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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. Enzyme-catalyzed, gas-phase reactions.

    PubMed

    Barzana, E; Klibanov, A M; Karel, M

    1987-06-01

    Dehydrated preparations of alcohol oxidase adsorbed on DEAE-cellulose vigorously catalyze a gas-phase oxidation of ethanol vapors with molecular oxygen. The gas-phase reaction is strongly dependent on the water activity of the system. The enzymatic activity is severely inhibited by the product hydrogen peroxide. This inhibition can be alleviated, however, by an addition of catalase or peroxidase to the dry preparation. Such dehydrated, bienzymic catalysts afford a complete and selective conversion of the substrate to acetaldehyde. Dry alcohol oxidase is much more thermostable than in aqueous solution. The results of this work suggest that dehydrated enzymes have potential applications in the analysis of gaseous compounds and in the development of novel gas-solid bioreactors.

  4. Representing Rate Equations for Enzyme-Catalyzed Reactions

    ERIC Educational Resources Information Center

    Ault, Addison

    2011-01-01

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

  5. Thermodynamics of Enzyme-Catalyzed Reactions: Part 4. Lyases

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.; Tewari, Yadu B.

    1995-09-01

    Equilibrium constants and enthalpy changes for reactions catalyzed by the lyase class of enzymes have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 106 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

  6. Thermodynamics of Enzyme-Catalyzed Reactions: Part 2. Transferases

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.; Tewari, Yadu B.

    1994-07-01

    Equilibrium constants and enthalpy changes for reactions catalyzed by the transferase class of enzymes have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 285 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

  7. Thermodynamics of Enzyme-Catalyzed Reactions. Part 3. Hydrolases

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.; Tewari, Yadu B.

    1994-11-01

    Equilibrium constants and enthalpy changes for reactions catalyzed by the hydrolase class of enzymes have been compiled. For each reaction the following information is given: The reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 145 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

  8. 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.

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

    PubMed

    Kanehisa, Minoru

    2013-09-02

    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.

  10. 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.

  11. Thermodynamics of Enzyme-Catalyzed Reactions: Part 1. Oxidoreductases

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.; Tewari, Yadu B.; Bell, Donna; Fazio, Kari; Anderson, Ellen

    1993-03-01

    Equilibrium constants and enthalpy changes for reactions catalyzed by oxidoreductases have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it. The thermodynamic conventions pertinent to the tabulation of equilibrium data are discussed. A distinction is made between those thermodynamic quantities which pertain to the overall biochemical reaction and those which pertain to a reference reaction that involves specific species. The data from 205 references have been examined and evaluated. Chemical Abstract Service Registry Numbers have been assigned to the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participated.

  12. Does metabolite channeling accelerate enzyme-catalyzed cascade reactions?

    PubMed Central

    Poshyvailo, Liubov; von Lieres, Eric

    2017-01-01

    Metabolite or substrate channeling is a direct transfer of metabolites from one enzyme to the next enzyme in a cascade. Among many potential advantages of substrate channeling, acceleration of the total reaction rate is considered as one of the most important and self-evident. However, using a simple model, supported by stochastic simulations, we show that it is not always the case; particularly at long times (i.e. in steady state) and high substrate concentrations, a channeled reaction cannot be faster, and can even be slower, than the original non-channeled cascade reaction. In addition we show that increasing the degree of channeling may lead to an increase of the metabolite pool size. We substantiate that the main advantage of channeling likely lies in protecting metabolites from degradation or competing side reactions. PMID:28234973

  13. Pericyclic reactions catalyzed by chorismate-utilizing enzymes.

    PubMed

    Lamb, Audrey L

    2011-09-06

    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.

  14. 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

  15. Thermodynamics of Enzyme-Catalyzed Reactions: Part 6--1999 Update

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.

    1999-07-01

    This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for enzyme-catalyzed reactions. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used]; the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 96 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

  16. Thermodynamics of Enzyme-Catalyzed Reactions: Part 5. Isomerases and Ligases

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.; Tewari, Yadu B.

    1995-11-01

    Equilibrium constants and enthalpy changes for reactions catalyzed by the isomerase and ligase classes of enzymes have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 176 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

  17. Thermodynamics of Enzyme-Catalyzed Reactions: Part 7-2007 Update

    NASA Astrophysics Data System (ADS)

    Goldberg, Robert N.; Tewari, Yadu B.; Bhat, Talapady N.

    2007-12-01

    This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for enzyme-catalyzed reactions. For each reaction, the following information is given: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used], the data and their evaluation, and, sometimes, commentary on the data and on any corrections which have been applied to the data or any calculations for which the data have been used. The review contains data from 119 references which have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

  18. 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.

  19. Changes in the standard transformed thermodynamic properties of enzyme-catalyzed reactions with ionic strength.

    PubMed

    Alberty, Robert A

    2007-04-12

    The ionic strength has significant effects on the thermodynamic properties of ionic species and on the transformed thermodynamic properties of biochemical reactants at specified pH values. These effects are discussed for species, reactants, and enzyme-catalyzed reactions. This has led to three new thermodynamic properties: (z(j)(2) - NH(j)), (z(2) - N(H))(i), and Delta(r)(z((2)-N(H)), which are referred to as ionic strength coefficients. The first of these is a property of a species, the second is a property of a reactant, and the third is the property of an enzyme-catalyzed reaction. The effects of ionic strength on standard thermodynamic properties of species, standard transformed thermodynamic properties of reactants, and standard transformed thermodynamic properties of enzyme-catalyzed reactions are proportional to these new thermodynamic properties.

  20. 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.

  1. 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.

  2. 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…

  3. A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase.

    PubMed

    Crehuet, Ramon; Field, Martin J

    2007-05-24

    The study of the chemical steps in enzyme-catalyzed reactions represents a challenge for molecular simulation techniques. One concern is how to calculate paths for the reaction. Common techniques include the definition of a reaction coordinate in terms of a small set of (normally) geometrical variables or the determination of minimum energy paths on the potential energy surface of the reacting system. Both have disadvantages, the former because it presupposes knowledge of which variables are likely to be important for reaction and the latter because it provides a static picture and dynamical effects are ignored. In this paper, we employ the transition path sampling method developed by Chandler and co-workers, which overcomes some of these limitations. The reaction that we have chosen is the chorismate-mutase-catalyzed conversion of chorismate into prephenate, which has become something of a test case for simulation studies of enzyme mechanisms. We generated an ensemble of approximately 1000 independent transition paths for the reaction in the enzyme and another approximately 500 for the corresponding reaction in solution. A large variety of analyses of these paths was performed, but we have concentrated on characterizing the transition state ensemble, particularly the flexibility of its structures with respect to other ligands of the enzyme and the time evolution of various geometrical and energetic properties as the reaction proceeds. We have also devised an approximate technique for locating transition state structures along the paths.

  4. Temperature effects on enzyme-catalyzed reactions within a cell: Monte Carlo simulations for coupled reaction and diffusion

    NASA Astrophysics Data System (ADS)

    Nangia, Shivangi; Anderson, James B.

    2013-01-01

    We report Monte Carlo simulations of temperature effects on single-step enzymatic reactions with varied rate constants and diffusion coefficients. For typical systems, where the intrinsic reaction rate is more sensitive to temperature than diffusion, the overall reaction is rate-limited at low temperatures and diffusion-limited at high temperatures. The effective activation energy shifts to a much lower value as temperature is increased. Our results show that the temperature dependence of enzyme-catalyzed reactions within a cell may be only loosely related to a potential energy barrier height. The effective activation energy may be strongly affected by coupling of reaction and diffusion.

  5. 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

  6. 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".

  7. Combined cross-linked enzyme aggregates of horseradish peroxidase and glucose oxidase for catalyzing cascade chemical reactions.

    PubMed

    Nguyen, Le Truc; Yang, Kun-Lin

    2017-05-01

    Cascade reactions involved unstable intermediates are often encountered in biological systems. In this study, we developed combined cross-linked enzyme aggregates (combi-CLEA) to catalyze a cascade reaction which involves unstable hydrogen peroxide as an intermediate. The combi-CLEA contains two enzymes̶ glucose oxidase (GOx) and horseradish peroxidase (HRP) which are cross-linked together as solid aggregates. The first enzyme GOx catalyzes the oxidation of glucose and produces hydrogen peroxide, which is used by the second enzyme HRP to oxidize 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). The apparent reaction rate of the cascade reaction reaches 10.5±0.5μM/min when the enzyme ratio is 150:1 (GOx:HRP). Interestingly, even in the presence of catalase, an enzyme that quickly decomposes hydrogen peroxide, the reaction rate only decreases by 18.7% to 8.3±0.3μM/min. This result suggests that the intermediate hydrogen peroxide is not decomposed by catalase due to a short diffusion distance between GOx and HRP in the combi-CLEA. Scanning electron microscopy images suggest that combi-CLEA particles are hollow spheres and have an average diameter around 250nm. Because of their size, combi-CLEA particles can be entrapped inside a nylon membrane for detecting glucose by using the cascade reaction.

  8. 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...

  9. 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.

  10. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

    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

  12. 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

  13. 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.

  14. 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.

  15. Bifurcations and asymptotic behavior of positive steady-states of an enzyme-catalyzed reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Ko, Wonlyul

    2016-12-01

    The current paper presents a better understanding of a diffusive enzyme-catalyzed system arising from glycolysis, describing a biochemical reaction in which a substrate is converted into a product with positive feedback and into a branched sink. Through theoretical analysis of the given partial differential system, the existence and nonexistence of nonconstant positive steady states are studied. Moreover, the global bifurcation structure and asymptotic behavior of the solutions are revealed. Our mathematical approach is based on bifurcation theory, index theory, and various elliptic estimates.

  16. Microwave-assisted enzyme-catalyzed reactions in various solvent systems.

    PubMed

    Lin, Shan-Shan; Wu, Chi-Hong; Sun, Mei-Chuan; Sun, Chung-Ming; Ho, Yen-Peng

    2005-04-01

    The work describes the accelerated enzymatic digestion of several proteins in various solvent systems under microwave irradiation. The tryptic fragments of the proteins were analyzed by matrix-assisted laser desorption/ionization mass spectrometry. Under the influence of rapid microwave heating, these enzymatic reactions can proceed in a solvent such as chloroform, which, under traditional digestion conditions, renders the enzyme inactive. The digestion efficiencies and sequence coverages were increased when the trypsin digestions occurred in acetonitrile-, methanol- and chloroform-containing solutions that were heated under microwave irradiation for 10 min using a commercial microwave applicator. The percentage of the protein digested under microwave irradiation increased with the relative acetonitrile content, but decreased as the methanol content was increased. These observations suggest that acetonitrile does not deactivate the enzyme during the irradiation period; in contrast, methanol does deactivate it. In all cases, the digestion efficiencies under microwave irradiation exceed those under conventional conditions.

  17. 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.

  18. Use of intermediate partitioning to calculate intrinsic isotope effects for the reaction catalyzed by malic enzyme

    SciTech Connect

    Grissom, C.B.; Cleland, W.W.

    1985-02-12

    For those enzymes that proceed via a stepwise reaction mechanism with a discrete chemical intermediate and where deuterium and /sup 13/C isotope effects are on separate steps, a new method has been developed to solve for the intrinsic deuterium and /sup 13/C kinetic isotope effects that relies on directly observing the partitioning of the intermediate between the forward and reverse directions. This observed partitioning ratio, along with the values of the primary deuterium, tritium, and /sup 13/C kinetic isotope effects on V/K for the substrate with the label being followed, allows an exact solution for the intrinsic deuterium and /sup 13/C isotope effects, the forward commitment for the deuterium-sensitive step, and the partition ratio for the intermediate in the reaction. This method allows portions of the reaction coordinate diagram to be defined precisely and the relative energy levels of certain activation barriers to be assigned exactly. With chicken liver triphosphopyridine nucleotide (TPN) malic enzyme activated by Mg/sup 2 +/, the partitioning of oxalacetate to pyruvate vs. malate in the presence of TPNH, 0.47, plus previously determined isotope effects gives an intrinsic deuterium isotope effect of 5.7 on hydride transfer and a /sup 13/C isotope effect of 1.044 on decarboxylation. Reverse hydride transfer is 10 times faster than decarboxylation, and the forward commitment for hydride transfer is 3.3. The /sup 13/C isotope effect is not significantly different with reduced acetylpyridine adenine dinucleotide phosphate replacing TPNH (although the pyruvate/malate partitioning ratio for oxalactate is now 9.9), but replacement of Mg/sup 2 +/ by Mn/sup 2 +/ raises the value to 1.065 (partition ratio 0.99).

  19. 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…

  20. 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…

  1. Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions

    PubMed Central

    Pelosi, Ludovic; Loiseau, Laurent; Barras, Frédéric; Schneider, Dominique; Junier, Ivan

    2016-01-01

    ABSTRACT The ubiquitous ATP synthase uses an electrochemical gradient to synthesize cellular energy in the form of ATP. The production of this electrochemical gradient relies on liposoluble proton carriers like ubiquinone (UQ), which is used in the respiratory chains of eukaryotes and proteobacteria. The biosynthesis of UQ requires three hydroxylation reactions on contiguous positions of an aromatic ring. In Escherichia coli, each of three UQ flavin monooxygenases (FMOs), called UbiF, UbiH, and UbiI, modifies a single position of the aromatic ring. This pattern of three hydroxylation reactions/three proteins has been accepted as a paradigm in UQ biology. Using a phylogenetic analysis, we found that UbiF, UbiH, and UbiI are detected only in a small fraction of proteobacteria, and we identified two new types of UQ FMOs: UbiM, which is distributed in members of the alpha, beta, and gamma classes of proteobacteria, and UbiL, which is restricted to members of the alphaproteobacteria. Remarkably, the ubiL and ubiM genes were found in genomes with fewer than three UQ hydroxylase-encoding genes. We demonstrated, using biochemical approaches, that UbiL from Rhodospirillum rubrum and UbiM from Neisseria meningitidis hydroxylate, respectively, two and three positions of the aromatic ring during UQ biosynthesis. We conclude that bacteria have evolved a large repertoire of hydroxylase combinations for UQ biosynthesis, including pathways with either three specialist enzymes or pathways with one or two generalist enzymes of broader regioselectivity. The emergence of the latter is potentially related to genome reduction events. IMPORTANCE UQ, a key molecule for cellular bioenergetics that is conserved from proteobacteria to humans, appeared in an ancestral proteobacterium more than 2 billion years ago. UQ biosynthesis has been studied only in a few model organisms, and thus, the diversity of UQ biosynthesis pathways is largely unknown. In the work reported here, we conducted a

  2. Thermodynamic parameters monitoring the equilibrium shift of enzyme-catalyzed hydrolysis/synthesis reactions in favor of synthesis in mixtures of water and organic solvent.

    PubMed

    Deschrevel, Brigitte; Vincent, Jean-Claude; Ripoll, Camille; Thellier, Michel

    2003-01-20

    The main strategy developed to shift the equilibrium state of a hydrolase-catalyzed hydrolysis/synthesis reaction consists in reducing water activity by addition of organic solvents in the reaction medium. We have used several mixtures of water and 1,4-butanediol, ranging from pure water to pure 1,4-butanediol, to study the hydrolysis/synthesis reaction of the N-Cbz-L-tryptophanyl-glycineamide dipeptide, catalyzed by alpha-chymotrypsin. In the presence of 1,4-butanediol, alpha-chymotrypsin also catalyzed the esterification reaction between this diol and N-Cbz-L-tryptophan; this ester hydrolysis/synthesis reaction has thus also been examined. The dipeptide and ester equilibrium concentrations increase when the water content of the reaction medium is decreased. Using our experimental data, we have determined the equilibrium constants of the hydrolysis/synthesis equilibria involving the nonionized forms of the protected amino acids, the estimated values of which are Ksp = 8 10(5) for the dipeptide and Kse = 78 for the ester respectively. They are true thermodynamic equilibrium constants, each related to a single, well-defined reaction equilibrium and with water activity being taken into account. If an organic solvent is added to the reaction medium these equilibria can be shifted towards synthesis by decreasing the water activity but also by modifying the ionization/neutralization equilibrium constant of the ionizable groups. These two effects depend both on the water content and on the nature of the organic solvent used, and, in particular, on its dielectric constant. Because of the importance of this parameter in our study, we discuss using it as an indicator to select an appropriate organic solvent to perform an enzyme-catalyzed synthesis.

  3. Advances in lipase-catalyzed esterification reactions.

    PubMed

    Stergiou, Panagiota-Yiolanda; Foukis, Athanasios; Filippou, Michalis; Koukouritaki, Maria; Parapouli, Maria; Theodorou, Leonidas G; Hatziloukas, Efstathios; Afendra, Amalia; Pandey, Ashok; Papamichael, Emmanuel M

    2013-12-01

    Lipase-catalyzed esterification reactions are among the most significant chemical and biochemical processes of industrial relevance. Lipases catalyze hydrolysis as well as esterification reactions. Enzyme-catalyzed esterification has acquired increasing attention in many applications, due to the significance of the derived products. More specifically, the lipase-catalyzed esterification reactions attracted research interest during the past decade, due to an increased use of organic esters in biotechnology and the chemical industry. Lipases, as hydrolyzing agents are active in environments, which contain a minimum of two distinct phases, where all reactants are partitioned between these phases, although their distribution is not fixed and changes as the reaction proceeds. The kinetics of the lipase-catalyzed reactions is governed by a number of factors. This article presents a thorough and descriptive evaluation of the applied trends and perspectives concerning the enzymatic esterification, mainly for biofuel production; an emphasis is given on essential factors, which affect the lipase-catalyzed esterification reaction. Moreover, the art of using bacterial and/or fungal strains for whole cell biocatalysis purposes, as well as carrying out catalysis by various forms of purified lipases from bacterial and fungal sources is also reviewed.

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

    PubMed

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

    2009-04-08

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

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

    PubMed

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

    2015-10-01

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

  6. Enzyme-Catalyzed Mutation in Breast Cancer

    DTIC Science & Technology

    2014-08-01

    instance, polycyclic aromatic hydrocarbons are converted by cellular cytochrome P450 enzymes into activated epox- ides, which can then react to form...Award Number: W81XWH-13-1-0247 TITLE: Enzyme -Catalyzed Mutation in Breast Cancer PRINCIPAL INVESTIGATOR: Reuben Harris CONTRACTING...CONTRACT NUMBER Enzyme -catalyzed Mutation in Breast Cancer 5b. GRANT NUMBER W81XWH-13-1-0247 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Reuben S. Harris

  7. 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.

  8. Enzyme catalyzed biochemical production in a polydimethylsiloxane microreactor

    NASA Astrophysics Data System (ADS)

    Dickey, Cynthia K.; Elmore, Bill B.; Jones, Francis

    2000-08-01

    Study of an aqueous-phase reaction in an enzyme- catalyzedpolydimethylsiloxane (PDMS) microreactor is underway. In the present work, urease - an enzyme that catalyzes urea to ammonia and carbon dioxide has been immobilized within open microchannels of 450 micrometers (micrometers ) in diameter or less. Microchannels are templated within PDMS. Preliminary results demonstrate the proof of concept for conversion biochemicals via a PDMS-based microreactor system.

  9. Enzyme catalyzed optofluidic biolaser for sensitive ion concentration detection

    NASA Astrophysics Data System (ADS)

    Gong, Chaoyang; Gong, Yuan; Oo, Maung Kyaw Khaing; Wu, Yu; Rao, Yunjiang; Fan, Xudong

    2016-12-01

    The enzyme horseradish peroxidase (HRP) has been extensively used in biochemistry for its ability to amplify a weak signal. By using HRP catalyzed substrate as the gain medium, we demonstrate sensitive ion concentration detection based on the optofluidic laser. The enzyme catalyzed reaction occurs in bulk solution inside a Fabry-Perot laser cavity, where the colorless, non-fluorescent 10-Acetyl-3,7-dihydroxyphenoxazine (ADHP) substrate is oxidized to produce highly fluorescent resorufin. Laser emission is achieved when pumped with the second harmonic wave of a Q-switched YAG laser. Further, we use sulfide anion (S2-) as an example to investigate the sensing performance of enzyme catalyzed optofluidic laser. The laser onset time difference between the sample to be tested and the reference is set to be the sensing output. Thanks to the amplification effects of both the enzymatic reaction and laser emission, we achieve a detection limit of 10 nM and a dynamic range of 3 orders of magnitude.

  10. A potential role for isothermal calorimetry in studies of the effects of thermodynamic non-ideality in enzyme-catalyzed reactions.

    PubMed

    Lonhienne, Thierry G A; Winzor, Donald J

    2004-01-01

    Attention is drawn to the feasibility of using isothermal calorimetry for the characterization of enzyme reactions under conditions bearing greater relevance to the crowded biological environment, where kinetic parameters are likely to differ significantly from those obtained by classical enzyme kinetic studies in dilute solution. An outline of the application of isothermal calorimetry to the determination of enzyme kinetic parameters is followed by considerations of the nature and consequences of crowding effects in enzyme catalysis. Some of those effects of thermodynamic non-ideality are then illustrated by means of experimental results from calorimetric studies of the effect of molecular crowding on the kinetics of catalysis by rabbit muscle pyruvate kinase. This review concludes with a discussion of the potential of isothermal calorimetry for the experimental determination of kinetic parameters for enzymes either in biological environments or at least in media that should provide reasonable approximations of the crowded conditions encountered in vivo.

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

    PubMed

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

    2016-02-01

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

  13. 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

  14. 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

  15. Unusual Cytochrome P450 Enzymes and Reactions*

    PubMed Central

    Guengerich, F. Peter; Munro, Andrew W.

    2013-01-01

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

  16. Production of L-malic acid with fixation of HCO3(-) by malic enzyme-catalyzed reaction based on regeneration of coenzyme on electrode modified by layer-by-layer self-assembly method.

    PubMed

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

    2009-01-01

    Malic enzyme prepared and purified from Brevundimonas diminuta IFO13182 catalyzed the decarboxylation reaction of malate to pyruvate and CO2 using NAD+ as the coenzyme, and the reverse reaction was used in the present study for L-malic acid production with fixation of HCO3(-) as a model compound for carbon source. The L-malic acid production was based on electrochemical regeneration of NADH on a carbon plate electrode modified by layer-by-layer adsorption of polymer-bound mediator (Alginic acid bound viologen derivative, Alg-V), polymer-bound coenzyme (Alginic acid bound NAD+, Alg-NAD+), and lipoamide dehydrogenase (LipDH). Electrochemical reduction of immobilized NAD+ catalyzed by LipDH in a multilayer film was achieved, and the L-malic acid production with HCO3(-) fixation system with layer-by-layer immobilization of Alg-V/LipDH/Alg-NAD+/malic enzyme multilayer film on the electrode gave an L-malic acid production of nearly 11.9 mmol and an HCO3(-) fixation rate of nearly 47.4% in a buffer containing only KHCO3 and pyruvic acid potassium salt, using a cation exchange membrane. The total turnover number of NADH within 48 h was about 19,000, which suggests that efficient NADH regeneration and fast electron transfer were achieved within the multilayer film, and that the modified electrode is a potential method for the fixation of HCO3(-) without addition of free coenzyme.

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

    PubMed Central

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

    2017-01-01

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

  18. Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer.

    PubMed

    Mohamed, Mark F; Hollfelder, Florian

    2013-01-01

    The observation that one enzyme can accelerate several chemically distinct reactions was at one time surprising because the enormous efficiency of catalysis was often seen as inextricably linked to specialization for one reaction. Originally underreported, and considered a quirk rather than a fundamental property, enzyme promiscuity is now understood to be important as a springboard for adaptive evolution. Owing to the large number of promiscuous enzymes that have been identified over the last decade, and the increased appreciation for promiscuity's evolutionary importance, the focus of research has shifted to developing a better understanding of the mechanistic basis for promiscuity and the origins of tolerant or restrictive specificity. We review the evidence for widespread crosswise promiscuity amongst enzymes that catalyze phosphoryl transfer, including several members of the alkaline phosphatase superfamily, where large rate accelerations between 10(6) and 10(17) are observed for both native and multiple promiscuous reactions. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.

  19. Secondary kinase reactions catalyzed by yeast pyruvate kinase.

    PubMed

    Leblond, D J; Robinson, J L

    1976-06-07

    1. Yeast pyruvate kinase (EC 2.7.1.40) catalyzes, in addition to the primary, physiologically important reaction, three secondary kinase reactions, the ATP-dependent phosphorylations of fluoride (fluorokinase), hydroxylamine (hydroxylamine kinase) and glycolate (glycolate kinase). 2. These reactions are accelerated by fructose-1,6-bisphosphate, the allosteric activator of the primary reaction. Wth Mg2+ as the required divalent cation, none of these reactions are observed in the absence of fructose-biphosphate. With Mn2+, fructose-bisphosphate is required for the glycolate kinase reaction, but merely stimulates the other reactions. 3. The effect of other divalent cations and pH on three secondary kinase reactions was also examined. 4. Results are compared with those obtained from muscle pyruvate kinase and the implications of the results for the mechanism of the yeast enzyme are discussed.

  20. 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

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed Central

    Míguez, David G.; Vanag, Vladimir K.; Epstein, Irving R.

    2007-01-01

    Waves and patterns in living systems are often driven by biochemical reactions with enzymes as catalysts and regulators. We present a reaction–diffusion system catalyzed by the enzyme glucose oxidase that exhibits traveling wave patterns in a spatially extended medium. Fronts and pulses propagate as a result of the coupling between the enzyme-catalyzed autocatalytic production and diffusion of hydrogen ions. A mathematical model qualitatively explains the experimental observations. PMID:17420460

  3. Horseradish-Peroxidase-Catalyzed Tyrosine Click Reaction.

    PubMed

    Sato, Shinichi; Nakamura, Kosuke; Nakamura, Hiroyuki

    2017-03-02

    The efficiency of protein chemical modification on tyrosine residues with N-methylluminol derivatives was drastically improved by using horseradish peroxidase (HRP). In the previous method, based on the use of hemin and H2 O2 , oxidative side reactions such as cysteine oxidation were problematic for functionalization of proteins selectively on tyrosine residues. Oxidative activation of N-methylluminol derivatives with a minimum amount of H2 O2 prevented the occurrence of oxidative side reactions under HRP-catalyzed conditions. As probes for HRP-catalyzed protein modification, N-methylluminol derivatives showed much higher efficiency than tyramide without inducing oligomerization of probe molecules. Tyrosine modification also proceeded in the presence of β-nicotinamide adenine dinucleotide (NADH, H2 O2 -free conditions).

  4. Metal Catalyzed Oligomerization Reactions of Organosiloxanes.

    DTIC Science & Technology

    1982-10-28

    metallacycle from a mixture of stereo- isomers of the starting disiloxane is observed. The catalytic activity of these complexes for the oligomeriza... catalysts were adsorbed on oxide supports. Although the goal of synthesizing stereoregular silicones has not yet been achieved, the results warrant further...implicated as intermediates in several transi- tion metal-catalyzed reactions, e.g. olefin metathesis . 1 3 Metallacycles are also probable

  5. 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.

  6. 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.

  7. 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.

    2016-11-15

    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.

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

    PubMed

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

    2014-03-14

    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.

  9. Thermodynamic limitations on microbially catalyzed reaction rates

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  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.

    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.

  11. Iodide effects in transition metal catalyzed reactions.

    PubMed

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

    2004-11-07

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

  12. 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.

  13. 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; ...

    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

  14. Firefly bioluminescence: a mechanistic approach of luciferase catalyzed reactions.

    PubMed

    Marques, Simone M; Esteves da Silva, Joaquim C G

    2009-01-01

    Luciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two-step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH(2)), with ATP-Mg(2+) generating inorganic pyrophosphate and an intermediate luciferyl-adenylate (LH(2)-AMP); the second is the oxidation and decarboxylation of LH(2)-AMP to oxyluciferin, the light emitter, producing CO(2), AMP, and photons of yellow-green light (550- 570 nm). In a dark reaction LH(2)-AMP is oxidized to dehydroluciferyl-adenylate (L-AMP). Luciferase also shows acyl-coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl-coenzyme A (L-CoA), luciferyl-coenzyme A (LH(2)-CoA), and fatty acyl-CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3'-phosphate chain plus an intact terminal pyrophosphate moiety. The LH(2) stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D-LH(2) or L-LH(2), has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging.

  15. 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.

  16. A procedure for the joint evaluation of substrate partitioning and kinetic parameters for reactions catalyzed by enzymes in reverse micellar solutions. I. Hydrolysis of 2-naphthyl acetate catalyzed by lipase in sodium 1,4-bis(2-ethylhexyl) sulphosuccinate (AOT)/buffer/heptane.

    PubMed

    Aguilar, L F; Abuin, E; Lissi, E

    2001-04-15

    A simple method useful for the joint evaluation of substrate partitioning and kinetic parameters for reactions catalyzed by enzymes entrapped in reverse micelles is proposed. The method is applied to the hydrolysis of 2-naphthyl acetate (2-NA) catalyzed by lipase in sodium 1,4-bis(2-ethylhexyl) sulfosuccinate (AOT)/buffer/heptane reverse micellar solutions. In the presence of micelles, the relationship between the initial reaction rate and the analytical concentration of 2-NA was dependent on AOT concentration at a constant W ([water]/[AOT]) value. The dependence of the initial reaction rate profiles with [AOT] was analyzed according with the method proposed to obtain the partition constant of 2-NA between the micelles and the external solvent, Kp. A value of Kp = 2.7 L mol(-1) was obtained irrespective of the water content of the micelles (W from 5 to 20). The catalytic rate constant kcat in the micellar solutions was independent of [AOT] but slightly decreased with an increase in W from 2 x 10(-6) mol g(-1) s(-1) at W = 5 to 1.2 x 10(-6) mol g(-1) s(-1) at W = 20. The apparent Michaelis constant determined in terms of the analytical concentration of 2-NA increased with [AOT] at a given W and moderately decreased with W at a fixed [AOT]. The increase with [AOT] is accounted for by considering the partitioning of the substrate. After correction for the partitioning of 2-NA values of (Km)corr were obtained as 3.9 x 10(-3) mol L(-1) (W = 5), 4.6 x 10(-3) mol L(-1) (W = 10), 2.3 x 10(-3) mol L(-1) (W = 15), and 1.7 x 10(-3) mol L(-1) (W = 20). The rate parameters in the aqueous phase in the absence of micelles, were obtained as (kcat)aq = 7.9 x 10(-6) mol g(-1) s(-1) and (Km)aq = 2.5 x 10(-3) mol L(-1). In order to compare the efficiency of the enzyme in the micellar solution with that in aqueous phase, the values of (Km)corr were in turn corrected to take into account differences in the substrate activity, obtaining so a set of (Km)*corr values. The efficiency of the

  17. 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.

  18. Copper-Catalyzed Click Reaction on/in Live Cells.

    PubMed

    Li, Siheng; Wang, Lin; Yu, Fei; Zhu, Zhiling; Shobaki, Dema; Chen, Haoqing; Wang, Mu; Wang, Jun; Qin, Guoting; Erasquin, Uriel J; Ren, Li; Wang, Yingjun; Cai, Chengzhi

    2017-03-01

    We demonstrated that copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction could be performed inside live mammalian cells without using a chelating azide. Under optimized conditions, the reaction was performed in human ovary cancer cell line OVCAR5 in which newly synthesized proteins were metabolically modified with homopropargylglycine (HPG). This model system allowed us to estimate the efficiency of the reaction on the cell membranes and in the cytosol using mass spectrometry. We found that the reaction was greatly promoted by a tris(triazolylmethyl)amine Cu(I) ligand tethering a cell-penetrating peptide. Uptake of the ligand, copper, and a biotin-tagged azide in the cells was determined to be 69 ± 2, 163 ± 3 and 1.3 ± 0.1 µM, respectively. After 10 minutes of reaction, the product yields on the membrane and cytosolic proteins were higher than 18% and 0.8%, respectively, while 75% cells remained viable. By reducing the biothiols in the system by scraping or treatment with N-ethylmalemide, the reaction yield on the cytosolic proteins was greatly improved to ~9% and ~14%, respectively, while the yield on the membrane proteins remained unchanged. The results indicate that out of many possibilities, deactivation of the current copper catalysts by biothiols is the major reason for the low yield of CuAAC reaction in the cytosol. Overall, we have improved the efficiency for CuAAC reaction on live cells by 3-fold. Despite the low yielding inside live cells, the products that strongly bind to the intracellular targets can be detected by mass spectrometry. Hence, the in situ CuAAC reaction can be potentially used for screening of cell-specific enzyme inhibitors or biomarkers containing 1,4-substituted 1,2,3-triazoles.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Masterson, Jean E.; Schwartz, Steven D.

    2014-10-01

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

  1. Stau-catalyzed big-bang nucleosynthesis reactions

    NASA Astrophysics Data System (ADS)

    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-) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X- particle has a lifetime of τX>~103 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- acts as a catalyst. Some of these X- catalyzed reactions have significantly large cross sections so that the inclusion of the reactions into the BBN network calculation can markedly change the abundances of some elements. We use a high-accuracy three-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

  2. 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.

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

    SciTech Connect

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

    2005-12-09

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

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

    PubMed Central

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

    2011-01-01

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

  5. 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%.

  6. 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.

  7. 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

  8. 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.

  9. New Stetter reactions catalyzed by thiamine diphosphate dependent MenD from E. coli.

    PubMed

    Beigi, Maryam; Waltzer, Simon; Zarei, Mostafa; Müller, Michael

    2014-12-10

    The intermolecular asymmetric Stetter reaction is a rarely found biocatalysts transformation. MenD, the second enzyme of the menaquinone biosynthetic pathway, catalyzes as a physiological reaction a Stetter-like addition of α-ketoglutarate to isochorismate. The substrate range of MenD for similar 1,4-additions is highly restricted. All other thiamine diphosphate dependent enzymes known to act as stetterases are members of the PigD enzyme subfamily, which accept aliphatic and aromatic α,β-unsaturated ketones and thioesters as Michael acceptor substrates. Here, we describe the unexpected activity of MenD with short-chain α,β-unsaturated acids and derivatives as substrates in Stetter reactions. MenD possesses a characteristic substrate range with respect to Michael acceptor substrates which is distinctly different from the classical stetterases. This provides biocatalytic access to new types of products which are not related to the products currently accessible by thiamine diphosphate dependent enzyme catalysis.

  10. Palladium-Catalyzed, Enantioselective Heine Reaction

    PubMed Central

    2016-01-01

    Aziridines are important synthetic intermediates for the generation of nitrogen-containing molecules. N-Acylaziridines undergo rearrangement by ring expansion to produce oxazolines, a process known as the Heine reaction. The first catalytic, enantioselective Heine reaction is reported for meso-N-acylaziridines where a palladium(II)–diphosphine complex is employed. The highly enantioenriched oxazoline products are valuable organic synthons and potential ligands for transition-metal catalysis. PMID:27398262

  11. Palladium-Catalyzed, Enantioselective Heine Reaction.

    PubMed

    Punk, Molly; Merkley, Charlotte; Kennedy, Katlyn; Morgan, Jeremy B

    2016-07-01

    Aziridines are important synthetic intermediates for the generation of nitrogen-containing molecules. N-Acylaziridines undergo rearrangement by ring expansion to produce oxazolines, a process known as the Heine reaction. The first catalytic, enantioselective Heine reaction is reported for meso-N-acylaziridines where a palladium(II)-diphosphine complex is employed. The highly enantioenriched oxazoline products are valuable organic synthons and potential ligands for transition-metal catalysis.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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,…

  17. 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

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

    PubMed

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

    2016-01-13

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

  19. Catalyzed reactions at illuminated semiconductor interfaces

    NASA Astrophysics Data System (ADS)

    Wrighton, M. S.

    1984-06-01

    It is pointed out that thermodynamically unfavorable chemical redox reactions can be effected by using optical energy as the driving force. To date, the best man-contrived systems for the direct conversion of optical energy to high energy redox products are semiconductor-based photoelectrochemical devices. The present investigation is concerned with the possibility that the minority carrier redox process at a semiconductor electrode may be too slow to compete with the recombination of photogenerated carriers. Attention is given to the photoelectrochemical generation of hydrogen, the photoelectrochemical reduction of carbon dioxide, the photo-oxidation of halides to halogens, and photo-oxidation of water. It is concluded that redox reactions of possible significance in solar fuel generation require rate acceleration to achieve high solar energy conversion efficiency.

  20. 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

  1. 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.

  2. 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.

  3. (Ligand intermediates in metal-catalyzed reactions)

    SciTech Connect

    Not Available

    1992-01-01

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

  4. 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.

  5. Adenosyl radical: reagent and catalyst in enzyme reactions

    PubMed Central

    Patterson, Dustin P.

    2010-01-01

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

  6. 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.

  7. 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

  8. Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

    PubMed Central

    Major, Dan T.; Heroux, Annie; Orville, Allen M.; Valley, Michael P.; Fitzpatrick, Paul F.; Gao, Jiali

    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. PMID:19926855

  9. One-pot lipase-catalyzed aldol reaction combination of in situ formed acetaldehyde.

    PubMed

    Wang, Na; Zhang, Wei; Zhou, Long-Hua; Deng, Qing-Feng; Xie, Zong-Bo; Yu, Xiao-Qi

    2013-12-01

    A facile tandem route to α,β-unsaturated aldehydes was developed by combining the two catalytic activities of the same enzyme in a one-pot strategy for the aldol reaction and in situ generation of acetaldehyde. Lipase from Mucor miehei was found to have conventional and promiscuous catalytic activities for the hydrolysis of vinyl acetate and aldol condensation with in situ formed acetaldehyde. The first reaction continuously provided material for the second reaction, which effectively reduced the volatilization loss, oxidation, and polymerization of acetaldehyde, as well as avoided a negative effect on the enzyme of excessive amounts of acetaldehyde. After optimizing the process, several substrates participated in the reaction and provided the target products in moderate to high yields using this single lipase-catalyzed one-pot biotransformation.

  10. 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.

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

    PubMed

    Saw, Mei Huey; Siew, Wai Lin

    2014-01-01

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

  12. Stereochemical course of enzyme-catalyzed aminopropyl transfer: spermidine synthase

    SciTech Connect

    Kullberg, D.W.; Orr, G.R.; Coward, J.K.

    1986-05-01

    The R and S enantionmers of S-adenosyl-3-(/sup 2/H)3-(methylthio)-1-propylamine (decarboxylated S-adenosylmethionine), previously synthesized in this laboratory, were incubated with (1,4-/sup 2/H/sub 4/)-putrescine in the presence of spermidine synthase from E. coli. The resulting chiral (/sup 2/H/sub 5/)spermidines were isolated and converted to their N/sub 1/,N/sub 7/-dibocspermidine-N/sub 4/-(1S,4R)-camphanamides. The derivatives were analyzed by 500 MHz /sup 1/H-NMR and the configuration of the chiral center assigned by correlation with the spectra of synthetic chiral (/sup 2/H/sub 3/)dibocspermidine camphanamide standards. The enzyme-catalyzed aminopropyl transfer was shown to occur with net retention of configuration, indicative of a double-displacement mechanism. This result concurs with that of a previous steady-state kinetics study of spermidine synthase isolated from E. coli, but contradicts the single-displacement mechanism suggested by a stereochemical analysis of chiral spermidines biosynthesized in E. coli treated with chirally deuterated methionines. It also indicates that this aminopropyltransferase is mechanistically distinct from the methyltransferases, which have been shown to act via a single-displacement mechanism (net inversion at -CH/sub 3/) in all cases studied to date.

  13. Asymptotic Expansion in Enzyme Reactions with High Enzyme Concentrations

    NASA Astrophysics Data System (ADS)

    Bersani, Alberto Maria; Dell'Acqua, Guido

    2010-09-01

    In this paper we find a new asymptotic expansion valid in enzymatic reactions where the total amount of enzyme exceeds greatly the total amount of substrate. In such case it is well known that the Michelis-Menten approximation is no longer valid; therefore our asymptotic expansion is a new tool to approximate in a closed form the concentrations of the reactants in presence of an enzyme excess.

  14. 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

  15. 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.

  16. 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.

  17. Rh(II)-catalyzed Reactions of Diazoesters with Organozinc Reagents

    PubMed Central

    Panish, Robert; Selvaraj, Ramajeyam; Fox, Joseph M.

    2015-01-01

    Rh(II)-catalyzed reactions of diazoesters with organozinc reagents are described. Diorganozinc reagents participate in reactions with diazo compounds by two distinct, catalyst-dependent mechanisms. With bulky diisopropylethylacetate ligands, the reaction mechanism is proposed to involve initial formation of a Rh-carbene and subsequent carbozincation to give a zinc enolate. With Rh2(OAc)4, it is proposed that initial formation of an azine precedes 1,2-addition by an organozinc reagent. This straightforward route to the hydrazone products provides a useful method for preparing chiral quaternary α-aminoesters or pyrazoles via the Paul-Knorr condensation with 1,3-diketones. Crossover and deuterium labeling experiments provide evidence for the mechanisms proposed. PMID:26241081

  18. Rh(II)-Catalyzed Reactions of Diazoesters with Organozinc Reagents.

    PubMed

    Panish, Robert; Selvaraj, Ramajeyam; Fox, Joseph M

    2015-08-21

    Rh(II)-catalyzed reactions of diazoesters with organozinc reagents are described. Diorganozinc reagents participate in reactions with diazo compounds by two distinct, catalyst-dependent mechanisms. With bulky diisopropylethyl acetate ligands, the reaction mechanism is proposed to involve initial formation of a Rh-carbene and subsequent carbozincation to give a zinc enolate. With Rh2(OAc)4, it is proposed that initial formation of an azine precedes 1,2-addition by an organozinc reagent. This straightforward route to the hydrazone products provides a useful method for preparing chiral quaternary α-aminoesters or pyrazoles via the Paul-Knorr condensation with 1,3-diketones. Crossover and deuterium labeling experiments provide evidence for the mechanisms proposed.

  19. Regioselective Versatility of Monooxygenase Reactions Catalyzed by CYP2B6 and CYP3A4: Examples with Single Substrates.

    PubMed

    Erratico, Claudio A; Deo, Anand K; Bandiera, Stelvio M

    2015-01-01

    Hepatic microsomal cytochrome P450 (CYP) enzymes have broad and overlapping substrate specificity and catalyze a variety of monooxygenase reactions, including aliphatic and aromatic hydroxylations, N-hydroxylations, oxygenations of heteroatoms (N, S, P and I), alkene and arene epoxidations, dehalogenations, dehydrogenations and N-, O- and S-dealkylations. Individual CYP enzymes typically catalyze the oxidative metabolism of a common substrate in a regioselective and stereoselective manner. In addition, different CYP enzymes often utilize different monooxygenase reactions when oxidizing a common substrate. This review examines various oxidative reactions catalyzed by a CYP enzyme acting on a single substrate. In the first example, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), a halogenated aromatic environmental contaminant, was oxidatively biotransformed by human CYP2B6. Nine different metabolites of BDE-47 were produced by CYP2B6 via monooxygenase reactions that included aromatic hydroxylation, with and without an NIH-shift, dealkylation and debromination. In the second example, lithocholic acid (3α-hydroxy-5β-cholan-24-oic acid), an endogenous bile acid, served as a substrate for human CYP3A4 and yielded five different metabolites via aliphatic hydroxylation and dehydrogenation reactions.

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

    PubMed

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

    2016-04-15

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

  1. 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)

  2. Cu-Catalyzed Click Reaction in Carbohydrate Chemistry.

    PubMed

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

    2016-03-09

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

  3. Reactions of ethyl diazoacetate catalyzed by methylrhenium trioxide

    SciTech Connect

    Zhu, Z.; Espenson, H.

    1995-11-03

    Methylrhenium trioxide (CH{sub 3}ReO{sub 3} or MTO) has found wise use in catalysis, including the epoxidation and metathesis of olefins, aldehyde olefination, and oxygen transfer. Extensive reports have now appeared in the area of MTO-catalyzed substrate oxidations with hydrogen peroxide. Certain catalytic applications of MTO for organic reactions that do not utilize peroxide have now been realized. In particular, a catalytic amount of MTO with ethyl diazoacetate (EDA) will convert aromatic imines to aziridines and convert aldehydes and ketones to epoxides. The aziridine preparation proceeds in high yields under anaerobic conditions more conveniently than with existing methods. Compounds with a three-membered heterocyclic ring can be obtained with the EDA/MTO catalytic system. Aromatic imines undergo cycloaddition reactions to give aziridines under mild conditions.

  4. 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.

  5. Palladium(II)-Catalyzed Enantioselective Reactions Using COP Catalysts.

    PubMed

    Cannon, Jeffrey S; Overman, Larry E

    2016-10-18

    Allylic amides, amines, and esters are key synthetic building blocks. Their enantioselective syntheses under mild conditions is a continuing pursuit of organic synthesis methods development. One opportunity for the synthesis of these building blocks is by functionalization of prochiral double bonds using palladium(II) catalysis. In these reactions, nucleopalladation mediated by a chiral palladium(II) catalyst generates a new heteroatom-substituted chiral center. However, reactions where nucleopalladation occurs with antarafacial stereoselectivity are difficult to render enantioselective because of the challenge of transferring chiral ligand information across the square-planar palladium complex to the incoming nucleophile. In this Account, we describe the development and use of enantiopure palladium(II) catalysts of the COP (chiral cobalt oxazoline palladacyclic) family for the synthesis of enantioenriched products from starting materials derived from prochiral allylic alcohols. We begin with initial studies aimed at rendering catalyzed [3,3]-sigmatropic rearrangements of allylic imidates enantioselective, which ultimately led to the identification of the significant utility of the COP family of Pd(II) catalysts. The first use of an enantioselective COP catalyst was reported by Richards' and our laboratories in 2003 for the enantioselective rearrangement of allylic N-arylimidates. Shortly thereafter, we discovered that the chloride-bridged COP dimer, [COP-Cl]2, was an excellent enantioselective catalyst for the rearrangement of (E)-allylic trichloroacetimidates to enantioenriched allylic trichloroacetamides, this conversion being the most widely used of the allylic imidate rearrangements. We then turn to discuss SN2' reactions catalyzed by the acetate-bridged COP dimer, [COP-OAc]2, which proceed by a unique mechanism to provide branched allylic esters and allylic phenyl ethers in high enantioselectivity. Furthermore, because of the unique nucleopalladation

  6. 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.

  7. [Chiral HPLC determination of conversion and enantiomeric excess of enzyme catalyzed stereoselective esterification of racemic ibuprofen].

    PubMed

    Xie, Y; Liu, H; Chen, J

    1998-01-01

    In the study of enzyme catalyzed kinetic resolution of racemates, it is imperative to assay how the optical yield varies with chemical conversion. In this paper, a method using one-time injection to determine enantiomeric excess and conversion of the stereoselective esterification of racemic ibuprofen with n-butanol catalyzed by lipase was developed with a commercially available HPLC CSP column Regis(S, S) Whelk-01. In the linear range of detector, all peak areas of products and substrates are proportional to their concentrations. Because the total mole concentration remains unchanged (equal to the initial value of ibuprofen) in the reaction process, the conversion could be calculated from the peak areas, provided the ratio of response factors was known. The calibration curves of two ibuprofen enantiomers with racemic ibuprofen as external standard were overlapped, indicating fiR = fiS. By investigating the variation of peak areas of products and substrates against conversion (determined by external standard), the ratio of peak area-concentration response factor of ibuprofen butyl ester to that of unreacted ibuprofen was determined to be 1 through linear regressions, from which the conversion could be directly determined by the self normalization of the peak areas. With a mobile phase of IPA/hexane/HAc/triethylamine (15/85/0.2/0.05, V/V, flow rate 0.4 mL/min), the resolution of ibuprofen enantiomers was sufficient for precise enantiomeric purity determination.

  8. 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.

  9. 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.

  10. 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.

  11. Lipase-catalyzed synthesis of ascorbyl oleate in acetone: optimization of reaction conditions and lipase reusability.

    PubMed

    Stojanović, Marija; Velićković, Dušan; Dimitrijević, Aleksandra; Milosavić, Nenad; Knežević-Jugović, Zorica; Bezbradica, Dejan

    2013-01-01

    Lipase-catalyzed ascorbyl oleate synthesis is eco-friendly and selective way of production of liposoluble biocompatible antioxidants, but still not present on an industrial level due to the high biocatalyst costs. In this study, response surface methodology was applied in order to estimate influence of individual experimental factors, identify interactions among them, and to determine optimum conditions for enzymatic synthesis of ascorbyl oleate in acetone, in terms of limiting substrate conversion, product yield, and yield per mass of consumed enzyme. As a biocatalyst, commercial immobilized preparation of lipase B from Candida antarctica, Novozym 435, was used. In order to develop cost-effective process, at reaction conditions at which maximum amount of product per mass of biocatalyst was produced (60°C, 0.018 % (v/v) of water, 0.135 M of vitamin C, substrates molar ratio 1:8, and 0.2 % (w/v) of lipase), possibilities for further increase of ester yield were investigated. Addition of molecular sieves at 4(th) hour of reaction enabled increase of yield from 16.7 mmol g⁻¹ to 19.3 mmol g⁻¹. Operational stability study revealed that after ten reaction cycles enzyme retained 48 % of its initial activity. Optimized synthesis with well-timed molecular sieves addition and repeated use of lipase provided production of 153 mmol per gram of enzyme. Further improvement of productivity was achieved using procedure for the enzyme reactivation.

  12. 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

  13. Heme oxygenase reveals its strategy for catalyzing three successive oxygenation reactions.

    PubMed

    Matsui, Toshitaka; Unno, Masaki; Ikeda-Saito, Masao

    2010-02-16

    Heme oxygenase (HO) is an enzyme that catalyzes the regiospecific conversion of heme to biliverdin IXalpha, CO, and free iron. In mammals, HO has a variety of physiological functions, including heme catabolism, iron homeostasis, antioxidant defense, cellular signaling, and O(2) sensing. The enzyme is also found in plants (producing light-harvesting pigments) and in some pathogenic bacteria, where it acquires iron from the host heme. The HO-catalyzed heme conversion proceeds through three successive oxygenations, a process that has attracted considerable attention because of its reaction mechanism and physiological importance. The HO reaction is unique in that all three O(2) activations are affected by the substrate itself. The first step is the regiospecific self-hydroxylation of the porphyrin alpha-meso carbon atom. The resulting alpha-meso-hydroxyheme reacts in the second step with another O(2) to yield verdoheme and CO. The third O(2) activation, by verdoheme, cleaves its porphyrin macrocycle to release biliverdin and free ferrous iron. In this Account, we provide an overview of our current understanding of the structural and biochemical properties of the complex self-oxidation reactions in HO catalysis. The first meso-hydroxylation is of particular interest because of its distinct contrast with O(2) activation by cytochrome P450. Although most heme enzymes oxidize exogenous substrates by high-valent oxo intermediates, HO was proposed to utilize the Fe-OOH intermediate for the self-hydroxylation. We have succeeded in preparing and characterizing the Fe-OOH species of HO at low temperature, and an analysis of its reaction, together with mutational and crystallographic studies, reveals that protonation of Fe-OOH by a distal water molecule is critical in promoting the unique self-hydroxylation. The second oxygenation is a rapid, spontaneous auto-oxidation of the reactive alpha-meso-hydroxyheme; its mechanism remains elusive, but the HO enzyme has been shown not to

  14. 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.

  15. Fundamental reaction mechanism and free energy profile for (-)-cocaine hydrolysis catalyzed by cocaine esterase.

    PubMed

    Liu, Junjun; Hamza, Adel; Zhan, Chang-Guo

    2009-08-26

    The fundamental reaction mechanism of cocaine esterase (CocE)-catalyzed hydrolysis of (-)-cocaine and the corresponding free energy profile have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations. On the basis of the QM/MM-FE results, the entire hydrolysis reaction consists of four reaction steps, including the nucleophilic attack on the carbonyl carbon of (-)-cocaine benzoyl ester by the hydroxyl group of Ser117, dissociation of (-)-cocaine benzoyl ester, nucleophilic attack on the carbonyl carbon of (-)-cocaine benzoyl ester by water, and finally dissociation between the (-)-cocaine benzoyl group and Ser117 of CocE. The third reaction step involving the nucleophilic attack of a water molecule was found to be rate-determining, which is remarkably different from (-)-cocaine hydrolysis catalyzed by wild-type butyrylcholinesterase (BChE; where the formation of the prereactive BChE-(-)-cocaine complex is rate-determining) or its mutants containing Tyr332Gly or Tyr332Ala mutation (where the first chemical reaction step is rate-determining). Besides, the role of Asp259 in the catalytic triad of CocE does not follow the general concept of the "charge-relay system" for all serine esterases. The free energy barrier calculated for the rate-determining step of CocE-catalyzed hydrolysis of (-)-cocaine is 17.9 kcal/mol, which is in good agreement with the experimentally derived activation free energy of 16.2 kcal/mol. In the present study, where many sodium ions are present, the effects of counterions are found to be significant in determining the free energy barrier. The finding of the significant effects of counterions on the free energy barrier may also be valuable in guiding future mechanistic studies on other charged enzymes.

  16. 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…

  17. Erythrocyte enzymes catalyze 1-nitropyrene and 3-nitrofluoranthene nitroreduction.

    PubMed

    Belisario, M A; Pecce, R; Garofalo, A; Sannolo, N; Malorni, A

    1996-04-15

    Nitroarenes are environmental contaminants produced during incomplete combustion processes. Nitroreduction, the most important pathway of nitroarene toxification, occurs mainly in the liver and intestine. In the present study, we show that human red cells may also possess the metabolic competence to reduce 1-nitropyrene (NP) and 3-nitrofluoranthene (NF), the nitroarenes chosen as model compounds, to their corresponding amino derivatives, 1-aminopyrene (AP) and 3-aminofluoranthene (AF). The requirement of the cofactor couple NADH/FMN suggests that erythrocyte nitroreductase activity occurs via one electron transfer. The presence of oxygen strongly inhibited the haemolysate-catalyzed nitroarene reduction, whether measured as amine formation or nitroarene disappearance. Intermediate reactive species, that bind covalently to haemoglobin and/or other erythrocyte proteins, are formed during nitroreduction catalyzed by human haemolysate. In fact, the reduced metabolites AP and AF were released after mild acid hydrolysis of red cell proteins exposed to NP and NF, thus suggesting that sulphinamide adducts have been formed.

  18. Evidence for coupled motion and hydrogen tunneling of the reaction catalyzed by glutamate mutase.

    PubMed

    Cheng, Mou-Chi; Marsh, E Neil G

    2007-01-23

    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 the 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 alpha-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5'-deoxyadenosine when glutamate mutase was reacted with [5'-(3)H]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.

  19. TBAF-catalyzed deacylation of cellulose esters: reaction scope and influence of reaction parameters.

    PubMed

    Zheng, Xueyan; Gandour, Richard D; Edgar, Kevin J

    2013-10-15

    In order to expand its utility and understand how to carry it out most efficiently, the scope of the highly regioselective, tetrabutylammonium fluoride (TBAF) catalyzed deacylation of cellulose acetates has been investigated, including the influence of key process parameters: solvent, temperature, and water content. Reactions in DMSO, THF, MEK and acetone afforded similar extents of deacylation and regioselectivity. Reaction with TBAF in DMSO at 50 °C for 18 h was the most efficient process providing regioselective deacylation at O-2/3. All results were consistent with our previous mechanistic proposals. Furthermore, we demonstrate that TBAF-catalyzed deacylation is also effective and regioselective with cellulose acetate, butyrate, and hexanoate triesters, and even with a cellulose ester devoid of alpha protons, cellulose tribenzoate. These reactions displayed regioselectivity for deacylation at O-2/3 similar to that observed earlier with cellulose acetate (DS 2.4).

  20. 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

  1. Trypsin-catalyzed multicomponent reaction: A novel and efficient one-pot synthesis of thiazole-2-imine derivatives.

    PubMed

    Zhou, Junbin; Huang, Xingtian; Zhang, Zhuan; Song, Ping; Li, Yiqun

    2017-01-10

    The first Trypsin from porcine pancreas catalyzed a novel one-pot three-component reaction of α-bromoketone, primary alkylamines, and phenylisothiocyanate for the synthesis of thiazole-imine derivatives with high yields (up to 98%) in a short time under mild conditions. The results revealed that Trypsin exhibited excellent catalytic activity and great tolerance for broad substrates. This Trypsin-catalyzed three component convergent method provides a novel strategy for the synthesis of thiazole-2-imine derivatives and expands the promiscuous functions of enzymes in organic synthesis.

  2. Kinetic analysis of the transglycosidation reaction catalyzed by rabbit spleen pyridine nucleotide glycohydrolase.

    PubMed

    Imai, T

    1989-11-01

    Properties of the transglycosidation reaction catalyzed by rabbit spleen pyridine nucleotide glycohydrolase were characterized using a modified cyanide addition method by which initial velocities of the transglycosidation (vT) and hydrolysis (vH) of pyridine nucleotides could be monitored simultaneously. (1) The vT was routinely determined with NMN and nicotinic acid used as substrates and was observed to be maximal at pH 6. Arrhenius plots of vT and vH indicated that the activation energies for transglycosidation and hydrolysis were 8.7 and 10.7 kcal/mol, respectively. (2) The enzyme showed a broad spectrum of substrate specificity with respect to both pyridine nucleotides and bases. Of the compounds tested, NMN and nicotinic acid were shown to be the best substrates when compared on the basis of Vmax/Km values. Kinetic constants for the enzyme-catalyzed transglycosidation reaction were as follows; Km(NMN) = 0.53 mM, Km(nicotinic acid), as acid form = 15 mM, apparent Vmax = 7.8 mumol/min/mg protein, in the presence of 0.2 M nicotinic acid. (3) The ratio of vT/vH was shown to be dependent on both pH and nicotinic acid concentration. However, transglycosidation versus hydrolysis partition at a fixed pH was constant regardless of the nicotinic acid concentration employed and approximated to be 1.2 x 10(4) at the maximal pH. (4) Nicotinamide, one of the most potent inhibitors for the enzyme-catalyzed hydrolysis, was shown to function as an antagonist for the transglycosidation reaction with NMN and nicotinic acid used as substrates. The inhibition mechanism with nicotinamide was purely noncompetitive with respect to nicotinic acid; on the other hand, the double reciprocal plot of the transglycosidation velocity against NMN concentration at a fixed concentration of nicotinamide was concave downwards. (5) The equilibrium constant of the reaction, NMN + 3-acetylpyridine----3-acetylpyridine mononucleotide + nicotinamide, was 0.61, whereas the conversion of NMN with

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

    PubMed

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

    2012-03-06

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

  4. Scaling and Continuum Percolation Model for Enzyme-Catalyzed Gel Degradation

    NASA Astrophysics Data System (ADS)

    Lairez, D.; Carton, J.-P.; Zalczer, G.; Pelta, J.

    2007-06-01

    Enzyme-catalyzed gel degradation is inherently controlled by diffusion of enzymes in the gel. We report kinetics measurements on the gelatin-thermolysin system, varying solvent viscosity as well as gel and enzyme concentrations. Scaling relations and reduced variables are proposed which are shown to account for the experimental results. Finally, we argue that the nontrivial experimental dependence on enzyme concentration for the degradation time demonstrates that enzyme random walk is self-attracting, leading to a continuum percolation model for gel degradation.

  5. Theoretical Study of the Mechanism of Exemestane Hydroxylation Catalyzed by Human Aromatase Enzyme.

    PubMed

    Viciano, Ignacio; Martí, Sergio

    2016-04-07

    Human aromatase (CYP19A1) aromatizes the androgens to form estrogens via a three-step oxidative process. The estrogens are necessary in humans, mainly in women, because of the role they play in sexual and reproductive development. However, these also are involved in the development and growth of hormone-dependent breast cancer. Therefore, inhibition of the enzyme aromatase, by means of drugs known as aromatase inhibitors, is the frontline therapy for these types of cancers. Exemestane is a suicidal third-generation inhibitor of aromatase, currently used in breast cancer treatment. In this study, the hydroxylation of exemestane catalyzed by aromatase has been studied by means of hybrid QM/MM methods. The Free Energy Perturbation calculations provided a free energy of activation for the hydrogen abstraction step (rate-limiting step) of 17 kcal/mol. The results reveal that the hydroxylation of exemestane is not the inhibition stage, suggesting a possible competitive mechanism between the inhibitor and the natural substrate androstenedione in the first catalytic subcycle of the enzyme. Furthermore, the analysis of the interaction energy for the substrate and the cofactor in the active site shows that the role of the enzymatic environment during this reaction consists of a transition state stabilization by means of electrostatic effects.

  6. 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.

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

    PubMed

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

    2015-03-09

    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.

  8. Copper-catalyzed cascade reactions of α,β-unsaturated esters with keto esters

    PubMed Central

    Wang, Chongnian; Li, Zengchang

    2015-01-01

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

  9. 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.

  10. 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.

  11. 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.

  12. Ultrasound assisted enzyme catalyzed degradation of Cetirizine dihydrochloride.

    PubMed

    Sutar, Rahul S; Rathod, Virendra K

    2015-05-01

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

  13. 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.

  14. Organic reactions catalyzed by methylrhenium trioxide: Reactions of ethyl diazoacetate and organic azides

    SciTech Connect

    Zhu, Z.; Espenson, J.H. |

    1996-10-16

    Methylrhenium trioxide (CH{sub 3}ReO{sub 3} or MTO) catalyzes several classes of reactions of ethyl diazoacetate, EDA. It is the first high valent oxo complex for carbene transfer. Under mild conditions and in the absence of other substrates, EDA was converted to a 9:1 mixture of diethyl maleate and diethyl fumarate. In the presence of alcohols, {alpha}-alkoxy ethyl acetates were obtained in good yield. The yields dropped for the larger and more branched alcohols, the balance of material being diethyl maleate and fumarate. An electron-donating group in the para position of phenols favors the formation of {alpha}-phenoxy ethyl acetates. The use of EDA to form {alpha}-thio ethyl acetates and N-substituted glycine ethyl esters, on the other hand, is hardly affected by the size or structure of the parent thiol or amine, with all of these reactions proceeding in high yield. MTO-catalyzed cycloaddition reactions occur between EDA and aromatic imines, olefins, and carbonyl compounds. Three-membered ring products are formed: aziridines, cyclopropanes, and epoxides, respectively. The reactions favor the formation of trans products, and provide a convenient route for the preparation of aziridines. Intermediate carbenoid and nitrenoid species have been proposed. In the presence of an oxygen source such as an epoxide, ethyl diazoacetate and azibenzil are converted to an oxalic acid monoethyl ester and to benzil; at the same time the epoxide was converted to an olefin. 75 refs., 1 fig., 7 tabs.

  15. 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.

  16. Asymmetric synthesis of dihydropyranones from ynones by sequential copper(I)-catalyzed direct aldol and silver(I)-catalyzed oxy-Michael reactions.

    PubMed

    Shi, Shi-Liang; Kanai, Motomu; Shibasaki, Masakatsu

    2012-04-16

    Ynones as diene surrogates: the asymmetric synthesis of enantiomerically enriched substituted dihydropyranones is described. The products are obtained in two steps by a copper(I)-catalyzed direct aldol reaction of ynones followed by a silver-catalyzed oxy-Michael reaction. This easy method is compatible with both aromatic and aliphatic substrates, and provides excellent chemoselectivity under mild reaction conditions.

  17. 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.

  18. 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

  19. 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.

  20. Laboratory Studies of Hydrogen Gas Generation Using the Cobalt Chloride Catalyzed Sodium Borohydride-Water Reaction

    DTIC Science & Technology

    2015-07-01

    TECHNICAL REPORT 2082 July 2015 Laboratory Studies of Hydrogen Gas Generation Using the Cobalt Chloride Catalyzed Sodium ...describes experiments to generate hydrogen gas using the cobalt chloride catalyzed sodium borohydride-water reaction. Space and Naval Warfare Systems...to inflate LTAs. Of the metal hydrides, we chose to explore the sodium borohydride chemistry. We chose this chemistry because of its energy density

  1. 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)

  2. Reaction rate modeling in cryoconcentrated solutions: alkaline phosphatase catalyzed DNPP hydrolysis.

    PubMed

    Champion, D; Blond, G; Le Meste, M; Simatos, D

    2000-10-01

    The hydrolysis of disodium p-nitrophenyl phosphate catalyzed by alkaline phosphatase was chosen as a model to study the kinetics of changes in frozen food products. The initial reaction rate was determined in concentrated sucrose solutions down to -24 degrees C, and the enzymatic characteristics K(M) and V(max) were calculated. The experimental data were compared to the kinetics predicted by assuming that the reaction was viscosity dependent. Indeed, an analysis of the enzymatic reaction demonstrated that both the diffusion of the substrate and the flexibility of the enzyme segments were controlled by the high viscosity of the media. When the temperature was too low for the viscosity to be measured simply, the Williams-Landel-Ferry equation was used to predict the viscosity, taking, as reference temperature, the glass transition temperature (T(g)) corresponding to the concentration of the freeze-concentrated phase at the test temperature. Predicted values of the reaction rate were very close to the experimental ones in the studied temperature range.

  3. Theoretical comparison of p-nitrophenyl phosphate and sulfate hydrolysis in aqueous solution: implications for enzyme-catalyzed sulfuryl transfer.

    PubMed

    Kamerlin, Shina Caroline Lynn

    2011-11-18

    analogue. Additionally, we show that the solvation effects upon moving from the ground state to the transition state are quite different for both reactions, suggesting that the enzymes that catalyze these reactions would need active sites with quite different electrostatic preorganization for the efficient catalysis of either reaction (despite which many enzymes can catalyze both phosphoryl and sulfuryl transfer). We believe that such a comparative study is an important foundation for understanding the molecular basis for phosphate-sulfate cross-promiscuity within members of the alkaline phosphatase superfamily.

  4. Tritium secondary kinetic isotope effect on phenylalanine ammonia-lyase-catalyzed reaction.

    PubMed

    Lewandowicz, A; Jemielity, J; Kańska, M; Zoń, J; Paneth, P

    1999-10-15

    The mechanism by which phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the reversible elimination of ammonia from phenylalanine yielding (E)-cinnamic acid has gained much attention in the recent years. Dehydroalanine is essential for the catalysis. It was assumed that this prostetic group acts as the electrophile, leading to a covalently bonded enzyme-intermediate complex with quarternary nitrogen of phenylalanine. Recently, an alternative mechanism has been suggested in which the enzyme-intermediate complex is formed in a Friedel-Crafts reaction between dehydroalanine and orthocarbon of the aromatic ring. Using semiempirical calculations we have shown that these two alternative mechanisms can be distinguished on the basis of the hydrogen secondary kinetic isotope effect when tritium label is placed in the orthopositions. Our calculations indicated also that the kinetic isotope effect measured using ring-labeled d(5)-phenylalanine could not be used to differentiate these alternative mechanisms. Measured secondary tritium kinetic isotope effect shows strong dependence on the reaction progress, starting at the inverse value of k(H)/k(T) = 0.85 for 5% conversion and reaching the normal value of about 1.15 as the conversion increases to 20%. This dependence has been interpreted in terms of a complex mechanism with initial formation of the Friedel-Crafts type intermediate.

  5. Fujiwara-Moritani Reaction of Weinreb Amides using a Ruthenium-Catalyzed C-H Functionalization Reaction.

    PubMed

    Das, Riki; Kapur, Manmohan

    2015-07-01

    The ruthenium-catalyzed Fujiwara-Moritani reaction (oxidative-Heck reaction) of Weinreb amides is reported herein. The reaction affords exclusively ortho-C-H olefination products, has excellent substrate scope and tolerates halogen functionalities, which increase the synthetic utility of the method. A variety of activated olefins as well as styrenes can be employed as coupling partners.

  6. Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease.

    PubMed

    Krzemińska, Agnieszka; Moliner, Vicent; Świderek, Katarzyna

    2016-12-21

    HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM subset of atoms described at semiempirical (AM1) and DFT (M06-2X) level. The results suggest that the most favorable reaction mechanism involves formation of a gem-diol intermediate, whose decomposition into the product complex would correspond to the rate-limiting step. The agreement between the activation free energy of this step with experimental data, as well as kinetic isotope effects (KIEs), supports this prediction. The role of the protein dynamic was studied by protein isotope labeling in the framework of the Variational Transition State Theory. The predicted enzyme KIEs, also very close to the values measured experimentally, reveal a measurable but small dynamic effect. Our calculations show how the contribution of dynamic effects to the effective activation free energy appears to be below 1 kcal·mol(-1). On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction. These electrostatic properties of the active site could be used as a mold for future drug design.

  7. 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.

  8. Cascade dearomatization of N-substituted tryptophols via Lewis acid-catalyzed Michael reactions.

    PubMed

    Liu, Chuan; Zhang, Wei; Dai, Li-Xin; You, Shu-Li

    2012-09-21

    Lewis acid-catalyzed cascade dearomatization of N-substituted tryptophols via Michael addition reaction was developed. The generality of the method has been demonstrated by the synthesis of versatile furoindoline derivatives with a quaternary carbon center in good yields.

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

    EPA Science Inventory

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

  10. Enantioselective synthesis of SSR 241586 by using an organo-catalyzed Henry reaction.

    PubMed

    Cochi, Anne; Métro, Thomas-Xavier; Pardo, Domingo Gomez; Cossy, Janine

    2010-08-20

    An organo-catalyzed Henry reaction, applied to an alpha-keto ester, has allowed the enantioselective synthesis of SSR 241586, a 2,2-disubstituted morpholine active in the treatment of schizophrenia and irritable bowel syndrome (IBS).

  11. Iron-catalyzed cross-coupling reactions of alkyl Grignards with aryl sulfamates and tosylates.

    PubMed

    Agrawal, Toolika; Cook, Silas P

    2013-01-04

    The iron-catalyzed cross-coupling of aryl sulfamates and tosylates has been achieved with primary and secondary alkyl Grignards. This study of iron-catalyzed cross-coupling reactions also examines the isomerization and β-hydride elimination problems that are associated with the use of isopropyl nucleophiles. While a variety of iron sources were competent in the reaction, the use of FeF(3)•3H(2)O was critical to minimize nucleophile isomerization.

  12. 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.

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

    PubMed

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

    2013-06-07

    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.

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

    PubMed

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

    2016-03-04

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

  15. Ultrasonic irradiation accelerated cyclopalladated ferrocenylimines catalyzed Suzuki reaction in neat water.

    PubMed

    Zhang, Jinli; Yang, Fan; Ren, Gerui; Mak, Thomas C W; Song, Maoping; Wu, Yangjie

    2008-02-01

    Both conventional heating and ultrasound effect on the cyclopalladated ferrocenylimines catalyzed Suzuki reaction of phenylboronic acid with a range of arylhalides in neat water was investigated. Heterogenous reaction of electron-withdrawing arylchlorides with phenylboronic acid could also result in good yields by using Cat. 2. It was found that the ultrasonic irradiation could dramatically accelerate the Suzuki reaction to achieve comparable results.

  16. Highly diastereoselective and regioselective copper-catalyzed nitrosoformate dearomatization reaction under aerobic-oxidation conditions.

    PubMed

    Yang, Weibo; Huang, Long; Yu, Yang; Pflästerer, Daniel; Rominger, Frank; Hashmi, A Stephen K

    2014-04-01

    An unprecedented copper-catalyzed acylnitroso dearomatization reaction, which expands the traditional acylnitroso ene reaction and acylnitroso Diels-Alder reaction to a new type of transformation, has been developed under aerobic oxidation. Intermolecular and intra-/intermolecular reaction modes demonstrate an entirely different N- or O-acylnitroso selectivity. Hence, we can utilize this reaction as a highly diastereoselective access to a series of new pyrroloindoline derivatives, which are important structural motifs for natural-product synthesis.

  17. Hypersensitive radical probe studies of chloroperoxidase-catalyzed hydroxylation reactions.

    PubMed

    Toy, P H; Newcomb, M; Hager, L P

    1998-07-01

    The oxidation of hypersensitive radical probes by chloroperoxidase from Caldariomyces fumago (CPO) was studied in an attempt to "time" a putative radical intermediate. Oxidation of (trans-2-phenylcyclopropyl)methane, previously studied by Zaks and Dodds [Zaks, A., and Dodds, D. R. (1995) J. Am. Chem. Soc. 115, 10419-10424] was reinvestigated. Unrearranged oxidation products were found as previously reported, and control experiments demonstrated that the cyclic alcohol from oxidation at the cyclopropylcarbinyl position, while subject to further oxidation, survives CPO oxidation as detectable species. However, in contrast to the report by Zaks and Dodds, the rearranged alcohol product expected from ring opening of a cyclopropylcarbinyl radical intermediate was shown to be unstable toward the enzyme oxidation reaction. Because of this instability, two new hypersensitive radical probes, (trans-2-phenylcyclopropyl)ethane and 2-(trans-2-phenylcyclopropyl)propane, and their potential cyclic and acyclic products from oxidation at the cyclopropylcarbinyl position were synthesized and tested. Oxidation of both of these probes at the cyclopropylcarbinyl position by CPO gave unrearranged alcohol products only, but control experiments again demonstrated that the rearranged alcohol products were unstable toward CPO oxidation conditions. From the combination of the probe and control studies, the lifetime of a putative radical intermediate must be less than 3 ps. Whereas the results are consistent with an insertion mechanism for production of alcohol product, they do not exclude a very short-lived intermediate.

  18. Iron-catalyzed cycloaddition reaction of diynes and cyanamides at room temperature.

    PubMed

    Wang, Chunxiang; Wang, Dongping; Xu, Fen; Pan, Bin; Wan, Boshun

    2013-04-05

    An iron-catalyzed [2 + 2 + 2] cycloaddition reaction of diynes and cyanamides at room temperature is reported. Highly substituted 2-aminopyridines were obtained in good to excellent yields with high regioselectivity. Insights toward the reaction process were investigated through in situ IR spectra and control experiments. In this iron-catalyzed cycloaddition reaction, the active iron species was generated only in the presence of both alkynes and nitriles. The lower reaction temperature, broad substrates scope, and inversed regioselectivity make it a complementary method to the previously developed iron catalytic system.

  19. Production of M-/GM-group aflatoxins catalyzed by the OrdA enzyme in aflatoxin biosynthesis.

    PubMed

    Yabe, Kimiko; Chihaya, Naomi; Hatabayashi, Hidemi; Kito, Masako; Hoshino, Sachiko; Zeng, Hongmei; Cai, Jingjing; Nakajima, Hiromitsu

    2012-09-01

    Aspergillus parasiticus produces the minor aflatoxins M(1) (AFM(1)), M(2) (AFM(2)), GM(1) (AFGM(1)), and GM(2) (AFGM(2)), as well as the major aflatoxins B(1) (AFB(1)), B(2) (AFB(2)), G(1) (AFG(1)), and G(2) (AFG(2)). Feeding of A. parasiticus with aspertoxin (12c-hydroxyOMST) caused AFM(1) and AFGM(1), and cell-free experiments using the microsomal fraction of A. parasiticus and aspertoxin caused production of AFM(1), indicating that aspertoxin is a precursor of AFM(1) and AFGM(1). Feeding of the same fungus with O-methylsterigmatocystin (OMST) caused AFM(1) and AFGM(1) together with AFB(1) and AFG(1); feeding with dihydroOMST (DHOMST) caused AFM(2) and AFGM(2) together with AFB(2) and AFG(2). Incubation of either the microsomal fraction or OrdA enzyme-expressing yeast with OMST caused production of aspertoxin together with AFM(1) and AFB(1). These results demonstrated that the OrdA enzyme catalyzes both 12c-hydroxylation reaction from OMST to aspertoxin and the successive reaction from aspertoxin to AFM(1). In contrast, feeding of the fungus with AFB(1) did not produce any AFM(1), demonstrating that M-/GM-aflatoxins are not produced from B-/G-aflatoxins. Furthermore, AFM(1) together with AFB(1) and AFG(1) was also produced from 11-hydroxyOMST (HOMST) in feeding experiment of A. parasiticus, whereas no aflatoxins were produced when used the ordA deletion mutant. These results demonstrated that OrdA enzyme can also catalyze 12c-hydroxylation of HOMST to produce 11-hydroxyaspertoxin, which serves as a precursor for the production of AFM(1) and AFGM(1). The same pathway may work for the production of AFM(2) and AFGM(2) from DHOMST and dihydroHOMST through the formation of dihydroaspertoxin and dihydro-11-hydroxyaspertoxin, respectively.

  20. 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

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

    PubMed

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

    2016-01-01

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

  2. A novel O-phospho-L-serine sulfhydrylation reaction catalyzed by O-acetylserine sulfhydrylase from Aeropyrum pernix K1.

    PubMed

    Mino, Koshiki; Ishikawa, Kazuhiko

    2003-09-11

    O-Acetylserine sulfhydrylase (OASS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, catalyzes the synthesis of L-cysteine from O-acetyl-L-serine and sulfide. O-Acetyl-L-serine is labile at high temperatures at which hyperthermophilic archaea live. Herein, a study of the substrate specificity of OASS from Aeropyrum pernix K1 with respect to O-acetyl-L-serine in L-cysteine synthesis is described. L-Azaserine, 3-chloro-L-alanine, and O-phospho-L-serine reacted with A. pernix OASS in a PLP-dependent manner. Sulfhydrylation reactions using these substrates reached a maximum in the pH range between 7.3 and 8.1. L-Azaserine and O-phospho-L-serine were found to be heat-stable substrates. The presence of FeCl3 or NiCl2 strongly inhibited the O-acetyl-L-serine sulfhydrylation reaction, whereas the O-phospho-L-serine sulfhydrylation reaction was only slightly inhibited. Kinetic analyses revealed that the O-phospho-L-serine sulfhydrylation reaction as well as the O-acetyl-L-serine sulfhydrylation reaction for A. pernix OASS followed a ping-pong bi-bi mechanism. In the case of the O-phospho-L-serine sulfhydrylation reaction at 85 degrees C, the K(m) values for O-phospho-L-serine and sulfide, and the rate constant were 250 mM, 12.5 mM, and 14000 s(-1), respectively. The reactivity of O-phospho-L-serine in the L-cysteine synthetic reaction provides a key for understanding the biosynthesis of L-cysteine by hyperthermophilic archaea. This is the first report of an enzyme that catalyzes the O-phospho-L-serine sulfhydrylation reaction.

  3. 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.

  4. 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

  5. REACTION MECHANISMS OF 15-HYDROPEROXYEICOSATETRAENOIC ACID CATALYZED BY HUMAN PROSTACYCLIN AND THROMBOXANE SYNTHASES

    PubMed Central

    Yeh, Hui-Chun; Tsai, Ah-Lim; Wang, Lee-Ho

    2007-01-01

    Prostacyclin synthase (PGIS) and thromboxane synthase (TXAS) are atypical cytochrome P450s. They do not require NADPH or dioxygen for isomerization of prostaglandin H2 (PGH2) to produce prostacyclin (PGI2) and thromboxane A2 (TXA2). PGI2 and TXA2 have opposing actions on platelet aggregation and blood vessel tone. In this report, we use a lipid hydroperoxide, 15-hydroperoxyeicosatetraenoic acid (15-HPETE), to explore the active site characteristics of PGIS and TXAS. The two enzymes transformed 15-HPETE not only into 13-hydroxy-14,15-epoxy-5,8,11-eicosatrienoic acid (13-OH-14,15-EET), like many microsomal P450s, but also to 15-ketoeicosatetraenoic acid (15-KETE) and 15-hydroxyeicosatetraenoic acid (15-HETE). 13-OH-14,15-EET and 15-KETE result from homolytic cleavage of the O–O bond, whereas 15-HETE results from heterolytic cleavage, a common peroxidase pathway. About 80% of 15-HPETE was homolytically cleaved by PGIS and 60% was homolytically cleaved by TXAS. The Vmax of homolytic cleavage is 3.5-fold faster than heterolytic cleavage for PGIS-catalyzed reactions (1100 min−1 vs. 320 min−1) and 1.4-fold faster for TXAS (170 min−1 vs. 120 min−1). Similar KM values for homolytic and heterolytic cleavages were found for PGIS (∼60 μM 15-HPETE) and TXAS (∼80 μM 15-HPETE), making PGIS a more efficient catalyst for the 15-HPETE reaction. PMID:17459323

  6. Transition-metal-catalyzed group transfer reactions for selective C-H bond functionalization of artemisinin.

    PubMed

    Liu, Yungen; Xiao, Wenbo; Wong, Man-Kin; Che, Chi-Ming

    2007-10-11

    Three types of novel artemisinin derivatives have been synthesized through transition-metal-catalyzed intramolecular carbenoid and nitrenoid C-H bond insertion reactions. With rhodium complexes as catalysts, lactone 11 was synthesized via carbene insertion reaction at the C16 position in 90% yield; oxazolidinone 13 was synthesized via nitrene insertion reaction at the C10 position in 87% yield based on 77% conversion; and sulfamidate 14 was synthesized via nitrene insertion reaction at the C8 position in 87% yield.

  7. Fluorometric assay protocol for protease-catalyzed transesterification reactions in organic solvents.

    PubMed

    Han, Min Su; Jung, Sang Oh; Kim, Mahn-Joo; Kim, Dong H

    2004-04-16

    A flourometric assay protocol for a subtilisin-catalyzed transesterification reaction in n-hexane has been developed. The method makes use of a Michael acceptor that forms a fluorescent adduct with thiophenol, one of the products generated in the transesterification reaction. The method may be employed for screening a biocatalyst useful for transesterification reactions in organic solvents and for optimizing the transesterification reaction conditions.

  8. 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.

  9. Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reaction: Scope, Mechanism, and Applications.

    PubMed

    Johansson, Johan R; Beke-Somfai, Tamás; Said Stålsmeden, Anna; Kann, Nina

    2016-12-14

    The ruthenium-catalyzed azide alkyne cycloaddition (RuAAC) affords 1,5-disubstituted 1,2,3-triazoles in one step and complements the more established copper-catalyzed reaction providing the 1,4-isomer. The RuAAC reaction has quickly found its way into the organic chemistry toolbox and found applications in many different areas, such as medicinal chemistry, polymer synthesis, organocatalysis, supramolecular chemistry, and the construction of electronic devices. This Review discusses the mechanism, scope, and applications of the RuAAC reaction, covering the literature from the last 10 years.

  10. Origins of Stereoselectivity of Chiral Vicinal Diamine-Catalyzed Aldol Reactions.

    PubMed

    Simon, Adam; Yeh, Alexander J; Lam, Yu-Hong; Houk, K N

    2016-12-16

    The sources of asymmetric induction in aldol reactions catalyzed by cinchona alkaloid-derived amines, and chiral vicinal diamines in general, have been determined by density functional theory calculations. Four vicinal diamine-catalyzed aldol reactions were examined. The cyclic transition states of these reactions involve nine-membered hydrogen-bonded rings in distinct conformations. Using nomenclature from eight-membered cycloalkanes, the heavy atoms of the low-energy transition states are in crown (chair-chair) and chair-boat conformations. The factors that control which of these are favored have been identified.

  11. 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

  12. ATP Recycling with Cell Lysate for Enzyme-Catalyzed Chemical Synthesis, Protein Expression and PCR.

    PubMed

    Alissandratos, Apostolos; Caron, Karine; Loan, Thomas D; Hennessy, James E; Easton, Christopher J

    2016-12-16

    E. coli lysate efficiently catalyzes acetyl phosphate-driven ATP regeneration in several important biotechnological applications. The utility of this ATP recycling strategy in enzyme-catalyzed chemical synthesis is illustrated through the conversion of uridine to UMP by the lysate from recombinant overexpression of uridine kinase with the E. coli. The UMP is further transformed into UTP through sequential phosphorylations by kinases naturally present in the lysate, in high yield. Cytidine and 5-fluorouridine also give the corresponding NMPs and NTPs with this system. Cell-free protein expression with a processed extract of lysate also proceeds readily when, instead of adding the required NTPs, all four are produced in situ from the NMPs, using acetyl phosphate and relying on endogenous kinase activity. Similarly, dNMPs can be used to produce the dNTPs necessary for DNA synthesis in PCR. These cheap alternative protocols showcase the potential of acetyl phosphate and ATP recycling with readily available cell lysate.

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  15. 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.

  16. The rhodium catalyzed three-component reaction of diazoacetates, titanium(IV) alkoxides and aldehydes.

    PubMed

    Lu, Chong-Dao; Liu, Hui; Chen, Zhi-Yong; Hu, Wen-Hao; Mi, Ai-Qiao

    2005-05-28

    The rhodium(II)-catalyzed three-component reaction of diazoacetates, titanium alkoxides and aldehydes is shown to give alpha-alkoxyl-beta-hydroxyl acid derivatives; the novel C-C bond formation reaction is proposed to occur through oxonium ylides derived from diazo compounds and titanium alkoxides, and followed by intermolecular trapping by aldehydes.

  17. Stereoselective synthesis of 2,5-disubstituted morpholines using a palladium-catalyzed hydroamination reaction.

    PubMed

    McGhee, Alicia; Cochran, Brian M; Stenmark, Torrey A; Michael, Forrest E

    2013-08-04

    A palladium-catalyzed hydroamination reaction is the key step in a stereoselective synthesis of 2,5-disubstituted and 2,3,5-trisubsituted morpholines from carbamate-protected aziridines. Aziridines are selectively attacked at the more substituted position by unsaturated alcohol nucleophiles using Lewis acid catalysts. Palladium-catalyzed hydroamination of the resulting aminoalkenes gives morpholines as a single diastereomer in excellent yield.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

    2015-01-01

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

  20. Change in heat capacity for enzyme catalysis determines temperature dependence of enzyme catalyzed rates.

    PubMed

    Hobbs, Joanne K; Jiao, Wanting; Easter, Ashley D; Parker, Emily J; Schipper, Louis A; Arcus, Vickery L

    2013-11-15

    The increase in enzymatic rates with temperature up to an optimum temperature (Topt) is widely attributed to classical Arrhenius behavior, with the decrease in enzymatic rates above Topt ascribed to protein denaturation and/or aggregation. This account persists despite many investigators noting that denaturation is insufficient to explain the decline in enzymatic rates above Topt. Here we show that it is the change in heat capacity associated with enzyme catalysis (ΔC(‡)p) and its effect on the temperature dependence of ΔG(‡) that determines the temperature dependence of enzyme activity. Through mutagenesis, we demonstrate that the Topt of an enzyme is correlated with ΔC(‡)p and that changes to ΔC(‡)p are sufficient to change Topt without affecting the catalytic rate. Furthermore, using X-ray crystallography and molecular dynamics simulations we reveal the molecular details underpinning these changes in ΔC(‡)p. The influence of ΔC(‡)p on enzymatic rates has implications for the temperature dependence of biological rates from enzymes to ecosystems.

  1. Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction

    PubMed Central

    Islam, Zahidul; Strutzenberg, Timothy S.; Ghosh, Ananda K.; Kohen, Amnon

    2015-01-01

    Thymidylate synthase (TSase) catalyzes the de novo biosynthesis of thymidylate, a precursor for DNA, and is thus an important target for chemotherapeutics and antibiotics. Two sequential C-H bond cleavages catalyzed by TSase are of particular interest: a reversible proton abstraction from the 2′-deoxy-uridylate substrate, followed by an irreversible hydride transfer forming the thymidylate product. QM/MM calculations of the former predicted a mechanism where the abstraction of the proton leads to formation of a novel nucleotide-folate intermediate that is not covalently bound to the enzyme (Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A. Biochemistry 2013, 52, 2348–2358). Existence of such intermediate would hold promise as a target for a new class of drugs. Calculations of the subsequent hydride transfer predicted a concerted H-transfer and elimination of the enzymatic cysteine (Kanaan, N.; Ferrer, S.; Marti, S.; Garcia-Viloca, M.; Kohen, A.; Moliner, V. J. Am. Chem. Soc. 2011, 133, 6692–6702). A key to both C-H activations is a highly conserved arginine (R166) that stabilizes the transition state of both H-transfers. Here we test these predictions by studying the R166 to lysine mutant of E. coli TSase (R166K) using intrinsic kinetic isotope effects (KIEs) and their temperature dependence to assess effects of the mutation on both chemical steps. The findings confirmed the predictions made by the QM/MM calculations, implicate R166 as an integral component of both reaction coordinates, and thus provide critical support to the nucleotide-folate intermediate as a new target for rational drug design. PMID:26576323

  2. 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.

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

    PubMed

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

    1999-10-07

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

  4. New Reactions and Products Resulting from Alternative Interactions between the P450 Enzyme and Redox Partners

    PubMed Central

    2015-01-01

    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. PMID:24521145

  5. 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.

  6. 1H NMR studies of substrate hydrogen exchange reactions catalyzed by L-methionine gamma-lyase.

    PubMed

    Esaki, N; Nakayama, T; Sawada, S; Tanaka, H; Soda, K

    1985-07-16

    Hydrogen exchange reactions of various L-amino acids catalyzed by L-methionine gamma-lyase (EC 4.4.1.11) have been studied. The enzyme catalyzes the rapid exchange of the alpha- and beta-hydrogens of L-methionine and S-methyl-L-cysteine with deuterium from the solvent. The rate of alpha-hydrogen exchange was about 40 times faster than that of the enzymatic elimination reaction of the sulfur-containing amino acids. The enzyme also catalyzes the exchange reaction of alpha- and beta-hydrogens of the following straight-chain L-amino acids which are not susceptible to elimination: norleucine, norvaline, alpha-aminobutyrate, and alanine. The exchange rates of the alpha-hydrogen and the total beta-hydrogens of L-alanine and L-alpha-aminobutyrate with deuterium followed first-order kinetics. For L-norvaline, L-norleucine, S-methyl-L-cysteine, and L-methionine, the rate of alpha-hydrogen exchange followed first-order kinetics, but the rate of total beta-hydrogen exchange decreased due to a primary isotope effect at the alpha-position. One beta-hydrogen of S-methyl-L-cysteine was exchanged faster than the other, although both the beta-hydrogens were exchanged completely with deuterium ultimately. L-Phenylalanine and L-tryptophan slowly underwent alpha-hydrogen exchange. The pro-R hydrogen of glycine was deuterated stereospecifically. None of the following amino acids were susceptible to the enzymatic hydrogen exchange: D isomers of the above amino acids, branched chain L-amino acids, acidic L-amino acids, and basic L-amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. 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.

  8. 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.

  9. Hyperpolarized 13C allows a direct measure of flux through a single enzyme-catalyzed step by NMR

    PubMed Central

    Merritt, Matthew E.; Harrison, Crystal; Storey, Charles; Jeffrey, F. Mark; Sherry, A. Dean; Malloy, Craig R.

    2007-01-01

    13C NMR is a powerful tool for monitoring metabolic fluxes in vivo. The recent availability of automated dynamic nuclear polarization equipment for hyperpolarizing 13C nuclei now offers the potential to measure metabolic fluxes through select enzyme-catalyzed steps with substantially improved sensitivity. Here, we investigated the metabolism of hyperpolarized [1-13C1]pyruvate in a widely used model for physiology and pharmacology, the perfused rat heart. Dissolved 13CO2, the immediate product of the first step of the reaction catalyzed by pyruvate dehydrogenase, was observed with a temporal resolution of ≈1 s along with H13CO3−, the hydrated form of 13CO2 generated catalytically by carbonic anhydrase. In hearts presented with the medium-chain fatty acid octanoate in addition to hyperpolarized [1-13C1]pyruvate, production of 13CO2 and H13CO3− was suppressed by ≈90%, whereas the signal from [1-13C1]lactate was enhanced. In separate experiments, it was shown that O2 consumption and tricarboxylic acid (TCA) cycle flux were unchanged in the presence of added octanoate. Thus, the rate of appearance of 13CO2 and H13CO3− from [1-13C1]pyruvate does not reflect production of CO2 in the TCA cycle but rather reflects flux through pyruvate dehydrogenase exclusively. PMID:18056642

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

    PubMed

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

    2016-01-11

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

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

    PubMed

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

    2016-04-15

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

  12. 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

    2016-04-08

    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.

  13. The source and characteristics of chemiluminescence associated with the oxygenase reaction catalyzed by Mn(2+)-ribulosebisphosphate carboxylase.

    PubMed

    Lilley, R M; Riesen, H; Andrews, T J

    1993-07-05

    We confirm the observation of Mogel and McFadden (Mogel, S.N., and McFadden, B. A. (1990) Biochemistry 29, 8333-8337) that ribulosebisphosphate carboxylase/oxygenase (rubisco) exhibits chemiluminescence while catalyzing its oxygenase reaction in the presence of Mn2+. However, our results with the spinach and Rhodospirillum rubrum enzymes differ markedly in the following respects. 1) Chemiluminescence intensity was directly proportional to enzyme concentration and behaved as if representing the rate of oxygenase catalysis. 2) The wavelength spectrum peaked at about 770 nm and extended beyond 810 nm. This seems inconsistent with chemiluminescence generated by simultaneous decay of pairs of singlet O2 molecules. It is consistent with manganese(II) luminescence and we discuss its possible sources. The time course of chemiluminescence (resolution, 0.25 s) was distinctively different for spinach and R. rubrum enzymes during the initial 5 s of catalysis, with the bacterial enzyme exhibiting a pronounced initial "burst." Chemiluminescence by the spinach enzyme responded to substrate concentrations in a manner consistent with known oxygenase properties, exhibiting Michaelis-Menten kinetics with ribulose-1,5-bisphosphate (Km 400 nM). Chemiluminescence required carbamylated enzyme with Mn2+ bound at the active site (activation energy, -57.1 KJ.mol-1). As an indicator of oxygenase activity, chemiluminescence represents an improvement over oxygen electrode measurements in response time and sensitivity by factors of at least 100.

  14. 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.

  15. Enzyme-catalyzed phase transition of alginate gels and gelatin-alginate interpenetrated networks.

    PubMed

    Doumèche, Bastien; Picard, Julien; Larreta-Garde, Véronique

    2007-11-01

    The enzyme-catalyzed gel-sol transition of calcium-alginate obtained by internal gelling strategy with the help of an entrapped alginate lyase is described. We show that alginate molecules and enzyme-produced oligoalginates shorten the gel time of physical gelatin gels (5% and 1.5%), probably due to local protein concentration increase. Interpenetrated networks composed of calcium-alginate and of gelatin were obtained only if elongation of gelatin helices inside a pre-existing calcium-alginate network could occur and only for low gelatin concentration (1.5%). The physical gelatin network is almost reversible inside the alginate one. Both networks can be obtained in the presence of alginate lyase, but gel-sol transition of calcium-alginate cannot be obtained in the presence of gelatin.

  16. Enzyme from an Uncultivated Sponge Bacterium Catalyzes S-Methylation in a Ribosomal Peptide.

    PubMed

    Helf, Maximilian J; Jud, Aurelia; Piel, Jörn

    2017-03-02

    Amino acid modifications are essential for the structural diversity and bioactivity of ribosomally synthesized and post-translationally modified peptide natural products (RiPPs). A particularly large and virtually untapped pool of unusual RiPPs and associated modifying enzymes is provided by uncultivated bacteria. An example is the chemically rich sponge symbiont "Candidatus Entotheonella factor", which produces the hypermodified polytheonamides of the poorly studied proteusin RiPP family. In addition to the polytheonamide genes, "E. factor" contains several further additional RiPP clusters of unknown function. Here we provide insights into one of these cryptic proteusin pathways by identifying an enzyme (PtyS) that catalyzes the S-methylation of cysteine residues. S-methylcysteine is rare in natural peptides and proteins, and the enzymatic activity was previously unknown for RiPPs, thus adding a new modification to the ribosomal peptide toolbox.

  17. Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A.

    PubMed

    Fujiwara, Kazuko; Maita, Nobuo; Hosaka, Harumi; Okamura-Ikeda, Kazuko; Nakagawa, Atsushi; Taniguchi, Hisaaki

    2010-03-26

    Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645-33651). Here, we report two new LplA structures, LplA.lipoyl-5'-AMP and LplA.octyl-5'-AMP.apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5'-AMP reaction intermediate and rotation of the C-terminal domain by about 180 degrees . These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys(133) residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes.

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

    PubMed

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

    2012-10-16

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

  19. 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.

  20. Enzyme-substrate reactions in very high magnetic fields. I.

    PubMed

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

    1967-03-01

    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.

  1. Kinetics of enzyme-catalyzed cross-linking of feruloylated arabinan from sugar beet.

    PubMed

    Zaidel, Dayang Norulfairuz Abang; Arnous, Anis; Holck, Jesper; Meyer, Anne S

    2011-11-09

    Ferulic acid (FA) groups esterified to the arabinan side chains of pectic polysaccharides can be oxidatively cross-linked in vitro by horseradish peroxidase (HRP) catalysis in the presence of hydrogen peroxide (H(2)O(2)) to form ferulic acid dehydrodimers (diFAs). The present work investigated whether the kinetics of HRP catalyzed cross-linking of FA esterified to α-(1,5)-linked arabinans are affected by the length of the arabinan chains carrying the feruloyl substitutions. The kinetics of the HRP-catalyzed cross-linking of four sets of arabinan samples from sugar beet pulp, having different molecular weights and hence different degrees of polymerization, were monitored by the disappearance of FA absorbance at 316 nm. MALDI-TOF/TOF-MS analysis confirmed that the sugar beet arabinans were feruloyl-substituted, and HPLC analysis verified that the amounts of diFAs increased when FA levels decreased as a result of the enzymatic oxidation treatment with HRP and H(2)O(2). At equimolar levels of FA (0.0025-0.05 mM) in the arabinan samples, the initial rates of the HRP-catalyzed cross-linking of the longer chain arabinans were slower than those of the shorter chain arabinans. The lower initial rates may be the result of the slower movement of larger molecules coupled with steric phenomena, making the required initial reaction of two FAs on longer chain arabinans slower than on shorter arabinans.

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

    SciTech Connect

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

    1987-06-30

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

  3. Asymmetric induction in the zirconium catalyzed ethylmagnesiation reaction

    SciTech Connect

    Bell, J.L.; Whitby, R.J.; Jones, R.V.H.

    1995-12-31

    In 1985 Dzhemilev reported the zirconium catalysed ethylmagnesiation of terminal alkenes. A chiral centre is formed during the reaction which occurs under mild conditions. The authors have applied this reaction to a number of substrates and a mechanism has been elucidated. In order to induce asymmetry into the reaction, several chiral literature catalysts were synthesised including Ethylenebis(tetrahydroindenyl)zirconium dichloride and two more hindered complexes reported by Erker. All of these catalysts displayed low activity and poor asymmetric induction with terminal alkenes. The synthesis and properties of two novel catalysts will be described. Results show high activity furnishing carbomagnesiated products in excellent yields with as little as 2 mol% catalyst. The enantiomeric excesses induced by the complexes are as high as 79% with terminal alkenes but are >95% with cyclic ethers. The catalyst has proved recoverable. Ethylmagnesiation of an amine followed by an acidic workup furnishes the chiral complex in a quantitative return.

  4. 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

  5. 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.

  6. 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

  7. An Investigation of Model Catalyzed Hydrocarbon Formation Reactions

    SciTech Connect

    Tysoe, W. T.

    2001-05-02

    Work was focused on two areas aimed at understanding the chemistry of realistic catalytic systems: (1) The synthesis and characterization of model supported olefin metathesis catalysts. (2) Understanding the role of the carbonaceous layer present on Pd(111) single crystal model catalysts during reaction.

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

    PubMed

    Elzainy, Tahany A; Ali, Thanaa H

    2005-02-01

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

  9. Dirhodium carboxylates catalyzed enantioselective coupling reactions of α-diazophosphonates, anilines, and electron-deficient aldehydes.

    PubMed

    Zhou, Cong-Ying; Wang, Jing-Cui; Wei, Jinhu; Xu, Zhen-Jiang; Guo, Zhen; Low, Kam-Hung; Che, Chi-Ming

    2012-11-05

    Chiral dirhodium carboxylate complexes ([Rh(2)(S-PTAD)(4)] or [Rh(2)(S-PTTL)(4)]) efficiently catalyze asymmetric three-component coupling reactions of α-diazophosphonates, anilines, and electron-deficient aldehydes to give α-amino-β-hydroxyphosphonates. The high level of enantiocontrol provides evidence for the intermediacy of metal-bound ammonium ylide in the product-forming step.

  10. 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).

  11. Efficient palladium-catalyzed coupling reactions of aryl bromides and chlorides with phenols.

    PubMed

    Hu, Tongjie; Schulz, Thomas; Torborg, Christian; Chen, Xiaorong; Wang, Jun; Beller, Matthias; Huang, Jun

    2009-12-21

    A convenient and general palladium-catalyzed coupling reaction of aryl bromides and chlorides with phenols was developed. Various functional groups such as nitriles, aldehydes, ketones and esters are well tolerated and the corresponding products are obtained in good to excellent yield.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Water-catalyzed gas-phase reaction of formic acid with hydroxyl radical: A computational investigation

    NASA Astrophysics Data System (ADS)

    Luo, Yi; Maeda, Satoshi; Ohno, Koichi

    2009-02-01

    The reaction of formic acid with hydroxyl radical, which is considered to be relevant to atmospheric chemistry, has been extensively studied. A water-catalyzed process of this reaction is computationally studied here for the first time. The scaled hypersphere search method was used for global exploration of pre-reaction complexes. Calculations were performed at high level of theory, such as CCSD(T)/cc-pVTZ//B3LYP/6-311+G(2df, 2p) and CCSD(T)/cc-pVTZ//MP2/aug-cc-pVDZ. It is found that the water-catalyzed process of this reaction is more kinetically favorable than its non-catalytic process. Such catalytic process may also be of interest for atmospheric chemistry, like the non-catalytic one.

  17. Enantioselective direct Mannich reactions of cyclic β-ketoesters catalyzed by chiral phosphine via a novel dual-reagent catalysis.

    PubMed

    Lou, Yan-Peng; Zheng, Chang-Wu; Pan, Ren-Ming; Jin, Qiao-Wen; Zhao, Gang; Li, Zhong

    2015-02-06

    A combination of an amino acid derived chiral phosphine catalyst and methyl acrylate efficiently catalyzed the direct Mannich reaction of cyclic β-ketoesters and N-Boc-aldimines. The dual-reagent catalysis was presumed to function through the formation of a zwitterion, which catalyzed the reaction with excellent stereocontrol via a hydrogen-bonding assisted chiral ion-pair pathway.

  18. Unexpected ring-opening reactions of aziridines with aldehydes catalyzed by nucleophilic carbenes under aerobic conditions.

    PubMed

    Liu, Yan-Kai; Li, Rui; Yue, Lei; Li, Bang-Jing; Chen, Ying-Chun; Wu, Yong; Ding, Li-Sheng

    2006-04-13

    [reaction: see text] The chemoselective ring opening of N-tosyl aziridines with aldehydes catalyzed by an N-heterocyclic carbene was investigated under aerobic conditions. Unexpected carboxylates of 1,2-amino alcohols from the corresponding aldehydes, rather than the acyl anion ring-opened beta-amino ketones, were exclusively obtained. A plausible mechanism for this unprecedented carbene-mediated reaction was also proposed.

  19. 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.

  20. Molecular cloning and characterization of a Perilla frutescens cytochrome P450 enzyme that catalyzes the later steps of perillaldehyde biosynthesis.

    PubMed

    Fujiwara, Yumi; Ito, Michiho

    2017-02-01

    Perilla produces the cyclohexanoid monoterpene perillaldehyde as a major constituent of an essential oil that is accumulated in its glandular trichomes. Perillaldehyde is a marker compound for quality control of soyo and has biological activities such as antibacterial, sedative, or vasodilatory effects. The predicted perillaldehyde formation involves the cyclization of geranyl diphosphate, hydroxylation, and oxidation, and cytochrome P450 plays a crucial role in perillaldehyde biosynthesis. In this study, a cytochrome P450-type enzyme with perillyl alcohol and perillaldehyde synthase activities was isolated by analyzing an expressed sequence tag library from several oil types of pure lines of perilla. A recombinant protein with a sequence that was highly specific for the type of perillaldehyde was expressed in Saccharomyces cerevisiae and evaluated by an in vitro enzymatic reaction. The recombinant protein catalyzed the hydroxylation and oxidation of limonene to perillyl alcohol and perillaldehyde. Cytochrome P450 limonene-7-hydroxylase cDNA from Perilla frutescens has been previously isolated. The cytochrome P450 isolated in this study shares 37% amino-acid identity with the previously isolated enzyme; however, it may have different characteristics.

  1. Enantioselective Nitroaldol Reaction of α-Ketoesters Catalyzed by Cinchona Alkaloids

    PubMed Central

    Li, Hongming; Wang, Baomin; Deng, Li

    2011-01-01

    The development of highly enantioselective and general catalytic nitroaldol (Henry) reactions with ketones is a challenging yet desirable task in organic synthesis. In this communication, we report an asymmetric nitroaldol reaction with α-ketoesters catalyzed by a new C6′-OH cinchona alkaloid catalyst. This is the first highly efficient organocatalytic asymmetric Henry reaction with ketones. This reaction is operationally simple and affords high enantioselectivity as well as good to excellent yield for a broad range of α-ketoesters. PMID:16417358

  2. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction.

    PubMed

    Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf

    2013-03-12

    The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.

  3. 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

  4. Forward design of a complex enzyme cascade reaction.

    PubMed

    Hold, Christoph; Billerbeck, Sonja; Panke, Sven

    2016-09-28

    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.

  5. 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.

  6. 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

    2011-02-02

    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.

  7. 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

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

    PubMed Central

    Cheatum, Christopher M.; Kohen, Amnon

    2015-01-01

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

  10. Enzyme deactivation due to metal-ion dissociation during turnover of the cobalt-beta-lactamase catalyzed hydrolysis of beta-lactams.

    PubMed

    Badarau, Adriana; Page, Michael I

    2006-09-12

    Metallo-beta-lactamases are native zinc enzymes that catalyze the hydrolysis of beta-lactam antibiotics but are also able to function with cobalt (II) and require one or two metal ions for catalytic activity. The kinetics of the hydrolysis of benzylpenicillin catalyzed by cobalt substituted beta-lactamase from Bacillus cereus (BcII) are biphasic. The dependence of enzyme activity on pH and metal-ion concentration indicates that only the di-cobalt enzyme is catalytically active. A mono-cobalt enzyme species is formed during the catalytic cycle, which is virtually inactive and requires the association of another cobalt ion for turnover. Two intermediates with different metal to enzyme stoichiometries are formed on a branched reaction pathway. The di-cobalt enzyme intermediate is responsible for the direct catalytic route, which is pH-independent between 5.5 and 9.5 but is also able to slowly lose one bound cobalt ion via the branching route to give the mono-cobalt inactive enzyme intermediate. This inactivation pathway of metal-ion dissociation occurs by both an acid catalyzed and a pH-independent reaction, which is dependent on the presence of an enzyme residue of pK(a) = 8.9 +/- 0.1 in its protonated form and shows a large kinetic solvent isotope effect (H(2)O/D(2)O) of 5.2 +/- 0.5, indicative of a rate-limiting proton transfer. The pseudo first-order rate constant to regenerate the di-cobalt beta-lactamase from the mono-cobalt enzyme intermediate has a first-order dependence on cobalt-ion concentration in the pH range 5.5-9.5. The second-order rate constant for metal-ion association is dependent on two groups of pK(a) 6.32 +/- 0.1 and 7.47 +/- 0.1 being in their deprotonated basic forms and one group of pK(a) 9.48 +/- 0.1 being in its protonated form.

  11. Catalyzed hydrolytic cleavage reaction of carbon-carbon bond

    SciTech Connect

    Ioffe, I.I.; Rubinskaya, E.V.

    1986-12-01

    The authors split the carbon-carbon bond for a series of simple and complex organic compounds in neutral aqueous solutions on a heterogeneous metal-containing catalyst, palladium on carbon. The experimental results are given. In each case, the catalytic effect was controlled by a blank experiment, without a catalyst, where there was no decomposition of the substrate. The occurrence of the heterogeneous-catalytic cleavage reaction of the carbon-carbon bonds in the molecules is indicated not only by their extensive conversion, but also by the almost complete depletion of the content of organic carbon, confirmed by a similar decrease in the chemical consumption of oxygen coefficient in the system, which is possible only in the complete decomposition of the organic compounds to gaseous products or with the formation of inappreciable amounts of low-molecular-weight water-soluble compounds.

  12. 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

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

    PubMed

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

    1996-12-13

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

  14. Fundamentals of enzyme kinetics.

    PubMed

    Seibert, Eleanore; Tracy, Timothy S

    2014-01-01

    This chapter provides a general introduction to the kinetics of enzyme-catalyzed reactions, with a focus on drug-metabolizing enzymes. A prerequisite to understanding enzyme kinetics is having a clear grasp of the meanings of "enzyme" and "catalysis." Catalysts are reagents that can increase the rate of a chemical reaction without being consumed in the reaction. Enzymes are proteins that form a subset of catalysts. These concepts are further explored below.

  15. Cumene hydroperoxide-supported demethylation reactions catalyzed by cytochrome P450 2B4 lacking the NH2-terminal sequence.

    PubMed

    Zhang, Y; Pernecky, S J

    1999-04-29

    Catalytic activities of cytochrome P450 2B4 lacking NH2-terminal amino acids 2-27 (wt Delta2B4) and that of truncated 2B4 containing a Pro to Ser mutation at position 221 were examined in a system supported by cumene hydroperoxide. Demethylation activities of either truncated 2B4 with N-methylaniline, N,N-dimethylaniline, and d-benzphetamine were lower than those of liver microsomal 2B4, whereas the rate of 1-phenylethanol oxidation to acetophenone catalyzed by liver microsomal and truncated 2B4 enzymes was nearly the same. The Km and Vmax values for cumene hydroperoxide in the demethylation of N-methylaniline by wt Delta2B4 were 20% and 28%, respectively, of those obtained for 2B4. The reaction with wt Delta2B4 displayed a lesser dependence on phospholipid than did that with 2B4, and a complex relationship between activity and substrate concentration. The results suggest that the NH2-terminal region contributes to interaction of oxidant, substrate, and phospholipid in cumene hydroperoxide-supported reactions catalyzed by cytochrome P450 2B4.

  16. Antioxidant activity of minimally processed red chicory (Cichorium intybus L.) evaluated in xanthine oxidase-, myeloperoxidase-, and diaphorase-catalyzed reactions.

    PubMed

    Lavelli, Vera

    2008-08-27

    Minimally processed red chicory products (Cichorium intybus L. var. silvestre) were studied for their polyphenol content and antioxidant activity evaluated by using the synthetic 2,2-diphenyl-1-(2,4,6-trinitrophenyl)hydrazyl radical and three model reactions catalyzed by relevant enzymatic sources of reactive oxygen species, namely, xanthine oxidase, myeloperoxidase, and diaphorase. Products were analyzed at the time of production and after storage at 4 degrees C within either a gas permeable film or a gas barrier film. The antioxidant activity and contents of hydroxycinnamic acids and flavonoids decreased by less than 20% during storage of the minimally processed red chicory products. Total phenolics were significantly correlated with the antioxidant activity evaluated with both the synthetic radical and the enzyme-catalyzed reactions. On a molar basis, red chicory phenolics were as efficient as the reference compound Trolox in scavenging the synthetic radical. However, red chicory phenolics had a much higher inhibitory activity than Trolox in the model enzymatic systems.

  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. Palladium-catalyzed cross-coupling reactions of silanolates: a paradigm shift in silicon-based cross-coupling reactions.

    PubMed

    Denmark, Scott E; Baird, John D

    2006-06-23

    This paper chronicles the conceptual development, proof of principle experiments, and recent advances in the palladium-catalyzed cross-coupling reactions of the conjugate bases of organosilanols. The discovery that led to the design and refinement of this process represents a classical illustration of how mechanistic studies can provide a fertile ground for the invention of new reactions. On the basis of a working hypothesis (which ultimately proved to be incorrect) and the desire to effect silicon-based cross-coupling without the agency of fluoride activation, a mild and practical palladium-catalyzed cross-coupling of alkenyl-, aryl-, and heteroaryl silanolates has been developed. The mechanistic underpinnings, methodological extensions, and the successful applications of this technology to the synthesis of complex molecules are described.

  19. 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.

  20. 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

    2015-12-04

    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.

  1. Palladium-catalyzed ring-opening reactions of cyclopropanated 7-oxabenzonorbornadiene with alcohols

    PubMed Central

    Tait, Katrina; Alrifai, Oday; Boutin, Rebecca; Haner, Jamie

    2016-01-01

    Summary Palladium-catalyzed ring-opening reactions of cyclopropanated 7-oxabenzonorbornadiene derivatives using alcohol nucleophiles were investigated. The optimal conditions were found to be 10 mol % PdCl2(CH3CN)2 in methanol, offering yields up to 92%. The reaction was successful using primary, secondary and tertiary alcohol nucleophiles and was compatible with a variety of substituents on cyclopropanated oxabenzonorbornadiene. With unsymmetrical C1-substituted cyclopropanated 7-oxabenzonorbornadienes, the regioselectivity of the reaction was excellent, forming only one regioisomer in all cases. PMID:27829926

  2. Combination of Microwave Reactions with Fluorous Separations in the Palladium-Catalyzed Synthesis of Aryl Sulfides

    PubMed Central

    Zhang, Wei; Lu, Yimin; Chen, Christine Hiu-Tung

    2007-01-01

    Coupling of microwave reactions with fluorous separations can dramatically increase the efficiency of high-speed synthesis. Described in this paper is a fluorous synthesis of aryl sulfides by palladium-catalyzed cross-coupling of aryl perfluoroalkylsulfonates (C8F17O2SOAr) with thiols (RSH) under microwave irradiation. Fluorous solid-phase extractions (F-SPE) are employed for the purification of reaction mixtures. No fluorous solvents are involved in reaction and separation processes. The fluorous synthesis is further extended to the multi-step synthesis of substituted hydantoin and amide scaffolds. PMID:14870851

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

    PubMed Central

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

    2015-01-01

    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

  4. 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.

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

    PubMed

    Halbwirth, Heidrun; Stich, Karl

    2006-06-01

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

  6. 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.

  7. Glutathiolactaldehyde as a probe of the overall stereochemical course of glyoxalase-I catalyzed reactions

    SciTech Connect

    Brush, E.J.; Kozarich, J.W.

    1986-05-01

    The overall stereochemical course of the reactions catalyzed by glyoxalase-I (GX-I) has remained elusive as the substrates are equilibrium mixtures of rapidly interconverting diastereomeric thiohemiacetals. However, with the discovery of inverse substrate processing by Kozarich and coworkers, it is possible to design GX-I substrate analogs that are intrinsically more stable than the thiohemiacetals. Hence, Chari and Kozarich reported that glutathiohydroxyacetone (GHA, GSCH/sub 2/COCH/sub 2/OH) undergoes GX-I catalyzed exchange of the pro-S hydroxymethyl proton with solvent deuterium. Their data suggest that GX-I processes a single diastereomeric thiohemiacetal, and are consistent with a cis-enediol intermediate. To test this hypothesis and to follow the overall stereochemistry on a single substrate, they have prepared glutathiolactaldehyde (GLA, GSCH/sub 2/CHOHCHO) as a potential inverse substrate. Human erythrocyte GX-I catalyzes the isomerization of GLA to GHA as evidenced by UV and NMR spectra of the product. Solvent deuterium is incorporated into the hydroxymethyl position, and NMR data suggest that incorporation is stereospecific. Furthermore, 50% of the expected amount of GHA is produced indicating that only one diastereomer of GLA is processed by GX-I. Identification of the absolute stereochemistry of the substrate diastereomer will lead to a clarification of the overall stereochemical and mechanistic course of GX-I catalyzed reactions.

  8. 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

  9. An enigmatic peptide ligation reaction: protease-catalyzed oligomerization of a native protein segment in neat aqueous solution.

    PubMed

    Kumaran, S; Datta, D; Roy, R P

    2000-04-01

    We report an enigmatic peptide ligation reaction catalyzed by Glu-specific Staphylococcus aureus V8 protease that occurs in neat aqueous solution around neutral pH utilizing a totally unprotected peptide substrate containing free alpha-carboxyl and alpha-amino groups. V8 protease catalyzed a chain of ligation steps between pH 6 and 8 at 4 degrees C, producing a gamut of covalent oligomers (dimer through octamer or higher) of a native protein segment TAAAKFE (S39) derived from ribonuclease A (RNAse A). Size-exclusion chromatography suggested the absence of strong interaction between the reacting peptides. The circular dichroism spectra of monomer through pentamer showed length-dependent enhancement of secondary structure in the oligomers, suggesting that protease-catalyzed ligation of a monomer to an oligomer resulted in a product that was more structured than its precursor. The relative conformational stability of the oligomers was reflected in their ability to resist proteolysis, indicating that the oligomerization reaction was facilitated as a consequence of the "conformational trapping" of the product. The ligation reaction proceeded in two phases-slow formation and accumulation of the dimer followed by a fast phase of oligomerization, implying that the conformational trap encountered in the oligomerization reaction was a two-step process. The Gly substitution at any position of the TAAAKFE sequence was deleterious, suggesting that the first step of the conformational trap, namely the dimerization reaction, that proceeded very slowly even with the parent peptide, was quite sensitive to amino acid sequence. In contrast, the oligomerization reaction of an Ala analog, AAAAKFE, occurred in much the same way as S39, albeit with faster rate, suggesting that Ala substitution stabilized the overall conformational trapping process. The results suggest the viability of the product-directed "conformational trap" as a mechanism to achieve peptide ligation of totally

  10. A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes.

    PubMed

    Sharma, Pankaz K; Chu, Zhen T; Olsson, Mats H M; Warshel, Arieh

    2007-06-05

    The catalytic power of enzymes containing coenzyme B(12) cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design.

  11. 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.

  12. 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

    2012-06-07

    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.

  13. Gold-Catalyzed Cycloisomerization of 1,5-Allenynes via Dual Activation of an Ene Reaction

    PubMed Central

    Cheong, Paul Ha-Yeon; Morganelli, Philip; Luzung, Michael R.; Houk, K. N.; Toste, F. Dean

    2010-01-01

    A tris-triphenylphosphinegold oxonium tetrafluoroborate, [(Ph3PAu)3O]BF4, catalyzes the rearrangement of 1,5-allenynes to produce cross-conjugated trienes. Experimental and computational evidence shows that the ene reaction proceeds through a unique nucleophilic addition of an allene double bond to a cationic phosphinegold(I) complexed phosphinegold(I) acetylide, followed by a 1,5-hydrogen shift. PMID:18327944

  14. Lewis acid catalyzed cascade reaction to carbazoles and naphthalenes via dehydrative [3 + 3]-annulation.

    PubMed

    Wang, Shaoyin; Chai, Zhuo; Wei, Yun; Zhu, Xiancui; Zhou, Shuangliu; Wang, Shaowu

    2014-07-03

    A novel Lewis acid catalyzed dehydrative [3 + 3]-annulation of readily available benzylic alcohols and propargylic alcohols was developed to give polysubstituted carbazoles and naphthalenes in moderate to good yields with water as the only byproduct. The reaction was presumed to proceed via a cascade process involving Friedel-Crafts-type allenylation, 1,5-hydride shift, 6π-eletrocyclization, and Wagner-Meerwein rearrangement.

  15. Chiral phosphoric acid catalyzed enantioselective 1,3-dipolar cycloaddition reaction of azlactones.

    PubMed

    Zhang, Zhenhua; Sun, Wangsheng; Zhu, Gongming; Yang, Junxian; Zhang, Ming; Hong, Liang; Wang, Rui

    2016-01-25

    The first chiral phosphoric acid catalyzed highly diastereo- and enantioselective 1,3-dipolar cycloaddition reaction of azlactones and methyleneindolinones was disclosed. By using a BINOL-derived chiral phosphoric acid as the catalyst, azlactones were activated as chiral anti N-protonated 1,3-dipoles to react with methyleneindolinones to yield biologically important 3,3'-pyrrolidonyl spirooxindole scaffolds in high yields, with good-to-excellent diastereo- and enantioselectivity.

  16. Chiral Calcium Phosphate Catalyzed Asymmetric Alkenylation Reaction of Arylglyoxals with 3-Vinylindoles.

    PubMed

    Li, Xiao-Yun; Yuan, Wen-Qiang; Tang, Sheng; Huang, Yi-Wei; Xue, Jia-Hui; Fu, Li Na; Guo, Qi-Xiang

    2017-03-03

    A highly efficient alkenylation reaction of arylglyoxals with 3-vinylindoles catalyzed by chiral calcium phosphate is described. Structurally diverse allylic alcohols bearing indole and carbonyl units are prepared in excellent yields, good diastereoselectivities, and high to excellent enantioselectivities. These products are good building blocks for the synthesis of polysubstituted chiral tetrahydrocarbozol-2-ones. The mechanism study indicates that the most likely role of the catalyst is to activate the hydrate of arylglyoxal and control the stereoselectivity via desymmetric coordination.

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

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

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

  18. A model reaction assesses contribution of H-tunneling and coupled motions to enzyme catalysis.

    PubMed

    Liu, Qi; Zhao, Yu; Hammann, Blake; Eilers, James; Lu, Yun; Kohen, Amnon

    2012-08-17

    To assess the contribution of physical features to enzyme catalysis, the enzymatic reaction has to be compared to a relevant uncatalyzed reaction. While such comparisons have been conducted for some hydrolytic and radical reactions, it is most challenging for biological hydride transfer and redox reactions in general. Here, the same experimental tools used to study the H-tunneling and coupled motions for enzymatic hydride transfer between two carbons were used in the study of an uncatalyzed model reaction. The enzymatic oxidations of benzyl alcohol and its substituted analogues mediated by alcohol dehydrogenases were compared to the oxidations by 9-phenylxanthylium cation (PhXn(+)). The PhXn(+) serves as an NAD(+) model, while the solvent, acetonitrile, models the protein environment. Experimental comparisons included linear free energy relations with Hammett reaction constant (ρ) of zero versus -2.7; temperature-independent versus temperature-dependent primary KIEs; deflated secondary KIEs with deuteride transfer (i.e., primary-secondary coupled motion) versus no coupling between secondary KIEs and H- or D-transfer; and large versus small secondary KIEs for the enzymatic versus uncatalyzed alcohol oxidation. Some of the differences may come from differences in the order of microscopic steps between the catalyzed versus uncatalyzed reactions. However, several of these comparative experiments indicate that in contrast to the uncatalyzed reaction the transition state of the enzymatic reaction is better reorganized for H-tunneling and its H-donor is better rehybridized prior to the C-H→C transfer. These findings suggest an important role for these physical features in enzyme catalysis.

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

    PubMed

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

    2015-12-23

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

  20. Asymmetric Petasis Borono-Mannich Allylation Reactions Catalyzed by Chiral Biphenols.

    PubMed

    Jiang, Yao; Schaus, Scott E

    2017-02-01

    Chiral biphenols catalyze the asymmetric Petasis borono-Mannich allylation of aldehydes and amines through the use of a bench-stable allyldioxaborolane. The reaction proceeds via a two-step, one-pot process and requires 2-8 mole % of 3,3'-Ph2 -BINOL as the optimal catalyst. Under microwave heating the reaction affords chiral homoallylic amines in excellent yields (up to 99 %) and high enantioselectivies (er up to 99:1). The catalytic reaction is a true multicomponent condensation reaction whereas both the aldehyde and the amine can possess a wide range of structural and electronic properties. Use of crotyldioxaborolane in the reaction results in stereodivergent products with anti- and syn-diastereomers both in good diastereoselectivities and enantioselectivities from the corresponding E- and Z-borolane stereoisomers.

  1. A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction.

    PubMed

    McGee, Philippe; Bétournay, Geneviève; Barabé, Francis; Barriault, Louis

    2017-01-12

    We have developed an innovative strategy for the formation of angular carbocycles via a gold(I)-catalyzed dehydro Diels-Alder reaction. This transformation provides rapid access to a variety of complex angular cores in excellent diastereoselectivities and high yields. The usefulness of this Au(I) -catalyzed cycloaddition was further demonstrated by accomplishing a 11-steps total synthesis of (±)-magellanine.

  2. 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.

  3. Computational analysis of the stereochemical outcome in the imidazolidinone-catalyzed enantioselective (4 + 3)-cycloaddition reaction.

    PubMed

    Krenske, Elizabeth H; Houk, K N; Harmata, Michael

    2015-01-16

    Computations show why the catalytic, asymmetric (4 + 3)-cycloaddition reaction developed in the Harmata laboratories proceeds with facial selectivity opposite to that for models proposed for related catalyzed Diels-Alder reactions. Computations with M06-2X/6-311+G(d,p)//B3LYP/6-31G(d) show that iminium ions derived from MacMillan's chiral 2-tert-butyl-5-benzylimidazolidinone and siloxypentadienals undergo (4 + 3)-cycloadditions with furans preferentially on the more crowded face. Conformational reorganization of the benzyl group, to avoid intramolecular interaction with the silyl group, is responsible for differentiating the activation barriers of top- and bottom-face attack.

  4. 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.

  5. 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

  6. 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.

  7. Stereoselective Synthesis of Saturated Heterocycles via Pd-Catalyzed Alkene Carboetherification and Carboamination Reactions

    PubMed Central

    Wolfe, John P.

    2009-01-01

    The development of Pd-catalyzed carboetherification and carboamination reactions between aryl/alkenyl halides and alkenes bearing pendant heteroatoms is described. These transformations effect the stereoselective construction of useful heterocycles such as tetrahydrofurans, pyrrolidines, imidazolidin-2-ones, isoxazolidines, and piperazines. The scope, limitations, and applications of these reactions are presented, and current stereochemical models are described. The mechanism of product formation, which involves an unusual intramolecular syn-insertion of an alkene into a Pd-Heteroatom bond is also discussed in detail. PMID:19183704

  8. Oscillatory enzyme reactions and Michaelis-Menten kinetics.

    PubMed

    Goldbeter, Albert

    2013-09-02

    Oscillations occur in a number of enzymatic systems as a result of feedback regulation. How Michaelis-Menten kinetics influences oscillatory behavior in enzyme systems is investigated in models for oscillations in the activity of phosphofructokinase (PFK) in glycolysis and of cyclin-dependent kinases in the cell cycle. The model for the PFK reaction is based on a product-activated allosteric enzyme reaction coupled to enzymatic degradation of the reaction product. The Michaelian nature of the product decay term markedly influences the period, amplitude and waveform of the oscillations. Likewise, a model for oscillations of Cdc2 kinase in embryonic cell cycles based on Michaelis-Menten phosphorylation-dephosphorylation kinetics shows that the occurrence and amplitude of the oscillations strongly depend on the ultrasensitivity of the enzymatic cascade that controls the activity of the cyclin-dependent kinase.

  9. Transition-metal-catalyzed enantioselective heteroatom-hydrogen bond insertion reactions.

    PubMed

    Zhu, Shou-Fei; Zhou, Qi-Lin

    2012-08-21

    Carbon-heteroatom bonds (C-X) are ubiquitous and are among the most reactive components of organic compounds. Therefore investigations of the construction of C-X bonds are fundamental and vibrant fields in organic chemistry. Transition-metal-catalyzed heteroatom-hydrogen bond (X-H) insertions via a metal carbene or carbenoid intermediate represent one of the most efficient approaches to form C-X bonds. Because of the availability of substrates, neutral and mild reaction conditions, and high reactivity of these transformations, researchers have widely applied transition-metal-catalyzed X-H insertions in organic synthesis. Researchers have developed a variety of rhodium-catalyzed asymmetric C-H insertion reactions with high to excellent enantioselectivities for a wide range of substrates. However, at the time that we launched our research, very few highly enantioselective X-H insertions had been documented primarily because of a lack of efficient chiral catalysts and indistinct insertion mechanisms. In this Account, we describe our recent studies of copper- and iron-catalyzed asymmetric X-H insertion reactions by using chiral spiro-bisoxazoline and diimine ligands. The copper complexes of chiral spiro-bisoxazoline ligands proved to be highly enantioselective catalysts for N-H insertions of α-diazoesters into anilines, O-H insertions of α-diazoesters into phenols and water, O-H insertions of α-diazophosphonates into alcohols, and S-H insertions of α-diazoesters into mercaptans. The iron complexes of chiral spiro-bisoxazoline ligands afforded the O-H insertion of α-diazoesters into alcohols and water with unprecedented enantioselectivities. The copper complexes of chiral spiro-diimine ligands exhibited excellent reactivity and enantioselectivity in the Si-H insertion of α-diazoacetates into a wide range of silanes. These transition-metal-catalyzed X-H insertions have many potential applications in organic synthesis because the insertion products, including chiral

  10. Purification and properties of the enzymes from Drosophila melanogaster that catalyze the conversion of dihydroneopterin triphosphate to the pyrimidodiazepine precursor of the drosopterins.

    PubMed

    Wiederrecht, G J; Brown, G M

    1984-11-25

    The enzyme system responsible for the conversion of 2-amino-4-oxo-6-(D-erythro-1',2',3'-trihydroxypropyl)-7,8-dihyd roptridine triphosphate (dihydroneopterin triphosphate or H2-NTP) to 2-amino-4-oxo-6-acetyl-7,8-dihydro-3H,9H-pyrimido[4,5-b]-[1,4]diazepine (pyrimidodiazepine or PDA), a precursor to the red eye pigments, he drosopterins, has been purified from the heads of Drosophila melanogaster. The PDA-synthesizing system consists of two components, a heat-stable enzyme and a heat-labile enzyme. The heat-stable enzyme can be replaced by sepiapterin synthase A, a previously purified enzyme required for the Mg2+-dependent conversion of H2-NTP to an unstable compound that appears to be 6-pyruvoyltetrahydropterin (pyruvoyl-H4-pterin). The heat-labile enzyme, purified to near-homogeneity and termed PDA synthase (Mr = 48,000), catalyzes the conversion of pyruvoyl-H4-pterin to PDA in a reaction requiring the presence of reduced glutathione. Because PDA is two electrons more reduced than pyruvoyl-H4-pterin, the reducing power required for this transformation is probably supplied by glutathione. The PDA-synthesizing system requires the presence of another thiol-containing compound such as 2-mercaptoethanol when incubation conditions 2-mercaptoethanol is no longer required. Evidence is presented to indicate that the Drosophila eye color mutant, sepia, is missing PDA synthase.

  11. Purification and characterization of cannabidiolic-acid synthase from Cannabis sativa L.. Biochemical analysis of a novel enzyme that catalyzes the oxidocyclization of cannabigerolic acid to cannabidiolic acid.

    PubMed

    Taura, F; Morimoto, S; Shoyama, Y

    1996-07-19

    We identified a unique enzyme that catalyzes the oxidocyclization of cannabigerolic acid to cannabidiolic acid (CBDA) in Cannabis sativa L. (CBDA strain). The enzyme, named CBDA synthase, was purified to apparent homogeneity by a four-step procedure: ammonium sulfate precipitation followed by chromatography on DEAE-cellulose, phenyl-Sepharose CL-4B, and hydroxylapatite. The active enzyme consists of a single polypeptide with a molecular mass of 74 kDa and a pI of 6.1. The NH2-terminal amino acid sequence of CBDA synthase is similar to that of Delta1-tetrahydrocannabinolic-acid synthase. CBDA synthase does not require coenzymes, molecular oxygen, hydrogen peroxide, and metal ion cofactors for the oxidocyclization reaction. These results indicate that CBDA synthase is neither an oxygenase nor a peroxidase and that the enzymatic cyclization does not proceed via oxygenated intermediates. CBDA synthase catalyzes the formation of CBDA from cannabinerolic acid as well as cannabigerolic acid, although the kcat for the former (0.03 s-1) is lower than that for the latter (0.19 s-1). Therefore, we conclude that CBDA is predominantly biosynthesized from cannabigerolic acid rather than cannabinerolic acid.

  12. 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)

  13. Digestion completeness of microwave-assisted and conventional trypsin-catalyzed reactions.

    PubMed

    Reddy, P Muralidhar; Hsu, Wan-Yu; Hu, Jun-Fu; Ho, Yen-Peng

    2010-03-01

    Microwave-assisted proteolytic digestion often yields misscleaved peptides, attributed to incomplete hydrolysis reactions between enzymes and substrates. The number of missed cleavages is an important parameter in proteome database searching. This study investigates how various factors affect digestion processes. Optimum conditions for microwave-assisted digestion (50 mM Tris buffer, 30 min at 60 degrees C, and enzyme to protein molar ratio of 1:5) were determined. The digestion products obtained from eight standard proteins were characterized based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Experimental results indicate that the digestion temperature, reaction time, enzyme to substrate ratio, and digestion buffer affect the number of misscleaved peptides and incomplete digestion percentages. Although all protein molecules in a sample could be digested into peptides within a few minutes under microwave irradiation, longer reaction times or methods to maximize the enzyme activity should be considered if digestion completeness is a major concern.

  14. 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

  15. 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.

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

    PubMed

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

    2015-06-21

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

  17. 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.

  18. Copper-catalyzed extended Pummerer reactions of ketene dithioacetal monoxides with alkynyl sulfides and ynamides with an accompanying oxygen rearrangement.

    PubMed

    Murakami, Kei; Imoto, Junichi; Matsubara, Hiroshi; Yoshida, Suguru; Yorimitsu, Hideki; Oshima, Koichiro

    2013-04-26

    The first examples of metal-catalyzed extended Pummerer reactions through the activation of sulfoxides are described. The copper-catalyzed reactions of ketene dithioacetal monoxides with alkynyl sulfides and ynamides provided a wide variety of γ,γ-disulfanyl-β,γ-unsaturated carbonyl compounds with an accompanying oxygen rearrangement. The products can be easily converted into 1,4-dicarbonyl compounds and substituted heteroaromatics. DFT calculations and mechanistic experiments revealed a new interesting stepwise addition/oxygen rearrangement mechanism.

  19. 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

  20. The mechanism of the NHC catalyzed aza-Morita-Baylis-Hillman reaction: insights into a new substrate-catalyzed bimolecular pathway.

    PubMed

    Verma, Pritha; Verma, Pragya; Sunoj, Raghavan B

    2014-04-14

    The first mechanistic study on the NHC-catalyzed aza-MBH reaction between cyclopentenone and N-mesylbenzaldimine using density functional theory reveals that a bimolecular mechanism, involving two molecules of benzaldimine in the proton transfer, is energetically more preferred over the conventional direct proton transfer.

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

    PubMed

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

    2014-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    PubMed

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

    2016-08-05

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

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

    PubMed Central

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

    2014-01-01

    Organic molecules and polymers with extended π-conjugation are appealing as advanced electronic materials, and have already found practical applications in thin-film transistors, light emitting diodes, and chemical sensors. Transition metal (TM)-catalyzed cross-coupling methodologies have evolved over the past four decades into one of the most powerful and versatile methods for C–C bond formation, enabling the construction of a diverse and sophisticated range of π-conjugated oligomers and polymers. In this review, we focus our discussion on recent synthetic developments of several important classes of π-conjugated systems using TM-catalyzed cross-coupling reactions, with a perspective on their utility for organic electronic materials. PMID:27877696

  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

    2016-02-05

    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.

  6. 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:27478280

  7. 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

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

    PubMed

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

    2006-01-06

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

  9. Silver-Catalyzed Formal Inverse Electron-Demand Diels-Alder Reaction of 1,2-Diazines and Siloxy Alkynes

    PubMed Central

    Türkmen, Yunus E.; Montavon, Timothy J.; Kozmin, Sergey A.; Rawal, Viresh H.

    2012-01-01

    A highly effective silver-catalyzed formal inverse electron-demand Diels-Alder reaction of 1,2-diazines and siloxy alkynes has been developed. The reactions provide ready access to a wide range of siloxy naphthalenes and anthracenes, which are formed in good to high yields, under mild reaction conditions, using low catalyst loadings. PMID:22607029

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Suga, Hiroyuki

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

  13. Simulating feedback and reversibility in substrate-enzyme reactions

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  15. Vitamin A as an enzyme that catalyzes the reduction of MTT to formazan by vitamin C.

    PubMed

    Chakrabarti, R; Kundu, S; Kumar, S; Chakrabarti, R

    2000-09-18

    The tetrazolium salt 3(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) is reduced to formazan by the succinate dehydrogenase system of active mitochondria, and hence, specifically used to assay for the viable cells, such as measurement of cell proliferation, cytotoxicity, and cell number. However, in the present study we have shown that some component specifically present in M199 but not in RPMI 1640 media can reduce MTT to formazan in the absence of a living system. Further study revealed that ascorbic acid reduced MTT to formazan, which was profoundly increased by a very small amount of retinol, whereas retinol alone had no effect. Oxidation of ascorbic acid by H(2)O(2) destroyed its ability to reduce MTT. The rate of MTT reduction was directly proportional to the concentration of MTT in the absence of retinol, but approached a zero-order state beyond a certain concentration of MTT in the presence of retinol. Furthermore, retinol remained unchanged after the completion of the reaction. Taken together, these results showed that retinol acts as a reductase that catalyzes the reduction of MTT to formazan using ascorbic acid as the cosubstrate (electron donor).

  16. Development of a synchronous enzyme-reaction system for a highly sensitive enzyme immunoassay.

    PubMed

    Inouye, Kuniyo; Ueno, Iori; Yokoyama, Shin-ichi; Sakaki, Toshiyuki

    2002-01-01

    A synchronous enzyme-reaction system using water-soluble formazan and a non-enzymatic electron mediator was developed and applied to an enzyme immunoassay (EIA). The reaction system consists of four steps: (I) dephosphorylation of NADP(+) to produce NAD(+) by alkaline phosphatase (ALP), (II) reduction of NAD(+) to produce NADH with oxidation of ethanol to yield acetaldehyde by alcohol dehydrogenase (ADH), (III) reduction of water-soluble tetrazolium salt (WST-1) to produce formazan by NADH via 1-methoxy-5-methyl-phenazinium methyl sulfate (PMS), and (IV) re-reduction of NAD(+) to produce NADH by ADH. During each cycle, one molecule of tetrazolium is converted to one molecule of formazan. The concentration of formazan during the reaction was given by second-order polynomials of the reaction time. Kinetic studies strongly suggested that the synchronous enzyme-reaction system had the potential to detect an analyte at the attomole level in EIA. On the basis of the kinetic studies, optimal conditions for EIA incorporating the synchronous system were examined. NADP(+) was purified thoroughly to remove minor traces of NAD(+) in the preparation, and an ADH preparation contaminated with the lowest level of ALP activity was used. When the synchronous system was applied to a sandwich-type EIA for human C-reactive protein, the protein was detected with a sensitivity of 50 attomole per well of a micro-titer plate (0.1 ml) in a 1-h reaction. In addition, EIA with water-soluble formazan showed a more quantitative and sensitive result than that with insoluble formazan. These findings indicated that the (WST-1)-PMS system introduced in this study has a great potential for highly sensitive enzyme immunoassay.

  17. 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.

  18. Deuterium isotope effect on the induction period of the cerium catalyzed Belousov-Zhabotinsky reaction

    NASA Astrophysics Data System (ADS)

    Rossi, Federico; Simoncini, Eugenio; Marchettini, Nadia; Tiezzi, Enzo

    2009-02-01

    In this work we present results about the deuterium isotopic effect on the global kinetics of a cerium catalyzed Belousov-Zhabotinsky reaction. A nonlinear dependence of the induction period upon the percentage of deuterated reactants was found in batch conditions. In order to understand this result, we investigated two reaction pathways responsible for the length of the induction period, namely: (a) the reaction between the enolic form of the malonic acid with molecular bromine and (b) the oxidation of malonic acid by the Ce(IV) ion. In both cases we obtained a linear dependence of the kinetic constants on the percentage of deuterated reactants. Nevertheless, by inserting the experimental values in the MBM (Marburg-Budapest-Missoula) model, we were able to qualitatively simulate the observed trend of the induction period.

  19. Organic carbonates as alternative solvents for palladium-catalyzed substitution reactions.

    PubMed

    Schäffner, Benjamin; Holz, Jens; Verevkin, Sergey P; Börner, Armin

    2008-01-01

    Organic carbonates, such as propylene carbonate, butylene carbonate, and diethyl carbonate, were tested in the Pd-catalyzed asymmetric allylic substitution reactions of rac-1,3-diphenyl-3-acetoxy-prop-1-ene with dimethyl malonate or benzylamine as nucleophiles. Bidentate diphosphanes were used as chiral ligands. The application of monodentate phosphanes capable of self-assembling with the metal was likewise tested. In the substitution reaction with dimethyl malonate, enantioselectivities up to 98% were achieved. In the amination reaction, the chiral product was obtained with up to 83% ee. The results confirm that these "green solvents" can be advantageously used for this catalytic transformation as an alternative to those solvents usually employed which run some risk of being harmful to the environment.

  20. Mild copper-catalyzed vinylation reactions of azoles and phenols with vinyl bromides.

    PubMed

    Taillefer, Marc; Ouali, Armelle; Renard, Brice; Spindler, Jean-Francis

    2006-07-05

    An efficient and straightforward copper-catalyzed method allowing vinylation of N- or O-nucleophiles with di- or trisubstituted vinyl bromides is reported. The procedure is applicable to a broad range of substrates since N-vinylation of mono-, di-, and triazoles as well as O-vinylation of phenol derivatives can be performed with catalytic amounts of copper iodide and inexpensive nitrogen ligands 3 or 8. In the case of more hindered vinyl bromides, the use of the original bidentate chelator 8 was shown to be more efficient to promote the coupling reactions than our key tetradentate ligand 3. The corresponding N-(1-alkenyl)azoles and alkenyl aryl ethers are obtained in high yields and selectivities under very mild temperature conditions (35-110 degrees C for N-vinylation reactions and 50-80 degrees C for O-vinylation reactions). Moreover, to our knowledge, this method is the first example of a copper-catalyzed vinylation of various azoles. Finally, this protocol, practical on a laboratory scale and easily adaptable to an industrial scale, is very competitive compared to the existing methods that allow the synthesis of such compounds.

  1. 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.

  2. N-heterocyclic carbene catalyzed asymmetric intermolecular Stetter reaction: origin of enantioselectivity and role of counterions.

    PubMed

    Kuniyil, Rositha; Sunoj, Raghavan B

    2013-10-04

    The mechanism and the role of KOtBu in an enantioselective NHC-catalyzed Stetter reaction between p-chlorobenzaldehyde and N-acylamido acrylate is established using DFT(M06-2X) methods. The Gibbs free energies are found to be significantly lower for transition states with explicit bound KOtBu as compared to the conventional pathways without the counterions. An intermolecular proton transfer from HOtBu to the prochiral carbon is identified as the stereocontrolling step. The computed enantioselectivities are in excellent agreement with the experimental results.

  3. Highly selective room-temperature copper-catalyzed C-N coupling reactions.

    PubMed

    Shafir, Alexandr; Buchwald, Stephen L

    2006-07-12

    Through the use of cyclic beta-diketones as supporting ligands, the copper-catalyzed coupling of aryl iodides with aliphatic amines occurs at room temperature in as little as 1 h. These high reaction rates allow for the coupling of a wide range of aryl and heteroaryl iodides at room temperature. This method is highly tolerant of a number of reactive functional groups, including -Br and aromatic -NH2 as well as phenolic and aliphatic -OH. The high selectivity of the CuI-beta-diketone catalyst for aliphatic amines represents a useful complement to the palladium-based methods.

  4. Isotope Effects and Mechanism of the Asymmetric BOROX Brønsted Acid Catalyzed Aziridination Reaction

    PubMed Central

    Vetticatt, Mathew J.; Desai, Aman A.; Wulff, William D.

    2013-01-01

    The mechanism of the chiral VANOL-BOROX Brønsted acid catalyzed aziridination reaction of imines and ethyldiazoacetate has been studied using a combination of experimental kinetic isotope effects and theoretical calculations. A stepwise mechanism where reversible formation of a diazonium ion intermediate precedes rate-limiting ring-closure to form the cis-aziridine is implicated. A revised model for the origin of enantio- and diastereoselectivity is proposed based on relative energies of the ring closing transition structures. PMID:23687986

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

    NASA Astrophysics Data System (ADS)

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

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

  6. 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.

  7. 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.)

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

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

    PubMed Central

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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 (ɛ 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 ɛ 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. ɛ values for Fenton-like oxidation of TCE were intermediate in those previously reported for aerobic biological processes (ɛ = - 1.1 to - 20.7‰). Thus, field-derived ɛ 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 ɛ values are less negative than those for Fenton-like oxidation.

  18. 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.

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

    PubMed

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

    2013-08-14

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

  20. A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase

    NASA Astrophysics Data System (ADS)

    Re, Suyong; Jung, Jaewoon; Ten-no, Seiichiro; Sugita, Yuji

    2009-10-01

    The phosphoryl transfer reaction from phospho- L-serine (pSer), catalyzed by phosphoserine phosphatase, is investigated using the hybrid quantum mechanics/molecular mechanics calculations. The two-dimensional energy surface along the phosphoryl and proton transfer distances reveals early protonation of the leaving group oxygen of pSer, prior to the transition state (TS), which triggers subsequent phosphoryl transfer reaction. Calculated electronic properties of the phosphoryl group at the active site suggest significant metaphosphate-like character of TS, which is consistent with kinetic experiments on related phosphatases. The features are not obtained with a one-dimensional search along the phosphoryl transfer coordinate, due to inadequate description of proton movement.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Alnemrat, Sufian; Vasiliev, Igor; Wang, Haobin

    2011-03-01

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

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

    PubMed

    Dorel, Ruth; Echavarren, Antonio M

    2015-08-07

    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.

  4. Progress of Chiral Schiff Bases with C1 Symmetry in Metal-Catalyzed Asymmetric Reactions.

    PubMed

    Hayashi, Masahiko

    2016-12-01

    In this Personal Account, various chiral Schiff base-metal-catalyzed enantioselective organic reactions are reported; the Schiff bases used were O,N,O- as well as N,N,P-tridentate ligands and N,N-bidentate ligands having C1 symmetry. In particular, the enantioselective addition of trimethylsilyl cyanide, dialkylzinc, and organozinc halides to aldehydes, enantioselective 1,4-addition of dialkylzinc to cyclic and acyclic enones, and asymmetric allylic oxidation are reported. Typically, ketimine-type Schiff base-metal complexes exhibited higher reactivity and enantioselectivity compared with the corresponding aldimine-type Schiff base-metal complexes. Notably, remarkable ligand acceleration was observed for all reactions. The obtained products can be used as key intermediates for optically active natural products and pharmaceuticals.

  5. The Onset Of Fluctuations In The Ferroin-Catalyzed Belousov-Zhabotinski Reaction

    NASA Astrophysics Data System (ADS)

    Hastings, Harold M.; Sobel, Sabrina G.; Fenton, Flavio H.; Chaterpaul, Stephen; Frank, Claudia; Pekor, Jordan; Russell, Elizabeth

    2003-08-01

    We report on an experimental study of the onset of target waves in the ferroin-catalyzed Belousov-Zhabotinski (BZ) reaction. In the cardiac electrical system, another excitable medium, spontaneous activity can initiate ventricular tachycardia by interacting with normal or other spontaneous electrical activity to generate spiral waves. In normal hearts, these spiral waves generally break down to cause ventricular fibrillation (VF), leading to sudden cardiac death. Our results for the BZ reaction: (1) centers of target waves are spatially correlated, with the correlation likely due to mixing effects and long range modes arising in the "clocking phase", (2) activitations begin after concentrations track an equilibrium through a Hopf bifurcation into an unstable "supercritical" state, (3) allowing very small fluctuations can generate targets.

  6. Dynamics of the onset of target waves in the ferroin-catalyzed Belousov-Zhabotinski reaction

    NASA Astrophysics Data System (ADS)

    Hastings, Harold M.; Sobel, Sabrina G.; Chaterpaul, Stephen; Frank, Claudia; Pekor, Jordan; Russell, Elizabeth; Fenton, Flavio

    2002-03-01

    We report on an experimental study of the onset of target waves in the excitable ferroin-catalyzed Belousov-Zhabotinski (BZ) reaction. In the cardiac electrical system, another excitable medium, the onset of spontaneous activity can initiate ventricular tachycardia by interacting with normal or other spontaneous electrical activity to generate spiral waves. In normal hearts, these spiral waves then generally break down to cause ventricular fibrillation (VF), and thus sudden cardiac death. Our results for the BZ reaction: (1) the onset of activity is a complex, multi-scale process, (2) centers of target waves are spatially correlated, (3) there are several spatial scales in the mm range, larger than the critical radius and the diffusion scale, and (4) simulations suggest how a chemical amplifier, suggested previously as a mechanism for microscopic fluctuations to generate chemical chaos [N Ganapathisubramanian and RM Noyes, J. Phys. Chem 76, 1770 (1982)], might play a similar role in the onset of activity.

  7. 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

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

    SciTech Connect

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

    2010-01-01

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

  9. PtI2-catalyzed tandem 3,3-rearrangement/Nazarov reaction of arylpropargylic esters: synthesis of indanone derivatives.

    PubMed

    Zheng, Huaiji; Xie, Xingang; Yang, Juan; Zhao, Changgui; Jing, Peng; Fang, Bowen; She, Xuegong

    2011-10-26

    An efficient PtI(2)-catalyzed tandem reaction of arylpropargylic esters, involving 3,3-rearrangement and Nazarov reaction, has been developed to produce 3-substituted and 3,3-disubstituted indanone derivatives. This approach provided a pathway to the synthesis of indanone skeletons in natural products.

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

    PubMed

    Muntzeck, Maren; Wilhelm, René

    2016-06-01

    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.

  11. 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

  12. In(III)-catalyzed tandem reaction of chromone-derived Morita-Baylis-Hillman alcohols with amines.

    PubMed

    Wu, Chen; Liu, Yuliang; Zeng, Hao; Liu, Li; Wang, Dong; Chen, Yongjun

    2011-01-07

    The reaction of chromone-derived cyclic Morita-Baylis-Hillman alcohols with amines catalyzed by In(OTf)(3) in a one pot process was developed for the convenient and efficient synthesis of 2-substituted-3-aminomethylenechromans. The tandem allylic amination/chromen ring-opening/Michael cyclization reactions were involved in this protocol.

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

    PubMed Central

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

    2014-01-01

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

  14. Palladium-Catalyzed Cross-Coupling Reactions of Organosilanols and their Salts

    PubMed Central

    Denmark, Scott E.; Regens, Christopher S.

    2009-01-01

    Conspectus In the panoply of modern synthetic methods for forming carbon-carbon and carbon-heteroatom bonds, the transition metal-catalyzed cross coupling of organometallic nucleophiles with organic electrophiles enjoys a preeminent status. The preparative utility of these reactions is, in large measure, a consequence of the wide variety of organometallic donors that have been conscripted into service. The most common of these reagents are organic derivatives of tin, boron, and zinc, which each possess unique advantages and shortcomings. Because of their low cost, low toxicity, and high chemical stability, organosilanes have emerged as viable alternatives to the conventional reagents in recent years. However, unlike the tin- and zinc-based reactions that require no activation or the boron-based reactions that require only heating with mild bases, silicon-based cross-coupling reactions often require heating in the presence of a fluoride source; this has significantly hampered the widespread acceptance of organosilanes. To address the “fluoride problem”, we have introduced a new paradigm for palladium-catalyzed, silicon-based cross-coupling reactions that employs organosilanols, a previously underutilized class of silicon reagents. The use of organosilanols either in the presence of Brønsted bases or as their silanolate salts represents a simple and mild alternative to the classic fluoride-based activation method. Organosilanols are easily available by many well-established methods for introducing carbon-silicon bonds onto alkenes, alkynes and arenes, and heteroarenes. Moreover, we have developed four different protocols for the generation of alkali metal salts of, vinyl-, alkenyl-, alkynyl-, aryl-, and heteroarylsilanolates: (1) reversible deprotonation with weak Brønsted bases, (2) irreversible deprotonation with strong Brønsted bases, (3) isolation of the salts from irreversible deprotonation, and (4) silanolate exchange with disiloxanes. We have

  15. 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.

  16. 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

  17. 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.

  18. Estimation of kinetic parameters for enzyme-inhibition reaction models using direct time-dependent equations for reactant concentrations.

    PubMed

    Goličnik, Marko

    2012-03-01

    To facilitate the determination of a reaction type and its kinetics constants for reversible inhibitors of Michaelis-Menten-type enzymes using progress-curve analysis, I present here an explicit equation for direct curve fitting to full time-course data of inhibited enzyme-catalyzed reactions. This algebraic expression involves certain elementary functions where their values are readily available using any standard nonlinear regression program. Hence this allows easy analysis of experimentally observed kinetics without any data conversion prior to fitting. Its implementation gives correct parameter estimates that are in very good agreement with results obtained using both the numerically integrated Michaelis-Menten rate equation or its exact closed-form solution which is expressed in terms of the Lambert W function.

  19. Escherichia coli unsaturated fatty acid synthesis: complex transcription of the fabA gene and in vivo identification of the essential reaction catalyzed by FabB.

    PubMed

    Feng, Youjun; Cronan, John E

    2009-10-23

    Although the unsaturated fatty acid (UFA) synthetic pathway of Escherichia coli is the prototype of such pathways, several unresolved issues have accumulated over the years. The key players are the fabA and fabB genes. Earlier studies of fabA transcription showed that the gene was transcribed from two promoters, with one being positively regulated by the FadR protein. The other weaker promoter (which could not be mapped with the technology then available) was considered constitutive because its function was independent of FadR. However, the FabR negative regulator was recently shown to represses fabA transcription. We report that the weak promoter overlaps the FadR-dependent promoter and is regulated by FabR. This promoter is strictly conserved in all E. coli and Salmonella enterica genomes sequenced to date and is thought to provide insurance against inappropriate regulation of fabA transcription by exogenous saturated fatty acids. Also, the fabAup promoter, a mutant promoter previously isolated by selection for increased FabA activity, was shown to be a promoter created de novo by a four-base deletion within the gene located immediately upstream of fabA. Demonstration of the key UFA synthetic reaction catalyzed by FabB has been elusive, although it was known to catalyze an elongation reaction. Strains lacking FabB are UFA auxotrophs indicating that the enzyme catalyzes an essential step in UFA synthesis. Using thioesterases specific for hydrolysis of short chain acyl-ACPs, the intermediates of the UFA synthetic pathway have been followed in vivo for the first time. These experiments showed that a fabB mutant strain accumulated less cis-5-dodecenoic acid than the parental wild-type strain. These data indicate that the key reaction in UFA synthesis catalyzed by FabB is elongation of the cis-3-decenoyl-ACP produced by FabA.

  20. Efficient production of free fatty acids from ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate.

    PubMed

    Mi, Le; Qin, Dandan; Cheng, Jie; Wang, Dan; Li, Sha; Wei, Xuetuan

    2017-03-01

    Two engineered Escherichia coli strains, DQ101 (MG1655 fadD (-))/pDQTES and DQ101 (MG1655 fadD (-))/pDQTESZ were constructed to investigate the free fatty acid production using ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate as carbon source in this study. The plasmid, pDQTES, carrying an acyl-ACP thioesterase 'TesA of E. coli in pTrc99A was constructed firstly, and then (3R)-hydroxyacyl-ACP dehydratase was ligated after the TesA to give the plasmid pDQTESZ. These two strains exhibited efficient fatty acid production when glucose was used as the sole carbon source, with a final concentration of 2.45 and 3.32 g/L, respectively. The free fatty acid production of the two strains on xylose is not as efficient as that on glucose, which was 2.32 and 2.96 g/L, respectively. For mixed sugars, DQ101 (MG1655 fadD (-))-based strains utilized glucose and pentose sequentially under the carbon catabolite repression (CCR) regulation. The highest total FFAs concentration from the mixed sugar culture reached 2.81 g/L by DQ101 (MG1655 fadD (-))/pDQTESZ. Furthermore, when ionic liquid-based enzyme-catalyzed bamboo hydrolysate was used as the carbon source, the strain DQ101 (MG1655 fadD (-))/pDQTESZ could produce 1.23 g/L FFAs with a yield of 0.13 g/g, and while it just produced 0.65 g/L free fatty acid with the ionic liquid-based acid-catalyzed bamboo hydrolysate as the feedstock. The results suggested that enzymatic catalyzed bamboo hydrolysate with ionic liquid pretreatment could serve as an efficient feedstock for free fatty acid production.

  1. 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.

  2. 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.

  3. Application of Grote-Hynes theory to the reaction catalyzed by thymidylate synthase.

    PubMed

    Kanaan, Natalia; Roca, Maite; Tuñón, Iñaki; Martí, Sergio; Moliner, Vicent

    2010-10-28

    A theoretical study of dynamic effects on the rate-limiting step of the thymidylate synthase catalyzed reaction has been carried out by means of Grote-Hynes theory, successfully predicting the values of the recrossing effects for a chemical reaction that involves the transfer of a classical light particle. The transmission coefficients, obtained at 278, 293, 303, and 313 K, are almost invariant and in all cases far from unity, revealing a significant coupling of the environment motions and the reaction coordinate. Nevertheless, their energetic contribution to the activation free energy represents less than 0.50 kcal/mol for each of the four tested temperatures. Calculation of the transmission coefficient for the isotopically labeled hydride transfer has rendered almost the same values, in agreement with the experimentally observed temperature-independent KIEs. Fourier transform of the time-dependent friction kernel at these four temperatures has allowed obtaining the transition-state friction spectra, which present very small dependence with temperature. Their analysis has led to the identification of some key vibrational modes governing the coupling between the reaction coordinate and the protein environment, thus identifying the relevant motions in the active site and obtaining a full picture of the role of each amino acid.

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

    PubMed Central

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

    2011-01-01

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

  5. Biocatalytic Synthesis of Allylic and Allenyl Sulfides through a Myoglobin-Catalyzed Doyle-Kirmse Reaction.

    PubMed

    Tyagi, Vikas; Sreenilayam, Gopeekrishnan; Bajaj, Priyanka; Tinoco, Antonio; Fasan, Rudi

    2016-10-17

    The first example of a biocatalytic [2,3]-sigmatropic rearrangement reaction involving allylic sulfides and diazo reagents (Doyle-Kirmse reaction) is reported. Engineered variants of sperm whale myoglobin catalyze this synthetically valuable C-C bond-forming transformation with high efficiency and product conversions across a variety of sulfide substrates (e.g., aryl-, benzyl-, and alkyl-substituted allylic sulfides) and α-diazo esters. Moreover, the scope of this myoglobin-mediated transformation could be extended to the conversion of propargylic sulfides to give substituted allenes. Active-site mutations proved effective in enhancing the catalytic efficiency of the hemoprotein in these reactions as well as modulating the enantioselectivity, resulting in the identification of the myoglobin variant Mb(L29S,H64V,V68F), which is capable of mediating asymmetric Doyle-Kirmse reactions with an enantiomeric excess up to 71 %. This work extends the toolbox of currently available biocatalytic strategies for the asymmetric formation of carbon-carbon bonds.

  6. Fenton-like reaction catalyzed by the rare earth inner transition metal cerium.

    PubMed

    Heckert, Eric G; Seal, Sudipta; Self, William T

    2008-07-01

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

  7. Identification and in vitro analysis of the GatD/MurT enzyme-complex catalyzing lipid II amidation in Staphylococcus aureus.

    PubMed

    Münch, Daniela; Roemer, Terry; Lee, Sang Ho; Engeser, Marianne; Sahl, Hans Georg; Schneider, Tanja

    2012-01-01

    The peptidoglycan of Staphylococcus aureus is characterized by a high degree of crosslinking and almost completely lacks free carboxyl groups, due to amidation of the D-glutamic acid in the stem peptide. Amidation of peptidoglycan has been proposed to play a decisive role in polymerization of cell wall building blocks, correlating with the crosslinking of neighboring peptidoglycan stem peptides. Mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin. We identified the enzymes catalyzing the formation of D-glutamine in position 2 of the stem peptide. We provide biochemical evidence that the reaction is catalyzed by a glutamine amidotransferase-like protein and a Mur ligase homologue, encoded by SA1707 and SA1708, respectively. Both proteins, for which we propose the designation GatD and MurT, are required for amidation and appear to form a physically stable bi-enzyme complex. To investigate the reaction in vitro we purified recombinant GatD and MurT His-tag fusion proteins and their potential substrates, i.e. UDP-MurNAc-pentapeptide, as well as the membrane-bound cell wall precursors lipid I, lipid II and lipid II-Gly₅. In vitro amidation occurred with all bactoprenol-bound intermediates, suggesting that in vivo lipid II and/or lipid II-Gly₅ may be substrates for GatD/MurT. Inactivation of the GatD active site abolished lipid II amidation. Both, murT and gatD are organized in an operon and are essential genes of S. aureus. BLAST analysis revealed the presence of homologous transcriptional units in a number of gram-positive pathogens, e.g. Mycobacterium tuberculosis, Streptococcus pneumonia and Clostridium perfringens, all known to have a D-iso-glutamine containing PG. A less negatively charged PG reduces susceptibility towards defensins and may play a general role in innate immune signaling.

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

    PubMed

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

    2015-11-06

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

  9. Non-contact photothermal control of enzyme reactions on a microchip by using a compact diode laser.

    PubMed

    Tanaka, Y; Slyadnev, M N; Hibara, A; Tokeshi, M; Kitamori, T

    2000-10-13

    Photothermal temperature control of an enzyme-catalyzed reaction in a microchip using a diode laser was demonstrated. A laser beam with energy of 10 mW was used to irradiate an absorbing target placed on top of the microchip cover plate. Theoretical calculations have shown that temperature in the microchannel can be locally increased by 5-7 degrees C during short time intervals, due to heat released by the target. The rate of the enzyme reaction, which was initially inhibited due to cooling of the chip to low temperature, was increased when the target was irradiated. The products were detected by a thermal lens microscope. The product concentration was shown to depend on irradiation time, laser intensity and substrate concentration. Reaction characteristics (rate constant of the reaction) were then derived from these dependencies. The reaction volume and absolute quantity of the reaction product were estimated as 10 nl and 100 fmol, respectively. It was also demonstrated that a direct solvent heating method using infrared radiation could control the reaction in the microchannel.

  10. 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

  11. 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.

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

    PubMed

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

    2015-06-01

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

  13. 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.

  14. Multiple mechanisms in Pd(II)-catalyzed S(N)2' reactions of allylic alcohols.

    PubMed

    Ghebreghiorgis, Thomas; Kirk, Brian H; Aponick, Aaron; Ess, Daniel H

    2013-08-02

    Density functional calculations and experiments were used to examine mechanisms of Pd(II) catalyzed intramolecular cyclization and dehydration in acyclic and bicyclic monoallylic diols, a formal S(N)2' reaction. In contrast to the previously proposed syn-oxypalladation mechanism for acyclic monoallylic diols, calculations and experiments strongly suggest that hydrogen bonding templates a hydroxyl group and Pd addition across the alkene and provides a low energy pathway via anti-addition (anti-oxypalladation) followed by intramolecular proton transfer and anti-elimination of water. This anti-addition, anti-elimination pathway also provides a simple rationale for the observed stereospecificity. For bicyclic monoallylic diol compounds, Pd(II) is capable of promoting either anti- or syn-addition. In addition, palladium chloride ligands can mediate proton transfer to promote dehydration when direct intramolecular proton transfer between diol groups is impossible.

  15. Analyzing site selectivity in Rh2(esp)2-catalyzed intermolecular C-H amination reactions.

    PubMed

    Bess, Elizabeth N; DeLuca, Ryan J; Tindall, Daniel J; Oderinde, Martins S; Roizen, Jennifer L; Du Bois, J; Sigman, Matthew S

    2014-04-16

    Predicting site selectivity in C-H bond oxidation reactions involving heteroatom transfer is challenged by the small energetic differences between disparate bond types and the subtle interplay of steric and electronic effects that influence reactivity. Herein, the factors governing selective Rh2(esp)2-catalyzed C-H amination of isoamylbenzene derivatives are investigated, where modification to both the nitrogen source, a sulfamate ester, and substrate are shown to impact isomeric product ratios. Linear regression mathematical modeling is used to define a relationship that equates both IR stretching parameters and Hammett σ(+) values to the differential free energy of benzylic versus tertiary C-H amination. This model has informed the development of a novel sulfamate ester, which affords the highest benzylic-to-tertiary site selectivity (9.5:1) observed for this system.

  16. Holliday junctions generate super-bright antibodies and antibody fragments in sortase-catalyzed reactions

    PubMed Central

    Li, Zeyang; Theile, Christopher S.; Chen, Guan-Yu; Bilate, Angelina M.; Duarte, Joao N.; Avalos, Ana M.; Fang, Tao; Barberena, Roberto; Sato, Shuji; Ploegh, Hidde L.

    2015-01-01

    Site-specific modification of proteins with fluorophores can render a protein fluorescent without compromising its function. To avoid self-quenching of multiple fluorophores installed in close proximity, we used Holliday junctions to label proteins site-specifically. Holliday junctions enable modification with multiple fluorophores at reasonably precise spacing. We designed a Holliday junction with three of its four arms modified with a fluorophore of choice and the remaining arm equipped with a dibenzocyclooctyne substituent to render it reactive with an azide-modified, fluorescent single domain antibody fragment or an intact immunoglobulin, produced in a sortase-catalyzed reaction. We conclude that fluorescent Holliday junctions improve fluorescence yields for both single domain and full-sized antibodies, without deleterious effects on antigen binding. PMID:26252716

  17. 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.

  18. Recent developments in the metal-catalyzed reactions of metallocarbenoids from propargylic esters.

    PubMed

    Marco-Contelles, José; Soriano, Elena

    2007-01-01

    The transition-metal-catalyzed intramolecular cycloisomerization of propargylic carboxylates provides functionalized bicyclo[n.1.0]enol esters in a very diastereoselective manner and, depending on the structure, with partial or complete transfer of chirality from enantiomerically pure precursors. The subsequent methanolysis gives bicyclo[n.1.0] ketones, hence resulting in a very efficient two-step protocol for the syntheses of alpha,beta-unsaturated cyclopropyl ketones, key intermediates for the preparation of natural products. The results from mechanistic computational studies suggest that they probably proceed through cyclopropyl metallocarbenoids, formed by endo-cyclopropanation, that undergo a 1,2-acyl migration. Finally, the potential of the intermolecular reaction and the related pentannulation of propargylic esters bearing pendant aromatic rings are also discussed.

  19. 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.

  20. On the Need for Spin Polarization in Heterogeneously Catalyzed Reactions on Nonmagnetic Metallic Surfaces.

    PubMed

    Fajín, José L C; D S Cordeiro, M Natália; Gomes, José R B; Illas, Francesc

    2012-05-08

    A series of reactions including water, oxygen, hydrogen and nitric oxide dissociation and carbon monoxide or nitric oxide oxidations catalyzed by metallic surfaces have been investigated by means of periodic density functional calculations with the main aim of establishing the importance of spin polarization when the substrate is nonmagnetic. Numerical differences in the calculated total energies and bond lengths of the breaking/forming bonds corresponding to spin restricted or spin unrestricted formalisms are usually smaller than the inherent error of density functional theory based methods. Nevertheless, it is important to insist on the fact that the spin polarized solution exists and is lower in energy than the one corresponding to the spin restricted formalism, as one would expect, and from a practical point of view, results obtained without taking spin polarization into account lead to the same description of the potential energy surface.

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

    PubMed

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

    2006-10-12

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

  2. 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

  3. Enzyme-catalyzed modification of PES surfaces: reduction in adsorption of BSA, dextrin and tannin.

    PubMed

    Nady, Norhan; Schroën, Karin; Franssen, Maurice C R; Fokkink, Remco; Mohy Eldin, Mohamed S; Zuilhof, Han; Boom, Remko M

    2012-07-15

    Poly(ethersulfone) (PES) can be modified in a flexible manner using mild, environmentally benign components such as 4-hydroxybenzoic acid and gallic acid, which can be attached to the surface via catalysis by the enzyme laccase. This leads to grafting of mostly linear polymeric chains (for 4-hydroxybenzoic acid, and for gallic acid at low concentration and short modification time) and of networks (for gallic acid at high concentration and long exposure time). The reaction is stopped at a specific time, and the modified surfaces are tested for adsorption of BSA, dextrin and tannin using in-situ reflectometry and AFM imaging. At short modification times, the adsorption of BSA, dextrin and tannin is significantly reduced. However, at longer modification times, the adsorption increases again for both substrates. As the contact angle on modified surfaces at short modification times is reduced (indicative of more hydrophilic surfaces), and keeps the same low values at longer modification times, hydrophilicity is not the only determining factor for the measured differences. At longer modification times, intra-layer reactivity will increase the amount of cross-linking (especially for gallic acid), branching (for 4-hydroxybenzoic acid) and/or collapse of the polymer chains. This leads to more compact layers, which leads to increased protein adsorption. The modifications were shown to have clear potential for reduction of fouling by proteins, polysaccharides, and polyphenols, which could be related to the surface morphology.

  4. The reaction mechanism of methyl-coenzyme M reductase: How an enzyme enforces strict binding order

    DOE PAGES

    Wongnate, Thanyaporn; Ragsdale, Stephen W.

    2015-02-17

    Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productivemore » whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(NiI)·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s-1 at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(NiII)·CoB7S-·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. In conclusion, this first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.« less

  5. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order.

    PubMed

    Wongnate, Thanyaporn; Ragsdale, Stephen W

    2015-04-10

    Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.

  6. 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.

  7. 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.

  8. A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates

    SciTech Connect

    Netzel, D.A.

    1991-04-01

    Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center_dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

  9. 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.

  10. 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.

  11. Relative reactivity of alkenyl alcohols in the palladium-catalyzed redox-relay Heck reaction.

    PubMed

    Hilton, Margaret J; Cheng, Bin; Buckley, Benjamin R; Xu, Liping; Wiest, Olaf; Sigman, Matthew S

    2015-09-16

    The relative rates of alkenyl alcohols in the Pd-catalyzed redox-relay Heck reaction were measured in order to examine the effect of their steric and electronic properties on the rate-determining step. Competition experiments between an allylic alkenyl alcohol and two substrates with differing chain lengths revealed that the allylic alcohol reacts 3-4 times faster in either case. Competition between di- and trisubstituted alkenyl alcohols provided an interesting scenario, in which the disubstituted alkene was consumed first followed by reaction of the trisubstituted alkene. Consistent with this observation, the transition structures for the migratory insertion of the aryl group into the di- and trisubstituted alkenes were calculated with a lower barrier for the former. An internal competition between a substrate containing two alcohols with differing chain lengths demonstrated the catalyst's preference for migrating towards the closest alcohol. Additionally, it was observed that increasing the electron density in the arene boronic acid promotes a faster reaction, which correlates with Hammett σp values to give a ρ of -0.87.

  12. Identification of a suitable and selective inhibitor towards aldehyde oxidase catalyzed reactions.

    PubMed

    Nirogi, Ramakrishna; Kandikere, Vishwottam; Palacharla, Raghava Choudary; Bhyrapuneni, Gopinadh; Kanamarlapudi, Vijaya Bhargava; Ponnamaneni, Ranjith Kumar; Manoharan, Arun Kumar

    2014-03-01

    1. Aldehyde oxidase (AO) is a liver cytosolic molybdoflavoprotein enzyme whose importance in drug metabolism is gaining in the recent. The objective of this work is to find a potent and selective inhibitor for AO activity using phthalazine oxidation as a marker reaction. 2. Among organic solvents tested, it was identified that methanol was not a suitable choice for AO activity even at concentrations less than 0.2% v/v. Acetonitrile and DMSO did not show any effect till 0.5% v/v but thereafter activites tend to decrease. 3. For selectivity, 23 compounds were selected and evaluated for their effects on AO and nine CYP450 enzymes. Among the tested compounds chlorpromazine, estradiol, hydralazine, quetiapine and raloxifene were selected based on their potency of inhibition towards AO activity. 4. Raloxifene was found to be a non-specific inhibitor of all major tested CYP450 enzymes and was excluded as a selective inhibitor for AO. Quetiapine also showed a degree of inhibition towards the major CYP450 tested. Hydralazine used as a specific inhibitor during the past for AO activity demonstrated a stimulation of AO activity at high and low concentrations respectively and the inhibition noted to be time dependent while inhibiting other enzymes like monoamine oxidase. 5. Estradiol showed no inhibition towards the tested CYP450 enzymes and thus proved to be a selective and specific inhibitor for AO activity with an uncompetitive mode of inhibition.

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

    PubMed

    Cornil, Johan; Gonnard, Laurine; Bensoussan, Charlélie; Serra-Muns, Anna; Gnamm, Christian; Commandeur, Claude; Commandeur, Malgorzata; Reymond, Sébastien; Guérinot, Amandine; Cossy, Janine

    2015-03-17

    A myriad of natural and/or biologically active products include nitrogen- and oxygen-containing saturated heterocycles, which are thus considered as attractive scaffolds in the drug discovery process. As a consequence, a wide range of reactions has been developed for the construction of these frameworks, much effort being specially devoted to the formation of substituted tetrahydropyrans and piperidines. Among the existing methods to form these heterocycles, the metal-catalyzed heterocyclization of amino- or hydroxy-allylic alcohol derivatives has emerged as a powerful and stereoselective strategy that is particularly interesting in terms of both atom-economy and ecocompatibility. For a long time, palladium catalysts have widely dominated this area either in Tsuji-Trost reactions [Pd(0)] or in an electrophilic activation process [Pd(II)]. More recently, gold-catalyzed formation of saturated N- and O-heterocycles has received growing attention because it generally exhibits high efficiency and diastereoselectivity. Despite their demonstrated utility, Pd- and Au-complexes suffer from high costs, toxicity, and limited natural abundance, which can be barriers to their widespread use in industrial processes. Thus, the replacement of precious metals with less expensive and more environmentally benign catalysts has become a challenging issue for organic chemists. In 2010, our group took advantage of the ability of the low-toxicity and inexpensive FeCl3 in activating allylic or benzylic alcohols to develop iron-catalyzed N- and O-heterocylizations. We first focused on N-heterocycles, and a variety of 2,6-disubstituted piperidines as well as pyrrolidines were synthesized in a highly diastereoselective fashion in favor of the cis-compounds. The reaction was further extended to the construction of substituted tetrahydropyrans. Besides triggering the formation of heterocycles, the iron salts were shown to induce a thermodynamic epimerization, which is the key to reach the high

  14. 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.

  15. 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.

  16. Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

    PubMed

    Ranaghan, Kara E; Ridder, Lars; Szefczyk, Borys; Sokalski, W Andrzej; Hermann, Johannes C; Mulholland, Adrian J

    2004-04-07

    To investigate fundamental features of enzyme catalysis, there is a need for high-level calculations capable of modelling crucial, unstable species such as transition states as they are formed within enzymes. We have modelled an important model enzyme reaction, the Claisen rearrangement of chorismate to prephenate in chorismate mutase, by combined ab initio quantum mechanics/molecular mechanics (QM/MM) methods. The best estimates of the potential energy barrier in the enzyme are 7.4-11.0 kcal mol(-1)(MP2/6-31+G(d)//6-31G(d)/CHARMM22) and 12.7-16.1 kcal mol(-1)(B3LYP/6-311+G(2d,p)//6-31G(d)/CHARMM22), comparable to the experimental estimate of Delta H(++)= 12.7 +/- 0.4 kcal mol(-1). The results provide unequivocal evidence of transition state (TS) stabilization by the enzyme, with contributions from residues Arg90, Arg7, and Arg63. Glu78 stabilizes the prephenate product (relative to substrate), and can also stabilize the TS. Examination of the same pathway in solution (with a variety of continuum models), at the same ab initio levels, allows comparison of the catalyzed and uncatalyzed reactions. Calculated barriers in solution are 28.0 kcal mol(-1)(MP2/6-31+G(d)/PCM) and 24.6 kcal mol(-1)(B3LYP/6-311+G(2d,p)/PCM), comparable to the experimental finding of Delta G(++)= 25.4 kcal mol(-1) and consistent with the experimentally-deduced 10(6)-fold rate acceleration by the enzyme. The substrate is found to be significantly distorted in the enzyme, adopting a structure closer to the transition state, although the degree of compression is less than predicted by lower-level calculations. This apparent substrate strain, or compression, is potentially also catalytically relevant. Solution calculations, however, suggest that the catalytic contribution of this compression may be relatively small. Consideration of the same reaction pathway in solution and in the enzyme, involving reaction from a 'near-attack conformer' of the substrate, indicates that adoption of this

  17. Synergistic effect of two E2 ubiquitin conjugating enzymes in SCFhFBH1 catalyzed polyubiquitination

    PubMed Central

    Choi, Jin Sun; Kim, Sunhong; Kim, Kidae; Myung, Pyung Keun; Park, Sung Goo; Seo, Yeon-Soo; Park, Byoung Chul

    2015-01-01

    Ubiquitination is a post translational modification which mostly links with proteasome dependent protein degradation. This process has been known to play pivotal roles in the number of biological events including apoptosis, cell signaling, transcription and translation. Although the process of ubiquitination has been studied extensively, the mechanism of polyubiquitination by multi protein E3 ubiquitin ligase, SCF complex remains elusive. In the present study, we identified UbcH5a as a novel stimulating factor for poly-ubiquitination catalyzed by SCFhFBH1 using biochemical fractionations and MALDI-TOF. Moreover, we showed that recombinant UbcH5a and Cdc34 synergistically stimulate SCFhFBH1 catalyzed polyubiquitination in vitro. These data may provide an important cue to understand the mechanism how the SCF complex efficiently polyubiquitinates target substrates. [BMB Reports 2015; 48(1): 25-29] PMID:24667174

  18. Palladium-catalyzed cross-coupling reactions of arylsiloxanes with aryl halides: application to solid-supported organic synthesis.

    PubMed

    Traficante, Carla I; Delpiccolo, Carina M L; Mata, Ernesto G

    2014-05-12

    The solid-phase version of the Pd-catalyzed Hiyama reaction between a variety of aryltriethoxysilanes and immobilized aryl halides was developed. Smooth cross-coupling was achieved to afford the corresponding biaryl products in moderate to excellent yields. The described protocol would be particularly useful for the construction of 4'-substituted 1,1'-biphenyl derivatives.

  19. 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.

  20. A General and Highly Selective Cobalt-Catalyzed Hydrogenation of N-Heteroarenes under Mild Reaction Conditions.

    PubMed

    Adam, Rosa; Cabrero-Antonino, Jose R; Spannenberg, Anke; Junge, Kathrin; Jackstell, Ralf; Beller, Matthias

    2017-02-14

    Herein, a general and efficient method for the homogeneous cobalt-catalyzed hydrogenation of N-heterocycles, under mild reaction conditions, is reported. Key to success is the use of the tetradentate ligand tris(2-(diphenylphosphino)phenyl)phosphine). This non-noble metal catalyst system allows the selective hydrogenation of heteroarenes in the presence of a broad range of other sensitive reducible groups.

  1. Mechanistic Studies Lead to Dramatically Improved Reaction Conditions for the Cu-Catalyzed Asymmetric Hydroamination of Olefins

    PubMed Central

    2015-01-01

    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

  2. Of the ortho effect in palladium/norbornene-catalyzed reactions: a theoretical investigation.

    PubMed

    Maestri, Giovanni; Motti, Elena; Della Ca', Nicola; Malacria, Max; Derat, Etienne; Catellani, Marta

    2011-06-08

    Mechanistic questions concerning palladium and norbornene catalyzed aryl-aryl coupling reactions are treated in this paper: how aryl halides react with the intermediate palladacycles, formed by interaction of the two catalysts with an aryl halide, and what is the rational explanation of the "ortho effect" (caused by an ortho substituent in the starting aryl halide), which leads to aryl-aryl coupling with a second molecule of aryl halide rather than to aryl-norbornyl coupling. Two possible pathways have been proposed, one involving aryl halide oxidative addition to the palladacycle, the other passing through a palladium(II) transmetalation, also involving the palladacycle, as previously proposed by Cardenas and Echavarren. Our DFT calculations using M06 show that, in palladium-catalyzed reaction of aryl halides, not containing ortho substituents, and norbornene, the intermediate palladacycle formed has a good probability to undergo transmetalation, energetically favored over the oxidative addition leading to Pd(IV). The unselective sp(2)-sp(2) and sp(2)-sp(3) coupling, experimentally observed in this case, can be explained in the framework of the transmetalation pathway since the energetic difference between aryl attack onto the aryl or norbornyl carbon of the palladacycle intermediate is quite small. On the other hand, according to the experimentally observed "ortho effect", selective aryl-aryl coupling only occurs in the reactions of ortho-substituted metallacycles. The present work offers the first possible rationalization of this finding. These in situ formed palladacycles containing an ortho substituent could more easily undergo oxidative addition of an aryl halide rather than reductive elimination from the transmetalation intermediate as a result of a steric clash in the transition state of the latter. The now energetically accessible Pd(IV) intermediate, featuring a Y-distorted trigonal bipyramidal structure, can account for the reported selective aryl

  3. 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.

  4. Iodine-catalyzed disproportionation of aryl-substituted ethers under solvent-free reaction conditions.

    PubMed

    Jereb, Marjan; Vražič, Dejan

    2013-03-28

    Iodine was demonstrated to be an efficient catalyst for disproportionation of aryl-substituted ethers under solvent-free reaction conditions. Variously substituted 1,1,1',1'-tetraaryldimethyl ethers were transformed into the corresponding diarylketone and diarylmethane derivatives. I2-catalyzed transformation of 4-methoxyphenyl substituted ethers yielded mono- and dialkylated Friedel-Crafts products as well. Treatment of trityl alkyl and trityl benzyl ethers with a catalytic amount of iodine produced triphenylmethane and the corresponding aldehydes and ketones. The electron-donating substituents facilitated the reaction, while the electron-withdrawing groups retarded it; the difference in reactivity is not very high. Such an observation may be in favour of hydride transfer, predominantly from the less electron rich side of the ether with more stable carbocation formation. With the isotopic studies it was established that a substantial portion of the C-H bond scission took place in the rate-determining step, while the carbonyl oxygen atom originated from the starting ether, and not from the air. The transformation took place under air and under argon, and HI was not a functioning catalyst.

  5. 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

  6. Kinetic resolution of racemic 1-phenyl 1-propanol by lipase catalyzed enantioselective esterification reaction.

    PubMed

    Karadeniz, Fatma; Bayraktar, Emine; Mehmetoglu, Ulkü

    2010-10-01

    In this study, resolution of (R,S)-1-phenyl 1-propanol by lipase-catalyzed enantioselective esterification was achieved. To investigate the effect of lipase type on enantiomeric excess, three different lipases were used. Novozym 435 exhibited the highest enantioselectivity for resolution of (R,S)-1-phenyl 1-propanol. The effects of carbon length of fatty acids from C12 to C16, which were used as acyl donor, organic solvents with Log P values from 0.5 to 4.5, acyl donor/alcohol molar ratio (1:1, 3:2, 2:1, 3:1), amount of added molecular sieves (0-133.2 kg/m(3)), and temperature (10-60° C) on the enantioselectivity were investigated. The best reaction conditions were comprised of using toluene (Log P= 2.5) as solvent, lauric acid (12C) as acyl donor, 133.2 kg/m(3) molecular sieves at 50° C and acyl donor/alcohol molar ratio as 1:1. Under these conditions, the enantiomeric excess of S enantiomer ee (S) was obtained as 95% for a reaction time of 2.5 hours.

  7. 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.

  8. Scope and Mechanisms of Frustrated Lewis Pair Catalyzed Hydrogenation Reactions of Electron-Deficient C=C Double Bonds.

    PubMed

    Morozova, Varvara; Mayer, Peter; Berionni, Guillaume

    2015-11-23

    Several phosphonium and ammonium triarylborohydrides, which are intermediates in hydrogenation reactions catalyzed by frustrated Lewis pairs, were synthesized in high yield under mild conditions from triaryl boranes, ammonium or phosphonium halides, and triethylsilane. The kinetics and mechanisms of the reactions of these hydridoborate salts with benzhydrylium ions, iminium ions, quinone methides, and Michael acceptors were investigated, and their nucleophilicity was determined and compared with that of other hydride donors.

  9. An approach to the synthesis of dimeric resveratrol natural products via a palladium-catalyzed domino reaction

    PubMed Central

    Jeffrey, Jenna L.; Sarpong, Richmond

    2009-01-01

    A route for the rapid assembly of the carbon framework of several resveratrol natural products is presented. A palladium-catalyzed domino reaction of bromostilbene derivative 6 and tolane 7, involving two sequential Heck coupling reactions, provides access to the benzofulvene-based core of various resveratrol-derived natural products. The carbon skeleton of pallidol and its congeners is achieved by a Lewis acid-induced Nazarov-type oxidative cyclization of 9. PMID:20161322

  10. 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.

  11. A novel synthesis of 2-aryl-2H-indazoles via a palladium-catalyzed intramolecular amination reaction.

    PubMed

    Song, J J; Yee, N K

    2000-02-24

    [reaction: see text] A variety of 2-aryl-2H-indazoles were synthesized by the palladium-catalyzed intramolecular amination of the corresponding N-aryl-N(o-bromobenzyl)hydrazines. Of several sets of reaction conditions surveyed, the combination of Pd(OAc)2/dppf/tBuONa gave the best results. This method applies to a wide scope of substrates containing electron-donating and electron-withdrawing substituents.

  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. 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

  14. Enantioselective Lewis acid-catalyzed Mukaiyama-Michael reactions of acyclic enones. Catalysis by allo-threonine-derived oxazaborolidinones.

    PubMed

    Wang, Xiaowei; Adachi, Shinya; Iwai, Hiroyoshi; Takatsuki, Hiroshi; Fujita, Katsuhiro; Kubo, Mikako; Oku, Akira; Harada, Toshiro

    2003-12-26

    allo-Threonine-derived O-aroyl-B-phenyl-N-tosyl-1,3,2-oxazaborolidin-5-ones 1g,n catalyze the asymmetric Mukaiyama-Michael reaction of acyclic enones with a trimethylsilyl ketene S,O-acetal in high enantioselectivity. A range of alkenyl methyl ketones is successfully employed as Michael acceptors affording ee values of 85-90% by using 10 mol % of the catalyst. The use of 2,6-diisopropylphenol and tert-butyl methyl ether as additives is found to be essential to achieve high enantioselectivity in these reactions. The effects of the additives are discussed in terms of the retardation of an Si(+)-catalyzed racemic pathway, which seriously deteriorates the enantioselectivity of asymmetric Mukaiyama-Michael reactions. A working model for asymmetric induction is proposed based on correlation between catalyst structures and enantioselectivities.

  15. Impact of copper-catalyzed cross-coupling reactions in natural product synthesis: the emergence of new retrosynthetic paradigms.

    PubMed

    Evano, Gwilherm; Theunissen, Cédric; Pradal, Alexandre

    2013-12-01

    Copper-catalyzed Ullmann-Goldberg-type cross-coupling reactions have undergone nothing short of a renaissance over the last decade and an impressive number of procedures are now available for the formation of C-N, C-O and C-S bonds with remarkable efficiencies and surgical precision. These reactions have been recently integrated into natural product synthesis, which clearly resulted in the emergence of new retrosynthetic paradigms and bond disconnections. The impact of copper-catalyzed cross-coupling reactions in natural product synthesis will be overviewed in this article with an emphasis on the evolution of strategies due to copper catalysis, mostly by comparison with alternative tactics and their relative efficiencies.

  16. 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

  17. Reaction mechanism for cocaine esterase-catalyzed hydrolyses of (+)- and (-)-cocaine: unexpected common rate-determining step.

    PubMed

    Liu, Junjun; Zhao, Xinyun; Yang, Wenchao; Zhan, Chang-Guo

    2011-05-05

    First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to examine the catalytic mechanism for cocaine esterase (CocE)-catalyzed hydrolysis of (+)-cocaine in comparison with CocE-catalyzed hydrolysis of (-)-cocaine. It has been shown that the acylation of (+)-cocaine consists of nucleophilic attack of the hydroxyl group of Ser117 on the carbonyl carbon of (+)-cocaine benzoyl ester and the dissociation of (+)-cocaine benzoyl ester. The first reaction step of deacylation of (+)-cocaine, which is identical to that of (-)-cocaine, is rate-determining, indicating that CocE-catalyzed hydrolyses of (+)- and (-)-cocaine have a common rate-determining step. The computational results predict that the catalytic rate constant of CocE against (+)-cocaine should be the same as that of CocE against (-)-cocaine, in contrast with the remarkable difference between human butyrylcholinesterase-catalyzed hydrolyses of (+)- and (-)-cocaine. The prediction has been confirmed by experimental kinetic analysis on CocE-catalyzed hydrolysis of (+)-cocaine in comparison with CocE-catalyzed hydrolysis of (-)-cocaine. The determined common rate-determining step indicates that rational design of a high-activity mutant of CocE should be focused on the first reaction step of the deacylation. Furthermore, the obtained mechanistic insights into the detailed differences in the acylation between the (+)- and (-)-cocaine hydrolyses provide indirect clues for rational design of amino acid mutations that could more favorably stabilize the rate-determining transition state in the deacylation and, thus, improve the catalytic activity of CocE. This study provides a valuable mechanistic base for rational design of an improved esterase for therapeutic treatment of cocaine abuse.

  18. Mechanism of an Organoboron-Catalyzed Domino Reaction: Kinetic and Computational Studies of Borinic Acid-Catalyzed Regioselective Chloroacylation of 2,3-Epoxy Alcohols.

    PubMed

    Garrett, Graham E; Tanveer, Kashif; Taylor, Mark S

    2017-01-20

    A mechanistic study of the borinic acid-catalyzed chloroacylation of 2,3-epoxy alcohols is presented. In this unusual mode of catalysis, the borinic acid activates the substrate toward sequential reactions with a nucleophile (epoxide ring-opening by chloride) and an electrophile (O-acylation of the resulting alkoxide). Reaction progress kinetic analysis of data obtained through in situ FTIR spectroscopy is consistent with a mechanism involving turnover-limiting acylation of a chlorohydrin-derived borinic ester. This proposal is further supported by investigations of the effects of aroyl chloride substitution on reaction rate. The kinetics experiments also shed light on the effects of chloride concentration on reaction rate and indicate that the catalyst is subject to inhibition by the product of the chloroacylation reaction. Computational modeling is employed to gain insight into the effects of the organoboron catalyst on the regioselectivities of the epoxide ring-opening and acylation steps. The density functional theory calculations provide a plausible pathway for selective chlorinolysis at C-3 and benzoylation at O-1, as is observed experimentally.

  19. A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase

    SciTech Connect

    Lyubimov, Artem Y.; Chen, Lin; Sampson, Nicole S.; Vrielink, Alice

    2009-11-01

    The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine. Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k{sub cat}. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

  20. Synthesis of Active Hexafluoroisopropyl Benzoates through a Hydrogen-Bond-Enabled Palladium(II)-Catalyzed C-H Alkoxycarbonylation Reaction.

    PubMed

    Wang, Yang; Gevorgyan, Vladimir

    2017-03-13

    A Pd(II) -catalyzed ortho C-H alkoxycarbonylation reaction of aryl silanes toward active hexafluoroisopropyl (HFIP) benzoate esters has been developed. This efficient reaction features high selectivity and good functional-group tolerance. Notably, given the general nature of the silyl-tethered directing group, this method delivers products bearing two independently modifiable sites. NMR studies reveal the presence of hydrogen bonding between HFIP and a pyrimidine nitrogen atom of the directing group, and it is thought to be crucial for the success of this alkoxycarbonylation reaction.

  1. N-tosyloxycarbamates as a source of metal nitrenes: rhodium-catalyzed C-H insertion and aziridination reactions.

    PubMed

    Lebel, Hélène; Huard, Kim; Lectard, Sylvain

    2005-10-19

    The rhodium-catalyzed decomposition of N-tosyloxycarbamates to generate metal nitrenes which undergo intramolecular C-H insertion or aziridination reaction is described. Aliphatic N-tosyloxycarbamates produce oxazolidinones with high yields and stereospecificity through insertion in benzylic, tertiary, and secondary C-H bonds. Intramolecular aziridination occurs with allylic N-tosyloxycarbamates to produce aziridines as single diastereomers. The reaction proceeds at room temperature using a rhodium catalyst and an excess of potassium carbonate and does not require the use of strong oxidant, such as hypervalent iodine reagents. A rhodium nitrene species is presumably involved, as both reactions are stereospecific.

  2. 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.

  3. 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.

  4. 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.

  5. Synthesis of Octyl-β-Glucoside Catalyzed by Almond β-Glucosidase in Unconventional Reaction Media

    PubMed Central

    2016-01-01

    Summary The reaction system for octyl-β-glucoside synthesis catalysed by the almond-β-glucosidase has been characterised. The monophasic octanol saturated with different amounts of water served as a reaction medium. Both the glucose and the activated substrate p-nitrophenyl-β-glucoside were examined as glycon donors. The reverse hydrolysis and the transglycosylation were both used as reaction models for this enzymatically catalysed alkyl-β-glucoside synthesis. The rate of synthesis of octyl-β-glucoside (vS), the rate of hydrolysis, i.e. the glucose formation (vH) and the predicted yield (Y) were determined. The effect of water activity on the synthetic and hydrolytic activity of the enzyme was investigated. Both the rate of synthesis and the rate of hydrolysis increased with the increase of the water activity in the reaction system, showing their maximum values at the water activity close to the saturation level. Thus, the maximum ratio of vS/vH=0.165 was achieved at the water activity of 0.94. The predicted yields were 0.5, 0.75 and 14.19% and were lower than the actually achieved yields of 19.45, 38 and 36.40% at the water activities of 0.75, 0.84 and 0.94, respectively. The yield of octyl-β-glucoside in the reverse hydrolysis was only 15.2%, i.e. 3.25 times lower than the yield obtained in the transglycosylation reaction with the water activity of 0.94. The solubility of glucose in pure octanol was only 1.5 mmol/L at the saturation level of 12 mmol/L in the presence of 10 mmol/L of p-nitrophenyl-β-glucoside, and it increased to 15.5 mmol/L in the presence of octyl-β-glucoside. PMID:27904411

  6. Assessment of theoretical procedures for calculating barrier heights for a diverse set of water-catalyzed proton-transfer reactions.

    PubMed

    Karton, Amir; O'Reilly, Robert J; Radom, Leo

    2012-04-26

    Accurate electronic barrier heights are obtained for a set of nine proton-transfer tautomerization reactions, which are either (i) uncatalyzed, (ii) catalyzed by one water molecule, or (iii) catalyzed by two water molecules. The barrier heights for reactions (i) and (ii) are obtained by means of the high-level ab initio W2.2 thermochemical protocol, while those for reaction (iii) are obtained using the W1 protocol. These three sets of benchmark barrier heights allow an assessment of the performance of more approximate theoretical procedures for the calculation of barrier heights of uncatalyzed and water-catalyzed reactions. We evaluate initially the performance of the composite G4 procedure and variants thereof (e.g., G4(MP2) and G4(MP2)-6X), as well as that of standard ab initio procedures (e.g., MP2, SCS-MP2, and MP4). We find that the performance of the G4(MP2)-type thermochemical procedures deteriorates with the number of water molecules involved in the catalysis. This behavior is linked to deficiencies in the MP2-based basis-set-correction term in the G4(MP2)-type procedures. This is remedied in the MP4-based G4 procedure, which shows good performance for both the uncatalyzed and the water-catalyzed reactions, with mean absolute deviations (MADs) from the benchmark values lying below the threshold of "chemical accuracy" (arbitrarily defined as 1 kcal mol(-1) ≈ 4.2 kJ mol(-1)). We also examine the performance of a large number of density functional theory (DFT) and double-hybrid DFT (DHDFT) procedures. We find that, with few exceptions (most notably PW6-B95 and B97-2), the performance of the DFT procedures that give good results for the uncatalyzed reactions deteriorates with the number of water molecules involved in the catalysis. The DHDFT procedures, on the other hand, show excellent performance for both the uncatalyzed and catalyzed reactions. Specifically, almost all of them afford MADs below the "chemical accuracy" threshold, with ROB2-PLYP and B2K

  7. Intensification of heterogeneously catalyzed Suzuki-Miyaura cross-coupling reaction using ultrasound: Understanding effect of operating parameters.

    PubMed

    Sancheti, Sonam V; Gogate, Parag R

    2017-01-27

    Palladium-catalyzed Suzuki-Miyaura cross-coupling reaction is a significant reaction for obtaining industrially important products. The current research work deals with intensification of reaction of 4-bromoanisole and phenylboronic acid catalyzed with 5wt% Pd/C (5% by weight Pd supported on C available as commercial catalyst) using ultrasound and more importantly, without use of any additional phase transfer catalyst. Heterogeneous catalyst has been selected in the present work so as to harness the benefits of easy separation and the possible limitations of heterogeneous operation are minimized by introducing ultrasonic irradiations. The effect of operating parameters such as ultrasound power, temperature, catalyst loading and molar ratio on the progress of reaction has been investigated. It has been observed that an optimum power, temperature and catalyst loading exist for maximum benefits whereas higher molar ratio was found to be favourable for the progress of the reaction. Also, the use of ultrasound reduced the reaction time from 70min required in conventional approach to only 35min under conditions of frequency of 22kHz, power dissipation of 40W and catalyst loading as 1.5mol% (refers to total quantum of catalyst used in the work) in ethanol-water system under ambient conditions. The work also demonstrated successful results at ten times higher volume as compared to the normally used volumes in the case of simple ultrasonic horn. Overall, the work has successfully demonstrated process intensification benefits obtained due to the use of ultrasound for heterogeneously catalyzed Suzuki-Miyaura cross-coupling reaction.

  8. The reaction mechanism of methyl-coenzyme M reductase: How an enzyme enforces strict binding order

    SciTech Connect

    Wongnate, Thanyaporn; Ragsdale, Stephen W.

    2015-02-17

    Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(NiI)·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s-1 at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(NiII)·CoB7S-·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. In conclusion, this first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.

  9. Rhodium-catalyzed [(3+2)+1] carbocyclization reactions of alkynylidenecyclopropanes with carbon monoxide: regiospecific construction of polysubstituted phenols.

    PubMed

    Evans, P Andrew; Burnie, Andrew J; Negru, Daniela E

    2014-09-05

    The development of the rhodium-catalyzed [(3+2)+1] carbocyclization reaction of alkynylidenecyclopropanes with carbon monoxide to construct polysubstituted phenols is described. This work offers a convenient method for the selective formation of tetra- and pentasubstituted phenols, which provide important intermediates for target directed synthesis. Finally, the ability to regiospecifically functionalize the phenols using conventional methods further illustrates the utility of this process.

  10. Lewis acid catalyzed cascade reaction of 3-(2-benzenesulfonamide)propargylic alcohols to spiro[indene-benzosultam]s.

    PubMed

    Sun, Lang; Zhu, Yuanxun; Wang, Jing; Lu, Ping; Wang, Yanguang

    2015-01-16

    A highly efficient and convenient construction of the spiro[indene-benzosultam] skeleton from propargylic alcohols has been developed. The reaction proceeded in a Lewis acid catalyzed cascade process, including the trapping of allene carbocation with sulfonamide, electrophilic cyclization, and intramolecular Friedel-Crafts alkylation. In the presence of NIS or NBS, iodo/bromo-substituted spiro[indene-benzosultam]s could be prepared in excellent yields.

  11. Fluorination Enables a Ligand-Controlled Regiodivergent Palladium-Catalyzed Decarboxylative Allylation Reaction to Access α,α-Difluoroketones

    PubMed Central

    Yang, Ming–Hsiu; Orsi, Douglas L.

    2015-01-01

    α,α-Difluoroketones possess unique physicochemical properties that are useful for developing therapeutics and probes for chemical biology. In order to access the α-allyl-α,α-difluoroketone substructure, complementary Pd-catalyzed decarboxylative allylation reactions were developed to provide linear and branched α-allyl-α,α-difluoroketones. For these orthogonal processes, the regioselectivity was uniquely controlled by fluorination of the substrate and the structure of ligand. PMID:25581845

  12. Recent Advances in Recoverable Systems for the Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction (CuAAC).

    PubMed

    Mandoli, Alessandro

    2016-09-05

    The explosively-growing applications of the Cu-catalyzed Huisgen 1,3-dipolar cycloaddition reaction between organic azides and alkynes (CuAAC) have stimulated an impressive number of reports, in the last years, focusing on recoverable variants of the homogeneous or quasi-homogeneous catalysts. Recent advances in the field are reviewed, with particular emphasis on systems immobilized onto polymeric organic or inorganic supports.

  13. 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.

  14. Ni(II) Tol-BINAP-catalyzed enantioselective Michael reactions of beta-ketoesters and unsaturated N-acylthiazolidinethiones.

    PubMed

    Evans, David A; Thomson, Regan J; Franco, Francisco

    2005-08-10

    The enantioselective addition of beta-ketoesters to unsaturated N-acylthiazolidinethiones catalyzed by Ni(II) Tol-BINAP Lewis acid complexes is reported. Notable features of this reaction are its operation simplicity, the obviated need for the addition of an external base, and the ease with which the adducts are converted into a range of potentially useful derivatives. In particular, the dihydropyrone adducts are versatile scaffolds for further stereoselective elaboration.

  15. 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.

  16. Energy-Related Small Molecule Activation Reactions: Oxygen Reduction and Hydrogen and Oxygen Evolution Reactions Catalyzed by Porphyrin- and Corrole-Based Systems.

    PubMed

    Zhang, Wei; Lai, Wenzhen; Cao, Rui

    2017-02-22

    Globally increasing energy demands and environmental concerns related to the use of fossil fuels have stimulated extensive research to identify new energy systems and economies that are sustainable, clean, low cost, and environmentally benign. Hydrogen generation from solar-driven water splitting is a promising strategy to store solar energy in chemical bonds. The subsequent combustion of hydrogen in fuel cells produces electric energy, and the only exhaust is water. These two reactions compose an ideal process to provide clean and sustainable energy. In such a process, a hydrogen evolution reaction (HER), an oxygen evolution reaction (OER) during water splitting, and an oxygen reduction reaction (ORR) as a fuel cell cathodic reaction are key steps that affect the efficiency of the overall energy conversion. Catalysts play key roles in this process by improving the kinetics of these reactions. Porphyrin-based and corrole-based systems are versatile and can efficiently catalyze the ORR, OER, and HER. Because of the significance of energy-related small molecule activation, this review covers recent progress in hydrogen evolution, oxygen evolution, and oxygen reduction reactions catalyzed by porphyrins and corroles.

  17. Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

    PubMed Central

    Świderek, Katarzyna; Tuñón, Iñaki; Martí, Sergio; Moliner, Vicent

    2015-01-01

    In the last decade L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed from the 80s that the full catalytic process of LDH starts with the binding of the cofactor and the substrate followed by the enclosure of the active site by a mobile loop of the protein before the reaction to take place. In this paper we show that the chemical step of the LDH catalyzed reaction can proceed within the open loop conformation, and the different reactivity of the different protein conformations would be in agreement with the broad range of rate constants measured in single molecule spectrometry studies. Starting from a recently solved X-ray diffraction structure that presented an open loop conformation in two of the four chains of the tetramer, QM/MM free energy surfaces have been obtained at different levels of theory. Depending on the level of theory used to describe the electronic structure, the free energy barrier for the transformation of pyruvate into lactate with the open conformation of the protein varies between 12.9 and 16.3 kcal/mol, after quantizing the vibrations and adding the contributions of recrossing and tunneling effects. These values are very close to the experimentally deduced one (14.2 kcal·mol−1) and ~2 kcal·mol−1 smaller than the ones obtained with the closed loop conformer. Calculation of primary KIEs and IR spectra in both protein conformations are also consistent with our hypothesis and in agreement with experimental data. Our calculations suggest that the closure of the active site is mainly required for the inverse process; the oxidation of lactate to pyruvate. According to this hypothesis H4 type LDH enzyme molecules, where it has been propose that lactate is transformed into pyruvate, should have a better ability to close the mobile loop than the M4 type LDH molecules. PMID:25705562

  18. Palladium-catalyzed carbonylation reaction of aryl bromides with 2-hydroxyacetophenones to form flavones.

    PubMed

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

    2012-10-01

    Flavone of the month: a general and efficient method for the palladium-catalyzed carbonylative synthesis of flavones has been developed. Starting from aryl bromides and 2-hydroxyacetophenones, the corresponding flavones have been isolated in good yields.

  19. Synthesis of steroid-ferrocene conjugates of steroidal 17-carboxamides via a palladium-catalyzed aminocarbonylation--copper-catalyzed azide-alkyne cycloaddition reaction sequence.

    PubMed

    Szánti-Pintér, Eszter; Balogh, János; Csók, Zsolt; Kollár, László; Gömöry, Agnes; Skoda-Földes, Rita

    2011-11-01

    Steroids with the 17-iodo-16-ene functionality were converted to ferrocene labeled steroidal 17-carboxamides via a two step reaction sequence. The first step involved the palladium-catalyzed aminocarbonylation of the alkenyl iodides with prop-2-yn-1-amine as the nucleophile in the presence of the Pd(OAc)(2)/PPh(3) catalyst system. In the second step, the product N-(prop-2-ynyl)-carboxamides underwent a facile azide-alkyne cycloaddition with ferrocenyl azides in the presence of CuSO(4)/sodium ascorbate to produce the steroid-ferrocene conjugates. The new compounds were obtained in good yield and were characterized by (1)H and (13)C NMR, IR, MS and elemental analysis.

  20. Mechanistic insights into the rhenium-catalyzed alcohol-to-olefin dehydration reaction.

    PubMed

    Korstanje, Ties J; Jastrzebski, Johann T B H; Klein Gebbink, Robertus J M

    2013-09-23

    Rhenium-based complexes are powerful catalysts for the dehydration of various alcohols to the corresponding olefins. Here, we report on both experimental and theoretical (DFT) studies into the mechanism of the rhenium-catalyzed dehydration of alcohols to olefins in general, and the methyltrioxorhenium-catalyzed dehydration of 1-phenylethanol to styrene in particular. The experimental and theoretical studies are in good agreement, both showing the involvement of several proton transfers, and of a carbenium ion intermediate in the catalytic cycle.

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

    PubMed

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

    2014-08-20

    Only a few techniques, such as quartz crystal microbalance and surface plasmon resonance spectroscopy, enable the analysis of dynamic processes on solid supports. Here we have developed a straightforward assay based on flow cytometry to continuously follow enzymatic reactions directly on microparticle surfaces. We applied this real-time flow cytometry (RT-FCM) approach to study the covalent immobilization of green-fluorescent protein (GFPuv) on triglycine-modified polystyrene microbeads by the transpeptidase sortase A (SrtA) from Staphylococcus aureus. Though commonly treated as functionally identical catalysts, the SrtA variants SrtAΔ₅₉ and SrtAΔ₂₅, in which the N-terminal amino acid residues 1-59 and 1-25 of the native enzyme are truncated, were shown to perform very differently with regard to this particular immobilization reaction. While SrtAΔ₅₉ efficiently catalyzed the covalent attachment of GFPuv to the surface (as indicated by a linear increase of microbead fluorescence), SrtAΔ₂₅ was essentially inactive. Besides the length of the N-terminal amino acid extension on the SrtA construct, the position of the hexahistidine tag at either the N- or C-terminus affected the efficiency of enzymatic protein immobilization. Apart from three enzyme variants containing the native core structure of SrtA, we also included three recently evolved mutants of SrtA in this comparative study. With these mutants we observed a rapid initial attachment of the GFPuv target protein to the microbeads. However, with proceeding reaction time, cleavage of the covalently immobilized target protein from the surface prevailed over the coupling reaction, consequently causing a decline of microbead fluorescence. In general, the RT-FCM approach used herein represents a powerful analytical tool for qualitative dynamic studies of many heterogeneous enzymatic reactions or other binding events that influence the fluorescence properties of microparticle surfaces.

  2. An Improved Method for Studying the Enzyme-Catalyzed Oxidation of Glucose Using Luminescent Probes

    ERIC Educational Resources Information Center

    Bare, William D.; Pham, Chi V.; Cuber, Matthew; Demas, J. N.

    2007-01-01

    A new method is presented for measuring the rate of the oxidation of glucose in the presence of glucose oxidase. The improved method employs luminescence measurements to directly determine the concentration of oxygen in real time, thus obviating complicated reaction schemes employed in previous methods. Our method has been used to determine…

  3. Rh-Catalyzed reductive Mannich-type reaction and its application towards the synthesis of (±)-ezetimibe

    PubMed Central

    Isoda, Motoyuki; Sato, Kazuyuki; Kunugi, Yurika; Tokonishi, Satsuki; Tarui, Atsushi; Minami, Hideki

    2016-01-01

    Summary An effective synthesis for syn-β-lactams was achieved using a Rh-catalyzed reductive Mannich-type reaction. A rhodium–hydride complex (Rh–H) derived from diethylzinc (Et2Zn) and a Rh catalyst was used for the 1,4-reduction of an α,β-unsaturated ester to give a Reformatsky-type reagent, which in turn, reacted with an imine to give the syn-β-lactam. Additionally, the reaction was applied to the synthesis of (±)-ezetimibe, a potent β-lactamic cholesterol absorption inhibitor. PMID:27559413

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

    PubMed Central

    Smyslova, Petra; Popa, Igor; Lyčka, Antonín; Tejral, Gracian; Hlavac, Jan

    2015-01-01

    Copper-free click reactions between a dibenzoazocine derivative and azides derived from 5-methyluridine were investigated. The non-catalyzed reaction yielded both regioisomers in an approximately equivalent ratio. The NMR spectra of each regioisomer revealed conformational isomery. The ratio of isomers was dependent on the type of regioisomer and the type of solvent. The synthesis of various analogs, a detailed NMR study and computational modeling provided evidence that the isomery was dependent on the interaction of the azocine and pyrimidine parts. PMID:26673606

  5. Mild Cu(I)-catalyzed cascade reaction of cyclic diaryliodoniums, sodium azide, and alkynes: efficient synthesis of triazolophenanthridines.

    PubMed

    Liu, Zhenquan; Zhu, Daqian; Luo, Bingling; Zhang, Naiyuan; Liu, Qi; Hu, Yumin; Pi, Rongbiao; Huang, Peng; Wen, Shijun

    2014-11-07

    Linear iodoniums are widely used as arylating reagents. However, cyclic diaryl idodoniums are ignored despite their potential to initiate dual arylations, atom and step economically. In our current work, a three-component cascade reaction of cyclic diaryliodoniums, sodium azide, and alkynes has been successfully achieved under mild conditions, catalyzed by cheap copper species. The regioselectivity associated with unsymmetrical iodoniums was enhanced by installing two methyls ortho and para to the I(III) center. The reaction enables a rapid access to a variety of complex molecules, triazolophenanthridine derivatives.

  6. Solvent- and ligand-induced switch of selectivity in gold(I)-catalyzed tandem reactions of 3-propargylindoles

    PubMed Central

    Álvarez, Estela; Miguel, Delia; García-García, Patricia; Fernández-Rodríguez, Manuel A; Rodríguez, Félix

    2011-01-01

    Summary The selectivity of our previously described gold-catalyzed tandem reaction, 1,2-indole migration followed by aura-iso-Nazarov cyclization, of 3-propargylindoles bearing (hetero)aromatic substituents at both the propargylic and terminal positions, was reversed by the proper choice of the catalyst and the reaction conditions. Thus, 3-(inden-2-yl)indoles, derived from an aura-Nazarov cyclization (instead of an aura-iso-Nazarov cyclization), were obtained in moderate to good yields from a variety of 3-propargylindoles. PMID:21804873

  7. Bidentate Lewis Acid Catalyzed Domino Diels-Alder Reaction of Phthalazine for the Synthesis of Bridged Oligocyclic Tetrahydronaphthalenes.

    PubMed

    Schweighauser, Luca; Bodoky, Ina; Kessler, Simon N; Häussinger, Daniel; Donsbach, Carsten; Wegner, Hermann A

    2016-03-18

    A domino process consisting of an inverse and a normal electron-demand Diels-Alder reaction is presented for the formation of bridged tri- and tetracyclic 1,2,3,4-tetrahydronaphthalenes catalyzed by a bidentate Lewis acid. The products were synthesized in a one-pot reaction from commercially available starting materials and contain up to six stereogenic centers. The tetrahydronaphthalenes were isolated as single diastereomers and are derivatives of phenylethylamine, which is well-known as a scaffold of amphetamine or dopamine.

  8. Synthesis of Symmetric Bis(N-alkylaniline)triarylmethanes via Friedel-Crafts-Catalyzed Reaction between Secondary Anilines and Aldehydes.

    PubMed

    Gomes, Rafael F A; Coelho, Jaime A S; Frade, Raquel F M; Trindade, Alexandre F; Afonso, Carlos A M

    2015-10-16

    The first general protocol for the preparation of symmetric triarylmethanes bearing secondary anilines by ytterbium-catalyzed Friedel-Crafts reaction of hetero(aryl) aldehydes and secondary anilines is reported. Mechanistic studies indicated that the iminium ion intermediate is the electrophilic partner. The reaction is greatly accelerated by high pressure (9 kbar) and showed a broad substrate scope on the hetero(aryl) aldehyde. The new triarylmethanes exhibited activity against HT-29 cancer cell lines, with the best result scoring an IC50 of 1.74 μM.

  9. The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions.

    PubMed

    Hartmann, Tobias; Schrapers, Peer; Utesch, Tillmann; Nimtz, Manfred; Rippers, Yvonne; Dau, Holger; Mroginski, Maria Andrea; Haumann, Michael; Leimkühler, Silke

    2016-04-26

    Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal-containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pKa of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase.

  10. The Role of Metals in the Reaction Catalyzed by Metal-Ion-Independent Bacillary RNase

    PubMed Central

    Ulyanova, Vera; Zelenikhin, Pavel; Kolpakov, Alexey; Blokhin, Dmitriy; Müller, Dieter; Klochkov, Vladimir; Ilinskaya, Olga

    2016-01-01

    Extracellular enzymes of intestinal microbiota are the key agents that affect functional activity of the body as they directly interact with epithelial and immune cells. Several species of the Bacillus genus, like Bacillus pumilus, a common producer of extracellular RNase binase, can populate the intestinal microbiome as a colonizing organism. Without involving metal ions as cofactors, binase depolymerizes RNA by cleaving the 3′,5′-phosphodiester bond and generates 2′,3′-cyclic guanosine phosphates in the first stage of a catalytic reaction. Maintained in the reaction mixture for more than one hour, such messengers can affect the human intestinal microflora and the human body. In the present study, we found that the rate of 2′,3′-cGMP was growing in the presence of transition metals that stabilized the RNA structure. At the same time, transition metal ions only marginally reduced the amount of 2′,3′-cGMP, blocking binase recognition sites of guanine at N7 of nucleophilic purine bases. PMID:28096759

  11. Evidence of kinetic control of ligand binding and staged product release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed reactions .

    PubMed

    Jackson, Sean G; Zhang, Fuzhong; Chindemi, Paul; Junop, Murray S; Berti, Paul J

    2009-12-15

    MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k(cat)/K(M) of 520 M(-1) s(-1), was far slower than the normal reaction, and 3 x 10(5)-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new "staged" MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA.ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA.UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA.

  12. Silylium ion-catalyzed challenging Diels-Alder reactions: the danger of hidden proton catalysis with strong Lewis acids.

    PubMed

    Schmidt, Ruth K; Müther, Kristine; Mück-Lichtenfeld, Christian; Grimme, Stefan; Oestreich, Martin

    2012-03-07

    The pronounced Lewis acidity of tricoordinate silicon cations brings about unusual reactivity in Lewis acid catalysis. The downside of catalysis with strong Lewis acids is, though, that these do have the potential to mediate the formation of protons by various mechanisms, and the thus released Brønsted acid might even outcompete the Lewis acid as the true catalyst. That is an often ignored point. One way of eliminating a hidden proton-catalyzed pathway is to add a proton scavenger. The low-temperature Diels-Alder reactions catalyzed by our ferrocene-stabilized silicon cation are such a case where the possibility of proton catalysis must be meticulously examined. Addition of the common hindered base 2,6-di-tert-butylpyridine resulted, however, in slow decomposition along with formation of the corresponding pyridinium ion. Quantitative deprotonation of the silicon cation was observed with more basic (Mes)(3)P to yield the phosphonium ion. A deuterium-labeling experiment verified that the proton is abstracted from the ferrocene backbone. A reasonable mechanism of the proton formation is proposed on the basis of quantum-chemical calculations. This is, admittedly, a particular case but suggests that the use of proton scavengers must be carefully scrutinized, as proton formation might be provoked rather than prevented. Proton-catalyzed Diels-Alder reactions are not well-documented in the literature, and a representative survey employing TfOH is included here. The outcome of these catalyses is compared with our silylium ion-catalyzed Diels-Alder reactions, thereby clearly corroborating that hidden Brønsted acid catalysis is not operating with our Lewis acid. Several simple-looking but challenging Diels-Alder reactions with exceptionally rare dienophile/enophile combinations are reported. Another indication is obtained from the chemoselectivity of the catalyses. The silylium ion-catalyzed Diels-Alder reaction is general with regard to the oxidation level of the

  13. Papain-catalyzed peptide bond formation: enzyme-specific activation with guanidinophenyl esters.

    PubMed

    de Beer, Roseri J A C; Zarzycka, Barbara; Amatdjais-Groenen, Helene I V; Jans, Sander C B; Nuijens, Timo; Quaedflieg, Peter J L M; van Delft, Floris L; Nabuurs, Sander B; Rutjes, Floris P J T

    2011-09-19

    The substrate mimetics approach is a versatile method for small-scale enzymatic peptide-bond synthesis in aqueous systems. The protease-recognized amino acid side chain is incorporated in an ester leaving group, the substrate mimetic. This shift of the specific moiety enables the acceptance of amino acids and peptide sequences that are normally not recognized by the enzyme. The guanidinophenyl group (OGp), a known substrate mimetic for the serine proteases trypsin and chymotrypsin, has now been applied for the first time in combination with papain, a cheap and commercially available cysteine protease. To provide insight in the binding mode of various Z-X(AA)-OGp esters, computational docking studies were performed. The results strongly point at enzyme-specific activation of the OGp esters in papain through a novel mode of action, rather than their functioning as mimetics. Furthermore, the scope of a model dipeptide synthesis was investigated with respect to both the amino acid donor and the nucleophile. Molecular dynamics simulations were carried out to prioritize 22 natural and unnatural amino acid donors for synthesis. Experimental results correlate well with the predicted ranking and show that nearly all amino acids are accepted by papain.

  14. Efficient access to substituted silafluorenes by nickel-catalyzed reactions of biphenylenes with Et₂SiH₂.

    PubMed

    Breunig, Jens Michael; Gupta, Puneet; Das, Animesh; Tussupbayev, Samat; Diefenbach, Martin; Bolte, Michael; Wagner, Matthias; Holthausen, Max C; Lerner, Hans-Wolfram

    2014-11-01

    The reaction of biphenylene (1) with Et2SiH2 in the presence of [Ni(PPhMe2)4] results in the formation of a mixture of 2-diethylhydrosilylbiphenyl [2(Et2HSi)] and 9,9,-diethyl-9-silafluorene (3). Silafluorene 3 was isolated in 37.5% and 2(Et2HSi) in 36.9% yield. The underlying reaction mechanism was elucidated by DFT calculations. 4-Methyl-9,9-diethyl-9-silafluorene (7) was obtained selectively from the [Ni(PPhMe2)4]-catalyzed reaction of Et2SiH2 and 1-methylbiphenylene. By contrast, no selectivity could be found in the Ni-catalyzed reaction between Et2SiH2 and the biphenylene derivative that bears tBu substituents in the 2- and 7-positions. Therefore, two pairs of isomers of tBu-substituted silafluorenes and of the related diethylhydrosilylbiphenyls were formed in this reaction. However, a subsequent dehydrogenation of the diethylhydrosilylbiphenyls with Wilkinson's catalyst yielded a mixture of 2,7-di-tert-butyl-9,9-diethyl-9-silafluorene (8) and 3,6-di-tert-butyl-9,9-diethyl-9-silafluorene (9). Silafluorenes 8 and 9 were separated by column chromatography.

  15. Controlling thermo-reversibility of gelatin gels through a peroxidase-catalyzed reaction under mild conditions for mammalian cells.

    PubMed

    Sakai, Shinji; Moriyama, Kousuke; Kawakami, Koei

    2011-01-01

    A variety of cross-linking methods is used for obtaining gelatin gels having a tolerance to thermo-reversible gel-sol transition at physiological temperature. In this paper, we investigated the applicability of horseradish peroxidase-catalyzed cross-linking of tyrosine residues originally contained in native gelatin molecules for preparing such gelatin gels. The gelatin gels obtained through exposure to the enzymatic reaction showed a higher resistance to thermo-reversibility at 37°C than gels obtained through a thermally-induced gelation alone. In addition, the resistance property to thermo-reversible gel-sol transition was tunable by controlling enzymatic reaction conditions: higher peroxidase concentration and thermally-induced pre-gelation accomplished by cooling the gelatin solution prior to the enzymatic reaction produced gels with higher resistance to thermo-reversibility. Fibroblast cells enclosed in the gelatin gels obtained through the enzymatic reaction with thermally-induced pre-gelation showed 93% viability. These results demonstrate the feasibility of peroxidase-catalyzed reaction for obtaining gelatin gels having a tolerance to thermo-reversible gel-to-sol transition at physiological temperature toward applications in biomedical and biopharmaceutical fields.

  16. Reaction mechanism of WGS and PROX reactions catalyzed by Pt/oxide catalysts revealed by an FeO(111)/Pt(111) inverse model catalyst.

    PubMed

    Xu, Lingshun; Wu, Zongfang; Jin, Yuekang; Ma, Yunsheng; Huang, Weixin

    2013-08-07

    We have employed XPS and TDS to study the adsorption and surface reactions of H2O, CO and HCOOH on an FeO(111)/Pt(111) inverse model catalyst. The FeO(111)-Pt(111) interface of the FeO(111)/Pt(111) inverse model catalyst exposes coordination-unsaturated Fe(II) cations (Fe(II)CUS) and the Fe(II)CUS cations are capable of modifying the reactivity of neighbouring Pt sites. Water facilely dissociates on the Fe(II)CUS cations at the FeO(111)-Pt(111) interface to form hydroxyls that react to form both water and H2 upon heating. Hydroxyls on the Fe(II)CUS cations can react with CO(a) on the neighbouring Pt(111) sites to produce CO2 at low temperatures. Hydroxyls act as the co-catalyst in the CO oxidation by hydroxyls to CO2 (PROX reaction), while they act as one of the reactants in the CO oxidation by hydroxyls to CO2 and H2 (WGS reaction), and the recombinative reaction of hydroxyls to produce H2 is the rate-limiting step in the WGS reaction. A comparison of reaction behaviors between the interfacial CO(a) + OH reaction and the formate decomposition reaction suggest that formate is the likely surface intermediate of the CO(a) + OH reaction. These results provide some solid experimental evidence for the associative reaction mechanism of WGS and PROX reactions catalyzed by Pt/oxide catalysts.

  17. Characterization of a Cross-Linked Protein-Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

    SciTech Connect

    Silakov, Alexey; Grove, Tyler L.; Radle, Matthew I.; Bauerle, Matthew R.; Green, Michael T.; Rosenzweig, Amy C.; Boal, Amie K.; Booker, Squire J.

    2014-08-14

    RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl-13C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process

  18. Characterization of a Cross-Linked Protein–Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

    PubMed Central

    2015-01-01

    RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl-13C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process. PMID:24806349

  19. Advanced Low Energy Enzyme Catalyzed Solvent for CO{sub 2} Capture

    SciTech Connect

    Zaks, Alex; Reardon, John

    2013-09-30

    A proof-of-concept biocatalyst enhanced solvent process was developed and demonstrated in an integrated bench-scale system using coal post combustion flue gas. The biocatalyst was deployed as a coating on M500X structured packing. Rate enhancement was evaluated using a non-volatile and non- toxic 20 wt% potassium carbonate solution. Greater than 500-fold volumetric scale-up from laboratory to bench scale was demonstrated in this project. Key technical achievements included: 10-fold mass transfer enhancement demonstrated in laboratory testing relative to blank potassium carbonate at 45°C; ~ 7-fold enhancement over blank in bench-scale field testing at National Carbon Capture Center; aerosol emissions were below detection limits (< 0.8 ppm); 90% capture was demonstrated at ~19.5 Nm{sup 3}/hr (dry basis); and ~ 80% CO{sub 2} capture was demonstrated at ~ 30 Nm{sup 3}/hr (dry basis) for more than 2800-hrs on flue gas with minimal detectible decline in activity. The regeneration energy requirement was 3.5 GJ/t CO{sub 2} for this solvent, which was below the target of <2.1 GJ/t CO{sub 2}. Bench unit testing revealed kinetic limitations in the un-catalyzed stripper at around 85°C, but process modeling based on bench unit data showed that equivalent work of less than 300 kWh/t CO{sub 2} including all CO{sub 2} compression can be achieved at lower temperature stripping conditions. Cost analysis showed that 20% potassium carbonate in a basic solvent flow sheet with biocatalyst coated packing has economic performance comparable to the reference NETL Case-12, 30% MEA. A detailed techno-economic analysis indicated that addition of catalyst in the stripper could reduce the cost of capture by ~6% and cost of avoided CO{sub 2} by ~10% below reference NETL Case-12. Based on these results, a directional plan was identified to reduce the cost of CO{sub 2} capture in future work.

  20. Rapid removal of N-linked oligosaccharides using microwave assisted enzyme catalyzed deglycosylation

    NASA Astrophysics Data System (ADS)

    Sandoval, Wendy N.; Arellano, Fred; Arnott, David; Raab, Helga; Vandlen, Richard; Lill, Jennie R.

    2007-01-01

    The removal of N-linked oligosaccharides from glycoproteins is commonly performed during the preparation of samples for mass spectrometry. A reduction in the protein's structural heterogeneity is sometimes essential to obtain a mass for the intact protein. Alternatively, removal of the sugar may be desired to facilitate oligosaccharide analysis. A typical approach to deglycosylation employs overnight digestion with the enzyme peptide N-glycosidase F (PNGase F). We report a method for the accelerated removal of N-linked oligosaccharides using PNGase F assisted by microwave irradiation. Complete deglycosylation was achieved in less than 30 min for most proteins without compromising the integrity of protein samples. This method was tested on a variety of glycoproteins, including antibodies, at the microgram level.

  1. Reactivity of Cations and Zwitterions Formed in Photochemical and Acid-Catalyzed Reactions from m-Hydroxycycloalkyl-Substituted Phenol Derivatives.

    PubMed

    Cindro, Nikola; Antol, Ivana; Mlinarić-Majerski, Kata; Halasz, Ivan; Wan, Peter; Basarić, Nikola

    2015-12-18

    Three m-substituted phenol derivatives, each with a labile benzylic alcohol group and bearing either protoadamantyl 4, homoadamantyl 5, or a cyclohexyl group 6, were synthesized and their thermal acid-catalyzed and photochemical solvolytic reactivity studied, using preparative irradiations, fluorescence measurements, nanosecond laser flash photolysis, and quantum chemical calculations. The choice of m-hydroxy-substitution was driven by the potential for these phenolic systems to generate m-quinone methides on photolysis, which could ultimately drive the excited-state pathway, as opposed to forming simple benzylic carbocations in the corresponding thermal route. Indeed, thermal acid-catalyzed reactions gave the corresponding cations, which undergo rearrangement and elimination from 4, only elimination from 5, and substitution and elimination from 6. On the other hand, upon photoexcitation of 4-6 to S1 in a polar protic solvent, proton dissociation from the phenol, coupled with elimination of the benzylic OH (as hydroxide ion) gave zwitterions (formal m-quinone methides). The zwitterions exhibit reactivity different from the corresponding cations due to a difference in charge distribution, as shown by DFT calculations. Thus, protoadamantyl zwitterion has a less nonclassical character than the corresponding cation, so it does not undergo 1,2-shift of the carbon atom, as observed in the acid-catalyzed reaction.

  2. Radical S-adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis.

    PubMed

    Flühe, Leif; Marahiel, Mohamed A

    2013-08-01

    Sactipeptides represent a new emerging class of ribosomally assembled and posttranslationally modified peptides that show diverse bioactivities. Their common hallmark is an intramolecular thioether bond that crosslink the sulfur atom of a cysteine residue with the α-carbon of an acceptor amino acid. This review summarizes recent achievements concerning the biosynthesis of sactipeptides in general and with special focus on the common enzymatic radical SAM mechanism leading to the thioether linkage formation. In addition this mechanism is compared to the mechanism of thioether bond formation during lanthipeptide biosynthesis and to other radical based thioether bond forming reactions.

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

    PubMed

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

    2008-05-01

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

  4. Chiral diphosphine and monodentate phosphorus ligands on a spiro scaffold for transition-metal-catalyzed asymmetric reactions.

    PubMed

    Xie, Jian-Hua; Zhou, Qi-Lin

    2008-05-01

    The preparation of chiral compounds in enantiomerically pure form is a challenging goal in modern organic synthesis. The use of chiral metal complex catalysis is a powerful, economically feasible tool for the preparation of optically active organic compounds on both laboratory and industrial scales. In particular, the metals coordinated by one or more chiral phosphorus ligands exhibit amazing enantioselectivity and reactivity. Many chiral phosphorus ligands have been synthesized and used in transition-metal-catalyzed asymmetric reactions in past decades. However, a large number of reactions still lack effective chiral ligands, and the enantioselectivities in many reactions are substrate-dependent. The development of effective chiral phosphorus ligands, especially ligands having novel chiral backbones, is still an important task in the area of asymmetric catalysis. Molecules containing a spirocyclic framework are ubiquitous in nature. The synthesis of molecules with this spiro structure can be traced back to 100 years ago. However, the use of this spirocyclic framework to construct chiral phosphorus ligands is a recent event. This Account outlines the design and synthesis of a new family of chiral spiro phosphorus ligands including spiro diphosphines and spiro monodentate phosphorus ligands with 1,1'-spirobiindane and 9,9'-spirobifluorene backbone and their applications in transition-metal-catalyzed asymmetric hydrogenation and carbon-carbon bond formation reactions. The chiral spiro diphosphine lgands SDP with a 1,1'-spirobiindane backbone and SFDP with a 9,9'-spirobifluorene backbone, and the spiro monophosphorus ligands including phosphoramidites, phosphites, phosphonites, and phospholane with a 1,1'-spirobiindane backbone were synthesized in good yields from enantiomerically pure 1,1'-spirobiindane-7,7'-diol and 9,9'-spirobifluoren-1,1'-diol. The ruthenium complexes of chiral spiro diphosphine ligands proved to be very effective catalysts for asymmetric

  5. Synthesis of phosphatidylcholine with defined fatty acid in the sn-1 position by lipase-catalyzed esterification and transesterification reaction.

    PubMed

    Adlercreutz, Dietlind; Budde, Heike; Wehtje, Ernst

    2002-05-20

    The incorporation of caproic acid in the sn-1 position of phosphatidylcholine (PC) catalyzed by lipase from Rhizopus oryzae was investigated in a water activity-controlled organic medium. The reaction was carried out either as esterification or transesterification. A comparison between these two reaction modes was made with regard to product yield, product purity, reaction time, and byproduct formation as a consequence of acyl migration. The yield in the esterification and transesterification reaction was the same under identical conditions. The highest yield (78%) was obtained at a water activity (a(w)) of 0.11 and a caproic acid concentration of 0.8 M. The reaction time was shorter in the esterification reaction than in the transesterification reaction. The difference in reaction time was especially pronounced at low water activities and high fatty acid concentrations. The loss in yield due to acyl migration and consequent enzymatic side reactions was around 16% under a wide range of conditions. The incorporation of a fatty acid in the sn-1 position of PC proved to be thermodynamically much more favorable than the incorporation of a fatty acid in the sn-2 position.

  6. The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As†

    PubMed Central

    Xu, Qin; Guo, Hao-Bo; Wlodawer, Alexander; Nakayama, Toru; Guo, Hong

    2008-01-01

    Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations are performed to study the acylation reaction catalyzed by kumamolisin-As, a serine-carboxyl peptidase, and to elucidate the catalytic mechanism and the origin of substrate specificity. It is demonstrated that the nucleophilic attack by the serine residue on the substrate may not be the rate limiting step for the acylation of the GPH*FF substrate. The present study also confirms the earlier suggestions that Asp 164 acts as a general acid during the catalysis and that the electrostatic oxyanion-hole interactions may not be sufficient to lead a stable tetrahedral intermediate along the reaction pathway. Moreover, Asp 164 is found to act as a general base during the formation of the acyl-enzyme from the tetrahedral intermediate. The role of dynamic substrate assisted catalysis (DSAC) involving His at the P1 site of the substrate is examined for the acylation reaction. It is demonstrated that the bond breaking and making events at each stage of the reaction trigger a change of the position for the His sidechain and lead to the formation of the alternative hydrogen bonds. The back and forth movements of the His sidechain between the C=O group of Pro at P2 and Oδ2 of Asp 164 in a P1ng-pong-like mechanism and the formation of the alternative hydrogen bonds effectively lower the free energy barriers for both the nucleophilic attack and the acyl-enzyme formation and may therefore contribute to the relatively high activity of kumamolisin-As towards to the substrates with His at P1 site. PMID:17326662

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

    PubMed

    Fok, Pak-Wing; Chou, Tom

    2009-05-20

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

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

    PubMed

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

    2007-02-02

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

  9. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions.

    PubMed

    Dixit, M; Das, S; Mhashal, A R; Eitan, R; Major, D T

    2016-01-01

    This chapter aims to present some basic multiscale approaches available for enzyme simulations, and to point out practical details and pitfalls that are not often discussed in the literature, but can greatly influence the outcome of any in silico enzyme study. We cover principle methodological steps of multiscale studies of general enzyme reactions. This includes choice of starting structures, boundary conditions, potential energy surfaces, reaction coordinates, simulation methods, as well as the choice of method for the treatment of nuclear quantum effects. Together, these and additional steps are crucial for the success of enzyme-modeling projects and should be considered prior to embarking on multiscale modeling.

  10. Factors that Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase†‡

    PubMed Central

    Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Carrell, Christopher J.; Mathews, F. Scott; Jorns, Marilyn Schuman

    2009-01-01

    NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative 2-electron oxidation of P2C but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single 2-electron oxidation step. Wild-type and mutant enzyme exhibit identical rate constants for P2C oxidation to dihydropicolinate and isomerization of a reduced enzyme•dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Picolinate release from Tyr258Phe is 100-fold faster than turnover. The presence of bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10- to 75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate or 1-cyclohexenoate, a 1-deaza P2C analog. The reduced Tyr258Phe•1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD. PMID:19702312

  11. The proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction.

    PubMed

    Zhang, Xiaohua; Bruice, Thomas C

    2005-12-20

    A study of the Thermus thermophilus chorismate mutase (TtCM) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. The computed free energies of activation for the reactions in water and TtCM are comparable to the experimental values. The free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and TtCM, respectively. The near attack conformer stabilization contributes approximately 90% to the proficiency of the enzymatic reaction compared with the reaction in water. The transition state (TS) structures and partial atom charges are much the same in the enzymatic and water reactions. The difference in the electrostatic interactions of Arg-89 with O13 in the enzyme-substrate complex and enzyme-TS complex provides the latter with but 0.55 kcal/mol of 1.92 kcal/mol total TS stabilization. Differences in electrostatic interactions between components at the active site in the enzyme-substrate complex and enzyme-TS complex are barely significant, such that TS stabilization is of minor importance and the enzymatic catalysis is through an entropic advantage.

  12. Faox enzymes inhibited Maillard reaction development during storage both in protein glucose model system and low lactose UHT milk.

    PubMed

    Troise, Antonio Dario; Dathan, Nina A; Fiore, Alberto; Roviello, Giovanni; Di Fiore, Anna; Caira, Simonetta; Cuollo, Marina; De Simone, Giuseppina; Fogliano, Vincenzo; Monti, Simona M

    2014-02-01

    Fructosamines, also known as Amadori products, are formed by the condensation of glucose with the amino group of amino acids or proteins. These compounds are precursors of advanced glycation end products (AGEs) that can be formed either endogenously during aging and diabetes, and exogenously in heat-processed food. The negative effects of dietary AGEs on human health as well as their negative impact on the quality of dairy products have been widely described, therefore specific tools able to prevent the formation of glycation products are needed. Two fructosamine oxidase enzymes isolated from Aspergillus sp. namely, Faox I and Faox II catalyze the oxidative deglycation of Amadori products representing a potential tool for inhibiting the Maillard reaction in dairy products. In this paper, the ability of recombinant Faox I and II in limiting the formation of carboxy-methyl lysine (CML) and protein-bound hydroxymethyl furfurol (b-HMF) in a commercial UHT low lactose milk and a beta-lactoglobulin (β-LG) glucose model system was investigated. Results show a consistent reduction of CML and b-HMF under all conditions. Faox effects were particularly evident on b-HMF formation in low lactose commercial milk. Peptide analysis of the β-LG glucose system identified some peptides, derived from cyanogen bromide hydrolysis, as suitable candidates to monitor Faox action in milk-based products. All in all data suggested that non-enzymatic reactions in dairy products might be strongly reduced by implementing Faox enzymes.

  13. Enantioselective synthesis of coumarin derivatives by PYBOX-DIPH-Zn(II) complex catalyzed Michael reaction.

    PubMed

    Ray, Sumit K; Singh, Pradeep K; Molleti, Nagaraju; Singh, Vinod K

    2012-10-05

    A potential pharmacologically active chiral 3-substituted 4-hydroxy-2-oxo-2H-chromene skeleton has been synthesized by enantioselective Michael addition catalyzed by PYBOX-DIPH-Zn(OTf)(2) complex. The methodology has successfully been employed in the synthesis of (R)-Warfarin and another related compounds.

  14. Fe-Catalyzed Oxidation Reactions of Olefins, Alkanes, and Alcohols: Involvement of Oxo- and Peroxo Complexes

    NASA Astrophysics Data System (ADS)

    Schröder, Kristin; Junge, Kathrin; Bitterlich, Bianca; Beller, Matthias

    In this review, recent developments of iron-catalyzed oxidations of olefins (epoxidation), alkanes, arenes, and alcohols are summarized. Special focus is given on the ligand systems and the catalytic performance of the iron complexes. In addition, the mechanistic involvement of high-valent iron-oxo species is discussed.

  15. Computational enzyme design: transitioning from catalytic proteins to enzymes.

    PubMed

    Mak, Wai Shun; Siegel, Justin B

    2014-08-01

    The widespread interest in enzymes stem from their ability to catalyze chemical reactions under mild and ecologically friendly conditions with unparalleled catalytic proficiencies. While thousands of naturally occurring enzymes have been identified and characterized, there are still numerous important applications for which there are no biological catalysts capable of performing the desired chemical transformation. In order to engineer enzymes for which there is no natural starting point, efforts using a combination of quantum chemistry and force-field based protein molecular modeling have led to the design of novel proteins capable of catalyzing chemical reactions not catalyzed by naturally occurring enzymes. Here we discuss the current status and potential avenues to pursue as the field of computational enzyme design moves forward.

  16. ESolvent-free, enzyme-catalyzed biodiesel production from mango, neem, and shea oils via response surface methodology.

    PubMed

    Nde, Divine Bup; Astete, Carlos; Boldor, Dorin

    2015-12-01

    Mango, neem and shea kernels produce non-conventional oils whose potentials are not fully exploited. To give an added value to these oils, they were transesterified into biodiesel in a solvent-free system using immobilized enzyme lipozyme from Mucor miehei. The Doehlert experimental design was used to evaluate the methyl ester (ME) yields as influenced by enzyme concentration-EC, temperature-T, added water content-AWC, and reaction time-RT. Biodiesel yields were quantified by (1)H NMR spectroscopy and subsequently modeled by a second order polynomial equation with interactions. Lipozyme enzymes were more tolerant to high temperatures in neem and shea oils reaction media compared to that of mango oil. The optimum reaction conditions EC, T, AWC, and RT assuring near complete conversion were as follows: mango oil 7.25 %, 36.6 °C, 10.9 %, 36.4 h; neem oil EC = 7.19 %, T = 45.7 °C, AWC = 8.43 %, RT = 25.08 h; and shea oil EC = 4.43 %, T = 45.65 °C, AWC = 6.21 % and RT = 25.08 h. Validation experiments of these optimum conditions gave ME yields of 98.1 ± 1.0, 98.5 ± 1.6 and 99.3 ± 0.4 % for mango, neem and shea oils, respectively, which all met ASTM biodiesel standards.

  17. Optimizing Metalloporphyrin-Catalyzed Reduction Reactions for In Situ Remediation of DOE Contaminants

    SciTech Connect

    Schlautman, Mark A.

    2013-07-14

    Past activities have resulted in a legacy of contaminated soil and groundwater at Department of Energy facilities nationwide. Uranium and chromium are among the most frequently encountered and highest-priority metal and radionuclide contaminants at DOE installations. Abiotic chemical reduction of uranium and chromium at contaminated DOE sites can be beneficial because the reduced metal species are less soluble in water, less mobile in the environment, and less toxic to humans and ecosystems. Although direct biological reduction has been reported for U(VI) and Cr(VI) in laboratory studies and at some field sites, the reactions can sometimes be slow or even inhibited due to unfavorable environmental conditions. One promising approach for the in-situ remediation of DOE contaminants is to develop electron shuttle catalysts that can be delivered precisely to the specific subsurface locations where contaminants reside. Previous research has shown that reduction of oxidized organic and inorganic contaminants often can be catalyzed by electron shuttle systems. Metalloporphyrins and their derivatives are well known electron shuttles for many biogeochemical systems, and thus were selected to study their catalytic capabilities for the reduction of chromium and uranium in the presence of reducing agents. Zero valent iron (ZVI) was chosen as the primary electron donor in most experimental systems. Research proceeded in three phases and the key findings of each phase are reported here. Phase I examined Cr(VI) reduction and utilized micro- and nano-sized ZVI as the electron donors. Electron shuttle catalysts tested were cobalt- and iron-containing metalloporphyrins and Vitamin B12. To aid in the recycle and reuse of the nano-sized ZVI and soluble catalysts, sol-gels and calcium-alginate gel beads were tested as immobilization/support matrices. Although the nano-sized ZVI could be incorporated within the alginate gel beads, preliminary attempts to trap it in sol-gels were not

  18. Characterization of hydroxylaminobenzene mutase from pNBZ139 cloned from Pseudomonas pseudoalcaligenes JS45. A highly associated SDS-stable enzyme catalyzing an intramolecular transfer of hydroxy groups.

    PubMed

    He, Z; Nadeau, L J; Spain, J C

    2000-02-01

    Hydroxylaminobenzene mutase is the enzyme that converts intermediates formed during initial steps in the degradation of nitrobenzene to a novel ring-fission lower pathway in Pseudomonas pseudoalcaligenes JS45. The mutase catalyzes a rearrangement of hydroxylaminobenzene to 2-aminophenol. The mechanism of the reactions and the properties of the enzymes are unknown. In crude extracts, the hydroxylaminobenzene mutase was stable at SDS concentrations as high as 2%. A procedure including Hitrap-SP, Hitrap-Q and Cu(II)-chelating chromatography was used to partially purify the enzyme from an Escherichia coli clone. The partially purified enzyme was eluted in the void volume of a Superose-12 gel-filtration column even in the presence of 0.05% SDS in 25 mM Tris/HCl buffer, which indicated that it was highly associated. When the enzymatic conversion of hydroxylaminobenzene to 2-aminophenol was carried out in 18O-labeled water, the product did not contain 18O, as determined by GC-MS. The results indicate that the reaction proceeded by intramolecular transfer of the hydroxy group from the nitrogen to the C-2 position of the ring. The mechanism is clearly different from the intermolecular transfer of the hydroxy group in the non-enzymatic Bamberger rearrangement of hydroxylaminobenzene to 4-aminophenol and in the enzymatic hydroxymutation of chorismate to isochorismate.

  19. Efficient multi-enzyme-catalyzed CDP-choline production driven by an ATP donor module.

    PubMed

    Liu, Yingmiao; Wang, Junzhi; Xu, Chongmao; Chen, Yong; Yang, Junjie; Liu, Dong; Niu, Huanqing; Jiang, Yu; Yang, Sheng; Ying, Hanjie

    2017-02-01

    Cytidine diphosphate choline (CDP-choline) has been applied for treating acute craniocerebral injury and allowing recovery of consciousness after brain surgery. In this study, an acetate kinase (ACK)/acetyl phosphate system was used to supply ATP and combined with Escherichia coli-overexpressed CMP kinase (CMK), NDP kinase (NDK), choline phosphate cytidylyltransferase (CCT), and choline kinase (CKI) to produce CDP-choline from CMP and choline chloride. Within 1 h, 49 mM CDP-choline was produced, for a molar yield of 89.9 and 68.4 % based on CMP and choline chloride, respectively; the utilization efficiency of energy (UEE) was 79.5 %. Acetyl phosphate, sodium acetate, and CTP inhibited the reaction when the concentration exceeded 18.5, 600, and 30 mM, respectively. This inhibition could be overcome by controlling the rate of acetyl phosphate, CMP addition or using KOH instead of NaOH to regulate the pH in fed-batch transformation. After 24 h, the maximum titer was 124.1 ± 2.7 mM, the productivity was 5.1 ± 0.1 mM l(-1) h(-1), the molar yield to CMP and choline chloride were 83.8 and 63.7 %, respectively, and the UEE was 58.2 %. This high yield and productivity of CDP-choline through biocatalysis suggest future application at the industrial scale.

  20. Degradation of trichloroethene by siderite-catalyzed hydrogen peroxide and persulfate: Investigation of reaction mechanisms and degradation products

    PubMed Central

    Yan, Ni; Liu, Fei; Xue, Qiang; Brusseau, Mark L.; Liu, Yali; Wang, Junjie

    2015-01-01

    A binary catalytic system, siderite-catalyzed hydrogen peroxide (H2O2) coupled with persulfate (S2O82−), was investigated for the remediation of trichloroethene (TCE) contamination. Batch experiments were conducted to investigate reaction mechanisms, oxidant decomposition rates, and degradation products. By using high performance liquid chromatography (HPLC) coupled with electron paramagnetic resonance (EPR), we identified four radicals (hydroxyl (HO·), sulfate (SO4−·), hydroperoxyl (HO2·), and superoxide (O2−·)) in the siderite-catalyzed H2O2-S2O82− system. In the absence of S2O82− (i.e., siderite-catalyzed H2O2), a majority of H2O2 was decomposed in the first hour of the experiment, resulting in the waste of HO·. The addition of S2O82− moderated the H2O2 decomposition rate, producing a more sustainable release of hydroxyl radicals that improved the treatment efficiency. Furthermore, the heat released by H2O2 decomposition accelerated the activation of S2O82−, and the resultant SO4−· was the primary oxidative agent during the first two hours of the reaction. Dichloroacetic acid was firstly detected by ion chromatography (IC). The results of this study indicate a new insight to the reaction mechanism for the catalytic binary H2O2-S2O82− oxidant system, and the delineation of radicals and the discovery of the chlorinated byproduct provide useful information for efficient treatment of chlorinated-solvent contamination in groundwater. PMID:26236152

  1. Degradation of trichloroethene by siderite-catalyzed hydrogen peroxide and persulfate: Investigation of reaction mechanisms and degradation products.

    PubMed

    Yan, Ni; Liu, Fei; Xue, Qiang; Brusseau, Mark L; Liu, Yali; Wang, Junjie

    2015-08-15

    A binary catalytic system, siderite-catalyzed hydrogen peroxide (H2O2) coupled with persulfate (S2O8(2-)), was investigated for the remediation of trichloroethene (TCE) contamination. Batch experiments were conducted to investigate reaction mechanisms, oxidant decomposition rates, and degradation products. By using high performance liquid chromatography (HPLC) coupled with electron paramagnetic resonance (EPR), we identified four radicals (hydroxyl (HO·), sulfate (SO4(-)·), hydroperoxyl (HO2·), and superoxide (O2(-)·)) in the siderite-catalyzed H2O2-S2O8(2-) system. In the absence of S2O8(2-) (i.e., siderite-catalyzed H2O2), a majority of H2O2 was decomposed in the first hour of the experiment, resulting in the waste of HO·. The addition of S2O8(2-) moderated the H2O2 decomposition rate, producing a more sustainable release of hydroxyl radicals that improved the treatment efficiency. Furthermore, the heat released by H2O2 decomposition accelerated the activation of S2O8(2-), and the resultant SO4(-)· was the primary oxidative agent during the first two hours of the reaction. Dichloroacetic acid was firstly detected by ion chromatography (IC). The results of this study indicate a new insight to the reaction mechanism for the catalytic binary H2O2-S2O8(2-) oxidant system, and the delineation of radicals and the discovery of the chlorinated byproduct provide useful information for efficient treatment of chlorinated-solvent contamination in groundwater.

  2. Stereo-specificity for pro-(R) hydrogen of NAD(P)H during enzyme-catalyzed hydride transfer to CL-20

    SciTech Connect

    Bhushan, Bharat; Halasz, Annamaria; Hawari, Jalal . E-mail: jalal.hawari@nrc.ca

    2005-12-02

    A dehydrogenase from Clostridium sp. EDB2 and a diaphorase from Clostridium kluyveri were reacted with CL-20 to gain insights into the enzyme-catalyzed hydride transfer to CL-20, and the enzyme's stereo-specificity for either pro-R or pro-S hydrogens of NAD(P)H. Both enzymes biotransformed CL-20 at rates of 18.5 and 24 nmol/h/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated product with a molecular weight of 393 Da. In enzyme kinetics studies using reduced deuterated pyridine nucleotides, we found a kinetic deuterium isotopic effect of 2-fold on CL-20 biotransformation rate using dehydrogenase enzyme against (R)NADD as a hydride-source compared to either (S)NADD or NADH. Whereas, in case of diaphorase, the kinetic deuterium isotopic effect of about 1.5-fold was observed on CL-20 biotransformation rate using (R)NADPD as hydride-source. In a comparative study with LC-MS, using deuterated and non-deuterated NAD(P)H, we found a positive mass-shift of 1 Da in the N-denitrohydrogenated product suggesting the involvement of a deuteride (D{sup -}) transfer from NAD(P)D. The present study thus revealed that both dehydrogenase and diaphorase enzymes from the two Clostridium species catalyzed a hydride transfer to CL-20 and showed stereo-specificity for pro-R hydrogen of NAD(P)H.

  3. Enzyme inhibition studies by integrated Michaelis-Menten equation considering simultaneous presence of two inhibitors when one of them is a reaction product.

    PubMed

    Bezerra, Rui M F; Pinto, Paula A; Fraga, Irene; Dias, Albino A

    2016-03-01

    To determine initial velocities of enzyme catalyzed reactions without theoretical errors it is necessary to consider the use of the integrated Michaelis-Menten equation. When the reaction product is an inhibitor, this approach is particularly important. Nevertheless, kinetic studies usually involved the evaluation of other inhibitors beyond the reaction product. The occurrence of these situations emphasizes the importance of extending the integrated Michaelis-Menten equation, assuming the simultaneous presence of more than one inhibitor because reaction product is always present. This methodology is illustrated with the reaction catalyzed by alkaline phosphatase inhibited by phosphate (reaction product, inhibitor 1) and urea (inhibitor 2). The approach is explained in a step by step manner using an Excel spreadsheet (available as a template in Appendix). Curve fitting by nonlinear regression was performed with the Solver add-in (Microsoft Office Excel). Discrimination of the kinetic models was carried out based on Akaike information criterion. This work presents a methodology that can be used to develop an automated process, to discriminate in real time the inhibition type and kinetic constants as data (product vs. time) are achieved by the spectrophotometer.

  4. Studies of the Mechanism and Origins of Enantioselectivity for the Chiral Phosphoric Acid-Catalyzed Stereoselective Spiroketalization Reactions.

    PubMed

    Khomutnyk, Yaroslav Ya; Argüelles, Alonso J; Winschel, Grace A; Sun, Zhankui; Zimmerman, Paul M; Nagorny, Pavel

    2016-01-13

    Mechanistic and computational studies were conducted to elucidate the mechanism and the origins of enantiocontrol for asymmetric chiral phosphoric acid-catalyzed spiroketalization reactions. These studies were designed to differentiate between the S(N)1-like, S(N)2-like, and covalent phosphate intermediate-based mechanisms. The chiral phosphoric acid-catalyzed spiroketalization of deuterium-labeled cyclic enol ethers revealed a highly diastereoselective syn-selective protonation/nucleophile addition, thus ruling out long-lived oxocarbenium intermediates. Hammett analysis of the reaction kinetics revealed positive charge accumulation in the transition state (ρ = -2.9). A new computational reaction exploration method along with dynamics simulations supported an asynchronous concerted mechanism with a relatively short-lived polar transition state (average lifetime = 519 ± 240 fs), which is consistent with the observed inverse secondary kinetic isotope effect of 0.85. On the basis of these studies, a transition state model explaining the observed stereochemical outcome has been proposed. This model predicts the enantioselective formation of the observed enantiomer of the product with 92% ee, which matches the experimentally observed value.

  5. Two-dimensional reaction free energy surfaces of catalytic reaction: effects of protein conformational dynamics on enzyme catalysis.

    PubMed

    Min, Wei; Xie, X Sunney; Bagchi, Biman

    2008-01-17

    We introduce a two-dimensional (2D) multisurface reaction free energy description of the catalytic cycle that explicitly connects the recently observed multi-time-scale conformational dynamics as well as dispersed enzymatic kinetics to the classical Michaelis-Menten equation. A slow conformational motion on a collective enzyme coordinate Q facilitates the catalytic reaction along the intrinsic reaction coordinate X, providing a dynamic realization of Pauling's well-known idea of transition-state stabilization. The catalytic cycle is modeled as transitions between multiple displaced harmonic wells in the XQ space representing different states of the cycle, which is constructed according to the free energy driving force of the cycle. Subsequent to substrate association with the enzyme, the enzyme-substrate complex under strain exhibits a nonequilibrium relaxation toward a new conformation that lowers the activation energy of the reaction, as first proposed by Haldane. The chemical reaction in X is thus enslaved to the down hill slow motion on the Q surface. One consequence of the present theory is that, in spite of the existence of dispersive kinetics, the Michaelis-Menten expression of the catalysis rate remains valid under certain conditions, as observed in recent single-molecule experiments. This dynamic theory builds the relationship between the protein conformational dynamics and the enzymatic reaction kinetics and offers a unified description of enzyme fluctuation-assisted catalysis.

  6. Lanthanum(III)-Catalyzed Three-Component Reaction of Coumarin-3-carboxylates for the Synthesis of Indolylmalonamides and Analysis of Their Photophysical Properties.

    PubMed

    Jennings, Julia J; Bhatt, Chinmay P; Franz, Annaliese K

    2016-08-05

    New methodology has been developed for the Lewis acid catalyzed synthesis of malonamides. First, the scandium(III)-catalyzed addition of diverse nucleophiles (e.g., indoles, N,N-dimethyl-m-anisidine, 2-ethylpyrrole, and 2-methylallylsilane) to coumarin-3-carboxylates has been developed to afford chromanone-3-carboxylates in high yields as a single diastereomer. Upon investigating a subsequent lanthanum(III)-catalyzed amidation reaction, a new multicomponent reaction was designed by bringing together coumarin-3-carboxylates with indoles and amines to afford indolylmalonamides, which were identified to exhibit fluorescent properties. The photophysical properties for selected compounds have been analyzed, including quantum yield, molar absorptivity, and Stokes shift. Synthetic studies of several reaction byproducts involved in the network of reaction equilibria for the three-component reaction provide mechanistic insight for the development of this methodology.

  7. Phosphoryl transfer is not rate-limiting for the ROCK I-catalyzed kinase reaction.

    PubMed

    Futer, Olga; Saadat, Ahmad R; Doran, John D; Raybuck, Scott A; Pazhanisamy, S

    2006-06-27

    Rho-associated coiled-coil kinase, ROCK, is implicated in Rho-mediated cell adhesion and smooth muscle contraction. Animal models suggest that the inhibition of ROCK can ameliorate conditions, such as vasospasm, hypertension, and inflammation. As part of our effort to design novel inhibitors of ROCK, we investigated the kinetic mechanism of ROCK I. Steady-state bisubstrate kinetics, inhibition kinetics, isotope partition analysis, viscosity effects, and presteady-state kinetics were used to explore the kinetic mechanism. Plots of reciprocals of initial rates obtained in the presence of nonhydrolyzable ATP analogues and the small molecule inhibitor of ROCK, Y-27632, against the reciprocals of the peptide concentrations yielded parallel lines (uncompetitive pattern). This pattern is indicative of an ordered binding mechanism, with the peptide adding first. The staurosporine analogue K252a, however, gave a noncompetitive pattern. When a pulse of (33)P-gamma-ATP mixed with ROCK was chased with excess unlabeled ATP and peptide, 0.66 enzyme equivalent of (33)P-phosphate was incorporated into the product in the first turnover. The presence of ATPase activity coupled with the isotope partition data is a clear evidence for the existence of a viable [E-ATP] complex in the kinase reaction and implicates a random binding mechanism. The k(cat)/K(m) parameters were fully sensitive to viscosity (viscosity effects of 1.4 +/- 0.2 and 0.9 +/- 0.3 for ATP and peptide 5, respectively), and therefore, the barriers to dissociation of either substrate are higher than the barrier for the phosphoryl transfer step. As a consequence, not all the binding steps are at fast equilibrium. The observation of a burst in presteady-state kinetics (k(b) = 10.2 +/- 2.1 s(-)(1)) and the viscosity effect on k(cat) of 1.3 +/- 0.2 characterize the phosphoryl transfer step to be fast and the release of product and/or the enzyme isomerization step accompanying it as rate-limiting at V(max) conditions. From

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

    DOEpatents

    Shah, Manish M.; Campbell, James A.

    1998-01-01

    A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with oxygen sensitive nitroreductase enzymes, such as ferredoxin NADP oxidoreductase.

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

    DOEpatents

    Shah, M.M.; Campbell, J.A.

    1998-07-07

    A method is described for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with oxygen sensitive nitroreductase enzymes, such as ferredoxin NADP oxidoreductase. 6 figs.

  10. Method of reduction of nitroaromatics by enzymatic reaction with redox enzymes

    DOEpatents

    Shah, Manish M.

    2000-01-01

    A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with redox enzymes, such as Oxyrase (Trademark of Oxyrase, Inc., Mansfield, Ohio).

  11. Bulk gold catalyzed oxidation reactions of amines and isocyanides and iron porphyrin catalyzed N-H and O-H bond insertion/cyclization reactions of diamines and aminoalcohols

    SciTech Connect

    Klobukowski, Erik

    2011-01-01

    This work involves two projects. The first project entails the study of bulk gold as a catalyst in oxidation reactions of isocyanides and amines. The main goal of this project was to study the activation and reactions of molecules at metal surfaces in order to assess how organometallic principles for homogeneous processes apply to heterogeneous catalysis. Since previous work had used oxygen as an oxidant in bulk gold catalyzed reactions, the generality of gold catalysis with other oxidants was examined. Amine N-oxides were chosen for study, due to their properties and use in the oxidation of carbonyl ligands in organometallic complexes. When amine N-oxides were used as an oxidant in the reaction of isocyanides with amines, the system was able to produce ureas from a variety of isocyanides, amines, and amine N-oxides. In addition, the rate was found to generally increase as the amine N-oxide concentration increased, and decrease with increased concentrations of the amine. Mechanistic studies revealed that the reaction likely involves transfer of an oxygen atom from the amine N-oxide to the adsorbed isocyanide to generate an isocyanate intermediate. Subsequent nucleophilic attack by the amine yields the urea. This is in contrast to the bulk gold-catalyzed reaction mechanism of isocyanides with amines and oxygen. Formation of urea in this case was proposed to proceed through a diaminocarbene intermediate. Moreover, formation of the proposed isocyanate intermediate is consistent with the reactions of metal carbonyl ligands, which are isoelectronic to isocyanides. Nucleophilic attack at coordinated CO by amine N-oxides produces CO{sub 2} and is analogous to the production of an isocyanate in this gold system. When the bulk gold-catalyzed oxidative dehydrogenation of amines was examined with amine N-oxides, the same products were afforded as when O{sub 2} was used as the oxidant. When the two types of oxidants were directly compared using the same reaction system and

  12. Single-Molecule Imaging of Iron-Phthalocyanine-Catalyzed Oxygen Reduction Reaction by in Situ Scanning Tunneling Microscopy.

    PubMed

    Gu, Jing-Ying; Cai, Zhen-Feng; Wang, Dong; Wan, Li-Jun

    2016-09-27

    We report herein an in situ electrochemical scanning tunneling microscopy (ECSTM) investigation of iron-phthalocyanine (FePc)-catalyzed oxygen reduction reaction (ORR). A highly ordered FePc adlayer is revealed on a Au(111) electrode. The center ions in the FePc adlayer show uniform high contrast in an oxygen-saturated electrolyte, which is attributed to the formation of an FePc-O2 complex. In situ STM results reveal the sharp contrast change upon shifting the electrode potential to trigger the ORR. Theoretical simulation has supplied further evidence for the contrast difference of the adsorbed FePc species.

  13. Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme.

    PubMed

    Massey, Archna P; Sigurdsson, Snorri Th

    2004-01-01

    The chemical syntheses of RNA oligomers containing modifications on the 5'-carbon of the 5'-terminal nucleoside for crystallographic and mechanistic studies of the hairpin ribozyme are reported. Phosphoramidites 4 and 8 were prepared and used in solid phase syntheses of RNA oligomers containing the sequence 5'-N'UCCUCUCC, where N' indicates either 5'-chloro-5'-deoxyguanosine or 5'-amino-5'-deoxyguanosine, respectively. A ribozyme ligation assay with the 5'-chloro- and 5'-amino-modified RNA oligomers demonstrated their inhibition of the hairpin-catalyzed RNA-RNA ligation reaction.

  14. Mechanism and Stereoselectivity in an Asymmetric N-Heterocyclic Carbene-Catalyzed Carbon-Carbon Bond Activation Reaction.

    PubMed

    Pareek, Monika; Sunoj, Raghavan B

    2016-11-18

    The mechanism and origin of stereoinduction in a chiral N-heterocyclic carbene (NHC) catalyzed C-C bond activation of cyclobutenone has been established using B3LYP-D3 density functional theory computations. The activation of cyclobutenone as an NHC-bound vinyl enolate and subsequent reaction with the electrophilic sulfonyl imine leads to the lactam product. The most preferred stereocontrolling transition state exhibits a number of noncovalent interactions rendering additional stabilization. The computed enantio- and diastereoselectivities are in good agreement with the previous experimental observations.

  15. Exhaustive study of the noise-induced phase transition in a stochastic model of self-catalyzed reactions

    NASA Astrophysics Data System (ADS)

    Pham, T. M.; Virchenko, Yu. P.

    2016-08-01

    We completely investigate the stationary distribution density in the space of relative concentrations for the three-parameter stochastic Horsthemke-Lefever model of a binary self-catalyzed cyclic chemical reaction with perturbations produced by thermal fluctuations of reagents taken into account. This model is a stationary diffusion random process generated by a stochastic equation with the Stratonovich differential, whose marginal distribution density admits a bifurcation restructuring from the unimodal to the bimodal phase with increasing noise intensity, which is interpreted physically as a dynamical phase transition induced by fluctuations in the system.

  16. A Novel Glucosylation Reaction on Anthocyanins Catalyzed by Acyl-Glucose–Dependent Glucosyltransferase in the Petals of Carnation and Delphinium[C][W

    PubMed Central

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

    2010-01-01

    Glucosylation of anthocyanin in carnations (Dianthus caryophyllus) and delphiniums (Delphinium grandiflorum) involves novel sugar donors, aromatic acyl-glucoses, in a reaction catalyzed by the enzymes acyl-glucose–dependent anthocyanin 5(7)-O-glucosyltransferase (AA5GT and AA7GT). The AA5GT enzyme was purified from carnation petals, and cDNAs encoding carnation Dc AA5GT and the delphinium homolog Dg AA7GT were isolated. Recombinant Dc AA5GT and Dg AA7GT proteins showed AA5GT and AA7GT activities in vitro. Although expression of Dc AA5GT in developing carnation petals was highest at early stages, AA5GT activity and anthocyanin accumulation continued to increase during later stages. Neither Dc AA5GT expression nor AA5GT activity was observed in the petals of mutant carnations; these petals accumulated anthocyanin lacking the glucosyl moiety at the 5 position. Transient expression of Dc AA5GT in petal cells of mutant carnations is expected to result in the transfer of a glucose moiety to the 5 position of anthocyanin. The amino acid sequences of Dc AA5GT and Dg AA7GT showed high similarity to glycoside hydrolase family 1 proteins, which typically act as β-glycosidases. A phylogenetic analysis of the amino acid sequences suggested that other plant species are likely to have similar acyl-glucose–dependent glucosyltransferases. PMID:20971893

  17. In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways.

    PubMed

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

    2015-12-25

    All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO2-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO2 fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions.

  18. In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways*♦

    PubMed Central

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

    2015-01-01

    All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO2-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO2 fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions. PMID:26511314

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta-D-xylosidase from Selenomonas ruminantium is the best catalyst known for promoting hydrolysis of 1,4-beta-D-xylooligosaccharides and it has potential utility in industrial saccharification processes. Kinetic parameters, kcat and kcat/Km, are more than 10-fold larger than those reported for the...

  20. ENZYME CATALYZED POLYCONDENSATION REACTIONS FOR THE SYNTHESIS OF AROMATIC POLYCARBONATES AND POLYESTERS. (R825338)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...