. The residual enzyme activity, either only in the solution or both in the solution and on the precipitate during the polymerizing reaction, was measured. The results indicate that the main effect of impurities in the peroxidase solution was the suppression of the adsorption of peroxidase molecules on the polymerized precipitate.

  17. Enzyme-catalyzed production of biodiesel by ultrasound-assisted ethanolysis of soybean oil in solvent-free system.

    PubMed

    Trentin, Claudia M; Popiolki, Ariana S; Batistella, Luciane; Rosa, Clarissa Dalla; Treichel, Helen; de Oliveira, Débora; Oliveira, J Vladimir

    2015-03-01

    This work reports the transesterification of soybean oil with ethanol using a commercial immobilized lipase, Novozym 435, under the influence of ultrasound irradiation, in a solvent-free s. The experiments were performed in an ultrasonic water bath, following a sequence of experimental designs to evaluate the effects of temperature, enzyme and water concentrations, oil to ethanol molar ratio and output irradiation power on the reaction yield. Besides, a kinetic study varying the substrates molar ratio and enzyme concentration was also carried out. Results show that ultrasound-assisted lipase-catalyzed transesterification of soybean oil with ethanol in solvent-free system might be a potential alternative route to conventional alkali-catalyzed and/or traditional enzymatic methods, as high reaction yields (~78 wt%) were obtained at mild irradiation power supply (~132 W), and temperature (63 °C) in a relatively short reaction time, 1 h. Additionally, a study regarding the enzyme reuse was carried out at the experimental condition that afforded the best reaction yield. PMID:25362889

  18. 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

  19. Kinetic study of free fatty acid esterification reaction catalyzed by recoverable and reusable hydrochloric acid.

    PubMed

    Su, Chia-Hung

    2013-02-01

    The catalytic performance and recoverability of several homogeneous acid catalysts (hydrochloric, sulfuric, and nitric acids) for the esterification of enzyme-hydrolyzed free fatty acid (FFA) and methanol were studied. Although all tested catalysts drove the reaction to a high yield, hydrochloric acid was the only catalyst that could be considerably recovered and reused. The kinetics of the esterification reaction catalyzed by hydrochloric acid was investigated under varying catalyst loading (0.1-1M), reaction temperature (303-343K), and methanol/FFA molar ratio (1:1-20:1). In addition, a pseudo-homogeneous kinetic model incorporating the above factors was developed. A good agreement (r(2)=0.98) between the experimental and calculated data was obtained, thus proving the reliability of the model. Furthermore, the reusability of hydrochloric acid in FFA esterification can be predicted by the developed model. The recoverable hydrochloric acid achieved high yields of FFA esterification within five times of reuse.

  20. 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.

  1. Computational study of a model system of enzyme-mediated [4+2] cycloaddition reaction.

    PubMed

    Gordeev, Evgeniy G; Ananikov, Valentine P

    2015-01-01

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

  2. Iodine-catalyzed oxidative coupling reactions utilizing C - H and X - H as nucleophiles.

    PubMed

    Liu, Dong; Lei, Aiwen

    2015-04-01

    In recent decades, iodine-catalyzed oxidative coupling reactions utilizing C - H and X - H as nucleophiles have received considerable attention because they represent more efficient, greener, more atom-economical, and milder bond-formation strategies over transition-metal-catalyzed oxidative coupling reactions. This Focus Review gives a brief summary of recent development on iodine-catalyzed oxidative coupling reactions utilizing C - H and X - H as nucleophiles.

  3. 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

  4. A thermodynamic investigation of reactions catalyzed by tryptophan synthase.

    PubMed

    Kishore, N; Tewari, Y B; Akers, D L; Goldberg, R N; Miles, E W

    1998-07-27

    Microcalorimetry and high-performance liquid chromatography have been used to conduct a thermodynamic investigation of the following reactions catalyzed by the tryptophan synthase alpha 2 beta 2 complex (EC 4.2.1.20) and its subunits: indole(aq) + L-serine(aq) = L-tryptophan(aq) + H2O(1); L-serine(aq) = pyruvate(aq) + ammonia(aq); indole(aq) + D-glyceraldehyde 3-phosphate(aq) = 1-(indol-3-yl)glycerol 3-phosphate(aq); L-serine(aq) + 1-(indol-3-yl)glycerol 3-phosphate(aq) = L-tryptophan(aq) + D-glyceraldehyde 3-phosphate(aq) + H2O(1). The calorimetric measurements led to standard molar enthalpy changes for all four of these reactions. Direct measurements yielded an apparent equilibrium constant for the third reaction; equilibrium constants for the remaining three reactions were obtained by using thermochemical cycle calculations. The results of the calorimetric and equilibrium measurements were analyzed in terms of a chemical equilibrium model that accounted for the multiplicity of the ionic states of the reactants and products. Thermodynamic quantities for chemical reference reactions involving specific ionic forms have been obtained. These quantities permit the calculation of the position of equilibrium of the above four reactions as a function of temperature, pH, and ionic strength. Values of the apparent equilibrium constants and standard transformed Gibbs free energy changes delta r G'(m) degree under approximately physiological conditions are given. Le Châtelier's principle provides an explanation as to why, in the metabolic pathway leading to the synthesis of L-tryptophan, the third reaction proceeds in the direction of formation of indole and D-glyceraldehyde 3-phosphate even though the apparent equilibrium constant greatly favors the formation of 1-(indol-3-yl)glycerol 3-phosphate. PMID:9700925

  5. Evidence for Coupled Motion and Hydrogen Tunneling the Reaction Catalyzed by Glutamate Mutase:†

    PubMed Central

    Cheng, Mou-Chi; Marsh, E. Neil G.

    2008-01-01

    Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze unusual isomerizations that proceed through organic radical intermediates generated by homolytic fission of coenzyme's unique cobalt-carbon bond. These enzymes are part of a larger family of enzymes that catalyze radical chemistry in which a key step is the abstraction of a hydrogen atom from an otherwise inert substrate. To gain insight into the mechanism of hydrogen transfer we previously used pre-steady state, rapid quench techniques to measure the α-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5’-deoxyadenosine when glutamate mutase was reacted with [5’-3H]-adenosylcobalamin and L-glutamate. We showed that both the kinetic and equilibrium isotope effects are large and inverse, 0.76 and 0.72 respectively. We have now repeated these measurements using glutamate deuterated in the position of hydrogen abstraction. The effect of introducing a primary deuterium kinetic isotope effect on the hydrogen transfer step is to reduce the magnitude of the secondary kinetic isotope effect to a value close to unity, 1.05 ± 0.08, whereas the equilibrium isotope effect is unchanged. The significant reduction in the secondary kinetic isotope effect is consistent with motions of the 5’-hydrogen atoms being coupled in the transition state to the motion of the hydrogen undergoing transfer, in a reaction that involves a large degree of quantum tunneling. PMID:17223710

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

    PubMed

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

    2016-04-01

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

  7. 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…

  8. A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase.

    PubMed

    Richard, John P

    2012-04-01

    Triosephosphate isomerase (TIM) catalyzes the stereospecific 1,2-proton shift at dihydroxyacetone phosphate (DHAP) to give (R)-glyceraldehyde 3-phosphate through a pair of isomeric enzyme-bound cis-enediolate phosphate intermediates. The chemical transformations that occur at the active site of TIM were well understood by the early 1990s. The mechanism for enzyme-catalyzed isomerization is similar to that for the nonenzymatic reaction in water, but the origin of the catalytic rate acceleration is not understood. We review the results of experimental work that show that a substantial fraction of the large 12 kcal/mol intrinsic binding energy of the nonreacting phosphodianion fragment of TIM is utilized to activate the active site side chains for catalysis of proton transfer. Evidence is presented that this activation is due to a phosphodianion-driven conformational change, the most dramatic feature of which is closure of loop 6 over the dianion. The kinetic data are interpreted within the framework of a model in which activation is due to the stabilization by the phosphodianion of a rare, desolvated, loop-closed form of TIM. The dianion binding energy is proposed to drive the otherwise thermodynamically unfavorable desolvation of the solvent-exposed active site. This reduces the effective local dielectric constant of the active site, to enhance stabilizing electrostatic interactions between polar groups and the anionic transition state, and increases the basicity of the carboxylate side chain of Glu-165 that functions to deprotonate the bound carbon acid substrate. A rebuttal is presented to the recent proposal [Samanta, M., Murthy, M. R. N., Balaram, H., and Balaram, P. (2011) ChemBioChem 12, 1886-1895] that the cationic side chain of K12 functions as an active site electrophile to protonate the carbonyl oxygen of DHAP.

  9. Multi-enzyme catalyzed rapid ethanol lowering in vitro.

    PubMed

    Whitmire, D R; Chambers, R P; Dillon, A R

    1991-10-01

    Ethanol was oxidized to acetate by an enzyme system using yeast alcohol dehydrogenase (YADH), yeast aldehyde dehydrogenase (YALDH), and lactic dehydrogenase (LDH) recycling NAD in two model duodenal fluids and in canine duodenal aspirate in vitro. Sufficient enzyme activities were maintained to convert as much as 34% of the original ethanol to acetate with negligible acetaldehyde accumulation.

  10. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

    PubMed

    Almonacid, Daniel E; Yera, Emmanuel R; Mitchell, John B O; Babbitt, Patricia C

    2010-03-12

    Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine

  11. Deep eutectic solvents (DESs) are viable cosolvents for enzyme-catalyzed epoxide hydrolysis.

    PubMed

    Lindberg, Diana; de la Fuente Revenga, Mario; Widersten, Mikael

    2010-06-01

    A special group of ionic liquids, deep eutectic solvents (DESs) have been tested as cosolvents in enzyme-catalyzed hydrolysis of a chiral (1,2)-trans-2-methylstyrene oxide. The choline chloride:ethane diol (ET), choline chloride:glycerol (GLY) and choline:chloride:urea (REL) DESs were included in the reaction mixtures with epoxide and the potato epoxide hydrolase StEH1. The effect of the DESs on enzyme function was primarily elevations of K(M) (up to 20-fold) and with lesser effects on turnover numbers (twofold variation). The regioselectivity in hydrolysis of the (1R,2R)-2-trans-methylstyrene oxide was altered in the presence of GLY or ET to favor epoxide ring opening at the benzylic carbon (R=2.33), enhancing the regioselectivity observed in buffer-only systems (R=1.35). The DES solutions dissolved 1.5-fold higher epoxide concentrations as compared to phosphate buffer. The total conversion of high concentration (40 g/l) of (1S,2S)-MeSO was not negatively affected by addition of 40% GLY. PMID:20438773

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

    Kitahata, S; Chiba, S; Brewer, C F; Hehre, E J

    1991-07-01

    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 D2O by soybean beta-amylase was found to exhibit an unusually large solvent deuterium kinetic isotope effect (VH/VD = 6.5), a reaction rate linearly dependent on the mole fraction of deuterium, and 2-deoxy-[2(a)-2H]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. This is a different stereochemistry than reported for starch hydrolysis. With the hydration catalyzed in H2O and analyzed by gas-liquid chromatography, both sweet potato and soybean beta-amylase were found to convert maltal to the beta-anomer of 2-deoxymaltose. 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 starch, yet creates products of the same anomeric configuration from both. Such stereochemical dichotomy argues for the overriding role of protein structures in 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. PMID:1829637

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

    PubMed

    Kitahata, S; Chiba, S; Brewer, C F; Hehre, E J

    1991-07-01

    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 D2O by soybean beta-amylase was found to exhibit an unusually large solvent deuterium kinetic isotope effect (VH/VD = 6.5), a reaction rate linearly dependent on the mole fraction of deuterium, and 2-deoxy-[2(a)-2H]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. This is a different stereochemistry than reported for starch hydrolysis. With the hydration catalyzed in H2O and analyzed by gas-liquid chromatography, both sweet potato and soybean beta-amylase were found to convert maltal to the beta-anomer of 2-deoxymaltose. 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 starch, yet creates products of the same anomeric configuration from both. Such stereochemical dichotomy argues for the overriding role of protein structures in 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. RNA size is a critical factor for U-containing substrate selectivity and permanent pseudouridylated product release during the RNA:Ψ-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 (Ψ) 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 Ψ 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.

  17. 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.

  18. Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

    NASA Astrophysics Data System (ADS)

    Rod, Thomas H.; Rydberg, Patrik; Ryde, Ulf

    2006-05-01

    We compare free energy calculations for the methyl transfer reaction catalyzed by catechol O-methyltransferase using the quantum mechanical/molecular mechanical free energy method with implicit and explicit solvents. An analogous methylation reaction in a solution is also studied. For the explicit solvent model, we use the three-point transferable intermolecular potential model, and for the implicit model, we use the generalized Born molecular volume model as implemented in CHARMM. We find that activation and reaction free energies calculated with the two models are very similar, despite some structural differences that exist. A significant change in the polarization of the environment occurs as the reaction proceeds. This is more pronounced for the reaction in a solution than for the enzymatic reaction. For the enzymatic reaction, most of the changes take place in the protein rather than in the solvent, and, hence, the benefit of having an instantaneous relaxation of the solvent degrees of freedom is less pronounced for the enzymatic reaction than for the reaction in a solution. This is a likely reason why energies of the enzyme reaction are less sensitive to the choice of atomic radii than are energies of the reaction in a solution.

  19. Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase

    PubMed Central

    Saen-oon, Suwipa; Schramm, Vern L.; Schwartz, Steven D.

    2010-01-01

    The Transition Path Sampling (TPS) method is a powerful technique for studying rare events in complex systems, that allows description of reactive events in atomic detail without prior knowledge of reaction coordinates and transition states. We have applied TPS in combination with a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) method to study the enzyme human purine nucleoside phosphorylase (hPNP). This enzyme catalyzes the reversible phosphorolysis of 6-oxypurine (deoxy)nucleosides to generate the corresponding purine base and (deoxy)ribose 1-phosphate. Hundreds of reactive trajectories were generated. Analysis of this transition path ensembles provides insight into the detailed mechanistic dynamics of reaction in the enzyme. Our studies have indicated a reaction mechanism involving the cleavage of the N-ribosidic bond to form transition states with substantial ribooxacarbenium ion character, that is then followed by conformational changes in the enzyme and the ribosyl group leading to migration of the anomeric carbon of the ribosyl group toward phosphate to form the product ribose 1-phosphate. This latter process is crucial in PNP, because several strong H-bonds form between active site residues in order to capture and align the phosphate nucleophile. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. Analysis of these transition state structures showed that bond-breaking and bond-forming distances are not a good choice for the reaction coordinate, but that the pseudorotational phase of the ribose ring is also a significant variable. PMID:20664707

  20. Enzyme efficiency: An open reaction system perspective

    NASA Astrophysics Data System (ADS)

    Banerjee, Kinshuk; Bhattacharyya, Kamal

    2015-12-01

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

  1. Enzyme efficiency: An open reaction system perspective.

    PubMed

    Banerjee, Kinshuk; Bhattacharyya, Kamal

    2015-12-21

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

  2. Enzyme efficiency: An open reaction system perspective

    SciTech Connect

    Banerjee, Kinshuk; Bhattacharyya, Kamal

    2015-12-21

    A measure of enzyme efficiency is proposed for an open reaction network that, in suitable form, applies to closed systems as well. The idea originates from the description of classical enzyme kinetics in terms of cycles. We derive analytical expressions for the efficiency measure by treating the network not only deterministically but also stochastically. The latter accounts for any significant amount of noise that can be present in biological systems and hence reveals its impact on efficiency. Numerical verification of the results is also performed. It is found that the deterministic equation overestimates the efficiency, the more so for very small system sizes. Roles of various kinetics parameters and system sizes on the efficiency are thoroughly explored and compared with the standard definition k{sub 2}/K{sub M}. Study of substrate fluctuation also indicates an interesting efficiency-accuracy balance.

  3. A review on lipase-catalyzed reactions in ultrasound-assisted systems.

    PubMed

    Lerin, Lindomar A; Loss, Raquel A; Remonatto, Daniela; Zenevicz, Mara Cristina; Balen, Manuela; Netto, Vendelino Oenning; Ninow, Jorge L; Trentin, Cláudia M; Oliveira, J Vladimir; de Oliveira, Débora

    2014-12-01

    The named "green chemistry" has been receiving increasing prominence due to its environmentally friendly characteristics. The use of enzymes as catalysts in processes of synthesis to replace the traditional use of chemical catalysts present as main advantage the fact of following the principles of the green chemistry. However, processes of enzymatic nature generally provide lower yields when compared to the conventional chemical processes. Therefore, in the last years, the ultrasound has been extensively used in enzymatic processes, such as the production of esters with desirable characteristics for the pharmaceutical, cosmetics, and food industry, for the hydrolysis and glycerolysis of vegetable oils, production of biodiesel, etc. Several works found in the open literature suggest that the energy released by the ultrasound during the cavitation phenomena can be used to enhance mass transfer (substrate/enzyme), hence increasing the rate of products formation, and also contributing to enhance the enzyme catalytic activity. Furthermore, the ultrasound is considered a "green" technology due to its high efficiency, low instrumental requirement and significant reduction of the processing time in comparison to other techniques. The main goal of this review was to summarize studies available to date regarding the application of ultrasound in enzyme-catalyzed esterification, hydrolysis, glycerolysis and transesterification reactions. PMID:24906428

  4. Generic HPLC platform for automated enzyme reaction monitoring: Advancing the assay toolbox for transaminases and other PLP-dependent enzymes.

    PubMed

    Börner, Tim; Grey, Carl; Adlercreutz, Patrick

    2016-08-01

    Methods for rapid and direct quantification of enzyme kinetics independent of the substrate stand in high demand for both fundamental research and bioprocess development. This study addresses the need for a generic method by developing an automated, standardizable HPLC platform monitoring reaction progress in near real-time. The method was applied to amine transaminase (ATA) catalyzed reactions intensifying process development for chiral amine synthesis. Autosampler-assisted pipetting facilitates integrated mixing and sampling under controlled temperature. Crude enzyme formulations in high and low substrate concentrations can be employed. Sequential, small (1 µL) sample injections and immediate detection after separation permits fast reaction monitoring with excellent sensitivity, accuracy and reproducibility. Due to its modular design, different chromatographic techniques, e.g. reverse phase and size exclusion chromatography (SEC) can be employed. A novel assay for pyridoxal 5'-phosphate-dependent enzymes is presented using SEC for direct monitoring of enzyme-bound and free reaction intermediates. Time-resolved changes of the different cofactor states, e.g. pyridoxal 5'-phosphate, pyridoxamine 5'-phosphate and the internal aldimine were traced in both half reactions. The combination of the automated HPLC platform with SEC offers a method for substrate-independent screening, which renders a missing piece in the assay and screening toolbox for ATAs and other PLP-dependent enzymes.

  5. Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A.

    PubMed

    Oanca, Gabriel; Purg, Miha; Mavri, Janez; Shih, Jean C; Stare, Jernej

    2016-05-21

    The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier. PMID:27121693

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

    PubMed

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

    2016-01-01

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

  7. Nanoparticle-catalyzed reductive bleaching for fabricating turn-off and enzyme-free amplified colorimetric bioassays.

    PubMed

    Li, Wei; Qiang, Weibing; Li, Jie; Li, Hui; Dong, Yifan; Zhao, Yaju; Xu, Danke

    2014-01-15

    Nanoparticle-catalyzed reductive bleaching reactions of colored substrates are emerging as a class of novel indicator reactions for fabricating enzyme-free amplified colorimetric biosensing (turn-off mode), which are exactly opposite to the commonly used oxidative coloring processes of colorless substrates in traditional enzyme-catalyzed amplified colorimetric bioassays (turn-on mode). In this work, a simple theoretical analysis shows that the sensitivity of this colorimetric bioassay can be improved by increasing the amplification factor (kcatΔt), or enhancing the binding affinity between analyte and receptor (Kd), or selecting the colored substrates with high extinction coefficients (ε). Based on this novel strategy, we have developed a turn-off and cost-effective amplified colorimetric thrombin aptasensor. This aptasensor made full use of sandwich binding of two affinity aptamers for increased specificity, magnetic particles for easy separation and enrichment, and gold nanoparticle (AuNP)-catalyzed reductive bleaching reaction to generate the amplified colorimetric signal. With 4-nitrophenol (4-NP) as the non-dye colored substrate, colorimetric bioassay of thrombin was achieved by the endpoint method with a detection limit of 91pM. In particular, when using methylene blue (MB) as the substrate, for the first time, a more convenient and efficient kinetic-based colorimetric thrombin bioassay was achieved without the steps of acidification termination and magnetic removal of particles, with a low detection limit of 10pM, which was superior to the majority of the existing colorimetric thrombin aptasensors. The proposed colorimetric protocol is expected to hold great promise in field analysis and point-of-care applications.

  8. Adrenodoxin supports reactions catalyzed by microsomal steroidogenic cytochrome P450s

    SciTech Connect

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

    2007-02-16

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

  9. Access to 4-alkylaminopyridazine derivatives via nitrogen-assisted regioselective Pd-catalyzed reactions.

    PubMed

    Blaise, Emilie; Kümmerle, Arthur E; Hammoud, Hassan; de Araújo-Júnior, João Xavier; Bihel, Frédéric; Bourguignon, Jean-Jacques; Schmitt, Martine

    2014-11-01

    3-Substituted, 6-substituted, and unsymmetrical 3,6-disubstituted 4-alkylaminopyridazines were prepared from a sequence of three chemo- and regioselective reactions combining amination and palladium-catalyzed cross-coupling reactions, such as reductive dehalogenation and Suzuki-Miyaura reactions. Extension of the methodology to Sonogashira reaction yielded a novel class of 3-substituted pyrrolopyridazines. PMID:25310174

  10. In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.

    PubMed

    Zargar, K; Saville, R; Phelan, R M; Tringe, S G; Petzold, C J; Keasling, J D; Beller, H R

    2016-08-10

    Anaerobic bacterial biosynthesis of toluene from phenylacetate was reported more than two decades ago, but the biochemistry underlying this novel metabolism has never been elucidated. Here we report results of in vitro characterization studies of a novel phenylacetate decarboxylase from an anaerobic, sewage-derived enrichment culture that quantitatively produces toluene from phenylacetate; complementary metagenomic and metaproteomic analyses are also presented. Among the noteworthy findings is that this enzyme is not the well-characterized clostridial p-hydroxyphenylacetate decarboxylase (CsdBC). However, the toluene synthase under study appears to be able to catalyze both phenylacetate and p-hydroxyphenylacetate decarboxylation. Observations suggesting that phenylacetate and p-hydroxyphenylacetate decarboxylation in complex cell-free extracts were catalyzed by the same enzyme include the following: (i) the specific activity for both substrates was comparable in cell-free extracts, (ii) the two activities displayed identical behavior during chromatographic separation of cell-free extracts, (iii) both activities were irreversibly inactivated upon exposure to O2, and (iv) both activities were similarly inhibited by an amide analog of p-hydroxyphenylacetate. Based upon these and other data, we hypothesize that the toluene synthase reaction involves a glycyl radical decarboxylase. This first-time study of the phenylacetate decarboxylase reaction constitutes an important step in understanding and ultimately harnessing it for making bio-based toluene.

  11. In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.

    PubMed

    Zargar, K; Saville, R; Phelan, R M; Tringe, S G; Petzold, C J; Keasling, J D; Beller, H R

    2016-01-01

    Anaerobic bacterial biosynthesis of toluene from phenylacetate was reported more than two decades ago, but the biochemistry underlying this novel metabolism has never been elucidated. Here we report results of in vitro characterization studies of a novel phenylacetate decarboxylase from an anaerobic, sewage-derived enrichment culture that quantitatively produces toluene from phenylacetate; complementary metagenomic and metaproteomic analyses are also presented. Among the noteworthy findings is that this enzyme is not the well-characterized clostridial p-hydroxyphenylacetate decarboxylase (CsdBC). However, the toluene synthase under study appears to be able to catalyze both phenylacetate and p-hydroxyphenylacetate decarboxylation. Observations suggesting that phenylacetate and p-hydroxyphenylacetate decarboxylation in complex cell-free extracts were catalyzed by the same enzyme include the following: (i) the specific activity for both substrates was comparable in cell-free extracts, (ii) the two activities displayed identical behavior during chromatographic separation of cell-free extracts, (iii) both activities were irreversibly inactivated upon exposure to O2, and (iv) both activities were similarly inhibited by an amide analog of p-hydroxyphenylacetate. Based upon these and other data, we hypothesize that the toluene synthase reaction involves a glycyl radical decarboxylase. This first-time study of the phenylacetate decarboxylase reaction constitutes an important step in understanding and ultimately harnessing it for making bio-based toluene. PMID:27506494

  12. In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community

    PubMed Central

    Zargar, K.; Saville, R.; Phelan, R. M.; Tringe, S. G.; Petzold, C. J.; Keasling, J. D.; Beller, H. R.

    2016-01-01

    Anaerobic bacterial biosynthesis of toluene from phenylacetate was reported more than two decades ago, but the biochemistry underlying this novel metabolism has never been elucidated. Here we report results of in vitro characterization studies of a novel phenylacetate decarboxylase from an anaerobic, sewage-derived enrichment culture that quantitatively produces toluene from phenylacetate; complementary metagenomic and metaproteomic analyses are also presented. Among the noteworthy findings is that this enzyme is not the well-characterized clostridial p-hydroxyphenylacetate decarboxylase (CsdBC). However, the toluene synthase under study appears to be able to catalyze both phenylacetate and p-hydroxyphenylacetate decarboxylation. Observations suggesting that phenylacetate and p-hydroxyphenylacetate decarboxylation in complex cell-free extracts were catalyzed by the same enzyme include the following: (i) the specific activity for both substrates was comparable in cell-free extracts, (ii) the two activities displayed identical behavior during chromatographic separation of cell-free extracts, (iii) both activities were irreversibly inactivated upon exposure to O2, and (iv) both activities were similarly inhibited by an amide analog of p-hydroxyphenylacetate. Based upon these and other data, we hypothesize that the toluene synthase reaction involves a glycyl radical decarboxylase. This first-time study of the phenylacetate decarboxylase reaction constitutes an important step in understanding and ultimately harnessing it for making bio-based toluene. PMID:27506494

  13. Mechanistic insights into nickamine-catalyzed alkyl-alkyl cross-coupling reactions.

    PubMed

    Breitenfeld, Jan; Hu, Xile

    2014-01-01

    Within the last decades the transition metal-catalyzed cross-coupling of non-activated alkyl halides has significantly progressed. Within the context of alkyl-alkyl cross-coupling, first row transition metals spanning from iron, over cobalt, nickel, to copper have been successfully applied to catalyze this difficult reaction. The mechanistic understanding of these reactions is still in its infancy. Herein we outline our latest mechanistic studies that explain the efficiency of nickel, in particular nickamine-catalyzed alkyl-alkyl cross-coupling reactions.

  14. 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)

  15. Epoxide ring-opening and Meinwald rearrangement reactions of epoxides catalyzed by mesoporous aluminosilicates.

    PubMed

    Robinson, Mathew W C; Davies, A Matthew; Buckle, Richard; Mabbett, Ian; Taylor, Stuart H; Graham, Andrew E

    2009-06-21

    Mesoporous aluminosilicates efficiently catalyze the ring-opening of epoxides to produce beta-alkoxyalcohols in high yields under extremely mild reaction conditions. These materials also catalyze the corresponding Meinwald rearrangement in non-nucleophilic solvents to give aldehydes which can be trapped in situ to provide the corresponding acetals in an efficient tandem process.

  16. Recent developments in gold-catalyzed cycloaddition reactions.

    PubMed

    López, Fernando; Mascareñas, José L

    2011-01-01

    In the last years there have been extraordinary advances in the development of gold-catalyzed cycloaddition processes. In this review we will summarize some of the most remarkable examples, and present the mechanistic rational underlying the transformations.

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

    PubMed

    Tian, Xuemei; Zhang, Suoqin; Zheng, Liangyu

    2016-03-01

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

  18. 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...

  19. Origins of the double asymmetric induction on proline-catalyzed aldol reactions.

    PubMed

    Calderón, Félix; Doyagüez, Elisa G; Cheong, Paul Ha-Yeon; Fernández-Mayoralas, Alfonso; Houk, K N

    2008-10-17

    Computational studies to elucidate the origin of the double asymmetric induction on proline-catalyzed aldol reaction have been performed using HF/6-31G(d) calculations. The computed transition structures explain the experimental data obtained. PMID:18811197

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

    PubMed

    Bolleddula, Jayaprakasam; Chowdhury, Swapan K

    2015-01-01

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

  1. Investigating the mechanism of the selective hydrogenation reaction of cinnamaldehyde catalyzed by Ptn clusters.

    PubMed

    Li, Laicai; Wang, Wei; Wang, Xiaolan; Zhang, Lin

    2016-08-01

    Cinnamaldehyde (CAL) belongs to the group of aromatic α,β-unsaturated aldehydes; the selective hydrogenation of CAL plays an important role in the fine chemical and pharmaceutical industries. Using Ptn clusters as catalytic models, we studied the selective hydrogenation reaction mechanism for CAL catalyzed by Ptn (n = 6, 10, 14, 18) clusters by means of B3LYP in density functional theory at the 6-31+ G(d) level (the LanL2DZ extra basis set was used for the Pt atom). The rationality of the transition state was proved by vibration frequency analysis and intrinsic reaction coordinate computation. Moreover, atoms in molecules theory and nature bond orbital theory were applied to discuss the interaction among orbitals and the bonding characteristics. The results indicate that three kinds of products, namely 3-phenylpropyl aldehyde, 3-phenyl allyl alcohol and cinnamyl alcohol, are produced in the selective hydrogenation reaction catalyzed by Ptn clusters; each pathway possesses two reaction channels. Ptn clusters are more likely to catalyze the activation and hydrogenation of the C = O bond in CAL molecules, eventually producing cinnamic alcohol, which proves that Ptn clusters have a strong reaction selectivity to catalyze CAL. The reaction selectivity of the catalyzer cluster is closely related to the size of the Ptn cluster, with Pt14 clusters having the greatest reaction selectivity. Graphical Abstract The reaction mechanism for the selective hydrogenation reaction ofcinnamaldehyde catalyzed by Ptn clusters was studied by densityfunctional theory. The reactionselectivity of cluster catalyzer was concluded to be closely related to the size of Ptn clusters, with Pt14 clusters having the greatest reaction selectivity. PMID:27444877

  2. Investigating the mechanism of the selective hydrogenation reaction of cinnamaldehyde catalyzed by Ptn clusters.

    PubMed

    Li, Laicai; Wang, Wei; Wang, Xiaolan; Zhang, Lin

    2016-08-01

    Cinnamaldehyde (CAL) belongs to the group of aromatic α,β-unsaturated aldehydes; the selective hydrogenation of CAL plays an important role in the fine chemical and pharmaceutical industries. Using Ptn clusters as catalytic models, we studied the selective hydrogenation reaction mechanism for CAL catalyzed by Ptn (n = 6, 10, 14, 18) clusters by means of B3LYP in density functional theory at the 6-31+ G(d) level (the LanL2DZ extra basis set was used for the Pt atom). The rationality of the transition state was proved by vibration frequency analysis and intrinsic reaction coordinate computation. Moreover, atoms in molecules theory and nature bond orbital theory were applied to discuss the interaction among orbitals and the bonding characteristics. The results indicate that three kinds of products, namely 3-phenylpropyl aldehyde, 3-phenyl allyl alcohol and cinnamyl alcohol, are produced in the selective hydrogenation reaction catalyzed by Ptn clusters; each pathway possesses two reaction channels. Ptn clusters are more likely to catalyze the activation and hydrogenation of the C = O bond in CAL molecules, eventually producing cinnamic alcohol, which proves that Ptn clusters have a strong reaction selectivity to catalyze CAL. The reaction selectivity of the catalyzer cluster is closely related to the size of the Ptn cluster, with Pt14 clusters having the greatest reaction selectivity. Graphical Abstract The reaction mechanism for the selective hydrogenation reaction ofcinnamaldehyde catalyzed by Ptn clusters was studied by densityfunctional theory. The reactionselectivity of cluster catalyzer was concluded to be closely related to the size of Ptn clusters, with Pt14 clusters having the greatest reaction selectivity.

  3. Cu-catalyzed cross-coupling reactions of epoxides with organoboron compounds.

    PubMed

    Lu, Xiao-Yu; Yang, Chu-Ting; Liu, Jing-Hui; Zhang, Zheng-Qi; Lu, Xi; Lou, Xin; Xiao, Bin; Fu, Yao

    2015-02-11

    A copper-catalyzed cross-coupling reaction of epoxides with arylboronates is described. This reaction is not limited to aromatic epoxides, because aliphatic epoxides are also suitable substrates. In addition, N-sulfonyl aziridines can be successfully converted into the products. This reaction provides convenient access to β-phenethyl alcohols, which are valuable synthetic intermediates. PMID:25564373

  4. Gold(III)-catalyzed three-component coupling reaction (TCC) selective toward furans.

    PubMed

    Li, Jian; Liu, Li; Ding, Dong; Sun, Jiangtao; Ji, Yangxuan; Dong, Jialing

    2013-06-01

    An efficient three-component coupling reaction toward a variety of furan derivatives has been developed. This cascade transformation proceeds via the gold-catalyzed coupling reaction of phenylglyoxal derivatives, secondary amines, and terminal alkynes, under the reaction conditions, that undergoes cyclization into the furan core.

  5. The biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical S-adenosylmethionine enzymes.

    PubMed

    Jarrett, Joseph T

    2015-02-13

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

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

    PubMed Central

    Jarrett, Joseph T.

    2015-01-01

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

  7. Synthesis of Cyclooctatetraenes through a Palladium-Catalyzed Cascade Reaction.

    PubMed

    Blouin, Sarah; Gandon, Vincent; Blond, Gaëlle; Suffert, Jean

    2016-06-13

    Reported is a cascade reaction leading to fully substituted cyclooctatetraenes. This unexpected transformation likely proceeds through a unique 8π electrocyclization reaction of a ene triyne. DFT computations provide the mechanistic basis of this surprizing reaction. PMID:27135905

  8. Explaining the atypical reaction profiles of heme enzymes with a novel mechanistic hypothesis and kinetic treatment.

    PubMed

    Manoj, Kelath Murali; Baburaj, Arun; Ephraim, Binoy; Pappachan, Febin; Maviliparambathu, Pravitha Parapurathu; Vijayan, Umesh K; Narayanan, Sivaprasad Valiyaveettil; Periasamy, Kalaiselvi; George, Ebi Ashley; Mathew, Lazar T

    2010-01-01

    Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO) characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP), uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation) of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model) was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the "steady state kinetics" of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates) is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s) affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of "the product of interest" in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of "substrate concentration at maximum observed rate". The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes. PMID:20498847

  9. Explaining the Atypical Reaction Profiles of Heme Enzymes with a Novel Mechanistic Hypothesis and Kinetic Treatment

    PubMed Central

    Manoj, Kelath Murali; Baburaj, Arun; Ephraim, Binoy; Pappachan, Febin; Maviliparambathu, Pravitha Parapurathu; Vijayan, Umesh K.; Narayanan, Sivaprasad Valiyaveettil; Periasamy, Kalaiselvi; George, Ebi Ashley; Mathew, Lazar T.

    2010-01-01

    Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO) characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP), uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation) of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model) was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the “steady state kinetics” of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates) is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s) affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of “the product of interest” in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of “substrate concentration at maximum observed rate”. The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes. PMID:20498847

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

    NASA Astrophysics Data System (ADS)

    Yao, Yuan; Li, Ze-Sheng

    2012-01-01

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

  11. Tandem reactions initiated by copper-catalyzed cross-coupling: a new strategy towards heterocycle synthesis.

    PubMed

    Liu, Yunyun; Wan, Jie-Ping

    2011-10-21

    Copper-catalyzed cross-coupling reactions which lead to the formation of C-N, C-O, C-S and C-C bonds have been recognized as one of the most useful strategies in synthetic organic chemistry. During past decades, important breakthroughs in the study of Cu-catalyzed coupling processes demonstrated that Cu-catalyzed reactions are broadly applicable to a variety of research fields related to organic synthesis. Representatively, employing these coupling transformations as key steps, a large number of tandem reactions have been developed for the construction of various heterocyclic compounds. These tactics share the advantages of high atom economics of tandem reactions as well as the broad tolerance of Cu-catalyst systems. Therefore, Cu-catalyzed C-X (X = N, O, S, C) coupling transformation-initiated tandem reactions were quickly recognized as a strategy with great potential for synthesizing heterocyclic compounds and gained worldwide attention. In this review, recent research progress in heterocycle syntheses using tandem reactions initiated by copper-catalyzed coupling transformations, including C-N, C-O, C-S as well as C-C coupling processes are summarized. PMID:21879127

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

    PubMed Central

    2014-01-01

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

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2013-01-15

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

  15. Copper-catalyzed oxidative Heck reactions between alkyltrifluoroborates and vinyl arenes.

    PubMed

    Liwosz, Timothy W; Chemler, Sherry R

    2013-06-21

    We report herein that potassium alkyltrifluoroborates can be utilized in oxidative Heck-type reactions with vinyl arenes. The reaction is catalyzed by a Cu(OTf)2/1,10-phenanthroline with MnO2 as the stoichiometric oxidant. In addition to the alkyl Heck, amination, esterification, and dimerization reactions of alkyltrifluoroborates are demonstrated under analogous reaction conditions. Evidence for an alkyl radical intermediate is presented. PMID:23734764

  16. Bulk Gold-Catalyzed Reactions of Isocyanides, Amines, and Amine N-Oxides

    SciTech Connect

    Klobukowski, Erik; Angelici, Robert; Woo, Keith L.

    2012-01-26

    Bulk gold powder (5–50 μm particles) catalyzes the reactions of isocyanides with amines and amine N-oxides to produce ureas. The reaction of n-butyl isocyanide (nBu–N≡C) with di-n-propylamine and N-methylmorpholine N-oxide in acetonitrile, which was studied in the greatest detail, produced 3-butyl-1,1-dipropylurea (O═C(NHnBu)(NnPr2)) in 99% yield at 60 °C within 2 h. Sterically and electronically different isocyanides, amines, and amine N-oxides react successfully under these conditions. Detailed studies support a two-step mechanism that involves a gold-catalyzed reaction of adsorbed isocyanide with the amine N-oxide to form an isocyanate (RN═C═O), which rapidly reacts with the amine to give the urea product. These investigations show that bulk gold, despite its reputation for poor catalytic activity, is capable of catalyzing these reactions.

  17. Molybdenum-Catalyzed Asymmetric Allylic Alkylation of 3-Alkyloxindoles: Reaction Development and Applications

    PubMed Central

    Trost, Barry M.; Zhang, Yong

    2013-01-01

    We report a full account of our work towards the development of Mo-catalyzed asymmetric allylic alkylation reactions with 3-alkyloxindoles as nucleophiles. The reaction is complementary to the Pd-catalyzed reaction with regard to the scope of oxindole nucleophiles. A number of 3-alkyloxindoles were alkylated successfully under mild conditions to give products with excellent yields and good-to-excellent enantioselectivities. Applications of this method to the preparation of indoline alkaloids such as (−)-physostigmine, ent-(−)-debromoflustramine B, and the indolinoquinoline rings of communesin B are reported. PMID:21290436

  18. 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

  19. Synthesis of 2-vinylic indoles and derivatives via a Pd-catalyzed tandem coupling reaction.

    PubMed

    Fayol, Aude; Fang, Yuan-Qing; Lautens, Mark

    2006-09-14

    A novel one-step synthesis of valuable 2-vinylic indoles and their tricycle derivatives is described. This reaction, which utilizes a gem-dibromovinyl unit as a readily available starting material, occurs via an efficient Pd-catalyzed tandem Buchwald-Hartwig/Heck reaction. PMID:16956187

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  2. Highly enantioselective Henry reactions of aromatic aldehydes catalyzed by an amino alcohol-copper(II) complex.

    PubMed

    Qin, Dan-Dan; Lai, Wen-Han; Hu, Di; Chen, Zheng; Wu, An-An; Ruan, Yuan-Ping; Zhou, Zhao-Hui; Chen, Hong-Bin

    2012-08-20

    Amino alcohol-Cu(II) catalyst: Highly enantioselective Henry reactions between aromatic aldehydes and nitromethane have been developed. The reactions were catalyzed by an easily available and operationally simple amino alcohol-copper(II) catalyst. In total, 38 substrates were tested and the R-configured products were obtained in good yields with excellent enantioselectivities. PMID:22791567

  3. 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

  4. 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.

  5. Troglitazone quinone formation catalyzed by human and rat CYP3A: an atypical CYP oxidation reaction.

    PubMed

    He, K; Woolf, T F; Kindt, E K; Fielder, A E; Talaat, R E

    2001-07-15

    Oxidative ring opening of troglitazone (TGZ)(1) a thiazolidine 2,4-dione derivative used for the treatment of type II diabetes mellitus, leads to the formation of a quinone metabolite. The formation of TGZ quinone was shown to be NADPH dependent and to require active microsomal enzymes. Quinone formation was not affected by co-incubation with catalase or sodium azide and was partially inhibited (25%) by superoxide dismutase (SOD). Kinetic analysis of TGZ quinone formation in human liver microsomes implied single enzyme involvement. CYP3A isoforms were characterized as the primary enzymes involved in quinone formation by several lines of evidence including: (a) troleandomycin and ketoconazole almost completely inhibited microsomal quinone formation when SOD was present, whereas other CYP inhibitors had minimal effects (<20%); (b) TGZ quinone formation was highly correlated with regard to both contents (r(2): 0.9374) and activities (r(2): 0.7951) of CYP3A4 in human liver microsomes (HLM); (c) baculovirus insect cell-expressed human CYP3A4 was able to catalyze TGZ quinone formation at a higher capacity (V(max)/K(m)) than other human CYPs with the relative contribution of CYP3A4 in HLM estimated to be 20-fold higher than that of other CYPs; (d) TGZ quinone formation was increased by 350% in liver microsomes from rats pretreated with dexamethasone (DEX); and (e) plasma concentrations of TGZ quinone were increased by 260-680% in rats pretreated with DEX. The chemical nature of the quinone metabolite suggests an atypical CYP reaction consistent with a one-electron oxidation mechanism where an intermediate phenoxy radical combines with ferryl oxygen to subsequently form the quinone metabolite.

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

    PubMed

    Thakur, Ashish; Louie, Janis

    2015-08-18

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

  7. Acid-, base-, and lewis-acid-catalyzed heterolysis of methoxide from an alpha-hydroxy-beta-methoxy radical: models for reactions catalyzed by coenzyme B12-dependent diol dehydratase.

    PubMed

    Xu, Libin; Newcomb, Martin

    2005-11-11

    [Reaction: see text].A model for glycol radicals was employed in laser flash photolysis kinetic studies of catalysis of the fragmentation of a methoxy group adjacent to an alpha-hydroxy radical center. Photolysis of a phenylselenylmethylcyclopropane precursor gave a cyclopropylcarbinyl radical that rapidly ring opened to the target alpha-hydroxy-beta-methoxy radical (3). Heterolysis of the methoxy group in 3 gave an enolyl radical (4a) or an enol ether radical cation (4b), depending upon pH. Radicals 4 contain a 2,2-diphenylcyclopropane reporter group, and they rapidly opened to give UV-observable diphenylalkyl radicals as the final products. No heterolysis was observed for radical 3 under neutral conditions. In basic aqueous acetonitrile solutions, specific base catalysis of the heterolysis was observed; the pK(a) of radical 3 was determined to be 12.5 from kinetic titration plots, and the ketyl radical formed by deprotonation of 3 eliminated methoxide with a rate constant of 5 x 10(7) s(-1). In the presence of carboxylic acids in acetonitrile solutions, radical 3 eliminated methanol in a general acid-catalyzed reaction, and rate constants for protonation of the methoxy group in 3 by several acids were measured. Radical 3 also reacted by fragmentation of methoxide in Lewis-acid-catalyzed heterolysis reactions; ZnBr2, Sc(OTf)3, and BF3 were found to be efficient catalysts. Catalytic rate constants for the heterolysis reactions were in the range of 3 x 10(4) to 2 x 10(6) s(-1). The Lewis-acid-catalyzed heterolysis reactions are fast enough for kinetic competence in coenzyme B12 dependent enzyme-catalyzed reactions of glycols, and Lewis-acid-catalyzed cleavages of beta-ethers in radicals might be applied in synthetic reactions.

  8. Direct detection and kinetic analysis of covalent intermediate formation in the 4-amino-4-deoxychorismate synthase catalyzed reaction.

    PubMed

    He, Ze; Toney, Michael D

    2006-04-18

    Chorismate-utilizing enzymes catalyze diverse reactions, providing critical physiological functions unique to plants, bacteria, fungi, and some parasites. Their absence in animals makes them excellent targets for antimicrobials and herbicides. 4-Amino-4-deoxychorismate synthase (ADCS) catalyzes the first step in folate biosynthsis and shares a common core mechanism with isochorismate synthase (IS) and anthranilate synthase (AS), in which nucleophile addition at C2 initiates these reactions. Evidence was presented previously [He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-2385] that K274 is the nucleophile in ADCS, implying formation of a covalent intermediate. Herein, we report the direct detection of this covalent intermediate formed in ADCS-catalyzed reactions by ESI-MS. Difference spectra show the covalent intermediate has an absorption maximum at 310 nm. This was used to study the pre-steady-state kinetics of covalent intermediate formation under various conditions. Additionally, E258 in ADCS was shown to be critical to formation of the covalent intermediate by acting as a general acid catalyst for loss of the C4 hydroxyl group. The E258A/D mutants both exhibit very low activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH(4)(+)-dependent activities, respectively. Lastly, A213 in IS (structurally homologous to K274 in ADCS) was changed to lysine in an attempt to convert IS to an ADCS-like enzyme. HPLC studies support the formation of a covalent intermediate with this mutant. PMID:16605270

  9. Stereochemical Consequences of Vinylpyruvate Hydratase-Catalyzed Reactions.

    PubMed

    Johnson, William H; Stack, Tyler M M; Taylor, Stephanie M; Burks, Elizabeth A; Whitman, Christian P

    2016-07-26

    A stereochemical analysis has been carried out on two vinylpyruvate hydratases (VPH), which convert 2-hydroxy-2,4-pentadienoate to 2-keto-4S-hydroxypentanoate in meta-fission pathways. Bacterial strains with this pathway can use aromatic compounds as sole sources of energy and carbon. The analysis was carried out using the 5-methyl and 5-chloro derivatives of 2-hydroxy-2,4-pentadienoate with the enzymes from Pseudomonas putida mt-2 (Pp) and Leptothrix cholodnii SP-6 (Lc). In both organisms, VPH is in a complex with the preceding enzyme in the pathway, 4-oxalocrotonate decarboxylase (4-OD). In D2O, a deuteron is incorporated stereospecifically at the C-3 and C-5 positions of product by both Pp and Lc enzymes. Accordingly, the complexes generate (3S,5S)-3,5-[di-D]-2-keto-4S-hydroxyhexanoate and (3S,5R)-3,5-[di-D]-2-keto-4R-hydroxy-5-chloropentanoate (4R and 5R due to a priority numbering change). The substitution at C-5 (CH3 or Cl) or the source of the enzyme (Pp or Lc) does not change the stereochemical outcome. One mechanism that can account for the results is the ketonization of the 5-substituted dienol to the α,β-unsaturated ketone (placing a deuteron at C-5 in D2O), followed by the conjugate addition of water (placing a deuteron at C-3). The stereochemical outcome for VPH (from Pp and Lc) is the same as that reported for a related enzyme, 2-oxo-hept-4-ene-1,7-dioate hydratase, from Escherichia coli C. The combined observations suggest similar mechanisms for these three enzymes that could possibly be common to this group of enzymes. PMID:27362840

  10. 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.

  11. New reactions and products resulting from alternative interactions between the P450 enzyme and redox partners.

    PubMed

    Zhang, Wei; Liu, Yi; Yan, Jinyong; Cao, Shaona; Bai, Fali; Yang, Ying; Huang, Shaohua; Yao, Lishan; Anzai, Yojiro; Kato, Fumio; Podust, Larissa M; Sherman, David H; Li, Shengying

    2014-03-01

    Cytochrome P450 enzymes are capable of catalyzing a great variety of synthetically useful reactions such as selective C-H functionalization. Surrogate redox partners are widely used for reconstitution of P450 activity based on the assumption that the choice of these auxiliary proteins or their mode of action does not affect the type and selectivity of reactions catalyzed by P450s. Herein, we present an exceptional example to challenge this postulate. MycG, a multifunctional biosynthetic P450 monooxygenase responsible for hydroxylation and epoxidation of 16-membered ring macrolide mycinamicins, is shown to catalyze the unnatural N-demethylation(s) of a range of mycinamicin substrates when partnered with the free Rhodococcus reductase domain RhFRED or the engineered Rhodococcus-spinach hybrid reductase RhFRED-Fdx. By contrast, MycG fused with the RhFRED or RhFRED-Fdx reductase domain mediates only physiological oxidations. This finding highlights the larger potential role of variant redox partner protein-protein interactions in modulating the catalytic activity of P450 enzymes.

  12. Copper(II)-Catalyzed Nitroaldol (Henry) Reactions: Recent Developments.

    PubMed

    Murugavel, Govindarasu; Sadhu, Pradeep; Punniyamurthy, Tharmalingam

    2016-08-01

    Self-assembled copper(II) complexes are described as effective catalysts for nitroaldol (Henry) reactions on water. The protocol involves a heterogeneous process and the catalysts can be recovered and recycled without loss of activity. Further, C2-symmetric N,N'-substituted chiral copper(II) salan complexes are found to be more effective catalysts than chiral copper(II) salen complexes for reactions in homogeneous catalysis, with high enantioselectivities. The reactions involve bifunctional catalysis, bearing the properties of a Brønsted base, as well as a Lewis acid, to effect the reaction in the absence of external additives.

  13. DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction.

    PubMed

    Algasaier, Sana I; Exell, Jack C; Bennet, Ian A; Thompson, Mark J; Gotham, Victoria J B; Shaw, Steven J; Craggs, Timothy D; Finger, L David; Grasby, Jane A

    2016-04-01

    Human flap endonuclease-1 (hFEN1) catalyzes the essential removal of single-stranded flaps arising at DNA junctions during replication and repair processes. hFEN1 biological function must be precisely controlled, and consequently, the protein relies on a combination of protein and substrate conformational changes as a prerequisite for reaction. These include substrate bending at the duplex-duplex junction and transfer of unpaired reacting duplex end into the active site. When present, 5'-flaps are thought to thread under the helical cap, limiting reaction to flaps with free 5'-terminiin vivo Here we monitored DNA bending by FRET and DNA unpairing using 2-aminopurine exciton pair CD to determine the DNA and protein requirements for these substrate conformational changes. Binding of DNA to hFEN1 in a bent conformation occurred independently of 5'-flap accommodation and did not require active site metal ions or the presence of conserved active site residues. More stringent requirements exist for transfer of the substrate to the active site. Placement of the scissile phosphate diester in the active site required the presence of divalent metal ions, a free 5'-flap (if present), a Watson-Crick base pair at the terminus of the reacting duplex, and the intact secondary structure of the enzyme helical cap. Optimal positioning of the scissile phosphate additionally required active site conserved residues Tyr(40), Asp(181), and Arg(100)and a reacting duplex 5'-phosphate. These studies suggest a FEN1 reaction mechanism where junctions are bound and 5'-flaps are threaded (when present), and finally the substrate is transferred onto active site metals initiating cleavage.

  14. DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction*

    PubMed Central

    Algasaier, Sana I.; Exell, Jack C.; Bennet, Ian A.; Thompson, Mark J.; Gotham, Victoria J. B.; Shaw, Steven J.; Craggs, Timothy D.; Finger, L. David; Grasby, Jane A.

    2016-01-01

    Human flap endonuclease-1 (hFEN1) catalyzes the essential removal of single-stranded flaps arising at DNA junctions during replication and repair processes. hFEN1 biological function must be precisely controlled, and consequently, the protein relies on a combination of protein and substrate conformational changes as a prerequisite for reaction. These include substrate bending at the duplex-duplex junction and transfer of unpaired reacting duplex end into the active site. When present, 5′-flaps are thought to thread under the helical cap, limiting reaction to flaps with free 5′-termini in vivo. Here we monitored DNA bending by FRET and DNA unpairing using 2-aminopurine exciton pair CD to determine the DNA and protein requirements for these substrate conformational changes. Binding of DNA to hFEN1 in a bent conformation occurred independently of 5′-flap accommodation and did not require active site metal ions or the presence of conserved active site residues. More stringent requirements exist for transfer of the substrate to the active site. Placement of the scissile phosphate diester in the active site required the presence of divalent metal ions, a free 5′-flap (if present), a Watson-Crick base pair at the terminus of the reacting duplex, and the intact secondary structure of the enzyme helical cap. Optimal positioning of the scissile phosphate additionally required active site conserved residues Tyr40, Asp181, and Arg100 and a reacting duplex 5′-phosphate. These studies suggest a FEN1 reaction mechanism where junctions are bound and 5′-flaps are threaded (when present), and finally the substrate is transferred onto active site metals initiating cleavage. PMID:26884332

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

    PubMed

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

    2016-04-15

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

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

    PubMed

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

    2011-11-01

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

  17. 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.

  18. A General Copper-Catalyzed Vinylic Halogen Exchange Reaction.

    PubMed

    Nitelet, Antoine; Evano, Gwilherm

    2016-04-15

    An efficient and general system for the halogen exchange reaction in alkenyl halides has been developed. Upon reaction with catalytic amounts of copper iodide and trans-N,N'-dimethylcyclohexane-1,2-diamine in the presence of tetramethylammonium chloride or bromide, a wide range of easily accessible alkenyl iodides can be smoothly transformed to their far less available chlorinated and brominated derivatives in excellent yields and with full retention of the double bond geometry. This reaction also enables the chlorination of bromoalkenes and could be extended to the use of gem-dibromoalkenes. PMID:27031868

  19. 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-(β-d-erythrofuranosyl)orotic acid and 1-(β-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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Cody, G. D.

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

  2. Synthesis of polycyclic indole skeletons by a gold(I)-catalyzed cascade reaction.

    PubMed

    Wang, Tao; Shi, Shuai; Pflästerer, Daniel; Rettenmeier, Eva; Rudolph, Matthias; Rominger, Frank; Hashmi, A Stephen K

    2014-01-01

    The conversion of simple, easily available urea-substituted 3-phenylpropargyl alcohols catalyzed by a simple IPr-gold(I) catalyst in a gold(I)-catalyzed cascade reaction composing of a gold-catalyzed nucleophilic addition and a subsequent gold-catalyzed substitution reaction delivers 1H-imidazo[1,5-a]indol-3(2H)-ones. Other gold(I) catalysts or silver catalysts gave lower yields and often gave other side products. Gold(III) and copper(II) catalysts decomposed the starting material. Twelve examples, including donor and acceptor substituents on the distal nitrogen of the urea substructure, are provided. An X-ray crystal structure analysis confirmed the structural assignment. The mechanistic investigation including isolation and further conversion of intermediates and reactions with enantiopure starting materials indicated that after the nucleophilic-addition step, the substrate undergoes an S(N)1-type benzylic substitution reaction at the indolyl alcohol intermediate or an intramolecular hydroamination reaction of the 2-vinylindole intermediate. PMID:24375591

  3. Reaction progress kinetic analysis of a copper-catalyzed aerobic oxidative coupling reaction with N-phenyl tetrahydroisoquinoline.

    PubMed

    Scott, Martin; Sud, Abhishek; Boess, Esther; Klussmann, Martin

    2014-12-19

    The results from a kinetic investigation of a Cu-catalyzed oxidative coupling reaction between N-phenyl tetrahydroisoquinoline and a silyl enol ether using elemental oxygen as oxidant are presented. By using reaction progress kinetic analysis as an evaluation method for the obtained data, we discovered information regarding the reaction order of the substrates and catalysts. Based on this information and some additional experiments, a refined model for the initial oxidative activation of the amine substrate and the activation of the nucleophile by the catalyst was developed. The mechanistic information also helped to understand why silyl nucleophiles have previously failed in a related Cu-catalyzed reaction using tert-butyl hydroperoxide as oxidant and how to overcome this limitation. PMID:25203932

  4. Rational nanoconjugation improves biocatalytic performance of enzymes: aldol addition catalyzed by immobilized rhamnulose-1-phosphate aldolase.

    PubMed

    Ardao, Inés; Comenge, Joan; Benaiges, M Dolors; Álvaro, Gregorio; Puntes, Víctor F

    2012-04-17

    Gold nanoparticles (AuNPs) are attractive materials for the immobilization of enzymes due to several advantages such as high enzyme loading, absence of internal diffusion limitations, and Brownian motion in solution, compared to the conventional immobilization onto porous macroscopic supports. The affinity of AuNPs to different groups present at the protein surface enables direct enzyme binding to the nanoparticle without the need of any coupling agent. Enzyme activity and stability appear to be improved when the biocatalyst is immobilized onto AuNPs. Rhamnulose-1-phosphate aldolase (RhuA) was selected as model enzyme for the immobilization onto AuNPs. The enzyme loading was characterized by four different techniques: surface plasmon resonance (SPR) shift and intensity, dynamic light scattering (DLS), and transmission electron microscopy (TEM). AuNPs-RhuA complexes were further applied as biocatalyst of the aldol addition reaction between dihydroxyacetone phosphate (DHAP) and (S)-Cbz-alaninal during two reaction cycles. In these conditions, an improved reaction yield and selectivity, together with a fourfold activity enhancement were observed, as compared to soluble RhuA. PMID:22428999

  5. Proposed mechanism for the reaction catalyzed by a diterpene cyclase, aphidicolan-16beta-ol synthase: experimental results on biomimetic cyclization and examination of the cyclization pathway by ab initio calculations.

    PubMed

    Oikawa, Hideaki; Nakamura, Kensuke; Toshima, Hiroaki; Toyomasu, Tomonobu; Sassa, Takeshi

    2002-08-01

    To examine the mechanism of the cyclization reaction catalyzed by aphidicolan-16beta-ol synthase (ACS), which is a key enzyme in the biosynthesis of diterpene aphidicolin, a specific inhibitor of DNA polymerase alpha, skeletal rearrangement of 2a and biomimetic cyclization of 4b were employed. The structures of the reaction products, which reflect penultimate cation intermediates, allowed us to propose a detailed reaction pathway for the Lewis acid-catalyzed cyclizations and rearrangements. Isolation of these products in an aphidicolin-producing fungus led us to speculate that the mechanism of the ACS-catalyzed cyclization reaction is the same as that of a nonenzymatic reaction. Ab initio calculations of the acid-catalyzed reaction intermediates and the transition states indicate that the overall reaction catalyzed by ACS is an exothermic process though the reaction proceeds via an energetically disfavored secondary cation-like transition state. In conjunction with the solvent effect in the acid-catalyzed reactions, this indicates that the actual role of ACS is to provide a template which enforces conformations of the intermediate cations leading to the productive cyclization although it has been believed that the cation-pi interaction between cation intermediates and aromatic amino acid residues in the active site is important for the enzymatic catalysis. This study provided important information on the role of various cationic species, especially secondary cation-like structures, in both nonenzymatic and enzymatic reactions.

  6. Novel Enzyme Family Found in Filamentous Fungi Catalyzing trans-4-Hydroxylation of l-Pipecolic Acid

    PubMed Central

    Hibi, Makoto; Mori, Ryosuke; Miyake, Ryoma; Kawabata, Hiroshi; Kozono, Shoko; Takahashi, Satomi

    2016-01-01

    Hydroxypipecolic acids are bioactive compounds widely distributed in nature and are valuable building blocks for the organic synthesis of pharmaceuticals. We have found a novel hydroxylating enzyme with activity toward l-pipecolic acid (l-Pip) in a filamentous fungus, Fusarium oxysporum c8D. The enzyme l-Pip trans-4-hydroxylase (Pip4H) of F. oxysporum (FoPip4H) belongs to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily, catalyzes the regio- and stereoselective hydroxylation of l-Pip, and produces optically pure trans-4-hydroxy-l-pipecolic acid (trans-4-l-HyPip). Amino acid sequence analysis revealed several fungal enzymes homologous with FoPip4H, and five of these also had l-Pip trans-4-hydroxylation activity. In particular, the homologous Pip4H enzyme derived from Aspergillus nidulans FGSC A4 (AnPip4H) had a broader substrate specificity spectrum than other homologues and reacted with the l and d forms of various cyclic and aliphatic amino acids. Using FoPip4H as a biocatalyst, a system for the preparative-scale production of chiral trans-4-l-HyPip was successfully developed. Thus, we report a fungal family of l-Pip hydroxylases and the enzymatic preparation of trans-4-l-HyPip, a bioactive compound and a constituent of secondary metabolites with useful physiological activities. PMID:26801577

  7. Evidence That Does Not Support Pyruvate Kinase M2 (PKM2)-catalyzed Reaction as a Rate-limiting Step in Cancer Cell Glycolysis.

    PubMed

    Xie, Jiansheng; Dai, Chunyan; Hu, Xun

    2016-04-22

    It has been recognized that the rate-limiting function of pyruvate kinase M2 (PKM2) in glycolysis plays an important role in distributing glycolytic intermediates for anabolic and catabolic purposes in cancer cells. However, after analysis of the catalytic capacity of PKM2 relative to other glycolytic enzymes, the regulation range of PKM2 activity, metabolic flux control, and thermodynamics, we suggest that the PKM2-catalyzed reaction is not a rate-limiting step in cancer cell glycolysis. Hexokinase and phosphofructokinase 1 (PFK1), the first and third enzyme along the pathway, are rate-limiting enzymes that limit the overall glycolytic rate, whereas PKM2 and lactate dehydrogenase, the last two enzymes in the pathway, are for the fast removal of upstream intermediates to prevent the obstruction of the pathway. The argument is in accordance with the catalytic capacity of glycolytic enzymes, regulation range of enzyme activities, metabolic flux control, and thermodynamics.

  8. 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

  9. Graphene cover-promoted metal-catalyzed reactions.

    PubMed

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

    2014-12-01

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

  10. Enzyme-Substrate Reactions in Very High Magnetic Fields. I

    PubMed Central

    Rabinovitch, B.; Maling, J. E.; Weissbluth, M.

    1967-01-01

    The availability of very high magnetic fields of up to 170,000 gauss made it worthwhile to pursue the search for a critical change in the rate of four enzyme substrate reactions. The four enzymes were ribonuclease, polyphenol oxidase, peroxidase, and aldolase. The experiments showed that, to within ±3%, no detectable change was observable in the rate of reaction of any of the systems for periods of exposure to the magnetic field of up to 20 min. PMID:6048870

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

    PubMed Central

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

    2012-01-01

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

  12. Eutectic salt catalyzed environmentally benign and highly efficient Biginelli reaction.

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-11-01

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

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

    PubMed

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

    2016-11-01

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

  16. The spliceosome catalyzes debranching in competition with reverse of the first chemical reaction.

    PubMed

    Tseng, Chi-Kang; Cheng, Soo-Chen

    2013-07-01

    Splicing of nuclear pre-mRNA occurs via two steps of the transesterification reaction, forming a lariat intermediate and product. The reactions are catalyzed by the spliceosome, a large ribonucleoprotein complex composed of five small nuclear RNAs and numerous protein factors. The spliceosome shares a similar catalytic core structure with that of fungal group II introns, which can self-splice using the same chemical mechanism. Like group II introns, both catalytic steps of pre-mRNA splicing can efficiently reverse on the affinity-purified spliceosome. The spliceosome also catalyzes a hydrolytic spliced-exon reopening reaction as observed in group II introns, indicating a strong link in their evolutionary relationship. We show here that, by arresting splicing after the first catalytic step, the purified spliceosome can catalyze debranching of lariat-intron-exon 2. The debranching reaction, although not observed in group II introns, has similar monovalent cation preferences as those for splicing catalysis of group II introns. The debranching reaction is in competition with the reverse Step 1 reaction influenced by the ionic environment and the structure of components binding near the catalytic center, suggesting that the catalytic center of the spliceosome can switch between different conformations to direct different chemical reactions.

  17. Copper-catalyzed borylative allyl-allyl coupling reaction.

    PubMed

    Semba, Kazuhiko; Bessho, Naoto; Fujihara, Tetsuaki; Terao, Jun; Tsuji, Yasushi

    2014-08-18

    Borylative allyl-allyl coupling using allenes, bis(pinacolato)diboron, and allyl phosphates has been developed in the presence of a copper catalyst bearing an N-heterocyclic carbene ligand. The reaction affords boryl-substituted 1,5-diene derivatives in good to high yields with high regioselectivity and Z selectivity. PMID:24986738

  18. Particle growth by acid-catalyzed heterogeneous reactions of organic carbonyls on preexisting aerosols.

    PubMed

    Jang, Myoseon; Carroll, Brian; Chandramouli, Bharadwaj; Kamens, Richard M

    2003-09-01

    Aerosol growth by the heterogeneous reactions of different aliphatic and alpha,beta-unsaturated carbonyls in the presence/absence of acidified seed aerosols was studied in a 2 m long flow reactor (2.5 cm i.d.) and a 0.5-m3 Teflon film bag under darkness. For the flow reactor experiments, 2,4-hexadienal, 5-methyl-3-hexen-2-one, 2-cyclohexenone, 3-methyl-2-cyclopentenone, 3-methyl-2-cyclohexenone, and octanal were studied. The carbonyls were selected based on their reactivity for acid-catalyzed reactions, their proton affinity, and their similarity to the ring-opening products from the atmospheric oxidation of aromatics. To facilitate acid-catalyzed heterogeneous hemiacetal/acetal formation, glycerol was injected along with inorganic seed aerosols into the flow reactor system. Carbonyl heterogeneous reactions were accelerated in the presence of acid catalysts (H2SO4), leading to higher aerosol yields than in their absence. Aldehydes were more reactive than ketones for acid-catalyzed reactions. The conjugated functionality also resulted in higher organic aerosol yieldsthan saturated aliphatic carbonyls because conjugation with the olefinic bond increases the basicity of the carbonyl leading to increased stability of the protonated carbonyl. Aerosol population was measured from a series of sampling ports along the length of the flow reactor using a scanning mobility particle sizer. Fourier transform infrared spectrometry of either an impacted liquid aerosol layer or direct reaction of carbonyls as a thin liquid layer on a zinc selenide FTIR disk was employed to demonstrate the direct transformation of chemical functional groups via the acid-catalyzed reactions. These results strongly indicate that atmospheric multifunctional organic carbonyls, which are created by atmospheric photooxidation reactions, can contribute significantly to secondary organic aerosol formation through acid-catalyzed heterogeneous reactions. Exploratory studies in 25- and 190-m3 outdoor chambers

  19. Polymer-supported siloxane transfer agents for Pd-catalyzed cross-coupling reactions.

    PubMed

    Nguyen, Minh H; Smith, Amos B

    2013-08-16

    The design, synthesis, and validation of a ring-opening metathesis polymerization (ROMP) polymer supporting siloxane transfer agents have been achieved that permit efficient palladium-catalyzed cross-coupling reactions. The solubility properties of the polymer facilitate not only product purification but also polymer recycling without significant loss of cross-coupling activity.

  20. Towards Efficient and Wide-Scope Metal-Catalyzed Alkyl-Alkyl Cross-Coupling Reactions.

    PubMed

    Cárdenas

    1999-10-18

    The simplest organic fragment, C(sp(3))-C(sp(3)), is unfortunately the most difficult to prepare by metal-catalyzed cross-coupling reactions (shown schematically) in the presence of functional groups. Recent advances show, however, that alkane moieties can be built within functionalized molecules by a careful choice of catalysts and conditions.

  1. Symmetrical bisquinolones via metal-catalyzed cross-coupling and homocoupling reactions.

    PubMed

    Hashim, Jamshed; Glasnov, Toma N; Kremsner, Jennifer M; Kappe, C Oliver

    2006-02-17

    Functionalized 4,4'-bisquinolones can be efficiently synthesized by microwave-assisted palladium(0)-catalyzed one-pot borylation/Suzuki cross-coupling reactions or via nickel(0)-mediated homocouplings of 4-chloroquinolin-2(1H)-one precursors. Both methods are also applicable to other types of symmetrical biaryls.

  2. 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.

  3. 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.

  4. Chiral holmium complex-catalyzed Diels-Alder reaction of silyloxyvinylindoles: stereoselective synthesis of hydrocarbazoles.

    PubMed

    Harada, Shinji; Morikawa, Takahiro; Nishida, Atsushi

    2013-10-18

    The catalytic and asymmetric cycloaddition between 3-[1-(silyloxy)vinyl]indoles and electron-deficient olefins gave substituted hydrocarbazoles in up to 99% yield and 94% ee. This reaction was catalyzed by a novel chiral holmium(III) complex. Alkylation of the cycloadduct gave a tricyclic compound with four continuous chiral centers, one of which was a quaternary carbon.

  5. 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

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

    PubMed

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

    2015-05-21

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

  7. Iron-Catalyzed Stereoselective Cross-Coupling Reactions of Stereodefined Enol Carbamates with Grignard Reagents.

    PubMed

    Rivera, Ana Cristina Parra; Still, Raymond; Frantz, Doug E

    2016-06-01

    A practical and highly stereoselective iron-catalyzed cross-coupling reaction of stereodefined enol carbamates and Grignard reagents to yield tri- and tetrasubstituted acrylates is reported. A facile method for the stereoselective generation of these enol carbamates has also been developed. PMID:27088754

  8. Pd-catalyzed cascade allylic alkylation and dearomatization reactions of indoles with vinyloxirane.

    PubMed

    Gao, Run-Duo; Xu, Qing-Long; Dai, Li-Xin; You, Shu-Li

    2016-09-14

    We have developed Pd-catalyzed intermolecular Friedel-Crafts-type allylic alkylation and allylic dearomatization reactions of substituted indoles bearing a nucleophilic group with vinyloxirane, providing an efficient method to synthesize structurally diverse tetrahydrocarboline and spiroindolenine derivatives under mild conditions. PMID:27511802

  9. Enantioselective [2 + 2 + 2] cycloaddition reaction of isocyanates and allenes catalyzed by nickel.

    PubMed

    Miura, Tomoya; Morimoto, Masao; Murakami, Masahiro

    2010-11-17

    The enantioselective intermolecular [2 + 2 + 2] cycloaddition reaction of two molecules of isocyanate and one molecule of allene is catalyzed by a nickel(0)/(S,S)-i-Pr-FOXAP complex, providing an efficient access to enantiomerically enriched dihydropyrimidine-2,4-diones.

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

    PubMed

    Liu, Qifan; Wang, Weigang; Ge, Maofa

    2015-05-01

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

  11. Enzyme-free amplification for sensitive electrochemical detection of DNA via target-catalyzed hairpin assembly assisted current change.

    PubMed

    Qian, Yong; Wang, Chunyan; Gao, Fenglei

    2014-12-01

    An isothermal, enzyme-free and sensitive method for electrochemical detection of DNA is proposed based on target catalyzed hairpin assembly and for signal amplification. Molecular beacon 1 (MB1) contains a ferrocene (Fc) tag, which was immobilized on the gold electrode as recognition probe to hybridize with target DNA. Then, molecular beacon 2 hybridized with the opened MB1, allowing the target to be displaced. The displaced target again triggered the next round of strand exchange reaction resulting in many Fc far away from the GE to achieve signal amplification for sensitive DNA detection. The current signal amplification strategy is relatively simple and inexpensive owing to avoid the use of any kind of enzyme or sophisticated equipment. It can achieve a sensitivity of 42 fM with a wide linear dynamic range from 10(-13) to 10(-9)M and discriminate mismatched DNA from perfect matched target DNA with a high selectivity. The proposed method showed excellent specificity, high sensitivity and low detection limit, and could be applied in analysis of real samples.

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

    PubMed

    Nguyen, Minh H; Smith, Amos B

    2014-04-01

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

  13. Enantioselective aldol reaction between isatins and cyclohexanone catalyzed by amino acid sulphonamides.

    PubMed

    Wang, Jun; Liu, Qi; Hao, Qing; Sun, Yanhua; Luo, Yiming; Yang, Hua

    2015-04-01

    Sulphonamides derived from primary α-amino acid were successfully applied to catalyze the aldol reaction between isatin and cyclohexanone under neat conditions. More interestingly, molecular sieves, as privileged additives, were found to play a vital role in achieving high enantioselectivity. Consequently, high yields (up to 99%) along with good enantioselectivities (up to 92% ee) and diastereoselectivities (up to 95:5 dr) were obtained. In addition, this reaction was also conveniently scaled up, demonstrating the applicability of this protocol.

  14. Advances in metal-catalyzed cross-coupling reactions of halogenated quinazolinones and their quinazoline derivatives.

    PubMed

    Mphahlele, Malose Jack; Maluleka, Marole Maria

    2014-10-29

    Halogenated quinazolinones and quinazolines are versatile synthetic intermediates for the metal-catalyzed carbon-carbon bond formation reactions such as the Kumada, Stille, Negishi, Sonogashira, Suzuki-Miyaura and Heck cross-coupling reactions or carbon-heteroatom bond formation via the Buchwald-Hartwig cross-coupling to yield novel polysubstituted derivatives. This review presents an overview of the application of these methods on halogenated quinazolin-4-ones and their quinazolines to generate novel polysubstituted derivatives.

  15. Gold-catalyzed Hosomi-Sakurai type reaction for the total synthesis of herboxidiene.

    PubMed

    Thirupathi, Barla; Mohapatra, Debendra K

    2016-07-14

    Total synthesis of herboxidiene/GEX1A/TAN-1609 has been accomplished in the 22 longest linear sequences starting from 2-butyne-1,4-diol following our recently developed gold-catalyzed Hosomi-Sakurai type of reaction on lactols with allyltrimethyl silane and Stille cross coupling to assemble the advanced fragment. The synthesis of the C10-C19 fragment was accomplished by means of Sharpless epoxidation and asymmetric alkylation reactions starting from (R)-methyl lactate. PMID:27193332

  16. Recyclable Polystyrene-Supported Siloxane-Transfer Agent for Palladium-Catalyzed Cross-Coupling Reactions

    PubMed Central

    2015-01-01

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

  17. Monitoring of Eco RI-catalyzed cleavage reaction of fluorescent-labeled heterochiral DNA.

    PubMed

    Urata, Hidehito; Tamaki, Chihiro; Matsuno, Miki; Wada, Shun-Ichi; Akagi, Masao

    2007-01-01

    We have found the unusual reactivity of a heterochiral oligodeoxynucleotide toward restriction endonuclease Eco RI. To conduct the kinetic analysis of the reaction, fluorescent-labeled single-stranded oligodeoxynucleotide molecular beacons were designed and synthesized. The beacons showed a remarkable fluorescence response by addition of Eco RI. The results promise that the beacon could be an effective tool for the kinetic analysis of Eco RI-catalyzed cleavage reaction of the heterochiral oligodeoxynucleotide.

  18. Thiourea-catalyzed enantioselective iso-Pictet-Spengler reactions.

    PubMed

    Lee, Yunmi; Klausen, Rebekka S; Jacobsen, Eric N

    2011-10-21

    A one-pot condensation of isotryptamines and aldehydes that affords enantiomerically enriched 4-substituted tetrahydro-γ-carbolines is reported. The reaction is induced by a chiral thiourea/benzoic acid dual catalyst system. Purification of the N-Boc-protected products by trituration or crystallization provides the optically pure tetrahydro-γ-carboline derivatives in a scalable and highly practical procedure. PMID:21919478

  19. Cobalt(III) porphyrin catalyzed aza-Diels-Alder reaction.

    PubMed

    Wakabayashi, Ryota; Kurahashi, Takuya; Matsubara, Seijiro

    2012-09-21

    An efficient protocol for the aza-Diels-Alder reaction of electron-deficient 1,3-dienes with unactivated imines in the presence of a cationic cobalt(III) porphyrin complex was developed. The transformation proceeded smoothly to afford the desired piperidine scaffold within 2 h at ambient temperature. Highly chemoselective cycloaddition of imines with dienes in the presence of a variety of carbonyl compounds was also demonstrated.

  20. 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

  1. Secondary alkyl halides in transition-metal-catalyzed cross-coupling reactions.

    PubMed

    Rudolph, Alena; Lautens, Mark

    2009-01-01

    Enormous effort has gone into the development of metal-catalyzed cross-coupling reactions with alkyl halides as electrophilic coupling partners. Whereas a wide array of primary alkyl halides can now be used effectively in cross-coupling reactions, the synthetic potential of secondary alkyl halides is just beginning to be revealed. This Minireview summarizes selected examples of the use of secondary alkyl halides as electrophiles in cross-coupling reactions. Emphasis is placed on the transition metals employed, the mechanistic pathways involved, and implications in terms of the stereochemical outcome of reactions.

  2. Palladium-Catalyzed Alkene Carboamination Reactions of Electron-Poor Nitrogen Nucleophiles

    PubMed Central

    Peterson, Luke J.

    2015-01-01

    Modified reaction conditions that facilitate Pd-catalyzed alkene carboamination reactions of electron-deficient nitrogen nucleophiles are reported. Pent-4-enylamine derivatives bearing N-tosyl or N-trifluoroacetyl groups are coupled with aryl triflates to afford substituted pyrrolidines in good yield. These reactions proceed via a mechanism involving anti-aminopalladation of the alkene, which differs from previously reported analogous reactions of N-aryl and N-boc pentenylamines. The application of these conditions to a formal synthesis of (±)-aphanorphine is also described. PMID:26622222

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

    PubMed Central

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

    2014-01-01

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

  4. Ligand-controlled access to [4 + 2] and [4 + 3] cycloadditions in gold-catalyzed reactions of allene-dienes.

    PubMed

    Mauleón, Pablo; Zeldin, Rachel M; González, Ana Z; Toste, F Dean

    2009-05-13

    By adjustment of the electronic properties of the ancilliary ligands, high selectivity can be achieved for either [4 + 2] or [4 + 3] cycloaddition reactions of allene-dienes catalyzed by gold(I). Triarylphosphitegold(I) complexes are employed as catalysts for a [4 + 2] cycloaddition reaction leading to alkylidenecyclohexenes. Conversely, di-tert-butylbiphenylphosphinegold(I)-catalyzed reactions afford cycloheptadienes via [4 + 3] cycloaddition reactions.

  5. Odorant metabolism catalyzed by olfactory mucosal enzymes influences peripheral olfactory responses in rats.

    PubMed

    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

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

    PubMed Central

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

    2007-01-01

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

  7. First principle kinetic studies of zeolite-catalyzed methylation reactions.

    PubMed

    Van Speybroeck, Veronique; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Lesthaeghe, David; Ghysels, An; Marin, Guy B; Waroquier, Michel

    2011-02-01

    Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational techniques, to derive Arrhenius plots and rate constants from first principles that can directly be compared with the experimental data. For these key elementary reactions in the methanol to hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115-123; J. Catal.2005, 234, 385-400]. At 350 °C, apparent activation energies of 103, 69, and 45 kJ/mol and rate constants of 2.6 × 10(-4), 4.5 × 10(-3), and 1.3 × 10(-2) mol/(g h mbar) for ethene, propene, and butene were derived, giving following relative ratios for methylation k(ethene)/k(propene)/k(butene) = 1:17:50. In this work, rate constants including pre-exponential factors are calculated which give very good agreement with the experimental data: apparent activation energies of 94, 62, and 37 kJ/mol for ethene, propene, and butene are found, and relative ratios of methylation k(ethene)/k(propene)/k(butene) = 1:23:763. The entropies of gas phase alkenes are underestimated in the harmonic oscillator approximation due to the occurrence of internal rotations. These low vibrational modes were substituted by manually constructed partition functions. Overall, the absolute reaction rates can be calculated with near chemical accuracy, and qualitative trends are very well reproduced. In addition, the proposed scheme is computationally very efficient and constitutes significant progress in kinetic modeling of reactions in heterogeneous catalysis.

  8. Module degradation catalyzed by metal-encapsulation reactions

    NASA Technical Reports Server (NTRS)

    Gallagher, B. D.

    1983-01-01

    Four major properties are considered to be relevant in determining service life of a photovoltaic module: (1) Mechanical: creep resistance, modulus, tensile strength; (2) Optical: integrated transmission at 0.4 to 1.1 m wavelength; (3) Chemical: inertness with respect to metals and other components, retention of stabilizers, etc. and (4) Electrical; maintaining effective isolation of conductive components. These properties were measured after exposing polymer specimens to three types of accelerated stress: thermal, ultraviolet radiation and metal catalysts. These conditions give rise to a large number of complex interrelated free-radical reactions that result in the deterioration of polymeric materials.

  9. Characterization of Enzymes Catalyzing Transformations of Cysteine S-Conjugated Intermediates in the Lincosamide Biosynthetic Pathway.

    PubMed

    Ushimaru, Richiro; Lin, Chia-I; Sasaki, Eita; Liu, Hung-Wen

    2016-09-01

    Lincosamides such as lincomycin A, celesticetin, and Bu-2545, constitute an important group of antibiotics. These natural products are characterized by a thiooctose linked to a l-proline residue, but they differ with regards to modifications of the thioacetal moiety, the pyrrolidine ring, and the octose core. Here we report that the pyridoxal 5'-phosphate-dependent enzyme CcbF (celesticetin biosynthetic pathway) is a decarboxylating deaminase that converts a cysteine S-conjugated intermediate into an aldehyde. In contrast, the homologous enzyme LmbF (lincomycin biosynthetic pathway) catalyzes C-S bond cleavage of the same intermediate to afford a thioglycoside. We show that Ccb4 and LmbG (downstream methyltransferases) convert the aldehyde and thiol intermediates into a variety of methylated lincosamide compounds including Bu-2545. The substrates used in these studies are the β-anomers of the natural substrates. The findings not only provide insight into how the biosynthetic pathway of lincosamide antibiotics can bifurcate to generate different lincosamides, but also reveal the promiscuity of the enzymes involved. PMID:27431934

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed Central

    Fornwald, Ryan M.; Fritz, Jonathan A.

    2014-01-01

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

  12. Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.

    PubMed

    Martí-Arbona, Ricardo; Fresquet, Vicente; Thoden, James B; Davis, Melissa L; Holden, Hazel M; Raushel, Frank M

    2005-05-17

    Isoaspartyl dipeptidase (IAD) is a member of the amidohydrolase superfamily and catalyzes the hydrolytic cleavage of beta-aspartyl dipeptides. Structural studies of the wild-type enzyme have demonstrated that the active site consists of a binuclear metal center positioned at the C-terminal end of a (beta/alpha)(8)-barrel domain. Steady-state kinetic parameters for the hydrolysis of beta-aspartyl dipeptides were obtained at pH 8.1. The pH-rate profiles for the hydrolysis of beta-Asp-Leu were obtained for the Zn/Zn-, Co/Co-, Ni/Ni-, and Cd/Cd-substituted forms of IAD. Bell-shaped profiles were observed for k(cat) and k(cat)/K(m) as a function of pH for all four metal-substituted forms. The pK(a) of the group that must be unprotonated for catalytic activity varied according to the specific metal ion bound in the active site, whereas the pK(a) of the group that must be protonated for catalytic activity was relatively independent of the specific metal ion present. The identity of the group that must be unprotonated for catalytic activity was consistent with the hydroxide that bridges the two divalent cations of the binuclear metal center. The identity of the group that must be protonated for activity was consistent with the free alpha-amino group of the dipeptide substrate. Kinetic constants were obtained for the mutant enzymes at conserved residues Glu77, Tyr137, Arg169, Arg233, Asp285, and Ser289. The catalytic properties of the wild-type and mutant enzymes, coupled with the X-ray crystal structure of the D285N mutant complexed with beta-Asp-His, are consistent with a chemical reaction mechanism for the hydrolysis of dipeptides that is initiated by the polarization of the amide bond via complexation to the beta-metal ion of the binuclear metal center. Nucleophilic attack by the bridging hydroxide is facilitated by abstraction of its proton by the side chain carboxylate of Asp285. Collapse of the tetrahedral intermediate and cleavage of the carbon-nitrogen bond occur

  13. Forward design of a complex enzyme cascade reaction

    NASA Astrophysics Data System (ADS)

    Hold, Christoph; Billerbeck, Sonja; Panke, Sven

    2016-09-01

    Enzymatic reaction networks are unique in that one can operate a large number of reactions under the same set of conditions concomitantly in one pot, but the nonlinear kinetics of the enzymes and the resulting system complexity have so far defeated rational design processes for the construction of such complex cascade reactions. Here we demonstrate the forward design of an in vitro 10-membered system using enzymes from highly regulated biological processes such as glycolysis. For this, we adapt the characterization of the biochemical system to the needs of classical engineering systems theory: we combine online mass spectrometry and continuous system operation to apply standard system theory input functions and to use the detailed dynamic system responses to parameterize a model of sufficient quality for forward design. This allows the facile optimization of a 10-enzyme cascade reaction for fine chemical production purposes.

  14. Forward design of a complex enzyme cascade reaction

    PubMed Central

    Hold, Christoph; Billerbeck, Sonja; Panke, Sven

    2016-01-01

    Enzymatic reaction networks are unique in that one can operate a large number of reactions under the same set of conditions concomitantly in one pot, but the nonlinear kinetics of the enzymes and the resulting system complexity have so far defeated rational design processes for the construction of such complex cascade reactions. Here we demonstrate the forward design of an in vitro 10-membered system using enzymes from highly regulated biological processes such as glycolysis. For this, we adapt the characterization of the biochemical system to the needs of classical engineering systems theory: we combine online mass spectrometry and continuous system operation to apply standard system theory input functions and to use the detailed dynamic system responses to parameterize a model of sufficient quality for forward design. This allows the facile optimization of a 10-enzyme cascade reaction for fine chemical production purposes. PMID:27677244

  15. 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, α-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

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

    PubMed

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

    2016-02-01

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

  17. 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 α,β-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

  18. 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 π radical ferryl intermediate known as Compound I (CpdI) (Por•+FeIV=O), or its ferryl radical resonance form (FeIV-O•). CYP-mediated hydroxylations occur via a consensus H atom abstraction/oxygen rebound mechanism involving an initial abstraction by CpdI of a H atom from the substrate, generating a highly-reactive protonated Compound II (CpdII) intermediate (FeIV-OH) and a carbon-centered alkyl radical that rebounds onto the ferryl hydroxyl moiety to yield the hydroxylated substrate. CYP enzymes utilize hydroperoxides, peracids, perborate, percarbonate, periodate, chlorite, iodosobenzene and N-oxides as surrogate oxygen atom donors to oxygenate substrates via the shunt pathway in the absence of NAD(P)H/O2 and reduction-oxidation (redox) auxiliary proteins. It has been difficult to isolate the historically elusive CpdI intermediate in the native NAD(P)H/O2-supported monooxygenase pathway and to determine its precise electronic structure and kinetic and physicochemical properties because of its high reactivity, unstable nature (t½~2 ms) and short life cycle, prompting suggestions for participation in monooxygenation reactions of alternative CYP iron-oxygen intermediates such as the ferric-peroxo anion species (FeIII-OO-), ferric-hydroperoxo species (FeIII-OOH) and FeIII-(H2O2) complex.

  19. Hydroconversion reactions catalyzed by highly stable pillared clays

    SciTech Connect

    Gomez, S.A.; Mosqueira, L.; Espinosa, J.; Fuentes, G.A.

    1993-12-31

    Al-pillared clays (Al-PILC) and Al-X-PILC (X = Ga, Ni), structurally stable at high temperature - in the case of Ga above 800{degrees}C-have been synthesized by controlling intercalation steps and stabilization procedures. New bidimensional materials with an interlaminar distance about 10-12{angstrom} and with different chemical reactivities in the pillars have thus been produced. The analytical techniques employed to characterize the materials and the processes involved during stabilization include N{sub 2} adsorption, AA, XRD, NH{sub 3}-TPD, TGA-DTA, HR- and MAS-NMR (Al, Si, and Ga) and in-situ IR and DRIFTS. Chemical characterization using high pressure reactions with probe molecules such as diphenylmethane and tert-butylbenzene shows selectivity patterns than can be clearly associated with the microstructure of the PILC used, as well as an effect due to the composition of the pillars. Similar studies with zeolites give patterns that differ from those of PILC, probably because of the change in dimensionality of the internal structure. Poisoning studies with metal porphyrins prove that PLIC have improved resistance compared to standard catalysts. Hydrotreatment of Maya crude results a significant reduction in total sulfur under conditions suitable for commercial operation.

  20. 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

  1. Conversion of aminodeoxychorismate synthase into anthranilate synthase with Janus mutations: mechanism of pyruvate elimination catalyzed by chorismate enzymes.

    PubMed

    Culbertson, Justin E; Chung, Dong hee; Ziebart, Kristin T; Espiritu, Eduardo; Toney, Michael D

    2015-04-14

    The central importance of chorismate enzymes in bacteria, fungi, parasites, and plants combined with their absence in mammals makes them attractive targets for antimicrobials and herbicides. Two of these enzymes, anthranilate synthase (AS) and aminodeoxychorismate synthase (ADCS), are structurally and mechanistically similar. The first catalytic step, amination at C2, is common between them, but AS additionally catalyzes pyruvate elimination, aromatizing the aminated intermediate to anthranilate. Despite prior attempts, the conversion of a pyruvate elimination-deficient enzyme into an elimination-proficient one has not been reported. Janus, a bioinformatics method for predicting mutations required to functionally interconvert homologous enzymes, was employed to predict mutations to convert ADCS into AS. A genetic selection on a library of Janus-predicted mutations was performed. Complementation of an AS-deficient strain of Escherichia coli grown on minimal medium led to several ADCS mutants that allow growth in 6 days compared to 2 days for wild-type AS. The purified mutant enzymes catalyze the conversion of chorismate to anthranilate at rates that are ∼50% of the rate of wild-type ADCS-catalyzed conversion of chorismate to aminodeoxychorismate. The residues mutated do not contact the substrate. Molecular dynamics studies suggest that pyruvate elimination is controlled by the conformation of the C2-aminated intermediate. Enzymes that catalyze elimination favor the equatorial conformation, which presents the C2-H to a conserved active site lysine (Lys424) for deprotonation and maximizes stereoelectronic activation. Acid/base catalysis of pyruvate elimination was confirmed in AS and salicylate synthase by showing incorporation of a solvent-derived proton into the pyruvate methyl group and by solvent kinetic isotope effects on pyruvate elimination catalyzed by AS. PMID:25710100

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

    PubMed

    Dubbaka, Srinivas Reddy; Vogel, Pierre

    2005-12-01

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

  3. Enantioselective Synthesis of Spirocyclohexadienones by NHC-Catalyzed Formal [3+3] Annulation Reaction of Enals.

    PubMed

    Yetra, Santhivardhana Reddy; Mondal, Santigopal; Mukherjee, Subrata; Gonnade, Rajesh G; Biju, Akkattu T

    2016-01-01

    The enantioselective synthesis of pyrazolone-fused spirocyclohexadienones was demonstrated by the reaction of α,β-unsaturated aldehydes with α-arylidene pyrazolinones under oxidative N-heterocyclic carbene (NHC)catalysis. This atom-economic and formal [3+3] annulation reaction proceeds through a vinylogous Michael addition/spiroannulation/dehydrogenation cascade to afford spirocyclic compounds with an all-carbon quaternary stereocenter in moderate to good yields and excellent ee values. Key to the success of the reaction is the cooperative NHC-catalyzed generation of chiral α,β-unsaturated acyl azoliums from enals, and base-mediated tandem generation of dienolate/enolate intermediates from pyrazolinones. PMID:26487242

  4. Lewis Acid Catalyzed Selective Reactions of Donor-Acceptor Cyclopropanes with 2-Naphthols.

    PubMed

    Kaicharla, Trinadh; Roy, Tony; Thangaraj, Manikandan; Gonnade, Rajesh G; Biju, Akkattu T

    2016-08-16

    Lewis acid-catalyzed reactions of 2-substituted cyclopropane 1,1-dicarboxylates with 2-naphthols is reported. The reaction exhibits tunable selectivity depending on the nature of Lewis acid employed and proceed as a dearomatization/rearomatization sequence. With Bi(OTf)3 as the Lewis acid, a highly selective dehydrative [3+2] cyclopentannulation takes place leading to the formation of naphthalene-fused cyclopentanes. Interestingly, engaging Sc(OTf)3 as the Lewis acid, a Friedel-Crafts-type addition of 2-naphthols to cyclopropanes takes place, thus affording functionalized 2-naphthols. Both reactions furnished the target products in high regioselectivity and moderate to high yields. PMID:27391792

  5. Study of the mechanism of muon-catalyzed t + t fusion reaction

    SciTech Connect

    Bogdanova, L. N.; Demin, D. L.; Filchenkov, V. V.

    2015-01-15

    The mechanism for the muon catalyzed fusion reaction t + t → {sup 4}He + 2n + 11.33 MeV is investigated. The model of the cascade reaction with {sup 5}He as an intermediate state is considered, both the ground and the first exited states being taken into account. The neutron energy spectrum measured in the recent experiment is compared with the Monte-Carlo-simulated one. Varying reaction parameters, we obtain optimum values for the relative weights of the {sup 5}He ground and excited states and for the excitation energy and width of the excited state.

  6. Enantioselective Multicomponent Condensation Reactions of Phenols, Aldehydes, and Boronates Catalyzed by Chiral Biphenols.

    PubMed

    Barbato, Keith S; Luan, Yi; Ramella, Daniele; Panek, James S; Schaus, Scott E

    2015-12-01

    Chiral diols and biphenols catalyze the multicomponent condensation reaction of phenols, aldehydes, and alkenyl or aryl boronates. The condensation products are formed in good yields and enantioselectivities. The reaction proceeds via an initial Friedel-Crafts alkylation of the aldehyde and phenol to yield an ortho-quinone methide that undergoes an enantioselective boronate addition. A cyclization pathway was discovered while exploring the scope of the reaction that provides access to chiral 2,4-diaryl chroman products, the core of which is a structural motif found in natural products. PMID:26576776

  7. Peroxygenase-Catalyzed Oxyfunctionalization Reactions Promoted by the Complete Oxidation of Methanol.

    PubMed

    Ni, Yan; Fernández-Fueyo, Elena; Gomez Baraibar, Alvaro; Ullrich, René; Hofrichter, Martin; Yanase, Hideshi; Alcalde, Miguel; van Berkel, Willem J H; Hollmann, Frank

    2016-01-11

    Peroxygenases catalyze a broad range of (stereo)selective oxyfunctionalization reactions. However, to access their full catalytic potential, peroxygenases need a balanced provision of hydrogen peroxide to achieve high catalytic activity while minimizing oxidative inactivation. Herein, we report an enzymatic cascade process that employs methanol as a sacrificial electron donor for the reductive activation of molecular oxygen. Full oxidation of methanol is achieved, generating three equivalents of hydrogen peroxide that can be used completely for the stereoselective hydroxylation of ethylbenzene as a model reaction. Overall we propose and demonstrate an atom-efficient and easily applicable alternative to established hydrogen peroxide generation methods, which enables the efficient use of peroxygenases for oxyfunctionalization reactions.

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

    PubMed

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

    2016-03-18

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

  9. Biochemical and Molecular Characterization of Phenylacetate-Coenzyme A Ligase, an Enzyme Catalyzing the First Step in Aerobic Metabolism of Phenylacetic Acid in Azoarcus evansii

    PubMed Central

    El-Said Mohamed, Magdy

    2000-01-01

    Phenylacetate-coenzyme A ligase (PA-CoA ligase; AMP forming, EC 6.2.1.30), the enzyme catalyzing the first step in the aerobic degradation of phenylacetate (PA) in Azoarcus evansii, has been purified and characterized. The gene (paaK) coding for this enzyme was cloned and sequenced. The enzyme catalyzes the reaction of PA with CoA and MgATP to yield phenylacetyl-CoA (PACoA) plus AMP plus PPi. The enzyme was specifically induced after aerobic growth in a chemically defined medium containing PA or phenylalanine (Phe) as the sole carbon source. Growth with 4-hydroxyphenylacetate, benzoate, adipate, or acetate did not induce the synthesis of this enzyme. This enzymatic activity was detected very early in the exponential phase of growth, and a maximal specific activity of 76 nmol min−1 mg of cell protein−1 was measured. After 117-fold purification to homogeneity, a specific activity of 48 μmol min−1 mg of protein−1 was achieved with a turnover number (catalytic constant) of 40 s−1. The protein is a monomer of 52 kDa and shows high specificity towards PA; other aromatic or aliphatic acids were not used as substrates. The apparent Km values for PA, ATP, and CoA were 14, 60, and 45 μM, respectively. The PA-CoA ligase has an optimum pH of 8 to 8.5 and a pI of 6.3. The enzyme is labile and requires the presence of glycerol for stabilization. The N-terminal amino acid sequence of the purified protein showed no homology with other reported PA-CoA ligases. The gene encoding this enzyme is 1,320 bp long and codes for a protein of 48.75 kDa (440 amino acids) which shows high similarity with other reported PA-CoA ligases. An amino acid consensus for an AMP binding motif (VX2SSGTTGXP) was identified. The biochemical and molecular characteristics of this enzyme are quite different from those of the isoenzyme catalyzing the same reaction under anaerobic conditions in the same bacterium. PMID:10629172

  10. Spectral and kinetic characterization of intermediates in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.

    PubMed

    Bruckner, Robert C; Jorns, Marilyn Schuman

    2009-06-01

    The flavoenzyme nikD, a 2-electron acceptor, catalyzes a remarkable aromatization of piperideine-2-carboxylate (P2C) to picolinate, an essential component of nikkomycin antibiotics. Steady-state kinetic data are indicative of a sequential mechanism where oxygen reacts with a reduced enzyme.dihydropicolinate (DHP) complex. The kinetics observed for complex formation with competitive inhibitors are consistent with a one-step binding mechanism. The anaerobic reaction with P2C involves three steps. The first step yields an enzyme.substrate charge transfer complex likely to contain the electron-rich P2C enamine. Calculated rates of formation and dissociation of the nikD.P2C complex are similar to those observed for the enzyme.1-cyclohexenoate complex. Formation of a reduced enzyme.DHP complex, (EH(2).DHP)(ini), occurs in a second step that exhibits a hyperbolic dependence on substrate concentration. The limiting rate of nikD reduction is at least 10-fold faster than the turnover rate observed with unlabeled or [4,4,5,5,6,6-D(6)]-P2C and exhibits a kinetic isotope effect (KIE = 6.4). The observed KIE on K(d apparent) (4.7) indicates that P2C is a sticky substrate. Formation of a final reduced species, (EH(2).DHP)(fin), occurs in a third step that is independent of P2C concentration and equal to the observed turnover rate. The observed KIE (3.3) indicates that the final step involves cleavage of at least one C-H bond. Tautomerization, followed by isomerization, of the initial DHP intermediate can produce an isomer that could be oxidized to picolinate in a reaction that satisfies known steric constraints of flavoenzyme reactions without the need to reposition a covalently tethered flavin or tightly bound intermediate.

  11. Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme

    PubMed Central

    Zhou, Jing-Min; Zhou, De-Min; Takagi, Yasuomi; Kasai, Yasuhiro; Inoue, Atsushi; Baba, Tadashi; Taira, Kazunari

    2002-01-01

    The hammerhead ribozyme is generally accepted as a well characterized metalloenzyme. However, the precise nature of the interactions of the RNA with metal ions remains to be fully defined. Examination of metal ion-catalyzed hammerhead reactions at limited concentrations of metal ions is useful for evaluation of the role of metal ions, as demonstrated in this study. At concentrations of Mn2+ ions from 0.3 to 3 mM, addition of the ribozyme to the reaction mixture under single-turnover conditions enhances the reaction with the product reaching a fixed maximum level. Further addition of the ribozyme inhibits the reaction, demonstrating that a certain number of divalent metal ions is required for proper folding and also for catalysis. At extremely high concentrations, monovalent ions, such as Na+ ions, can also serve as cofactors in hammerhead ribozyme-catalyzed reactions. However, the catalytic efficiency of monovalent ions is extremely low and, thus, high concentrations are required. Furthermore, addition of monovalent ions to divalent metal ion-catalyzed hammerhead reactions inhibits the divalent metal ion-catalyzed reactions, suggesting that the more desirable divalent metal ion–ribozyme complexes are converted to less desirable monovalent metal ion–ribozyme complexes via removal of divalent metal ions, which serve as a structural support in the ribozyme complex. Even though two channels appear to exist, namely an efficient divalent metal ion-catalyzed channel and an inefficient monovalent metal ion-catalyzed channel, it is clear that, under physiological conditions, hammerhead ribozymes are metalloenzymes that act via the significantly more efficient divalent metal ion-dependent channel. Moreover, the observed kinetic data are consistent with Lilley’s and DeRose’s two-phase folding model that was based on ground state structure analyses. PMID:12034824

  12. Enzyme-catalyzed formation of beta-peptides: beta-peptidyl aminopeptidases BapA and DmpA acting as beta-peptide-synthesizing enzymes.

    PubMed

    Heck, Tobias; Kohler, Hans-Peter E; Limbach, Michael; Flögel, Oliver; Seebach, Dieter; Geueke, Birgit

    2007-09-01

    In recent studies, we discovered that the three beta-peptidyl aminopeptidases, BapA from Sphingosinicella xenopeptidilytica 3-2W4, BapA from S. microcystinivorans Y2, and DmpA from Ochrobactrum anthropi LMG7991, possess the unique feature of cleaving N-terminal beta-amino acid residues from beta- and alpha/beta-peptides. Herein, we investigated the use of the same three enzymes for the reverse reaction catalyzing the oligomerization of beta-amino acids and the synthesis of mixed peptides with N-terminal beta-amino acid residues. As substrates, we employed the beta-homoamino acid derivatives H-beta hGly-pNA, H-beta3 hAla-pNA, H-(R)-beta3 hAla-pNA, H-beta3 hPhe-pNA, H-(R)-beta3 hPhe-pNA, and H-beta3 hLeu-pNA. All three enzymes were capable of coupling the six beta-amino acids to oligomers with chain lengths of up to eight amino acid residues. With the enzyme DmpA as the catalyst, we observed very high conversion rates, which correspond to dimer yields of up to 76%. The beta-dipeptide H-beta3 hAla-beta3 hLeu-OH and the beta/alpha-dipeptide H-beta hGly-His-OH (carnosine) were formed with almost 50% conversion, when a five-fold excess of beta3-homoleucine or histidine was incubated with H-beta3 hAla-pNA and H-beta hGly-pNA, respectively, in the presence of the enzyme BapA from S. microcystinivorans Y2. BapA from S. xenopeptidilytica 3-2W4 turned out to be a versatile catalyst capable of coupling various beta-amino acid residues to the free N-termini of beta- and alpha-amino acids and even to an alpha-tripeptide. Thus, these aminopeptidases might be useful to introduce a beta-amino acid residue as an N-terminal protecting group into a 'natural' alpha-peptide, thereby stabilizing the peptide against degradation by other proteolytic enzymes. PMID:17886858

  13. Enzyme-catalyzed formation of beta-peptides: beta-peptidyl aminopeptidases BapA and DmpA acting as beta-peptide-synthesizing enzymes.

    PubMed

    Heck, Tobias; Kohler, Hans-Peter E; Limbach, Michael; Flögel, Oliver; Seebach, Dieter; Geueke, Birgit

    2007-09-01

    In recent studies, we discovered that the three beta-peptidyl aminopeptidases, BapA from Sphingosinicella xenopeptidilytica 3-2W4, BapA from S. microcystinivorans Y2, and DmpA from Ochrobactrum anthropi LMG7991, possess the unique feature of cleaving N-terminal beta-amino acid residues from beta- and alpha/beta-peptides. Herein, we investigated the use of the same three enzymes for the reverse reaction catalyzing the oligomerization of beta-amino acids and the synthesis of mixed peptides with N-terminal beta-amino acid residues. As substrates, we employed the beta-homoamino acid derivatives H-beta hGly-pNA, H-beta3 hAla-pNA, H-(R)-beta3 hAla-pNA, H-beta3 hPhe-pNA, H-(R)-beta3 hPhe-pNA, and H-beta3 hLeu-pNA. All three enzymes were capable of coupling the six beta-amino acids to oligomers with chain lengths of up to eight amino acid residues. With the enzyme DmpA as the catalyst, we observed very high conversion rates, which correspond to dimer yields of up to 76%. The beta-dipeptide H-beta3 hAla-beta3 hLeu-OH and the beta/alpha-dipeptide H-beta hGly-His-OH (carnosine) were formed with almost 50% conversion, when a five-fold excess of beta3-homoleucine or histidine was incubated with H-beta3 hAla-pNA and H-beta hGly-pNA, respectively, in the presence of the enzyme BapA from S. microcystinivorans Y2. BapA from S. xenopeptidilytica 3-2W4 turned out to be a versatile catalyst capable of coupling various beta-amino acid residues to the free N-termini of beta- and alpha-amino acids and even to an alpha-tripeptide. Thus, these aminopeptidases might be useful to introduce a beta-amino acid residue as an N-terminal protecting group into a 'natural' alpha-peptide, thereby stabilizing the peptide against degradation by other proteolytic enzymes.

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

    PubMed

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

    2010-01-01

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

  15. 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

  16. Evidence for the formation of an enamine species during aldol and Michael-type addition reactions promiscuously catalyzed by 4-oxalocrotonate tautomerase.

    PubMed

    Poddar, Harshwardhan; Rahimi, Mehran; Geertsema, Edzard M; Thunnissen, Andy-Mark W H; Poelarends, Gerrit J

    2015-03-23

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which has a catalytic N-terminal proline residue (Pro1), can promiscuously catalyze various carbon-carbon bond-forming reactions, including aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde, and Michael-type addition of acetaldehyde to a wide variety of nitroalkenes to yield valuable γ-nitroaldehydes. To gain insight into how 4-OT catalyzes these unnatural reactions, we carried out exchange studies in D2 O, and X-ray crystallography studies. The former established that H-D exchange within acetaldehyde is catalyzed by 4-OT and that the Pro1 residue is crucial for this activity. The latter showed that Pro1 of 4-OT had reacted with acetaldehyde to give an enamine species. These results provide evidence of the mechanism of the 4-OT-catalyzed aldol and Michael-type addition reactions in which acetaldehyde is activated for nucleophilic addition by Pro1-dependent formation of an enamine intermediate.

  17. Envisioning an enzymatic Diels-Alder reaction by in situ acid-base catalyzed diene generation.

    PubMed

    Linder, Mats; Johansson, Adam Johannes; Manta, Bianca; Olsson, Philip; Brinck, Tore

    2012-06-01

    We present and evaluate a new and potentially efficient route for enzyme-mediated Diels-Alder reactions, utilizing general acid-base catalysis. The viability of employing the active site of ketosteroid isomerase is demonstrated.

  18. A General Palladium-Catalyzed Hiyama Cross-Coupling Reaction of Aryl and Heteroaryl Chlorides.

    PubMed

    Yuen, On Ying; So, Chau Ming; Man, Ho Wing; Kwong, Fuk Yee

    2016-05-01

    A general palladium-catalyzed Hiyama cross-coupling reaction of aryl and heteroaryl chlorides with aryl and heteroaryl trialkoxysilanes by a Pd(OAc)2 /L2 catalytic system is presented. A newly developed water addition protocol can dramatically improve the product yields. The conjugation of the Pd/L2 system and the water addition protocol can efficiently catalyze a broad range of electron-rich, -neutral, -deficient, and sterically hindered aryl chlorides and heteroaryl chlorides with excellent yields within three hours and the catalyst loading can be down to 0.05 mol % Pd for the first time. Hiyama coupling of heteroaryl chlorides with heteroaryl silanes is also reported for the first time. The reaction can be easily scaled up 200 times (100 mmol) without any degasification and purification of reactants; this facilitates the practical application in routine synthesis.

  19. 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

  20. Synthesis of Cyclic Peptidomimetics via a Pd-Catalyzed Macroamination Reaction.

    PubMed

    Hopkins, Brett A; Smith, Graham F; Sciammetta, Nunzio

    2016-08-19

    A new method to access cyclic peptidomimetics via a Pd-catalyzed macroamination reaction is presented. Natural amino acid amines are revealed as proficient coupling partners in these transformations. With a commercially available CPhos G3 catalyst system and substrates bearing diverse amino acid and aryl halide backbones, the unique head to side-chain (or side-chain mimic) macrocycles are afforded with ring sizes from 11 to 23 members in yields up to 84%. PMID:27508926

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

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

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

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

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

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

  3. New insights into the mechanism of iron-catalyzed cross-coupling reactions.

    PubMed

    Bekhradnia, Ahmadreza; Norrby, Per-Ola

    2015-03-01

    The mechanism of the iron-catalyzed cross-coupling of alkyl halides with aryl Grignard reagents is studied by a combination of GC monitoring and DFT calculation. Herein, we investigate two possible reaction pathways, the regular oxidative addition (OA) pathway and the atom transfer (AT) pathway that might occur in the rate-limiting step. The computational studies revealed that the AT pathway requires less energy than the regular OA pathway. PMID:25649755

  4. Brønsted Acid-Catalyzed Cascade Reactions Involving 1,2-Indole Migration.

    PubMed

    Álvarez, Estela; Nieto Faza, Olalla; Silva López, Carlos; Fernández-Rodríguez, Manuel A; Sanz, Roberto

    2015-09-01

    A cascade reaction of indoles with propargylic diols involving an unprecedented metal-free 1,2-indole migration onto an alkyne was carried out. DFT calculations support a mechanism consisting of a concerted nucleophilic attack of the indole nucleus with loss of water, followed by the 1,2-migration and subsequent Nazarov cyclization. This Brønsted acid-catalyzed protocol affords indole-functionalized benzofulvene derivatives in high yields. PMID:26211757

  5. N-tosylhydrazones: versatile reagents for metal-catalyzed and metal-free cross-coupling reactions.

    PubMed

    Shao, Zhihui; Zhang, Hongbin

    2012-01-21

    Transition metal-catalyzed cross-coupling reactions have been established as one of the most powerful tools for the construction of C-C and C-X bonds. In this context, the development of novel metal-catalyzed cross-coupling processes that do not require stoichiometric organometallic reagents is particularly attractive. Recently, N-tosylhydrazones have emerged as a new type of versatile coupling partners for transition metal-catalyzed cross-coupling reactions as well as metal-free cross-coupling reactions, and have attracted increasing attention. This tutorial review summarizes recent important developments in this area with N-tosylhydrazones as versatile coupling partners.

  6. Biorefining: heterogeneously catalyzed reactions of carbohydrates for the production of furfural and hydroxymethylfurfural.

    PubMed

    Karinen, Reetta; Vilonen, Kati; Niemelä, Marita

    2011-08-22

    Furfurals are important intermediates in the chemical industry. They are typically produced by homogeneous catalysis in aqueous solutions. However, heterogeneously catalyzed processes would be beneficial in view of the principles of green chemistry: the elimination of homogeneous mineral acids makes the reaction mixtures less corrosive, produces less waste, and facilitates easy separation and recovery of the catalyst. Finding an active and stable water-tolerant solid acid catalyst still poses a challenge for the production of furfural (furan-2-carbaldehyde) and 5-(hydroxymethyl)-2-furaldehyde (HMF). Furfural is produced in the dehydration of xylose, and HMF is formed from glucose and fructose in the presence of an acidic catalyst. Bases are not active in dehydration reaction but do catalyze the isomerization of monosaccharides, which is favorable when using glucose as a raw material. In addition to the desired dehydration of monosaccharides, many undesired side reactions take place, reducing the selectivity and deactivating the catalyst. In addition, the catalyst properties play an important role in the selectivity. In this Review, catalytic conversion approaches are summarized, focusing on the heterogeneously catalyzed formation of furfural. The attractiveness of catalytic concepts is evaluated, keeping in mind productivity, sustainability, and environmental footprint. PMID:21728248

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

    PubMed

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

    2016-01-01

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

  8. Macromolecular crowding effect upon in vitro enzyme kinetics: mixed activation-diffusion control of the oxidation of NADH by pyruvate catalyzed by lactate dehydrogenase.

    PubMed

    Balcells, Cristina; Pastor, Isabel; Vilaseca, Eudald; Madurga, Sergio; Cascante, Marta; Mas, Francesc

    2014-04-17

    Enzyme kinetics studies have been usually designed as dilute solution experiments, which differ substantially from in vivo conditions. However, cell cytosol is crowded with a high concentration of molecules having different shapes and sizes. The consequences of such crowding in enzymatic reactions remain unclear. The aim of the present study is to understand the effect of macromolecular crowding produced by dextran of different sizes and at diverse concentrations in the well-known reaction of oxidation of NADH by pyruvate catalyzed by L-lactate dehydrogenase (LDH). Our results indicate that the reaction rate is determined by both the occupied volume and the relative size of dextran obstacles with respect to the enzyme present in the reaction. Moreover, we analyzed the influence of macromolecular crowding on the Michaelis-Menten constants, vmax and Km. The obtained results show that only high concentrations and large sizes of dextran reduce both constants suggesting a mixed activation-diffusion control of this enzymatic reaction due to the dextran crowding action. From our knowledge, this is the first experimental study that depicts mixed activation-diffusion control in an enzymatic reaction due to the effect of crowding.

  9. More than bystanders: the effect of olefins on transition-metal-catalyzed cross-coupling reactions.

    PubMed

    Johnson, Jeffrey B; Rovis, Tomislav

    2008-01-01

    Olefins and alkynes are ubiquitous in transition-metal catalysis, whether introduced by the substrate, the catalyst, or as an additive. Whereas the impact of metals and ligands is relatively well understood, the effects of olefins in these reactions are generally underappreciated, even though numerous examples of olefins influencing the outcome of a reaction, through increased activity, stability, or selectivity, have been reported. This Review provides an overview of the interaction of olefins with transition metals and documents examples of olefins influencing the outcome of catalytic reactions, in particular cross-coupling reactions. It should thus provide a basis for the improved understanding and further utilization of olefin and alkyne effects in transition-metal-catalyzed reactions.

  10. Parameterization of the ReaxFF reactive force field for a proline-catalyzed aldol reaction.

    PubMed

    Hubin, Pierre O; Jacquemin, Denis; Leherte, Laurence; Vercauteren, Daniel P

    2016-11-01

    A parameterization of the ReaxFF reactive FF is performed using a Monte Carlo Simulated Annealing procedure for the modeling of a proline-catalyzed aldol reaction. Emphasis is put on the accurate reproduction of the relative stabilities of several key intermediates of the reaction, as well as, on the description of the reaction path bridging these intermediates based on quantum mechanical calculations. Our training sets include new criteria based on geometry optimizations and short Molecular Dynamics simulations to ensure that the trained ReaxFF potentials adequately predict the structures of all key intermediates. The transferability of the sets of parameters obtained is assessed for various steps of the considered aldol reaction, as well as for different substrates, catalysts, and reagents. This works indeed highlights the challenge of reaching transferable parameters for several reaction steps. © 2016 Wiley Periodicals, Inc.

  11. 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

  12. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane.

    PubMed

    Reimann, Joachim; Jetten, Mike S M; Keltjens, Jan T

    2015-01-01

    Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world. PMID:25707470

  13. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane.

    PubMed

    Reimann, Joachim; Jetten, Mike S M; Keltjens, Jan T

    2015-01-01

    Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.

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

    PubMed

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

    2016-01-18

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

  15. 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

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

    PubMed

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

    2016-07-18

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

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

    PubMed

    Doi, Ryohei; Ohashi, Masato; Ogoshi, Sensuke

    2016-01-01

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

  18. Assembly of 3-Sulfenylbenzofurans and 3-Sulfenylindoles by Palladium-Catalyzed Cascade Annulation/Arylthiolation Reaction.

    PubMed

    Li, Jianxiao; Li, Chunsheng; Yang, Shaorong; An, Yanni; Wu, Wanqing; Jiang, Huanfeng

    2016-04-01

    A novel and efficient palladium-catalyzed cascade annulation/arylthiolation reaction has been developed to afford functionalized 3-sulfenylbenzofuran and 3-sulfenylindole derivatives in moderate to good yields from readily available 2-alkynylphenols and 2-alkynylamines in ionic liquids. This protocol provides a valuable synthetic tool for the assembly of a wide range of 3-sulfenylbenzofuran and 3-sulfenylindole derivatives with high atom- and step-economy and exceptional functional group tolerance. Moreover, the employment of ionic liquids under mild reaction conditions makes this transformation green and practical. Furthermore, this approach enriched current C-S bond formation chemistry, making a valuable and practical method in synthetic and medicinal chemistry. PMID:26980622

  19. 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.

  20. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zahn, Dirk

    2004-05-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C⋯O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate.

  1. 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)

  2. Enzyme-catalyzed synthesis of unsaturated aliphatic polyesters based on green monomers from renewable resources.

    PubMed

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

    2013-08-12

    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.

  3. 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

  4. The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide.

    PubMed

    Bruender, Nathan A; Bandarian, Vahe

    2016-05-24

    Ribosomally synthesized post-translationally modified peptides (RiPPs) are encoded in the genomes of a wide variety of microorganisms, in the proximity of open reading frames that encode enzymes that conduct extensive modifications, many of which are novel. Recently, members of the radical S-adenosyl-l-methionine (SAM) superfamily have been identified in these biosynthetic clusters. Herein, we demonstrate the putative radical SAM enzyme, MftC, oxidatively decarboxylates the C-terminus of the MftA peptide in the presence of the accessory protein MftB. The reaction catalyzed by MftC expands the repertoire of peptide-based radical SAM chemistry beyond the intramolecular cross-links. PMID:27158836

  5. Rh(I)-catalyzed intramolecular [3 + 2] cycloaddition reactions of 1-ene-, 1-yne- and 1-allene-vinylcyclopropanes.

    PubMed

    Jiao, Lei; Lin, Mu; Yu, Zhi-Xiang

    2010-02-21

    New Rh(I)-catalyzed intramolecular [3 + 2] cycloaddition reactions of 1-ene-, 1-yne and 1-allene-vinylcyclopropanes have been developed, affording an efficient and versatile synthesis of cyclopentane- and cyclopentene-embedded bicyclic structures.

  6. Proline catalyzed α-aminoxylation reaction in the synthesis of biologically active compounds.

    PubMed

    Kumar, Pradeep; Dwivedi, Namrata

    2013-02-19

    The search for new and efficient ways to synthesize optically pure compounds is an active area of research in organic synthesis. Asymmetric catalysis provides a practical, cost-effective, and efficient method to create a variety of complex natural products containing multiple stereocenters. In recent years, chemists have become more interested in using small organic molecules to catalyze organic reactions. As a result, organocatalysis has emerged both as a promising strategy and as an alternative to catalysis with expensive proteins or toxic metals. One of the most successful and widely studied secondary amine-based organocatalysts is proline. This small molecule can catalyze numerous reactions such as the aldol, Mannich, Michael addition, Robinson annulation, Diels-Alder, α-functionalization, α-amination, and α-aminoxylation reactions. Catalytic and enantioselective α-oxygenation of carbonyl compounds is an important reaction to access a variety of useful building blocks for bioactive molecules. Proline catalyzed α-aminoxylation using nitrosobenzene as oxygen source, followed by in situ reduction, gives enantiomerically pure 1,2-diol. This molecule can then undergo a variety of organic reactions. In addition, proline organocatalysis provides access to an assortment of biologically active natural products including mevinoline (a cholesterol lowering drug), tetrahydrolipstatin (an antiobesity drug), R(+)-α-lipoic acid, and bovidic acid. In this Account, we present an iterative organocatalytic approach to synthesize both syn- and anti-1,3-polyols, both enantio- and stereoselectively. This method is primarily based on proline-catalyzed sequential α-aminoxylation and Horner-Wadsworth-Emmons (HWE) olefination of aldehyde to give a γ-hydroxy ester. In addition, we briefly illustrate the broad application of our recently developed strategy for 1,3-polyols, which serve as valuable, enantiopure building blocks for polyketides and other structurally diverse and

  7. 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.

  8. 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/β-cyclodextrins/poly(amidoamine) dendrimer-encapsulated Au nanoparticles (Fc-Fc/β-CD/PAMAM-Au) for procalcitonin (PCT) detection has been developed in this study. The signal probe was constructed as follows: amine-terminated β-CD was adsorbed to PAMAM-Au first, and then the prepared Fc-Fc was recognized by the β-CD to form stable host-guest nanonets. Next, secondary antibodies (Ab2) were attached into the formed netlike nanostructure of Fc-Fc/β-CD/PAMAM-Au by chemical absorption between PAMAM-Au and -NH2 of β-CD. Herein, the PAMAM-Au act not only as nanocarriers for anchoring large amounts of the β-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 β-CD as well as improving solubility by the hydrophilic exterior of β-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 β-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.

  9. Human Milk Oligosaccharides (HMOS): Structure, Function, and Enzyme-Catalyzed Synthesis.

    PubMed

    Chen, Xi

    2015-01-01

    The important roles played by human milk oligosaccharides (HMOS), the third major component of human milk, in the health of breast-fed infants have been increasingly recognized, as the structures of more than 100 different HMOS have now been elucidated. Despite the recognition of the various functions of HMOS as prebiotics, antiadhesive antimicrobials, and immunomodulators, the roles and the applications of individual HMOS species are less clear. This is mainly due to the limited accessibility to large amounts of individual HMOS in their pure forms. Current advances in the development of enzymatic, chemoenzymatic, whole-cell, and living-cell systems allow for the production of a growing number of HMOS in increasing amounts. This effort will greatly facilitate the elucidation of the important roles of HMOS and allow exploration into the applications of HMOS both as individual compounds and as mixtures of defined structures with desired functions. The structures, functions, and enzyme-catalyzed synthesis of HMOS are briefly surveyed to provide a general picture about the current progress on these aspects. Future efforts should be devoted to elucidating the structures of more complex HMOS, synthesizing more complex HMOS including those with branched structures, and developing HMOS-based or HMOS-inspired prebiotics, additives, and therapeutics. PMID:26613816

  10. Keratin Protein-Catalyzed Nitroaldol (Henry) Reaction and Comparison with Other Biopolymers.

    PubMed

    Häring, Marleen; Pettignano, Asja; Quignard, Françoise; Tanchoux, Nathalie; Díaz Díaz, David

    2016-01-01

    Here we describe a preliminary investigation on the ability of natural keratin to catalyze the nitroaldol (Henry) reaction between aldehydes and nitroalkanes. Both aromatic and heteroaromatic aldehydes bearing strong or moderate electron-withdrawing groups were converted into the corresponding β-nitroalcohol products in both DMSO and in water in the presence of tetrabutylammonium bromide (TBAB) as a phase transfer catalyst. Negligible background reactions (i.e., negative control experiment in the absence of keratin protein) were observed in these solvent systems. Aromatic aldehydes bearing electron-donating groups and aliphatic aldehydes showed poor or no conversion, respectively. In general, the reactions in water/TBAB required twice the amount of time than in DMSO to achieve similar conversions. Moreover, comparison of the kinetics of the keratin-mediated nitroaldol (Henry) reaction with other biopolymers revealed slower rates for the former and the possibility of fine-tuning the kinetics by appropriate selection of the biopolymer and solvent. PMID:27571051

  11. Mechanism of silver- and copper-catalyzed decarboxylation reactions of aryl carboxylic acids.

    PubMed

    Xue, Liqin; Su, Weiping; Lin, Zhenyang

    2011-11-28

    Silver- and copper-catalyzed decarboxylation reactions of aryl carboxylic acids were investigated with the aid of density functional theory calculations. The reaction mechanism starts with a carboxylate complex of silver or copper. Decarboxylation occurs via ejecting CO(2) from the carboxylate complex followed by protodemetallation with an aryl carboxylic acid molecule to regenerate the starting complex. Our results indicated that the primary factor to affect the overall reaction barriers is the ortho steric destabilization effect on the starting carboxylate complexes for most cases. Certain ortho substituents that are capable of coordinating with the catalyst metal center without causing significant ring strain stabilize the decarboxylation transition states and reduce the overall reaction barriers. However, the coordination effect is found to be the secondary factor when compared with the ortho effect. PMID:21979246

  12. Keratin Protein-Catalyzed Nitroaldol (Henry) Reaction and Comparison with Other Biopolymers.

    PubMed

    Häring, Marleen; Pettignano, Asja; Quignard, Françoise; Tanchoux, Nathalie; Díaz Díaz, David

    2016-08-25

    Here we describe a preliminary investigation on the ability of natural keratin to catalyze the nitroaldol (Henry) reaction between aldehydes and nitroalkanes. Both aromatic and heteroaromatic aldehydes bearing strong or moderate electron-withdrawing groups were converted into the corresponding β-nitroalcohol products in both DMSO and in water in the presence of tetrabutylammonium bromide (TBAB) as a phase transfer catalyst. Negligible background reactions (i.e., negative control experiment in the absence of keratin protein) were observed in these solvent systems. Aromatic aldehydes bearing electron-donating groups and aliphatic aldehydes showed poor or no conversion, respectively. In general, the reactions in water/TBAB required twice the amount of time than in DMSO to achieve similar conversions. Moreover, comparison of the kinetics of the keratin-mediated nitroaldol (Henry) reaction with other biopolymers revealed slower rates for the former and the possibility of fine-tuning the kinetics by appropriate selection of the biopolymer and solvent.

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

    PubMed

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

    2016-05-17

    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

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

    PubMed

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

    2016-05-17

    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

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

    PubMed

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

    2016-08-01

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

  16. EzCatDB: the enzyme reaction database, 2015 update.

    PubMed

    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.

  17. EzCatDB: the enzyme reaction database, 2015 update.

    PubMed

    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

  18. 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.

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

    PubMed

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

    2013-04-19

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

  20. A general synthesis of fluoroalkylated alkenes by palladium-catalyzed Heck-type reaction of fluoroalkyl bromides.

    PubMed

    Feng, Zhang; Min, Qiao-Qiao; Zhao, Hai-Yang; Gu, Ji-Wei; Zhang, Xingang

    2015-01-19

    An efficient palladium-catalyzed Heck-type reaction of fluoroalkyl halides, including perfluoroalkyl bromides, trifluoromethyl iodides, and difluoroalkyl bromides, has been developed. The reaction proceeds under mild reaction conditions with high efficiency and broad substrate scope, and provides a general and straightforward access to fluoroalkylated alkenes which are of interest in life and material sciences.

  1. Sulfuric, hydrochloric, and nitric acid-catalyzed triacetone triperoxide (TATP) reaction mixtures: an aging study.

    PubMed

    Fitzgerald, Mark; Bilusich, Daniel

    2011-09-01

    The organic peroxide explosive triacetone triperoxide (TATP) is regularly encountered by law enforcement agents in various stages of its production. This study utilizes solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS) to examine sulfuric acid-, hydrochloric acid-, and nitric acid-catalyzed TATP syntheses during the initial 24 h of these reactions at low temperatures (5-9°C). Additionally, aging of the reaction mixtures was examined at both low and ambient temperatures (19-21°C) for a further 9 days. For each experiment, TATP could be readily identified in the headspace above the reaction mixture 1 h subsequent to the combination of reagents; at 24 h, TATP and diacetone diperoxide (DADP) were prominent. TATP degraded more rapidly than DADP. Additionally, chlorinated acetones chloroacetone and 1,1,-dichloroacetone were identified in the headspace above the hydrochloric acid-catalyzed TATP reaction mixture. These were not present when the catalyst was sulfuric acid or nitric acid. PMID:21595692

  2. Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member.

    PubMed

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

    2011-11-01

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

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

    PubMed

    Jee, Elizabeth; Bánsági, Tamás; Taylor, Annette F; Pojman, John A

    2016-02-01

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

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

    PubMed Central

    Jee, Elizabeth; Bánsági, Tamás

    2016-01-01

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

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

    PubMed

    Jee, Elizabeth; Bánsági, Tamás; Taylor, Annette F; Pojman, John A

    2016-02-01

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

  6. Plant lipases: biocatalyst aqueous environment in relation to optimal catalytic activity in lipase-catalyzed synthesis reactions.

    PubMed

    Caro, Yanis; Pina, Michel; Turon, Fabrice; Guilbert, Stephane; Mougeot, Estelle; Fetsch, David V; Attwool, Philip; Graille, Jean

    2002-03-20

    Adsorption and desorption isotherms of two commercial enzyme preparations of papain and bromelain were determined with a Dynamic Vapor System. The Guggenheim-Anderson-deBoer (GAB) modeling of the obtained sorption isotherms allowed the definition of different levels of hydration of those samples. Afterward, these enzyme preparations were used as biocatalysts in water and solvent-free esterification and alcoholysis reactions. The evolution of the obtained fatty acid ester level as a function of the initial hydration level of the biocatalyst, i.e., thermodynamic water activity (a(w)) and water content, was studied. The results show an important correlation between the initial hydration level of the biocatalyst and its catalytic activity during the lipase-catalyzed synthesis reactions. Thus, the Carica papaya lipase (crude papain preparation) catalytic activity is highly dependent on the biocatalyst hydration state. The optimized synthesis reaction yield is obtained when the a(w) value of the enzyme preparation is stabilized at 0.22, which corresponds to 2% water content. This optimal level of hydration occurs on the linear part of the biocatalyst's sorption isotherm, where the water molecules can form a mono- or multiple layer with the protein network. The synthesis reaction yield decreases when the a(w) of the preparation is higher than 0.22, because the excess water molecules modify the system equilibrium leading to the reverse and competitive reaction, i.e., hydrolysis. These results show also that an optimal storage condition for the highly hydrophilic crude papain preparation is a relative humidity strictly lower than 70% to avoid an irreversible structural transition leading to a useless biocatalyst. Concerning the bromelain preparation, no effect of the hydration level on the catalytic activity during esterification reactions was observed. This biocatalyst has too weak a catalytic activity which makes it difficult to observe any differences. Furthermore, the

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

    PubMed

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

    2016-01-01

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

  8. 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.

  9. Enzymes in Analytical Chemistry.

    ERIC Educational Resources Information Center

    Fishman, Myer M.

    1980-01-01

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

  10. Metal-Catalyzed Cyclization Reactions of 2,3,4-Trien-1-ols: A Joint Experimental-Computational Study.

    PubMed

    Alcaide, Benito; Almendros, Pedro; Cembellín, Sara; Fernández, Israel; Martínez Del Campo, Teresa

    2016-08-01

    Controlled preparation of tri- and tetrasubstituted furans, as well as carbazoles has been achieved through chemo- and regioselective metal-catalyzed cyclization reactions of cumulenic alcohols. The gold- and palladium-catalyzed cycloisomerization reactions of cumulenols, including indole-tethered 2,3,4-trien-1-ols, to trisubstituted furans was effective, due to a 5-endo-dig oxycyclization by attack of the hydroxy group onto the central cumulene double bond. In contrast, palladium-catalyzed heterocyclization/coupling reactions with 3-bromoprop-1-enes furnished tetrasubstituted furans. Also studied was the palladium-catalyzed cyclization/coupling sequence involving protected indole-tethered 2,3,4-trien-1-ols and 3-bromoprop-1-enes that exclusively generated trisubstituted carbazole derivatives. These results could be explained through a selective 6-endo-dig cumulenic hydroarylation, followed by aromatization. DFT calculations were carried out to understand this difference in reactivity. PMID:27383332

  11. 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.

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

    PubMed

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

    2011-04-15

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

  13. Imparting Catalyst-Control upon Classical Palladium-Catalyzed Alkenyl C–H Bond Functionalization Reactions

    PubMed Central

    Sigman, Matthew S.; Werner, Erik W.

    2011-01-01

    Conspectus The functional group transformations carried out by the palladium-catalyzed Wacker and Heck reactions are radically different, but they are both alkenyl C-H bond functionalization reactions that have found extensive use in organic synthesis. The synthetic community depends heavily on these important reactions, but selectivity issues arising from control by the substrate, rather than control by the catalyst, have prevented the realization of their full potential. Because of important similarities in the respective selectivity-determining nucleopalladation and β-hydride elimination steps of these processes, we posit that the mechanistic insight garnered through the development of one of these catalytic reactions may be applied to the other. In this Account, we detail our efforts to develop catalyst-controlled variants of both the Wacker oxidation and the Heck reaction to address synthetic limitations and provide mechanistic insight into the underlying organometallic processes of these reactions. In contrast to previous reports, we discovered that electrophilic palladium catalysts with non-coordinating counterions allowed for the use of a Lewis basic ligand to efficiently promote TBHP-mediated Wacker oxidation reactions of styrenes. This discovery led to the mechanistically guided development of a Wacker reaction catalyzed by a palladium complex with a bidentate ligand. This ligation may prohibit coordination of allylic heteroatoms, thereby allowing for the application of the Wacker oxidation to substrates that were poorly behaved under classical conditions. Likewise, we unexpectedly discovered that electrophilic Pd-σ-alkyl intermediates are capable of distinguishing between electronically inequivalent C–H bonds during β-hydride elimination. As a result, we have developed E-styrenyl selective oxidative Heck reactions of previously unsuccessful electronically non-biased alkene substrates using arylboronic acid derivatives. The mechanistic insight gained

  14. Peroxygenase-Catalyzed Oxyfunctionalization Reactions Promoted by the Complete Oxidation of Methanol.

    PubMed

    Ni, Yan; Fernández-Fueyo, Elena; Gomez Baraibar, Alvaro; Ullrich, René; Hofrichter, Martin; Yanase, Hideshi; Alcalde, Miguel; van Berkel, Willem J H; Hollmann, Frank

    2016-01-11

    Peroxygenases catalyze a broad range of (stereo)selective oxyfunctionalization reactions. However, to access their full catalytic potential, peroxygenases need a balanced provision of hydrogen peroxide to achieve high catalytic activity while minimizing oxidative inactivation. Herein, we report an enzymatic cascade process that employs methanol as a sacrificial electron donor for the reductive activation of molecular oxygen. Full oxidation of methanol is achieved, generating three equivalents of hydrogen peroxide that can be used completely for the stereoselective hydroxylation of ethylbenzene as a model reaction. Overall we propose and demonstrate an atom-efficient and easily applicable alternative to established hydrogen peroxide generation methods, which enables the efficient use of peroxygenases for oxyfunctionalization reactions. PMID:26607550

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

    NASA Astrophysics Data System (ADS)

    Abideen, Saqib Ul

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

  16. Palladium-catalyzed cross-coupling reactions of 4a,8a-azaboranaphthalene.

    PubMed

    Sun, Feiye; Lv, Lily; Huang, Min; Zhou, Zhaohui; Fang, Xiangdong

    2014-10-01

    A concise and effective three-step synthesis of 4a,8a-azaboranaphthalene (ABN) has been developed in gram scale. Electrophilic aromatic substitution reactions of ABN provide excellent functional-group-tolerant cross-coupling partners in various Pd-catalyzed cross-coupling reactions (e.g., Sonogashira, Suzuki-Miyaura, or Heck reaction). Photophysical, electrochemical, and DFT calculations all suggest a narrowed HOMO-LUMO gap with extended π-conjugation characters in the cross-coupled molecules. The ABN moiety as a new fluorophore has a distinct and selective fluorescence response toward Zn(II) and Cd(II) ions, demonstrating great potential for the ABN structural motif in fluorescent chemosensors.

  17. 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 γ-amido-acid derivatives and γ-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 α-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.

  18. Enzyme stabilization via bio-templated silicification reactions.

    PubMed

    Johnson, Glenn R; Luckarift, Heather R

    2011-01-01

    Effective entrapment of enzymes in solid-phase materials is critical to their practical application. The entrapment generally stabilizes biological activity compared to soluble molecules and the material simplifies catalyst integration significantly. A silica sol-gel process based upon biological mechanisms of inorganic material formation (biomineralization) supports protein immobilization reactions within minutes. The material has high protein binding capacity and the catalytic activity of the enzyme is retained. We have demonstrated that both oligopeptides and selected proteins will mediate the biomineralization of silica and allow effective co-encapsulation of other proteins present in the reaction mixture. The detailed methods described here provide a simple and effective approach for molecular biologists, biochemists, and bioengineers to create stable, solid-phase biocatalysts that may be integrated within sensors, synthetic processes, reactive barriers, energy conversion materials, and other biotechnology concepts.

  19. 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

  20. 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.

  1. Palladium-catalyzed C-H functionalization of acyldiazomethane and tandem cross-coupling reactions.

    PubMed

    Ye, Fei; Qu, Shuanglin; Zhou, Lei; Peng, Cheng; Wang, Chengpeng; Cheng, Jiajia; Hossain, Mohammad Lokman; Liu, Yizhou; Zhang, Yan; Wang, Zhi-Xiang; Wang, Jianbo

    2015-04-01

    Palladium-catalyzed C-H functionalization of acyldiazomethanes with aryl iodides has been developed. This reaction is featured by the retention of the diazo functionality in the transformation, thus constituting a novel method for the introduction of diazo functionality to organic molecules. Consistent with the experimental results, the density functional theory (DFT) calculation indicates that the formation of Pd-carbene species in the catalytic cycle through dinitrogen extrusion from the palladium ethyl diazoacetate (Pd-EDA) complex is less favorable. The reaction instead proceeds through Ag2CO3 assisted deprotonation and subsequently reductive elimination to afford the products with diazo functionality remained. This C-H functionalization transformation can be further combined with the recently evolved palladium-catalyzed cross-coupling reaction of diazo compounds with aryl iodides to develop a tandem coupling process for the synthesis of α,α-diaryl esters. DFT calculation supports the involvement of Pd-carbene as reactive intermediate in the catalytic cycle, which goes through facile carbene migratory insertion with a low energy barrier (3.8 kcal/mol). PMID:25794590

  2. Palladium-catalyzed C-H functionalization of acyldiazomethane and tandem cross-coupling reactions.

    PubMed

    Ye, Fei; Qu, Shuanglin; Zhou, Lei; Peng, Cheng; Wang, Chengpeng; Cheng, Jiajia; Hossain, Mohammad Lokman; Liu, Yizhou; Zhang, Yan; Wang, Zhi-Xiang; Wang, Jianbo

    2015-04-01

    Palladium-catalyzed C-H functionalization of acyldiazomethanes with aryl iodides has been developed. This reaction is featured by the retention of the diazo functionality in the transformation, thus constituting a novel method for the introduction of diazo functionality to organic molecules. Consistent with the experimental results, the density functional theory (DFT) calculation indicates that the formation of Pd-carbene species in the catalytic cycle through dinitrogen extrusion from the palladium ethyl diazoacetate (Pd-EDA) complex is less favorable. The reaction instead proceeds through Ag2CO3 assisted deprotonation and subsequently reductive elimination to afford the products with diazo functionality remained. This C-H functionalization transformation can be further combined with the recently evolved palladium-catalyzed cross-coupling reaction of diazo compounds with aryl iodides to develop a tandem coupling process for the synthesis of α,α-diaryl esters. DFT calculation supports the involvement of Pd-carbene as reactive intermediate in the catalytic cycle, which goes through facile carbene migratory insertion with a low energy barrier (3.8 kcal/mol).

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

    PubMed

    He, Nan; Li, Zhen Hua

    2016-04-21

    Formic acid decomposition (FAD) reaction has been an innovative way for hydrogen energy. Noble metal catalysts, especially palladium-containing nanoparticles, supported or unsupported, perform well in this reaction. Herein, we considered the simplest model, wherein one Pd atom is used as the FAD catalyst. With high-level theoretical calculations of CCSD(T)/CBS quality, we investigated all possible FAD pathways. The results show that FAD catalyzed by one Pd atom follows a different mechanism compared with that catalyzed by surfaces or larger clusters. At the initial stage of the reaction, FAD follows a dehydration route and is quickly poisoned by CO due to the formation of very stable PdCO. PdCO then becomes the actual catalyst for FAD at temperatures approximately below 1050 K. Beyond 1050 K, there is a switch of catalyst from PdCO to Pd atom. The results also show that dehydration is always favoured over dehydrogenation on either the Pd-atom or PdCO catalyst. On the Pd-atom catalyst, neither dehydrogenation nor dehydration follows the formate mechanism. In contrast, on the PdCO catalyst, dehydrogenation follows the formate mechanism, whereas dehydration does not. We also systematically investigated the performance of 24 density functional theory methods. We found that the performance of the double hybrid mPW2PLYP functional is the best, followed by the B3LYP, B3PW91, N12SX, M11, and B2PLYP functionals.

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

    PubMed

    He, Nan; Li, Zhen Hua

    2016-04-21

    Formic acid decomposition (FAD) reaction has been an innovative way for hydrogen energy. Noble metal catalysts, especially palladium-containing nanoparticles, supported or unsupported, perform well in this reaction. Herein, we considered the simplest model, wherein one Pd atom is used as the FAD catalyst. With high-level theoretical calculations of CCSD(T)/CBS quality, we investigated all possible FAD pathways. The results show that FAD catalyzed by one Pd atom follows a different mechanism compared with that catalyzed by surfaces or larger clusters. At the initial stage of the reaction, FAD follows a dehydration route and is quickly poisoned by CO due to the formation of very stable PdCO. PdCO then becomes the actual catalyst for FAD at temperatures approximately below 1050 K. Beyond 1050 K, there is a switch of catalyst from PdCO to Pd atom. The results also show that dehydration is always favoured over dehydrogenation on either the Pd-atom or PdCO catalyst. On the Pd-atom catalyst, neither dehydrogenation nor dehydration follows the formate mechanism. In contrast, on the PdCO catalyst, dehydrogenation follows the formate mechanism, whereas dehydration does not. We also systematically investigated the performance of 24 density functional theory methods. We found that the performance of the double hybrid mPW2PLYP functional is the best, followed by the B3LYP, B3PW91, N12SX, M11, and B2PLYP functionals. PMID:27005983

  5. A novel glucosylation reaction on anthocyanins catalyzed by acyl-glucose-dependent glucosyltransferase in the petals of carnation and delphinium.

    PubMed

    Matsuba, Yuki; Sasaki, Nobuhiro; Tera, Masayuki; Okamura, Masachika; Abe, Yutaka; Okamoto, Emi; Nakamura, Haruka; Funabashi, Hisakage; Takatsu, Makoto; Saito, Mikako; Matsuoka, Hideaki; Nagasawa, Kazuo; Ozeki, Yoshihiro

    2010-10-01

    Glucosylation of anthocyanin in carnations (Dianthus caryophyllus) and delphiniums (Delphinium grandiflorum) involves novel sugar donors, aromatic acyl-glucoses, in a reaction catalyzed by the enzymes acyl-glucose-dependent anthocyanin 5(7)-O-glucosyltransferase (AA5GT and AA7GT). The AA5GT enzyme was purified from carnation petals, and cDNAs encoding carnation Dc AA5GT and the delphinium homolog Dg AA7GT were isolated. Recombinant Dc AA5GT and Dg AA7GT proteins showed AA5GT and AA7GT activities in vitro. Although expression of Dc AA5GT in developing carnation petals was highest at early stages, AA5GT activity and anthocyanin accumulation continued to increase during later stages. Neither Dc AA5GT expression nor AA5GT activity was observed in the petals of mutant carnations; these petals accumulated anthocyanin lacking the glucosyl moiety at the 5 position. Transient expression of Dc AA5GT in petal cells of mutant carnations is expected to result in the transfer of a glucose moiety to the 5 position of anthocyanin. The amino acid sequences of Dc AA5GT and Dg AA7GT showed high similarity to glycoside hydrolase family 1 proteins, which typically act as β-glycosidases. A phylogenetic analysis of the amino acid sequences suggested that other plant species are likely to have similar acyl-glucose-dependent glucosyltransferases.

  6. Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions.

    PubMed

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

    2012-11-13

    Density functional theory (DFT) based quantum mechanical/molecular mechanical (QM/MM) calculations have provided valuable insight into the reactivity of the cytochrome P450 family of enzymes (P450s). A failure of commonly used DFT methods, such as B3LYP, is the neglect of dispersion interactions. An empirical dispersion correction has been shown to improve the accuracy of gas phase DFT calculations of P450s. The current work examines the effect of the dispersion correction in QM/MM calculations on P450s. The hydrogen abstraction from camphor, and hydrogen abstraction and C-O addition of cyclohexene and propene by P450cam have been modeled, along with the addition of benzene to Compound I in CYP2C9, at the B3LYP-D2/CHARMM27 level of theory. Single point energy calculations were also performed at the B3LYP-D3//B3LYP-D2/CHARMM27 level. The dispersion corrections lower activation energy barriers significantly (by ∼5 kcal/mol), as seen for gas phase calculations, but has a small effect on optimized geometries.These effects are likely to be important in modeling reactions catalyzed by other enzymes also. Given the low computational cost of including such dispersion corrections, we recommend doing so in all B3LYP based QM/MM calculations.

  7. Convergent Synthesis of 2-Aryl-Substituted Quinolines by Gold-Catalyzed Cascade Reaction.

    PubMed

    Ueda, Hirofumi; Yamaguchi, Minami; Tokuyama, Hidetoshi

    2016-01-01

    Gold-catalyzed auto-tandem catalysis has been developed for synthesizing 2-aryl-substituted quinolines. The reaction of an aniline bearing an acetal moiety with an aryl alkyne proceeded via formal [4+2]-cycloaddition, which involved the addition of gold acetylide to an oxonium ion to give amino alkyne intermediate and sequential 6-endo-dig cyclization of amino alkyne intermediate by attacking of nitrogen to alkyne moiety activated by gold catalyst. The cationic gold catalyst promoted two different processes by enhancing the nucleophilicity and electrophilicity of alkyne. This convergent synthetic methodology enabled the synthesis of a variety of 2-aryl-substituted quinolines. PMID:27373638

  8. Total Synthesis of (-)-Lepadiformine A Utilizing Hg(OTf)2-Catalyzed Cycloisomerization Reaction.

    PubMed

    Nishikawa, Keisuke; Kikuchi, Seiho; Ezaki, Shinnosuke; Koyama, Tomoyuki; Nokubo, Haruka; Kodama, Takeshi; Tachi, Yoshimitsu; Morimoto, Yoshiki

    2015-12-01

    A cytotoxic marine alkaloid (-)-lepadiformine A (1) possesses a unique structure characterized by the trans-1-azadecalin AB ring system fused with the AC spiro-cyclic ring. In this research, we found that a cycloisomerization reaction from amino ynone 2 to a 1-azaspiro[4.5]decane skeleton 3, corresponding to the AC ring system of 1, is promoted by Hg(OTf)(2). Thus, we have accomplished the efficient total synthesis of (-)-lepadiformine A in 28% overall yield by featuring the novel Hg(OTf)(2)-catalyzed cycloisomerization. PMID:26584002

  9. Plant carotene cis-trans isomerase CRTISO: a new member of the FAD(RED)-dependent flavoproteins catalyzing non-redox reactions.

    PubMed

    Yu, Qiuju; Ghisla, Sandro; Hirschberg, Joseph; Mann, Varda; Beyer, Peter

    2011-03-11

    The carotene cis-trans isomerase CRTISO is a constituent of the carotene desaturation pathway as evolved in cyanobacteria and prevailing in plants, in which a tetra-cis-lycopene species, termed prolycopene, is formed. CRTISO, an evolutionary descendant of the bacterial carotene desaturase CRTI, catalyzes the cis-to-trans isomerization reactions leading to all-trans-lycopene, the substrate for the subsequent lycopene cyclization to form all-trans-α/β-carotene. CRTISO and CRTI share a dinucleotide binding motif at the N terminus. Here we report that this site is occupied by FAD in CRTISO. The reduced form of this cofactor catalyzes a reaction not involving net redox changes. Results obtained with C(1)- and C(5)-deaza-FAD suggest mechanistic similarities with type II isopentenyl diphosphate: dimethylallyl diphosphate isomerase (IDI-2). CRTISO, together with lycopene cyclase CRTY and IDI-2, thus represents the third enzyme in isoprenoid metabolism belonging to the class of non-redox enzymes depending on reduced flavin for activity. The regional specificity and the kinetics of the isomerization reaction were investigated in vitro using purified enzyme and biphasic liposome-based systems carrying specific cis-configured lycopene species as substrates. The reaction proceeded from cis to trans, recognizing half-sides of the symmetrical prolycopene and was accompanied by one trans-to-cis isomerization step specific for the C(5)-C(6) double bond. Rice lycopene β-cyclase (OsLCY-b), when additionally introduced into the biphasic in vitro system used, was found to be stereospecific for all-trans-lycopene and allowed the CRTISO reaction to proceed toward completion by modifying the thermodynamics of the overall reaction. PMID:21209101

  10. ZnS quantum dots as pH probes for study of enzyme reaction kinetics.

    PubMed

    Wu, Dudu; Chen, Zhi

    2012-06-10

    Water soluble ZnS quantum dots (QDs) modified by mercaptoacetic acid (MAA) were used to determinate proton concentration in aqueous solutions by fluorescence spectroscopic technique. The results showed that the fluorescence of the water-soluble QDs could be quenched by proton concentration and the fluorescence intensity of the water-soluble QDs decreased linearly as the pH varied from 4.5 to 7.0. Based on this phenomenon, a convenient, rapid and specific method to determine of enzyme reaction kinetics was proposed. The modified ZnS QDs were successfully used as pH probes in monitoring the hydrolysis of glycidyl butyrate catalyzed by porcine pancreatic lipase (PPL). The proposed method was found to improve stability, sensitivity and a monitoring range for determination proton concentration as compared to the already described analytical methods based on p-Nitrophenoxide (PNP).

  11. 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.)

  12. Study of enzyme adsorption and reaction kinetics for cellulose hydrolysis

    SciTech Connect

    Gilbert, I.G.

    1982-01-01

    Enzymatic hydrolysis of cellulose occurs due to the combined catalytic action of two types of cellulase components commonly referred to as C/sub 1/ and C/sub x/. However, before the hydrolysis reaction can begin, it is necessary for these enzymes to first adsorb onto the accessible surfaces of the insoluble cellulose substrate. The objective of the study was to gain a better understanding of the relationships between the adsorption of these enzyme components, the hydrolysis kinetics, the cellulosic surface area accessible to the enzymes, and the cellulose crystallinity. These relationships were investigated by passing a Trichoderma viride cellulase solution through columns of cellulose powder having different accessibility and crystallinity, and then analyzing the quantities of the different enzyme components and the hydrolysis product in the effluent. The amounts of the different cellulase components were analyzed using high-performance anion-exchange chromatography. Additional adsorption and hydrolysis experiments were done using columns of cellulose beads specially developed to provide amodel substrate for this analysis. A mathematical model has been formulated to describe the kinetics of enzyme adsorption and the resultant, initial hydrolysis rate in cellulose column. The analytical solutions obtained have been linearized into a convenient form so that the kinetic parameters of the model can be readily determined from experimental breakthrough curves.

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

    SciTech Connect

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

    2010-11-03

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

  14. 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.

  15. Mechanistic insights on platinum- and palladium-pincer catalyzed coupling and cyclopropanation reactions between olefins.

    PubMed

    Rajeev, Ramanan; Sunoj, Raghavan B

    2012-07-21

    The mechanism of M(II)-PNP-pincer catalyzed reaction between (i) ethene, (ii) trans-butene with 2-methylbut-2-ene, 2,3-dimethylbut-2-ene and tert-butylbutene is examined by using density functional theory methods (where M = Pt or Pd). All key intermediates and transition states involved in the reaction are precisely located on the respective potential energy surfaces using the popular DFT functionals such as mPW1K, M06-2X, and B3LYP in conjunction with the 6-31+G** basis set. The reaction between these olefins can lead to a linear coupling product or a substituted cyclopropane. The energetic comparison between coupling as well as cyclopropanation pathways involving four pairs of olefins for both platinum (1-4) and palladium (5-8) catalyzed reactions is performed. The key events in the lower energy pathway in the mechanistic course involves (i) a C-C bond formation between the metal bound olefin (ethene or trans-butene) and a free olefin, and (ii) two successive [1,2] hydrogen migrations in the ensuing carbocationic intermediates (1c-4c, and 1d-4d), toward the formation of the coupling product. The computed barriers for these steps in the reaction of metal bound ethene to free tert-butylbutene (or other butenes) are found to be much lower than the corresponding steps when trans-butene is bound to the metal pincer. The Gibbs free energy differences between the transition states leading to the coupling product (TS(d-e)) and that responsible for cyclopropanated product (TS(d-g)) are found to be diminishingly closer in the case of the platinum pincer as compared to that in the palladium system. The computed energetics indicate that the coupled product prefers to remain as a metal olefin complex, consistent with the earlier experimental reports.

  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

    2015-01-07

    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.

  17. 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

  18. 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

  19. Atom-efficient metal-catalyzed cross-coupling reaction of indium organometallics with organic electrophiles.

    PubMed

    Pérez, I; Sestelo, J P; Sarandeses, L A

    2001-05-01

    The novel metal-catalyzed cross-coupling reaction of indium organometallics with organic electrophiles is described. Triorganoindium compounds (R(3)In) containing alkyl, vinyl, aryl, and alkynyl groups are efficiently prepared from the corresponding lithium or magnesium organometallics by reaction with indium trichloride. The cross-coupling reaction of R(3)In with aryl halides and pseudohalides (iodide 2, bromide 5, and triflate 4), vinyl triflates, benzyl bromides, and acid chlorides proceeds under palladium catalysis in excellent yields and with high chemoselectivity. Indium organometallics also react with aryl chlorides as under nickel catalysis. In the cross-coupling reaction the triorganoindium compounds transfer, in a clear example of atom economy, all three of the organic groups attached to the metal, as shown by the necessity of using only 34 mol % of indium. The feasibility of using R(3)In in reactions with different electrophiles, along with the high yields and chemoselectivities obtained, reveals indium organometallics to be useful alternatives to other organometallics in cross-coupling reactions.

  20. Metal-Catalyzed Chemical Reaction of Single Molecules Directly Probed by Vibrational Spectroscopy.

    PubMed

    Choi, Han-Kyu; Park, Won-Hwa; Park, Chan-Gyu; Shin, Hyun-Hang; Lee, Kang Sup; Kim, Zee Hwan

    2016-04-01

    The study of heterogeneous catalytic reactions remains a major challenge because it involves a complex network of reaction steps with various intermediates. If the vibrational spectra of individual molecules could be monitored in real time, one could characterize the structures of the intermediates and the time scales of reaction steps without ensemble averaging. Surface-enhanced Raman scattering (SERS) spectroscopy does provide vibrational spectra with single-molecule sensitivity, but typical single-molecule SERS signals exhibit spatial heterogeneities and temporal fluctuations, making them difficult to be used in single-molecule kinetics studies. Here we show that SERS can monitor the single-molecule catalytic reactions in real time. The surface-immobilized reactants placed at the junctions of well-defined nanoparticle-thin film structures produce time-resolved SERS spectra with discrete, step-transitions of photoproducts. We interpret that such SERS-steps correspond to the reaction events of individual molecules occurring at the SERS hotspot. The analyses of the yield, dynamics, and the magnitude of such SERS steps, along with the associated spectral characteristics, fully support our claim. In addition, a model that is based on plasmonic field enhancement and surface photochemistry reproduces the key features of experimental observation. Overall, the result demonstrates that it is possible, under well-controlled conditions, to differentiate the chemical and physical processes contributing to the single-molecule SERS signals, and thus shows the use of single-molecule SERS as a tool for studying the metal-catalyzed organic reactions.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  2. Stereospecific Nickel-Catalyzed Cross-Coupling Reactions of Benzylic Ethers with Isotopically-Labeled Grignard Reagents

    PubMed Central

    2015-01-01

    In this manuscript we highlight the potential of stereospecific nickel-catalyzed cross-coupling reactions for applications in the pharmaceutical industry. Using an inexpensive and sustainable nickel catalyst, we report a gram-scale Kumada cross-coupling reaction. Reactions are highly stereospecific and proceed with inversion at the benzylic position. We also expand the scope of our reaction to incorporate isotopically labeled substituents. PMID:27458328

  3. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai A; De Ronde, Wiet H; Daniels, Bryan C; Mugler, Andrew

    2008-01-01

    Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.

  4. Transition-metal-catalyzed Suzuki-Miyaura cross-coupling reactions: a remarkable advance from palladium to nickel catalysts.

    PubMed

    Han, Fu-She

    2013-06-21

    In the transition-metal-catalyzed cross-coupling reactions, the use of the first row transition metals as catalysts is much more appealing than the precious metals owing to the apparent advantages such as cheapness and earth abundance. Within the last two decades, particularly the last five years, explosive interests have been focused on the nickel-catalyzed Suzuki-Miyaura reactions. This has greatly advanced the chemistry of transition-metal-catalyzed cross-coupling reactions. Most notably, a broad range of aryl electrophiles such as phenols, aryl ethers, esters, carbonates, carbamates, sulfamates, phosphates, phosphoramides, phosphonium salts, and fluorides, as well as various alkyl electrophiles, which are conventionally challenging, by applying palladium catalysts can now be coupled efficiently with boron reagents in the presence of nickel catalysts. In this review, we would like to summarize the progress in this reaction.

  5. Nitrous Oxide-dependent Iron-catalyzed Coupling Reactions of Grignard Reagents.

    PubMed

    Döhlert, Peter; Weidauer, Maik; Enthaler, Stephan

    2015-01-01

    The formation of carbon-carbon bonds is one of the fundamental transformations in chemistry. In this regard the application of palladium-based catalysts has been extensively investigated during recent years, but nowadays research focuses on iron catalysis, due to sustainability, costs and toxicity issues; hence numerous examples for iron-catalyzed cross-coupling reactions have been established, based on the coupling of electrophiles (R(1)-X, X = halide) with nucleophiles (R(2)-MgX). Only a small number of protocols deals with the iron-catalyzed oxidative coupling of nucleophiles (R(1)-MgX + R(2)-MgX) with the aid of oxidants (1,2-dihaloethanes). However, some issues arise with these oxidants; hence more recently the potential of the industrial waste product nitrous oxide (N(2)O) was investigated, because the unproblematic side product N(2) is formed. Based on that, we demonstrate the catalytic potential of easily accessible iron complexes in the oxidative coupling of Grignard reagents. Importantly, nitrous oxide was essential to obtain yields up to >99% at mild conditions (e.g. 1 atm, ambient temperature) and low catalyst loadings (0.1 mol%) Excellent catalyst performance is realized with turnover numbers of up to 1000 and turnover frequencies of up to 12000 h(-1). Moreover, a good functional group tolerance is observed (e.g. amide, ester, nitrile, alkene, alkyne). Afterwards the reaction of different Grignard reagents revealed interesting results with respect to the selectivity of cross-coupling product formation. PMID:26507477

  6. Stable carbon isotope fractionation during trichloroethene degradation in magnetite-catalyzed Fenton-like reaction.

    PubMed

    Liu, Yunde; Zhou, Aiguo; Gan, Yiqun; Liu, Cunfu; Yu, Tingting; Li, Xiaoqian

    2013-02-01

    Mineral-catalyzed Fenton-like oxidation of chlorinated ethylenes is an attractive technique for in situ soil and groundwater remediation. Stable carbon isotope enrichment factors associated with magnetite-catalyzed Fenton-like oxidation of trichloroethylene (TCE) have been determined, to study the possibility of applying stable carbon isotope analysis as a technique to assess the efficacy of remediation implemented by Fenton-like oxidation. The carbon enrichment factors (ε values) ranged from -2.7‰ to -3.6‰ with a mean value of -3.3±0.3‰, and only small differences were observed for different initial reactive conditions. The ε values were robust and reproducible, and were relatively insensitive to a number of environmental factors such as ratios of reactants and PCE co-contamination, which can reduce the uncertainty associated with application of isotope enrichment factors for quantification of in situ remediation by Fenton-like reaction. ε values for Fenton-like oxidation of TCE were intermediate in those previously reported for aerobic biological processes (ε=-1.1 to -20.7‰). Thus, field-derived ε values that are more negative than those for Fenton-like oxidation, may indicate the occurrence of aerobic biodegradation at contaminated sites undergoing in situ remediation with Fenton-like reaction. However, stable carbon isotope analysis is unable to determine whether there is the occurrence of biodegradation processes if field-derived ε values are less negative than those for Fenton-like oxidation.

  7. Mixed-ligand catalysts: a powerful tool in transition-metal- catalyzed cross-coupling reactions.

    PubMed

    Fan, Yuting; Cong, Mei; Peng, Ling

    2014-03-01

    Transition-metal-catalyzed cross-coupling reactions have fundamentally revolutionized organic synthesis, empowering the otherwise difficult to achieve products with rapid and convenient accesses alongside excellent yields. Within these reactions, ligands often play a critical role in specifically and effectively advocating the corresponding catalysis. Consequently, a myriad of ligands have been created and applied to make a fine tuning of electronic and steric effect of catalysts, remarkably promoting catalytic efficiency and applicability. The "mixed-ligand" concept has recently emerged; by combining and capitalizing on the superiority of each individual ligand already available, an expedient way can be achieved to reach a larger extent of catalytic diversity and efficacy. Given the availability of a wealth of ligands, it is reasonable to have great expectations for the original application of mixed-ligand catalytic systems and their important value in organic synthesis.

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

    PubMed

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

    2013-08-14

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

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

    PubMed

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

    2013-08-14

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

  10. The Palladium-Catalyzed Aerobic Kinetic Resolution of Secondary Alcohols: Reaction Development, Scope, and Applications

    PubMed Central

    Ebner, David C.; Bagdanoff, Jeffrey T.; Ferreira, Eric M.; McFadden, Ryan M.; Caspi, Daniel D.; Trend, Raissa M.

    2010-01-01

    The first palladium-catalyzed enantioselective oxidation of secondary alcohols has been developed, utilizing the readily available diamine (−)-sparteine as chiral ligand and molecular oxygen as the stoichiometric oxidant. Mechanistic insights regarding the role of base and hydrogen bond donors have resulted in several improvements to the original system. Namely, addition of cesium carbonate and tert-butyl alcohol greatly enhances reaction rates, promoting rapid resolutions. The use of chloroform as solvent allows the use of ambient air as the terminal oxidant at 23 °C, resulting in enhanced catalyst selectivity. These improved reaction conditions have permitted the successful kinetic resolution of benzylic, allylic, and cyclopropyl secondary alcohols to high enantiomeric excess with good to excellent selectivity factors. This catalyst system has also been applied to the desymmetrization of meso-diols, providing high yields of enantioenriched hydroxyketones. PMID:19904777

  11. 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

  12. 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.

  13. Influence of Ionic Liquids on an Iron(III) Catalyzed Three-Component Coupling/Hydroarylation/Dehydrogenation Tandem Reaction.

    PubMed

    Muntzeck, Maren; Wilhelm, René

    2016-01-01

    A three-component oxidative dehydrogenation tandem reaction via the coupling and hydroarylation of benzaldehyde, aniline and phenylacetylene to a quinoline derivate was catalyzed by an iron-containing ionic liquid. The reaction was air mediated and could be performed under neat conditions. The iron(III) of the ionic liquid was the oxidizing species. PMID:27258264

  14. Influence of Ionic Liquids on an Iron(III) Catalyzed Three-Component Coupling/Hydroarylation/Dehydrogenation Tandem Reaction

    PubMed Central

    Muntzeck, Maren; Wilhelm, René

    2016-01-01

    A three-component oxidative dehydrogenation tandem reaction via the coupling and hydroarylation of benzaldehyde, aniline and phenylacetylene to a quinoline derivate was catalyzed by an iron-containing ionic liquid. The reaction was air mediated and could be performed under neat conditions. The iron(III) of the ionic liquid was the oxidizing species. PMID:27258264

  15. 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...

  16. On the mechanism of N-heterocyclic carbene-catalyzed reactions involving acyl azoliums.

    PubMed

    Mahatthananchai, Jessada; Bode, Jeffrey W

    2014-02-18

    Catalytic reactions promoted by N-heterocyclic carbenes (NHCs) have exploded in popularity since 2004 when several reports described new fundamental reactions that extended beyond the long-studied generation of acyl anion equivalents. These new NHC-catalyzed reactions allow chemists to generate unique reactive species from otherwise inert starting materials, all under simple, mild reaction conditions and with exceptional selectivities. In analogy to transition metal catalysis, the use of NHCs has introduced a new set of elementary steps that operate via discrete reactive species, including acyl anion, homoenolate, and enolate equivalents, usually generated by oxidation state reorganization ("redox neutral" reactions). Nearly all NHC-catalyzed reactions offer operationally simple reactions, proceed at room temperature without the need for stringent exclusion of air, and do not generate reaction byproducts. Variation of the catalyst or reaction conditions can profoundly influence reaction outcomes, and researchers can tune the desired selectivities through careful choice of NHC precursor and base. The catalytically generated homoenolate and enolate equivalents are nucleophilic species. In contrast, the catalytically generated acyl azolium and α,β-unsaturated acyl azoliums are electrophilic cationic species with unique and unprecedented chemistry. For example, when generated catalytically, these species transformed an α-functionalized aldehyde to an ester under redox neutral conditions without coupling reagents or waste. In addition to providing new approaches to catalytic esterifications, acyl azoliums offer unique reactivities that chemists can exploit for selective reactions. This Account focuses on the discovery and mechanistic investigation of the catalytic generation of acyl azoliums and α,β-unsaturated acyl azoliums. These chemical species are fascinating, and their catalytic generation is an important development. Studies of their unusual chemistry

  17. Chemoselective chromium(II)-catalyzed cross-coupling reactions of dichlorinated heteroaromatics with functionalized aryl grignard reagents.

    PubMed

    Steib, Andreas K; Kuzmina, Olesya M; Fernandez, Sarah; Malhotra, Sushant; Knochel, Paul

    2015-01-26

    Chromium(II) chloride catalyzes the chemoselective cross-coupling reaction of dichloropyridines with a range of functionalized (hetero)aromatic Grignard reagents at room temperature. Functional groups, such as esters and acetals, are well tolerated in this transformation. Previously challenging substrates, quinolines and isoquinolines, participate in the selective Cr-catalyzed cross-coupling in cyclopentyl methyl ether (CPME) as the solvent. The effective purging of Cr salts is demonstrated by using various solid supports. PMID:25470669

  18. 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.

  19. Roles of the redox-active disulfide and histidine residues forming a catalytic dyad in reactions catalyzed by 2-ketopropyl coenzyme M oxidoreductase/carboxylase.

    PubMed

    Kofoed, Melissa A; Wampler, David A; Pandey, Arti S; Peters, John W; Ensign, Scott A

    2011-09-01

    NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC), an atypical member of the disulfide oxidoreductase (DSOR) family of enzymes, catalyzes the reductive cleavage and carboxylation of 2-ketopropyl-coenzyme M [2-(2-ketopropylthio)ethanesulfonate; 2-KPC] to form acetoacetate and coenzyme M (CoM) in the bacterial pathway of propylene metabolism. Structural studies of 2-KPCC from Xanthobacter autotrophicus strain Py2 have revealed a distinctive active-site architecture that includes a putative catalytic triad consisting of two histidine residues that are hydrogen bonded to an ordered water molecule proposed to stabilize enolacetone formed from dithiol-mediated 2-KPC thioether bond cleavage. Site-directed mutants of 2-KPCC were constructed to test the tenets of the mechanism proposed from studies of the native enzyme. Mutagenesis of the interchange thiol of 2-KPCC (C82A) abolished all redox-dependent reactions of 2-KPCC (2-KPC carboxylation or protonation). The air-oxidized C82A mutant, as well as wild-type 2-KPCC, exhibited the characteristic charge transfer absorbance seen in site-directed variants of other DSOR enzymes but with a pK(a) value for C87 (8.8) four units higher (i.e., four orders of magnitude less acidic) than that for the flavin thiol of canonical DSOR enzymes. The same higher pK(a) value was observed in native 2-KPCC when the interchange thiol was alkylated by the CoM analog 2-bromoethanesulfonate. Mutagenesis of the flavin thiol (C87A) also resulted in an inactive enzyme for steady-state redox-dependent reactions, but this variant catalyzed a single-turnover reaction producing a 0.8:1 ratio of product to enzyme. Mutagenesis of the histidine proximal to the ordered water (H137A) led to nearly complete loss of redox-dependent 2-KPCC reactions, while mutagenesis of the distal histidine (H84A) reduced these activities by 58 to 76%. A redox-independent reaction of 2-KPCC (acetoacetate decarboxylation) was not decreased for any of the

  20. Coupling Reaction of Enol Derivatives with Silyl Ketene Acetals Catalyzed by Gallium Trihalides.

    PubMed

    Nishimoto, Yoshihiro; Kita, Yuji; Ueda, Hiroki; Imaoka, Hiroto; Chiba, Kouji; Yasuda, Makoto; Baba, Akio

    2016-08-01

    A cross-coupling reaction between enol derivatives and silyl ketene acetals catalyzed by GaBr3 took place to give the corresponding α-alkenyl esters. GaBr3 showed the most effective catalytic ability, whereas other metal salts such as BF3 ⋅OEt2 , AlCl3 , PdCl2 , and lanthanide triflates were not effective. Various types of enol ethers and vinyl carboxylates as enol derivatives are amenable to this coupling. The scope of the reaction with silyl ketene acetals was also broad. We successfully observed an alkylgallium intermediate by using NMR spectroscopy, suggesting a mechanism involving anti-carbogallation among GaBr3 , an enol derivative, and a silyl ketene acetal, followed by syn-β-alkoxy elimination from the alkylgallium. Based on kinetic studies, the turnover-limiting step of the reaction using a vinyl ether and a vinyl carboxylate involved syn-β-alkoxy elimination and anti-carbogallation, respectively. Therefore, the leaving group had a significant effect on the progress of the reaction. Theoretical calculations analysis suggest that the moderate Lewis acidity of gallium would contribute to a flexible conformational change of the alkylgallium intermediate and to the cleavage of the carbon-oxygen bond in the β-alkoxy elimination process, which is the turnover-limiting step in the reaction between a vinyl ether and a silyl ketene acetal. PMID:27400389

  1. Coupling Reaction of Enol Derivatives with Silyl Ketene Acetals Catalyzed by Gallium Trihalides.

    PubMed

    Nishimoto, Yoshihiro; Kita, Yuji; Ueda, Hiroki; Imaoka, Hiroto; Chiba, Kouji; Yasuda, Makoto; Baba, Akio

    2016-08-01

    A cross-coupling reaction between enol derivatives and silyl ketene acetals catalyzed by GaBr3 took place to give the corresponding α-alkenyl esters. GaBr3 showed the most effective catalytic ability, whereas other metal salts such as BF3 ⋅OEt2 , AlCl3 , PdCl2 , and lanthanide triflates were not effective. Various types of enol ethers and vinyl carboxylates as enol derivatives are amenable to this coupling. The scope of the reaction with silyl ketene acetals was also broad. We successfully observed an alkylgallium intermediate by using NMR spectroscopy, suggesting a mechanism involving anti-carbogallation among GaBr3 , an enol derivative, and a silyl ketene acetal, followed by syn-β-alkoxy elimination from the alkylgallium. Based on kinetic studies, the turnover-limiting step of the reaction using a vinyl ether and a vinyl carboxylate involved syn-β-alkoxy elimination and anti-carbogallation, respectively. Therefore, the leaving group had a significant effect on the progress of the reaction. Theoretical calculations analysis suggest that the moderate Lewis acidity of gallium would contribute to a flexible conformational change of the alkylgallium intermediate and to the cleavage of the carbon-oxygen bond in the β-alkoxy elimination process, which is the turnover-limiting step in the reaction between a vinyl ether and a silyl ketene acetal.

  2. Role of substituents on the reactivity and product selectivity in reactions of naphthalene derivatives catalyzed by the orphan thermostable cytochrome P450, CYP175A1.

    PubMed

    Banerjee, Shibdas; Goyal, Sandeep; Mazumdar, Shyamalava

    2015-10-01

    The thermostable nature of CYP175A1 enzyme is of potential interest for the biocatalysis at ambient temperature or at elevated temperature under environmentally benign conditions. Although little is known about the substrate selectivity of this enzyme, the biocatalytic activities of CYP175A1 on different substituted naphthalenes have been studied in oxidative pathway, and the effect of the substituent on the reaction has been determined. The enzyme first acts as a peroxygenase to convert these substituted naphthalenes to the corresponding naphthols, which subsequently undergo in-situ oxidative dimerization to form dyes of different colors possibly by the peroxidase-type activity of CYP175A1. The product analyses and kinetic measurements suggested that the presence of electron releasing substituent (ERS) in the substrate enhanced the substrate conversion, whereas the presence of electron withdrawing substituent (EWS) in the substrate drastically reduced the substrate conversion. The position of the ERS in the substrate was also found to play an important role in the transformation of the substrate. The results further demonstrate that mutation of the Leu80 residue to Phe enhances the reactivity of the enzyme by favoring the substrate association in the active site. The observed rates of the enzymatic oxygenation reaction of the substituted naphthalenes followed the Hammett correlation of substituent effect, supporting aromatic electrophilic substitution mechanism catalyzed by the cytochrome P450 enzyme. PMID:26312734

  3. Role of substituents on the reactivity and product selectivity in reactions of naphthalene derivatives catalyzed by the orphan thermostable cytochrome P450, CYP175A1.

    PubMed

    Banerjee, Shibdas; Goyal, Sandeep; Mazumdar, Shyamalava

    2015-10-01

    The thermostable nature of CYP175A1 enzyme is of potential interest for the biocatalysis at ambient temperature or at elevated temperature under environmentally benign conditions. Although little is known about the substrate selectivity of this enzyme, the biocatalytic activities of CYP175A1 on different substituted naphthalenes have been studied in oxidative pathway, and the effect of the substituent on the reaction has been determined. The enzyme first acts as a peroxygenase to convert these substituted naphthalenes to the corresponding naphthols, which subsequently undergo in-situ oxidative dimerization to form dyes of different colors possibly by the peroxidase-type activity of CYP175A1. The product analyses and kinetic measurements suggested that the presence of electron releasing substituent (ERS) in the substrate enhanced the substrate conversion, whereas the presence of electron withdrawing substituent (EWS) in the substrate drastically reduced the substrate conversion. The position of the ERS in the substrate was also found to play an important role in the transformation of the substrate. The results further demonstrate that mutation of the Leu80 residue to Phe enhances the reactivity of the enzyme by favoring the substrate association in the active site. The observed rates of the enzymatic oxygenation reaction of the substituted naphthalenes followed the Hammett correlation of substituent effect, supporting aromatic electrophilic substitution mechanism catalyzed by the cytochrome P450 enzyme.

  4. Heavy atom isotope effects on the reaction catalyzed by the oxalate decarboxylase from Bacillus subtilis.

    PubMed

    Reinhardt, Laurie A; Svedruzic, Drazenka; Chang, Christopher H; Cleland, W Wallace; Richards, Nigel G J

    2003-02-01

    Oxalate decarboxylase (OxDC) catalyzes a remarkable transformation in which the C-C bond in oxalate is cleaved to give carbon dioxide and formate. Like the native OxDC isolated from Aspergillus niger, the recombinant, bacterial OxDC from Bacillus subtilis contains Mn(II) in its resting state and requires catalytic dioxygen for activity. The most likely mechanism for OxDC-catalyzed C-C bond cleavage involves the participation of free radical intermediates, although this hypothesis remains to be unequivocally demonstrated. Efforts to delineate the catalytic mechanism have been placed on a firm foundation by the high-resolution crystal structure of recombinant, wild type B. subtilis OxDC (Anand et al., Biochemistry 2002, 41, 7659-7669). We now report the results of heavy-atom kinetic isotope effect measurements for the OxDC-catalyzed decarboxylation of oxalate, in what appear to be the first detailed studies of the mechanism employed by OxDC. At pH 4.2, the OxDC-catalyzed formation of formate and CO(2) have normal (13)C isotope effects of 1.5% +/- 0.1% and 0.5% +/- 0.1%, respectively, while the (18)O isotope effect on the formation of formate is 1.1% +/- 0.2% normal. Similarly at pH 5.7, the production of formate and CO(2) exhibits normal (13)C isotope effects of 1.9% +/- 0.1% and 0.8% +/- 0.1%, respectively, and the (18)O isotope effect on the formation of formate is 1.0% +/- 0.2% normal. The (18)O isotope effect on the formation of CO(2), however, 0.7% +/- 0.2%, is inverse at pH 5.7. These results are consistent with a multistep model in which a reversible, proton-coupled, electron transfer from bound oxalate to the Mn-enzyme gives an oxalate radical, which decarboxylates to yield a formate radical anion. Subsequent reduction and protonation of this intermediate then gives formate.

  5. 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

  6. Effect of osmolytes on protein dynamics in the lactate dehydrogenase-catalyzed reaction.

    PubMed

    Zhadin, Nickolay; Callender, Robert

    2011-03-15

    Laser-induced temperature jump relaxation spectroscopy was used to probe the effect of osmolytes on the microscopic rate constants of the lactate dehydrogenase-catalyzed reaction. NADH fluorescence and absorption relaxation kinetics were measured for the lactate dehydrogenase (LDH) reaction system in the presence of varying amounts of trimethylamine N-oxide (TMAO), a protein-stabilizing osmolyte, or urea, a protein-destabilizing osmolyte. Trimethylamine N-oxide (TMAO) at a concentration of 1 M strongly increases the rate of hydride transfer, nearly nullifies its activation energy, and also slightly increases the enthalpy of hydride transfer. In 1 M urea, the hydride transfer enthalpy is almost nullified, but the activation energy of the step is not affected significantly. TMAO increases the preference of the closed conformation of the active site loop in the LDH·NAD(+)·lactate complex; urea decreases it. The loop opening rate in the LDH·NADH·pyruvate complex changes its temperature dependence to inverse Arrhenius with TMAO. In this complex, urea accelerates the loop motion, without changing the loop opening enthalpy. A strong, non-Arrhenius decrease in the pyruvate binding rate in the presence of TMAO offers a decrease in the fraction of the open loop, pyruvate binding competent form at higher temperatures. The pyruvate off rate is not affected by urea but decreases with TMAO. Thus, the osmolytes strongly affect the rates and thermodynamics of specific events along the LDH-catalyzed reaction: binding of substrates, loop closure, and the chemical event. Qualitatively, these results can be understood as an osmolyte-induced change in the energy landscape of the protein complexes, shifting the conformational nature of functional substates within the protein ensemble.

  7. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Sieffert, Nicolas; Bühl, Michael

    2010-06-16

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

  11. 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.

  12. 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 β-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

  13. Palladium(0)/NHC-Catalyzed Reductive Heck Reaction of Enones: A Detailed Mechanistic Study.

    PubMed

    Raoufmoghaddam, Saeed; Mannathan, Subramaniyan; Minnaard, Adriaan J; de Vries, Johannes G; Reek, Joost N H

    2015-12-14

    We have studied the mechanism of the palladium-catalyzed reductive Heck reaction of para-substituted enones with 4-iodoanisole by using N,N-diisopropylethylamine (DIPEA) as the reductant. Kinetic studies and in situ spectroscopic analysis have provided a detailed insight into the reaction. Progress kinetic analysis demonstrated that neither catalyst decomposition nor product inhibition occurred during the catalysis. The reaction is first order in the palladium and aryl iodide, and zero order in the activated alkene, N-heterocyclic carbene (NHC) ligand, and DIPEA. The experiments with deuterated solvent ([D7]DMF) and deuterated base ([D15]Et3N) supported the role of the amine as a reductant in the reaction. The palladium complex [Pd(0)(NHC)(1)] has been identified as the resting state. The kinetic experiments by stopped-flow UV/Vis also revealed that the presence of the second substrate, benzylideneacetone 1, slows down the oxidative addition of 4-iodoanisole through its competing coordination to the palladium center. The kinetic and mechanistic studies indicated that the oxidative addition of the aryl iodide is the rate-determining step. Various scenarios for the oxidative addition step have been analyzed by using DFT calculations (bp86/def2-TZVP) that supported the inhibiting effect of substrate 1 by formation of resting state [Pd(0)(NHC)(1)] species at the cost of further increase in the energy barrier of the oxidative addition step. PMID:26561034

  14. CuBr catalyzed C-N cross coupling reaction of purines and diaryliodonium salts to 9-arylpurines.

    PubMed

    Niu, Hong-Ying; Xia, Chao; Qu, Gui-Rong; Zhang, Qian; Jiang, Yi; Mao, Run-Ze; Li, De-Yang; Guo, Hai-Ming

    2011-07-21

    CuBr was found to be an efficient catalyst for the C-N cross coupling reaction of purine and diaryliodonium salts. 9-Arylpurines were synthesized in excellent yields with short reaction times (2.5 h). The method represents an alternative to the synthesis of 9-arylpurines via Cu(II) catalyzed C-N coupling reaction with arylboronic acids as arylating agents. PMID:21660365

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2015-11-01

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

  17. Iron-Catalyzed Enantioselective Cross-Coupling Reactions of α-Chloroesters with Aryl Grignard Reagents.

    PubMed

    Jin, Masayoshi; Adak, Laksmikanta; Nakamura, Masaharu

    2015-06-10

    The first iron-catalyzed enantioselective cross-coupling reaction between an organometallic compound and an organic electrophile is reported. Synthetically versatile racemic α-chloro- and α-bromoalkanoates were coupled with aryl Grignard reagents in the presence of catalytic amounts of an iron salt and a chiral bisphosphine ligand, giving the products in high yields with acceptable and synthetically useful enantioselectivities (er up to 91:9). The produced α-arylalkanoates were readily converted to the corresponding α-arylalkanoic acids with high optical enrichment (er up to >99:1) via simple deprotections/recrystallizations. The results of radical probe experiments are consistent with a mechanism that involves the formation of an alkyl radical intermediate, which undergoes subsequent enantioconvergent arylation in an intermolecular manner. The developed asymmetric coupling offers not only facile and practical access to various chiral α-arylalkanoic acid derivatives, which are of significant pharmaceutical importance, but also a basis of controlling enantioselectivity in an iron-catalyzed organometallic transformation. PMID:25955413

  18. Quantum mechanical/molecular mechanical study of catalytic mechanism and role of key residues in methylation reactions catalyzed by dimethylxanthine methyltransferase in caffeine biosynthesis.

    PubMed

    Yue, Yufei; Guo, Hong

    2014-02-24

    The caffeine biosynthetic pathway is of considerable importance for the beverage and pharmaceutical industries which produces two blockbuster products: theobromine and caffeine. The major biochemistry in caffeine biosynthesis starts from the initial substrate of xanthosine and ends with the final product caffeine, with theobromine serving as an intermediate. The key enzyme, S-adenosyl-l-methionine (SAM) dependent 3,7-dimethyl-xanthine methyltransferase (DXMT), catalyzes two important methyl transfer steps in caffeine biosynthesis: (1) methylation of N3 of 7-methylxanthine (7mX) to form theobromine (Tb); (2) methylation of N1 of theobromine to form caffeine (Cf). Although DXMT has been structurally characterized recently, our understanding of the detailed catalytic mechanism and role of key catalytic residues is still lacking. In this work, the quantum mechanical/molecular mechanical (QM/MM) MD and free energy simulations are performed to elucidate the catalytic mechanism of the enzyme-catalyzed reactions and to explain experimental observations concerning the activity of this enzyme. The roles of certain active-site residues are studied, and the results of computer simulation seem to suggest that a histidine residue (His160) at the active site of DXMT may act as a general base/acid catalyst during the methyl transfer process.

  19. 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

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

    PubMed

    Fructos, Manuel R; Urbano, Juan; Díaz-Requejo, M Mar; Pérez, Pedro J

    2015-01-01

    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.

  1. The Contribution of Electrostatic and van der Waals Interactions to the Stereospecificity of the Reaction Catalyzed by Lactate Dehydrogenase

    PubMed Central

    van Beek, Jeroen; Callender, Robert; Gunner, M. R.

    1997-01-01

    Continuum electrostatic calculations in conjunction with molecular dynamics simulations have been used to investigate the source of the stereospecificity in the hydride transfer reaction catalyzed by lactate dehydrogenase (LDH). These studies show that favorable electrostatic interactions between the carboxamide group of the reduced nicotinamide adenine dinucleotide coenzyme and protein residues of the active site of LDH can account for much if not all of the stereospecificity of the LDH-catalyzed reaction, with A-side hydride transfer more than 107 times greater than B-side transfer. Unfavorable steric interactions within the binding complex for B-side transfer are not found. ImagesFIGURE 2 PMID:9017191

  2. 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

  3. 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

  4. Stereospecific Nickel-Catalyzed Cross-Coupling Reactions of Benzylic Ethers and Esters

    PubMed Central

    2015-01-01

    Conspectus 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

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

    PubMed

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

    2010-11-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  7. Whole-Cell-Catalyzed Multiple Regio- and Stereoselective Functionalizations in Cascade Reactions Enabled by Directed Evolution.

    PubMed

    Li, Aitao; Ilie, Adriana; Sun, Zhoutong; Lonsdale, Richard; Xu, Jian-He; Reetz, Manfred T

    2016-09-19

    Biocatalytic cascade reactions using isolated stereoselective enzymes or whole cells in one-pot processes lead to value-added chiral products in a single workup. The concept has been restricted mainly to starting materials and intermediate products that are accepted by the respective wild-type enzymes. In the present study, we exploited directed evolution as a means to create E. coli whole cells for regio- and stereoselective cascade sequences that are not possible using man-made catalysts. The approach is illustrated using P450-BM3 in combination with appropriate alcohol dehydrogenases as catalysts in either two-, three-, or four-step cascade reactions starting from cyclohexane, cyclohexanol, or cyclohexanone, respectively, leading to either (R,R)-, (S,S)-, or meso-cyclohexane-1,2-diol. The one-pot conversion of cyclohexane into (R)- or (S)-2-hydroxycyclohexanone in the absence of ADH is also described. PMID:27573978

  8. 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.

  9. Determination of selenium via the fluorescence quenching effect of selenium on hemoglobin-catalyzed peroxidative reaction.

    PubMed

    Chen, Ya-Hong; Zhang, Ya-Nan; Tian, Feng-Shou

    2015-05-01

    A new method for the determination of selenium based on its fluorescence quenching on the hemoglobin-catalyzed reaction of H2 O2 and l-tyrosine has been established. The effect of pH, foreign ions and the optimization of variables on the determination of selenium was examined. The calibration curve was found to be linear between the fluorescence quenching (F0 /F) and the concentration of selenium within the range of 0.16-4.00 µg/mL. The detection limit was 1.96 ng/mL and the relative standard deviation was 3.14%. This method can be used for the determination of selenium in Se-enriched garlic bulbs with satisfactory results.

  10. Heterometallic Metal-Organic Frameworks That Catalyze Two Different Reactions Sequentially.

    PubMed

    Saha, Debraj; Hazra, Dipak K; Maity, Tanmoy; Koner, Subratanath

    2016-06-20

    A series of copper- and alkaline-earth-metal-based multidimensional metal-organic frameworks, {[CuMg(pdc)2(H2O)4]·2H2O}n (1), [CuCa(pdc)2]n (2), [CuSr(pdc)2(H2O)3]n (3), and {[CuBa(pdc)2(H2O)5]·H2O}n (4), where H2Pdc = pyridine-2,5-dicarboxylic acid, were hydrothermally synthesized and characterized. Two different metals act as the active center to catalyze two kinds of reactions, viz., olefin to its epoxide followed by epoxide ring opening to afford the corresponding vicinal diol in a sequential manner. PMID:27232433

  11. DFT studies on the palladium-catalyzed dearomatization reaction between naphthalene allyl chloride and allyltributylstannane.

    PubMed

    Cao, Wei; Tian, Dongxu; Han, Dongxue

    2015-10-01

    The Pd-catalyzed dearomatization of naphthalene allyl chloride with allyltributylstannane has been investigated using density functional theory (DFT) calculations at the B3LYP level. The calculations indicate that the (ŋ(1)-allyl)(ŋ(3)-allyl)Pd(PH3) complex is responsible for the formation of ortho-dearomatized product. Moreover it is easy to produce the ortho-dearomatized product when reductive elimination starts from (ŋ(3)-allylnaphthalene)(ŋ(1)-allyl)Pd complex 7, while it is easy to form the para-dearomatized product when reductive elimination starts from (ŋ(3)-allylnaphthalene)(ŋ(1)-allyl)Pd complex 9. The Stille coupling products can't be produced due to high reaction energy barrier. Graphical Abstract Two mechanisms of dearomatization are investigated by DFT, and (ŋ(1)-allyl)(ŋ(3)-allyl)Pd(PH3) complexes are the main intermediates for ortho-dearomatized product.

  12. 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.

  13. Transition-metal-catalyzed carbonylation reactions of olefins and alkynes: a personal account.

    PubMed

    Wu, Xiao-Feng; Fang, Xianjie; Wu, Lipeng; Jackstell, Ralf; Neumann, Helfried; Beller, Matthias

    2014-04-15

    Carbon monoxide was discovered and identified in the 18th century. Since the first applications in industry 80 years ago, academic and industrial laboratories have broadly explored CO's use in chemical reactions. Today organic chemists routinely employ CO in organic chemistry to synthesize all kinds of carbonyl compounds. Despite all these achievements and a century of carbonylation catalysis, many important research questions and challenges remain. Notably, apart from academic developments, industry applies carbonylation reactions with CO on bulk scale. In fact, today the largest applications of homogeneous catalysis (regarding scale) are carbonylation reactions, especially hydroformylations. In addition, the vast majority of acetic acid is produced via carbonylation of methanol (Monsanto or Cativa process). The carbonylation of olefins/alkynes with nucleophiles, such as alcohols and amines, represent another important type of such reactions. In this Account, we discuss our work on various carbonylations of unsaturated compounds and related reactions. Rhodium-catalyzed isomerization and hydroformylation reactions of internal olefins provide straightforward access to higher value aldehydes. Catalytic hydroaminomethylations offer an ideal way to synthesize substituted amines and even heterocycles directly. More recently, our group has also developed so-called alternative metal catalysts based on iridium, ruthenium, and iron. What about the future of carbonylation reactions? CO is already one of the most versatile C1 building blocks for organic synthesis and is widely used in industry. However, because of CO's high toxicity and gaseous nature, organic chemists are often reluctant to apply carbonylations more frequently. In addition, new regulations have recently made the transportation of carbon monoxide more difficult. Hence, researchers will need to develop and more frequently use practical and benign CO-generating reagents. Apart from formates, alcohols, and metal

  14. 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.

  15. Palladium-Based Nanomaterials: A Platform to Produce Reactive Oxygen Species for Catalyzing Oxidation Reactions.

    PubMed

    Long, Ran; Huang, Hao; Li, Yaping; Song, Li; Xiong, Yujie

    2015-11-25

    Oxidation reactions by molecular oxygen (O2 ) over palladium (Pd)-based nanomaterials are a series of processes crucial to the synthesis of fine chemicals. In the past decades, investigations of related catalytic materials have mainly been focused on the synthesis of Pd-based nanomaterials from the angle of tailoring their surface structures, compositions and supporting materials, in efforts to improve their activities in organic reactions. From the perspective of rational materials design, it is imperative to address the fundamental issues associated with catalyst performance, one of which should be oxygen activation by Pd-based nanomaterials. Here, the fundamentals that account for the transformation from O2 to reactive oxygen species over Pd, with a focus on singlet O2 and its analogue, are introduced. Methods for detecting and differentiating species are also presented to facilitate future fundamental research. Key factors for tuning the oxygen activation efficiencies of catalytic materials are then outlined, and recent developments in Pd-catalyzed oxygen-related organic reactions are summarized in alignment with each key factor. To close, we discuss the challenges and opportunities for photocatalysis research at this unique intersection as well as the potential impact on other research fields.

  16. 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.

  17. 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.

  18. Novel palladium complex-catalyzed reaction of magnesium amides with allylic electrophiles

    SciTech Connect

    Dzhemilev, U.M.; Ibragimov, A.G.; Minsker, D.L.; Muslukhov, R.R.

    1987-08-20

    In order to develop an efficient method for the synthesis of higher order unsaturated tertiary amines, and also to explore a new method for the formation of C-N bonds, they have investigated the transition metal complex-catalyzed reaction of magnesium amides with electrophiles; the electrophiles selected for study included allyl ethers and esters, as well as sulfones, sulfides and quaternized allylamines. The effects of the nature and structure of the catalyst components, as well as of the reaction conditions, on product yield were examined in the case of the reaction of diethyl (bromomagnesium)amine with diallyl ether, and revealed that the highest yield of diethylallyl-amine (I) was achieved using Pd(acac)/sub 2/ (3-5 mole %) and Ph/sub 3/P (1:2) as catalyst in THF solution at 50/sup 0/C for 5 h. Other transition metal (Ni, Fe, Zr, Ti, Cu) compounds were also examined as catalysts, but the yield of (I) did not exceed 15% with these compounds. Bimetallic catalysts based on Zr (Cp/sub 2/ZrCl, Py/sub 2/ZrCl/sub 6/, (RO)/sub 4/Zr) and Ni (Ni(acac)/sub 2/ and NiCl/sub 2/) were successful in forming (I) from diethyl (bromomagnesium)amine and diallyl ether in 60% yield.

  19. Palladium-Based Nanomaterials: A Platform to Produce Reactive Oxygen Species for Catalyzing Oxidation Reactions.

    PubMed

    Long, Ran; Huang, Hao; Li, Yaping; Song, Li; Xiong, Yujie

    2015-11-25

    Oxidation reactions by molecular oxygen (O2 ) over palladium (Pd)-based nanomaterials are a series of processes crucial to the synthesis of fine chemicals. In the past decades, investigations of related catalytic materials have mainly been focused on the synthesis of Pd-based nanomaterials from the angle of tailoring their surface structures, compositions and supporting materials, in efforts to improve their activities in organic reactions. From the perspective of rational materials design, it is imperative to address the fundamental issues associated with catalyst performance, one of which should be oxygen activation by Pd-based nanomaterials. Here, the fundamentals that account for the transformation from O2 to reactive oxygen species over Pd, with a focus on singlet O2 and its analogue, are introduced. Methods for detecting and differentiating species are also presented to facilitate future fundamental research. Key factors for tuning the oxygen activation efficiencies of catalytic materials are then outlined, and recent developments in Pd-catalyzed oxygen-related organic reactions are summarized in alignment with each key factor. To close, we discuss the challenges and opportunities for photocatalysis research at this unique intersection as well as the potential impact on other research fields. PMID:26422795

  20. 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.

  1. Electrogenic steps in the redox reactions catalyzed by photosynthetic reaction-centre complex from Rhodopseudomonas viridis.

    PubMed

    Dracheva, S M; Drachev, L A; Konstantinov, A A; Semenov AYu; Skulachev, V P; Arutjunjan, A M; Shuvalov, V A; Zaberezhnaya, S M

    1988-01-15

    Electrogenic and redox events in the reaction-centre complexes from Rhodopseudomonas viridis have been studied. In contrast to the previous points of view it is shown that all the four hemes of the tightly bound cytochrome c have different Em values (-60, +20, +310 and +380 mV). The first three hemes reveal alpha absorption maxima at 554 nm, 552 nm and 556 nm respectively. The 380-mV heme displays a split alpha band with a maximum at 559 nm and a shoulder at 552 nm. Such a splitting is due to non-degenerated Qx and Qy transitions in the iron-porphyrin ring as demonstrated by magnetic circular dichroism spectra. Fast kinetic measurements show that, at redox potentials when only high-potential hemes c-559 and c-556 are reduced, heme c-559 appears to be the electron donor to P-960+ (tau = 0.32 microsecond) whereas heme c-556 serves to rereduce c-559 (tau = 2.5 microsecond). Upon reduction of the third heme (c-552), the P-960+ reduction rate increases twofold (tau = 0.17 microsecond) and all photoinduced redox events within the cytochrome appear to be complete in less than 1 microsecond after the flash. The following sequence of the redox centers is tentatively suggested: c-554, c-556, c-552, c-559, P-960. To study electrogenesis, the reaction-centre complexes from Rps. viridis were incorporated into asolectin liposomes, and fast kinetics of laser flash-induced electric potential difference has been measured in proteoliposomes adsorbed on a phospholipid-impregnated film. The electrical difference induced by a single 15-ns flash was found to be as high as 100 mV. The photoelectric response has been found to involve four electrogenic stages associated with (I) QA reduction by P-960; (II) reduction of P-960+ by heme c-559; (III) reduction of c-559 by c-556 and (IV) protonation of Q2-B. The relative contributions of stages I, II, III and IV are found to be equal to 70%, 15%, 5% and 10%, respectively, of the overall electrogenic process. At the same time, the first three

  2. Formation of a complex pattern of sinapate esters in Brassica napus seeds, catalyzed by enzymes of a serine carboxypeptidase-like acyltransferase family?

    PubMed

    Baumert, Alfred; Milkowski, Carsten; Schmidt, Jürgen; Nimtz, Manfred; Wray, Victor; Strack, Dieter

    2005-06-01

    Members of the Brassicaceae accumulate complex patterns of sinapate esters, as shown in this communication with seeds of oilseed rape (Brassica napus). Fifteen seed constituents were isolated and identified by a combination of high-field NMR spectroscopy and high resolution electrospray ionisation mass spectrometry. These include glucose, gentiobiose and kaempferol glycoside esters as well as sinapine (sinapoylcholine), sinapoylmalate and an unusual cyclic spermidine amide. One of the glucose esters (1,6-di-O-sinapoylglucose), two gentiobiose esters (1-O-caffeoylgentiobiose and 1,2,6'-tri-O-sinapoylgentiobiose) and two kaempferol conjugates [4'-(6-O-sinapoylglucoside)-3,7-di-O-glucoside and 3-O-sophoroside-7-O-(2-O-sinapoylglucoside)] seem to be new plant products. Serine carboxypeptidase-like (SCPL) acyltransferases catalyze the formation of sinapine and sinapoylmalate accepting 1-O-beta-acetal esters (1-O-beta-glucose esters) as acyl donors. To address the question whether the formation of other components of the complex pattern of the sinapate esters in B. napus seeds is catalyzed via 1-O-sinapoyl-beta-glucose, we performed a seed-specific dsRNAi-based suppression of the sinapate glucosyltransferase gene (BnSGT1) expression. In seeds of BnSGT1-suppressing plants the amount of sinapoylglucose decreased below the HPLC detection limit resulting in turn in the disappearance or marked decrease of all the other sinapate esters, indicating that formation of the complex pattern of these esters in B. napus seeds is dependent on sinapoylglucose. This gives rise to the assumption that enzymes of an SCPL acyltransferase family catalyze the appropriate transfer reactions to synthesize the accumulating esters. PMID:15907956

  3. 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

  4. 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.

  5. Cinchona Urea-Catalyzed Asymmetric Sulfa-Michael Reactions: The Brønsted Acid-Hydrogen Bonding Model.

    PubMed

    Grayson, Matthew N; Houk, K N

    2016-07-27

    The cinchona alkaloid-derived urea-catalyzed asymmetric conjugate addition of aromatic thiols to cycloalkenones was studied using density functional theory (DFT). Deprotonation of the thiol gives a protonated amine that activates the electrophile by Brønsted acid catalysis, while the urea group binds the nucleophilic thiolate by hydrogen bonding. These results demonstrate the generality of the Brønsted acid-hydrogen bonding transition state (TS) model for cinchona alkaloid catalysis that we recently showed to be favored over Wynberg's widely accepted ion pair-hydrogen bonding model and represent the first detailed mechanistic study of a cinchona urea-catalyzed reaction. The conformation of the catalyst methoxy group has a strong effect on the TS, an effect overlooked in previous mechanistic studies of reactions catalyzed by cinchona alkaloids.

  6. 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.

  7. Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

    PubMed

    Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

    2008-01-01

    A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

  8. Diazo compounds and N-tosylhydrazones: novel cross-coupling partners in transition-metal-catalyzed reactions.

    PubMed

    Xiao, Qing; Zhang, Yan; Wang, Jianbo

    2013-02-19

    Transition-metal-catalyzed carbene transformations and cross-couplings represent two major reaction types in organometallic chemistry and organic synthesis. However, for a long period of time, these two important areas have evolved separately, with essentially no overlap or integration. Thus, an intriguing question has emerged: can cross-coupling and metal carbene transformations be merged into a single reaction cycle? Such a combination could facilitate the development of novel carbon-carbon bond-forming methodologies. Although this concept was first explored about 10 years ago, rapid developments inthis area have been achieved recently. Palladium catalysts can be used to couple diazo compounds with a wide variety of organic halides. Under oxidative coupling conditions, diazo compounds can also react with arylboronic acids and terminal alkynes. Both of these coupling reactions form carbon-carbon double bonds. As the key step in these catalytic processes, Pd carbene migratory insertion plays a vital role in merging the elementary steps of Pd intermediates, leading to novel carbon-carbon bond formations. Because the diazo substrates can be generated in situ from N-tosylhydrazones in the presence of base, the N-tosylhydrazones can be used as reaction partners, making this type of cross-coupling reaction practical in organic synthesis. N-Tosylhydrazones are easily derived from the corresponding aldehydes or ketones. The Pd-catalyzed cross-coupling of N-tosylhydrazones is considered a complementary reaction to the classic Shapiro reaction for converting carbonyl functionalities into carbon-carbon double bonds. It can also serve as an alternative approach for the Pd-catalyzed cross-coupling of carbonyl compounds, which is usually achieved via triflates. The combination of carbene formation and cross-coupling in a single catalytic cycle is not limited to Pd-catalyzed reactions. Recent studies of Cu-, Rh-, Ni-, and Co-catalyzed cross-coupling reactions with diazo

  9. Metal-ligand binding affinity vs reactivity: qualitative studies in Rh(I)-catalyzed asymmetric ring-opening reactions.

    PubMed

    Tsui, Gavin Chit; Dougan, Patrick; Lautens, Mark

    2013-06-01

    Rh(I)-catalyzed asymmetric ring opening (ARO) of oxabenzonorbornadiene is used as a model system to qualitatively study reactions involving multiple metal-ligand interactions. The key feature of this approach is the use of product ee as an indicator to quickly gain important information such as the relative ligand binding affinity and relative reactivity of catalysts.

  10. 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.

  11. New efficient ligand for sub-mol % copper-catalyzed C-N cross-coupling reactions running under air.

    PubMed

    Larsson, Per-Fredrik; Astvik, Peter; Norrby, Per-Ola

    2012-01-01

    A new efficient ligand, N,N''-dimethyldiethylene triamine (DMDETA), has been synthesized and evaluated for sub-mol % copper-catalyzed C-N cross-coupling reactions. The efficiency of the ligand was determined by kinetic methods. DMDETA proved to display efficiency similar to DMEDA and, in addition, the resulting catalyst was tolerant to air. PMID:23209530

  12. New efficient ligand for sub-mol % copper-catalyzed C–N cross-coupling reactions running under air

    PubMed Central

    Larsson, Per-Fredrik; Astvik, Peter

    2012-01-01

    Summary A new efficient ligand, N,N’’-dimethyldiethylene triamine (DMDETA), has been synthesized and evaluated for sub-mol % copper-catalyzed C–N cross-coupling reactions. The efficiency of the ligand was determined by kinetic methods. DMDETA proved to display efficiency similar to DMEDA and, in addition, the resulting catalyst was tolerant to air. PMID:23209530

  13. Evidence for the involvement of acid/base chemistry in the reaction catalyzed by the type II isopentenyl diphosphate/dimethylallyl diphosphate isomerase from Staphylococcus aureus.

    PubMed

    Thibodeaux, Christopher J; Mansoorabadi, Steven O; Kittleman, William; Chang, Wei-chen; Liu, Hung-wen

    2008-02-26

    The type II isopentenyl diphosphate/dimethylallyl diphosphate isomerase (IDI-2) is a flavin mononucleotide (FMN)-dependent enzyme that catalyzes the reversible isomerization of isopentenyl pyrophosphate (IPP) to dimethylallyl pyrophosphate (DMAPP), a reaction with no net change in redox state of the coenzyme or substrate. Here, UV-vis spectral analysis of the IDI-2 reaction revealed the accumulation of a reduced neutral dihydroflavin intermediate when the reduced enzyme was incubated with IPP or DMAPP. When IDI-2 was reconstituted with 1-deazaFMN and 5-deazaFMN, similar reduced neutral forms of the deazaflavin analogues were observed in the presence of IPP. Single turnover stopped-flow absorbance experiments indicated that this flavin intermediate formed and decayed at kinetically competent rates in the pre-steady-state and, thus, most likely represents a true intermediate in the catalytic cycle. UV-vis spectra of the reaction mixtures reveal trace amounts of a neutral semiquinone, but evidence for the presence of IPP-based radicals could not be obtained by EPR spectroscopy. Rapid-mix chemical quench experiments show no burst in DMAPP formation, suggesting that the rate determining step in the forward direction (IPP to DMAPP) occurs prior to DMAPP formation. A solvent deuterium kinetic isotope effect (D2OVmax = 1.5) was measured on vo in steady-state kinetic experiments at saturating substrate concentrations. A substrate deuterium kinetic isotope effect was also measured on the initital velocity (DVmax = 1.8) and on the decay rate of the flavin intermediate (Dks = 2.3) in single-turnover stopped-flow experiments using (R)-[2-2H]-IPP. Taken together, these data suggest that the C2-H bond of IPP is cleaved in the rate determining step and that general acid/base catalysis may be involved during turnover. Possible mechanisms for the IDI-2 catalyzed reaction are presented and discussed in terms of the available X-ray crystal structures.

  14. Inhibitors of enzymes catalyzing modifications to histone lysine residues: structure, function and activity.

    PubMed

    Lillico, Ryan; Stesco, Nicholas; Khorshid Amhad, Tina; Cortes, Claudia; Namaka, Mike P; Lakowski, Ted M

    2016-05-01

    Gene expression is partly controlled by epigenetic mechanisms including histone-modifying enzymes. Some diseases are caused by changes in gene expression that can be mitigated by inhibiting histone-modifying enzymes. This review covers the enzyme inhibitors targeting histone lysine modifications. We summarize the enzymatic mechanisms of histone lysine acetylation, deacetylation, methylation and demethylation and discuss the biochemical roles of these modifications in gene expression and in disease. We discuss inhibitors of lysine acetylation, deacetylation, methylation and demethylation defining their structure-activity relationships and their potential mechanisms. We show that there are potentially indiscriminant off-target effects on gene expression even with the use of selective epigenetic enzyme inhibitors.

  15. 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

  16. Mechanistic Studies Lead to Dramatically Improved Reaction Conditions for the Cu-Catalyzed Asymmetric Hydroamination of Olefins.

    PubMed

    Bandar, Jeffrey S; Pirnot, Michael T; Buchwald, Stephen L

    2015-11-25

    Enantioselective copper(I) hydride (CuH)-catalyzed hydroamination has undergone significant development over the past several years. To gain a general understanding of the factors governing these reactions, kinetic and spectroscopic studies were performed on the CuH-catalyzed hydroamination of styrene. Reaction profile analysis, rate order assessment, and Hammett studies indicate that the turnover-limiting step is regeneration of the CuH catalyst by reaction with a silane, with a phosphine-ligated copper(I) benzoate as the catalyst resting state. Spectroscopic, electrospray ionization mass spectrometry, and nonlinear effect studies are consistent with a monomeric active catalyst. With this insight, targeted reagent optimization led to the development of an optimized protocol with an operationally simple setup (ligated copper(II) precatalyst, open to air) and short reaction times (<30 min). This improved protocol is amenable to a diverse range of alkene and alkyne substrate classes. PMID:26522837

  17. Conversion of acetyl-coenzyme A into 3-hydroxy-3-methylglutaryl-coenzyme A in radish seedlings. Evidence of a single monomeric protein catalyzing a FeII/quinone-stimulated double condensation reaction.

    PubMed

    Weber, T; Bach, T J

    1994-02-10

    We solubilized from radish membranes and purified to apparent homogeneity a monomeric protein (55.5 kDa) capable of catalyzing the two-step conversion of acetyl-CoA into 3-hydroxy-3-methylglutaryl(HMG)-CoA. Unlike the situation described for other eukaryotes (yeast, animals), both enzyme activities needed for HMG-CoA synthesis (acetoacetyl-CoA thiolase, AACT and HMG-CoA synthase, HMGS) appear to be localized on a single polypeptide. Thus, the enzyme system is further referred to as AACT/HMGS. The reaction as catalyzed by purified AACT/HMGS is strongly stimulated in vitro in presence of FeII-chelates (namely EDTA) and of quinone cofactors with pyrroloquinoline quinone (PQQ) being by far the most effective one studied so far. Whereas the FeII stimulation is apparently due to a Vmax effect, PQQ increases the affinity of the enzyme system towards acetyl-CoA (1.9 microM vs. 5.9 microM, at 50 microM FeII, 100 microM EDTA, 20 microM PQQ). Stimulation by naphthoquinone (NQ) can be overcome in the presence of halogenated NQ-derivatives, while activation by PQQ remains unaffected, possibly indicating a much more specific-binding of the latter cofactor. Gel filtration experiments of enzyme after preincubation in presence of PQQ indicate that there is no covalent-binding of the quinone cofactor to the enzyme. As is also shown with partially purified enzyme from maize membranes, phenylhydrazine, known to react with PQQ as the prosthetic group of quinoproteins (see van der Meer et al. (1987) FEBS Lett. 221, 299-304), efficiently inhibits the reaction. The data lead us to suggest a reaction mechanism that involves radical formation by the redox couple FeII/PQQ, thereby possibly facilitating the energetically unfavorable Claisen condensation as catalyzed during the first partial (AACT) reaction.

  18. 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.

  19. Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

    PubMed

    Chan, Kui K; Wood, B McKay; Fedorov, Alexander A; Fedorov, Elena V; Imker, Heidi J; Amyes, Tina L; Richard, John P; Almo, Steven C; Gerlt, John A

    2009-06-23

    The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (k(cat)/k(non), 7.1 x 10(16)) and proficiency [(k(cat)/K(M))/k(non), 4.8 x 10(22) 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 (>or=10(10)). The origin of the "missing" contribution, or=10(10)), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of k(cat) for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of k(ex) 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 a vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and

  20. Palladium-Catalyzed α-Arylation of Zinc Enolates of Esters: Reaction Conditions and Substrate Scope

    PubMed Central

    Hama, Takuo; Ge, Shaozhong; Hartwig, John F.

    2013-01-01

    The intermolecular α-arylation of esters by palladium-catalyzed coupling of aryl bromides with zinc enolates of esters is reported. Reactions of three different types of zinc enolates have been developed. α-Arylation of esters occurs in high yields with isolated Reformatsky reagents, with Reformatsky reagents generated from α-bromo esters and activated zinc, and with zinc enolates generated by quenching lithium enolates of esters with zinc chloride. The use of zinc enolates, instead of alkali metal enolates, greatly expands the scope of the arylation of esters. The reactions occur at room temperature or at 70 °C with bromoarenes containing cyano, nitro, ester, keto, fluoro, enolizable hydrogen, hydroxyl or amino functionality and with bromopyridines. The scope of esters encompasses acyclic acetates, propionates, and isobutyrates, α-alkoxyesters, and lactones. The arylation of zinc enolates of esters was conducted with catalysts bearing the hindered pentaphenylferrocenyl di-tert-butylphosphine (Q-phos) or the highly reactive dimeric Pd(I) complex {[P(t-Bu)3]PdBr}2. PMID:23931445

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

    SciTech Connect

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

    2013-09-06

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

  2. Computational study of gold-catalyzed homo- and cross-coupling reactions.

    PubMed

    Nieto Faza, Olalla; Silva López, Carlos

    2013-05-17

    The role of gold as the organizing metal in homo- and cross-coupling reactions is explored in this paper combining DFT calculations with QTAIM, NBO, and the energetic span model analysis. For the gold(III) complex 7, a key intermediate in the experimental oxidative coupling scheme by Zhang et al., we describe the mechanisms corresponding to a cross-coupling after transmetalation with boron compounds and to a homocoupling after transmetalation with the original gold(I) complex 6, a new example of dual role of this metal in homogeneous catalysis. We predict for the first path a two-step transmetalation with a low energy rate-limiting step characterized by a four-center transition structure, where fluorine plays an essential role, followed by a reductive elimination where the C-C bond formation is coupled to the departure of fluorine from the gold center. The homocoupling path follows a similar mechanism, with a two-step transmetalation with interesting changes in bonding around the Au(I) center and a rate-limiting reductive elimination. Our findings on the competition between mechanisms, and the effect of ligands and solvent, agree with the experimental results and provide new insights into the mechanism of gold-catalyzed cross-coupling reactions. PMID:23597253

  3. Analysis of the HindIII-catalyzed reaction by time-resolved crystallography

    PubMed Central

    Kawamura, Takashi; Kobayashi, Tomoki; Watanabe, Nobuhisa

    2015-01-01

    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. PMID:25664735

  4. Polyoxymetalate liquid-catalyzed polyol fuel cell and the related photoelectrochemical reaction mechanism study

    NASA Astrophysics Data System (ADS)

    Wu, Weibing; Liu, Wei; Mu, Wei; Deng, Yulin

    2016-06-01

    A novel design of liquid catalyzed fuel cell (LCFC), which uses polyoxometalates (POMs) as the photocatalyst and charge carrier has been reported previously. In this paper, the adaptability of biomass fuels (e.g., glycerol and glucose) to the LCFC and corresponding cell performance were studied in detail here. An interesting finding that greatly differs from conventional fuel cell is that high molecular weight fuels rather than small molecule fuels (e.g., methanol and ethylene glycol) are favored by the novel LCFC with respect to the power densities. The power output of LCFC strongly depends on the number and structure of hydroxyl groups in the biomass fuels. The evidence of UV-Vis and 1H NMR spectra shows that the preassociation between POM and alcohol fuels, which determines the photoelectrochemical reaction pathway of POM, is enhanced as the number of hydroxyl increases. Experimental results also demonstrate that more hydroxyl groups in the molecules lead to faster photoelectrochemical reaction between POM and fuels, higher reduction degree of POM, and further higher power output of LCFC. Our study reveals that biomass-based polyhydroxyl compounds such as starch, hemicellulose and cellulose are potential high-performance fuels for LCFC.

  5. Lewis Acid Catalyzed Regiospecific Cross-Dehydrative Coupling Reaction of 2-Furylcarbinols with β-Keto Amides or 4-Hydroxycoumarins: A Route to Furyl Enols.

    PubMed

    Miao, Maozhong; Luo, Yi; Li, Hongli; Xu, Xin; Chen, Zhengkai; Xu, Jianfeng; Ren, Hongjun

    2016-06-17

    Lewis acid catalyzed directly dehydrative carbon-carbon bond formation reaction of 2-furylcarbinols with β-keto amides provides a straightforward method for regioselective synthesis of (Z)-furyl enols. Moreover, this Lewis acid catalyzed cross-coupling reaction can be extended to an interesting heterocyclic version featuring a functionalized 3-furyl-4-hydroxycoumarin synthesis. PMID:27224045

  6. Rapid formation of triarylphosphines by microwave-assisted transition metal-catalyzed C-p cross-coupling reactions.

    PubMed

    Stadler, Alexander; Kappe, C Oliver

    2002-10-01

    Rapid, direct transition metal-catalyzed C-P(III) cross-coupling reactions were performed by microwave dielectric heating, employing diphenylphosphine and aryl halides/triflates as substrates. Depending on the specific aryl halide/triflate precursor, the highest yields were obtained utilizing heterogeneous or homogeneous Pd or Ni catalysts in DMF or NMP in the presence of KOAc or DABCO as a base. [reaction: see text

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

    PubMed

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

    2014-06-01

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

  8. From a Sequential to a Concurrent Reaction in Aqueous Medium: Ruthenium-Catalyzed Allylic Alcohol Isomerization and Asymmetric Bioreduction.

    PubMed

    Ríos-Lombardía, Nicolás; Vidal, Cristian; Liardo, Elisa; Morís, Francisco; García-Álvarez, Joaquín; González-Sabín, Javier

    2016-07-18

    The ruthenium-catalyzed redox isomerization of allylic alcohols was successfully coupled with the enantioselective enzymatic ketone reduction (mediated by KREDs) in a concurrent process in aqueous medium. The overall transformation, formally the asymmetric reduction of allylic alcohols, took place with excellent conversions and enantioselectivities, under mild reaction conditions, employing commercially and readily available catalytic systems, and without external coenzymes or cofactors. Optimization resulted in a multistep approach and a genuine cascade reaction where the metal catalyst and biocatalyst coexist from the beginning.

  9. Hydrolase-catalyzed biotransformations in deep eutectic solvents.

    PubMed

    Gorke, Johnathan T; Srienc, Friedrich; Kazlauskas, Romas J

    2008-03-14

    Hydrolases show good catalytic activity in deep eutectic solvents, despite the presence of urea, which can denature enzymes, or alcohols, which can interfere with hydrolase-catalyzed reactions. PMID:18309428

  10. Lecithin-cholesterol acyltransferase (LCAT) catalyzes transacylation of intact cholesteryl esters. Evidence for the partial reversal of the forward LCAT reaction

    SciTech Connect

    Sorci-Thomas, M.; Babiak, J.; Rudel, L.L. )

    1990-02-15

    Lecithin-cholesterol acyltransferase (LCAT) catalyzes the intravascular synthesis of lipoprotein cholesteryl esters by converting cholesterol and lecithin to cholesteryl ester and lysolecithin. LCAT is unique in that it catalyzes sequential reactions within a single polypeptide sequence. In this report we find that LCAT mediates a partial reverse reaction, the transacylation of lipoprotein cholesteryl oleate, in whole plasma and in a purified, reconstituted system. As a result of the reverse transacylation reaction, a linear accumulation of (3H)cholesterol occurred during incubations of plasma containing high density lipoprotein labeled with (3H)cholesteryl oleate. When high density lipoprotein labeled with cholesteryl (14C)oleate was also included in the incubation the labeled fatty acyl moiety remained in the cholesteryl (14C)oleate pool showing that the formation of labeled cholesterol did not result from hydrolysis of the doubly labeled cholesteryl esters. The rate of release of (3H)cholesterol was only about 10% of the forward rate of esterification of cholesterol using partially purified human LCAT and was approximately 7% in whole monkey plasma. Therefore, net production of cholesterol via the reverse LCAT reaction would not occur. (3H)Cholesterol production from (3H)cholesteryl oleate was almost completely inhibited by a final concentration of 1.4 mM 5,5'-dithiobis(nitrobenzoic acid) during incubation with either purified LCAT or whole plasma. Addition of excess lysolecithin to the incubation system did not result in the formation of (14C)oleate-labeled lecithin, showing that the reverse reaction found here for LCAT was limited to the last step of the reaction. To explain these results we hypothesize that LCAT forms a (14C)oleate enzyme thioester intermediate after its attack on the cholesteryl oleate molecule.

  11. G protein activation by G protein coupled receptors: ternary complex formation or catalyzed reaction?

    PubMed

    Roberts, David J; Waelbroeck, Magali

    2004-09-01

    G protein coupled receptors catalyze the GDP/GTP exchange on G proteins, thereby activating them. The ternary complex model, designed to describe agonist binding in the absence of GTP, is often extended to G protein activation. This is logically unsatisfactory as the ternary complex does not accumulate when G proteins are activated by GTP. Extended models taking into account nucleotide binding exist, but fail to explain catalytic G protein activation. This review puts forward an enzymatic model of G protein activation and compares its predictions with the ternary complex model and with observed receptor phenomenon. This alternative model does not merely provide a new set of formulae but leads to a new philosophical outlook and more readily accommodates experimental observations. The ternary complex model implies that, HRG being responsible for efficient G protein activation, it should be as stable as possible. In contrast, the enzyme model suggests that although a limited stabilization of HRG facilitates GDP release, HRG should not be "too stable" as this might trap the G protein in an inactive state and actually hinder G protein activation. The two models also differ completely in the definition of the receptor "active state": the ternary complex model implies that the active state corresponds to a single active receptor conformation (HRG); in contrast, the catalytic model predicts that the active receptor state is mobile, switching smoothly through various conformations with high and low affinities for agonists (HR, HRG, HRGGDP, HRGGTP, etc.).

  12. Cobalamin- and Corrinoid-Dependent Enzymes

    PubMed Central

    Matthews, Rowena G.

    2011-01-01

    This chapter will review the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyltransfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations. PMID:20877792

  13. 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.

  14. Structural Characterization of a 140 degrees Domain Movement in the Two-Step Reaction Catalyzed by 4-Chlorobenzoate:CoA Ligase

    SciTech Connect

    Reger,A.; Wu, R.; Dunaway-Mariano, D.; Gulick, A.

    2008-01-01

    Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PPi, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140 to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

  15. I2-Catalyzed Multicomponent Reactions for Accessing Densely Functionalized Pyrazolo[1,5-a]pyrimidines and Their Disulphenylated Derivatives.

    PubMed

    Sun, Jun; Qiu, Jiang-Kai; Jiang, Bo; Hao, Wen-Juan; Guo, Cheng; Tu, Shu-Jiang

    2016-04-15

    New I2-catalyzed multicomponent bicyclization reactions of β-ketonitriles with sulfonyl hydrazides have been established, providing a direct and metal-free access toward unreported pyrazolo[1,5-a]pyrimidin-4-ium sulfonates. The latter could be quantitatively converted into densely functionalized pyrazolo[1,5-a]pyrimidines in the presence of bases. Using sulfonyl hydrazides as a sulfenylating agent, the resulting pyrazolo[1,5-a]pyrimidines enabled I2-catalyzed unprecedented disulphenylations to access fully substituted pyrazolo[1,5-a]pyrimidines through direct C(sp(2))-H bond bifunctionalization. PMID:26991413

  16. Mechanistic study of chemoselectivity in Ni-catalyzed coupling reactions between azoles and aryl carboxylates.

    PubMed

    Lu, Qianqian; Yu, Haizhu; Fu, Yao

    2014-06-11

    Itami et al. recently reported the C-O electrophile-controlled chemoselectivity of Ni-catalyzed coupling reactions between azoles and esters: the decarbonylative C-H coupling product was generated with the aryl ester substrates, while C-H/C-O coupling product was generated with the phenol derivative substrates (such as phenyl pivalate). With the aid of DFT calculations (M06L/6-311+G(2d,p)-SDD//B3LYP/6-31G(d)-LANL2DZ), the present study systematically investigated the mechanism of the aforementioned chemoselective reactions. The decarbonylative C-H coupling mechanism involves oxidative addition of C(acyl)-O bond, base-promoted C-H activation of azole, CO migration, and reductive elimination steps (C-H/Decar mechanism). This mechanism is partially different from Itami's previous proposal (Decar/C-H mechanism) because the C-H activation step is unlikely to occur after the CO migration step. Meanwhile, C-H/C-O coupling reaction proceeds through oxidative addition of C(phenyl)-O bond, base-promoted C-H activation, and reductive elimination steps. It was found that the C-O electrophile significantly influences the overall energy demand of the decarbonylative C-H coupling mechanism, because the rate-determining step (i.e., CO migration) is sensitive to the steric effect of the acyl substituent. In contrast, in the C-H/C-O coupling mechanism, the release of the carboxylates occurs before the rate-determining step (i.e., base-promoted C-H activation), and thus the overall energy demand is almost independent of the acyl substituent. Accordingly, the decarbonylative C-H coupling product is favored for less-bulky group substituted C-O electrophiles (such as aryl ester), while C-H/C-O coupling product is predominant for bulky group substituted C-O electrophiles (such as phenyl pivalate). PMID:24823646

  17. The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    We consider the role of quantum effects in the transfer of hydrogen-like species in enzyme-catalyzed reactions. This review is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects (KIEs) implies that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We review the path integral approach and the Caldeira-Leggett model, which provides a general framework to describe and understand tunneling in a quantum system that interacts with a noisy environment at nonzero temperature. Here the quantum system is the active site of the enzyme, and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature T0, which is determined by the curvature of the potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. We review typical values for the parameters in the Caldeira-Leggett Hamiltonian, including the frequency-dependent friction and noise due to the environment. For physically reasonable parameters, we show that quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of KIEs for two classes of enzymes that have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction and noise due to the environment are weak and only slightly modify the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental fluctuations with frequencies much less than 1000 cm-1 do not have a significant effect on quantum corrections to the reaction rate. This is essentially because the time scales associated with the dynamics of proton transfer are faster than

  18. 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

  19. Rhodium catalyzed chelation-assisted C-H bond functionalization reactions.

    PubMed

    Colby, Denise A; Tsai, Andy S; Bergman, Robert G; Ellman, Jonathan A

    2012-06-19

    Over the last several decades, researchers have achieved remarkable progress in the field of organometallic chemistry. The development of metal-catalyzed cross-coupling reactions represents a paradigm shift in chemical synthesis, and today synthetic chemists can readily access carbon-carbon and carbon-heteroatom bonds from a vast array of starting compounds. Although we cannot understate the importance of these methods, the required prefunctionalization to carry out these reactions adds cost and reduces the availability of the starting reagents. The use of C-H bond activation in lieu of prefunctionalization has presented a tantalizing alternative to classical cross-coupling reactions. Researchers have met the challenges of selectivity and reactivity associated with the development of C-H bond functionalization reactions with an explosion of creative advances in substrate and catalyst design. Literature reports on selectivity based on steric effects, acidity, and electronic and directing group effects are now numerous. Our group has developed an array of C-H bond functionalization reactions that take advantage of a chelating directing group, and this Account surveys our progress in this area. The use of chelation control in C-H bond functionalization offers several advantages with respect to substrate scope and application to total synthesis. The predictability and decreased dependence on the inherent stereoelectronics of the substrate generally result in selective and high yielding transformations with broad applicability. The nature of the chelating moiety can be chosen to serve as a functional handle in subsequent elaborations. Our work began with the use of Rh(I) catalysts in intramolecular aromatic C-H annulations, which we further developed to include enantioselective transformations. The application of this chemistry to the simple olefinic C-H bonds found in α,β-unsaturated imines allowed access to highly substituted olefins, pyridines, and piperidines. We

  20. Practical Iron- and Cobalt-Catalyzed Cross-Coupling Reactions between N-Heterocyclic Halides and Aryl or Heteroaryl Magnesium Reagents.

    PubMed

    Kuzmina, Olesya M; Steib, Andreas K; Fernandez, Sarah; Boudot, Willy; Markiewicz, John T; Knochel, Paul

    2015-05-26

    The reaction scope of iron- and cobalt-catalyzed cross-coupling reactions in the presence of isoquinoline (quinoline) in the solvent mixture tBuOMe/THF has been further investigated. Various 2-halogenated pyridine, pyrimidine, and triazine derivatives were arylated under these mild conditions in excellent yields. The presence of isoquinoline allows us to perform Fe-catalyzed cross-coupling reactions between 6-chloroquinoline and aryl magnesium reagents. Furthermore, it was found that the use of 10% N,N-dimethylquinoline-8-amine increases the yields of some Co-catalyzed cross-coupling reactions with chloropyridines bearing electron-withdrawing substituents. PMID:25899175

  1. Adenylate-forming enzymes.

    PubMed

    Schmelz, Stefan; Naismith, James H

    2009-12-01

    Thioesters, amides, and esters are common chemical building blocks in a wide array of natural products. The formation of these bonds can be catalyzed in a variety of ways. For chemists, the use of an activating group is a common strategy and adenylate enzymes are exemplars of this approach. Adenylating enzymes activate the otherwise unreactive carboxylic acid by transforming the normal hydroxyl leaving group into adenosine monophosphate. Recently there have been a number of studies of such enzymes and in this review we suggest a new classification scheme. The review highlights the diversity in enzyme fold, active site architecture, and metal coordination that has evolved to catalyze this particular reaction. PMID:19836944

  2. Effect of carbon on the Ni catalyzed methane cracking reaction: A DFT study

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    To understand the effects of carbon atoms on the Ni catalyzed methane cracking reactions, methane dissociation on clean, surface-carbon-covered, and subsurface-carbon-accumulated Ni(1 1 1) surfaces were investigated using density functional theory (DFT). The results show that the existence of surface and subsurface C atoms destabilized the adsorption of the surface hydrocarbon species when compared to the clean Ni(1 1 1) surface. The projected density state (PDOS) analysis shows that the deposition of C atoms on and into the Ni surface modified the electronic structure of the Ni surface, and thus reduced the catalytic activity of the bonded Ni atoms. Moreover, it was found that the presence carbon atoms increase the CHx (x = 4-1) species activation barriers especially on the surface carbon covered (1/4 ML) Ni(1 1 1) surface, where CHx (x = 4-1) species encounter highest energy barrier for dissociation due to the electronic deactivation induced by Csbnd Ni bonding and the strong repulsive carbon sbnd CHx interaction. The calculations also show that CHx dissociation barriers are not affected by its neighboring C atom at low surface carbon coverage (1/9 ML). This work can be used to estimate more realistic kinetic parameters for this system.

  3. The Origin of Anti-Markovnikov Regioselectivity in Alkene Hydroamination Reactions Catalyzed by [Rh(DPEphos)](.).

    PubMed

    Couce-Rios, Almudena; Lledós, Agustí; Ujaque, Gregori

    2016-06-27

    The development of regioselective anti-Markovnikov alkene's hydroamination is a long-standing goal in catalysis. The [Rh(COD)(DPEphos)](+) complex is the most general and regioselective group 9 catalyst for such a process. The reaction mechanism for intermolecular hydroamination of alkenes catalyzed by [Rh(DPEphos)](+) complex is analyzed by means of DFT calculations. Hydroamination (alkene vs. amine activation routes) as well as oxidative amination pathways are analyzed. According to the computational results the operating mechanism can be generally described by alkene coordination, amine nucleophilic addition, proton transfer through the metal center and reductive elimination steps. The mechanism for the formation of the oxidative amination side product goes via a β-elimination after the nucleophilic addition and metal center protonation steps. The origin of the regioselectivity for the addition process (Markovnikov vs. anti-Markovnikov additions) is shown to be not charge but orbitally driven. Remarkably, η(2) to η(1) slippage degree on the alkene coordination mode is directly related to the regioselective outcome.

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

    PubMed

    Yemiş, 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. The Origin of Anti-Markovnikov Regioselectivity in Alkene Hydroamination Reactions Catalyzed by [Rh(DPEphos)](.).

    PubMed

    Couce-Rios, Almudena; Lledós, Agustí; Ujaque, Gregori

    2016-06-27

    The development of regioselective anti-Markovnikov alkene's hydroamination is a long-standing goal in catalysis. The [Rh(COD)(DPEphos)](+) complex is the most general and regioselective group 9 catalyst for such a process. The reaction mechanism for intermolecular hydroamination of alkenes catalyzed by [Rh(DPEphos)](+) complex is analyzed by means of DFT calculations. Hydroamination (alkene vs. amine activation routes) as well as oxidative amination pathways are analyzed. According to the computational results the operating mechanism can be generally described by alkene coordination, amine nucleophilic addition, proton transfer through the metal center and reductive elimination steps. The mechanism for the formation of the oxidative amination side product goes via a β-elimination after the nucleophilic addition and metal center protonation steps. The origin of the regioselectivity for the addition process (Markovnikov vs. anti-Markovnikov additions) is shown to be not charge but orbitally driven. Remarkably, η(2) to η(1) slippage degree on the alkene coordination mode is directly related to the regioselective outcome. PMID:27226329

  6. New insights into atrazine degradation by cobalt catalyzed peroxymonosulfate oxidation: kinetics, reaction products and transformation mechanisms.

    PubMed

    Ji, Yuefei; Dong, Changxun; Kong, Deyang; Lu, Junhe

    2015-03-21

    The widespread occurrence of atrazine in waters poses potential risk to ecosystem and human health. In this study, we investigated the underlying mechanisms and transformation pathways of atrazine degradation by cobalt catalyzed peroxymonosulfate (Co(II)/PMS). Co(II)/PMS was found to be more efficient for ATZ elimination in aqueous solution than Fe(II)/PMS process. ATZ oxidation by Co(II)/PMS followed pseudo-first-order kinetics, and the reaction rate constant (k(obs)) increased appreciably with increasing Co(II) concentration. Increasing initial PMS concentration favored the decomposition of ATZ, however, no linear relationship between k(obs) and PMS concentration was observed. Higher efficiency of ATZ oxidation was observed around neutral pH, implying the possibility of applying Co(II)/PMS process under environmental realistic conditions. Natural organic matter (NOM), chloride (Cl(-)) and bicarbonate (HCO3(-)) showed detrimental effects on ATZ degradation, particularly at higher concentrations. Eleven products were identified by applying solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC/MS) techniques. Major transformation pathways of ATZ included dealkylation, dechlorination-hydroxylation, and alkyl chain oxidation. Detailed mechanisms responsible for these transformation pathways were discussed. Our results reveal that Co(II)/PMS process might be an efficient technique for remediation of groundwater contaminated by ATZ and structurally related s-triazine herbicides.

  7. Photoinduced Vesicle Formation via the Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction.

    PubMed

    Konetski, Danielle; Gong, Tao; Bowman, Christopher N

    2016-08-16

    Synthetic vesicles have a wide range of applications from drug and cosmetic delivery to artificial cell and membrane studies, making simple and controlled formation of vesicles a large focus of the field today. Here, we report the use of the photoinitiated copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction using visible light to introduce spatiotemporal control into the formation of vesicles. Upon the establishment of the spatiotemporal control over vesicle formation, it became possible to adjust initiation conditions to modulate vesicle sizes resulting in the formation of controllably small or large vesicles based on light intensity or giant vesicles when the formation was initiated in flow-free conditions. Additionally, this photoinitiated method enables vesicle formation at a density 400-fold higher than initiation using sodium ascorbate as the catalyst. Together, these advances enable the formation of high-density, controlled size vesicles using low-energy wavelengths while producing enhanced control over the formation characteristics of the vesicle. PMID:27443396

  8. 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.

  9. A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase

    SciTech Connect

    Lyubimov, Artem Y.; Chen, Lin; Sampson, Nicole S.; Vrielink, Alice

    2009-11-01

    The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine. Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k{sub cat}. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

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

    PubMed

    Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

    2013-05-17

    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.

  11. Synthesis of Branched Alkylboronates by Copper-Catalyzed Allylic Substitution Reactions of Allylic Chlorides with 1,1-Diborylalkanes.

    PubMed

    Kim, Junghoon; Park, Sangwoo; Park, Jinyoung; Cho, Seung Hwan

    2016-01-22

    Reported herein is a copper-catalyzed S(N)2'-selective allylic substitution reaction using readily accessible allylic chlorides and 1,1-diborylalkanes, a reaction which proceeds with chemoselective C-B bond activation of the 1,1-diborylalkanes. In the presence of a catalytic amount of [Cu(IMes)Cl] [IMes=1,3-bis(2,4,6-trimethylphenyl)imidazole-2-ylidene] and LiOtBu as a base, a range of primary and secondary allylic chlorides undergo the S(N)2'-selective allylic substitution reaction to produce branched alkylboronates. The synthetic utilities of the obtained alkylboronates are also presented. PMID:26666468

  12. Nickel and cobalt-catalyzed coupling of alkyl halides with alkenes via heck reactions and radical conjugate addition.

    PubMed

    Qian, Qun; Zang, Zhenhua; Chen, Yang; Tong, Weiqi; Gong, Hegui

    2013-05-01

    Cross-coupling of alkyl halides with alkenes leading to Heck-type and addition products is summarized. The development of Heck reaction with aliphatic halides although has made significant progress in the past decade and particularly recently, it was much less explored in comparison with the aryl halides. The use of Ni- and Co-catalyzed protocols allowed efficient Heck coupling of activated and unactivated alkenes with 1°, 2° and 3° alkyl halides. In addition, radical conjugate addition to activated alkenes has become a well-established method that has led to efficient construction of many natural products. The utilization of Ni- and Co-catalyzed strategies would avoid toxic tin reagents, and therefore worth exploring. The recent development of Ni- and Co-catalyzed addition of alkyl halides to alkenes displays much improved reactivity and functional group tolerance. In this mini-review, we also attempt to overview the mechanisms that are proposed in the reactions, aiming at providing insight into the nickel and cobalt-catalyzed coupling of alkyl halides with alkenes.

  13. A coumarin-specific prenyltransferase catalyzes the crucial biosynthetic reaction for furanocoumarin formation in parsley.

    PubMed

    Karamat, Fazeelat; Olry, Alexandre; Munakata, Ryosuke; Koeduka, Takao; Sugiyama, Akifumi; Paris, Cedric; Hehn, Alain; Bourgaud, Frédéric; Yazaki, Kazufumi

    2014-02-01

    Furanocoumarins constitute a sub-family of coumarin compounds with important defense properties against pathogens and insects, as well as allelopathic functions in plants. Furanocoumarins are divided into two sub-groups according to the alignment of the furan ring with the lactone structure: linear psoralen and angular angelicin derivatives. Determination of furanocoumarin type is based on the prenylation position of the common precursor of all furanocoumarins, umbelliferone, at C6 or C8, which gives rise to the psoralen or angelicin derivatives, respectively. Here, we identified a membrane-bound prenyltransferase PcPT from parsley (Petroselinum crispum), and characterized the properties of the gene product. PcPT expression in various parsley tissues is increased by UV irradiation, with a concomitant increase in furanocoumarin production. This enzyme has strict substrate specificity towards umbelliferone and dimethylallyl diphosphate, and a strong preference for the C6 position of the prenylated product (demethylsuberosin), leading to linear furanocoumarins. The C8-prenylated derivative (osthenol) is also formed, but to a much lesser extent. The PcPT protein is targeted to the plastids in planta. Introduction of this PcPT into the coumarin-producing plant Ruta graveolens showed increased consumption of endogenous umbelliferone. Expression of PcPT and a 4-coumaroyl CoA 2'-hydroxylase gene in Nicotiana benthamiana, which does not produce furanocoumarins, resulted in formation of demethylsuberosin, indicating that furanocoumarin production may be reconstructed by a metabolic engineering approach. The results demonstrate that a single prenyltransferase, such as PcPT, opens the pathway to linear furanocoumarins in parsley, but may also catalyze the synthesis of osthenol, the first intermediate committed to the angular furanocoumarin pathway, in other plants.

  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. Access to Isoquinolines and Isoquinolin-3-ols via Rh(III)-Catalyzed Coupling/Cyclization Cascade Reaction of Arylimidates and Diazo Compounds.

    PubMed

    Li, Xing Guang; Sun, Min; Jin, Qiao; Liu, Kai; Liu, Pei Nian

    2016-05-01

    A Rh(III)-catalyzed coupling/cyclization cascade reaction is described, which involves arylimidates and diazo compounds and proceeds via intermolecular C-C bond formation and subsequent intramolecular C-N bond formation. Mechanistic investigation revealed that the reaction is a two-step process: the initial Rh(III)-catalyzed coupling/cyclization proceeds very fast and the following dehydration is rather slow. The reaction provides a direct approach to isoquinolines and isoquinolin-3-ols without any oxidants. PMID:27042947

  16. Synthesis of chiral biphenol-based diphosphonite ligands and their application in palladium-catalyzed intermolecular asymmetric allylic amination reactions.

    PubMed

    Shi, Ce; Chien, Chih-Wei; Ojima, Iwao

    2011-02-01

    A library of new 2,2'-bis(diphenylphosphinoyloxy)-1,1'-binaphthyl (binapo)-type chiral diphosphonite ligands was designed and synthesized based on chiral 3,3',5,5',6,6'-hexasubstituted biphenols. These bop ligands have exhibited excellent efficiency in a palladium-catalyzed intermolecular allylic amination reaction, which provides a key intermediate for the total synthesis of Strychnos indole alkaloids with enantiopurities of up to 96% ee. PMID:21254441

  17. Convergent Synthesis of Diverse Nitrogen Heterocycles via Rh(III)-Catalyzed C-H Conjugate Addition/Cyclization Reactions.

    PubMed

    Weinstein, Adam B; Ellman, Jonathan A

    2016-07-01

    The development of Rh(III)-catalyzed C-H conjugate addition/cyclization reactions that provide access to synthetically useful fused bi- and tricyclic nitrogen heterocycles is reported. A broad scope of C-H functionalization substrates and electrophilic olefin coupling partners is effective, and depending on the nature of the directing group, cyclic imide, amide, or heteroaromatic products are obtained. An efficient synthesis of a pyrrolophenanthridine alkaloid natural product, oxoassoanine, highlights the utility of this method.

  18. 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.

  19. In Vivo and in Vitro Evidence for Biochemical Coupling of Reactions Catalyzed by Lysophosphatidylcholine Acyltransferase and Diacylglycerol Acyltransferase*

    PubMed Central

    Pan, Xue; Chen, Guanqun; Kazachkov, Michael; Greer, Michael S.; Caldo, Kristian Mark P.; Zou, Jitao; Weselake, Randall J.

    2015-01-01

    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-[14C]acyl-PC, formation of [14C]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 14C-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

  20. Convergent Synthesis of Diverse Nitrogen Heterocycles via Rh(III)-Catalyzed C-H Conjugate Addition/Cyclization Reactions.

    PubMed

    Weinstein, Adam B; Ellman, Jonathan A

    2016-07-01

    The development of Rh(III)-catalyzed C-H conjugate addition/cyclization reactions that provide access to synthetically useful fused bi- and tricyclic nitrogen heterocycles is reported. A broad scope of C-H functionalization substrates and electrophilic olefin coupling partners is effective, and depending on the nature of the directing group, cyclic imide, amide, or heteroaromatic products are obtained. An efficient synthesis of a pyrrolophenanthridine alkaloid natural product, oxoassoanine, highlights the utility of this method. PMID:27337641