Sample records for enzyme catalyzed reactions

  1. Thermodynamics of Enzyme-Catalyzed Reactions Database

    National Institute of Standards and Technology Data Gateway

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

  2. Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Timescales

    E-print Network

    Paul, Mark

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

  3. Representing Rate Equations for Enzyme-Catalyzed Reactions

    ERIC Educational Resources Information Center

    Ault, Addison

    2011-01-01

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

  4. Molecular Mechanism by which One Enzyme Catalyzes Two Reactions

    NASA Astrophysics Data System (ADS)

    Nishimasu, Hiroshi; Fushinobu, Shinya; Wakagi, Takayoshi

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

  5. 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.

  6. Thermodynamics of industrially-important, enzyme-catalyzed reactions

    Microsoft Academic Search

    Yadu B. Tewari

    1990-01-01

    The thermodynamics of 10 industrially-important, enzyme-catalyzed reactions are examined. The reactions discussed are: the\\u000a conversions of penicillin G to 6-amino-penicillinic acid using the enzyme penicillin acylase; starch to glucose using amylases;\\u000a glucose to fructose using glucose (xylose) isomerase; cellulose to glucose using cellulase; fumaric acid and ammonia to l-aspartic\\u000a acid using l-aspartase; transcinnamic acid and ammonia to l-phenylalanine using l-phenylalanine

  7. Thermodynamics of Enzyme-Catalyzed Reactions: Part 7--2007 Update Robert N. Goldberg,a...

    E-print Network

    Magee, Joseph W.

    Thermodynamics of Enzyme-Catalyzed Reactions: Part 7--2007 Update Robert N. Goldberg,a... Yadu B 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

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

    E-print Network

    van Vliet, Lucas J.

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

  9. 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.

  10. ENZO: A Web Tool for Derivation and Evaluation of Kinetic Models of Enzyme Catalyzed Reactions

    PubMed Central

    Bevc, Staš; Konc, Janez; Stojan, Jure; Hodoš?ek, Milan; Penca, Matej; Praprotnik, Matej; Janeži?, Dušanka

    2011-01-01

    We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si. PMID:21818304

  11. USE OF CRITICAL CARBON DIOXIDE TO OPTIMIZE AN ENZYME CATALYZED REACTION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It was hypothesized that the equilibrium point of an enzyme-catalyzed reaction could be shifted to the right if the product could be partitioned into an immiscible carbon dioxide (CO2) phase. The molar ratios of starting material to product in CO2 were compared over a range of temperatures and pres...

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

    Microsoft Academic Search

    V. Renganathan; Keiji Miki; Michael H. Gold

    1987-01-01

    Lignin peroxidase (ligninase, LiP) an HâOâ-dependent lignin-degrading heme enzyme from the basidiomycetous fungus Phanerochaete chrysosporium, catalyzes the oxidation of a variety of lignin model compounds. In this paper the authors examine the haloperoxidase reactions of LiP. In the presence of HâOâ, homogeneous LiP oxidized bromide and iodide but not chloride. Halide oxidation was measured by the halogenation of monochlorodimedone (MCD)

  13. Determination of Rapid-Equilibrium Kinetic Parameters of Ordered and Random Enzyme-Catalyzed Reaction A + B = P + Q

    E-print Network

    Alberty, Robert A.

    This article deals with the rapid-equilibrium kinetics of the forward and reverse reactions together for the ordered and random enzyme-catalyzed A + B = P + Q and emphasizes the importance of reporting the values of the ...

  14. 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.

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

    PubMed

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

    2014-04-18

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

  16. Triosephosphate isomerase: energetics of the reaction catalyzed by the yeast enzyme expressed in Escherichia coli

    SciTech Connect

    Nickbarg, E.B.; Knowles, J.R.

    1988-08-09

    Triosephosphate isomerase from bakers' yeast, expressed in Escherichia coli strain DF502(p12), has been purified to homogeneity. The kinetics of the reaction in each direction have been determined at pH 7.5 and 30 degrees C. Deuterium substitution at the C-2 position of substrate (R)-glyceraldehyde phosphate and at the 1-pro-R position of substrate dihydroxyacetone phosphate results in kinetic isotope effects on kcat of 1.6 and 3.4, respectively. The extent of transfer of tritium from (1(R)-TH)dihydroxyacetone phosphate to product (R)-glyceraldehyde phosphate during the catalyzed reaction is only 3% after 66% conversion to product, indicating that the enzymic base that mediates proton transfer is in rapid exchange with solvent protons. When the isomerase-catalyzed reaction is run in tritiated water in each direction, radioactivity is incorporated both into the remaining substrate and into the product. In the exchange-conversion experiment with dihydroxyacetone phosphate as substrate, the specific radioactivity of remaining dihydroxyacetone phosphate rises as a function of the extent of reaction with a slope of about 0.3, while the specific radioactivity of the products is 54% that of the solvent. In the reverse direction with (R)-glyceraldehyde phosphate as substrate, the specific radioactivity of the product formed is only 11% that of the solvent, while the radioactivity incorporated into the remaining substrate (R)-glyceraldehyde phosphate also rises as a function of the extent of reaction with a slope of 0.3. These results have been analyzed according to the protocol described earlier to yield the free energy profile of the reaction catalyzed by the yeast isomerase.

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

    SciTech Connect

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

    1987-08-11

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

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

    SciTech Connect

    Malik, Radhika; Viola, Ronald E. (Toledo)

    2010-10-28

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

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

    ERIC Educational Resources Information Center

    Bozlee, Brian J.

    2007-01-01

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

  20. Enzyme Reactions

    NSDL National Science Digital Library

    Minerva Deland School

    2011-10-03

    This video shows an enzyme reaction lab. The teacher demonstrates how the enzyme, catalase, reacts with hydrogen peroxide (a substrate found in cells). The teacher first demonstrates a normal enzyme reaction. He or she then goes on to show how manipulating temperature and pH will affect the reaction of an enzyme.

  1. Catalyzed enzyme electrodes

    DOEpatents

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

    1993-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-06-01

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

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

    ERIC Educational Resources Information Center

    Sims, Paul A.

    2009-01-01

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

  4. Enzyme Reactions

    NSDL National Science Digital Library

    Maryland Virtual High School

    The enzyme reaction rate activity allows students to simulate the effects of variables such as temperature and pH on the reaction rate of the enzyme catalase. This computer simulation is best used after the students have done a wet lab experiment. The value of the simulation is that it requires the students to interpret and analyze the graphical representation of data and it enables the running of mutiple experiments in a short amount of time.

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

    PubMed

    Natsume, Tomotaka; Yoshimoto, Makoto

    2014-03-12

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

  6. 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…

  7. Enzyme-Catalyzed Processes in Organic Solvents

    Microsoft Academic Search

    Aleksey Zaks; Alexander M. Klibanov

    1985-01-01

    Three different lipases (porcine pancreatic, yeast, and mold) can vigorously act as catalysts in a number of nearly anhydrous organic solvents. Various transesterification reactions catalyzed by porcine pancreatic lipase in hexane obey Michaelis-Menten kinetics. The dependence of the catalytic activity of the enzyme in organic media on the pH of the aqueous solution from which it was recovered is bell-shaped,

  8. Mechanism of enzyme-catalyzed phospho group transfer

    SciTech Connect

    Hansen, D.E.

    1986-01-01

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

  9. Oxygen isotope effects of enzyme-catalyzed organophosphorus hydrolysis reactions: implications for interpretation of dissolved PO4 ?18O values in natural waters

    NASA Astrophysics Data System (ADS)

    Liang, Y.; Blake, R. E.

    2002-12-01

    The geochemical cycling of P in Earth surface environments is controlled largely by biota. It has been recently demonstrated that intracellular cycling of P in microbial cultures and biological turnover of P in natural waters leads to temperature-dependent O isotope equilibrium between dissolved inorganic PO4 (Pi) and ambient water, and that the ?18O of Pi can be a useful tracer of biological reactions and P cycling in aquatic systems/sediments. Oxygen isotope exchange between Pi and water during biological turnover of P is catalyzed by enzymes at low-temperature. Phosphoenzymes play a crucial role in the intracellular functions of all living organisms and also have important extracellular functions in aquatic ecosystems such as regeneration of Pi from organophosphorus compounds (e.g., phosphoesters). Laboratory experiments indicate that extracellular enzyme reactions may result in incomplete Pi turnover and non-equilibrium Pi-water O isotope exchange. Determination of the O isotope effects of phosphoenzyme-catalyzed reactions is fundamental to the understanding of mechanisms of PO4-water O isotope exchange, pathways of biogeochemical P cycling, and interpretation of PO4 ?18O values from natural systems. Here we report on the O isotope fractionation between enzymatically-released Pi and water, in cell-free abiotic systems. Alkaline phosphatase (Apase) is a non-specific phosphohydrolase commonly found in fresh and marine coastal waters that catalyzes the hydrolysis of Pi from phosphomonoesters. We examined the O isotope effects of Apase derived from both microbial and eukaryotic sources and acting on different phosphomonoester substrates (e.g., ?-D-Glucose 1-Phosphate, ?-Glycerophosphate, AMP) in 18O-labeled waters. Oxygen isotope ratios of Pi released by Apase indicate that only 1 of the 4 O atoms in PO4 is incorporated from water with little or no apparent O isotopic fractionation at the site of incorporation. This observation is consistent with phosphomonoester structure and the Apase active site configuration and reaction mechanism. 5'-nucleotidase is another important phosphoenzyme identified in marine ecosystems. The O isotope effects of 5'-nucleotidase- catalyzed reactions will also be presented and implications of these results for interpretation of PO4 ?18O values in natural systems will be discussed.

  10. Janus-faced Enzymes Yeast Tgl3p and Tgl5p Catalyze Lipase and Acyltransferase Reactions

    PubMed Central

    Rajakumari, Sona

    2010-01-01

    In the yeast, mobilization of triacylglycerols (TAGs) is facilitated by the three TAG lipases Tgl3p, Tgl4p, and Tgl5p. Motif search analysis, however, indicated that Tgl3p and Tgl5p do not only contain the TAG lipase motif GXSXG but also an H-(X)4-D acyltransferase motif. Interestingly, lipid analysis revealed that deletion of TGL3 resulted in a decrease and overexpression of TGL3 in an increase of glycerophospholipids. Similar results were obtained with TGL5. Therefore, we tested purified Tgl3p and Tgl5p for acyltransferase activity. Indeed, both enzymes not only exhibited lipase activity but also catalyzed acylation of lysophosphatidylethanolamine and lysophosphatidic acid, respectively. Experiments using variants of Tgl3p created by site-directed mutagenesis clearly demonstrated that the two enzymatic activities act independently of each other. We also showed that Tgl3p is important for efficient sporulation of yeast cells, but rather through its acyltransferase than lipase activity. In summary, our results demonstrate that yeast Tgl3p and Tgl5p play a dual role in lipid metabolism contributing to both anabolic and catabolic processes. PMID:20016004

  11. Strictosidine Synthase: Mechanism of a Pictet–Spengler Catalyzing Enzyme

    PubMed Central

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

    2010-01-01

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

  12. Analysis of enzyme-catalyzed nucleotide modification by aldose reductase

    SciTech Connect

    Grimshaw, C.E.

    1987-05-01

    Homogeneous bovine kidney aldose reductase catalyzes two reactions in addition to the normal aldehyde-dependent oxidation of NADPH. First, adduct formation between the oxidized nucleotide and the oxidized substrate is observed during turnover due to initial formation of a reversible E:NADP/sup +/:R-CHO ternary complex, which subsequently reacts to give the covalent complex (E:NADP/sup +/-R-CHO). The reaction is enzyme-catalyzed with substantial enhancement of both the pseudo-first order rate constant and the overall K/sub eq/ relative to the reaction with free NADP/sup +/ in aqueous buffer. Analysis of the concentration dependence and time-course for reversible dead-end and covalent complex formation are described for several aldehyde and nucleotide substrates. Non-linear time courses for aldehyde reduction and substrate inhibition by the aldehyde substrate in initial velocity studies are completely accounted for by this mechanism, thereby eliminating a simple Dalziel-type explanation for the substrate activation by aldehyde which is also observed. Second, enzyme-catalyzed oxidation of NADPH occurs in the absence of aldehyde substrate with a rate equal to .03% of V/sub max/ for the normal reduction of glyceraldehyde. By 500 MHz /sup 1/H-NMR, the enzyme-catalyzed oxidation of (4-/sup 2/H)NADPH appears to be greater than 95% stereospecific. Spectroscopic evidence for a similar oxidation reaction is observed for the covalent E:NADP/sup +/-R-CHO adduct with glyceraldehyde, but not with glycolaldehyde.

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

    PubMed Central

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

    2015-01-01

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

  14. 4-alkyl-o-quinone/2-hydroxy-p-quinone methide isomerase from the larval hemolymph of Sarcophaga bullata. I. Purification and characterization of enzyme-catalyzed reaction.

    PubMed

    Saul, S J; Sugumaran, M

    1990-10-01

    An enzyme which catalyzes the conversion of certain 4-alkyl-o-benzoquinones to 2-hydroxy-p-quinone methides has been purified to apparent homogeneity from the hemolymph of Sarcophaga bullata by employing conventional protein purification techniques. The purified enzyme migrated with an approximate molecular weight of 98,000 on gel filtration chromatography. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, it migrated as a single band with a molecular weight of 46,000, indicating that it is made up of two identical subunits. It exhibited a pH optimum of 6.0 and readily converted chemically synthesized as well as enzymatically generated quinones derived from N-acetyldopamine, N-beta-alanyldopamine, and 3,4-dihydroxyphenethyl alcohol to highly unstable 2-hydroxy-p-quinone methides. The quinone methides thus formed were rapidly and nonenzymatically hydrated to form side chain hydroxylated o-diphenols as the stable product. In support of this proposition, when the enzyme reaction with N-acetyldopamine quinone was conducted in the presence of 10% methanol, racemic beta-methoxy-N-acetyldopamine was recovered as an additional product. The quinones of N-acetylnorepinephrine, N-beta-alanylnorepinephrine, and 3,4-dihydroxyphenylglycol were also attacked by the isomerase, resulting in the formation of N-acetylarterenone, N-beta-alanylarterenone and 2-hydroxy-3',4'-dihydroxyacetophenone, respectively as the stable products. The isomerase converted the dihydrocaffeiyl methyl amide quinone to its quinone methide analog which rapidly tautomerized to yield caffeiyl methyl amide. The importance of quinone isomerase in insect immunity and sclerotization of insect cuticle is discussed. PMID:2211605

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

    PubMed

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

    2015-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. Enzyme-catalyzed resolution of racemate using enzyme functionalized silica nanoparticles in the presence of surfactants

    Microsoft Academic Search

    Yoon Seok Song; Hee Uk Lee; Jong Ho Lee; Seung Wook Kim

    2011-01-01

    The enzyme-catalyzed resolution of racemic naproxen 2,2,2-trifluoroethyl thioester was performed by the immobilization of lipase on silica nanoparticles using a covalent bonding method. To increase the conversion and reaction rate of this resolution, we investigated the effect of non-ionic surfactants (M-SA 1025 and SM 20). The optimal reaction conditions such as temperature and loading amount of immobilized lipase were also

  18. Enzyme Reaction Annotation Using Cloud Techniques

    PubMed Central

    Huang, Chuan-Ching

    2013-01-01

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

  19. Enzyme reaction annotation using cloud techniques.

    PubMed

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

    2013-01-01

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

  20. Enzyme catalysed tandem reactions.

    PubMed

    Oroz-Guinea, Isabel; García-Junceda, Eduardo

    2013-04-01

    To transfer to the laboratory, the excellent efficiency shown by enzymes in Nature, biocatalysis, had to mimic several synthetic strategies used by the living organisms. Biosynthetic pathways are examples of tandem catalysis and may be assimilated in the biocatalysis field for the use of isolated multi-enzyme systems in the homogeneous phase. The concurrent action of several enzymes that work sequentially presents extraordinary advantages from the synthetic point of view, since it permits a reversible process to become irreversible, to shift the equilibrium reaction in such a way that enantiopure compounds can be obtained from prochiral or racemic substrates, reduce or eliminate problems due to product inhibition or prevent the shortage of substrates by dilution or degradation in the bulk media, etc. In this review we want to illustrate the developments of recent studies involving in vitro multi-enzyme reactions for the synthesis of different classes of organic compounds. PMID:23490810

  1. Paper microfluidic-based enzyme catalyzed double microreactor.

    PubMed

    Ferrer, Ivonne M; Valadez, Hector; Estala, Lissette; Gomez, Frank A

    2014-08-01

    We describe a paper microfluidic-based enzyme catalyzed double microreactor assay using fluorescent detection. Here, solutions of lactate dehydrogenase (LDH) and diaphorase (DI) were directly spotted onto the microfluidic paper-based analytical device (?PAD). Samples containing lactic acid, resazurin, and nicotinamide adenine dinucleotide oxidized form (NAD(+) ), potassium chloride (KCl), and BSA, in MES buffer were separately spotted onto the ?PAD and MES buffer flowed through the device. A cascade reaction occurs upon the sample spot overlapping with LDH to form pyruvate and nicotinamide adenine dinucleotide reduced form (NADH). Subsequently, NADH is used in the conversion of resazurin to fluorescent resorufin by DI. The ?PAD avoids the need of surface functionalization or enzyme immobilization steps. These microreactor devices are low cost and easy to fabricate and effect reaction based solely on buffer capillary action. PMID:24913741

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  4. Enzyme-catalyzed Acylation of (R,S)-1-phenylethanol in 1-butyl-3-methylimidazolium Based Ionic Liquids

    Microsoft Academic Search

    Maja Habulin

    Ionic liquids represent an exciting new class of reaction solvents for catalysis, which have been used successfully for enzyme-catalyzed reactions. In present research, three different ionic liquids, 1-butyl-3-methylimidazolium tetrafluoro- borate, 1-butyl-3-methylimidazolium hexafluorophosphate, and 1-ethyl-3-methylimidazolium bis((trifluoromethyl)sul- fonyl))amide, were synthesized. They were used as a reaction medium for enzyme-catalyzed acylation of (R,S)-1- phenylethanol with vinyl acetate. Mentioned enzymatic reaction was performed in

  5. Enantioselective iron-catalyzed intramolecular cyclopropanation reactions.

    PubMed

    Shen, Jun-Jie; Zhu, Shou-Fei; Cai, Yan; Xu, Huan; Xie, Xiu-Lan; Zhou, Qi-Lin

    2014-11-24

    An iron-catalyzed asymmetric intramolecular cyclopropanation was realized in high yields and excellent enantioselectivity (up to 97%?ee) by using the iron complexes of chiral spiro-bisoxazoline ligands as catalysts. The superiority of iron catalysts exhibited in this reaction demonstrated the potential abilities of this sustainable metal in asymmetric carbenoid transformation reactions. PMID:25283384

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

    E-print Network

    Cao, Yang

    1 Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction Yang Cao a) Dept, Santa Barbara, Santa Barbara, CA 93106 Abstract: The enzyme-catalyzed conversion of a substrate this process, the intermediate enzyme-substrate complex is usually much more likely to decay into its original

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

    E-print Network

    Tsai, Ming-Daw

    -containing enzymes which carry out p replacement and/or a$ elimina- tion reactions of amino acids, the reaction and the cofactor to an enzyme-bound Schiff s base between pyridoxal phosphate and cr-aminoacrylic acidStereochemistry and Mechanism of Reactions Catalyzed by Tryptophan Synthetase and Its p2 Subunit

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

    NASA Astrophysics Data System (ADS)

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

    1997-11-01

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

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

    E-print Network

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

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

  10. Enzyme-catalyzed synthesis of aliphatic-aromatic oligoamides.

    PubMed

    Stavila, E; Alberda van Ekenstein, G O R; Loos, K

    2013-05-13

    Enzymatically catalyzed polycondensation of p-xylylenediamine and diethyl sebacate resulted in oligo(p-xylylene sebacamide) with high melting temperatures (223-230 °C) and the enzymatic polycondensation of dimethyl terephthalate and 1,8-diaminooctane leads to oligo(octamethylene terephthalamide) with two melting temperatures at 186 and 218 °C. No oligoamides, but products 1 and 2, were formed from the enzymatic reaction of dimethyl terephthalate and p-xylylenediamine. All reactions were catalyzed by CAL-B, icutinase, or CLEA cutinase. All reactions catalyzed by CAL-B show higher conversion than reactions catalyzed by icutinase or CLEA cutinase. The highest DPmax of 15 was achieved in a one-step and two-step synthesis of oligo(p-xylylene sebacamide) catalyzed by CLEA cutinase. PMID:23544613

  11. 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

  12. Surface catalyzed mercury transformation reactions

    NASA Astrophysics Data System (ADS)

    Varanasi, Patanjali

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

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

    E-print Network

    Spiteri, Raymond J.

    a carbon acid substrate. Gerlt and Gassman have applied Marcus formalism to such proton transfer reactions to argue that transition states for concerted general acid-general base catalyzed enolization at enzyme from Carbon Acid Substrates Stephen L. Bearne, * and Raymond J. Spiteri§ Department of Biochemistry

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

    Microsoft Academic Search

    Diana Lindberg; Mario de la Fuente Revenga; Mikael Widersten

    2010-01-01

    A special group of ionic liquids, deep eutectic solvents (DESs) have been tested as cosolvents in enzyme-catalyzed hydrolysis of a chiral (1,2)-trans-2-methylstyrene oxide. The choline chloride:ethane diol (ET), choline chloride:glycerol (GLY) and choline:chloride:urea (REL) DESs were included in the reaction mixtures with epoxide and the potato epoxide hydrolase StEH1. The effect of the DESs on enzyme function was primarily elevations

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed Central

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

    2014-01-01

    We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems. PMID:24628210

  17. 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. PMID:24628210

  18. Mechanism of the reaction catalyzed by mandelate racemase. 3. Asymmetry in reactions catalyzed by the H297N mutant

    SciTech Connect

    Landro, J.A.; Kallarakal, A.T.; Ransom, S.C.; Gerlt, J.A.; Kozarich, J.W. (Univ. of Maryland, College Park (United States)); Neidhart, D.J. (Abbott Labs., Abbott Park, IL (United States)); Kenyon, G.L. (Univ. of California, San Francisco (United States))

    1991-09-24

    Two preceding papers suggest that the active site of mandelate racemase (MR) contains two distinct general acid/base catalysts: Lys 166, which abstracts the {alpha}-proton from (s)-mandelate, and His 297, which abstracts the {alpha}-proton from (R)-mandelate. In this paper the authors report on the properties of the mutant of MR in which His 297 has been converted to asparagine by site-directed mutagenesis (H297N). The structure of H297N, solved by molecular replacement at 2.2-{angstrom} resolution, reveals that no conformational alterations accompany the substitution. As expected, h297N has no detectable MR activity. However, H297N catalyzes the stereospecific elimination of bromide ion from racemic {rho}-(bromomethyl) mandelate to give {rho}-(methyl)-benzoylformate in 45% yield at a rate equal to that measured for wild-type enzyme. The pD dependence of the rate of the exchange reaction catalyzed by H297N reveals a pK{sub a} of 6.4 in D{sub 2}O which is assigned to Lys 166. These observations provide persuasive evidence that the reaction catalyzed by MR does, in fact, proceed via a two-base mechanism in which Lys 166 abstracts the {alpha}-proton from (S)-mandelate and His 297 abstracts the {alpha}-proton from (R)-mandelate. These studies demonstrate the power of site-directed mutagenesis in providing otherwise inaccessible detail about the mechanism of an enzyme-catalyzed reaction.

  19. Biginelli Reaction Catalyzed by Copper Nanoparticles

    PubMed Central

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

    2012-01-01

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

  20. Hydrolase-catalyzed reactions in membrane reactors at atmospheric and high pressure

    Microsoft Academic Search

    Mateja Primoži?; Muzafera Paljevac; Željko Knez

    2009-01-01

    Membrane reactors could serve as a tool for enzyme-catalyzed reactions and they enable the performance of catalytic reaction, enzyme recovery and product isolation as a one-step process. In the presented work, the use of continuous flat-shape and continuous tubular membrane enzymatic reactors for different enzymatic systems at atmospheric pressure and at supercritical conditions are described. In a high-pressure continuous enzymatic

  1. Mammalian Tyrosinase Catalyzes Three Reactions in the Biosynthesis of Melanin

    Microsoft Academic Search

    Ann Korner; John Pawelek

    1982-01-01

    The biosynthesis of melanin is initiated by the catalytic oxidation of tyrosine to dopa by tyrosinase in a reaction that requires dopa as a cofactor. Tyrosinase then catalyzes the dehydrogenation of dopa to dopaquinone. The subsequent reactions can proceed spontaneously in vitro. Tyrosinase, purified from murine melanomas and the skins of brown mice, has now been shown to catalyze a

  2. Reaction kinetics of catalyzed competitive heteropolymer cleavage.

    PubMed

    Sadiq, S Kashif; Könnyü, Balázs; Müller, Viktor; Coveney, Peter V

    2011-09-22

    A theoretical formulation for complete heteropolymer degradation is developed in terms of Michaelis-Menten reaction kinetics under the quasi-steady-state approximation. This allows the concentration of the entire intermediate decomposition cascade to be accounted for as well as each species of emerging final product. The formulation is implemented computationally and results in stable reaction kinetics across a range of orders of magnitude for K(M) and k(cat). The model is compared with experiment, specifically in vitro HIV-1 protease-catalyzed retroviral Gag-polyprotein processing. Using an experimentally determined cleavage-polypeptide parameter set, good qualitative agreement is reached with Gag degradation kinetics, given the difference in experimental conditions. A parameter search within 1 order of magnitude of variation of the experimental set results in the determination of an optimal parameter set in complete agreement with experiment which allows the time evolution of each individual as well as intermediate species in Gag to be accurately followed. Future investigations that determine the required enzymatic parameters to populate such a scheme will allow for the model to be refined in order to track the time for viral maturation and infectivity. PMID:21823648

  3. Enzyme-catalyzed oxidation facilitates the return of fluorescence for single-walled carbon nanotubes.

    PubMed

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

    2013-09-11

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

  4. 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.

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

    E-print Network

    Chen, Chuo

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

  6. USE OF NEURAL NETWORKS IN THE MATHEMATICAL MODELING OF THE ENZYMIC SYNTHESIS OF AMOXICILLIN CATALYZED BY PENICILLIN G ACYLASE IMMOBILIZED IN CHITOSAN

    Microsoft Academic Search

    James A. Silva; Wellington S. Adriano; Andrea L. O. Ferreira; Luciana R. B. Gonçalves

    The specificity of enzymes and their ability to catalyze reactions make them attractive for applications in biochemical and industrial fields. One major advantage of this biocatalyst specificity is the achievement of targets free of side products. Immobilization offers some operational advantages over free enzymes, such as choice of batch or continuous processes, rapid termination of reactions, controlled product formation, ease

  7. The role and source of 5P-deoxyadenosyl radical in a carbon skeleton rearrangement catalyzed by a plant enzyme

    E-print Network

    Rétey, János

    in analogous rearrangements catalyzed by coenzyme BIP- dependent enzymes. Possible roles of S speculated that coenzyme BIP is involved in the reaction [2^4]. Since, in spite of some claims [5 and bacteria coenzyme BIP is the major source of 5P-deoxyadenosyl radical [13]. More re- cently, S

  8. Ruthenium-Catalyzed Concurrent Tandem Reactions University of North Carolina

    E-print Network

    Johnson, Jeff S.

    Ruthenium-Catalyzed Concurrent Tandem Reactions Greg Boyce University of North Carolina February 8. Enyne Cascades I. Dienyne Metathesis II. Ring Rearrangement Metathesis III. Metathesis/Non-Metathesis I of Tandem Reactions ­ Sequential tandem reactions involve coupling transformations that operate

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

    PubMed Central

    Zhang, Qi; Liu, Wen

    2011-01-01

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

  10. Influencing Enzymes: A Lesson on Enzyme Reactions

    NSDL National Science Digital Library

    Camia Steinmann (Clear Creek High School)

    2007-08-01

    This teaching resource was developed by a K-12 science teacher in the American Physiological SocietyÂ?s 2007 Frontiers in Physiology Program. For more information on this program, please visit www.frontiersinphys.org. Students will investigate the catabolic properties of the enzyme amylase and its role in digestion of breaking down starch molecules. Prior to this activity, students should be able to identify the structural and functional properties of carbohydrates and proteins. Upon completion of this activity, students will be able to predict the effect of different environments on enzyme activity.

  11. Mechanistic approaches to palladium-catalyzed alkene difunctionalization reactions

    PubMed Central

    Jensen, Katrina H.; Sigman, Matthew S.

    2009-01-01

    Alkene difunctionalization, the addition of two functional groups across a double bond, exemplifies a class of reactions with significant synthetic potential. This emerging area examines recent developments of palladium-catalyzed difunctionalization reactions, with a focus on mechanistic strategies that allow for functionalization of a common palladium alkyl intermediate. PMID:18972034

  12. Ti-Catalyzed Reactions of Hindered Isocyanates with Alcohols

    E-print Network

    Spino, Claude

    Hydrochloric acid7a and copper(I) chloride6,9b are two frequently utilized acid catalysts for that reaction chloride was incapable of catalyzing their reaction with alcohols, and hydrochloric acid as well as many that would be both mildly Lewis acidic and yet contain ligands capable of acting as a base would procure

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

    PubMed Central

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

    2007-01-01

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

  14. Rearrangement Reactions Catalyzed by Cytochrome P450s

    PubMed Central

    Ortiz de Montellano, Paul R.; Nelson, Sidney D.

    2010-01-01

    Cytochrome P450s promote a variety of rearrangement reactions both as a consequence of the nature of the radical and other intermediates generated during catalysis, and of the neighboring structures in the substrate that can interact either with the initial radical intermediates or with further downstream products of the reactions. This article will review several kinds of previously published cytochrome P450-catalyzed rearrangement reactions, including changes in stereochemistry, radical clock reactions, allylic rearrangements, “NIH” and related shifts, ring contractions and expansions, and cyclizations that result from neighboring group interactions. Although most of these reactions can be carried out by many members of the cytochrome P450 superfamily, some have only been observed with select P450s, including some reactions that are catalyzed by specific endoperoxidases and cytochrome P450s found in plants. PMID:20971058

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

    PubMed Central

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

    2014-01-01

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

  16. Diamine ligands in copper-catalyzed reactions

    E-print Network

    Surry, David S.

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

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

    PubMed Central

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

    2013-01-01

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

  18. 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.

  19. Evaluation of true kinetic parameters for reversible immobilized enzyme reactions

    SciTech Connect

    Ishikawa, H.; Tanaka, T.; Kurose, K.; Hikita, H.

    1987-06-01

    For a reversible one-substrate reaction system that follows the Haldane reaction mechanism, a new and effective method has been proposed to extract true or intrinsic kinetic parameters of immobilized enzymes from diffusion limited rate data. The method utilizes the effectiveness factors correlated in terms of the general modulus defined by Aris and Bischoff, and a new modulus defined in the present study. It requires a trial-and-error calculation, but only a few data points. Furthermore, it provides a saving of materials such as substrates and enzymes, and takes less time for experiments compared to the initial rate methods. The usefulness of the method is demonstrated by determining the kinetic parameters for membrane bound fumarase which catalyzes the reaction of the conversion of fumarate to L-malate, for which the equilibrium constant is circa 4. (Refs. 20).

  20. 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

  1. 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,…

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

    SciTech Connect

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

    2009-01-01

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

  3. 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

  4. 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. PMID:25082205

  5. Lewis acid template-catalyzed asymmetric diels-alder reaction.

    PubMed

    Ishihara, Jun; Nakadachi, Shino; Watanabe, Yuki; Hatakeyama, Susumi

    2015-02-20

    An asymmetric Diels-Alder reaction of 2,4-dienols and methyl acrylate utilizing a chiral Zn(II)/Mg(II) bimetallic template with low catalyst loading was successfully achieved. The bimetallic Lewis acid template derived from (R)-5,5',6,6',7,7',8,8'-octahydro-1,1'-bi-2-naphthol catalyzed the Diels-Alder reaction in the presence of molecular sieves 4 Å to afford various functionalized bicyclic ?-lactones with high enantiomeric purities. PMID:25621816

  6. Stereochemistry and Mechanism of Reactions Catalyzed by Tryptophanase from Escherichia coZi*

    E-print Network

    Tsai, Ming-Daw

    base complex of the amino acid and pyridoxal phosphate with elimination of the p substituent (indoleStereochemistry and Mechanism of Reactions Catalyzed by Tryptophanase from Escherichia co reactions catalyzed by tryptophanase from Escherichia coli are shown to proceed stereospecifically

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

    PubMed

    Saw, Mei Huey; Siew, Wai Lin

    2014-01-01

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

  8. Stau-catalyzed big-bang nucleosynthesis reactions

    SciTech Connect

    Kamimura, Masayasu [Department of Physics, Kyushu University, Fukuoka 812-8581 (Japan); Kino, Yasushi [Department of Physics, Tohoku University, Sendai 980-8578 (Japan); Hiyama, Emiko [RIKEN Nishina Center, Wako 351-0198 (Japan)

    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.

  9. Phase transfer catalyzed reactions on polymers

    Microsoft Academic Search

    Antoni S. Gó?d?

    1982-01-01

    Linear high-molecular weight polyepichlorohydrin elastomer (PECH) was reacted with potassium Superoxide in benzene and benzene-dimethylsulfoxide solutions in the presence of 18-crown-6 as a phase-transfer catalyst. Elemental analysis, spectroscopic studies, and viscosity measurements showed that Superoxide ion attacks both the chloromethyl group leading to the formation of various oxygen-containing groups, and main chain, causing its rapid degradation. A reaction mechanism has

  10. Enzyme Reactions in Nanoporous, Picoliter Volume Containers

    SciTech Connect

    Siuti, Piro [ORNL; Retterer, Scott T [ORNL; Choi, Chang Kyoung [Michigan Technological University; Doktycz, Mitchel John [ORNL

    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. Accelerated stochastic simulation of the stiff enzyme-substrate reaction Department of Computer Science, University of California, Santa Barbara,

    E-print Network

    Petzold, Linda R.

    Accelerated stochastic simulation of the stiff enzyme-substrate reaction Yang Caoa Department; accepted 11 August 2005; published online 13 October 2005 The enzyme-catalyzed conversion of a substrate this process, the intermediate enzyme-substrate complex is usually much more likely to decay into its original

  12. Density Functional Study of Mo-Carbonyl-Catalyzed Alkynol Cycloisomerization: Comparison with W-Catalyzed Reaction

    PubMed Central

    Nowroozi-Isfahani, Taraneh; Musaev, Djamaladdin G.; McDonald, Frank E.; Morokuma, Keiji

    2006-01-01

    Mo-catalyzed endo-cycloisomerizations of alkynes tethered to alcohols have been studied using density functional theory, and comparisons were made with the W-catalyzed reaction. The cycloisomerization is initiated with the formation of metal alkyne ? complex and is followed by the rate-determining step, which transforms the ? complex to a vinylidene carbene complex, considered to be critical for endo-mode cyclization. Several different alkynols have been selected to investigate five- and six-membered ring endo-cycloisomerizations in the presence of Mo(CO)5 catalyst. The energy barriers calculated for five- and six-membered ring cycloisomerizations are within a range of 25–30 kcal/mol for most cases studied, showing no significant energy difference between the two metals. The stabilization effect of THF and Et3N solvents and the substitution reaction of THF by alkynol substrates in the reaction process with Mo and W complexes are studied as well. The principal difference between Mo- and W-catalyzed cycloisomerization processes appears to be the initial formation of a ? complex, which is more stabilizing for formation of the W-alkyne vs Mo-alkyne complexes. PMID:16601823

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

    PubMed

    Qian, Deyun; Zhang, Junliang

    2015-02-01

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

  14. Investigations into Transition Metal Catalyzed Arene Trifluoromethylation Reactions

    PubMed Central

    Ye, Yingda; Sanford, Melanie S.

    2015-01-01

    Trifluoromethyl-substituted arenes and heteroarenes are widely prevalent in pharmaceuticals and agrochemicals. As a result, the development of practical methods for the formation of aryl–CF3 bonds has become an active field of research. Over the past five years, transition metal catalyzed cross-coupling between aryl–X (X = halide, organometallic, or H) and various “CF3” reagents has emerged as a particularly exciting approach for generating aryl–CF3 bonds. Despite many recent advances in this area, current methods generally suffer from limitations such as poor generality, harsh reaction conditions, the requirement for stoichiometric quantities of metals, and/or the use of costly CF3 sources. This Account describes our recent efforts to address some of these challenges by: (1) developing aryl trifluoromethylation reactions involving high oxidation state Pd intermediates, (2) exploiting AgCF3 for C–H trifluoromethylation, and (3) achieving Cu-catalyzed trifluoromethylation with photogenerated CF3•.

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

    PubMed

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

    2014-11-15

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

  16. 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

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

    PubMed

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

    2015-03-01

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

  18. Biotransformations catalyzed by multimeric enzymes: stabilization of tetrameric ampicillin acylase permits the optimization of ampicillin synthesis under dissociation conditions.

    PubMed

    Fernández-Lafuente, R; Hernández-Jústiz, O; Mateo, C; Terreni, M; Fernández-Lorente, G; Moreno, M A; Alonso, J; García-López, J L; Guisan, J M

    2001-01-01

    The importance of the stabilization of the quaternary structure of multimeric enzymes has been illustrated using a model reaction with great industrial relevance: the enzymatic synthesis of ampicillin from 6-amino penicillanic acid (6APA) and phenylglycine methyl ester (PGM) catalyzed by the tetrameric enzyme alpha-amino acid ester hydrolase from Acetobacter turbidans. The stabilization of the multimeric structure of the enzyme was achieved by multi-subunit immobilization of the enzyme followed by its further solid-phase chemical intersubunit cross-linking with polyfunctional macromolecules (dextran-aldehyde). This stabilized derivative has permitted the study of the reaction under conditions where nonstabilized enzyme molecules tended to dissociate (e.g., absence of phosphate ions). Synthetic yields improved from around 65%, under conditions where the nonstabilized derivative was stable, to around 85% in conditions where only the stabilized derivative could be utilized (40% methanol and absence of phosphate ions). When using high concentrations of PGM, a significant worsening of the reaction performance was detected with a significant decrease in the yields (below 55%, using 50 mM 6APA and PGM). This problem has been sorted out by using a fed-batch reaction system. By addition of PGM continuously to the reaction mixture (to maintain the concentration between 0.5 and 3 mM), 95% of 6-APA could be transformed to antibiotic (47.5 mM) by only using a 20% excess of acylating ester. PMID:11749160

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

    E-print Network

    Vallino, Joseph J.

    from yeast cells the enzymes catalyzing alcoholic fermentation. This achievement clearly demonstrated of biochemistry is the history of en- zyme research. The name enzyme ("in yeast") was not used until 1877, but much earlier it was suspected that biological catalysts are involved in the fermentation of sugar

  20. [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. PMID:11324481

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

    E-print Network

    Baik, Mu-Hyun

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

  2. Development and application of transition metal-catalyzed cross-coupling reactions

    E-print Network

    Chae, Junghyun, 1973-

    2004-01-01

    Chapter 1. PALLADIUM-CATALYZED REGIOSELECTIVE HYDRODEBROMINATION OF DIBROMOINDOLES A novel approach to the selective preparation of 4-bromoindoles has been developed via a Pd-catalyzed reaction. A variety of 4,6-dibromoindoles, ...

  3. 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…

  4. The use of molecular modelling in the understanding of configurational specificity (R or S) in asymmetric reactions catalyzed by Saccharomyces cerevisiae or isolated dehydrogenases

    Microsoft Academic Search

    Ricardo de Souza Pereira; Fernando Pavão; Glaucius Oliva

    1998-01-01

    This method gives a general ideal how to use crystallographic information of enzymes to understand reactions catalyzed by these biocatalysts, commonly used by biochemists to produce chiral products. The interactions of three acetoacetic esters with the enzymes L-lactate dehydrogenase and alcohol dehydrogenase were studied through molecular modelling computer program. These artificial substrates have been widely used to produce chiral synthons.

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

    PubMed

    Alcaide, Benito; Almendros, Pedro

    2014-03-18

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

  6. 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)

  7. Enzyme catalysis Enzyme catalysis is the catalysis of chemical reactions by

    E-print Network

    Cavanagh, John

    Enzyme catalysis Enzyme catalysis is the catalysis of chemical reactions by specialized proteins known as enzymes. Catalysis of biochemical reactions in the cell is vital due to the very low reaction rates of the uncatalysed reactions. The mechanism of enzyme catalysis is similar in principle to other

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

    PubMed

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

    2010-06-01

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

  9. Effect of enzyme dehydration on alcalase-catalyzed dipeptide synthesis in near-anhydrous organic media.

    PubMed

    Vossenberg, Petra; Beeftink, Rik; Stuart, Martien Cohen; Tramper, Hans

    2013-01-01

    The effect of enzyme dehydration by molecular sieves on the coupling of phenylalanine amide and the carbamoylmethyl ester of N-protected phenylalanine in near-anhydrous tetrahydrofuran was investigated. This coupling was catalyzed by Alcalase covalently immobilized onto macroporous acrylic beads (Cov); these immobilized enzymes were hydrated prior to use. The dehydration kinetics of Cov by molecular sieve powder were determined by incubating Cov with different amounts of molecular sieve powder for different periods of time (0-80 h). Subsequently, the remaining coupling activity of Cov was measured. Dehydration-induced inactivation of Cov by molecular sieve powder was found to occur in three phases: (1) an initial, rapid, major dehydration-induced inactivation that takes place during the first activity measurement, (2) a phase of first-order inactivation, and (3) a plateau phase in activity. These dehydration kinetics were incorporated into a previously found reaction kinetics model. The resulting model was then used to fit progress curve data of the coupling in the presence of different amounts of molecular sieve powder. Upon establishment of parameter values, the model was used to predict independent data sets and found to work well. PMID:23554404

  10. Enzyme Reactions in Nanoporous, Picoliter Volume Containers

    PubMed Central

    Siuti, Piro; Retterer, Scott T.; Choi, Chang-Kyoung; Doktycz, Mitchel J.

    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. Assessment of small molecule and Green Fluorescent Protein diffusion from the vessels indicates that pore sizes on order of 10 nm can be obtained, allowing capture of proteins and diffusive exchange of small molecules. 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 (Km and Vmax) 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. PMID:22148720

  11. Enzyme reactions in nanoporous, picoliter volume containers.

    PubMed

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

    2012-01-17

    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. Assessment of small-molecule and green fluorescent protein diffusion from the vessels indicates that pore sizes on the order of 10 nm can be obtained, allowing capture of proteins and diffusive exchange of small molecules. 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 (K(m) and V(max)) 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. PMID:22148720

  12. Enzyme-catalyzed and enzyme-triggered pathways in dioxygenation of 1-monolinoleoyl-rac-glycerol by potato tuber lipoxygenase.

    PubMed

    Butovich, I A; Reddy, C C

    2001-04-01

    It was shown for the first time that potato tuber lipoxygenase (ptLOX) catalyzed the aerobic oxidation of 1-monolinoleoyl-rac-glycerol (mLG) in a mixed micellar reaction solution with the non-ionic detergent monododecyl ether of decaoxyethylene glycol. No hydrolysis of mLG occurred during the reaction. The four major reaction products obtained at 23 degrees C were identified as 1-[9-hydroperoxy-10E,12Z-octadecadienoyl]-rac-glycerol (9-(E,Z)HPODE-GE, 41%), 1-[13-hydroperoxy-9Z,11E-octadecadienoyl]-rac-glycerol (13-(Z,E)-HPODE-GE, 17%), and their all-trans isomers ( approximately 21% each). The molar fraction of all-trans isomers depended on the temperature of the reaction solution; it was found that at 0 degrees C their molar fractions were approximately 15.5% each, while 9-(E,Z)HPODE-GE and 13-(Z,E)-HPODE-GE gave 42% and 27%, respectively, of the overall product. A free radical scavenger, 4-hydroxy-TEMPO, dramatically increased the molar fraction of 9-(E,Z)HPODE-GE, yielding 83% at 23 degrees C, at the expense of all other products. Chiral HPLC of 9-(E,Z)HPODE-GE formed in the presence of 4-hydroxy-TEMPO revealed that it was composed of approximately 94% S and approximately 6% (R) isomers. This assures largely a uniform orientation of mLG molecules in the ptLOX active center, with their methyl end most likely deepened into the protein globule. The second major product, 13-(Z,E)-HPODE-GE, which yielded approximately 9% of the total product formed in the presence of 4-hydroxy-TEMPO, was racemic, and so were the all-trans isomers. Therefore, the last three cannot be considered the true products of the enzyme reaction, which is known to be stereospecific. It appears that they were formed as a result of (i) leakage of the pentadienyl radicals from the ptLOX active center and their subsequent non-enzymatic dioxygenation, and/or (ii) leakage of the peroxyl radicals leading to a free radical chain reaction affording all positional, geometrical and stereoisomers of the products. This reaction resembles ptLOX oxidation of another non-ionizable substrate, linoleyl alcohol [I.A. Butovich, S.M. Luk'yanova, C.C. Reddy, Arch. Biochem. Biophys. 378 (2000) 65-77], and differed substantially from oxidation of ionizable linoleic acid. Consequently, formation of large amounts of the non-specific oxidation products might be considered a universal characteristic of ptLOX oxidation of non-ionizable compounds. PMID:11295443

  13. Iodine-catalyzed oxidative coupling reactions utilizing c?h and x?h as nucleophiles.

    PubMed

    Liu, Dong; Lei, Aiwen

    2015-04-01

    In recent decades, iodine-catalyzed oxidative coupling reactions utilizing C?H and X?H as nucleophiles have received considerable attention because they represent more efficient, greener, more atom-economical, and milder bond-formation strategies over transition-metal-catalyzed oxidative coupling reactions. This Focus Review gives a brief summary of recent development on iodine-catalyzed oxidative coupling reactions utilizing C?H and X?H as nucleophiles. PMID:25683644

  14. Good vibrations in enzyme-catalysed reactions

    NASA Astrophysics Data System (ADS)

    Hay, Sam; Scrutton, Nigel S.

    2012-03-01

    Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.

  15. Fundamental Reaction Mechanism and Free Energy Profile for (?)-Cocaine Hydrolysis Catalyzed by Cocaine Esterase

    PubMed Central

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

    2009-01-01

    Fundamental reaction mechanism of cocaine esterase (CocE)-catalyzed hydrolysis of (?)-cocaine and the corresponding free energy profile have been studied by performing pseudobond first-principle quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Based on the QM/MM-FE results, the entire hydrolysis reaction consists of four reaction steps, including the nucleophilic attack on carbonyl carbon of (?)-cocaine benzoyl ester by hydroxyl group of Ser117, dissociation of (?)-cocaine benzoyl ester, nucleophilic attack on carbonyl carbon of (?)-cocaine benzoyl ester by water, and finally the dissociation between (?)-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 (where the formation of prereactive BChE-(?)-cocaine complex is rate-determining) or its mutants containing Tyr332Gly or Tyr332Gly 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 present study, where many sodium ions are present, the effects of counter ions are found to be significant in determining the free energy barrier. The finding of the significant effects of counter ions on the free energy barrier may also be valuable in guiding future mechanistic studies on other charged enzymes. PMID:19642701

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

    E-print Network

    RajanBabu, T. V. "Babu"

    . Stoichiometric reaction of complexes 10e* and 10j* with the sodium salt of diethyl malonate gave malonate adducts-Catalyzed Allylation Reaction: Making Both Enantiomers of a Product in High Optical Purity Using the Same Source in the palladium-catalyzed asymmetric allylation reaction between 1,3-diphe- nylprop-2-en-1-yl acetate

  17. Highly Enantioselective Rh-Catalyzed Intramolecular AlderEne Reactions for the

    E-print Network

    Zhang, Xumu

    Highly Enantioselective Rh-Catalyzed Intramolecular Alder±Ene Reactions for the Syntheses of Chiral, the enantioselective processes of metal-catalyzed Alder±ene reactions are relatively unex- plored and the development intramolecular Alder±ene reactions of enynes using a [{Rh(diphos)Cl}2] precursor.[4] Enantioselectivities between

  18. Does nature click? Theoretical prediction of an enzyme-catalyzed transannular 1,3-dipolar cycloaddition in the biosynthesis of lycojaponicumins A and B.

    PubMed

    Krenske, Elizabeth H; Patel, Ashay; Houk, K N

    2013-11-20

    Biosynthetic 1,3-dipolar cycloadditions are rare. No enzymes have yet been identified whose function is to catalyze this class of reactions. Recently, however, a 1,3-dipolar cycloaddition was proposed as a key step in the biosynthesis of two Lycopodium alkaloids, lycojaponicumins A and B. The lycojaponicumins' fused bicyclic tetrahydroisoxazole ring system was proposed to originate from a transannular 1,3-dipolar cycloaddition between a nitrone and an enone in a nine-membered macrocycle. We have used quantum mechanical calculations to predict whether this cycloaddition could constitute a feasible step in a biosynthetic pathway. Our calculations define a general computational approach for analyzing whether a putative biosynthetic reaction is likely to be enzyme-catalyzed. The quantum mechanically predicted rate of the uncatalyzed reaction in water is compared with the rate enhancement theoretically achievable when the reaction is catalyzed by a theozyme (theoretical enzyme). Density functional theory calculations (M06-2X) predict that the uncatalyzed transannular 1,3-dipolar cycloaddition of the putative lycojaponicumin precursor in water is moderately facile (?G(++) = 21.5 kcal/mol, k = 10(-3) s(-1)) and that an enzyme could accelerate the cycloaddition by placing hydrogen bond donors around the enone while maintaining an otherwise nonpolar active site. The theoretical enzyme-catalyzed process has ?G(++) ? 17 kcal/mol, corresponding to a 2000-fold rate enhancement, and the predicted kcat (2 s(-1)) is similar to those of known enzymes involved in secondary metabolic pathways. Thus, theory predicts that the proposed transannular 1,3-dipolar cycloaddition is a plausible step in a biosynthetic pathway leading to the lycojaponicumins and suggests that dipolar cycloadditions can be accelerated by enzyme catalysis. PMID:24195703

  19. Theoretical study on the BF3-catalyzed Meinwald rearrangement reaction.

    PubMed

    Fraile, José María; Mayoral, José Antonio; Salvatella, Luis

    2014-07-01

    The mechanisms of the BF3-catalyzed Meinwald rearrangement reactions of five epoxides in dichloromethane solution have been studied at the M062X/6-311++G(2df,2pd) level. Accordingly, the Lewis acid-epoxide complex can react through several alternative pathways, though three phases (ring opening, C-C bond rotation, and hydrogen or alkyl group migration) are required in any path. In some cases, a concerted pathway (involving all three successive phases) is found. Otherwise, the reaction takes place through a reaction mechanism involving a zwitterion or a BF3 addition compound (formed by fluoride transfer from the BF3 moiety to the incipient carbocationic center generated by C-O bond rupture) or both as reaction intermediate(s). The BF2-bound fluorohydrin yields the reaction product through a concerted process involving fluoride transfer from the C-F bond to the OBF2 group and hydrogen or alkyl group migration, as first demonstrated in this work. Effects of a number of features (solvent effects, concurrent hydrogen/alkyl group migration, carbocation substitution, benzylic conjugation) are also discussed. PMID:24893807

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

    SciTech Connect

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

    2000-06-15

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

  1. 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.

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

    PubMed

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

    2014-03-18

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

  3. 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 100W, 25kHz frequency and 50% duty cycle with agitation speed of 200rpm. It is observed that enzymatic degradation of Cetirizine dihydrochloride under the influence of ultrasound irradiation not only enhances the degradation but also reduces the time of degradation as compared to conventional enzymatic degradation technique. PMID:25515235

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

    PubMed

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

    2015-03-01

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

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

    E-print Network

    Ng, Sze-Sze

    2008-01-01

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

  6. One substrate, five products: reactions catalyzed by the dihydroneopterin aldolase from Mycobacterium tuberculosis

    PubMed Central

    Czekster, Clarissa M.; Blanchard, John S.

    2012-01-01

    Tetrahydrofolate cofactors are required for one carbon transfer reactions involved in the synthesis of purines, amino acids, and thymidine. Inhibition of tetrahydrofolate biosynthesis is a powerful therapeutic strategy in the treatment of several diseases, and the possibility of using antifolates to inhibit enzymes from Mycobacterium tuberculosis has been explored. This work focuses on the study of the first enzyme in tetrahydrofolate biosynthesis that is unique to bacteria, dihydroneopterin aldolase (MtDHNA). This enzyme requires no metals or cofactors, and does not form a protein mediated Schiff base with the substrate, unlike most aldolases. Here, we were able to demonstrate that the reaction catalyzed by MtDHNA generates three different pterin products, one of which is not produced by other wild type DHNAs. The enzyme-substrate complex partitions 51% in the first turnover to form the aldolase product, 24% to the epimerase product, and 25% to the oxygenase product. The aldolase reaction is strongly pH-dependent, and apparent pKa values were obtained for the first time for this class of enzyme. Furthermore, chemistry is rate-limiting for the aldolase reaction, and the analysis of solvent kinetic isotope effects in steady-state and pre-steady-state conditions, combined with proton inventory studies revealed that two protons and a likely solvent contribution are involved in formation and breakage of a common intermediate. This study provides information about the plasticity required from a catalyst that possesses high substrate specificity while being capable of utilizing two distinct epimers with the same efficiency to generate five distinct products. PMID:23150985

  7. THE TRIACYLGLYCEROL SYNTHESIS ENZYME DGAT1 ALSO CATALYZES THE SYNTHESIS OF DIACYLGLYCEROLS, WAXES, AND RETINYL ESTERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The final step of triacylglycerol biosynthesis is catalyzed by acyl CoA:diacylglycerol acyltransferase (DGAT) enzymes. The two known DGATs, DGAT1 and DGAT2, are encoded by unrelated genes. Although both DGAT1 and DGAT2 knockout mice have reduced tissue triacylglycerol contents, they have disparate p...

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

    PubMed

    Chelucci, Giorgio; Baldino, Salvatore; Baratta, Walter

    2015-02-17

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

  9. 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.

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

    PubMed

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

    2014-01-15

    Nanoparticle-catalyzed reductive bleaching reactions of colored substrates are emerging as a class of novel indicator reactions for fabricating enzyme-free amplified colorimetric biosensing (turn-off mode), which are exactly opposite to the commonly used oxidative coloring processes of colorless substrates in traditional enzyme-catalyzed amplified colorimetric bioassays (turn-on mode). In this work, a simple theoretical analysis shows that the sensitivity of this colorimetric bioassay can be improved by increasing the amplification factor (kcat?t), or enhancing the binding affinity between analyte and receptor (Kd), or selecting the colored substrates with high extinction coefficients (?). Based on this novel strategy, we have developed a turn-off and cost-effective amplified colorimetric thrombin aptasensor. This aptasensor made full use of sandwich binding of two affinity aptamers for increased specificity, magnetic particles for easy separation and enrichment, and gold nanoparticle (AuNP)-catalyzed reductive bleaching reaction to generate the amplified colorimetric signal. With 4-nitrophenol (4-NP) as the non-dye colored substrate, colorimetric bioassay of thrombin was achieved by the endpoint method with a detection limit of 91pM. In particular, when using methylene blue (MB) as the substrate, for the first time, a more convenient and efficient kinetic-based colorimetric thrombin bioassay was achieved without the steps of acidification termination and magnetic removal of particles, with a low detection limit of 10pM, which was superior to the majority of the existing colorimetric thrombin aptasensors. The proposed colorimetric protocol is expected to hold great promise in field analysis and point-of-care applications. PMID:23962710

  11. Acid-catalyzed reactions of epoxides for atmospheric nanoparticle growth.

    PubMed

    Xu, Wen; Gomez-Hernandez, Mario; Guo, Song; Secrest, Jeremiah; Marrero-Ortiz, Wilmarie; Zhang, Annie L; Zhang, Renyi

    2014-11-01

    Although new particle formation accounts for about 50% of the global aerosol production in the troposphere, the chemical species and mechanism responsible for the growth of freshly nucleated nanoparticles remain largely uncertain. Here we show large size growth when sulfuric acid nanoparticles of 4-20 nm are exposed to epoxide vapors, dependent on the particle size and relative humidity. Composition analysis of the nanoparticles after epoxide exposure reveals the presence of high molecular weight organosulfates and polymers, indicating the occurrence of acid-catalyzed reactions of epoxides. Our results suggest that epoxides play an important role in the growth of atmospheric newly nucleated nanoparticles, considering their large formation yields from photochemical oxidation of biogenic volatile organic compounds. PMID:25338124

  12. Reaction Pathway and Free Energy Profile for Cocaine Hydrolase-Catalyzed Hydrolysis of (?)-Cocaine

    PubMed Central

    Liu, Junjun; Zhan, Chang-Guo

    2012-01-01

    Reaction pathway of (?)-cocaine hydrolysis catalyzed by our recently discovered most efficient cocaine hydrolase, which is the A199S/F227A/S287G/A328W/Y332G mutant of human butyrylcholinesterase (BChE), and the corresponding free energy profile have been studied by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Based on the QM/MM-FE results, the catalytic hydrolysis process consists of four major reaction steps, including the nucleophilic attack on carbonyl carbon of (?)-cocaine benzoyl ester by hydroxyl group of S198, dissociation of (?)-cocaine benzoyl ester, nucleophilic attack on carbonyl carbon of (?)-cocaine benzoyl ester by water, and finally the dissociation between (?)-cocaine benzoyl group and S198 of the enzyme. The second reaction step is rate-determining. The calculated free energy barrier associated with the transition state for the rate-determining step is ~15.0 kcal/mol, which is in excellent agreement with the experimentally-derived activation free energy of ~14.7 kcal/mol. The mechanistic insights obtained from the present study will be valuable for rational design of more active cocaine hydrolase against (?)-cocaine. In particular, future efforts aiming at further increasing the catalytic activity of the enzyme against (?)-cocaine should focus on stabilization of the transition state for the second reaction step in which the benzoyl ester of (?)-cocaine dissociates. PMID:23066354

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

    PubMed

    Sugumaran, M; Ricketts, D

    1995-01-01

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

  14. Pd/C catalyzed Suzuki-Miyaura cross coupling reaction: Is it heterogeneous or homogeneous?

    NASA Astrophysics Data System (ADS)

    Hoang, Tony Phuc

    The Suzuki-Miyaura cross-coupling reaction is a popular industrial method of creating covalent bonds between two carbons. This reaction can be catalyzed by a myriad of palladium catalyst including heterogeneous and homogeneous. The objective of this research is to study whether the Suzuki cross coupling reaction catalyzed by solid supported palladium catalysts is truly heterogeneous in nature (i.e. does the reaction occurs on the surface of the catalyst or does palladium leach from the solid support and catalyze the reaction in a homogenous manner).

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

    PubMed Central

    Wang, Chongnian; Li, Zengchang

    2015-01-01

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

  16. Enantioselective carbonyl-ene reactions catalyzed by chiral cationic dirhodium(II,III) carboxamidates.

    PubMed

    Xu, Xichen; Wang, Xiaochen; Liu, Yuxiao; Doyle, Michael P

    2014-12-19

    An enantioselective carbonyl-ene reaction of glyoxylate esters with 1,1-disubstituted alkenes catalyzed by chiral cationic dirhodium(II,III) carboxamidates is described. The paddlewheel dirhodium(II,III) carboxamidates having one open coordination site at each rhodium smoothly catalyze the carbonyl-ene reaction to afford homoallylic alcohol products in good isolated yields with high enantioselectivities. PMID:25084486

  17. 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

    Both phosphoryl and sulfuryl transfers are ubiquitous in biology, being involved in a wide range of processes, ranging from cell division to apoptosis. Additionally, it is becoming increasingly clear that enzymes that can catalyze phosphoryl transfer can often cross-catalyze sulfuryl transfer (and vice versa). However, while there have been extensive experimental and theoretical studies performed on phosphoryl transfer, the body of available research on sulfuryl transfer is comparatively much smaller. The present work presents a direct theoretical comparison of p-nitrophenyl phosphate and sulfate monoester hydrolysis, both of which are considered prototype systems for probing phosphoryl and sulfuryl transfer, respectively. Specifically, free energy surfaces have been generated using density functional theory, by initial geometry optimization in PCM using the 6-31+G* basis set and the B3LYP density functional, followed by single-point calculations using the larger 6-311+G** basis set and the COSMO continuum model. The resulting surfaces have been then used to identify the relevant transition states, either by further unconstrained geometry optimization or from the surface itself where possible. Additionally, configurational entropies were evaluated using a combination of the quasiharmonic approximation and the restraint release approach and added to the calculated activation barriers as a correction. Finally, the overall activation entropy was estimated by approximating the solvent contribution to the total activation entropy using the Langevin dipoles solvation model. We have reproduced both the experimentally observed activation barriers and the observed trend in the activation entropies with reasonable accuracy, as well as providing a comparison of calculated and observed (15)N and (18)O kinetic isotope effects. We demonstrate that, counterintuitively, the hydrolysis of the p-nitrophenyl sulfate proceeds through a more expansive pathway than its phosphate 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. PMID:21981415

  18. 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)

  19. Enzyme-catalyzed and enzyme-triggered pathways in dioxygenation of 1-monolinoleoyl- rac-glycerol by potato tuber lipoxygenase

    Microsoft Academic Search

    I. A. Butovich; C. Channa Reddy

    2001-01-01

    It was shown for the first time that potato tuber lipoxygenase (ptLOX) catalyzed the aerobic oxidation of 1-monolinoleoyl-rac-glycerol (mLG) in a mixed micellar reaction solution with the non-ionic detergent monododecyl ether of decaoxyethylene glycol. No hydrolysis of mLG occurred during the reaction. The four major reaction products obtained at 23°C were identified as 1-[9-hydroperoxy-10E,12Z-octadecadienoyl]-rac-glycerol (9-(E,Z)HPODE-GE, 41%), 1-[13-hydroperoxy-9Z,11E-octadecadienoyl]-rac-glycerol (13-(Z,E)-HPODE-GE, 17%), and

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

    PubMed

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

    2014-12-01

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

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

    E-print Network

    Moslin, Ryan Thomas McLeod

    2007-01-01

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

  2. Reactions of biological antioxidants: I. Fe(III)-catalyzed reactions of lipid hydroperoxides with ?-tocopherol

    Microsoft Academic Search

    E. H. Gruger; A. L. Tappel

    1970-01-01

    Rates of ?-tocopherol oxidation were measured for free-radical reactions produced by Fe(III)-catalyzed dissociations of hydroperoxides.\\u000a The kinetics were treated as first-order in ?-tocopherol. The hydroperoxides were preformed from methyl linoleate, methyl\\u000a linolenate, ethyl arachidonate, methyl eicosapentaenoate, and a fraction of polyunsaturated fatty esters of menhaden oil.\\u000a The degree of unsaturation of the lipid hydroperoxides had little effect on the rates

  3. Tandem three-component reactions of aldehyde, alkyl acrylate, and dialkylmalonate catalyzed by ethyl diphenylphosphine.

    PubMed

    Jang, Yeong-Jiunn; Syu, Siang-En; Jhang, Yi-Wun; Lee, Yu-Ting; Lee, Chia-Jui; Chen, Ko-Wei; Das, Utpal; Lin, Wenwei

    2012-01-01

    A new highly efficient three-component reaction of alkyl acrylate, aldehyde and dialkyl malonate using ethyl diphenylphosphine as organocatalyst has been described. Various highly functional compounds bearing hydroxyl groups and the ester functions can be easily prepared in moderate to good yields according to our one-step procedure. The reactions are believed to proceed via Morita-Baylis-Hillman reactions of alkyl acrylate and aldehydes, followed by the Michael addition reactions of dialkyl malonates. Our reactions indicated that the intermediate species formed in the phosphine-catalyzed MBH reaction are an effective organic base to catalyze the Michael addition reactions of dialkyl malonates to the preformed MBH adducts. PMID:22446986

  4. Direct transfer of the phosphoryl moiety of mannitol 1-phosphate to [14C]mannitol catalyzed by the enzyme II complexes of the phosphoenolpyruvate: mannitol phosphotransferase systems in Spirochaeta aurantia and Salmonella typhimurium.

    PubMed

    Saier, M H; Newman, M J

    1976-06-25

    Spirochaeta aurantia possesses a phosphoenolpyruvate:mannitol phosphotransferase system which catalyzes the transmembrane transport and phosphorylation of mannitol. In vitro studies showed that both phosphoenolpyruvate and mannitol 1-phosphate could serve as phosphate donors. The phosphoenolpyruvate-dependent reaction required two soluble proteins, Enzyme SI and HPr, and an integral membrane complex, Enzyme SII. Only Enzyme SII was required for the mannitol 1-phosphate-dependent reaction. Enzyme II-dependent transphosphorylation of sugars was also demonstrated in eubacterial extracts. The results lead to the suggestion that the Enzyme II complexes of bacterial phosphotransferase systems possess nonoverlapping binding sites for sugar and sugar phosphate. PMID:819432

  5. CYP3As catalyze nifedipine oxidation in pig liver microsomes: Enzyme kinetics, inhibition and functional expression

    Microsoft Academic Search

    Jun Jiang; Junping Wang; Hua Cai; Kangbai Li; Yiqun Deng

    2011-01-01

    Cytochrome P450 (CYP) 3As have received much attention because of their importance in drug metabolism. However, information on CYP3As in pigs is still largely incomplete. Herein, we focused on the involvement of CYP3As in nifedipine oxidation in pig liver microsomes. Enzyme kinetics, inhibition and immunochemical studies indicated that CYP3As might catalyze nifedipine oxidation and that ketoconazole could strongly inhibit this

  6. Exploring chain length selectivity in HIC-catalyzed polycondensation reactions.

    PubMed

    Feder, David; Gross, Richard A

    2010-03-01

    Polyester synthesis activity of immobilized Humicola insolens (HiC) was systematically studied with three-series of substrates varying in (i) omega-hydroxyalkanoic acid (omegaHA), (ii) alpha,omega-n-alkane diol, and (iii) alpha,omega-n-alkane diacid chain length. Covalent immobilization of HiC on Amberzyme oxirane (AO) resin (i.e., AO-HiC) was prepared. HiC-AO's activity for omegaHA substrates with 6, 10, 12, and 16 carbons was C16 > C12, where C10-omegaHA and C6-omegaHA were not polymerized. In contrast, N435's activity for omegaHA substrates was C16 = C12 > C10, where C6-omegaHA was not polymerized. HiC-AO activity for copolymerization of sebacic acid (C10-diacid) with alpha,omega-n-alkane diols with 3-, 4-, 5-, 6-, and 8-carbon chain lengths was C8 > C6, where C3, C4, and C5 diols were not polymerized. N435's relative activity for diol substrates was C8 = C6 = C5 > C4 > C3. HiC-AO activity for copolymerizations of 1,8-octanediol with alpha,omega-n-alkane diacids with 6-, 8-, 9-, 10-, and 13-carbon chain lengths was C13 = C10, where HiC showed little activity for C6, C8, and C9 diacid copolymerization. N435 displayed similar activity for all these diacid chain lengths. Thus, N435 has a broader substrate promiscuity than HiC-AO. This is most apparent for shorter chain length omegaHA, diol, and diacid monomers. These trends were similarly observed for a series of small molecule esterification reactions. Comparison of HiC-AO- and N435-catalyzed C16-HA homopolymerization at 8 h gave polymers with M(n) 40.4 and 25.5 kg/mol, respectively. Furthermore, HiC-AO- and N435-catalyzed copolymerization of 1,8-octanediol/C13-diacid polymerizations at 8 h gave polymers with M(n) of 11.0 and 9.6 kg/mol, respectively. PMID:20095578

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

    E-print Network

    Naber, John R. (John Robert)

    2010-01-01

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

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

    E-print Network

    Strieter, Eric R

    2005-01-01

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

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

    E-print Network

    Teverovskiy, Georgiy

    2013-01-01

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

  10. Mechanism and Transition-State Structures for Nickel-Catalyzed Reductive Alkyne?Aldehyde Coupling Reactions

    E-print Network

    McCarren, P. R.

    The mechanism of nickel-catalyzed reductive alkyne?aldehyde coupling reactions has been investigated using density functional theory. The preferred mechanism involves oxidative cyclization to form the nickeladihydrofuran ...

  11. An efficient route to highly strained cyclobutenes: indium-catalyzed reactions of enynals with alkynes.

    PubMed

    Liang, Renxiao; Jiang, Huanfeng; Zhu, Shifa

    2015-03-12

    A catalytic method to synthesize the highly strained cyclobutene was developed. The reaction was believed to proceed through a formal indium-catalyzed [2+2] cycloaddition between electron-deficient enynals and various alkynes. PMID:25578629

  12. Nickel-catalyzed reaction of thioisatins and alkynes: a facile synthesis of thiochromones.

    PubMed

    Inami, Tasuku; Kurahashi, Takuya; Matsubara, Seijiro

    2014-11-01

    A new synthetic method for thiochromones was developed by using nickel-catalyzed decarbonylative cycloaddition of readily available thioisatins with alkynes. This reaction proceeded under very mild conditions and has quite high functional group compatibility. PMID:25347619

  13. Chemoenzymatic synthesis of thiazolyl Peptide natural products featuring an enzyme-catalyzed formal [4 + 2] cycloaddition.

    PubMed

    Wever, Walter J; Bogart, Jonathan W; Baccile, Joshua A; Chan, Andrew N; Schroeder, Frank C; Bowers, Albert A

    2015-03-18

    Thiocillins from Bacillus cereus ATCC 14579 are members of the well-known thiazolyl peptide class of natural product antibiotics, the biosynthesis of which has recently been shown to proceed via post-translational modification of ribosomally encoded precursor peptides. It has long been hypothesized that the final step of thiazolyl peptide biosynthesis involves a formal [4 + 2] cycloaddition between two dehydroalanines, a unique transformation that had eluded enzymatic characterization. Here we demonstrate that TclM, a single enzyme from the thiocillin biosynthetic pathway, catalyzes this transformation. To facilitate characterization of this new class of enzyme, we have developed a combined chemical and biological route to the complex peptide substrate, relying on chemical synthesis of a modified C-terminal fragment and coupling to a 38-residue leader peptide by means of native chemical ligation (NCL). This strategy, combined with active enzyme, provides a new chemoenzymatic route to this promising class of antibiotics. PMID:25742119

  14. Fundamental Reaction Pathway and Free Energy Profile for Butyrylcholinesterase-Catalyzed Hydrolysis of Heroin

    PubMed Central

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

    2013-01-01

    The pharmacological function of heroin requires an activation process which transforms heroin into 6-monoacetylmorphine (6-MAM) which is the most active form. The primary enzyme responsible for this activation process in human plasma is butyrylcholinesterase (BChE). The detailed reaction pathway of the activation process via BChE-catalyzed hydrolysis has been explored computationally, for the first time, in the present study by performing molecular dynamics simulation and first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the whole reaction process includes acylation and deacylation stages. The acylation consists of two reaction steps, i.e. the nucleophilic attack on the carbonyl carbon of 3-acetyl group of heroin by the hydroxyl oxygen of Ser198 side chain and the dissociation of 6-MAM. The deacylation also consists of two reaction steps, i.e. the nucleophilic attack on the carbonyl carbon of the acyl-enzyme intermediate by a water molecule and the dissociation of the acetic acid from Ser198. The calculated free energy profile reveals that the second transition state (TS2) should be rate-determining. The structural analysis reveals that the oxyanion hole of BChE plays an important role in the stabilization of the rate-determining transition state TS2. The free energy barrier (15.9±0.2 or 16.1±0.2 kcal/mol) calculated for the rate-determining step is in good agreement with the experimentally-derived activation free energy (~16.2 kcal/mol), suggesting that the mechanistic insights obtained from the present computational study are reliable. The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse. PMID:23992153

  15. Heterogeneous catalyzed decomposition reactions of dichlorodifluoromethane in the presence of water on ?-alumina

    Microsoft Academic Search

    E. Kemnitz; A. Kohne; E. Lieske

    1997-01-01

    The heterogeneous catalyzed decomposition of CCl2F2 (CFC-12) in the presence of water was investigated, employing ?-alumina as catalyst. The catalyzed hydrolysis reaction yields very high conversion degrees of CFC-12 in the first reaction stage. For a period of about 3 h there is a remarkable lack of balance between the amount of liberated HF and HCl owing to the uptake

  16. A free-standing condensation enzyme catalyzing ester bond formation in C-1027 biosynthesis.

    PubMed

    Lin, Shuangjun; Van Lanen, Steven G; Shen, Ben

    2009-03-17

    Nonribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of many biologically active peptides and typically are modular, with each extension module minimally consisting of a condensation, an adenylation, and a peptidyl carrier protein domain responsible for incorporation of an amino acid into the growing peptide chain. C-1027 is a chromoprotein antitumor antibiotic whose enediyne chromophore consists of an enediyne core, a deoxy aminosugar, a benzoxazolinate, and a beta-amino acid moiety. Bioinformatics analysis suggested that the activation and incorporation of the beta-amino acid moiety into C-1027 follows an NRPS mechanism whereby biosynthetic intermediates are tethered to the peptidyl carrier protein SgcC2. Here, we report the biochemical characterization of SgcC5, an NRPS condensation enzyme that catalyzes ester bond formation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core. SgcC5 uses (S)-3-chloro-5-hydroxy-beta-tyrosyl-SgcC2 as the donor substrate and exhibits regiospecificity for the C-2 hydroxyl group of the enediyne core mimic as the acceptor substrate. Remarkably, SgcC5 is also capable of catalyzing amide bond formation, albeit with significantly reduced efficiency, between (S)-3-chloro-5-hydroxy-beta-tyrosyl-(S)-SgcC2 and (R)-2-amino-1-phenyl-1-ethanol, an alternative enediyne core mimic bearing an amine at its C-2 position. Thus, SgcC5 is capable of catalyzing both ester and amide bond formation, providing an evolutionary link between amide- and ester-forming condensation enzymes. PMID:19246381

  17. 4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate

    E-print Network

    Herschlag, Dan

    4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate nucleophilic substitution reactions of the phosphate diester, methyl 2,4-dinitrophenylphosphate monoanion in enzymatic reactions of phosphate diesters are discussed. Asulfur atom has been substituted for a nonbridging

  18. ENZYME: Enzyme Nomenclature Database

    NSDL National Science Digital Library

    Recently updated, the ENZYME: Enzyme Nomenclature Database is based mainly on recommendations by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and "describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided." An online user manual describes how to access and use the database, which may be searched by EC number, enzyme class, official description or alternative name(s), chemical compound, or cofactor. Typical returns include Names, Reaction catalyzed, Comments, Human Genetic Diseases, and a host of hyperlinked cross-references. ENZYME is provided by the Swiss Institute of Bioinformatics.

  19. Enzyme-catalyzed conversion of chemical structures on the surface of gold nanorods.

    PubMed

    Kusaka, Eriko; Ito, Takeo; Tanabe, Kazuhito; Nishimoto, Sei-ichi

    2013-09-18

    For developing metal nanoparticles of which surface chemical structures could be altered by enzymes in the cells, functional linkers caged by coumaric acids have been synthesized. Synthesized gold nanorod (GNR) conjugates possessing coumaric acid precursors underwent (porcine liver) esterase-catalyzed hydrolysis on their surface to afford GNRs coated with amino-functionalized polyethylene glycol and fluorescent coumarins as reporter molecules for monitoring the conversion. The chemical structural conversion on the GNR surfaces was successfully observed inside cells by fluorescence microscopy when GNR conjugates were incubated with tumor cells. PMID:23889000

  20. 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.

  1. IAA-synthase, an enzyme complex from Arabidopsis thaliana catalyzing the formation of indole-3-acetic acid from (S)-tryptophan.

    PubMed

    Müller, A; Weiler, E W

    2000-08-01

    An enzyme complex was isolated from Arabidopsis thaliana that catalyzes the entire pathway of biosynthesis of the major plant growth hormone, indole-3-acetic acid (IAA), from (S)-tryptophan. The 160-180 kDa, soluble complex catalyzes a strictly O2-dependent reaction which requires no further added factors and is stereospecific for the substrate (S)-tryptophan (app. Km = 120 microM). H2(18)O labeling proved that both oxygen atoms of IAA were delivered via H2O. This, as well as immunological evidence for the presence of a nitrilase-like protein in the complex, suggests the reaction to proceed via the intermediate indole-3-acetonitrile. IAA-synthase forms a tight metabolite channel committed to IAA production and occurs in shoots, roots and cell cultures of A. thaliana. PMID:11030425

  2. Role of asparagine 510 in the relative timing of substrate bond cleavages in the reaction catalyzed by choline oxidase.

    PubMed

    Rungsrisuriyachai, Kunchala; Gadda, Giovanni

    2010-03-23

    The flavoprotein choline oxidase catalyzes the oxidation of choline to glycine betaine with transient formation of an aldehyde intermediate and molecular oxygen as final electron acceptor. The enzyme has been grouped in the glucose-methanol-choline oxidoreductase enzyme superfamily, which shares a highly conserved His-Asn catalytic pair in the active site. In this study, the conserved asparagine residue at position 510 in choline oxidase was replaced with alanine, aspartate, histidine, or leucine by site-directed mutagenesis, and the resulting mutant enzymes were purified and characterized in their biochemical and mechanistic properties. All of the substitutions resulted in low incorporation of FAD into the protein. The Asn510Asp enzyme was not catalytically active with choline and had 75% of the flavin associated noncovalently. The most notable changes in the catalytic parameters with respect to wild-type choline oxidase were seen in the Asn510Ala enzyme, with decreases of 4300-fold in the k(cat)/K(choline), 600-fold in the k(red), 660-fold in the k(cat), and 50-fold in the k(cat)/K(oxygen) values. Smaller, but nonetheless similar, changes were seen also in the Asn510His enzyme. Both the K(d) and K(m) values for choline changed < or = 7-fold. These data are consistent with Asn510 participating in both the reductive and oxidative half-reactions but having a minimal role in substrate binding. Substrate, solvent, and multiple kinetic isotope effects on the k(red) values indicated that the substitution of Asn510 with alanine, but not with histidine, resulted in a change from stepwise to concerted mechanisms for the cleavages of the OH and CH bonds of choline catalyzed by the enzyme. PMID:20163155

  3. 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

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

    PubMed

    Abeysinghe, Thelma; Kohen, Amnon

    2015-01-01

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

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

    PubMed

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

    2012-10-16

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

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

    PubMed

    Lyons, Thomas W; Brookhart, Maurice

    2013-07-29

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

  8. An alternative approach to aldol reactions: gold-catalyzed formation of boron enolates from alkynes.

    PubMed

    Körner, Cindy; Starkov, Pavel; Sheppard, Tom D

    2010-05-01

    A new method for enolate generation via the gold-catalyzed addition of boronic acids to alkynes is reported. The formation of boron enolates from readily accessible ortho-alkynylbenzeneboronic acids proceeds rapidly with 2 mol % PPh(3)AuNTf(2) at ambient temperature. The enolates undergo aldol reaction with an aldehyde present in the reaction mixture to give cyclic boronate esters, which can be subsequently transformed into phenols, biaryls, or dihydrobenzofurans via oxidation, Suzuki-Miyaura, or intramolecular Chan-Lam coupling, respectively. A combined gold/boronic acid catalyzed aldol condensation reaction of an alkynyl aldehyde was also successfully achieved. PMID:20380452

  9. The Use of Tertiary Alkylmagnesium Nucleophiles in Ni-Catalyzed Cross-Coupling Reactions

    PubMed Central

    Joshi-Pangu, Amruta

    2013-01-01

    Nickel-catalyzed cross-coupling reactions of unactivated tertiary alkyl nucleophiles and aryl bromides have been developed using N-heterocyclic carbene ligands. These processes are reviewed alongside earlier attempts to employ unactivated tertiary alkyl nucleophiles in cross-coupling reactions. Potential mechanisms for the transformations, and future challenges in this field are discussed. PMID:23641126

  10. Palladium-catalyzed three-component cascade reaction: facial access to densely functionalized indolizines.

    PubMed

    Liu, Ren-Rong; Lu, Chuan-Jun; Zhang, Ming-Di; Gao, Jian-Rong; Jia, Yi-Xia

    2015-05-01

    A palladium-catalyzed three-component cascade reaction of 2-(2-enynyl)pyridines with nucleophiles and allyl halides has been developed, enabling the synthesis of densely functionalized indolizines in moderate to good yields. The newly developed methodology offers several practical advantages, including operational simplicity, ready availability of starting materials, and mild reaction conditions. PMID:25808277

  11. N-Heterocyclic Carbene-Catalyzed Radical Reactions for Highly Enantioselective ?-Hydroxylation of Enals.

    PubMed

    Zhang, Yuexia; Du, Yu; Huang, Zhijian; Xu, Jianfeng; Wu, Xingxing; Wang, Yuhuang; Wang, Ming; Yang, Song; Webster, Richard D; Chi, Yonggui Robin

    2015-02-25

    An N-heterocyclic carbene-catalyzed ?-hydroxylation of enals is developed. The reaction goes through a pathway involving multiple radical intermediates, as supported by experimental observations. This oxidative single-electron-transfer reaction allows for highly enantioselective access to ?-hydroxyl esters that are widely found in natural products and bioactive molecules. PMID:25651161

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

    Microsoft Academic Search

    Kui K. Chan; M Wood; Alexander A. Fedorov; Elena V. Fedorov; Heidi J. Imker; Tina L. Amyes; John P. Richard; Steven C. Almo; John A. Gerlt

    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

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

    PubMed Central

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

    2013-01-01

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

  14. A Bifunctional Enzyme in a Single Gene Catalyzes the Incorporation of GlcN into the Aeromonas Core Lipopolysaccharide*

    PubMed Central

    Jimenez, Natalia; Vilches, Silvia; Lacasta, Anna; Regué, Miguel; Merino, Susana; Tomás, Juan M.

    2009-01-01

    The core lipopolysaccharide (LPS) of Aeromonas hydrophila AH-3 and Aeromonas salmonicida A450 is characterized by the presence of the pentasaccharide ?-d-GlcN-(1?7)-l-?-d-Hep-(1?2)-l-?-d-Hep-(1?3)-l-?-d-Hep-(1?5)-?-Kdo. Previously it has been suggested that the WahA protein is involved in the incorporation of GlcN residue to outer core LPS. The WahA protein contains two domains: a glycosyltransferase and a carbohydrate esterase. In this work we demonstrate that the independent expression of the WahA glycosyltransferase domain catalyzes the incorporation of GlcNAc from UDP-GlcNAc to the outer core LPS. Independent expression of the carbohydrate esterase domain leads to the deacetylation of the GlcNAc residue to GlcN. Thus, the WahA is the first described bifunctional glycosyltransferase enzyme involved in the biosynthesis of core LPS. By contrast in Enterobacteriaceae containing GlcN in their outer core LPS the two reactions are performed by two different enzymes. PMID:19805547

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

    PubMed Central

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

    2007-01-01

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

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

    E-print Network

    Baik, Mu-Hyun

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

  17. [Analogs of pyrophosphate in a pyrophosphorolysis reaction catalyzed by DNA polymerases].

    PubMed

    Rozovskaia, T A; Tarusova, N B; Minasian, Sh Kh; Atrazhev, A M; Kukhanova, M K

    1989-01-01

    The reaction of pyrophosphorolysis catalyzed by Escherichia coli DNA polymerase I Klenov fragment, calf thymus DNA polymerase alpha, rat liver DNA polymerase beta and AMV reverse transcriptase was studied. Some pyrophosphate (PPi) analogs were taken as low molecular weight substrates. It was shown that only imidodiphosphonic acid acted as the PPi substrate analog for the reactions catalyzed by DNA polymerases I and alpha, both imidodiphosphonic acid and methylenediphosphonic acid were active in the case of DNA polymerase beta and reverse transcriptase. Other analogs tested were neither nucleotide residue acceptors, nor inhibitors of the pyrophosphorolysis reaction with PPi. The abilities of some PPi analogs to inhibit the DNA elongation catalyzed by reverse transcriptase were investigated. The principles of specificity of low molecular substrates recognition by DNA polymerases and some problems concerning the mechanisms of DNA synthesis inhibition by PPi analogues are discussed. PMID:2549402

  18. 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.

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

    PubMed Central

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

    2013-01-01

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

  20. Imidazole-Catalyzed Henry Reactions in Aqueous Medium

    Microsoft Academic Search

    Mridula Phukan; Kalyan Jyoti Borah; Ruli Borah

    2008-01-01

    2-Nitroalkanols can be efficiently synthesized using imidazole as a mild Lewis basic catalyst in aqueous medium as well as in organic solvents. The products have been found in good yields without purification (> 95% purity by H NMR) for aromatic aldehydes. Additionally, the very mild reaction conditions prevent the particular side reactions such as aldol condensation, Cannizzaro reaction, or dehydration of

  1. Ionic Liquid Catalyzed the Internal Redox Esterification Reaction

    Microsoft Academic Search

    Yinyin Yu; Li Hua; Wenwen Zhu; Yu Shi; Ting Cao; Yunxiang Qiao; Zhenshan Hou

    2012-01-01

    The internal redox esterification of ?, ?-unsaturated aldehydes and alcohols was carried out using different ionic liquids (ILs) as catalysts and reaction solvent. The basic ionic liquid, 1-butyl-3-methylimidazolium acetate ([bmim]OAc) exhibited highest activity for this reaction among them. The influences of the amount of ionic liquid catalyst, and reaction time on yield of saturated ester have been investigated subsequently. The

  2. Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles

    E-print Network

    Boxer, Steven G.

    states of the reactions they catalyze (6, 7) and, combined with physical models to describe the enzyme­transition=kuncat = KS D KTS D ; [1] where kcat and kuncat are the enzyme-catalyzed and uncatalyzed unimolecular rate

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

    Microsoft Academic Search

    Yurie Mine; Lin Zhang; Kimitoshi Fukunaga; Yoshiaki Sugimura

    2005-01-01

    The solvent effects of cyclopentyl methyl ether (CPME) on the reaction rates and enzyme enantioselectivity in the enantioselective transesterifications of racemic 6-methyl-5-hepten-2-ol (racemic sulcatol: SUL) and racemic 2,2-dimethyl-1,3-dioxolane-4-methanol (racemic solketal: SOL) with a series of enol esters catalyzed by Pseudomonas cepacia lipase co-lyophilized with cyclodextrins (a-, ß-, ?-, partially methylated ß-,?and 2,3,6-tri-O-methyl-ß-cyclodextrin: aCyD; ßCyD; ?CyD; Me1.78 ßCyD; Me3ßCyD) were investigated

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

    PubMed

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

    2015-04-14

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

  5. L-cysteine desulfidase: an [4Fe-4S] enzyme isolated from Methanocaldococcus jannaschii that catalyzes the breakdown of L-cysteine into pyruvate, ammonia, and sulfide.

    PubMed

    Tchong, Shih-I; Xu, Huimin; White, Robert H

    2005-02-01

    A [4Fe-4S] enzyme that decomposes L-cysteine to hydrogen sulfide, ammonia, and pyruvate has been isolated and characterized from Methanocaldococcus jannaschii. The sequence of the isolated enzyme demonstrated that the protein was the product of the M. jannaschii MJ1025 gene. The protein product of this gene was recombinantly produced in Escherichia coli and purified to homogeneity. Both the isolated and recombinant enzymes are devoid of pyridoxal phosphate (PLP) and are rapidly inactivated upon exposure to air. The air-inactivated enzyme is activated by reaction with Fe2+ and dithiothreitol in the absence of air. The air-inactivated enzyme contains 3 mol of iron per subunit (43 kDa, SDS gel electrophoresis), and the native enzyme has a measured molecular mass of 135 kDa (gel filtration), indicating it is a trimer. The enzyme is very specific for L-cysteine, with no activity being detected with D-cysteine, L-homocysteine, 3-mercaptopropionic acid (cysteine without the amino group), cysteamine (cysteine without the carboxylic acid), or mercaptolactate (the hydroxyl analogue of cysteine). The activity of the enzyme was stimulated by 40% when the enzyme was assayed in the presence of methyl viologen (4 mM) and inhibited by 70% when the enzyme was assayed in the presence of EDTA (7.1 mM). Preincubation of the enzyme with iodoacetamide (17 mM) completely abolishes activity. The enzymatic activity has a half-life of 8 or 12 min when the enzyme is treated at room temperature with 0.42 mM N-ethylmaleimide (NEM) or 0.42 mM iodoacetamide, respectively. MALDI analysis of the NEM-inactivated enzyme showed Cys25 as the site of alkylation. Site-directed mutagenesis of each of four of the cysteines conserved in the orthologues of the enzyme reduced the catalytic efficiency and thermal stability of the enzyme. The enzyme was found to catalyze exchange of the C-2 hydrogen of the L-cysteine with solvent. These results are consistent with three of the conserved cysteines being involved in the formation of the [4Fe-4S] center and the thiolate of Cys25 serving as a base to abstract the alpha-hydrogen in the first step of the elimination. Although the enzyme has no sequence homology to any known enzymes, including the non-PLP-dependent serine/threonine dehydratases or aconitases, the mechanisms of action of all of these enzymes are similar, in that each catalyzes an alpha,beta-elimination reaction adjacent to a carboxylate group. It is proposed that the enzyme may be responsible for the production of sulfide required for the biosynthesis of iron-sulfur centers in this archaea. A mechanism of action of the enzyme is proposed. PMID:15683250

  6. An enzyme-free and amplified colorimetric detection strategy via target-aptamer binding triggered catalyzed hairpin assembly.

    PubMed

    Quan, Ke; Huang, Jin; Yang, Xiaohai; Yang, Yanjing; Ying, Le; Wang, He; He, Yong; Wang, Kemin

    2015-01-18

    Here we introduce an enzyme-free and colorimetric detection strategy for small molecule adenosine. The approach is based on the adenosine-aptamer binding triggered liberation of an initiator strand that consecutively catalyzes DNA hairpins hybridized from singles to couples. These couples induce gold nanoparticles assembled via crosslinking, which could be visualized by a color change. PMID:25435498

  7. The Enolase Superfamily: A General Strategy for Enzyme-Catalyzed Abstraction of the R-Protons of Carboxylic Acids

    E-print Network

    Rayment, Ivan

    -Protons of Carboxylic Acids Patricia C. Babbitt,*, Miriam S. Hasson,§,| Joseph E. Wedekind,,# David R. J. Palmer by their ability to catalyze the abstraction of the R-proton of a carboxylic acid to form an enolic intermediate specialized enzymes: mandelate racemase, galactonate dehydratase, glucarate dehydratase, muconate

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

    PubMed

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

    2014-12-19

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

  9. Enantioselective direct Mannich reactions of cyclic ?-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

    2015-02-01

    A combination of an amino acid derived chiral phosphine catalyst and methyl acrylate efficiently catalyzed the direct Mannich reaction of cyclic ?-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. PMID:25621822

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  11. Task-specific ionic liquid as base, ligand and reaction medium for the palladium-catalyzed Heck reaction

    Microsoft Academic Search

    Lei Wang; Hongji Li; Pinhua Li

    2009-01-01

    A novel ionic liquid, which was based on ethanolamine-functionalized quaternary ammonium salt was designed and synthesized. 4-Di(hydroxyethyl)aminobutyl tributylammonium bromide (DHEABTBAB) 1, a task-specific ionic liquid, which acts as a base, ligand and reaction medium, exhibits a very high activity and recyclability to palladium-catalyzed Heck reaction. The olefinations of iodoarenes, bromoarenes and chloroarenes with olefins generated the corresponding cross-coupling products in

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

    PubMed

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

    2003-09-01

    Aerosol growth by the heterogeneous reactions of different aliphatic and alpha,beta-unsaturated carbonyls in the presence/absence of acidified seed aerosols was studied in a 2 m long flow reactor (2.5 cm i.d.) and a 0.5-m3 Teflon film bag under darkness. For the flow reactor experiments, 2,4-hexadienal, 5-methyl-3-hexen-2-one, 2-cyclohexenone, 3-methyl-2-cyclopentenone, 3-methyl-2-cyclohexenone, and octanal were studied. The carbonyls were selected based on their reactivity for acid-catalyzed reactions, their proton affinity, and their similarity to the ring-opening products from the atmospheric oxidation of aromatics. To facilitate acid-catalyzed heterogeneous hemiacetal/acetal formation, glycerol was injected along with inorganic seed aerosols into the flow reactor system. Carbonyl heterogeneous reactions were accelerated in the presence of acid catalysts (H2SO4), leading to higher aerosol yields than in their absence. Aldehydes were more reactive than ketones for acid-catalyzed reactions. The conjugated functionality also resulted in higher organic aerosol yieldsthan saturated aliphatic carbonyls because conjugation with the olefinic bond increases the basicity of the carbonyl leading to increased stability of the protonated carbonyl. Aerosol population was measured from a series of sampling ports along the length of the flow reactor using a scanning mobility particle sizer. Fourier transform infrared spectrometry of either an impacted liquid aerosol layer or direct reaction of carbonyls as a thin liquid layer on a zinc selenide FTIR disk was employed to demonstrate the direct transformation of chemical functional groups via the acid-catalyzed reactions. These results strongly indicate that atmospheric multifunctional organic carbonyls, which are created by atmospheric photooxidation reactions, can contribute significantly to secondary organic aerosol formation through acid-catalyzed heterogeneous reactions. Exploratory studies in 25- and 190-m3 outdoor chambers were also implemented to demonstrate the formation of high molecular weight organic structures. The reaction of ozone with alpha-pinene to generate secondary organic aerosols (SOAs) was performed in the presence of background aerosol consisting of a mixture of wood soot and diesel soot. Results strongly suggest that indigenous sulfuric acid associated with the combustion of fossil fuels (e.g., diesel soot) can initiate acid-catalyzed heterogeneous reactions of SOAs on the particle phase. PMID:12967102

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

    E-print Network

    Rainka, Matthew P. (Matthew Paul)

    2005-01-01

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

  14. 9422 Stratospheric ice catalyzes chlorine reactions 9428 Fusing silk and silica

    E-print Network

    McFadden, Geoff

    9422 Stratospheric ice catalyzes chlorine reactions 9428 Fusing silk and silica 9482 Identifying, and Mario J. Molina (see pages 9422­9427) CHEMISTRY Fusing silk and silica An engineered protein combining the flexibility and tensile strength of spider silk with the resilience of silica has been developed. The result

  15. Polymer-Supported Siloxane Transfer Agents for Pd-Catalyzed Cross-Coupling Reactions

    PubMed Central

    Nguyen, Minh H.; Smith, Amos B.

    2013-01-01

    The design, synthesis and validation of a ROMP polymer supporting siloxane transfer agents have been achieved that permit efficient palladium-catalyzed cross-coupling reactions. The solubility properties of the polymer not only facilitate product purification, but also recycling without significant loss of cross-coupling activity. PMID:23901881

  16. 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.

  17. Asymmetric aldol reactions in poly(ethylene glycol) catalyzed by l-proline

    Microsoft Academic Search

    S. Chandrasekhar; Ch. Narsihmulu; N. Ramakrishna Reddy; S. Shameem Sultana

    2004-01-01

    A rapid l-proline catalyzed direct aldol reaction between various aldehydes and acetone was achieved using PEG as the solvent with comparable enantioselectivities and yields to those obtained in other solvents. Recycling the catalyst and solvent (PEG) was possible 10 times without loss of activity.

  18. Ligand-Controlled Regiodivergent Palladium-Catalyzed Decarboxylative Allylation Reaction to Access ?,?-Difluoroketones.

    PubMed

    Yang, Ming-Hsiu; Orsi, Douglas L; Altman, Ryan A

    2015-02-16

    ?,?-Difluoroketones possess unique physicochemical properties that are useful for developing therapeutics and probes for chemical biology. To access the ?-allyl-?,?-difluoroketone substructure, complementary palladium-catalyzed decarboxylative allylation reactions were developed to provide linear and branched ?-allyl-?,?-difluoroketones. For these orthogonal processes, the fluorination pattern of the substrate enabled the ligands to dictate the regioselectivity of the transformations. PMID:25581845

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

    Microsoft Academic Search

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

    2006-01-01

    The capability of mushroom tyrosinase to catalyze the oxidation of tyrosine residues of Bombyx mori silk fibroin was studied under heterogeneous reaction conditions, by using a series of silk substrates differing in surface and bulk morphology and structure, i.e. hydrated and insoluble gels, mechanically generated powder and fibre. Tyrosinase was able to oxidize 10–11% of the tyrosine residues of silk

  20. Enantioselective Arylative Dearomatization of Indoles via Pd-Catalyzed Intramolecular Reductive Heck Reactions.

    PubMed

    Shen, Chong; Liu, Ren-Rong; Fan, Ren-Jie; Li, Ying-Long; Xu, Teng-Fei; Gao, Jian-Rong; Jia, Yi-Xia

    2015-04-22

    A highly enantioselective intramolecular arylative dearomatization of indoles via palladium-catalyzed reductive Heck reactions was developed. The new strategy led to a series of optically active indolines bearing C2-quaternary stereocenters in modest to good yields with excellent enantioselectivities (up to 99% ee). PMID:25849154

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

    E-print Network

    Elrod, Matthew J.

    Atmospheric Environment 40 (2006) 6863­6878 Acid-catalyzed reactions of hexanal on sulfuric acid the uptake of gas- phase hexanal into ammonium sulfate and sulfuric acid aerosols. While both deliquesced condensation product was formed only at initial concentrations of 75­96 wt% sulfuric acid in water

  2. 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.

  3. Chiral N,N'-dioxide-In(OTf)3-catalyzed asymmetric vinylogous Mukaiyama aldol reactions.

    PubMed

    Fu, Kai; Zheng, Jianfeng; Lin, Lili; Liu, Xiaohua; Feng, Xiaoming

    2015-02-01

    Chiral N,N'-dioxide-In(OTf)3 complexes were developed as efficient catalysts to catalyze the vinylogous Mukaiyama aldol reaction of the silyl dienol ester with aldehydes. The corresponding ?-hydroxy-?,?-unsaturated esters were obtained in up to 99% yield and 98% ee. Moreover, the obtained (R)-3v can be easily transformed to natural bioactive products. PMID:25597692

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

    NASA Astrophysics Data System (ADS)

    Cody, G. D.

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

  5. Metal-catalyzed cascade reactions: useful synthetic tools for the preparation of polycyclic arenes.

    PubMed

    Feng, Chieh-Ning; Hsieh, Ya-Chu; Wu, Yao-Ting

    2015-02-01

    This account summarizes our recent efforts to synthesize numerous important and interesting polycyclic arenes under mild conditions using metal-catalyzed protocols. The palladium-catalyzed annulations of 2-iodobiphenyls or 2,2'-diiodobiphenyls with alkynes efficiently generated phenanthrene derivatives. This synthetic method was utilized as the key step when preparing phenanthrene-based alkaloids, tetrabenzopyracylenes and persubstituted [8]circulenes. Depending on whether a palladium or nickel catalytic system was used, 1-ethynyl-8-iodonaphthalenes underwent either a cyclodimerization or a nitrile-incorporated cascade reaction to produce zethrenes or pyrroloarenes, respectively. Methylene-bridged polyarenes are generated easily from 2-halo-2'-methylbiaryls through benzylic C-H bond activation and subsequent carbon-carbon bond formation, and palladium complexes promote the arylation of methylene carbons. The palladium-catalyzed annulations of 1,8-bis(arylethynyl)naphthalene derivatives with o-diiodoarenes yielded benzo[k]fluoranthene-based linear acenes, which can be applied to synthesize highly curved fragments of fullerenes. The self-reactions of diarylethynes formed either dihydrocyclopenta[a]indenes or octaaryl-1,3,5,7-octatetraenes through palladium-catalyzed cycloisomerization or nickel-catalyzed tetramerization, respectively. In the presence of palladium catalysts, the hydroalkynylation of terminal arylalkynes directly generated angular trimerization adduct dienynes. PMID:25376430

  6. Enrichment of ?-linolenic acid from borage oil via lipase-catalyzed reactions

    Microsoft Academic Search

    Fang-Cheng Huang; Yi-Hsu Ju; Cheng-Wei Huang

    1997-01-01

    Three lipase-catalyzed reactions were utilized to enrich ?-linolenic acid in borage oil: (i) selective hydrolysis in isooctane\\u000a by Candida rugosa lipase immobilized on microporous polypropylene, (ii) selective esterification of free fatty acid from saponified borage\\u000a oil and n-butanol by Lipozyme IM-20, and (iii) acidolysis of the products of the previous two reactions, that is, unhydrolyzed acylglycerols\\u000a and unesterified free fatty

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

    PubMed Central

    2015-01-01

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

  8. Synthesis of biaryls via decarboxylative Pd-catalyzed cross-coupling reaction.

    PubMed

    Becht, Jean-Michel; Catala, Cédric; Drian, Claude Le; Wagner, Alain

    2007-04-26

    [reaction: see text] A simple and efficient route to biaryls via Pd-catalyzed decarboxylative cross-couplings of arene carboxylic acids and aryl iodides is reported. The PdCl2/AsPh3 catalytic system in the presence of Ag2CO3 in DMSO was found to be particularly efficient to perform this transformation. This reaction can be extended to the synthesis of various biaryls, including sterically hindered biaryls, with yields ranging from 58% to 90%. PMID:17411063

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

    PubMed

    Nguyen, Minh H; Smith, Amos B

    2014-04-01

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

  10. One-pot three-component Mannich reaction catalyzed by iodine under solvent-free conditions

    Microsoft Academic Search

    Li Gang; Long Ruiling; Yang Jiangli

    2011-01-01

    One-pot three-component Mannich reactions of ketones with aromatic aldehydes and aromatic amines are effectively catalyzed\\u000a by molecular iodine at room temperature under solvent-free conditions to afford the corresponding ?-amino carbonyl compounds\\u000a with moderate to excellent yields. The method has the following advantages: no use of solvent, mild condition, high reaction\\u000a speed and small quantity of catalyst.

  11. Iodine catalyzed one-pot five-component reactions for direct synthesis of densely functionalized piperidines

    Microsoft Academic Search

    Abu T. Khan; Kranthi K. R. Bannuru

    2010-01-01

    A simple and convenient one-pot multicomponent reaction (MCR) has been developed for the synthesis of highly functionalized piperidines catalyzed by molecular iodine. This strategy demonstrated five-component reactions of 1,3-dicarbonyl compounds, amines and aromatic aldehydes in methanol using 10 mol % of iodine at room temperature. This methodology provides an alternative approach for easy access of highly and fully substituted piperidines in moderate

  12. Gold-catalyzed multiple cascade reaction of 2-alkynylphenylazides with propargyl alcohols.

    PubMed

    Li, Nan; Wang, Tian-Yi; Gong, Liu-Zhu; Zhang, Liming

    2015-02-23

    An unprecedented gold-catalyzed multiple cascade reaction between 2-alkynyl arylazides and alkynols has been developed, allowing for the step-economical synthesis of pyrroloindolone derivatives with a wide range of structural diversity. In this reaction, the gold complex participates in triple catalysis in tandem fashion. Moreover, the efficient chirality transfer from optically pure alkynol substrates enables facile access to chiral pyrroloindolone derivatives with two stereogenic centers, including a quaternary one, with excellent levels of optical purity. PMID:25639254

  13. Synthesis of substituted tetrahydroindoloisoquinoline derivatives via intramolecular Pd-catalyzed alkene carboamination reactions.

    PubMed

    Alicea, Jeremiah; Wolfe, John P

    2014-05-01

    Intramolecular Pd-catalyzed alkene carboamination reactions of substituted 2-allyl-N-(2-bromobenzyl)anilines are described. The substrates for these reactions are generated in two steps from readily available 2-allylanilines and 2-bromobenzaldehyde derivatives. The transformations afford substituted tetrahydroindoloisoquinolines, an uncommon class of fused bicyclic heterocycles, in good yield. The mechanism of these transformations is described, and a model that accounts for the observed product stereochemistry is proposed. PMID:24724560

  14. Tandem gold-catalyzed dehydrative cyclization/diels-alder reactions: facile access to indolocarbazole alkaloids.

    PubMed

    Borrero, Nicholas V; DeRatt, Lindsey G; Ferreira Barbosa, Lais; Abboud, Khalil A; Aponick, Aaron

    2015-04-01

    A gold-catalyzed synthesis of cyclic 2-oxodienes from readily prepared propargyl alcohols and the subsequent Diels-Alder reaction are reported. The dehydrative cyclization reactions proceeded smoothly, and the dienes formed in situ were demonstrated to undergo cycloaddition with a variety of dienophiles. This method offers a new strategy for the synthesis of indolocarbazole alkaloids, whereby the convergent synthetic design allows for differentiation between the indole nitrogens. PMID:25797466

  15. The role of silica gel in lipase-catalyzed esterification reactions of high-polar substrates

    Microsoft Academic Search

    Edmundo Castillo; Valérie Dossat; Alain Marty; J. Stéphane Condoret; Didier Combes

    1997-01-01

    The crucial role of silica gel in lipase-catalyzed esterification reactions using adsorbed high-polar substates was established.\\u000a It was found that in these kinds of reactions, the presence of silica gel-adsorbed substrates did not alter the kinetic mechanisms\\u000a of the synthesis of acylglycerides but improved significantly the conversion yields. An explanation for the critical role\\u000a of silica gel in these kinds

  16. Indium(III) bromide-catalyzed preparation of dihydropyrimidinones: improved protocol conditions for the Biginelli reaction

    Microsoft Academic Search

    Nan-Yan Fu; Yao-Feng Yuan; Zhong Cao; Shan-Wei Wang; Ji-Tao Wang; Clovis Peppe

    2002-01-01

    Indium(III) bromide efficiently catalyzes the three-component coupling of ?-keto esters, aldehydes and urea (or thiourea) to afford the corresponding dihydropyrimidinones. This new protocol for the Biginelli reaction includes the following important features: produces excellent yields, allows the recycling of catalyst with no loss in its activity, and leads to zero-discharge during the process. The reaction of ethyl acetoacetate, salicylaldehyde and

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

    PubMed

    Mphahlele, Malose Jack; Maluleka, Marole Maria

    2014-01-01

    Halogenated quinazolinones and quinazolines are versatile synthetic intermediates for the metal-catalyzed carbon-carbon bond formation reactions such as the Kumada, Stille, Negishi, Sonogashira, Suzuki-Miyaura and Heck cross-coupling reactions or carbon-heteroatom bond formation via the Buchwald-Hartwig cross-coupling to yield novel polysubstituted derivatives. This review presents an overview of the application of these methods on halogenated quinazolin-4-ones and their quinazolines to generate novel polysubstituted derivatives. PMID:25356566

  18. Phosphine-free palladium acetate catalyzed Suzuki reaction in water.

    PubMed

    Liu, Leifang; Zhang, Yuhong; Wang, Yanguang

    2005-07-22

    Pd(OAc)(2) in a mixture of water and poly(ethylene glycol) (PEG) is shown to be an extremely active catalyst for the Suzuki reaction of aryl iodides and bromides. The reaction can be conducted under mild conditions (50 degrees C) without the use of a microwave or phosphine ligand in high yields. The isolation of the products is readily performed by the extraction of diethyl ether, and the Pd(OAc)(2)-PEG can be reused without significant loss in activity. PMID:16018716

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

    PubMed Central

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

    2012-01-01

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

  20. Nickel-catalyzed reactions of enone with ethylene

    NASA Astrophysics Data System (ADS)

    Nishimura, A.; Haba, T.; Ohashi, M.; Ogoshi, S.

    2010-06-01

    The reaction of (E)-1-phenylbut-2-en-1-one with ethylene in the presence of a catalytic amount of Ni(cod)2 and PCy3 at room temperature gave two kinds of three-component addition products; one is 1,6-enone composed of an enone and two ethylene molecules, and the other is 1,5-diketone composed of two enones and an ethylene. The reactions might proceed via oxidative cyclization of an enone and an ethylene with nickel(0).

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

    E-print Network

    Masayasu Kamimura; Yasushi Kino; Emiko Hiyama

    2009-06-13

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

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

    PubMed

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  4. Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

    Microsoft Academic Search

    David Yu Zhang; Andrew J. Turberfield; Bernard Yurke; Erik Winfree

    2007-01-01

    Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input

  5. Enzyme Reaction Rates at Limited Water Activities

    Microsoft Academic Search

    J. J. Skujins; A. D. McLaren

    1967-01-01

    A well-mixed powder consisting of dry urea and urease exposed to air containing discrete amounts of water vapor showed a release of carbon-14 dioxide above 60-percent relative humidity. The relative activity of urease followed the water-vapor adsorption isotherm of urease. The minimum amount of water required for the reaction observed was 1.3 moles per mole of side-chain polar groups of

  6. Evidence for the Formation of an Enamine Species during Aldol and Michael-type Addition Reactions Promiscuously Catalyzed by 4-Oxalocrotonate Tautomerase.

    PubMed

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

    2015-03-23

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which has a catalytic N-terminal proline residue (Pro1), can promiscuously catalyze various carbon-carbon bond-forming reactions, including aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde, and Michael-type addition of acetaldehyde to a wide variety of nitroalkenes to yield valuable ?-nitroaldehydes. To gain insight into how 4-OT catalyzes these unnatural reactions, we carried out exchange studies in D2 O, and X-ray crystallography studies. The former established that H-D exchange within acetaldehyde is catalyzed by 4-OT and that the Pro1 residue is crucial for this activity. The latter showed that Pro1 of 4-OT had reacted with acetaldehyde to give an enamine species. These results provide evidence of the mechanism of the 4-OT-catalyzed aldol and Michael-type addition reactions in which acetaldehyde is activated for nucleophilic addition by Pro1-dependent formation of an enamine intermediate. PMID:25728471

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

    E-print Network

    Bothma, Jacques P; McKenzie, Ross H

    2009-01-01

    We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative descr...

  8. Barrier compression and tunneling in enzyme catalysed reactions

    NASA Astrophysics Data System (ADS)

    Scrutton, Nigel

    2011-03-01

    Nuclear quantum mechanical tunneling is important in enzyme-catalysed H-transfer reactions. This viewpoint has arisen after a number of experimental studies have described enzymatic reactions with kinetic isotope effects that are significantly larger than the semi-classical limit. Other experimental evidence for tunneling, and the potential role of promoting vibrations that transiently compress the reaction barrier, is more indirect, being derived from the interpretation of e.g. mutational analyses of enzyme systems and temperature perturbation studies of reaction rates/kinetic isotope effects. Computational simulations have, in some cases, determined exalted kinetic isotope effects and tunneling contributions, and identified putative promoting vibrations. In this presentation, we present the available evidence -- both experimental and computational -- for environmentally-coupled H-tunneling in several enzyme systems, from our recent work on redox enzyme systems. We then consider the relative importance of tunneling contributions to these reactions. We find that the tunneling contribution to these reactions confers a rate enhancement of approx. 1000-fold. Without tunneling, a 1000-fold reduction in activity would seriously impair cellular metabolism. We infer that tunneling is crucial to host organism viability thereby emphasising the general importance of tunneling in biology.

  9. Temperature optima of enzyme-catalysed reactions in microemulsion systems

    Microsoft Academic Search

    K. Mlejnek; B. Seiffert; T. Demberg; M. Kämper; M. Hoppert

    2004-01-01

    Ternary phase systems (water\\/surfactant\\/organic solvent) were utilised to increase and broaden the temperature optima of enzyme-catalysed reactions. Alcohol dehydrogenases from yeast and Thermoanaerobium brockii (EC 1.1.1.1 and EC 1.1.1.2), lactate dehydrogenase from Lactobacillus delbrueckii (EC 1.1.1.28) and the particulate hydrogenase from Ralstonia eutropha (EC 1.18.99.1) were used as model enzymes in microemulsions, consisting of the surfactant Aerosol OT, and various

  10. 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.)

  11. Isofunctional Enzymes PAD1 and UbiX Catalyze Formation of a Novel Cofactor Required by Ferulic Acid Decarboxylase and 4-Hydroxy-3-polyprenylbenzoic Acid Decarboxylase.

    PubMed

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

    2015-04-17

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

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

    PubMed

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

    2015-02-25

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

  13. 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

  14. Reaction Kinetics of Substrate Transglycosylation Catalyzed by TreX of Sulfolobus solfataricus and Effects on Glycogen Breakdown

    PubMed Central

    Nguyen, Dang Hai Dang; Park, Jong-Tae; Shim, Jae-Hoon; Tran, Phuong Lan; Oktavina, Ershita Fitria; Nguyen, Thi Lan Huong; Lee, Sung-Jae; Park, Cheon-Seok; Li, Dan; Park, Sung-Hoon; Stapleton, David; Lee, Jin-Sil

    2014-01-01

    We studied the activity of a debranching enzyme (TreX) from Sulfolobus solfataricus on glycogen-mimic substrates, branched maltotetraosyl-?-cyclodextrin (Glc4-?-CD), and natural glycogen to better understand substrate transglycosylation and the effect thereof on glycogen debranching in microorganisms. The validation test of Glc4-?-CD as a glycogen mimic substrate showed that it followed the breakdown process of the well-known yeast and rat liver extract. TreX catalyzed both hydrolysis of ?-1,6-glycosidic linkages and transglycosylation at relatively high (>0.5 mM) substrate concentrations. TreX transferred maltotetraosyl moieties from the donor substrate to acceptor molecules, resulting in the formation of two positional isomers of dimaltotetraosyl-?-1,6-?-cyclodextrin [(Glc4)2-?-CD]; these were 61,63- and 61,64-dimaltotetraosyl-?-1,6-?-CD. Use of a modified Michaelis-Menten equation to study substrate transglycosylation revealed that the kcat and Km values for transglycosylation were 1.78 × 103 s?1 and 3.30 mM, respectively, whereas the values for hydrolysis were 2.57 × 103 s?1 and 0.206 mM, respectively. Also, enzyme catalytic efficiency (the kcat/Km ratio) increased as the degree of polymerization of branch chains rose. In the model reaction system of Escherichia coli, glucose-1-phosphate production from glycogen by the glycogen phosphorylase was elevated ?1.45-fold in the presence of TreX compared to that produced in the absence of TreX. The results suggest that outward shifting of glycogen branch chains via transglycosylation increases the number of exposed chains susceptible to phosphorylase action. We developed a model of the glycogen breakdown process featuring both hydrolysis and transglycosylation catalyzed by the debranching enzyme. PMID:24610710

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

    PubMed

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

    2013-07-01

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

  16. A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides.

    PubMed

    Piletic, Ivan R; Edney, Edward O; Bartolotti, Libero J

    2013-11-01

    Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase. Specifically, the importance of acid catalysis and solvent polarity are investigated using a variety of epoxides and nucleophiles. The condensed phase is modeled using molecular clusters immersed in a dielectric continuum and a majority of the calculations are performed with the M062x density functional and the 6-311++G** basis set. Calculations of acid catalyzed epoxide hydrolysis transition states for simple primary, secondary and tertiary epoxides are consistent with an A-2 mechanism where the nucleophile (water) interacts with an epoxide carbon in the transition state. By applying transition state theory to this mechanism, the overall rate constants of epoxide reactions such as hydrolysis, organosulfate formation, organonitrate formation and oligomerization are determined. The calculations indicate that the acid catalyzed hydrolysis rate constant of 2-methyl-2,3-epoxybutane-1,4-diol (?-IEPOX--an isoprene epoxide produced under low NOx conditions) is approximately 30 times greater than 2-methyl-2,3-epoxypropanoic acid (MAE--methacrylic acid epoxide derived from isoprene and produced at high NOx concentrations). Furthermore, acid catalyzed organosulfate formation and epoxide oligomerization reactions are competitive and appear to be kinetically favorable over the hydrolysis of IEPOX. PMID:24061334

  17. Lewis Acid and/or Lewis Base catalyzed [3+2] cycloaddition reaction: Synthesis of pyrazoles and pyrazolines

    E-print Network

    Paris-Sud XI, Université de

    1 Lewis Acid and/or Lewis Base catalyzed [3+2] cycloaddition reaction: Synthesis of pyrazoles is reported. All the reactions were carried out under no strong bases/acids, solvent free conditions+2] cycloaddition reaction strategy to form five membered ring systems through the reaction partners of 1,3-dipoles

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

    PubMed Central

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

    2001-01-01

    We have previously reported that bacterial flavohemoglobin (HMP) catalyzes both a rapid reaction of heme-bound O2 with nitric oxide (NO) to form nitrate [HMP-Fe(II)O2 + NO ? HMP-Fe(III) + NO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\mathrm{_{3}^{-}}}\\end{equation*}\\end{document}] and, under anaerobic conditions, a slower reduction of heme-bound NO to an NO? equivalent (followed by the formation of N2O), thereby protecting against nitrosative stress under both aerobic and anaerobic conditions, and rationalizing our finding that NO is rapidly consumed across a wide range of O2 concentrations. It has been alternatively suggested that HMP activity is inhibited at low pO2 because the enzyme is then in the relatively inactive nitrosyl form [koff/kon for NO (0.000008 ?M) ? koff/kon for O2 (0.012 ?M) and KM for O2 = 30–100 ?M]. To resolve this discrepancy, we have directly measured heme-ligand turnover and NADH consumption under various O2/NO concentrations. We find that, at biologically relevant O2 concentrations, HMP preferentially binds NO (not O2), which it then reacts with oxygen to form nitrate (in essence NO? + O2 ? NO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\mathrm{_{3}^{-}}}\\end{equation*}\\end{document}). During steady-state turnover, the enzyme can be found in the ferric (FeIII) state. The formation of a heme-bound nitroxyl equivalent and its subsequent oxidation is a novel enzymatic function, and one that dominates the oxygenase activity under biologically relevant conditions. These data unify the mechanism of HMP/NO interaction with those recently described for the nematode Ascaris and mammalian hemoglobins, and more generally suggest that the peroxidase (FeIII)-like properties of globins have evolved for handling of NO. PMID:11517313

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

    PubMed

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

    2014-06-16

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

  20. GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase\\/reductase family that catalyzes two distinct reactions at the same active site

    Microsoft Academic Search

    William S Somers; Mark L Stahl; Francis X Sullivan

    1998-01-01

    Background: In all species examined, GDP-fucose is synthesized from GDP-mannose in a three-step reaction catalyzed by two enzymes, GDP-mannose 4,6 dehydratase and a dual function 3,5-epimerase-4-reductase named GDP-fucose synthetase. In this latter aspect fucose biosynthesis differs from that of other deoxy and dideoxy sugars, in which the epimerase and reductase activities are present as separate enzymes. Defects in GDP-fucose biosynthesis

  1. ?-Linolenic acid-rich triacylglycerols derived from borage oil via lipase-catalyzed reactions

    Microsoft Academic Search

    Fang-Cheng Huang; Yi-Hsu Ju; Jen-Chung Chiang

    1999-01-01

    ?-Linolenic acid (GLA), a precursor of arachidonic acid, possesses physiological functions of modulating immune and inflammatory\\u000a response. Highly purified GLA is desired both as a medicine and as an ingredient of cosmetics. In this work, urea fractionation\\u000a and lipase-catalyzed reactions were employed for the enrichment of GLA in borage oil. GLA content in free fatty acids from\\u000a saponified borage oil

  2. Biaryl synthesis via decarboxylative Pd-catalyzed reactions of arenecarboxylic acids and diaryliodonium triflates.

    PubMed

    Becht, Jean-Michel; Le Drian, Claude

    2008-07-17

    A novel simple and efficient synthesis of biaryls via a Pd-catalyzed decarboxylative cross-coupling reaction of arenecarboxylic acids and diaryliodonium triflates is described. The PdCl2/DPEphos catalytic system in the presence of Ag2CO3 in DMSO was found to be the most efficient. Various biaryls, including sterically hindered biaryls, were synthesized with yields ranging from 37 to 85%. PMID:18553969

  3. The rapid and enhanced reduction of graphene oxide by microwave assisted acid catalyzed reaction.

    PubMed

    Tien, Huynh Ngoc; Luan, Van Hoang; Hoa, Le Thuy; Lee, Tae Kyu; Kong, Byung-Seon; Chung, Jin Suk; Kim, Eui Jung; Hur, Seung Hyun

    2013-10-01

    We report a novel synthetic route to fabricate reduced graphene oxide (rGO) from graphene oxide (GO) using a microwave assisted acid catalyzed reaction in organic solvent. The obtained rGO in this study exhibited 4 times higher electrical conductivity, less oxygen content and better ordered structure than that of conventional solvothermally fabricated ones. By using microwave irradiation, high quality rGO can be obtained in several minutes. PMID:24245202

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

    PubMed

    Bekhradnia, Ahmadreza; Norrby, Per-Ola

    2015-02-17

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

  5. Enzyme Homologues Have Distinct Reaction Paths through Their Transition States.

    PubMed

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

    2015-03-01

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

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

    PubMed Central

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

    2015-01-01

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

  7. Atom-transfer radical addition reactions catalyzed by RuCp* complexes: a mechanistic study.

    PubMed

    Fernández-Zúmel, Mariano A; Thommes, Katrin; Kiefer, Gregor; Sienkiewicz, Andrzej; Pierzchala, Katarzyna; Severin, Kay

    2009-11-01

    Kinetic and spectroscopic analyses were performed to gain information about the mechanism of atom-transfer radical reactions catalyzed by the complexes [RuCl2Cp*(PPh3)] and [RuClCp*(PPh3)2] (Cp*=pentamethylcyclopentadienyl), in the presence and in the absence of the reducing agent magnesium. The reactions of styrene with ethyl trichloroacetate, ethyl dichloroacetate, or dichloroacetonitrile were used as test reactions. The results show that for substrates with high intrinsic reactivity, such as ethyl trichloroacetate, the oxidation state of the catalyst in the resting state is +3, and that the reaction is zero-order with respect to the halogenated compound. Furthermore, the kinetic data suggest that the metal catalyst is not directly involved in the rate-limiting step of the reaction. PMID:19750528

  8. Theoretical investigation for the reaction of NO 2 with CO catalyzed by Sc +

    NASA Astrophysics Data System (ADS)

    Wang, Yong-Cheng; Zhang, Jian-Hui; Geng, Zhi-Yuan; Chen, Dong-Ping; Liu, Ze-Yu; Yang, Xiao-Yan

    2007-09-01

    The mechanism of the reaction NO(2A)+CO(1?+)?NO(2?)+CO(1?g+) catalyzed by Sc + has been investigated by means of UB3LYP/6-311+G(2d) level. Our calculated results strongly indicate that both the reactions NO 2( 2A 1) + Sc +(X 3D) ? NO( 2?) + ScO +(X 1? +) and ScO(X1?+)+CO(1?+)?Sc(XD)+CO(1?g+) are spin-forbidden reactions. The crossing points (CPs) that are involved and the possible spin inversion processes are discussed using the intrinsic reaction coordinate (IRC) approach. On the basis of Hammond postulate, they are typical 'two-state reactivity' (TSR) reactions. And the O-atom affinities (OA) testified that the argumentation is thermodynamically allowed.

  9. PGH2 degradation pathway catalyzed by GSH-heme complex bound microsomal prostaglandin E2 synthase type 2: the first example of a dual-function enzyme.

    PubMed

    Yamada, Taro; Takusagawa, Fusao

    2007-07-17

    Prostaglandin E2 synthase (PGES) catalyzes the isomerization of PGH2 to PGE2. PGES type 2 (mPGES-2) is a membrane-associated enzyme, whose N-terminal section is apparently inserted into the lipid bilayer. Both intact and N-terminal truncated enzymes have been isolated and have similar catalytic activity. The recombinant N-terminal truncated enzyme purified from Escherichia coli HB101 grown in LB medium containing delta-aminolevulinate and Fe(NO3)3 has a red color, while the same enzyme purified from the same E. coli grown in minimal medium has no color. The red-colored enzyme has been characterized by mass, fluorescence, and EPR spectroscopies and X-ray crystallography. The enzyme is found to contain bound glutathione (GSH) and heme. GSH binds to the active site with six H-bonds, while a heme is complexed with bound GSH forming a S-Fe coordination bond with no polar interaction with mPGES-2. There is a large open space between the heme and the protein, where a PGH2 might be able to bind. The heme dissociation constant is 0.53 microM, indicating that mPGES-2 has relatively strong heme affinity. Indeed, expression of mPGES-2 in E. coli stimulates heme biosynthesis. Although mPGES-2 has been reported to be a GSH-independent PGES, the crystal structure and sequence analysis indicate that mPGES-2 is a GSH-binding protein. The GSH-heme complex-bound enzyme (mPGES-2h) catalyzes formation of 12(S)-hydroxy-5(Z),8(E),10(E)-heptadecatrienoic acid and malondialdehyde from PGH2, but not formation of PGE2. The following kinetic parameters at 37 degrees C were determined: KM = 56 microM, kcat = 63 s-1, and kcat/KM = 1.1 x 10(6) M-1 s-1. They suggest that mPGES-2h has significant catalytic activity for PGH2 degradation. It is possible that both GSH-heme complex-free and -bound enzymes are present in the same tissues. mPGES-2 in heme-rich liver is most likely to become the form of mPGES-2h and might be involved in degradation reactions similar to that of cytochrome P450. Since mPGES-2 is an isomerase and mPGES-2h is a lyase, mPGES-2 cannot simply be classified into one of six classes set by the International Union of Biochemistry and Molecular Biology. PMID:17585783

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

    NASA Astrophysics Data System (ADS)

    Kamimura, M.; Kino, Y.; Hiyama, E.

    2009-05-01

    An accurate quantum three-body calculation is performed for 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 ?_X ? 10^3 s, it can capture a light element previously synthesized in standard BBN and form a Coulombic bound state, for example, (^7Be X^-) at temperature T_9 ? 0.4 (in units of 10^9 K), (? X^-) at T_9 ? 0.1 and (p X^-) at T_9 ? 0.01. The bound state, an exotic atom, is expected to induce the following reactions in which X^- acts as a catalyst: i) ?-transfer reactions such as (? X^-)+d to ^6Li + X, ii) radiative capture reactions such as (^7Be X^-) + p to (^8B X^-) + ?, iii) three-body breakup reactions such as (^7Li X^-) + p to ? + ? + X^-, iv) charge-exchange reactions such as (p X^-) + ? to (? X^-) +p and v) neutron induced reactions such as (^8Be X^-) + n to ^9Be + X^-. In recent papers it has been claimed that 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, giving not only a solution to the ^6Li-^7Li problem (the calculated underproduction of ^6Li by a factor of ˜ 1000 and overproduction of ^7Li+$^7Be by a factor of ˜ 3) but also a constraint on the lifetime and primordial abundance of the elementary particle X^-. However, most of these calculations of the reaction cross sections in the literature were performed assuming too naive models or approximations that are unsuitable for these complicated low-energy nuclear reactions. We use a high-accuracy few-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

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

    E-print Network

    Woodin, Katrina Sue

    2007-01-01

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

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

    E-print Network

    McAvoy, Camille Z

    2012-01-01

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

  13. 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

  14. 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 ?-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. Chirality 27:314-319, 2015. © 2015 Wiley Periodicals, Inc. PMID:25691447

  15. Knoevenagel condensation reaction catalyzed by task-specific ionic liquid under solvent-free conditions

    Microsoft Academic Search

    Caibo Yue; Aiqin Mao; Yunyang Wei; Minjie Lü

    2008-01-01

    A task-specific ionic liquid, [H3N+–CH2–CH2–OH][CH3COO?] was synthesized and used as catalyst in the Knoevenagel condensation reaction of various kinds of aromatic aldehydes with ethyl cyanoacetate or malononitrile. ?,?-Unsaturated carbonyl compounds were obtained in reasonable yields when the [H3N+–CH2–CH2–OH][CH3COO?] catalyzed Knoevenagel reaction was carried out at room temperature for several to 60min under solvent-free conditions. Only E-isomers were detected. The task-specific

  16. 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

  17. Facile One-Pot Assembly of Imidazotriazolobenzodiazepines via Indium(III)-Catalyzed Multicomponent Reactions

    PubMed Central

    Nguyen, Huy H.; Palazzo, Teresa A.; Kurth, Mark J.

    2013-01-01

    An operationally simple, one-pot multicomponent reaction has been developed for the assembly of 9H-benzo[f]imidazo[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepines adorned with three diversification points via an atom-economical transformation incorporating ?-diketones, o-azidobenzaldehydes, propargylic amines, and ammonium acetate. This process involves tandem InCl3-catalyzed cyclocondensation and intramolecular azide-alkyne 1,3-dipolar cycloaddition reactions; optimization data, substrate scope, and mechanistic insights are discussed. PMID:23961714

  18. A New Class of Ligands for Aqueous, Lanthanide-Catalyzed, Enantioselective Mukaiyama Aldol Reactions

    PubMed Central

    Mei, Yujiang; Dissanayake, Prabani; Allen, Matthew J.

    2010-01-01

    The development of aqueous methods to generate enantiopure ?-hydroxy carbonyl compounds is an important goal because these subunits compose many bioactive compounds, and the ability to synthesis these groups in water has environmental and cost benefits. In this communication, we report a new class of ligands for aqueous, lanthanide-catalyzed, asymmetric Mukaiyama aldol reactions to synthesize chiral ?-hydroxy ketones. Furthermore, we use luminescence-decay measurements to unveil mechanistic information regarding the catalytic reaction via changes of water-coordination number. The precatalysts presented here yielded ?-hydroxy carbonyls from aliphatic and aryl substrates with outstanding syn:anti ratios and enantiometric excesses of up to 49:1 and 97%. PMID:20806902

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

    SciTech Connect

    Ye, Xinhao [Virginia Polytechnic Institute and State University (Virginia Tech); Wang, Yiran [Virginia Polytechnic Institute and State University (Virginia Tech); Hopkins, Robert C. [University of Georgia, Athens, GA; Adams, Michael W. W. [University of Georgia, Athens, GA; Evans, Barbara R [ORNL; Mielenz, Jonathan R [ORNL; Zhang, Y.-H. Percival [Virginia Polytechnic Institute and State University (Virginia Tech)

    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.

  20. EzCatDB: the enzyme reaction database, 2015 update

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    E-print Network

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

    2009-10-07

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

  3. Proline catalyzed ?-aminoxylation reaction in the synthesis of biologically active compounds.

    PubMed

    Kumar, Pradeep; Dwivedi, Namrata

    2013-02-19

    The search for new and efficient ways to synthesize optically pure compounds is an active area of research in organic synthesis. Asymmetric catalysis provides a practical, cost-effective, and efficient method to create a variety of complex natural products containing multiple stereocenters. In recent years, chemists have become more interested in using small organic molecules to catalyze organic reactions. As a result, organocatalysis has emerged both as a promising strategy and as an alternative to catalysis with expensive proteins or toxic metals. One of the most successful and widely studied secondary amine-based organocatalysts is proline. This small molecule can catalyze numerous reactions such as the aldol, Mannich, Michael addition, Robinson annulation, Diels-Alder, ?-functionalization, ?-amination, and ?-aminoxylation reactions. Catalytic and enantioselective ?-oxygenation of carbonyl compounds is an important reaction to access a variety of useful building blocks for bioactive molecules. Proline catalyzed ?-aminoxylation using nitrosobenzene as oxygen source, followed by in situ reduction, gives enantiomerically pure 1,2-diol. This molecule can then undergo a variety of organic reactions. In addition, proline organocatalysis provides access to an assortment of biologically active natural products including mevinoline (a cholesterol lowering drug), tetrahydrolipstatin (an antiobesity drug), R(+)-?-lipoic acid, and bovidic acid. In this Account, we present an iterative organocatalytic approach to synthesize both syn- and anti-1,3-polyols, both enantio- and stereoselectively. This method is primarily based on proline-catalyzed sequential ?-aminoxylation and Horner-Wadsworth-Emmons (HWE) olefination of aldehyde to give a ?-hydroxy ester. In addition, we briefly illustrate the broad application of our recently developed strategy for 1,3-polyols, which serve as valuable, enantiopure building blocks for polyketides and other structurally diverse and complex natural products. Other research groups have also applied similar strategies to prepare such bioactive molecules as littoralisone, brasoside and (+)-cytotrienin A. Among the various synthetic approaches reported for 1,3-polyols, our organocatalytic iterative approach appears to be very promising and robust. This method combines the merit of organocatalytic reaction with an easy access to both enantiomerically pure forms of proline, mild reaction conditions, and tolerance to both air and moisture. In this Account, we present the latest applications of organocatalysis and how organic chemists can use this new tool for the total synthesis of complex natural products. PMID:23148510

  4. Target-catalyzed dynamic assembly-based pyrene excimer switching for enzyme-free nucleic acid amplified detection.

    PubMed

    Qing, Zhihe; He, Xiaoxiao; Huang, Jin; Wang, Kemin; Zou, Zhen; Qing, Taiping; Mao, Zhengui; Shi, Hui; He, Dinggeng

    2014-05-20

    Because of the intrinsic importance of nucleic acid as biotargets, the simple and sensitive detection of nucleic acid is very essential for biological studies and medical diagnostics. Herein, a new strategy for enzyme-free nucleic acid amplified detection has been opened up by combining the signal-amplification capability of target-catalyzed dynamic assembly with the spatially sensitive fluorescent signal of the pyrene excimer. In this strategy, three metastable pyrene-labeled hairpin DNA probes were designed as assembly components, which were kinetically handicapped from cross-opening in the absence of the target DNA. However, in the presence of the target, the dynamic assembly of branched junctions was circularly catalyzed and accompanied by the switching of the pyrene excimer which emits at ~488 nm. Thus, the target DNA could be detected by this simple mix-and-detect amplification method, without expensive and perishable protein enzymes. A good detection capability exhibited with a detectable minimum target concentration of 10 pM, which was comparable to or even better than some reported enzyme-dependent amplification methods, and the potential for the target detection from complex fluids was verified. In addition, as a novel transformation of dynamic DNA assembly technology into enzyme-free signal-amplification analytical application, we infer that the proposed strategy will hold promising potential for application in a wider range of fields, including aptamer-based non-nucleic acid target sensing, biomedicine, and bioimaging. PMID:24749630

  5. Site-Specific Bioconjugation of a Murine Dihydrofolate Reductase Enzyme by Copper(I)-Catalyzed Azide-Alkyne Cycloaddition with Retained Activity

    PubMed Central

    Lim, Sung In; Mizuta, Yukina; Takasu, Akinori; Kim, Yong Hwan; Kwon, Inchan

    2014-01-01

    Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is an efficient reaction linking an azido and an alkynyl group in the presence of copper catalyst. Incorporation of a non-natural amino acid (NAA) containing either an azido or an alkynyl group into a protein allows site-specific bioconjugation in mild conditions via CuAAC. Despite its great potential, bioconjugation of an enzyme has been hampered by several issues including low yield, poor solubility of a ligand, and protein structural/functional perturbation by CuAAC components. In the present study, we incorporated an alkyne-bearing NAA into an enzyme, murine dihydrofolate reductase (mDHFR), in high cell density cultivation of Escherichia coli, and performed CuAAC conjugation with fluorescent azide dyes to evaluate enzyme compatibility of various CuAAC conditions comprising combination of commercially available Cu(I)-chelating ligands and reductants. The condensed culture improves the protein yield 19-fold based on the same amount of non-natural amino acid, and the enzyme incubation under the optimized reaction condition did not lead to any activity loss but allowed a fast and high-yield bioconjugation. Using the established conditions, a biotin-azide spacer was efficiently conjugated to mDHFR with retained activity leading to the site-specific immobilization of the biotin-conjugated mDHFR on a streptavidin-coated plate. These results demonstrate that the combination of reactive non-natural amino acid incorporation and the optimized CuAAC can be used to bioconjugate enzymes with retained enzymatic activity. PMID:24887377

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

    E-print Network

    Colby Davie, Elizabeth A. (Elizabeth Anne)

    2005-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Suga, Hiroyuki

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

  8. A logarithmic approximation to initial rates of enzyme reactions.

    PubMed

    Lu, Wei-Ping; Fei, Lin

    2003-05-01

    A straightforward and empirical regression method based on a logarithmic approximation has been developed to accurately estimate initial rates from nonlinear progress curves of enzyme reactions. The principle of this parametric approach is to use a relatively large number of observations, while averaging out random errors, to predict the curvature at time zero, which has the highest rate of change. The usual linear regression of a few initial time points lacks prediction power at time zero and therefore underestimates the true initial rate. Application of this nonlinear regression approach to enzyme reactions demonstrated satisfactory results. This approach is less subjective in choosing initial time points to be used for rate determination, and much more robust to random errors. Moreover, it is relatively easy to realize with commonly available software. PMID:12694727

  9. 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.

  10. Iron-catalyzed decarboxylative cross coupling reactions and palladium-catalyzed sp2-sp3 coupling of coumarins.

    E-print Network

    Trivedi, Rushi

    2009-12-15

    The thesis details the development of a decarboxylative synthesis of aryl ethers using a relatively new Iron catalyst and a novel decarboxylative coupling of coumarins catalyzed by palladium. Aryl allyl carbonates underwent facile decarboxylative...

  11. Palladium-catalyzed C-h functionalization of acyldiazomethane and tandem cross-coupling reactions.

    PubMed

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

    2015-04-01

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

  12. Platinum-catalyzed asymmetric ring-opening reactions of oxabenzonorbornadienes with phenols.

    PubMed

    Meng, Ling; Yang, Wen; Pan, Xuejing; Tao, Meng; Cheng, Guo; Wang, Sanyong; Zeng, Heping; Long, Yuhua; Yang, Dingqiao

    2015-03-01

    A platinum(II)-catalyzed asymmetric ring opening of oxabenzonorbornadienes with phenols was developed, which afforded the corresponding cis-2-(un)substituted phenoxy-1,2-dihydronaphthalen-1-ol products rather than the trans ones in excellent yields (up to 99%) with moderate to good enantioselectivities (up to 87% ee) under mild conditions. In addition, the cis-configuration of product 2b was confirmed by X-ray diffraction analysis. Based on the results, a potential mechanism for the present catalytic reaction was proposed. PMID:25679332

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

    PubMed

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

    2010-01-01

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

  14. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai A [Los Alamos National Laboratory; De Ronde, Wiet H [AMOLF; Daniels, Bryan C [CORNELL; Mugler, Andrew [COLUMBIA

    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.

  15. Non-precious metals catalyze formal [4 + 2] cycloaddition reactions of 1,2-diazines and siloxyalkynes under ambient conditions.

    PubMed

    Sumaria, Chintan S; Türkmen, Yunus E; Rawal, Viresh H

    2014-06-20

    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

  16. Formation of a complex pattern of sinapate esters in Brassica napus seeds, catalyzed by enzymes of a serine carboxypeptidase-like acyltransferase family?

    PubMed

    Baumert, Alfred; Milkowski, Carsten; Schmidt, Jürgen; Nimtz, Manfred; Wray, Victor; Strack, Dieter

    2005-06-01

    Members of the Brassicaceae accumulate complex patterns of sinapate esters, as shown in this communication with seeds of oilseed rape (Brassica napus). Fifteen seed constituents were isolated and identified by a combination of high-field NMR spectroscopy and high resolution electrospray ionisation mass spectrometry. These include glucose, gentiobiose and kaempferol glycoside esters as well as sinapine (sinapoylcholine), sinapoylmalate and an unusual cyclic spermidine amide. One of the glucose esters (1,6-di-O-sinapoylglucose), two gentiobiose esters (1-O-caffeoylgentiobiose and 1,2,6'-tri-O-sinapoylgentiobiose) and two kaempferol conjugates [4'-(6-O-sinapoylglucoside)-3,7-di-O-glucoside and 3-O-sophoroside-7-O-(2-O-sinapoylglucoside)] seem to be new plant products. Serine carboxypeptidase-like (SCPL) acyltransferases catalyze the formation of sinapine and sinapoylmalate accepting 1-O-beta-acetal esters (1-O-beta-glucose esters) as acyl donors. To address the question whether the formation of other components of the complex pattern of the sinapate esters in B. napus seeds is catalyzed via 1-O-sinapoyl-beta-glucose, we performed a seed-specific dsRNAi-based suppression of the sinapate glucosyltransferase gene (BnSGT1) expression. In seeds of BnSGT1-suppressing plants the amount of sinapoylglucose decreased below the HPLC detection limit resulting in turn in the disappearance or marked decrease of all the other sinapate esters, indicating that formation of the complex pattern of these esters in B. napus seeds is dependent on sinapoylglucose. This gives rise to the assumption that enzymes of an SCPL acyltransferase family catalyze the appropriate transfer reactions to synthesize the accumulating esters. PMID:15907956

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

    PubMed

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

    2012-04-01

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

  18. Synthesis of Acyclic r, -Unsaturated Ketones via Pd(II)-Catalyzed Intermolecular Reaction of Alkynamides and Alkenes

    E-print Network

    Liu, David R.

    Synthesis of Acyclic r, -Unsaturated Ketones via Pd(II)-Catalyzed Intermolecular Reaction ketone.3 Here we describe the development of an analogous intermolecular oxidative coupling reaction between alkynamides and terminal alkenes to generate acyclic R, -unsat- urated ketones4 (eq 1). Our

  19. Versatile post-functionalization of polyoxometalate platforms by using an unprecedented range of palladium-catalyzed coupling reactions.

    PubMed

    Lorion, Mélanie M; Matt, Benjamin; Alves, Sandra; Proust, Anna; Poli, Giovanni; Oble, Julie; Izzet, Guillaume

    2013-09-16

    Handy POMs: Several palladium-catalyzed coupling reactions have been applied to polyoxometalate post-functionalization. The feasibility of each reaction with one model substrate was investigated and each set of synthetic conditions was optimized to obtain full conversions and high purity hybrid compounds. PMID:23983072

  20. Chiral phosphoric acid catalyzed highly enantioselective Friedel-Crafts alkylation reaction of C3-substituted indoles to ?,?-unsaturated ?-ketimino esters.

    PubMed

    Bi, Bo; Lou, Qin-Xin; Ding, Yu-Yang; Chen, Sheng-Wei; Zhang, Sha-Sha; Hu, Wen-Hui; Zhao, Jun-Ling

    2015-02-01

    A highly enantioselective C2 Friedel-Crafts alkylation reaction of 3-substituted indoles to ?,?-unsaturated ?-ketimino esters has been developed. This reaction was efficiently catalyzed by a chiral phosphoric acid catalyst. The corresponding C2-substituted indole derivatives, bearing an ?-ketimino ester motif, were obtained in moderate to high yields (up to 93%) and with high enantioselectivities (up to >99% ee). PMID:25594307

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

    E-print Network

    Epstein, Irving R.

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

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

    E-print Network

    Venkataraman, Dhandapani "DV"

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

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

    PubMed

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

    2014-07-01

    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

  4. A comparative mechanistic study of Cu-catalyzed oxidative coupling reactions with N-phenyltetrahydroisoquinoline.

    PubMed

    Boess, Esther; Schmitz, Corinna; Klussmann, Martin

    2012-03-21

    A comparative mechanistic study of Cu-catalyzed oxidative coupling reactions of N-phenyltetrahydroisoquinoline with different nucleophiles was conducted. Two previously reported combinations of catalyst and oxidant were studied, CuCl(2)·2H(2)O/O(2) and CuBr/tert-butyl hydroperoxide (TBHP). On the basis of a synthetic study with different nucleophiles, the electrophilicity of the intermediate iminium ion was estimated and differences between the two methods were revealed. The key intermediate in the aerobic method is shown to be an iminium ion, formed through oxidation by copper(II), which can react with any nucleophile of sufficient reactivity. The role of oxygen is the reoxidation of the reduced catalyst. In the CuBr/TBHP system, an ?-amino peroxide is proposed as a true intermediate within the catalytic cycle, formed from the amine and TBHP by a Cu-catalyzed radical reaction pathway and acting as a precursor to the iminium ion intermediate. PMID:22338603

  5. Gold- and silver-catalyzed reactions of propargylic alcohols in the presence of protic additives.

    PubMed

    Pennell, Matthew N; Turner, Peter G; Sheppard, Tom D

    2012-04-10

    A wide range of primary, secondary and tertiary propargylic alcohols undergo a Meyer-Schuster rearrangement to give enones at room temperature in the presence of a gold(I) catalyst and small quantities of MeOH or 4-methoxyphenylboronic acid. The syntheses of the enone natural products isoegomaketone and daphenone were achieved using this reaction as the key step. The rearrangement of primary propargylic alcohols can readily be combined in a one-pot procedure with the addition of a nucleophile to the resulting terminal enone, to give ?-aryl, ?-alkoxy, ?-amino or ?-sulfido ketones. Propargylic alcohols bearing an adjacent electron-rich aryl group can also undergo silver-catalyzed substitution of the alcohol with oxygen, nitrogen and carbon nucleophiles. This latter reaction was initially observed with a batch of gold catalyst that was probably contaminated with small quantities of silver salt. PMID:22374879

  6. Reaction pathways in the decomposition of hydrogen peroxide catalyzed by copper(II).

    PubMed

    Perez-Benito, Joaquin F

    2004-03-01

    The kinetics of the decomposition of H(2)O(2) catalyzed by Cu(II) has been studied by the initial-rate method in aqueous phosphate media at near physiological pH. The activity of the catalyst is increased by [Fe(CN)(6)](3-) and decreased by VO(3)(-), CrO(4)(2-) and Zn(II). Three reaction pathways are involved in the Cu(II)-H(2)O(2) reaction, the kinetic orders of the catalyst being 1 (rate constant k1), 2 (rate constant k2) and 3 (rate constant k3). The three pathways present fractional apparent orders (>1) in H(2)O(2) and base catalysis. The apparent activation energies associated to rate constants k1, k2 and k3 are 102+/-4, 65+/-8 and 61+/-5 kJ mol(-1). Free-radical chain mechanisms are proposed for the three pathways. PMID:14987843

  7. 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. PMID:25525966

  8. Enantioselective Synthesis of Tetrahydroquinolines, Tetrahydroquinoxalines, and Tetrahydroisoquinolines via Pd-Catalyzed Alkene Carboamination Reactions.

    PubMed

    Hopkins, B A; Wolfe, J P

    2014-12-01

    A catalyst composed of Pd2(dba)3 and (S)-Siphos-PE provides excellent results in Pd-catalyzed alkene carboamination reactions between aniline derivatives bearing pendant alkenes and aryl or alkenyl halides. These transformations generate tetrahydroquinolines and tetrahydroquinoxalines that contain quaternary carbon stereocenters with high levels of asymmetric induction. In addition this catalyst also effects the asymmetric synthesis of tetrahydroisoquinolines via related transformations of 2-allylbenzylamines. In contrast to most other approaches to the asymmetric synthesis of these compounds, which frequently involve functional group interconversion or a single C-C or C-N bond-forming event, the carboamination reactions generate both a C-N bond, a C-C bond, and a stereocenter. PMID:25431650

  9. 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. PMID:24479684

  10. Gold(I)-catalyzed cycloisomerization reactions of allenes: An exploration of ligand effects and the total synthesis of flinderole B and C

    E-print Network

    Zeldin, Rachel Motove

    2011-01-01

    For examples of enantioselective gold(I)-reactions in totalenantioselective rendition of the gold(I)- catalyzed hydroarylation reactionreactions, we were interested in rendering these transformations enantioselective.

  11. Mechanism and stereoselection in a Y-catalyzed transacylation reaction. A computational modeling study.

    PubMed

    Sanan, Toby T; Rajanbabu, T V; Hadad, Christopher M

    2010-04-01

    Density functional theory calculations were performed to evaluate the proposed mechanism of a yttrium-salen complex-catalyzed acylation of secondary alcohols using an enol acetate as the acyl-transfer agent. A key step in the proposed mechanism is an intramolecular nucleophilic reaction between the coordinated alcohol and enol ester, brought into close proximity by the yttrium catalyst. The use of the BP86 pure density functional for reproduction of the geometry of the yttrium complex was validated by comparison with the experimental crystal structure. Mapping of the free energy surface of the reaction followed, employing both the BP86 and B3LYP functionals, and results suggest that the proposed mechanism (Org. Lett. 2002, 4, 1607-1610) is a reasonable pathway for the reaction. Reproduction of the experimentally observed enantioselectivity of the reaction was subsequently attempted, with diastereomeric transition states identified for the turnover-limiting step in the reaction, the intramolecular nucleophilic attack of the alcohol into the enol ester reagent. The predicted experimental enantioselectivities were successfully reproduced for the three ligands studied, although the energetic predictions did not perfectly correlate with the experimental enantioselectivities. PMID:20222696

  12. Rhodium(II)-catalyzed reactions of 3-diazo-2,4-chromenediones. First one-step synthesis of pterophyllin 2

    Microsoft Academic Search

    Yong Rok Lee; Jung Yup Suk; Byung So Kim

    1999-01-01

    Rhodium(II)-catalyzed reactions of 3-diazo-2,4-chromenediones 1–3 with a variety of substrates are described. Reactions of 1 with nitriles, isocyanates, and ketones give the corresponding 5-membered heterocycles in moderate yields, whereas those of 1 with acid chlorides afford ?-chloroenones in moderate yields. Reactions of 1 with electron-rich and -deficient olefins such as vinyl ethers and allyl iodide give dihydrofurocoumarins as a single

  13. EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions

    PubMed Central

    Cuesta, Sergio Martinez; Furnham, Nicholas; Holliday, Gemma L.

    2014-01-01

    EC-BLAST is an algorithm for quantitative similarity searches between enzyme reactions at three levels a) bond change, b) reaction centre and c) reaction structure similarity. It exploits the knowledge of bond changes and reaction patterns for all known biochemical reactions derived from atom-atom mapping (AAM) across each reaction. This has the potential to improve the established enzyme classification system, to find novel biochemical transformations, to improve the assignment of enzyme function to sequences, as well as for the re-engineering of enzymes. EC-BLAST URL: http://www.ebi.ac.uk/thornton-srv/software/rbl/ PMID:24412978

  14. 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 ?m). 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. PMID:25691570

  15. Asymmetric cascade reaction to allylic sulfonamides from allylic alcohols by palladium(II)/base-catalyzed rearrangement of allylic carbamates.

    PubMed

    Bauer, Johannes Moritz; Frey, Wolfgang; Peters, René

    2014-07-14

    A regio- and enantioselective tandem reaction is reported capable of directly transforming readily accessible achiral allylic alcohols into chiral sulfonyl-protected allylic amines. The reaction is catalyzed by the cooperative action of a chiral ferrocene palladacycle and a tertiary amine base and combines high step-economy with operational simplicity (e.g. no need for inert-gas atmosphere or catalyst activation). Mechanistic studies support a Pd(II)-catalyzed [3,3] rearrangement of allylic carbamates--generated in situ from the allylic alcohol and an isocyanate--as the key step, which is followed by a decarboxylation. PMID:24898109

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

    PubMed

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

    2014-09-12

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

  17. Identification and quantitation of reaction intermediates and residuals in lipase-catalyzed transesterified oils by HPLC.

    PubMed

    Aryee, Alberta N A; Phillip, Leroy E; Cue, Roger I; Simpson, Benjamin K

    2011-09-01

    A high-performance liquid chromatography (HPLC) unit equipped with size exclusion column and a refractive index detector was used for simultaneous monitoring, identification, and quantitation of the reaction components from lipase-catalyzed transesterification of three oils. The procedure simultaneously separated and detected the unreacted triacylglycerols (TAG), diacyl-, and monoacyl-glycerol (DAG and MAG) co-products, residual alcohol as well as free fatty acid (FFA) based on retention times. The chromatograms showed well separated and resolved peaks. The elution of the components from the transesterification reaction in increasing order was: TAG?reaction components and products of transesterification reactions without the need for additional derivatization steps. PMID:21523356

  18. Mechanistic Insights into a BINOL-Derived Phosphoric Acid-Catalyzed Asymmetric Pictet-Spengler Reaction.

    PubMed

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

    2015-03-01

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

  19. No Selenium Required: Reactions Catalyzed By Mammalian Thioredoxin Reductase That Are Independent of a Selenocysteine Residue.†

    PubMed Central

    Lothrop, Adam P.; Ruggles, Erik L.; Hondal, Robert J.

    2009-01-01

    Mammalian thioredoxin reductase (TR) contains a rare selenocysteine (Sec) residue in a conserved redox active tetrapeptide of sequence Gly-Cys1-Sec2-Gly. The high chemical reactivity of the Sec residue is thought to confer broad substrate specificity to the enzyme. In addition to utilizing thioredoxin (Trx) as a substrate, other substrates are: protein disulfide isomerase, glutaredoxin, glutathione peroxidase, NK-lysin/granulsin, HIV Tat protein, H2O2, lipid hydroperoxides, vitamin K, ubiquinone, juglone, ninhydrin, alloxan, dehydroascorbate, DTNB, lipoic acid/lipoamide, S-nitrosoglutathione, selenodiglutathione, selenite, methylseleninate, and selenocystine. Here we show that the Cys2-mutant enzyme or the N- terminal reaction center alone can reduce Se-containing substrates selenocystine and selenite with only slightly less activity than the wild type enzyme, in stark contrast to when Trx is used as the substrate when the enzyme suffers a 175- to 550-fold reduction in kcat. Our data supports the use of alternative mechanistic pathways for the Se-containing substrates that bypass a critical ring-forming step when Trx is the substrate. We also show that lipoic acid can be reduced through a Sec-independent mechanism that involves the N-terminal reaction center. These results show that the broad substrate specificity of the mammalian enzyme is not due to the presence of the rare Sec residue, but is due to the catalytic power of the N-terminal reaction center. We hypothesize that the N-terminal reaction center can reduce substrates: (i) with good leaving groups such as DTNB, (ii) that are highly electrophilic such as selenite, (iii) or are activated by strain such as lipoic acid/lipoamide. We also show that the absence of Sec only changed the IC50 for aurothioglucose by a factor of 1.7 in the full-length mammalian enzyme (83 nM to 142 nM), but surprisingly the truncated enzyme showed much stronger inhibition (25 nM). This contrasts with auranofin, where the absence of Sec more strongly perturbed inhibition. PMID:19366212

  20. ENZYME ISOFORMS MAY INCREASE PHENOTYPIC ROBUSTNESS

    Microsoft Academic Search

    Maurizio Tomaiuolo; Richard Bertram; David Houle

    2008-01-01

    Enzyme isoforms are found in many cellular reactions, and can differ in the kind of reaction they catalyze, in their substrate affinity, or in their reaction rates. The evolutionary significance of enzyme isoforms is only partially understood. We used mathematical modeling to investigate the hypothesis that isoforms may be favored by selection because they can increase the phenotypic robustness of

  1. 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.

  2. The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily.

    PubMed

    Nguyen, Tinh T; Fedorov, Alexander A; Williams, Lakenya; Fedorov, Elena V; Li, Yingchun; Xu, Chengfu; Almo, Steven C; Raushel, Frank M

    2009-09-22

    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 k(cat) and k(cat)/K(m) 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 beta-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. PMID:19678710

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

    E-print Network

    Chou, Tom

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

  4. Diffusion fronts in enzyme-catalysed reactions G.P. Boswell

    E-print Network

    Davidson, Fordyce A.

    Diffusion fronts in enzyme-catalysed reactions G.P. Boswell and F.A. Davidson Division: Michaelis-Menten, quasi-steady state, open system, diffusible substrate Running Head: enzyme-catalysed- Menten type kinetics for enzyme-catalysed biochemical reactions is studied. Previous work has in the main

  5. 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.

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

    PubMed

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

    2013-08-01

    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. PMID:23862564

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

    SciTech Connect

    Hegedus, L.S.; Sestrick, M.R.; Michaelson, E.T.; Harrington, P.J. (Colorado State Univ., Fort Collins (USA))

    1989-08-18

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

  8. Mechanistic insight into the Staudinger reaction catalyzed by N-heterocyclic carbenes.

    PubMed

    Hans, Morgan; Wouters, Johan; Demonceau, Albert; Delaude, Lionel

    2013-07-15

    Four zwitterions were prepared by treating 1,3-dimesitylimidazolin-2-ylidene (SIMes) or 1,3-dimesitylimidazol-2-ylidene (IMes) with either N-tosyl benzaldimine or diphenylketene. They were isolated in high yields and characterized by IR and NMR spectroscopy. The molecular structures of three of them were determined by using X-ray crystallography and their thermal stability was monitored by using thermogravimetric analysis. The imidazol(in)ium-2-amides were rather labile white solids that did not show any tendency to tautomerize into the corresponding 1,2,2-triaminoethene derivatives. They displayed a mediocre catalytic activity in the Staudinger reaction of N-tosyl benzaldimine with diphenylketene. In contrast, the imidazol(in)ium-2-enolates were orange-red crystalline materials that remained stable over extended periods of time. Despite their greater stability, these zwitterions turned out to be efficient promoters for the model cycloaddition under scrutiny. As a matter of fact, their catalytic activity matched those recorded with the free carbenes. Altogether, these results provide strong experimental insight into the mechanism of the Staudinger reaction catalyzed by N-heterocyclic carbenes. They also highlight the superior catalytic activity of the imidazole-based carbene IMes compared with its saturated analogue SIMes in the reaction under consideration. PMID:23754585

  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. 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.

  11. Structural Characterization of a 140 Degree Domain Movement in the Two-Step Reaction Catalyzed By 4-Chlorobenzoate:CoA Ligase

    SciTech Connect

    Reger, A.S.; Wu, R.; Dunaway-Mariano, D.; Gulick, A.M.

    2009-05-21

    Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PP{sub 1}, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140{sup o} to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue [Wu et al. (2008) Biochemistry 47, 8026-8039]. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

  12. Use of the Extraordinary Infrared Transmission of Metallic Subwavelength Arrays To Study the Catalyzed Reaction of Methanol to Formaldehyde on Copper Oxide

    E-print Network

    the Catalyzed Reaction of Methanol to Formaldehyde on Copper Oxide Shaun M. Williams, Kenneth R. Rodriguez scattered out of an incident beam. Commercial nickel mesh has been coated with copper to reduce the hole processes on the Cu surface. The copper oxide catalyzed reaction of methanol has been studied by recording

  13. Lecithin-cholesterol acyltransferase (LCAT) catalyzes transacylation of intact cholesteryl esters. Evidence for the partial reversal of the forward LCAT reaction

    SciTech Connect

    Sorci-Thomas, M.; Babiak, J.; Rudel, L.L. (Wake Forest Univ., Winston-Salem, NC (USA))

    1990-02-15

    Lecithin-cholesterol acyltransferase (LCAT) catalyzes the intravascular synthesis of lipoprotein cholesteryl esters by converting cholesterol and lecithin to cholesteryl ester and lysolecithin. LCAT is unique in that it catalyzes sequential reactions within a single polypeptide sequence. In this report we find that LCAT mediates a partial reverse reaction, the transacylation of lipoprotein cholesteryl oleate, in whole plasma and in a purified, reconstituted system. As a result of the reverse transacylation reaction, a linear accumulation of (3H)cholesterol occurred during incubations of plasma containing high density lipoprotein labeled with (3H)cholesteryl oleate. When high density lipoprotein labeled with cholesteryl (14C)oleate was also included in the incubation the labeled fatty acyl moiety remained in the cholesteryl (14C)oleate pool showing that the formation of labeled cholesterol did not result from hydrolysis of the doubly labeled cholesteryl esters. The rate of release of (3H)cholesterol was only about 10% of the forward rate of esterification of cholesterol using partially purified human LCAT and was approximately 7% in whole monkey plasma. Therefore, net production of cholesterol via the reverse LCAT reaction would not occur. (3H)Cholesterol production from (3H)cholesteryl oleate was almost completely inhibited by a final concentration of 1.4 mM 5,5'-dithiobis(nitrobenzoic acid) during incubation with either purified LCAT or whole plasma. Addition of excess lysolecithin to the incubation system did not result in the formation of (14C)oleate-labeled lecithin, showing that the reverse reaction found here for LCAT was limited to the last step of the reaction. To explain these results we hypothesize that LCAT forms a (14C)oleate enzyme thioester intermediate after its attack on the cholesteryl oleate molecule.

  14. Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase alpha-, beta-, and alpha beta-reactions.

    PubMed

    Woehl, E; Dunn, M F

    1999-06-01

    The alpha-subunit of the tryptophan synthase bienzyme complex catalyzes the formation of indole from the cleavage of 3-indolyl-D-glyceraldehyde 3'-phosphate, while the beta-subunit utilizes L-serine and the indole produced at the alpha-site to form tryptophan. The replacement reaction catalyzed by the beta-subunit requires pyridoxal 5'-phosphate (PLP) as a cofactor. The beta-reaction occurs in two stages: in stage I, the first substrate, L-Ser, reacts with the enzyme-bound PLP cofactor to form an equilibrating mixture of the L-Ser Schiff base, E(Aex1), and the alpha-aminoacrylate Schiff base intermediate, E(A-A); in stage II, this intermediate reacts with the second substrate, indole, to form tryptophan. Monovalent cations (MVCs) are effectors of these processes [Woehl, E., and Dunn, M. F. (1995) Biochemistry 34, 9466-9476]. Herein, detailed kinetic dissections of stage II are described in the absence and in the presence of MVCs. The analyses presented complement the results of the preceding paper [Woehl, E., and Dunn, M. F. (1999) Biochemistry 38, XXXX-XXXX], which examines stage I, and confirm that the chemical and conformational processes in stage I establish the presence of two slowly interconverting conformations of E(A-A) that exhibit different reactivities in stage II. The pattern of kinetic isotope effects on the overall activity of the beta-reaction shows an MVC-mediated change in rate-limiting steps. In the absence of MVCs, the reaction of E(A-A) with indole becomes the rate-limiting step. In the presence of Na+ or K+, the conversion of E(Aex1) to E(A-A) is rate limiting, whereas some third process not subject to an isotope effect becomes rate determining for the NH4+-activated enzyme. The combined results from the preceding paper and from this study define the MVC effects, both for the reaction catalyzed by the beta-subunit and for the allosteric communication between the alpha- and beta-sites. Partial reaction-coordinate free energy diagrams and simulation studies of MVC effects on the proposed mechanism of the beta-reaction are presented. PMID:10353823

  15. Iron- and Indium-Catalyzed Reactions toward Nitrogen- and Oxygen-Containing Saturated Heterocycles.

    PubMed

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

    2015-03-17

    A myriad of natural and/or biologically active products include nitrogen- and oxygen-containing saturated heterocycles, which are thus considered as attractive scaffolds in the drug discovery process. As a consequence, a wide range of reactions has been developed for the construction of these frameworks, much effort being specially devoted to the formation of substituted tetrahydropyrans and piperidines. Among the existing methods to form these heterocycles, the metal-catalyzed heterocyclization of amino- or hydroxy-allylic alcohol derivatives has emerged as a powerful and stereoselective strategy that is particularly interesting in terms of both atom-economy and ecocompatibility. For a long time, palladium catalysts have widely dominated this area either in Tsuji-Trost reactions [Pd(0)] or in an electrophilic activation process [Pd(II)]. More recently, gold-catalyzed formation of saturated N- and O-heterocycles has received growing attention because it generally exhibits high efficiency and diastereoselectivity. Despite their demonstrated utility, Pd- and Au-complexes suffer from high costs, toxicity, and limited natural abundance, which can be barriers to their widespread use in industrial processes. Thus, the replacement of precious metals with less expensive and more environmentally benign catalysts has become a challenging issue for organic chemists. In 2010, our group took advantage of the ability of the low-toxicity and inexpensive FeCl3 in activating allylic or benzylic alcohols to develop iron-catalyzed N- and O-heterocylizations. We first focused on N-heterocycles, and a variety of 2,6-disubstituted piperidines as well as pyrrolidines were synthesized in a highly diastereoselective fashion in favor of the cis-compounds. The reaction was further extended to the construction of substituted tetrahydropyrans. Besides triggering the formation of heterocycles, the iron salts were shown to induce a thermodynamic epimerization, which is the key to reach the high diastereoselectivities observed in favor of the most stable cis-isomers. It is worth noting that spiroketals could be prepared by using this method, which was successfully applied to a synthetic approach toward natural products belonging to the bistramide family. We then turned our attention to heterocycles incorporating two heteroatoms such as isoxazolidines. These frameworks can be found in biologically active natural products, and in addition, they can be transformed into 1,3-amino alcohols, which are of importance in organic chemistry. The use of FeCl3·6H2O allowed the access to a large variety of 3,5-disubstituted isoxazolidines from ?-hydroxylamino allylic alcohol derivatives with good yields and diastereoselectivities in favor of the cis-isomer. Recently, a Lewis acid-catalyzed synthesis of six- and five-membered ring carbonates starting from linear tert-butyl carbonates was reported. In some cases, the mild and chemoselective InCl3 was preferred over FeCl3·6H2O to avoid side-product formation. The resulting cyclic carbonates were easily transformed into 1,3- or 1,2-diols, and a total synthesis of (3S,5S)-alpinikatin was achieved. PMID:25674664

  16. Enzymes containing porous polymersomes as nano reaction vessels for cascade reactions.

    PubMed

    Kuiper, Suzanne M; Nallani, Madhavan; Vriezema, Dennis M; Cornelissen, Jeroen J L M; van Hest, Jan C M; Nolte, Roeland J M; Rowan, Alan E

    2008-12-01

    Polystyrene(40)-b-poly(isocyanoalanine(2-thiophen-3-yl-ethyl)amide)(50) (PS-PIAT) polymersomes have the unique property of being sufficiently porous to allow diffusion of small (organic) substrates while retaining large biomolecules such as enzymes inside. Herein we report on the encapsulation and protection of glucose oxidase (GOx) and horse radish peroxidase (HRP) in PS-PIAT polymersomes and the successful employment of these functionalised nanoreactors in a cascade reaction. The demonstrated concept allows for further application in other enzymatic cascade reactions, bio-organic hybrid systems and biosensing devices. PMID:19005589

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

    E-print Network

    Toste, Dean

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

  18. 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....

  19. Synthesis of 6-(Arylthio)phenanthridines by Copper-Catalyzed Tandem Reactions of 2-Biaryl Isothiocyanates with Diaryliodonium Salts.

    PubMed

    Guo, Weisi; Li, Shoulei; Tang, Lin; Li, Ming; Wen, Lirong; Chen, Chao

    2015-03-01

    A novel copper-catalyzed tandem C-S/C-C bond-forming reaction of 2-biaryl isothiocyanates with diaryliodonium salts was developed. This is the first general approach to synthesize phenanthridines from 2-biaryl isothiocyanates. This methodology has been successfully applied to the synthesis of trisphaeridine. PMID:25719267

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

    PubMed Central

    Shaikh, Tanveer Mahamadali

    2013-01-01

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

  1. Temperature dependence of internal friction in enzyme reactions.

    PubMed

    Rauscher, Anna Á; Simon, Zoltán; Szöllosi, Gergely J; Gráf, László; Derényi, Imre; Malnasi-Csizmadia, Andras

    2011-08-01

    Our aim was to elucidate the physical background of internal friction of enzyme reactions by investigating the temperature dependence of internal viscosity. By rapid transient kinetic methods, we directly measured the rate constant of trypsin 4 activation, which is an interdomain conformational rearrangement, as a function of temperature and solvent viscosity. We found that the apparent internal viscosity shows an Arrhenius-like temperature dependence, which can be characterized by the activation energy of internal friction. Glycine and alanine mutations were introduced at a single position of the hinge of the interdomain region to evaluate how the flexibility of the hinge affects internal friction. We found that the apparent activation energies of the conformational change and the internal friction are interconvertible parameters depending on the protein flexibility. The more flexible a protein was, the greater proportion of the total activation energy of the reaction was observed as the apparent activation energy of internal friction. Based on the coupling of the internal and external movements of the protein during its conformational change, we constructed a model that quantitatively relates activation energy, internal friction, and protein flexibility. PMID:21555355

  2. 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

    2012-03-01

    The pronounced Lewis acidity of tricoordinate silicon cations brings about unusual reactivity in Lewis acid catalysis. The downside of catalysis with strong Lewis acids is, though, that these do have the potential to mediate the formation of protons by various mechanisms, and the thus released 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 ?,?-unsaturated dienophile (carbonyl and carboxyl), whereas proton catalysis is limited to carbonyl compounds. PMID:22309027

  3. Several dinucleoside polyphosphates are acceptor substrates in the T4 RNA ligase catalyzed reaction.

    PubMed

    Atencia, E A; Montes, M; Günther Sillero, M A; Sillero, A

    2000-03-01

    Several dinucleoside polyphosphates accept cytidine-3', 5'-bisphosphate from the adenylylated donor 5'-adenylylated cytidine 5',3'-bisphosphate in the T4 RNA ligase catalyzed reaction. The 5'-adenylylated cytidine 5',3'-bisphosphate synthesized in a first step, from ATP and cytidine-3',5'-bisphosphate, is used as a substrate to transfer the cytidine-3',5'-bisphosphate residue to the 3'-OH group(s) of diguanosine tetraphosphate (Gp4G) giving rise to Gp4GpCp and pCpGp4GpCp in a ratio of approximately 10 : 1, respectively. The synthesized Gp4GpCp was characterized by treatment with snake venom phosphodiesterase and alkaline phosphatase and analysis (chromatographic position and UV spectra) of the reaction products by HPLC. The apparent Km values measured for Gp4G and 5'-adenylylated cytidine 5',3'-bisphosphate in this reaction were approximately 4 mM and 0.4 mM, respectively. In the presence of 0.5 mM ATP and 0.5 mM cytidine-3',5'-bisphosphate, the relative efficiencies of the following nucleoside(5')oligophospho(5')nucleosides as acceptors of cytidine-3',5'-bisphosphate from 5'-adenylylated cytidine 5', 3'-bisphosphate are indicated in parentheses: Gp4G (100); Gp5G (101); Ap4G (47); Ap4A (39). Gp2G, Gp3G and Xp4X were not substrates of the reaction. Dinucleotides containing two guanines and at least four inner phosphates were the preferred acceptors of cytidine-3', 5'-bisphosphate at their 3'-OH group(s). PMID:10712602

  4. Theoretical investigations on the stereoselectivity of the proline catalyzed Mannich reaction in DMSO.

    PubMed

    Parasuk, Waraporn; Parasuk, Vudhichai

    2008-12-01

    The stereocontrol steps of the (S)-proline catalyzed Mannich reaction of cyclohexanone, formaldehyde, and aniline were theoretically investigated. The geometries of reactants, products, and transition states were optimized using density functional theory using the B3LYP functional with the 6-31++G(d,p) basis set. The energies of these compounds were then more accurately determined at the MP2 level, and the effect of DMSO as the solvent was included using a polarizable continuum model (PCM). The reaction was modeled from the previously proposed mechanism that cyclohexanone reacts with (S)-proline to generate an enamine, while formaldehyde reacts with aniline to produce an imine, and that the conformation around the C-N bond of the enamine 1 is crucial for the further enantioselective step. The formation of two conformations of the enamine via a proton transfer process was examined, revealing activation barriers for syn- and anti-enamine proton transfer of 10.2 and 17.9 kcal/mol, respectively. The transformation of syn- to anti-enamine through C-N bond rotation, however, was predicted to require only 4.2 kcal/mol, while the (S)- and (R)-intermediates could be obtained from subsequent reactions between enamine and imine with energy barriers of 8.5 and 12.4 kcal/mol, respectively. The difference between these barriers, but not the C-N rotation energy, becomes larger at the MP2 level and when DMSO as a solvent is included. This predicted enantioselective reaction, through the kinetic and thermodynamic favoring of the (S)-pathway, is in agreement with experimental results, which have reported the (S)-configuration as the major product. PMID:18954108

  5. Multiple Hydrogen Kinetic Isotope Effects for Enzymes Catalyzing Exchange with Solvent: Application to Alanine Racemase

    E-print Network

    Toney, Michael

    .824 in D2O. Similar reductions are also observed at 65 °C, the temperature to which the Bacillus stearothermophilus enzyme is adapted. These data strongly support a stepwise racemization of stereoisomeric aldimine the acidity of the CR proton. Previous work has established that racemization in the Bacillus

  6. Critical role of DNA intercalation in enzyme-catalyzed nucleotide flipping

    PubMed Central

    Hendershot, Jenna M.; O'Brien, Patrick J.

    2014-01-01

    Nucleotide flipping is a common feature of DNA-modifying enzymes that allows access to target sites within duplex DNA. Structural studies have identified many intercalating amino acid side chains in a wide variety of enzymes, but the functional contribution of these intercalating residues is poorly understood. We used site-directed mutagenesis and transient kinetic approaches to dissect the energetic contribution of intercalation for human alkyladenine DNA glycosylase, an enzyme that initiates repair of alkylation damage. When AAG flips out a damaged nucleotide, the void in the duplex is filled by a conserved tyrosine (Y162). We find that tyrosine intercalation confers 140-fold stabilization of the extrahelical specific recognition complex, and that Y162 functions as a plug to slow the rate of unflipping by 6000-fold relative to the Y162A mutant. Surprisingly, mutation to the smaller alanine side chain increases the rate of nucleotide flipping by 50-fold relative to the wild-type enzyme. This provides evidence against the popular model that DNA intercalation accelerates nucleotide flipping. In the case of AAG, DNA intercalation contributes to the specific binding of a damaged nucleotide, but this enhanced specificity comes at the cost of reduced speed of nucleotide flipping. PMID:25324304

  7. The gas phase reaction of singlet dioxygen with water: a water-catalyzed mechanism.

    PubMed

    Xu, Xin; Muller, Richard P; Goddard, William A

    2002-03-19

    Stimulated by the recent surprising results from Wentworth et al. [Wentworth, A. D., Jones, L. H., Wentworth, P., Janda, K. D. & Lerner, R. A. (2000) Proc. Natl. Acad. Sci. USA 97, 10930-10935] that Abs efficiently catalyze the conversion of molecular singlet oxygen ((1)O(2)) plus water to hydrogen peroxide (HOOH), we used quantum chemical methods (B3LYP density functional theory) to delineate the most plausible mechanisms for the observed efficient conversion of water to HOOH. We find two reasonable pathways. In Pathway I, (i) H(2)O catalyzes the reaction of (1)O(2) with a second water to form HOOOH; (ii) two HOOOH form a dimer, which rearranges to form the HOO-HOOO + H(2)O complex; (iii) HOO-HOOO rearranges to HOOH-OOO, which subsequently reacts with H(2)O to form H(2)O(4) + HOOH; and (iv) H(2)O(4) rearranges to the cyclic dimer (HO(2))(2), which in turn forms HOOH plus (1)O(2) or (3)O(2). Pathway II differs in that step ii is replaced with the reaction between HOOOH and (1)O(2), leading to the formation of HOO-HOOO. This then proceeds to similar products. For a system with (18)O H(2)O, Pathway I leads to a 2.2:1 ratio of (16)O:(18)O in the product HOOH, whereas Pathway II leads to 3:1. These ratios are in good agreement with the 2.2:1 ratio observed in isotope experiments by Wentworth et al. These mechanisms lead to two HOOH per initial (1)O(2) or one, depending on whether the product of step iv is (1)O(2) or (3)O(2), in good agreement with the experimental result of 2.0. In addition to the Ab-induced reactions, the hydrogen polyoxides (H(2)O(3) and H(2)O(4)) formed in these mechanisms and their decomposition product polyoxide radicals (HO(2), HO(3)) may play a role in combustion, explosions, atmospheric chemistry, and the radiation chemistry in aqueous systems. PMID:11891316

  8. Mechanism of the Orotidine 5’-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence for Substrate Destabilization†

    PubMed Central

    Chan, Kui K.; Wood, B. McKay; Fedorov, Alexander A.; Fedorov, Elena V.; Imker, Heidi J.; Amyes, Tina L.; Richard, John P.; Almo, Steven C.; Gerlt, John A.

    2009-01-01

    The reaction catalyzed by orotidine 5’-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (kcat/knon, 7.1 × 1016) and proficiency [(kcat/KM)/knon, 4.8 × 1022 M?1] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (? 1010). The origin of the “missing” contribution, ? 107 (?1017 total - ? 1010), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc Natl Acad Sci U S A 97, 2017?2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of kcat for decarboxylation of FOMP (a more reactive substrate analog) but have little effect on the value of kex for exchange of H6 of FUMP with solvent deuterium; the structures of wild type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis á vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization. PMID:19435314

  9. 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.

  10. Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

    PubMed

    Chan, Kui K; Wood, B McKay; Fedorov, Alexander A; Fedorov, Elena V; Imker, Heidi J; Amyes, Tina L; Richard, John P; Almo, Steven C; Gerlt, John A

    2009-06-23

    The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (k(cat)/k(non), 7.1 x 10(16)) and proficiency [(k(cat)/K(M))/k(non), 4.8 x 10(22) M(-1)] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (>or=10(10)). The origin of the "missing" contribution, or=10(10)), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of k(cat) for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of k(ex) for exchange of H6 of FUMP with solvent deuterium; the structures of wild-type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild-type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis a vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization. PMID:19435314

  11. 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. PMID:20831353

  12. Analysis of the HindIII-catalyzed reaction by time-resolved crystallography

    PubMed Central

    Kawamura, Takashi; Kobayashi, Tomoki; Watanabe, Nobuhisa

    2015-01-01

    In order to investigate the mechanism of the reaction catalyzed by HindIII, structures of HindIII–DNA complexes with varying durations of soaking time in cryoprotectant buffer containing manganese ions were determined by the freeze-trap method. In the crystal structures of the complexes obtained after soaking for a longer duration, two manganese ions, indicated by relatively higher electron density, are clearly observed at the two metal ion-binding sites in the active site of HindIII. The increase in the electron density of the two metal-ion peaks followed distinct pathways with increasing soaking times, suggesting variation in the binding rate constant for the two metal sites. DNA cleavage is observed when the second manganese ion appears, suggesting that HindIII uses the two-metal-ion mechanism, or alternatively that its reactivity is enhanced by the binding of the second metal ion. In addition, conformational change in a loop near the active site accompanies the catalytic reaction. PMID:25664735

  13. Palladium-Catalyzed ?-Arylation of Zinc Enolates of Esters: Reaction Conditions and Substrate Scope

    PubMed Central

    Hama, Takuo; Ge, Shaozhong; Hartwig, John F.

    2013-01-01

    The intermolecular ?-arylation of esters by palladium-catalyzed coupling of aryl bromides with zinc enolates of esters is reported. Reactions of three different types of zinc enolates have been developed. ?-Arylation of esters occurs in high yields with isolated Reformatsky reagents, with Reformatsky reagents generated from ?-bromo esters and activated zinc, and with zinc enolates generated by quenching lithium enolates of esters with zinc chloride. The use of zinc enolates, instead of alkali metal enolates, greatly expands the scope of the arylation of esters. The reactions occur at room temperature or at 70 °C with bromoarenes containing cyano, nitro, ester, keto, fluoro, enolizable hydrogen, hydroxyl or amino functionality and with bromopyridines. The scope of esters encompasses acyclic acetates, propionates, and isobutyrates, ?-alkoxyesters, and lactones. The arylation of zinc enolates of esters was conducted with catalysts bearing the hindered pentaphenylferrocenyl di-tert-butylphosphine (Q-phos) or the highly reactive dimeric Pd(I) complex {[P(t-Bu)3]PdBr}2. PMID:23931445

  14. Reaction Pathways and Energetics of Etheric C?O Bond Cleavage Catalyzed by Lanthanide Triflates

    SciTech Connect

    Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.

    2013-07-15

    Efficient and selective cleavage of etheric C?O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C?O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C?O cleavage occurs via a C?H ? O?H proton transfer in concert with weakening of the C?O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C?O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.

  15. 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.

  16. Transglycosylation reaction catalyzed by a class V chitinase from cycad, Cycas revoluta: a study involving site-directed mutagenesis, HPLC, and real-time ESI-MS.

    PubMed

    Taira, Toki; Fujiwara, Maho; Dennhart, Nicole; Hayashi, Hiroko; Onaga, Shoko; Ohnuma, Takayuki; Letzel, Thomas; Sakuda, Shohei; Fukamizo, Tamo

    2010-04-01

    Class V chitinase from cycad, Cycas revoluta, (CrChi-A) is the first plant chitinase that has been found to possess transglycosylation activity. To identify the structural determinants that bring about transglycosylation activity, we mutated two aromatic residues, Phe166 and Trp197, which are likely located in the acceptor binding site, and the mutated enzymes (F166A, W197A) were characterized. When the time-courses of the enzymatic reaction toward chitin oligosaccharides were monitored by HPLC, the specific activity was decreased to about 5-10% of that of the wild type and the amounts of transglycosylation products were significantly reduced by the individual mutations. From comparison between the reaction time-courses obtained by HPLC and real-time ESI-MS, we found that the transglycosylation reaction takes place under the conditions used for HPLC but not under the ESI-MS conditions. The higher substrate concentration (5 mM) used for the HPLC determination is likely to bring about chitinase-catalyzed transglycosylation. Kinetic analysis of the time-courses obtained by HPLC indicated that the sugar residue affinity of +1 subsite was strongly reduced in both mutated enzymes, as compared with that of the wild type. The IC(50) value for the inhibitor allosamidin determined by real-time ESI-MS was not significantly affected by the individual mutations, indicating that the state of the allosamidin binding site (from -3 to -1 subsites) was not changed in the mutated enzymes. We concluded that the aromatic side chains of Phe166 and Trp197 in CrChi-A participate in the transglycosylation acceptor binding, thus controlling the transglycosylation activity of the enzyme. PMID:19879383

  17. Can laccases catalyze bond cleavage in lignin?

    PubMed

    Munk, Line; Sitarz, Anna K; Kalyani, Dayanand C; Mikkelsen, J Dalgaard; Meyer, Anne S

    2015-01-01

    Modification of lignin is recognized as an important aspect of the successful refining of lignocellulosic biomass, and enzyme-assisted processing and upcycling of lignin is receiving significant attention in the literature. Laccases (EC 1.10.3.2) are taking the centerstage of this attention, since these enzymes may help degrading lignin, using oxygen as the oxidant. Laccases can catalyze polymerization of lignin, but the question is whether and how laccases can directly catalyze modification of lignin via catalytic bond cleavage. Via a thorough review of the available literature and detailed illustrations of the putative laccase catalyzed reactions, including the possible reactions of the reactive radical intermediates taking place after the initial oxidation of the phenol-hydroxyl groups, we show that i) Laccase activity is able to catalyze bond cleavage in low molecular weight phenolic lignin model compounds; ii) For laccases to catalyze inter-unit bond cleavage in lignin substrates, the presence of a mediator system is required. Clearly, the higher the redox potential of the laccase enzyme, the broader the range of substrates, including o- and p-diphenols, aminophenols, methoxy-substituted phenols, benzenethiols, polyphenols, and polyamines, which may be oxidized. In addition, the currently available analytical methods that can be used to detect enzyme catalyzed changes in lignin are summarized, and an improved nomenclature for unequivocal interpretation of the action of laccases on lignin is proposed. PMID:25560931

  18. Pd(II)-Catalyzed C–H Activation/C–C Cross-Coupling Reactions: Versatility and Practicality

    PubMed Central

    Chen, Xiao; Engle, Keary M.; Wang, Dong-Hui; Yu, Jin-Quan

    2009-01-01

    In the past decade, palladium-catalyzed C–H activation/C–C bond forming reactions have emerged as promising new catalytic transformations; however, development in this field is still at an early stage compared to the state of the art in cross-coupling reactions using aryl and alkyl halides. This Review begins with a brief introduction of four extensively investigated modes of catalysis for forming C–C bonds from C–H bonds: Pd(II)/Pd(0), Pd(II)/Pd(IV), Pd(0)/Pd(II)/Pd(IV) and Pd(0)/Pd(II) catalysis. More detailed discussion is then directed towards the recent development of Pd(II)-catalyzed coupling of C–H bonds with organometallic reagents through a Pd(II)/Pd(0) catalytic cycle. Despite much progress made to date, improving the versatility and practicality of this new reaction remains a tremendous challenge. PMID:19557755

  19. Fundamental reaction pathways for cytochrome P450-catalyzed 5'-hydroxylation and N-demethylation of nicotine.

    PubMed

    Li, Dongmei; Wang, Yong; Han, Keli; Zhan, Chang-Guo

    2010-07-15

    The reaction pathways for 5'-hydroxylation and N-demethylation of nicotine catalyzed by cytochrome P450 were investigated by performing a series of first-principle electronic structure calculations on a catalytic reaction model system. The computational results indicate that 5'-hydroxylation of nicotine occurs through a two-state stepwise process, that is, an initial hydrogen atom transfer from nicotine to Cpd I (i.e., the HAT step) followed by a recombination of the nicotine moiety with the iron-bound hydroxyl group (i.e., the rebound step) on both the high-spin (HS) quartet and low-spin (LS) doublet states. The HAT step is the rate-determining one. This finding represents the first case that exhibits genuine rebound transition state species on both the HS and the LS states for C(alpha)-H hydroxylation of amines. N-Demethylation of nicotine involves a N-methylhydroxylation to form N-(hydroxymethyl)nornicotine, followed by N-(hydroxymethyl)nornicotine decomposition to nornicotine and formaldehyde. The N-methylhydroxylation step is similar to 5'-hydroxylation, namely, a rate-determining HAT step followed by a rebound step. The decomposition process occurs on the deprotonated state of N-(hydroxymethyl)nornicotine assisted by a water molecule, and the energy barrier is significantly lower than that of the N-methylhydroxylation process. Comparison of the rate-determining free energy barriers for the two reaction pathways predicts a preponderance of 5'-hydroxylation over the N-demethylation by roughly a factor of 18:1, which is in excellent agreement with the factor of 19:1 derived from available experimental data. PMID:20572647

  20. Radiolysis of water vapor and a surface-catalyzed isotope-exchange reaction

    SciTech Connect

    Richter, H.W.; Firestone, R.F.

    1981-08-26

    The steady-state radiolysis of deuterium oxide vapor has been examined using protium, perprotiopropane, or mixtures of these two as free-radical scavengers. Tritiated water was used as an internal radiation source, and glass irradiation vessels were employed. D atoms are produced in the radiolytic decomposition of D/sub 2/O, and HD is formed by reaction of this species with the added radical scavengers. It was assumed previously that the yield of HD molecules could be equated with the yield of radiolytically produced D atoms. However, the experimental results of the present investigation demonstrate conclusively that when H/sub 2/ is used as a radical scavenger there are two pathways for HD formation: (1) homogeneous scavenging of the radiolytically produced D atoms by H/sub 2/, as expected, and (2) heterogeneous combination of H atoms produced in the scavenging reaction (D + H/sub 2/ ..-->.. HD + H) with D atoms absorbed on the vessel surface, where the adsorbed D atoms are generated by a surface-catalyzed isotope-exchange reaction between H atoms adsorbed from the volume and D/sub 2/O. From the results of this investigation, it appears that the yield of D atoms produced in the radiolysis of D/sub 2/O is G/sub D/ = 7.0 atoms/100 eV absorbed energy, i.e., the G(HD) found in experiments using propane as the radical scavenger. G/sub D/sub 2// is shown to be 0.65 molecules/100 eV.

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

    PubMed

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

    2004-10-01

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

  2. Reaction Mechanism for Cocaine Esterase-Catalyzed Hydrolyses of (+)- and (?)-Cocaine: Unexpected Common Rate-Determining Step

    PubMed Central

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

    2011-01-01

    First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations have been performed to examine 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 hydroxyl group of Ser117 on 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. Further, 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. PMID:21486046

  3. Real-time detection of dopamine released from a nerve model cell by an enzyme-catalyzed luminescence method and its application to drug assessment.

    PubMed

    Shinohara, Hiroaki; Wang, Feifei

    2007-01-01

    A real-time observation of neurotransmitter release from a nerve cell is a useful method for not only neuroscience research, but also assessing of the influence of chemicals, including drugs, on the human nervous system. In this study, a more simple and sensitive method for real-time monitoring of dopamine release from a nerve model cell was developed. Highly sensitive detection of dopamine was performed by using tyramine oxidase for dopamine oxidation, which was followed by a luminol luminescence reaction. This enzyme-catalyzed luminescence method was applied to observe dopamine release from the PC12 cell as a nerve model cell upon stimulation with acetylcholine and an acetylcholine receptor agonist. The results demonstrated that the real-time monitoring of the activation of the PC12 cell was easily performed by this method. This method possessed many advantages, such as high sensitivity, rapid measurement and no pretreatment for cells. It might be applied to drug screening and the assessment of harmful influences of food additives and pesticides on the nerves. PMID:17213629

  4. Rhodium catalyzed chelation-assisted C-H bond functionalization reactions

    PubMed Central

    Colby, Denise A.; Tsai, Andy S.; Bergman, Robert G.; Ellman, Jonathan A.

    2011-01-01

    Conspectus Over the last several decades, researchers have achieved remarkable progress in the field of organometallic chemistry. The development of metal-catalyzed cross-coupling reactions represents a paradigm shift in chemical synthesis, and today synthetic chemists can readily access carbon-carbon and carbon-heteroatom bonds from a vast array of starting compounds. Although we cannot understate the importance of these methods, the required pre-functionalization to carry out these reactions adds cost and reduces the availability of the starting reagents. The use of C-H bond activation in lieu of pre-functionalization has presented a tantalizing alternative to classical cross-coupling reactions. Researchers have met the challenges of selectivity and reactivity associated with the development of C-H bond functionalization reactions with an explosion of creative advances in substrate and catalyst design. Literature reports on selectivity based on steric effects, acidity, and electronic and directing group effects are now numerous. Our group has developed an array of C-H bond functionalization reactions that take advantage of a chelating directing group, and this Account surveys our progress in this area. The use of chelation control in C-H bond functionalization offers several advantages with respect to substrate scope and application to total synthesis. The predictability and decreased dependence on the inherent stereoelectronics of the substrate generally result in selective and high yielding transformations with broad applicability. The nature of the chelating moiety can be chosen to serve as a functional handle in subsequent elaborations. Our work began with the use of Rh(I) catalysts in intramolecular aromatic C-H annulations, which we further developed to include enantioselective transformations. The application of this chemistry to the simple olefinic C-H bonds found in ?,?-unsaturated imines allowed access to highly substituted olefins, pyridines, and piperidines. We observed complementary reactivity with Rh(III) catalysts and developed an oxidative coupling with unactivated alkenes. Further studies on the Rh(III) catalysts led us to develop methods for the coupling of C-H bonds to polarized ? bonds such as those in imines and isocyanates. In several cases the methods that we have developed for chelation-controlled C-H bond functionalization have been applied to the total synthesis of complex molecules such as natural products, highlighting the utility of these methods in organic synthesis. PMID:22148885

  5. A new route to methyl (R,E)-(-)-tetradeca-2,4,5-trienoate (pheromone of Acanthoscelides obtectus) utilizing a palladium-catalyzed asymmetric allene formation reaction.

    PubMed

    Ogasawara, Masamichi; Nagano, Takashi; Hayashi, Tamio

    2005-07-01

    [reaction: see text] A formal total synthesis of the sex attractant of male dried bean beetle, methyl (R,E)-(-)-tetradeca-2,4,5-trienoate, was achieved by a new efficient route utilizing the Pd-catalyzed asymmetric allene synthesis reaction. It was found that the atropisomeric biaryl bisphosphine (R)-segphos showed better enantioselectivity than (R)-binap in the Pd-catalyzed reaction for preparing alkyl-substituted axially chiral allenes. PMID:15989370

  6. 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…

  7. Enzyme-catalyzed hydrolysis of cellulose in ionic liquids: a green approach toward the production of biofuels.

    PubMed

    Bose, Sayantan; Armstrong, Daniel W; Petrich, Jacob W

    2010-06-24

    We investigated the reactivity and stability of a commercial mixture of cellulases in eight ionic liquids by optical and calorimetric techniques. First, hydrolysis by cellulases from Tricoderma reesei in these ionic liquids was benchmarked against that in aqueous buffer. Only 1-methylimidazolium chloride (mim Cl) and tris-(2-hydroxyethyl)methylammonium methylsulfate (HEMA) provided a medium in which hydrolysis could occur. While hydrolysis at 65 degrees C is initially much faster in buffer than in these two liquids, it reaches a plateau after 2 h, whereas the reaction progresses monotonically in the two ionic liquids. This difference in the rate of hydrolysis is largely attributed to two factors: (1) the higher viscosity of the ionic liquids and (2) the enzymes are irreversibly denatured at 50 degrees C in buffer while they are stable to temperatures as high as 115 degrees C in HEMA. We explored whether fluorescence quenching of aromatic amino acids of the enzymes was indeed a signature of protein denaturation, as has been suggested in the literature, and concluded that quenching is not necessarily associated with denaturation. When it does occur, for example, in the presence of ionic liquids formed from imidazolium cations and chloride anions, it arises from the imidazolium rather than the chloride. Finally, we conclude that HEMA is a promising, novel, green medium for performing cellulose hydrolysis reactions to convert biomass into biofuels. Because of the thermal stability it imparts to enzymes, its ability to solubilize biomass, and the fact that it does not quench tryptophyl fluorescence (thus permitting monitoring of the enzymes by fluorescence spectroscopy), HEMA provides an ideal starting point for the design of ionic liquids, not only for the hydrolysis of biomass, but also for use with a wide spectrum of enzymatic reactions. PMID:20509703

  8. Enzyme-catalyzed change of antioxidants content and antioxidant activity of asparagus juice.

    PubMed

    Sun, Ting; Powers, Joseph R; Tang, Juming

    2007-01-10

    A pectolytic enzyme preparation from Aspergillus niger (pectinase AN) decreased most rutin content and antioxidant activity of asparagus juice. To investigate the mechanism of such loss, we analyzed several possible related enzyme activities in pectinase AN. We found that the activity of pectinase AN to oxidize guaiacol had no significant difference with or without the presence of H2O2; thus it was laccase activity, not peroxidase (PO) activity, that pectinase AN contained. We did not find any polyphenol oxidase (PPO) activity in pectinase AN. Laccase in pectinase AN could be the major cause of loss of rutin and antioxidant activity of asparagus juice. When most laccase activity of pectinase AN was inactivated after heating at 70 degrees C for 1.5 min and incubated with asparagus juice, the loss rate of rutin was only 9% of that treated with unheated pectinase AN, and the antioxidant activity was even increased. Rhamnosidase activity was detected in pectinase AN and can change rutin in asparagus juice to quercetin-3-glucoside, which has higher antioxidant activity than rutin. This may explain the increase of antioxidant activity of asparagus juice treated with heated pectinase AN that still contained some rhamnosidase activity. The discovery of our research is helpful to produce juice with high antioxidant activity and high health benefits in the juice industry. PMID:17199313

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

    PubMed

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

    2011-04-01

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

  10. (Hydroxyalkyl)cob(III)alamins as Competitive Inhibitors in Coenzyme B12-Dependent Enzymic Reactions: 1

    E-print Network

    Rétey, János

    (Hydroxyalkyl)cob(III)alamins as Competitive Inhibitors in Coenzyme B12-Dependent Enzymic Reactions-(p-tolyl)cobamide] (HOÃ?PTC) were tested with two coenzyme-B12-dependent enzymes: glycerol dehydratase (GDH) and propane-1 as strong competitive inhibitors of coenzyme B12 (5'-deoxy-5'-adenosylcobalamin, AdoÃ?Cbl) for both enzymes

  11. Global stability of the attracting set of an enzyme-catalysed reaction system

    E-print Network

    Davidson, Fordyce A.

    remain small, even when the values of kinetic parameters (e.g. maximum enzyme activities) changeGlobal stability of the attracting set of an enzyme-catalysed reaction system y F.A. Davidson of reaction rate on metabolite concentration taking the form of saturation kinetics. It has been recently

  12. Effect of mass transfer on the oxygen reduction reaction catalyzed by platinum dendrimer encapsulated nanoparticles

    PubMed Central

    Dumitrescu, Ioana; Crooks, Richard M.

    2012-01-01

    Here we report on the effect of the mass transfer rate (kt) on the oxygen reduction reaction (ORR) catalyzed by Pt dendrimer-encapsulated nanoparticles (DENs) comprised of 147 and 55 atoms (Pt147 and Pt55). The experiments were carried out using a dual-electrode microelectrochemical device, which enables the study of the ORR under high kt conditions with simultaneous detection of H2O2. At low kt (0.02 to 0.12 cm s-1) the effective number of electrons involved in ORR, neff, is 3.7 for Pt147 and 3.4 for Pt55. As kt is increased, the mass-transfer-limited current for the ORR becomes significantly lower than the value predicted by the Levich equation for a 4-electron process regardless of catalyst size. However, the percentage of H2O2 detected remains constant, such that neff barely changes over the entire kt range explored (0.02 cm s-1). This suggests that mass transfer does not affect neff, which has implications for the mechanism of the ORR on Pt nanoparticles. Interestingly, there is a significant difference in neff for the two sizes of Pt DENs (neff = 3.7 and 3.5 for Pt147 and Pt55, respectively) that cannot be assigned to mass transfer effects and that we therefore attribute to a particle size effect. PMID:22665772

  13. 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.

  14. de novo computational enzyme design.

    PubMed

    Zanghellini, Alexandre

    2014-10-01

    Recent advances in systems and synthetic biology as well as metabolic engineering are poised to transform industrial biotechnology by allowing us to design cell factories for the sustainable production of valuable fuels and chemicals. To deliver on their promises, such cell factories, as much as their brick-and-mortar counterparts, will require appropriate catalysts, especially for classes of reactions that are not known to be catalyzed by enzymes in natural organisms. A recently developed methodology, de novo computational enzyme design can be used to create enzymes catalyzing novel reactions. Here we review the different classes of chemical reactions for which active protein catalysts have been designed as well as the results of detailed biochemical and structural characterization studies. We also discuss how combining de novo computational enzyme design with more traditional protein engineering techniques can alleviate the shortcomings of state-of-the-art computational design techniques and create novel enzymes with catalytic proficiencies on par with natural enzymes. PMID:24794534

  15. 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.

  16. PURIFICATION AND ISOLATION OF THE PHOSPHOGLYCERATE KINASE ENZYME

    E-print Network

    Collins, Gary S.

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

  17. Isomerization, but not oxidation, is suppressed by a single point mutation, E361Q, in the reaction catalyzed by cholesterol oxidase

    SciTech Connect

    Sampson, N.S.; Kass, I.J. [State Univ. of New York, Stony Brook, NY (United States)] [State Univ. of New York, Stony Brook, NY (United States)

    1997-02-05

    The putative active site base of cholesterol oxidase from Streptomyces has been removed by site-directed mutagenesis and the mutant enzyme characterized. When glutamate-361 is mutated to a glutamine, the isomerization chemistry catalyzed by cholesterol oxidase is suppressed and the intermediate cholest-5-ene-3-one is isolated. The specific activity for oxidation is 20-fold slower than the wild-type reaction, though the specific activity for isomerization is 10,000-fold slower. Furthermore, incubation of cholest-5-ene-3-one with the E361Q cholesterol oxidase resulted in the production of cholest-4-ene-6{beta}-hydroperoxy-3-one (6%), cholest-4-ene-3,6-dione (32%), cholest-4-ene-6{beta}-ol-3-one (36%), and cholest-4-ene-6{alpha}-hydroperoxy-3-one/ cholest-4-ene-6{alpha}-ol-3-one (13%), in addition to cholest-4-ene-3-one (13%). Measurement of reaction stoichiometry eliminated the possibility that H{sub 2}O{sub 2} or the C4a-hydroperoxy flavin was the oxygenation agent. It is proposed that cholest-4-ene-6-hydroperoxy-3-one is the product of radical chain autoxidation and that cholest-4-ene-3,6-dione and cholest-4-ene-6-ol-3-one are decomposition products of the hydroperoxy steroid radical. The characterization of the E361Q mutant chemistry has illuminated the importance of intermediate sequestration in enzyme catalysis. 42 refs., 5 figs., 2 tabs.

  18. Evidence of Kinetic Control of Ligand Binding and Staged Product Release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed Reactions

    SciTech Connect

    Jackson, S.; Zhang, F; Chindemi, P; Junop, M; Berti, P

    2009-01-01

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

  19. 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. PMID:25541815

  20. Platinum-catalyzed tandem cycloisomerization reaction of benzoendiynyl esters: regioselective long-range 1,5-acyl migration.

    PubMed

    Chen, Zhiyuan; Jia, Xuegong; Huang, Jiapian; Yuan, Jianjun

    2014-11-01

    A Pt(II)-catalyzed intramolecular chemo- and regioselective pentannulation/long-range 1,5-acyl migration reaction is described. This cascade cycloisomerization protocol produces a wide variety of benzofulvene diketones in good to excellent yields with exclusively the Z configuration of the exocyclic double bond of the final product. The (18)O isotope experiment together with (13)C NMR, HRMS, and HMBC analyses confirmed an interesting long-range acyl rearrangement process in this transformation. PMID:25266509

  1. 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.

  2. Regio- and stereoselective synthesis of benzothiazolo-pyrimidinones via an NHC-catalyzed Mannich/lactamization domino reaction.

    PubMed

    Ni, Qijian; Song, Xiaoxiao; Xiong, Jiawen; Raabe, Gerhard; Enders, Dieter

    2015-01-25

    An NHC-catalyzed regio- and stereoselective Mannich/lactamization domino reaction of N-(benzothiazolyl)imines with ?-chloroaldehydes has been developed. This new protocol provides a facile approach for the asymmetric synthesis of benzothiazolo-pyrimidinones and a pyrrolo[1,2-a]indolone in moderate to good yields (34-78%) and excellent stereoselectivities (87-99% ee, up to >20?:?1 d.r.). PMID:25476422

  3. Au-catalyzed ring-opening reactions of 2-(1-alkynyl-cyclopropyl)pyridines with nucleophiles.

    PubMed

    Liu, Ren-Rong; Ye, Shi-Chun; Lu, Chuan-Jun; Xiang, Bin; Gao, Jianrong; Jia, Yi-Xia

    2015-04-22

    A novel method for the C-C bond cleavage of cyclopropanes was developed by gold-catalyzed cycloisomerization of 2-(1-alkynyl-cyclopropyl)pyridine with nucleophiles, which provides efficient access to structurally diverse indolizines under mild conditions. A series of N-, C- and O-based nucleophiles were involved in this reaction to afford the corresponding indolizines in modest to excellent yields. PMID:25832795

  4. Process optimization of enzyme catalyzed production of dietary diacylglycerol (DAG) using TLIM as biocatalyst.

    PubMed

    Dhara, Rupali; Singhal, Rekha S

    2014-01-01

    Diacylglycerol (DAG)-rich sunflower oil was prepared and the optimal conditions for synthesis of DAG-rich oil by glycerolysis using biocatalyst TLIM was determined. A maximum production of 59.8% DAG was obtained after 5 h of constant reaction under vacuum (756 mm of Hg). The optimum temperature for glycerolysis was found to be 50°C, while stoichiometric molar ratio of sunflower oil:glycerol was 2:1 for this reaction. A minimum acid value of 0.48 mg of KOH.g(-1) of oil was observed under these conditions. The fatty acid composition of DAG-rich oil was found to be similar to the original TAG-rich sunflower oil used in the work. The lipase catalysed glycerolysis using 1,3 specific lipase was used to promote the formation of 1,3 isoform of DAG as this isoform is known to possess anti-obesity effect. DAG content was determined by HPTLC and GCMS. The DAG-rich oil contained 59.75% DAG of which 63.34% was found as 1,3-DAG and 36.65% was 1,2-DAG/2,3-DAG. PMID:24500104

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

    PubMed

    Bhushan, Bharat; Halasz, Annamaria; Hawari, Jalal

    2005-12-01

    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 24nmol/h/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated product with a molecular weight of 393Da. 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 1Da in the N-denitrohydrogenated product suggesting the involvement of a deuteride (D(-)) 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. PMID:16225844

  6. Enzyme-catalyzed synthesis of poly[(R)-(-)-3-hydroxybutyrate]: Formation of macroscopic granules in vitro

    SciTech Connect

    Gerngross, T.U.; Martin, D.P. [Metabolix, Inc., Cambridge, MA (United States)

    1995-07-03

    A combined chemical and enzymatic procedure has been developed to synthesize macroscopic poly[(R)-(-)-3-hydroxybutyrate] (PHB) granules in vitro. The granules form in a matter of minutes when purified polyhydroxyalkanoate (PHA) synthase from Alcaligenes eutrophus is exposed to synthetically prepared (R)-3-hydroxybutyryl coenzyme A, thereby establishing the minimal requirements for PHB granule formation. The artificial granules are spherical with diameters of up to 3 {mu}m and significantly larger than their native counterparts (0.5 {mu}m). The isolated PHB was characterized by {sup 1}H and {sup 13}C NMR, gel-permeation chromatography, and chemical analysis. The in vitro polymerization system yields PHB with a molecular mass > 10 x 10{sup 6} Da, exceeding by an order of magnitude the mass of PHAs typically extracted from microorganisms. We also demonstrate that the molecular mass of the polymer can be controlled by the initial PHA synthase concentration. Preliminary kinetic analysis of de novo granule formation confirms earlier findings of a lag time for the enzyme but suggests the involvement of an additional granule assembly step. Minimal requirements for substrate recognition were investigated. Since substrate analogs lacking the adenosine 3{prime}, 5{prime}-bisphosphate moiety of (R)-3-hydroxybutyryl coenzyme A were not accepted by the PHA synthase, we provide evidence that this structural element of the substrate is essential for catalysis. PHAs provide a range of natural, renewable, biodegradable thermoplastics with a broad range of useful material properties. 33 refs., 6 figs., 1 tab.

  7. Expanding the scope of asymmetric electrophilic atom-transfer reactions: titanium- and ruthenium-catalyzed hydroxylation of beta-ketoesters.

    PubMed

    Toullec, Patrick Y; Bonaccorsi, Cristina; Mezzetti, Antonio; Togni, Antonio

    2004-04-20

    The enantioselective formation of a quaternary stereogenic center coinciding with a hydroxylation process is a very rare reaction from a homogeneous catalysis point of view. Indeed, to our knowledge, no asymmetric transition-metal-catalyzed direct hydroxylation has been reported before. We describe here our initial study concerning the enantioselective alpha-hydroxylation of various beta-ketoesters catalyzed by Lewis-acidic complexes. Specifically, it was found that the Ti complex [TiCl(2)((R,R)-1-Np-TADDOLato)(MeCN)(2)] affords the hydroxylated products in high yield and enantioselectivities up to 94% enantiomeric excess when using 2-(phenylsulphonyl)-3-(4-nitrophenyl)oxaziridine as the oxidizing agent. Chiral enantiopure compounds of the latter type have been used previously in stoichiometric asymmetric hydroxylation reactions. We also show that, in a complementary approach with H(2)O(2) as the oxidant, the Ru(II) complex [RuCl(OE(2))((S,S)-PNNP)]PF(6) catalyzes the same type of transformation in a case of substrates showing a very substantial extent of enolization under reaction conditions; being, however, unreactive toward only weakly enolized beta-ketoesters. PMID:15071186

  8. Expanding the scope of asymmetric electrophilic atom-transfer reactions: Titanium- and ruthenium-catalyzed hydroxylation of ?-ketoesters

    PubMed Central

    Toullec, Patrick Y.; Bonaccorsi, Cristina; Mezzetti, Antonio; Togni, Antonio

    2004-01-01

    The enantioselective formation of a quaternary stereogenic center coinciding with a hydroxylation process is a very rare reaction from a homogeneous catalysis point of view. Indeed, to our knowledge, no asymmetric transition-metal-catalyzed direct hydroxylation has been reported before. We describe here our initial study concerning the enantioselective ?-hydroxylation of various ?-ketoesters catalyzed by Lewis-acidic complexes. Specifically, it was found that the Ti complex [TiCl2((R,R)-1-Np-TADDOLato)(MeCN)2] affords the hydroxylated products in high yield and enantioselectivities up to 94% enantiomeric excess when using 2-(phenylsulphonyl)-3-(4-nitrophenyl)oxaziridine as the oxidizing agent. Chiral enantiopure compounds of the latter type have been used previously in stoichiometric asymmetric hydroxylation reactions. We also show that, in a complementary approach with H2O2 as the oxidant, the Ru(II) complex [RuCl(OE2)((S,S)-PNNP)]PF6 catalyzes the same type of transformation in a case of substrates showing a very substantial extent of enolization under reaction conditions; being, however, unreactive toward only weakly enolized ?-ketoesters. PMID:15071186

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

    E-print Network

    Gomez Ruiz, Alejandro

    1998-01-01

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

  10. MACiE: a database of enzyme reaction mechanisms

    E-print Network

    Holliday, Gemma L; Bartlett, Gail J; Almonacid, Daniel E; O'Boyle, Noel M; Murray-Rust, Peter; Thornton, Janet M; Mitchell, John B O

    2005-09-27

    MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a...

  11. CALIX[6]ARENE DERIVATIVES BEARING SULFONATE AND ALKYL GROUPS AS SURFACTANTS IN SC(OTF)3-CATALYZED MUKAIYAMA ALDOL REACTIONS IN WATER. (R822668)

    EPA Science Inventory

    Abstract Amphiphilic calix[6]arene derivatives 1a¯b were found to be efficient surfactants for Sc(OTf)3-catalyzed Mukaiyama aldol reaction of silyl enol ethers with aldehydes in water. The results indicated t...

  12. Collective synthesis of cladiellins based on the gold-catalyzed cascade reaction of 1,7-diynes.

    PubMed

    Yue, Guozong; Zhang, Yun; Fang, Lichao; Li, Chuang-Chuang; Luo, Tuoping; Yang, Zhen

    2014-02-10

    The cladiellin family of natural products, which includes molecules with various biological activities, continues to invite new synthetic studies. A gold-catalyzed tandem reaction of 1,7-diynes to construct the 6-5-bicyclic ring systems that are present in a number of natural products was developed. This reaction was applied as the key step to realize the formal and total syntheses of nine members of the cladiellin family in an enantio- and diastereoselective manner. This modular and efficient approach could also be used for the construction of other cladiellins, as well as their analogues, for follow-up studies. PMID:24474595

  13. Re2O7-catalyzed reaction of hemiacetals and aldehydes with O-, S-, and C-nucleophiles

    PubMed Central

    Sittiwong, Wantanee; Richardson, Michael W; Schiaffo, Charles E; Fisher, Thomas J

    2013-01-01

    Summary Re(VII) oxides catalyze the acetalization, monoperoxyacetalization, monothioacetalization and allylation of hemiacetals. The reactions, which take place under mild conditions and at low catalyst loadings, can be conducted using hemiacetals, the corresponding O-silyl ethers, and, in some cases, the acetal dimers. Aldehydes react under similar conditions to furnish good yields of dithioacetals. Reactions of hemiacetals with nitrogen nucleophiles are unsuccessful. 1,2-Dioxolan-3-ols (peroxyhemiacetals) undergo Re(VII)-promoted etherification but not allylation. Hydroperoxyacetals (1-alkoxyhydroperoxides) undergo selective exchange of the alkoxide group in the presence of either Re2O7 or a Brønsted acid. PMID:23946852

  14. 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

  15. 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

    2014-11-01

    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. PMID:25338129

  16. Impact of in situ MAS NMR techniques to the understanding of the mechanisms of zeolite catalyzed reactions.

    PubMed

    Ivanova, Irina I; Kolyagin, Yuriy G

    2010-12-01

    The in situ MAS NMR studies of the mechanisms of zeolite catalyzed reactions are reviewed. The first part of the critical review contains brief information on the different experimental approaches used for the in situ MAS NMR studies under batch and flow conditions. In the second part, a cross reference index between the reactions studied, the catalysts used, the mechanistic information obtained and the corresponding literature sources is established. Finally, in the last part the most widely studied areas are discussed in more detail. In particular, the impact of in situ MAS NMR to unravel the mechanisms of olefin, alcohol and alkanes transformations over zeolite catalysts is analyzed (232 references). PMID:21038049

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

    E-print Network

    Pak-Wing Fok; Tom Chou

    2009-05-20

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

  18. DOI:10.1002/ejic.201300710 Reaction Mechanism of Water Oxidation Catalyzed by

    E-print Network

    Liao, Rongzhen

    to the opening of the benzene ring, which explains the observation of fast catalyst degrada- tion. The lack a quite fast catalyst degradation. Kinetic studies also sug- gest that the formation of O2 catalyzed

  19. Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.

    PubMed

    Wise, Eric L; Yew, Wen Shan; Gerlt, John A; Rayment, Ivan

    2003-10-28

    3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism. PMID:14567674

  20. Rapid-Equilibrium Enzyme Kinetics

    ERIC Educational Resources Information Center

    Alberty, Robert A.

    2008-01-01

    Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics is…

  1. Reaction pathway and free energy profile for papain-catalyzed hydrolysis of N-acetyl-Phe-Gly 4-nitroanilide

    PubMed Central

    Wei, Donghui; Huang, Xiaoqin; Tang, Mingsheng; Zhan, Chang-Guo

    2013-01-01

    Possible reaction pathways for papain-catalyzed hydrolysis of N-acetyl-Phe-Gly 4-nitroanilide (APGNA) have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy (QM/MM-FE) calculations. The whole hydrolysis process includes two stages: acylation and deacylation. For the acylation stage of the catalytic reaction, we have explored three possible paths (A, B, and C) and the corresponding free energy profiles along the reaction coordinates. It has been demonstrated that the most favorable reaction path in this stage is path B consisting of two reaction steps: the first step is a proton transfer to form a zwitterionic form (i.e. Cys-S?/His-H+ ion-pair), and the second step is the nucleophilic attack on the carboxyl carbon of the substrate accompanied with the dissociation of 4-nitroanilide. The deacylation stage includes the nucleophilic attack of a water molecule on the carboxyl carbon of the substrate and dissociation between the carboxyl carbon of the substrate and the sulfhydryl sulfur of Cys25 side chain. The free energy barriers calculated for the acylation and deacylation stages are 20.0 kcal/mol and 10.7 kcal/mol, respectively. Thus, the acylation is rate-limiting. The overall free energy barrier calculated for papain-catalyzed hydrolysis of APGNA is 20.0 kcal/mol, which is reasonably close to the experimentally derived activation free energy of 17.9 kcal/mol. PMID:23862626

  2. Potassium acetate-catalyzed acetylation of wood: reaction rates at low temperatures

    Microsoft Academic Search

    Eiichi Obataya; Kazuya Minato

    2009-01-01

    Spruce wood blocks were acetylated in the presence of potassium acetate (KAc) at 20, 40, 60, 80 and 120°C. At 20°C, the weight\\u000a percent gain (WPG) due to the KAc-catalyzed acetylation reached 20% in 18 days, whereas that due to pyridine-catalyzed acetylation\\u000a did not exceed 8%. The hygroscopicity and dimensional stability of the KAc-acetylated wood were the same as those of

  3. 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 (?-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 ?-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. PMID:23604465

  4. An Isothermal Titration Calorimetric Method to Determine the Kinetic Parameters of Enzyme Catalytic Reaction

    E-print Network

    Luhua, Lai

    of enzyme. The molar reaction heat was calculated from the titration peak area divided by substrate moles per titration, and the initial catalytic reaction rate in the presence of vari- ous concentrations of product can be calculated from the peak height and the molar reaction heat. From Michaelis­Menten function

  5. Development of Stereocontrolled Palladium(II)-Catalyzed Domino Heck/Suzuki ?,?-Diarylation Reactions with Chelating Vinyl Ethers and Arylboronic Acids

    PubMed Central

    Trejos, Alejandro; Odell, Luke R; Larhed, Mats

    2012-01-01

    A stereoselective and 1,4-benzoquinone-mediated palladium(II)-catalyzed Heck/Suzuki domino reaction involving metal coordinating cyclic methylamino vinyl ethers and a number of electronically diverse arylboronic acids has been developed and studied. Diastereomeric ratios up to 39:1 and 78 % isolated yields were obtained. The stereoselectivity of the reaction was found to be highly dependent on the nature of the arylboronic acid and the amount of water present in the reaction mixture. Thus, a domino ?,?-diarylation–reduction of chelating vinyl ethers can now be accomplished and stereochemically controlled, given that optimized conditions and an appropriate chiral auxiliary are used. To the best of our knowledge, this represents the first example of a stereoselective, oxidative Heck/Suzuki domino reaction in the literature. PMID:24551492

  6. Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products

    SciTech Connect

    Achyuthan, Komandoor; Adams, Paul; Simmons, Blake; Singh, Anup

    2011-07-13

    Lignin composition (monolignol types of coniferyl, sinapyl or p-coumaryl alcohol) is causally related to biomass recalcitrance. We describe multiwavelength (220, 228, 240, 250, 260, 290, 295, 300, 310 or 320 nm) absorption spectroscopy of coniferyl alcohol and its laccase- or peroxidase-catalyzed products during real time kinetic, pseudo-kinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 mu L volumes demonstrated assay miniaturization and high throughput screening capabilities. Bathochromic and hypsochromic shifts along with hyperchromicity or hypochromicity accompanied enzymatic oxidations by laccase or peroxidase. The limits of detection and quantitation of coniferyl alcohol averaged 2.4 and 7.1 mu M respectively, with linear trend lines over 3 to 4 orders of magnitude. Coniferyl alcohol oxidation was evident within 10 minutes or with 0.01 mu g/mL laccase and 2 minutes or 0.001 mu g/mL peroxidase. Detection limit improved to 1.0 mu M coniferyl alcohol with Km of 978.7 +/- 150.7 mu M when examined at 260 nm following 30 minutes oxidation with 1.0 mu g/mL laccase. Our assays utilized the intrinsic spectroscopic properties of coniferyl alcohol or its oxidation products for enabling detection, without requiring chemical synthesis or modification of the substrate or product(s). These studies facilitate lignin compositional analyses and augment pretreatment strategies for reducing biomass recalcitrance.

  7. FINAL REPORT. CHARACTERIZATION OF CHEMICALLY MODIFIED ENZYMES FOR BIOREMEDIATION REACTIONS

    EPA Science Inventory

    Remediation processes frequently involve species possessing limited solubility in water. For this project, we were interested in novel strategies using molecularly modified enzymes with enhanced activity and stability for remediation of recalcitrant compounds in organic solvents....

  8. Identification in Haloferax volcanii of Phosphomevalonate Decarboxylase and Isopentenyl Phosphate Kinase as Catalysts of the Terminal Enzyme Reactions in an Archaeal Alternate Mevalonate Pathway

    PubMed Central

    VanNice, John C.; Skaff, D. Andrew; Keightley, Andrew; Addo, James K.; Wyckoff, Gerald J.

    2014-01-01

    Mevalonate (MVA) metabolism provides the isoprenoids used in archaeal lipid biosynthesis. In synthesis of isopentenyl diphosphate, the classical MVA pathway involves decarboxylation of mevalonate diphosphate, while an alternate pathway has been proposed to involve decarboxylation of mevalonate monophosphate. To identify the enzymes responsible for metabolism of mevalonate 5-phosphate to isopentenyl diphosphate in Haloferax volcanii, two open reading frames (HVO_2762 and HVO_1412) were selected for expression and characterization. Characterization of these proteins indicated that one enzyme is an isopentenyl phosphate kinase that forms isopentenyl diphosphate (in a reaction analogous to that of Methanococcus jannaschii MJ0044). The second enzyme exhibits a decarboxylase activity that has never been directly attributed to this protein or any homologous protein. It catalyzes the synthesis of isopentenyl phosphate from mevalonate monophosphate, a reaction that has been proposed but never demonstrated by direct experimental proof, which is provided in this account. This enzyme, phosphomevalonate decarboxylase (PMD), exhibits strong inhibition by 6-fluoromevalonate monophosphate but negligible inhibition by 6-fluoromevalonate diphosphate (a potent inhibitor of the classical mevalonate pathway), reinforcing its selectivity for monophosphorylated ligands. Inhibition by the fluorinated analog also suggests that the PMD utilizes a reaction mechanism similar to that demonstrated for the classical MVA pathway decarboxylase. These observations represent the first experimental demonstration in H. volcanii of both the phosphomevalonate decarboxylase and isopentenyl phosphate kinase reactions that are required for an alternate mevalonate pathway in an archaeon. These results also represent, to our knowledge, the first identification and characterization of any phosphomevalonate decarboxylase. PMID:24375100

  9. Industrial Enzymes and Biocatalysis

    NASA Astrophysics Data System (ADS)

    McAuliffe, Joseph C.; Aehle, Wolfgang; Whited, Gregory M.; Ward, Donald E.

    All life processes are the result of enzyme activity. In fact, life itself, whether plant or animal, involves a complex network of enzymatic reactions. An enzyme is a protein that is synthesized in a living cell. It catalyzes a thermodynamically possible reaction so that the rate of the reaction is compatible with the numerous biochemical processes essential for the growth and maintenance of a cell. The synthesis of an enzyme thus is under tight metabolic regulations and controls that can be genetically or environmentally manipulated sometimes to cause the overproduction of an enzyme by the cell. An enzyme, like chemical catalysts, in no way modifies the equilibrium constant or the free energy change of a reaction.

  10. Low-temperature superacid catalysis: Reactions of n-butane catalyzed by iron- and manganese-promoted sulfated zirconia

    SciTech Connect

    Cheung, T.K.; D`Itri, J.L.; Gates, B.C. [Univ. of California, Davis, CA (United States)] [Univ. of California, Davis, CA (United States)

    1995-02-01

    Environmental concerns are leading to the replacement of aromatic hydrocarbons in gasoline with high-octane-number branched paraffins and oxygenated compounds such as methyl t-butyl ether, which is produced from methanol and isobutylene. The latter can be formed from n-butane by isomerization followed by dehydrogenation. To meet the need for improved catalysts for isomerization of n-butane and other paraffins, researchers identified solid acids that are noncorrosive and active at low temperatures. Sulfated zirconia catalyzes the isomerization of n-butane even at 25{degrees}C, and the addition of Fe and Mn promoters increases its activity by three orders of magnitude. Little is known about this new catalyst. Here the authors provide evidence of its performance for n-butane conversion, demonstrating that isomerization is accompanied by disproportionation and other, less well understood, acid-catalyzed reactions and undergoes rapid deactivation associated with deposition of carbonaceous material. 10 refs., 3 figs.

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

    DOEpatents

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

    1998-01-01

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

  12. Method of reduction of nitroaromatics by enzymatic reaction with redox enzymes

    DOEpatents

    Shah, Manish M. (Richland, WA)

    2000-01-01

    A method for the controlled reduction of nitroaromatic compounds such as nitrobenzene and 2,4,6-trinitrotoluene by enzymatic reaction with redox enzymes, such as Oxyrase (Trademark of Oxyrase, Inc., Mansfield, Ohio).

  13. 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.

  14. A theoretical and experimental study of the effects of silyl substituents in enantioselective reactions catalyzed by diphenylprolinol silyl ether.

    PubMed

    Hayashi, Yujiro; Okamura, Daichi; Yamazaki, Tatsuya; Ameda, Yasuto; Gotoh, Hiroaki; Tsuzuki, Seiji; Uchimaru, Tadafumi; Seebach, Dieter

    2014-12-15

    The effect of silyl substituents in diphenylprolinol silyl ether catalysts was investigated. Mechanistically, reactions catalyzed by diphenylprolinol silyl ether can be categorized into three types: two that involve an iminium ion intermediate, such as for the Michael-type reaction (type?A) and the cycloaddition reaction (type?B), and one that proceeds via an enamine intermediate (type?C). In the Michael-type reaction via iminium ions (type?A), excellent enantioselectivity is realized when the catalyst with a bulky silyl moiety is employed, in which efficient shielding of a diastereotopic face of the iminium ion is directed by the bulky silyl moiety. In the cycloaddition reaction of iminium ions (type?B) and reactions via enamines (type?C), excellent enantioselectivity is obtained even when the silyl group is less bulky and, in this case, too much bulk reduces the reaction rate. In other cases, the yield increases when diphenylprolinol silyl ethers with bulky substituents are employed, presumably by suppressing side reactions between the nucleophilic catalyst and the reagent. The conformational behaviors of the iminium and enamine species have been determined by theoretical calculations. These data explain the effect of the bulkiness of the silyl substituent on the enantioselectivity and reactivity of the catalysts. PMID:25348681

  15. Activity of enzymes catalyzing formation of beta-L-fucosyl phosphate and GDP-beta-L-fucose in amphibian tissues and their application in chemo-enzymic synthesis of GDP-beta-L-fucose.

    PubMed

    Druzhinina, T N; Utkina, N S; Chan, K; Strecker, G; Shibaev, V N

    1999-07-01

    Amphibian oviduct and liver were shown to contain enzymes that catalyze the formation of GDP-beta-L-fucose from GDP-alpha-D-mannose or L-fucose. The conversion of L-fucose into beta-L-fucopyranosyl phosphate was achieved on a preparative scale using high-activity fucokinase in toad liver extracts. For chemo-enzymic preparation of GDP-beta-L-fucose, a convenient modification for pyrophosphate synthesis through phosphomorpholidate which does not require anhydrous conditions is suggested. PMID:10424902

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

    E-print Network

    Tas, A. Cuneyt

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

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

    PubMed

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

    2014-07-01

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

  18. Aminoglycoside Antibiotic-Inactivating Enzymes in Actinomycetes Similar to those Present in Clinical Isolates of Antibiotic-Resistant Bacteria

    Microsoft Academic Search

    Raoul Benveniste; Julian Davies

    1973-01-01

    Various species of Streptomyces possess aminoglycoside-modifying enzymes. Streptomyces kanamyceticus contains an enzyme that acetylates the 6'-amino group of kanamycin A and B, gentamicin C1a, and neomycin. Streptomyces spectabilis produces an enzyme that acetylates the 2'-amino group of the hexose ring of gentamicin C1a. These enzymes catalyze reactions identical to those catalyzed by enzymes found in gram-negative bacteria containing R (antibiotic

  19. Cloning and expression of cytochrome P450 enzymes catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of cyanogenic glucosides in Triglochin maritima.

    PubMed

    Nielsen, J S; Møller, B L

    2000-04-01

    Two cDNA clones encoding cytochrome P450 enzymes belonging to the CYP79 family have been isolated from Triglochin maritima. The two proteins show 94% sequence identity and have been designated CYP79E1 and CYP79E2. Heterologous expression of the native and the truncated forms of the two clones in Escherichia coli demonstrated that both encode multifunctional N-hydroxylases catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of the two cyanogenic glucosides taxiphyllin and triglochinin in T. maritima. This renders CYP79E functionally identical to CYP79A1 from Sorghum bicolor, and unambiguously demonstrates that cyanogenic glucoside biosynthesis in T. maritima and S. bicolor is catalyzed by analogous enzyme systems with p-hydroxyphenylacetaldoxime as a free intermediate. This is in contrast to earlier reports stipulating p-hydroxyphenylacetonitrile as the only free intermediate in T. maritima. L-3,4-Dihydroxyphenyl[3-(14)C]Ala (DOPA) was not metabolized by CYP79E1, indicating that hydroxylation of the phenol ring at the meta position, as required for triglochinin formation, takes place at a later stage. In S. bicolor, CYP71E1 catalyzes the subsequent conversion of p-hydroxyphenylacetaldoxime to p-hydroxymandelonitrile. When CYP79E1 from T. maritima was reconstituted with CYP71E1 and NADPH-cytochrome P450 oxidoreductase from S. bicolor, efficient conversion of tyrosine to p-hydroxymandelonitrile was observed. PMID:10759528

  20. Cloning and Expression of Cytochrome P450 Enzymes Catalyzing the Conversion of Tyrosine to p-Hydroxyphenylacetaldoxime in the Biosynthesis of Cyanogenic Glucosides in Triglochin maritima1

    PubMed Central

    Nielsen, John Strikart; Møller, Birger Lindberg

    2000-01-01

    Two cDNA clones encoding cytochrome P450 enzymes belonging to the CYP79 family have been isolated from Triglochin maritima. The two proteins show 94% sequence identity and have been designated CYP79E1 and CYP79E2. Heterologous expression of the native and the truncated forms of the two clones in Escherichia coli demonstrated that both encode multifunctional N-hydroxylases catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of the two cyanogenic glucosides taxiphyllin and triglochinin in T. maritima. This renders CYP79E functionally identical to CYP79A1 from Sorghum bicolor, and unambiguously demonstrates that cyanogenic glucoside biosynthesis in T. maritima and S. bicolor is catalyzed by analogous enzyme systems with p-hydroxyphenylacetaldoxime as a free intermediate. This is in contrast to earlier reports stipulating p-hydroxyphenylacetonitrile as the only free intermediate in T. maritima. l-3,4-Dihydroxyphenyl[3-14C]Ala (DOPA) was not metabolized by CYP79E1, indicating that hydroxylation of the phenol ring at the meta position, as required for triglochinin formation, takes place at a later stage. In S. bicolor, CYP71E1 catalyzes the subsequent conversion of p-hydroxyphenylacetaldoxime to p-hydroxymandelonitrile. When CYP79E1 from T. maritima was reconstituted with CYP71E1 and NADPH-cytochrome P450 oxidoreductase from S. bicolor, efficient conversion of tyrosine to p-hydroxymandelonitrile was observed. PMID:10759528

  1. Nonlinear Dynamics of the Peroxidase-Oxidase Reaction: I. Bistability and Bursting Oscillations at Low Enzyme Concentrations

    E-print Network

    Schaffer, William M.

    Nonlinear Dynamics of the Peroxidase-Oxidase Reaction: I. Bistability and Bursting Oscillations conditions, the horseradish peroxidase (HRP)-catalyzed peroxidase-oxidase (PO) reaction evidences a wide were reported1 in 1977 for the peroxidase-oxidase (PO) reaction, a system in which oscillatory dynamics

  2. Synthesis of 2,4-diarylsubstituted-pyridines through a Ru-catalyzed four component reaction.

    PubMed

    Bai, Yang; Tang, Lichang; Huang, Huawen; Deng, Guo-Jun

    2015-03-31

    A ruthenium-catalyzed one-pot synthesis of 2,4-diarylsubstituted pyridines from acetophenones, ammonium acetate and DMF under an oxygen atmosphere is described. The carbon atom situated at C6 of the pyridine ring comes from the methyl group of DMF and the nitrogen atom comes from ammonium acetate. PMID:25764281

  3. A facile route to flavone and neoflavone backbones via a regioselective palladium catalyzed oxidative Heck reaction.

    PubMed

    Khoobi, Mehdi; Alipour, Masoumeh; Zarei, Samaneh; Jafarpour, Farnaz; Shafiee, Abbas

    2012-03-21

    A straightforward and atom-economical base-free palladium-catalyzed regioselective direct arylation of coumarins and chromenones is devised. This protocol is compatible with a wide variety of electron-donating and -withdrawing substituents and allows construction of various biologically important flavone and neoflavone backbones. PMID:22318701

  4. Palladium-catalyzed decarboxylative cross-coupling reactions: a route for regioselective functionalization of coumarins.

    PubMed

    Jafarpour, Farnaz; Zarei, Samaneh; Olia, Mina Barzegar Amiri; Jalalimanesh, Nafiseh; Rahiminejadan, Soraya

    2013-04-01

    A straightforward, regioselective, and step-economical ligand-free palladium-catalyzed decarboxylative functionalization of coumarin-3-carboxylic acids is devised. This protocol is compatible with a wide variety of electron-donating and -withdrawing substituents and allows for construction of various biologically important ?-electron extended coumarins. PMID:23445254

  5. 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.

  6. Gold(I)-catalyzed 1,4- and/or 1,5-heteroaryl migration reactions through regiocontrolled cyclizations.

    PubMed

    Wang, Chengyu; Xie, Xin; Liu, Jun; Liu, Yuanhong; Li, Yuxue

    2015-01-01

    Gold(I)-catalyzed regioselective cycloisomerizations of furan-ynes have been described. The reaction provides a concise access to stereodefined trisubstituted alkenes by endo cyclization with concomitant 1,5-migration of the furanyl group in the presence of unactivated 3?Å molecular sieves. In the absence of molecular sieves, indene products are generated by exo cyclization, followed by 1,4-furanyl migration/cyclization. The scope for 1,5-migrations can be extended to other heterocycles, such as benzofurans, thiophenes, and pyrroles. PMID:25411108

  7. Rapid and efficient copper-catalyzed Finkelstein reaction of (hetero)aromatics under continuous-flow conditions.

    PubMed

    Chen, Mao; Ichikawa, Saki; Buchwald, Stephen L

    2015-01-01

    A general, rapid, and efficient method for the copper-catalyzed Finkelstein reaction of (hetero)aromatics has been developed using continuous flow to generate a variety of aryl iodides. The described method can tolerate a broad spectrum of functional groups, including N-H and O-H groups. Additionally, in lieu of isolation, the aryl iodide solutions were used in two distinct multistep continuous-flow processes (amidation and Mg-I exchange/nucleophilic addition) to demonstrate the flexibility of this method. PMID:25378244

  8. 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...

  9. The study of the stereospecificity in enzyme-catalyzed reactions of glyceryl acetonide derivatives

    E-print Network

    Chauvet, Christine Jeanne

    1987-01-01

    -d-ala-glycerol acetonide) was studied in the presence of papain. In all those studies the enantiomeric excess was determined by optical rotation or by 3 P NMR spectroscopy. ACKNOWLEDGEMENTS I would like, first, to thank my advisor Dr. Chi-Huey Wong for his help, his..., was converted into the corresponding 1, 2:5, 6-bisacetonide 3 in moderate yield; the resulting diol was cleaved with lead tetraacetate to give R-2a. The unstable glyceraldehyde intermediate was not isolated but was catalytically reduced to S-la by hydrogen...

  10. BETA-D-XYLOSIDASE FROM SELENOMONAS RUMINANTIUM: THERMODYNAMICS OF ENZYME-CATALYZED AND NONCATALYZED REACTIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta-D-xylosidase from Selenomonas ruminantium has been revealed as the best catalyst known for promoting hydrolysis of 1,4-beta-D-xylooligosaccharides, and it has potential utility in saccharification processes. Kinetic parameters, kcat and kcat/Km, are more than 10-fold larger than those reported...

  11. Measurement of positional isotope exchange rates in enzyme catalyzed reactions by fast atom bombardment mass spectrometry

    E-print Network

    Hilscher, Larry Wayne

    1985-01-01

    . Instead it offers a direct analysis method based on the 0. 02 ppm upfield shift induced by 18 0 substitution. This method has, however, sufferd. from decreased sensitivity as compared to mass spectrometry. At least 100x more material is required... solution wa, s titrated to pq 7. 6 with KCH. KC10 wa" allowed to precipita+e at 0 0 and then removed by centrifugation. The supernatant wa, s diluted to 100 mL, readjusted to PH 7. 6, and applied to a DEAE-cellulose column (1. 8 x 60 cm). The column...

  12. Purification and properties of the enzymes from Drosophila melanogaster that catalyze the synthesis of sepiapterin from Dihydroneopterin triphosphate

    Microsoft Academic Search

    Gwen G. Krivi; Gene M. Brown

    1979-01-01

    Sepiapterin synthase, the enzyme system responsible for the synthesis of sepiapterin from dihydroneopterin triphosphate, has been partially purified from extracts of the heads of young adult fruit flies (Drosophila melanogaster). The sepiapterin synthase system consists of two components, termed “enzyme A” (MW 82,000) and “enzyme B” (MW 36,000). Some of the properties of the enzyme system are as follows: NADPH

  13. Stereocontrolled synthesis of bicyclic sulfamides via Pd-catalyzed alkene carboamination reactions. Control of 1,3-asymmetric induction by manipulating mechanistic pathways.

    PubMed

    Babij, Nicholas R; McKenna, Grace M; Fornwald, Ryan M; Wolfe, John P

    2014-06-20

    A new annulation strategy for the synthesis of trans-bicyclic sulfamides is described. The Pd-catalyzed alkene carboamination reactions of 2-allyl and cis-2,5-diallyl pyrrolidinyl sulfamides with aryl and alkenyl triflates afford the fused bicyclic compounds in good yields and with good diastereoselectivity (up to 13:1 dr). Importantly, by employing reaction conditions that favor an anti-aminopalladation mechanism, the relative stereochemistry between the C3 and C4a stereocenters of the products is reversed relative to related Pd-catalyzed carboamination reactions that proceed via syn-aminopalladation. PMID:24916343

  14. Synthesis of pyrazines from rhodium-catalyzed reaction of 2H-Azirines with N-sulfonyl 1,2,3-triazoles.

    PubMed

    Ryu, Taekyu; Baek, Yonghyeon; Lee, Phil Ho

    2015-02-20

    An efficient synthetic route to a wide range of trisubstituted pyrazines is developed from Rh-catalyzed reaction of 2H-azirines with N-sulfonyl-1,2,3-triazoles through the elimination of nitrogen molecule and arylsulfinic acid. The present reaction proceeds through formation of in situ generated dihydropyrazines. PMID:25619593

  15. Palladium-catalyzed cross-coupling reaction of diazo compounds and vinyl boronic acids: an approach to 1,3-diene compounds.

    PubMed

    Xia, Yamu; Xia, Ying; Liu, Zhen; Zhang, Yan; Wang, Jianbo

    2014-08-15

    A palladium-catalyzed oxidative cross-coupling of vinyl boronic acids and cyclic ?-diazocarbonyl compounds has been reported. The reaction constitutes an efficient method for the synthesis of 1,3-diene compounds bearing a ring structure. Mechanistically, the reaction involves migratory insertion of palladium carbene as the key step. PMID:25019414

  16. A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme

    PubMed Central

    Yoshinari, Koichi; Taira, Kazunari

    2000-01-01

    We synthesized three types of 11mer substrate, namely the natural substrate S11O and the thiosubstituted substrates S11SpS and S11RpS, in which the respective pro-Sp and pro-Rp oxygen atoms were replaced by sulfur, and subjected them to detailed kinetic analysis in the cleavage reaction catalyzed by a hammerhead ribozyme. In agreement with previous findings, in the presence of Mg2+ or Ca2+ ions the rate of ribozyme-catalyzed cleavage of S11SpS was as high as that of S11O, whereas the corresponding rate for S11RpS was nearly four orders of magnitude lower than that for either S11O or S11SpS. However, the rate of the ribozyme-catalyzed reaction with each of the three substrates was enhanced by Cd2+ ions. Such results have generally been taken as evidence that supports the direct interaction of the sulfur atom at the Rp position of the cleavage site with the added Cd2+ ion. However, our present analysis demonstrates that (i) the added Cd2+ ion binds at the P9 site; (ii) the bound Cd2+ ion at the P9 site replaces two Mg2+ or two Ca2+ ions, an observation that suggests a different mode of interaction with the added Cd2+ ion; and, most importantly and in contrast to the conclusion reached by other investigators, (iii) the Cd2+ ion does not interact with the sulfur atom at the Rp position of the scissile phosphate either in the ground state or in the transition state. PMID:10734192

  17. Initial reaction(s) in biotransformation of CL-20 is catalyzed by salicylate 1-monooxygenase from Pseudomonas sp. strain ATCC 29352.

    PubMed

    Bhushan, Bharat; Halasz, Annamaria; Spain, Jim C; Hawari, Jalal

    2004-07-01

    CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) (C(6)H(6)N(12)O(12)), a future-generation high-energy explosive, is biodegradable by Pseudomonas sp. strain FA1 and Agrobacterium sp. strain JS71; however, the nature of the enzyme(s) involved in the process was not understood. In the present study, salicylate 1-monooxygenase, a flavin adenine dinucleotide (FAD)-containing purified enzyme from Pseudomonas sp. strain ATCC 29352, biotransformed CL-20 at rates of 0.256 +/- 0.011 and 0.043 +/- 0.003 nmol min(-1) mg of protein(-1) under anaerobic and aerobic conditions, respectively. The disappearance of CL-20 was accompanied by the release of nitrite ions. Using liquid chromatography/mass spectrometry in the negative electrospray ionization mode, we detected a metabolite with a deprotonated mass ion [M - H](-) at 345 Da, corresponding to an empirical formula of C(6)H(6)N(10)O(8), produced as a result of two sequential N denitration steps on the CL- 20 molecule. We also detected two isomeric metabolites with [M - H](-) at 381 Da corresponding to an empirical formula of C(6)H(10)N(10)O(10). The latter was a hydrated product of the metabolite C(6)H(6)N(10)O(8) with addition of two H(2)O molecules, as confirmed by tests using (18)O-labeled water. The product stoichiometry showed that each reacted CL-20 molecule produced about 1.7 nitrite ions, 3.2 molecules of nitrous oxide, 1.5 molecules of formic acid, and 0.6 ammonium ion. Diphenyliodonium-mediated inhibition of salicylate 1-monooxygenase and a comparative study between native, deflavo, and reconstituted enzyme(s) showed that FAD site of the enzyme was involved in the biotransformation of CL-20 catalyzed by salicylate 1-monooxygenase. The data suggested that salicylate 1-monooxygenase catalyzed two oxygen-sensitive single-electron transfer steps necessary to release two nitrite ions from CL-20 and that this was followed by the secondary decomposition of this energetic chemical. PMID:15240281

  18. Molecular Scissors: RNA Enzymes Go Commercial

    Microsoft Academic Search

    Ann Gibbons

    1991-01-01

    When Thomas Cech of the University of Colorado discovered in 1982 that RNA can act as an enzyme, catalyzing specific biological reactions, the result surprised molecular biologists. Only proteins, they thought, could act as enzymes. The work not only led to a Nobel Prize for Cech, it prompted prophecies of a new kind of genetic engineering - one based on

  19. Positional Assembly of Enzymes on Bacterial Outer Membrane Vesicles for Cascade Reactions

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

    Schlautman, Mark A. [Clemson University, Clemson, SC (United States)

    2013-07-14

    Past activities have resulted in a legacy of contaminated soil and groundwater at Department of Energy facilities nationwide. Uranium and chromium are among the most frequently encountered and highest-priority metal and radionuclide contaminants at DOE installations. Abiotic chemical reduction of uranium and chromium at contaminated DOE sites can be beneficial because the reduced metal species are less soluble in water, less mobile in the environment, and less toxic to humans and ecosystems. Although direct biological reduction has been reported for U(VI) and Cr(VI) in laboratory studies and at some field sites, the reactions can sometimes be slow or even inhibited due to unfavorable environmental conditions. One promising approach for the in-situ remediation of DOE contaminants is to develop electron shuttle catalysts that can be delivered precisely to the specific subsurface locations where contaminants reside. Previous research has shown that reduction of oxidized organic and inorganic contaminants often can be catalyzed by electron shuttle systems. Metalloporphyrins and their derivatives are well known electron shuttles for many biogeochemical systems, and thus were selected to study their catalytic capabilities for the reduction of chromium and uranium in the presence of reducing agents. Zero valent iron (ZVI) was chosen as the primary electron donor in most experimental systems. Research proceeded in three phases and the key findings of each phase are reported here. Phase I examined Cr(VI) reduction and utilized micro- and nano-sized ZVI as the electron donors. Electron shuttle catalysts tested were cobalt- and iron-containing metalloporphyrins and Vitamin B12. To aid in the recycle and reuse of the nano-sized ZVI and soluble catalysts, sol-gels and calcium-alginate gel beads were tested as immobilization/support matrices. Although the nano-sized ZVI could be incorporated within the alginate gel beads, preliminary attempts to trap it in sol-gels were not successful. Conversely, the water-soluble catalysts could be trapped within sol-gel matrices but they tended to leach out of the alginate gel beads during use. In general, immobilization of the nano-sized ZVI in gel beads and of the catalysts in sol-gels tended to result in slower rates of Cr(VI) reduction, but these effects could be overcome to some extent by using higher reactant/catalyst concentrations. In addition, the lowering of their effectiveness would likely be offset by the benefits obtained when recycling and reusing the materials because they were immobilized. Addition of the catalytic electron shuttles will be most useful when the micro-sized or nano-sized ZVI becomes less reactive with reaction time. Continued work in Phase II in the area of nano-sized ZVI immobilization led to procedures that were successful in incorporating the iron particles in sol-gel matrices. The water-soluble reductants sodium dithionite and L-ascorbic acid were also tested, but their use appeared to lead to formation of complexes with the uranyl cation which limited their effectiveness. Also, although the sol-gel supported nano-sized ZVI showed some promise at reducing uranium, the fluoride used in the sol-gel synthesis protocol appeared to lead to formation of uranyl-fluoride complexes that were less reactive. Because hexavalent chromium is an anion which does not form complexes with fluoride, it was used to demonstrate the intrinsic reactivity of the sol-gel immobilized nano-sized ZVI. Consistent with our observations in Phase I, the sol-gel matrix once again slowed down the reduction reaction but the expected benefits of recycle/reuse should outweigh this adverse effect. The major emphasis in Phase III of this study was to simultaneously incorporate nano-sized ZVI and water-soluble catalysts in the same sol-gel matrix. The catalysts utilized were cobalt complexes of uroporphyrin and protoporphyrin and Cr(VI) reduction was used to test the efficacy of the combined "catalyst + reductant" sol-gel matrix. When enough catalyst was added to the sol-gels, enhancement of the Cr(VI)

  1. Friedel–Crafts Acylation and Related Reactions Catalyzed by Heteropoly Acids

    Microsoft Academic Search

    J. Kaur; E. F. Kozhevnikova; K. Griffin; B. Harrison; I. V. Kozhevnikov

    2003-01-01

    The Friedel–Crafts acylation of anisole (AN) with acetic anhydride (AA) and the Fries rearrangement of phenyl acetate in the liquid phase catalyzed by bulk and silica-supported heteropoly acids (HPA), mainly H3PW12O40 (PW), have been studied. In anisole acylation, PW exhibits very high activity, yielding up to 98% para and 2–4% ortho isomer of methoxyacetophenone (MOAP) at 90-110°C and an AN\\/AA

  2. Facile surface PEGylation via tyrosinase-catalyzed oxidative reaction for the preparation of non-fouling surfaces.

    PubMed

    Lee, Yunki; Park, Kyung Min; Bae, Jin Woo; Park, Ki Dong

    2013-02-01

    The control of biological interactions that occur at material-cell/blood interfaces is of great importance to help maximize in vitro and in vivo performance of biomedical devices. PEGylation has been extensively used as an effective surface modification tool that can alter biological responses on device surfaces. Herein, we report a new surface PEGylation method using a tyrosinase-catalyzed oxidative reaction. Tyramine (TA), an enzymatically active phenolic compound, was chemically conjugated to methoxy poly(ethylene glycol) (mPEG). Surface immobilization of mPEG-TA onto various substrates was accomplished simply and rapidly by adding tyrosinase under mild conditions. It was shown that the water contact angles on all surfaces modified with mPEG-TA were decreased, indicating successful introduction of hydrophilic PEG. In addition, the X-ray photoelectron spectroscopy (XPS) spectra demonstrated the differences in the atomic composition on the TiO(2) surface after treatment with mPEG-TA. Non-fouling surfaces prevent non-specific interactions with proteins and cells; consistently, the PEGylated TiO(2) surface clearly showed a decrease in both levels of bovine serum albumin (BSA) adsorption and NIH3T3 cell attachment. Therefore, the facile surface PEGylation using a tyrosinase-catalyzed oxidative reaction should be useful for designing non-fouling surfaces of biomedical devices. PMID:23104029

  3. Fluctuating reaction rate and non-exponential blinking statistics in single-enzyme kinetics

    NASA Astrophysics Data System (ADS)

    Tang, Jau; Yeh, Yi-Cheun; Tai, Po-Tse

    2008-09-01

    Extending the Michaelis-Menten kinetic scheme, we consider a three-state diffusion-controlled reaction model to investigate the effects of fluctuating reaction rate on the blinking statistics of single-enzyme catalytic reactions. As a result of conformational changes, the barrier-height and the reaction rate for the bottleneck enzymatic reaction could fluctuate in time, leading to non-exponential blinking statistics. To illustrate model applications, some reported experimental data for single ?-galactosidase molecules were reanalyzed here to extract useful kinetic parameters.

  4. DFT study of the spin-forbidden reaction of N 2O and CO catalyzed by Pt +

    NASA Astrophysics Data System (ADS)

    Wang, Yong-Cheng; Wang, Qing-Yun; Geng, Zhi-Yuan; Si, Yu-Bing; Zhang, Jian-Hui; Li, Hui-Zhen; Zhang, Qing-Li

    2008-07-01

    The gas-phase reaction of N 2O and CO catalyzed by Pt + has been investigated by means of the relativistic effective core potential (RECP) of Stuttgart basis sets on platinum and UB3LYP/6-311+G(2d) level on nonmetal atoms. The involving crossings between the doublet and quartet potential energy surfaces have been discussed by means of the intrinsic reaction coordinate approach used by Yoshizawa et al, and corresponding MECPs we obtained by the mathematical algorithm proposed by Harvey et al. has also been employed. In addition, the crossing caused by SOC is efficient. And the O-atom affinities (OA) testified that the argumentation is thermodynamically allowed.

  5. Origin of chemoselectivity in N-heterocyclic carbene catalyzed cross-benzoin reactions: DFT and experimental insights.

    PubMed

    Langdon, Steven M; Legault, Claude Y; Gravel, Michel

    2015-04-01

    An exploration into the origin of chemoselectivity in the NHC-catalyzed cross-benzoin reaction reveals several key factors governing the preferred pathway. In the first computational study to explore the cross-benzoin reaction, a piperidinone-derived triazolium catalyst produces kinetically controlled chemoselectivity. This is supported by (1)H NMR studies as well as a series of crossover experiments. Major contributors include the rapid and preferential formation of an NHC adduct with alkyl aldehydes, a rate-limiting carbon-carbon bond formation step benefiting from a stabilizing ?-stacking/?-cation interaction, and steric penalties paid by competing pathways. The energy profile for the analogous pyrrolidinone-derived catalyst was found to be remarkably similar, despite experimental data showing that it is less chemoselective. The chemoselectivity could not be improved through kinetic control; however, equilibrating conditions show substantial preference for the same cross-benzoin product kinetically favored by the piperidinone-derived catalyst. PMID:25734574

  6. Enzyme

    MedlinePLUS

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  7. Poly(ethyleneglycol) (PEG): a rapid and recyclable reaction medium for the DABCO-catalyzed Baylis–Hillman reaction

    Microsoft Academic Search

    S Chandrasekhar; Ch Narsihmulu; B Saritha; S Shameem Sultana

    2004-01-01

    PEG (400) has been used as a rapid and recyclable reaction medium for the Baylis–Hillman reaction with the conventional basic catalyst DABCO (20mol%) with very good yields of products. Recyclability is achieved with no further addition of DABCO to the reaction medium for over four runs without substantial loss in yields. Incidentally, DABCO is recycled for the first time in

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

    PubMed

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

    2014-06-01

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

  9. Chain transfer reaction catalyzed by various polyhydroxyalkanoate synthases with poly(ethylene glycol) as an exogenous chain transfer agent.

    PubMed

    Tomizawa, Satoshi; Saito, Yuta; Hyakutake, Manami; Nakamura, Yoshiyuki; Abe, Hideki; Tsuge, Takeharu

    2010-07-01

    Polyhydroxyalkanoate (PHA) synthases catalyze chain transfer (CT) reaction after polymerization reaction of PHA by transferring PHA chain from PHA synthase to a CT agent, resulting in covalent bonding of CT agent to PHA chain at the carboxyl end. Previous studies have shown that poly(ethylene glycol) (PEG) is an effective exogenous CT agent. This study aimed to compare the effects of PEG on CT reaction during poly[(R)-3-hydroxybutyrate] [P(3HB)] synthesis by using six PHA synthases in Escherichia coli JM109. The synthesized P(3HB) polymers were characterized in terms of molecular weight and end-group structure. Supplementation of PEG to the culture medium reduced P(3HB) molecular weights by up to 96% due to PEG-induced CT reaction. The P(3HB) polymers were subjected to (1)H NMR analysis to confirm the formation of a covalent bond between PEG and P(3HB) chain at the carboxyl end. This study revealed the reactivity of PHA synthases to PEG with respect to CT reaction in E. coli. PMID:20422180

  10. Observing metal-catalyzed chemical reactions in situ using surface-enhanced Raman spectroscopy on Pd-Au nanoshells.

    PubMed

    Heck, Kimberly N; Janesko, Benjamin G; Scuseria, Gustavo E; Halas, Naomi J; Wong, Michael S

    2008-12-10

    Insight into the nature of transient reaction intermediates and mechanistic pathways involved in heterogeneously catalyzed chemical reactions is obtainable from a number of surface spectroscopic techniques. Carrying out these investigations under actual reaction conditions is preferred but remains challenging, especially for catalytic reactions that occur in water. Here, we report the direct spectroscopic study of the catalytic hydrodechlorination of 1,1-dichloroethene in H2O using surface-enhanced Raman spectroscopy (SERS). With Pd islands grown on Au nanoshell films, this reaction can be followed in situ using SERS, exploiting the high enhancements and large active area of Au nanoshell SERS substrates, the transparency of Raman spectroscopy to aqueous solvents, and the catalytic activity enhancement of Pd by the underlying Au metal. The formation and subsequent transformation of several adsorbate species was observed. These results provide the first direct evidence of the room-temperature catalytic hydrodechlorination of a chlorinated solvent, a potentially important pathway for groundwater cleanup, as a sequence of dechlorination and hydrogenation steps. More broadly, the results highlight the exciting prospects of studying catalytic processes in water in situ, like those involved in biomass conversion and proton-exchange membrane fuel cells. PMID:19554693

  11. Simulation studies in biochemical signaling and enzyme reactions

    NASA Astrophysics Data System (ADS)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  12. Resolution of component proteins in an enzyme complex from Methanosarcina thermophila catalyzing the synthesis or cleavage of acetyl-CoA

    SciTech Connect

    Abbanat, D.R.; Ferry, J.G. (Virginia Inst. and State Univ., Blacksburg (United States))

    1991-04-15

    An enzyme complex was isolated from acetate-grown Methanosarcina thermophila that oxidized CO and catalyzed the synthesis or cleavage of acetyl-CoA. The complex consisted of five subunits ({alpha}1{beta}1{gamma}1{delta}1{epsilon}1) of 89, 71, 60, 58, and 19 kDa. The complex contained nickel, iron, acid-labile sulfide, and cobalt in a corrinoid cofactor. Two components were resolved by anion-exchange chromatography of the complex in the presence of dodecyltrimethylammonium bromide and Triton X-100: a 200-kDa nickel/iron-sulfur protein with the 89-and 19-kDa ({alpha}{sub 2}{epsilon}{sub x}) subunits and a 100-kDa corrinoid/iron-sulfur protein with the 60- and 58-kDa subunits ({gamma}1{delta}1). Both components contained iron-sulfur centers. The nickel/iron-sulfur component oxidized CO and reduced methyl viologen or a ferredoxin isolated from M. thermophila. UV-visible spectroscopy indicated that the reduced corrinoid/iron-sulfur component could be methylated with CH{sub 3}I. The results suggest that the enzyme complex from M. thermophila contained at least two enzyme components, each with a specific function. The properties of the component enzymes support a mechanism proposed for acetyl-CoA synthesis (or cleavage) by the enzyme complex.

  13. ?-Bond activation of small molecules and reactions catalyzed by transition-metal complexes: theoretical understanding of electronic processes.

    PubMed

    Guan, Wei; Sayyed, Fareed Bhasha; Zeng, Guixiang; Sakaki, Shigeyoshi

    2014-07-01

    ?-Bond activations of R1-R2 and R1-X1 (R1, R2 = H, alkyl, aromatics, etc.; X1 = electronegative group) by transition-metal complexes are classified into two main categories: ?-bond activation by a metal (M) center and that by a metal-ligand bond. The former is classified into two subcategories: concerted oxidative addition to M and stepwise oxidative addition via nucleophilic attack of M. The latter is also classified into two subcategories: heterolytic activaton by M-X2 (X2 = anion ligand) and oxidative addition to M-L (L = neutral ligand). In the concerted oxidative addition, charge transfer (CT) occurs from the M d orbital to the ?* antibonding orbital of R1-R2, the clear evidence of which is presented here. The concerted oxidative additions of Ph-CN, Me-CN, and Ph-Cl to a nickel(0) complex are discussed as examples. The stepwise oxidative addition occurs through nucleophilic attack of M to R1-X1 to form an ion-pair intermediate. In the nucleophilic attack, CT occurs from the M d? to either the ?* orbital or empty p? orbital of R1-X1. Solvation plays a crucial role in stabilizing the transition state and ion-pair intermediate. The oxidative addition reactions of Ph-I, CH3-Br, and Br2B(OSiH3) to platinum(0), platinum(II), and palladium(0) complexes are discussed. In the heterolytic activation of R1-R2 by an M-X2 bond, R1 and R2 are bound with M and X2, respectively, indicating that R1 becomes anion-like and R2 becomes cation-like. CT mainly occurs from the X2 ligand to the ?* antibonding orbital of R1-R2 and also from R1 to the M empty d orbital. In the oxidative addition to an M-L moiety, R1 is bound with M, R2 is bound with L, and thus-formed L-R2 is bound with M. The oxidative addition reaction of the Si-H bond of silane to Cp2Zr(C2H4) and that of the H-H bond of H2 to Ni[MesB(o-Ph2PC6H4)2] are discussed as examples. The importance of the ?-bond activation in such catalytic reactions as nickel(0)-catalyzed phenylcyanation of alkyne, nickel(0)-catalyzed carboxylation of phenyl chloride, ruthenium(II)-catalyzed hydrogenation of carbon dioxide, and the Hiyama cross-coupling reaction is discussed based on theoretical studies. PMID:24784994

  14. Transformation pathways of MeO-PBDEs catalyzed by active center of P450 enzymes: a DFT investigation employing 6-MeO-BDE-47 as a case.

    PubMed

    Wang, Xingbao; Chen, Jingwen; Wang, Yong; Xie, Hongbin; Fu, Zhiqiang

    2015-02-01

    Recent in vivo and in vitro experiments indicated that methoxylated polybrominated diphenyl ethers (MeO-PBDEs) can be biotransformed into hydroxylated PBDEs (HO-PBDEs) that are more toxic than PBDEs and MeO-PBDEs. Nevertheless, the enzymatic transformation mechanism is not clear. We hypothesized that cytochrome P450 enzymes (CYPs) play a key role in the transformation and employed the density functional theory calculations to unveil the mechanism. The transformation of a model compound, 6-MeO-BDE-47, catalyzed by the active center of CYPs (Compound I), was computed. For the first time, our results show that the energy barriers for the addition of Compound I to the C atoms on the phenyl of 6-MeO-BDE-47 are much higher than that for hydroxylation of the methoxyl, indicating that O-demethylation is a dominating metabolic pathway. This is in line with experimental observations performed by others. The pathways for the transformation of 6-MeO-BDE-47 catalyzed by Compound I were clarified. A C-H bond of the methoxyl is activated by Compound I, followed by radical rebound to form carbinol intermediates, then the carbinols decompose to form 6-HO-BDE-47 with the assistance of water molecules. The computational method can be potentially employed to develop models that predict biotransformation of xenobiotics catalyzed by CYPs. PMID:25462307

  15. Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

    PubMed Central

    Náray-Szabó, Gábor; Oláh, Julianna; Krámos, Balázs

    2013-01-01

    Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods. PMID:24970187

  16. Mechanistic studies on a Cu-catalyzed aerobic oxidative coupling reaction with N-phenyl tetrahydroisoquinoline: structure of intermediates and the role of methanol as a solvent.

    PubMed

    Boess, Esther; Sureshkumar, Devarajulu; Sud, Abhishek; Wirtz, Cornelia; Farès, Christophe; Klussmann, Martin

    2011-06-01

    The mechanism of an aerobic copper-catalyzed oxidative coupling reaction with N-phenyl tetrahydroisoquinoline was investigated. The oxidized species formed from the reaction of the amine with the copper catalyst were analyzed by NMR-spectroscopy. An iminium dichlorocuprate was found to be the reactive intermediate and could be structurally characterized by X-ray crystallography. The effect of methanol to effectively stabilize the iminium ion was investigated and shown to be beneficial in an oxidative allylation reaction. PMID:21561084

  17. Two-step sequential reaction catalyzed by layer-by-layer assembled urease and arginase multilayers

    Microsoft Academic Search

    Sandeep Disawal; Jianhong Qiu; Bill B. Elmore; Yuri M. Lvov

    2003-01-01

    Layer-by-layer (LbL) self-assembly was used to build multi-component thin films containing polyions and enzymes: urease (Ur), and arginase (Ar). These multilayers were shown to participate catalytically in a two step sequential decomposition of l-arginine to urea and subsequently to ammonia. Deposition of multilayers was characterized with quartz crystal microbalance (QCM). The following enzyme monolayer stacking architectures were studied: (Ur\\/PDDA)n, (Ar\\/PDDA)n,

  18. Monte Carlo Simulations of Enzyme Reactions in Two Dimensions: Fractal Kinetics and Spatial Segregation

    Microsoft Academic Search

    Hugues Berry

    2002-01-01

    Conventional equations for enzyme kinetics are based on mass-action laws, that may fail in low-dimensional and disordered media such as biological membranes. We present Monte Carlo simulations of an isolated Michaelis–Menten enzyme reaction on two-dimensional lattices with varying obstacle densities, as models of biological membranes. The model predicts that, as a result of anomalous diffusion on these low-dimensional media, the

  19. On the radical nature of iron-catalyzed cross-coupling reactions.

    PubMed

    Hedström, Anna; Izakian, Zakieh; Vreto, Irma; Wallentin, Carl-Johan; Norrby, Per-Ola

    2015-04-01

    The radical nature of iron-catalyzed cross-coupling between Grignard reagents and alkyl halides has been studied by using a combination of competitive kinetic experiments and DFT calculations. In contrast to the corresponding coupling with aryl halides, which commences through a classical two-electron oxidative addition/reductive elimination sequence, the presented data suggest that alkyl halides react through an atom-transfer-initiated radical pathway. Furthermore, a general iodine-based quenching methodology was developed to enable the determination of highly accurate concentrations of Grignard reagents, a capability that facilitates and increases the information output of kinetic investigations based on these substrates. PMID:25703202

  20. Redox Reactions of Metalloporphyrins and their Role in Catalyzed Reduction of Carbon Dioxide

    SciTech Connect

    Neta, P.

    2002-09-01

    Pulse radiolysis and laser photolysis are used to study redox processes of metalloporphyrins and related complexes in order to evaluate these light absorbing molecules as sensitizers and intermediates in solar energy conversion schemes. The main thrust of the current studies is to investigate the role of reduced metalloporphyrins as intermediates in the catalyzed reduction of carbon dioxide. Studies involve cobalt and iron porphyrins, phthalocyanines, corroles, and corrins as homogeneous catalysts for reduction of carbon dioxide in solution. The main aim is to understand the mechanisms of these photochemical schemes in order to facilitate their potential utilization.

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

    E-print Network

    Straube, Arthur V.

    Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction

  2. An Altered Transition State for the Reaction of an RNA Model Catalyzed by a Dinuclear Zinc(II) Catalyst

    PubMed Central

    Humphry, Tim; Iyer, Subashree; Iranzo, Olga; Morrow, Janet R.; Richard, John P.; Paneth, Piotr

    2009-01-01

    The cyclization of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group (18klg = 1.0064 ± 0.0009 and 15k = 1.0002 ± 0.0002), and that nucleophilic bond formation occurs in the rate-determining step (18knuc = 1.0326 ± 0.0008). In the catalyzed reaction, larger leaving group isotope effects (18klg = 1.0113 ± 0.0005 and 15k = 1.0015 ± 0.0005) and a smaller nucleophile isotope effect (18knuc = 1.0116 ± 0.0010) indicate a later TS with greater leaving group bond fission, and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2’-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer. PMID:19053445

  3. Mechanism of the reaction catalyzed by mandelate racemase. 1. Chemical and kinetic evidence for a two-base mechanism

    SciTech Connect

    Powers, V.M.; Koo, C.W.; Kenyon, G.L. (Univ. of California, San Francisco (United States)); Gerlt, J.A.; Kozarich, J.W. (Univ. of Maryland, College Park (United States))

    1991-09-24

    The fate of the {alpha}-hydrogen of mandelate in the reaction catalyzed by mandelate racemase has been investigated by a mass spectroscopic method. The method entails the incubation of (R)- or (S)-({alpha}-{sup 1}H) mandelate in buffered D{sub 2}O to a low extent of turnover (about 5-8%), esterification of the resulting mixture of mandelates with diazomethane, derivatization of the methyl esters with a chiral derivatizing agent, and quantitation of the isotope content of the {alpha}-hydrogen of both substrate and product by gas chromatography/mass spectrometric analysis. No significant substrate-derived {alpha}-protium was found in the product for racemization in either direction. In addition, in the (R) to (S) direction almost no exchange of the {alpha}-hydrogen in the remaining (R) substrate pool occurred, but in the (S) to (R) direction 3.5-5.1% exchange of the {alpha}-hydrogen in the remaining substrate (after 5.1-7.2% net turnover) was found. Qualitatively similar results were obtained in the (S) to (R) direction in H{sub 2}O when (S)-({alpha}-{sup 2}H)mandelate was used as substrate. In other experiments, an overshoot in the progress curve was observed when the racemization of either enantiomer of ({alpha}-{sup 1}H) mandelate in D{sub 2}O was monitored by following the change in ellipticity of the reaction mixture; the magnitude of the overshoot was greater in the (R) to (S) than in the (S) to (R) direction. All of the available data indicate that the reaction catalyzed by mandelate racemase proceeds by a two-base mechanism, in contrast to earlier proposals.

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

    PubMed

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

    2014-12-24

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

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

    PubMed Central

    Hong, Allen Y.

    2014-01-01

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

  6. Asymmetric Glyoxylate-Ene Reactions Catalyzed by Chiral Pd(II) Complexes in the Ionic Liquid [bmim][PF6

    PubMed Central

    He, Xi Jun; Shen, Zhen Lu; Mo, Wei Min; Hu, Bao Xiang; Sun, Nan

    2007-01-01

    The room temperature ionic liquid [bmim][PF6] was employed as the reaction medium in the asymmetric glyoxylate-ene reaction of ?-methyl styrene (4a) with ethyl glyoxylate using chiral palladium(II) complexes as the catalysts. [Pd(S-BINAP)(3,5-CF3-PhCN)2](SbF6)2 (1b) showed the highest catalytic activity. Under the reaction conditions of 40 °C, 0.5 h, and 1b/4a molar ratio of 0.05, ethyl ?-hydroxy-4-phenyl-4-pentenoate was obtained in excellent chemical yield (94 %) with high enantioselectivity (70 %). Other ?-hydroxy esters can also be obtained in high chemical yields and enantioselectities through the glyoxylate-ene reactions of alkenes with glyoxylates catalyzed by 1b in [bmim][PF6]. Moreover, the ionic liquid [bmim][PF6] which contained the palladium(II) complex could be recycled and reused several times without significant loss of the catalytic activity.

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

    NASA Astrophysics Data System (ADS)

    Zhao, Haiying; Dou, Xiaoming

    2005-01-01

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

  8. L-proline-catalyzed enantioselective one-pot cross-Mannich reaction of aldehydes.

    PubMed

    Hayashi, Yujiro; Urushima, Tatsuya; Tsuboi, Wataru; Shoji, Mitsuru

    2007-01-01

    This protocol describes a procedure for the synthesis of syn-beta-amino alpha-substituted aldehydes, versatile intermediates in synthetic organic chemistry, via asymmetric, direct, one-pot, three-component, cross-Mannich reaction of two different aldehydes. The reaction consists of two steps; one is the formation of imine by the reaction of aldehyde and p-anisidine in the presence of Pro, and the second step is the enantioselective addition reaction of enamine generated from the other aldehyde and Pro with the imine generated in the first step. As the aldehyde easily racemizes, gamma-amino alcohol was isolated and characterized after reduction. The yield and diastereo- and enantioselectivities are generally excellent. It will take approximately 26 h to complete the protocol: 0.5 h to set up the reaction, 20.5 h for the reaction and 5 h for the isolation and purification. PMID:17401345

  9. The roles of counterion and water in a stereoselective cysteine-catalyzed Rauhut-Currier reaction: A challenge for computational chemistry

    PubMed Central

    Dermenci, Alpay; Miller, Scott J.

    2013-01-01

    The stereoselective Rauhut-Currier (RC) reaction catalyzed by a cysteine derivative has been explored computationally with DFT (M06-2X) theory. Both methanethiol and a chiral cysteine derivative were studied as nucleophiles. The complete reaction pathway involves rate-determining elimination of the thiol catalyst from the Michael addition product. The stereoselective Rauhut-Currier reaction, catalyzed by a cysteine derivative as nucleophile, has also been studied in detail. This reaction was experimentally found to be extremely sensitive to the reaction conditions, such as the number of water equivalents and the effect of potassium counterion. The E1cB process for catalyst elimination has been explored computationally for the 8 possible stereoisomers. The effect of explicit water solvation and the presence of counterion (either K+ or Na+) has been studied for the lowest energy enantiomer pair (1S, 2R, 3S)/(1R, 2S, 3R). PMID:24038400

  10. The roles of counterion and water in a stereoselective cysteine-catalyzed Rauhut-Currier reaction: a challenge for computational chemistry.

    PubMed

    Osuna, Sílvia; Dermenci, Alpay; Miller, Scott J; Houk, K N

    2013-10-11

    The stereoselective Rauhut-Currier (RC) reaction catalyzed by a cysteine derivative has been explored computationally with density functional theory (M06-2X). Both methanethiol and a chiral cysteine derivative were studied as nucleophiles. The complete reaction pathway involves rate-determining elimination of the thiol catalyst from the Michael addition product. The stereoselective Rauhut-Currier reaction, catalyzed by a cysteine derivative as a nucleophile, has also been studied in detail. This reaction was experimentally found to be extremely sensitive to the reaction conditions, such as the number of water equivalents and the effect of potassium counterion. The E1cB process for catalyst elimination has been explored computationally for the eight possible stereoisomers. The effect of explicit water solvation and the presence of counterion (either K(+) or Na(+) ) has been studied for the lowest energy enantiomer pair (1S, 2R, 3S)/(1R, 2S, 3R). PMID:24038400

  11. Factors Affecting Reaction Kinetics of Glucose Oxidase

    Microsoft Academic Search

    Kristin A. Johnson

    2002-01-01

    Basic principles of enzyme kinetics are demonstrated using the enzyme glucose oxidase. The glucose oxidase enzymatic reaction is coupled to horseradish peroxidase, which in turn catalyzes the oxidation of a dye to a bright blue-green color. The appearance of the blue-green dye is used to monitor the course of the reaction and is quite visible in a classroom setting. A

  12. Reactions and enzymes in the metabolism of drugs and other xenobiotics.

    PubMed

    Testa, Bernard; Pedretti, Alessandro; Vistoli, Giulio

    2012-06-01

    In this article, we offer an overview of the compared quantitative importance of biotransformation reactions in the metabolism of drugs and other xenobiotics, based on a meta-analysis of current research interests. Also, we assess the relative significance the enzyme (super)families or categories catalysing these reactions. We put the facts unveiled by the analysis into a drug discovery context and draw some implications. The results confirm the primary role of cytochrome P450-catalysed oxidations and UDP-glucuronosyl-catalysed glucuronidations, but they also document the marked significance of several other reactions. Thus, there is a need for several drug discovery scientists to better grasp the variety of drug metabolism reactions and enzymes and their consequences. PMID:22305937

  13. Enzyme-catalysed reactions between some 2-substituted 5-nitrofuran derivatives and glutathione

    PubMed Central

    Boyland, E.; Speyer, B. E.

    1970-01-01

    1. A glutathione transferase present in rat and human liver supernatant catalyses the reaction of some 2-substituted 5-nitrofuran derivatives with GSH, with formation of a conjugate and release of the nitro group as inorganic nitrite. Some of the substrates undergo the same reaction at a slower rate in the absence of enzyme. Nitrofuran derivatives commonly used as drugs, and five other drugs containing nitro groups, did not react. 2. Substrate activity in the nitrofuran derivatives showed an approximate correlation with the lability of the nitro group to alkali. 3. Optimum pH values ranging from 6.6 to 9.0 were found for the enzymic reaction with various derivatives, the values being influenced by alkali-lability and pK values of the compounds. 4. Tenfold purification of rat liver glutathione S-aryl-transferase resulted in an equal purification of the activities that catalyse the reaction of two of the nitrofuran derivatives with GSH. PMID:5533198

  14. Aromatic amide-derived non-biaryl atropisomers as highly efficient ligands in silver-catalyzed asymmetric cycloaddition reactions.

    PubMed

    Bai, Xing-Feng; Song, Tao; Xu, Zheng; Xia, Chun-Gu; Huang, Wei-Sheng; Xu, Li-Wen

    2015-04-20

    The synthesis of a series of aromatic amide-derived non-biaryl atropisomers with a phosphine group and multiple stereogenic centers is reported. The novel phosphine ligands exhibit high diastereo- and enantioselectivities (up to >99:1 d.r., 95-99?% ee) as well as yields in the silver-catalyzed asymmetric [3+2] cycloaddition of aldiminoesters with nitroalkenes, which provides a highly enantioselective strategy for the synthesis of optically pure nitro-substituted pyrrolidines. In addition, the experimental results with regard to the carbon stereogenic center as well as the amide stereochemistry confirmed the potential of hemilabile atropisomers as chiral ligand in catalytic asymmetric [3+2] cycloaddition reaction. PMID:25728216

  15. Synthesis of a double helicene by a palladium-catalyzed cross-coupling reaction: structure and physical properties.

    PubMed

    Kashihara, Hitoshi; Asada, Toshio; Kamikawa, Ken

    2015-04-20

    For this study, twisted ?-extended helicene 1 and double helicene 2 with a helicene framework were synthesized through palladium-catalyzed C?H arylation or Suzuki-Miyaura coupling reaction. X-ray crystallography revealed grossly twisted structures that were soluble in various conventional organic solvents. Optical properties based on UV/Vis and fluorescence spectra were measured. Electrochemical properties were also studied by measurements of cyclic voltammetry in 1 and 2, which revealed their HOMO and the LUMO energies. Theoretical calculation supports their HOMO and LUMO energies and molecular orbitals. Furthermore, a racemization process of 2 predicted that the activation free energy at 300?K would be 31.8?kcal?mol(-1) by DFT calculation, which indicated the static helicity at 300?K. PMID:25754221

  16. Cytochrome P-450 model reactions: efficient and highly selective oxidation of alcohols with tetrabutylammonium peroxymonosulfate catalyzed by Mn-porphyrins.

    PubMed

    Rezaeifard, Abdolreza; Jafarpour, Maasoumeh; Moghaddam, Gholamreza Kardan; Amini, Fatemeh

    2007-04-15

    A novel biomimetic method for rapid oxidation of a wide range of benzylic, allylic, aliphatic, primary and secondary alcohols to the related aldehydes and ketones using Bu(4)NHSO(5) catalyzed by Mn(TPP)OAc/pyridine system with high to excellent yields and excellent selectivity has been developed. The high turnover rates obtained in this catalytic system represent a high efficiency and also relative stability of Mn-porphyrin catalyst towards oxidative degradation. The presence of an electron-withdrawing group on the phenyl ring of both benzyl alcohol and porphyrin ligand increases the reactivity of substrate as well as catalytic activity of Mn-porphyrin catalyst in the oxidation reaction. PMID:17293117

  17. The enantioselective construction of tetracyclic diterpene skeletons with Friedel-Crafts alkylation and palladium-catalyzed cycloalkenylation reactions.

    PubMed

    Burke, Sarah J; Malachowski, William P; Mehta, Sharan K; Appenteng, Roselyn

    2015-02-18

    Due to the profound extent to which natural products inspire medicinal chemists in drug discovery, there is demand for innovative syntheses of these often complex materials. This article describes the synthesis of tricarbocyclic natural product architectures through an extension of the enantioselective Birch-Cope sequence with intramolecular Friedel-Crafts alkylation reactions. Additionally, palladium-catalyzed enol silane cycloalkenylation of the tricarbocyclic structures afforded the challenging bicyclo[3.2.1]octane C/D ring system found in the gibberellins and the ent-kauranes, two natural products with diverse medicinal value. In the case of the ent-kaurane derivative, an unprecedented alkene rearrangement converted four alkene isomers to one final product. PMID:25598198

  18. Importance of glutamate 87 and the substrate ?-amine for the reaction catalyzed by d-arginine dehydrogenase.

    PubMed

    Ball, Jacob; Bui, Quan V V; Gannavaram, Swathi; Gadda, Giovanni

    2015-02-15

    Pseudomonas aeruginosad-arginine dehydrogenase (PaDADH) catalyzes the oxidation of d-arginine to iminoarginine, which is non-enzymatically hydrolyzed to 2-ketoarginine and ammonia. Here, site-directed mutagenesis and pH effects were used to investigate binding and catalysis of zwitterionic and cationic substrates for the enzyme. An unprotonated group with apparent pKa value ?7.9 is required for binding d-arginine or d-lysine, but not d-methionine or d-leucine. This group is E87, as suggested by its replacement with leucine. An unprotonated group with pKa of 9.5, which persists in the H48F and E87L variants, is required for amine oxidation with all substrates. Since Y53 and Y249 were previously ruled out, the pKa is assigned to the substrate ?-NH3(+) group, which previous QM/MM and Kd pH-profile demonstrated to be protonated for preferred binding to the enzyme. Lack of pH effects on the (D)kred with d-leucine established 9.5 as the intrinsic pKa, and d-leucine as a non-sticky substrate. d-Arginine, d-lysine and d-methionine and their corresponding iminoproducts were significantly stickier than d-leucine, as indicated by apparent pKa values <9.5 in both kcat/Km and kcat. Restricted proton movements in catalysis were established from hollowed kcat pH profiles in wild-type PaDADH with d-lysine and in the H48F and E87L enzymes with d-arginine. PMID:25637657

  19. Enantioselective Synthesis of Functionalized Pyrazoles by NHC-Catalyzed Reaction of Pyrazolones with ?,?-Unsaturated Aldehydes.

    PubMed

    Yetra, Santhivardhana Reddy; Mondal, Santigopal; Suresh, Eringathodi; Biju, Akkattu T

    2015-03-20

    The N-heterocyclic carbene (NHC)-organocatalyzed enantioselective annulation reaction of pyrazolones with ?,?-unsaturated aldehydes proceeding via the chiral ?,?-unsaturated acyl azolium intermediates under oxidative conditions is presented. The reaction afforded dihydropyranone-fused pyrazoles in moderate to good yields and good er values under operationally simple and base-free conditions. PMID:25723547

  20. Platinum-catalyzed domino reaction with benziodoxole reagents for accessing benzene-alkynylated indoles.

    PubMed

    Li, Yifan; Waser, Jerome

    2015-04-27

    Indoles are omnipresent in natural products, bioactive molecules, and organic materials. Consequently, their synthesis or functionalization are important fields of research in organic chemistry. Most works focus on installation or modification of the pyrrole ring. To access benzene-ring-functionalized indoles with an unsubstituted pyrrole ring remains more challenging. Reported herein is a platinum-catalyzed cyclization/alkynylation domino process to selectively obtain C5- or C6-functionalized indoles starting from easily available pyrroles. The work combines, for the first time, a platinum catalyst with ethynylbenziodoxole hypervalent iodine reagents in a domino process for the synthesis of polyfunctionalized arene rings and gives access to important building blocks for the synthesis of bioactive compounds and organic materials. PMID:25759194

  1. Oxygen reduction reaction catalyzed with titanyl phthalocyanines in nonaqueous and aqueous media.

    PubMed

    Demir, Faruk; Erdo?mu?, Ali; Koca, At?f

    2013-10-14

    Electrochemical and in situ spectroelectrochemical behaviors and electrocatalytic reduction of molecular oxygen with titanyl phthalocyanines (TiPc) bearing 3,4-(methylenedioxy)-phenoxy substituents were performed in aprotic solvents. Multi electrons and metal-based and ring-based redox processes of TiPcs indicate their possible electrocatalytic activity toward many target species. Different numbers and positions of the substituents of the complexes affect the peaks' character and assignment of the processes. The presence of O2 in the electrolyte system influences the electrochemical and spectral responses of TiPcs. Electrochemical and in situ spectroelectrochemical analysis indicates interaction of molecular oxygen with TiPcs and these interaction mechanisms depend on both the substituent environments of the complexes and the electrolyte system. Langmuir-Blodgett films of the complexes also catalyze molecular oxygen in aqueous media, which is a desired property for their practical application. PMID:23949120

  2. Low-temperature superacid catalysis: Reactions of n - butane and propane catalyzed by iron- and manganese-promoted sulfated zirconia

    SciTech Connect

    Tsz-Keung, Cheung; d`Itri, J.L.; Lange, F.C.; Gates, B.C. [Univ. of California, Davis, CA (United States)

    1995-12-31

    The primary goal of this project is to evaluate the potential value of solid superacid catalysts of the sulfated zirconia type for light hydrocarbon conversion. The key experiments catalytic testing of the performance of such catalysts in a flow reactor fed with streams containing, for example, n-butane or propane. Fe- and Mn-promoted sulfated zirconia was used to catalyze the conversion of n-butane at atmospheric pressure, 225-450{degrees}C, and n-butane partial pressures in the range of 0.0025-0.01 atm. At temperatures <225{degrees}C, these reactions were accompanied by cracking; at temperatures >350{degrees}C, cracking and isomerization occurred. Catalyst deactivation, resulting at least in part from coke formation, was rapid. The primary cracking products were methane, ethane, ethylene, and propylene. The observation of these products along with an ethane/ethylene molar ratio of nearly 1 at 450{degrees}C is consistent with cracking occurring, at least in part, by the Haag-Dessau mechanism, whereby the strongly acidic catalyst protonates n-butane to give carbonium ions. The rate of methane formation from n-butane cracking catalyzed by Fe- and Mn-promoted sulfated zirconia at 450{degrees}C was about 3 x 10{sup -8} mol/(g of catalyst {center_dot}s). The observation of butanes, pentanes, and methane as products is consistent with Olah superacid chemistry, whereby propane is first protonated by a very strong acid to form a carbonium ion. The carbonium ion then decomposes into methane and an ethyl cation which undergoes oligocondensation reactions with propane to form higher molecular weight alkanes. The results are consistent with the identification of iron- and manganese-promoted sulfated zirconia as a superacid.

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

    PubMed

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

    2014-12-01

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

  4. A review of multiscale modeling of metal-catalyzed reactions: Mechanism development for complexity and emergent behavior

    SciTech Connect

    Salciccioli, Michael [Univ. of Delaware, Newark, DE (United States); Stamatakis, Michail [Univ. of Delaware, Newark, DE (United States); Caratzoulas, S. [Univ. of Delaware, Newark, DE (United States); Vlachos, Dion G. [Univ. of Delaware, Newark, DE (United States)

    2011-10-01

    We review and provide a perspective on multiscale modeling of catalytic reactions with emphasis on mechanism development and application to complex and emergent systems. We start with an overview of length and time scales, objectives, and challenges in first-principles modeling of reactive systems. Subsequently, we review various methods that ensure thermodynamic consistency of mean-field microkinetic models. Next, we describe estimation of reaction rate constants via quantum mechanical and statistical–mechanical methods as well as semi-empirical methods. Among the latter, we discuss the bond-order conservation method for thermochemistry and activation energy estimation. In addition, we review the newly developed group-additivity method on adsorbate/metal systems and linear free energy or Brønsted–Evans–Polanyi (BEP) relations, and their parameterization using DFT calculations to generate databases of activation energies and reaction free energies. Linear scaling relations, which can enable transfer of reaction energetics among metals, are discussed. Computation-driven catalyst design is reviewed and a new platform for discovery of materials with emergent behavior is introduced. The effect of parameter uncertainty on catalyst design is discussed; it is shown that adsorbate–adsorbate interactions can profoundly impact materials design. Spatiotemporal averaging of microscopic events via the kinetic Monte Carlo method for realistic reaction mechanisms is discussed as an alternative to mean-field modeling. A hierarchical multiscale modeling strategy is proposed as a means of addressing (some of) the complexity of catalytic reactions. Structure-based microkinetic modeling is next reviewed to account for nanoparticle size and shape effects and structure sensitivity of catalytic reactions. It is hypothesized that catalysts with multiple sites of comparable activity can exhibit structure sensitivity that depends strongly on operating conditions. It is shown that two descriptor models are necessary to describe the thermochemistry of adsorbates on nanoparticles. Multiscale and accelerated methods for computing free energies in solution, while accounting explicitly for solvent effects in catalytic reactions, are briefly touched upon with the acid catalyzed dehydration of fructose in water as an example. The above methods are illustrated with several reactions, such as the CO oxidation on Au; the hydrogenation of ethylene and hydrogenolysis of ethane on Pt; the glycerol decomposition to syngas on Pt-based materials; the NH? decomposition on single metals and bimetallics; and the dehydration of fructose in water. Finally, we provide a summary and outlook.

  5. Asymmetric disulfonimide-catalyzed synthesis of ?-amino-?-ketoester derivatives by vinylogous Mukaiyama-Mannich reactions.

    PubMed

    Wang, Qinggang; van Gemmeren, Manuel; List, Benjamin

    2014-12-01

    An organocatalytic asymmetric synthesis of ?-amino-?-ketoester derivatives has been developed. A chiral disulfonimide (DSI) serves as a highly efficient precatalyst for a vinylogous Mukaiyama-Mannich reaction of readily available dioxinone-derived silyloxydienes with N-Boc-protected imines, delivering products in excellent yields and enantioselectivities. The synthetic utility of this reaction is illustrated in various transformations, including a new C?C bond-forming reaction, which provide useful enantioenriched building blocks. The methodology is applied in a formal synthesis of (-)-lasubin. PMID:25348924

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

    PubMed Central

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

    2014-01-01

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

  7. Palladium- and Nickel-Catalyzed Carbon–Carbon Bond Insertion Reactions with Alkylidenesilacyclopropanes

    PubMed Central

    Buchner, Kay M.; Woerpel, K. A.

    2010-01-01

    Palladium and nickel catalysts promoted highly selective carbon–carbon bond insertion reactions with di-tert-butyl-alkylidenesilacyclopropanes. Pd(PPh3)4 was demonstrated to be the optimal catalyst, allowing for a variety of carbon–carbon ?-bond insertion reactions. Depending on the nature of the carbon–carbon ? bond, the insertion reaction proceeded with either direct insertion into the carbon(sp2)–silicon bond or with allylic transposition. Ring-substituted alkylidenesilacyclopropanes required a nickel catalyst to afford insertion products. Using Ni(cod)2 as the carbon–carbon bond insertion catalyst, new double alkyne insertion products and alkene isomerization products were observed. PMID:20419110

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

    SciTech Connect

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

    2003-12-11

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

  9. Mechanisms of Enzyme-Catalyzed Reduction of Two Carcinogenic Nitro-Aromatics, 3-Nitrobenzanthrone and Aristolochic Acid I: Experimental and Theoretical Approaches

    PubMed Central

    Stiborová, Marie; Frei, Eva; Schmeiser, Heinz H.; Arlt, Volker M.; Martínek, Václav

    2014-01-01

    This review summarizes the results found in studies investigating the enzymatic activation of two genotoxic nitro-aromatics, an environmental pollutant and carcinogen 3-nitrobenzanthrone (3-NBA) and a natural plant nephrotoxin and carcinogen aristolochic acid I (AAI), to reactive species forming covalent DNA adducts. Experimental and theoretical approaches determined the reasons why human NAD(P)H:quinone oxidoreductase (NQO1) and cytochromes P450 (CYP) 1A1 and 1A2 have the potential to reductively activate both nitro-aromatics. The results also contributed to the elucidation of the molecular mechanisms of these reactions. The contribution of conjugation enzymes such as N,O-acetyltransferases (NATs) and sulfotransferases (SULTs) to the activation of 3-NBA and AAI was also examined. The results indicated differences in the abilities of 3-NBA and AAI metabolites to be further activated by these conjugation enzymes. The formation of DNA adducts generated by both carcinogens during their reductive activation by the NOQ1 and CYP1A1/2 enzymes was investigated with pure enzymes, enzymes present in subcellular cytosolic and microsomal fractions, selective inhibitors, and animal models (including knock-out and humanized animals). For the theoretical approaches, flexible in silico docking methods as well as ab initio calculations were employed. The results summarized in this review demonstrate that a combination of experimental and theoretical approaches is a useful tool to study the enzyme-mediated reaction mechanisms of 3-NBA and AAI reduction. PMID:24918288

  10. 13C NMR Characterization of an Exchange Reaction between CO and CO2 Catalyzed by Carbon Monoxide Dehydrogenase†

    PubMed Central

    2008-01-01

    Carbon monoxide dehydrogenase (CODH) catalyzes the reversible oxidation of CO to CO2 at a nickel?iron?sulfur cluster (the C-cluster). CO oxidation follows a ping-pong mechanism involving two-electron reduction of the C-cluster followed by electron transfer through an internal electron transfer chain to external electron acceptors. We describe 13C NMR studies demonstrating a CODH-catalyzed steady-state exchange reaction between CO and CO2 in the absence of external electron acceptors. This reaction is characterized by a CODH-dependent broadening of the 13CO NMR resonance; however, the chemical shift of the 13CO resonance is unchanged, indicating that the broadening is in the slow exchange limit of the NMR experiment. The 13CO line broadening occurs with a rate constant (1080 s?1 at 20 °C) that is approximately equal to that of CO oxidation. It is concluded that the observed exchange reaction is between 13CO and CODH-bound 13CO2 because 13CO line broadening is pH-independent (unlike steady-state CO oxidation), because it requires a functional C-cluster (but not a functional B-cluster) and because the 13CO2 line width does not broaden. Furthermore, a steady-state isotopic exchange reaction between 12CO and 13CO2 in solution was shown to occur at the same rate as that of CO2 reduction, which is approximately 750-fold slower than the rate of 13CO exchange broadening. The interaction between CODH and the inhibitor cyanide (CN?) was also probed by 13C NMR. A functional C-cluster is not required for 13CN? broadening (unlike for 13CO), and its exchange rate constant is 30-fold faster than that for 13CO. The combined results indicate that the 13CO exchange includes migration of CO to the C-cluster, and CO oxidation to CO2, but not release of CO2 or protons into the solvent. They also provide strong evidence of a CO2 binding site and of an internal proton transfer network in CODH. 13CN? exchange appears to monitor only movement of CN? between solution and its binding to and release from CODH. PMID:18589895

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

    E-print Network

    Miller, Karen M. (Karen Marie)

    2005-01-01

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

  12. [Pyrophosphate analogs in the pyrophosphorolysis reaction catalyzed by Escherichia coli RNA polymerase].

    PubMed

    Rozovskaia, T A; Chenchik, A A; Tarusova, N B; Bibilashvili, R Sh; Khomutov, R M

    1981-01-01

    Processive pyrophosphorolysis of RNA from ternary RNA polymerase-nascent RNA-delta D111 T7 DNA complex has been followed in the absence of nucleoside triphosphates. Series of inorganic pyrophosphate analogs were investigated for their ability to sustain the reaction and to compete with inorganic pyrophosphate for the reaction. Methylenediphosphonic, imidodiphosphonic, phosphonacetic acids, inorganic triphosphate, methylenediphosphonic and phosphate were found to be capable of substituting the inorganic pyrophosphate in RNA degradation reaction with tantamount efficiency. They give rise to nucleoside monophosphates for phosphonoacetic acid, nucleoside triphosphates for inorganic pyrophosphate and inorganic triphosphate, nucleoside triphosphates analogs for methylenediphosphonic, imidodiphosphonic acids and methylenediphosphonic acid phosphate as the low molecular weight product of the reaction. The problem of specific interaction of RNA polymerase with nucleoside triphosphates and inorganic pyrophosphate is discussed in the terms of structural requirements for the compounds to be a potent substrate for RNA polymerase. PMID:6275257

  13. DNA-Catalyzed Henry Reaction in Pure Water and the Striking Influence of Organic Buffer Systems.

    PubMed

    Häring, Marleen; Pérez-Madrigal, Maria M; Kühbeck, Dennis; Pettignano, Asja; Quignard, Françoise; Díaz, David Díaz

    2015-01-01

    In this manuscript we report a critical evaluation of the ability of natural DNA to mediate the nitroaldol (Henry) reaction at physiological temperature in pure water. Under these conditions, no background reaction took place (i.e., control experiment without DNA). Both heteroaromatic aldehydes (e.g., 2-pyridinecarboxaldehyde) and aromatic aldehydes bearing strong or moderate electron-withdrawing groups reacted satisfactorily with nitromethane obeying first order kinetics and affording the corresponding ?-nitroalcohols in good yields within 24 h. In contrast, aliphatic aldehydes and aromatic aldehydes having electron-donating groups either did not react or were poorly converted. Moreover, we discovered that a number of metal-free organic buffers efficiently promote the Henry reaction when they were used as reaction media without adding external catalysts. This constitutes an important observation because the influence of organic buffers in chemical processes has been traditionally underestimated. PMID:25749682

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

    EPA Science Inventory

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

  15. Metal-Catalyzed Double Migratory Cascade Reactions of Propargylic Esters and Phosphates

    PubMed Central

    Shiroodi, Roohollah Kazem

    2013-01-01

    Propargylic esters and phosphates are easily accessible substrates, which exhibit rich and tunable reactivities in the presence of transition metal catalysts. ?-acidic metals, mostly gold and platinum salts, activate these substrates for an initial 1,2- or 1,3-acyloxy and phosphatyloxy migration processes to form reactive intermediates. These intermediates are able to undergo further cascade reactions leading to a variety of diverse structures. This tutorial review systematically introduces the double migratory reactions of propargylic esters and phosphates as a novel synthetic method, in which further cascade reaction of the reactive intermediate is accompanied by a second migration of a different group, thus offering a rapid route to a wide range of functionalized products. The serendipitous observations, as well as designed approaches involving the double migratory cascade reactions, will be discussed with emphasis placed on the mechanistic aspects and the synthetic utilities of the obtained products. PMID:23443274

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

    E-print Network

    Müller, Peter

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

  17. An Efficient Process for Pd-Catalyzed C?N Cross-Coupling Reactions of Aryl Iodides: Insight Into Controlling Factors

    E-print Network

    Fors, Brett P.

    An investigation into Pd-catalyzed C?N cross-coupling reactions of aryl iodides is described. NaI is shown to have a significant inhibitory effect on these processes. By switching to a solvent system in which the iodide ...

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

    E-print Network

    Toste, Dean

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Zhou, Xiaoli; Liu, Meiling; Lai, Yingjun; Yang, Tangtao

    2014-01-01

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

  1. Molybdenum Reduction to Molybdenum Blue in Serratia sp. Strain DRY5 Is Catalyzed by a Novel Molybdenum-Reducing Enzyme

    PubMed Central

    Shukor, M. Y.; Halmi, M. I. E.; Rahman, M. F. A.; Shamaan, N. A.; Syed, M. A.

    2014-01-01

    The first purification of the Mo-reducing enzyme from Serratia sp. strain DRY5 that is responsible for molybdenum reduction to molybdenum blue in the bacterium is reported. The monomeric enzyme has an apparent molecular weight of 105?kDalton. The isoelectric point of this enzyme was 7.55. The enzyme has an optimum pH of 6.0 and maximum activity between 25 and 35°C. The Mo-reducing enzyme was extremely sensitive to temperatures above 50°C (between 54 and 70°C). A plot of initial rates against substrate concentrations at 15?mM 12-MP registered a Vmax for NADH at 12.0?nmole Mo blue/min/mg protein. The apparent Km for NADH was 0.79?mM. At 5?mM NADH, the apparent Vmax and apparent Km values for 12-MP of 12.05?nmole/min/mg protein and 3.87?mM, respectively, were obtained. The catalytic efficiency (kcat/Km) of the Mo-reducing enzyme was 5.47?M?1?s?1. The purification of this enzyme could probably help to solve the phenomenon of molybdenum reduction to molybdenum blue first reported in 1896 and would be useful for the understanding of the underlying mechanism in molybdenum bioremediation involving bioreduction. PMID:24724104

  2. Metal-organic frameworks catalyzed C-C and C-heteroatom coupling reactions.

    PubMed

    Dhakshinamoorthy, Amarajothi; Asiri, Abdullah M; Garcia, Hermenegildo

    2015-04-01

    Metal organic frameworks (MOFs) are porous crystalline solids whose structure is formed by metal ions or clusters of a few metal ions held in place by bi- or multipodal organic linkers. In some cases, the metal nodes in MOFs have exchangeable coordination positions that allow them to participate as active sites promoting organic reactions. There is much current interest in exploiting the advantages that MOFs offer as catalysts, including a large surface area, high metal content, flexibility in the design of the active sites in the framework, together with the easy synthesis of these materials. In the present review we describe the use of MOFs as catalysts to promote cross-coupling reactions involving organometallic reaction intermediates and catalysis by Lewis acid sites. These types of reactions are of large synthetic utility due to the high yields achieved, mild conditions and compatibility with other functional groups. The content includes C-C bond forming reactions, such as Suzuki-Miyaura, Mizoroki-Heck, Sonogashira, Stille and Ullmann, but also C-O and C-N cross-couplings. The final section summarizes our views on future developments and targets in these types of reactions. The core of the review is references that have appeared in 2010 or after, which give an idea of the novelty and current interest in this area. PMID:25608717

  3. A new approach to carbon-carbon bond formation: Development of aerobic Pd-catalyzed reductive coupling reactions of organometallic reagents and styrenes

    PubMed Central

    Gligorich, Keith M.; Iwai, Yasumasa; Cummings, Sarah A.; Sigman, Matthew S.

    2009-01-01

    Alkenes are attractive starting materials for organic synthesis and the development of new selective functionalization reactions are desired. Previously, our laboratory discovered a unique Pd-catalyzed hydroalkoxylation reaction of styrenes containing a phenol. Based upon deuterium labeling experiments, a mechanism involving an aerobic alcohol oxidation coupled to alkene functionalization was proposed. These results inspired the development of a new Pd-catalyzed reductive coupling reaction of alkenes and organometallic reagents that generates a new carbon-carbon bond. Optimization of the conditions for the coupling of both organostannanes and organoboronic esters is described and the initial scope of the transformation is presented. Additionally, several mechanistic experiments are outlined and support the rationale for the development of the reaction based upon coupling alcohol oxidation to alkene functionalization. PMID:20161306

  4. Kinetic Isotope Effects for Alkaline Phosphatase Reactions: Implications for the Role of Active-Site Metal Ions in Catalysis

    E-print Network

    Herschlag, Dan

    Kinetic Isotope Effects for Alkaline Phosphatase Reactions: Implications for the Role of Active@stanford.edu; hengge@cc.usu.edu Abstract: Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested kinetic isotope effects (KIEs) for AP-catalyzed hydrolysis reactions with several phosphate monoester

  5. Homogeneous silicone modified primary amine-Brønsted acid salt catalyzed aldol reaction: unexpected synergistic effect of polysiloxane with remarkable improvement of efficiency and stereoselectivity

    Microsoft Academic Search

    Li-Wen Xu; Ya-Dong Ju; Li Li; Hua-Yu Qiu; Jian-Xiong Jiang; Guo-Qiao Lai

    2008-01-01

    We have developed a new strategy to improve the stereoselectivity in enamine catalysis by the introduction of super-hydrophobic long-chain silicone\\/polysiloxane as support\\/functional group for a model aldol reaction. The homogeneous direct aldol reaction of cyclic ketones with different aromatic aldehydes catalyzed by polysiloxane-derived primary amines has been reported with high yields, good diastereoselectivity, and up to 99% ee.

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

    ERIC Educational Resources Information Center

    Barlag, Rebecca; Nyasulu, Frazier

    2010-01-01

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

  7. NHC-Catalyzed Reactions of Aryloxyacetaldehydes: A Domino Elimination/Conjugate Addition/Acylation Process for the Synthesis of Substituted Coumarins

    PubMed Central

    Phillips, Eric M.; Wadamoto, Manabu; Roth, Howard S.; Ott, Andrew W.; Scheidt, Karl A.

    2009-01-01

    N-Heterocyclic carbenes (NHCs) catalyze a domino Michael addition/acylation reaction to form 3,4-dihydrocoumarins. The reaction proceeds through addition of the NHC to an aryloxyaldehyde followed by elimination of a phenoxide leaving group, generating an enol intermediate. This transient nucleophile generated in situ performs a 1,4-addition onto a conjugate acceptor and the carbene catalyst is regenerated upon acylation of the phenoxide anion resulting in formation of 3,4-dihydrocoumarins. PMID:19049403

  8. Immune response to enzyme replacement therapy: clinical signs of hypersensitivity reactions and altered enzyme distribution in a high titre rat model

    Microsoft Academic Search

    Doug A. Brooks; John J. Hopwood; Barbara M. King

    1998-01-01

    Immune responses to enzyme replacement therapy (ERT) have been reported and can result in a hypersensitivity\\/anaphylactic reaction during or immediately after enzyme infusion. We have investigated the infusion of the lysosomal enzyme N-acetylgalactosamine 4-sulphatase (4-sulphatase) into immunized, high titre rats as a model of immune response to ERT. To simulate ERT, high and low titre rats were infused with different

  9. [Molybdenum-catalyzed heteroatom removal reactions: The effect of promoters on reaction]. [Annual report, December 1, 1992--November 1, 1993

    SciTech Connect

    Friend, C.M.

    1993-12-01

    A general method was developed for determine mechanisms for surface reactions, and desulfurization and deoxygenation processes were modeled on clean and S-covered Mo(110). Efforts were aimed at accurately describing the bonding and structure of adsorbed reactants. Thiol desulfurization on Co-covered Mo(110) was studied. Kinetics and selectivity for thiol hydrogenolysis depend on structure and composition of interface.

  10. Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products

    E-print Network

    Achyuthan, Komandoor

    2013-01-01

    enzyme [10,11] and further predicated on its high efficiency ligninlignin [6] either directly through the oxidative, demethylating and demethoxylating activities of phenoloxidative enzymesenzymes for biofuels is the ?-glucosidase, especially those involved in hydrolyzing the lignin

  11. A Group of Sequence-Related Sphingomonad Enzymes Catalyzes Cleavage of ?-Aryl Ether Linkages in Lignin ?-Guaiacyl and ?-Syringyl Ether Dimers

    PubMed Central

    2014-01-01

    Lignin biosynthesis occurs via radical coupling of guaiacyl and syringyl hydroxycinnamyl alcohol monomers (i.e., “monolignols”) through chemical condensation with the growing lignin polymer. With each chain-extension step, monolignols invariably couple at their ?-positions, generating chiral centers. Here, we report on activities of bacterial glutathione-S-transferase (GST) enzymes that cleave ?-aryl ether bonds in lignin dimers that are composed of different monomeric units. Our data reveal that these sequence-related enzymes from Novosphingobium sp. strain PP1Y, Novosphingobium aromaticivorans strain DSM12444, and Sphingobium sp. strain SYK-6 have conserved functions as ?-etherases, catalyzing cleavage of each of the four dimeric ?-keto-?-aryl ether-linked substrates (i.e., guaiacyl-?-guaiacyl, guaiacyl-?-syringyl, syringyl-?-guaiacyl, and syringyl-?-syringyl). Although each ?-etherase cleaves ?-guaiacyl and ?-syringyl substrates, we have found that each is stereospecific for a given ?-enantiomer in a racemic substrate; LigE and LigP ?-etherase homologues exhibited stereospecificity toward ?(R)-enantiomers whereas LigF and its homologues exhibited ?(S)-stereospecificity. Given the diversity of lignin’s monomeric units and the racemic nature of lignin polymers, we propose that bacterial catabolic pathways have overcome the existence of diverse lignin-derived substrates in nature by evolving multiple enzymes with broad substrate specificities. Thus, each bacterial ?-etherase is able to cleave ?-guaiacyl and ?-syringyl ether-linked compounds while retaining either ?(R)- or ?(S)-stereospecificity. PMID:25232892

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

    PubMed

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

    2013-01-23

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

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

    PubMed Central

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

    2014-01-01

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

  14. A Bifunctional Enzyme (Delta^1Pyrroline5Carboxylate Synthetase) Catalyzes the First Two Steps in Proline Biosynthesis in Plants

    Microsoft Academic Search

    Chien-An A. Hu; Ashton J. Delauney; Desh Pal S. Verma

    1992-01-01

    Many plants synthesize and accumulate proline in response to osmotic stress. Despite the importance of this pathway, however, the exact metabolic route and enzymes involved in the synthesis of proline in plants have not been unequivocally identified. We report here the isolation of a mothbean (Vigna aconitifolia) cDNA clone encoding a bifunctional enzyme, Delta^1-pyrroline-5-carboxylate synthetase (P5CS), with both gamma-glutamyl kinase

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

    E-print Network

    Minnesota, University of

    Isotope Effects, Enzyme Kinetics, and Solvent Effects. Abstract: A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: (1) combined quantum for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble

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

    PubMed

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

    2013-11-01

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

  17. Palladium-Catalyzed Reactions of Arylindium Reagents Prepared Directly from Aryl Iodides and Indium Metal

    PubMed Central

    Papoian, Vardan

    2008-01-01

    Treatment of aryl iodides with indium metal in the presence of lithium chloride leads to the formation of an organoindium reagent capable of participating in cross-coupling reactions under transition-metal catalysis. Combination with aryl halides in the presence of 5 mol% Cl2Pd(dppf) furnishes biaryl compounds in good yields; similarly, reaction with acyl halides or allylic acetates/carbonates in the presence of 5–10 mol % palladium catalyst leads to arylketones and allylic substitution products, respectively, in moderate yields. The reactions are tolerant of the presence of protic solvents, and ~85% of the indium metal employed can be recovered by reduction of the residual indium salts with zinc(0). PMID:18722408

  18. Primary and secondary reaction pathways in ruthenium-catalyzed hydrocarbon synthesis

    SciTech Connect

    Madon, R.J.; Reyes, S.C.; Iglesia, E. (Exxon Research and Engineering Co., Annandale, NJ (United States))

    1991-10-03

    Residence time studies show that n-paraffins, {alpha}-olefins, and cis-2-olefins are primary products during hydrocarbon synthesis on Ru catalysts. Their formation, as well as that of branched isomers, is consistent with previously proposed surface reactions of alkyl groups on metal surfaces. Secondary hydrogenation and hydrogenolysis of {alpha}-olefins are inhibited by the water product of the synthesis step. However, {alpha}-olefin readsorption and surface chain initiation and cis-to-trans isomerization take place as secondary reactions. The decrease in {alpha}-olefin readsorption and surface chain initiation and cis-to-trans isomerization take place as secondary reactions. The decrease in {alpha}-olefin readsorption and surface chain initiation and cis-to-trans isomerization take place as secondary reactions. The decrease in {alpha}-olefin readsorption and surface chain initiation and cis-to-trans isomerization take place as secondary reactions. The decrease in {alpha}-olefin selectivity with increasing CO conversion and molecular size reflects the greater extent of readsorption as bed and pore residence times of {alpha}-olefin increase. Readsorption of {alpha}-olefins and chain initiation increases with molecular size because the rate of removal of olefins from liquid-filled catalyst pores is decreased due to intraparticle diffusion limitations. This diffusion-enhanced olefin readsorption accounts for the observed deviations of carbon number distributions from those predicted by Flory polymerization kinetics. Chain growth probability increases with chain length until an asymptotic value is reached. Readsorption decreases the contribution of termination via hydrogen abstraction to chain growth kinetics. In effect, differences in selectivity between small and large hydrocarbons are due to the increasing influence of pore residence times and the decreasing influence of bed residence times on secondary reactions as olefin size increases.

  19. Hydrogen-borrowing and interrupted-hydrogen-borrowing reactions of ketones and methanol catalyzed by iridium.

    PubMed

    Shen, Di; Poole, Darren L; Shotton, Camilla C; Kornahrens, Anne F; Healy, Mark P; Donohoe, Timothy J

    2015-01-26

    Reported herein is the use of catalytic [{Ir(cod)Cl}2 ] to facilitate hydrogen-borrowing reactions of ketone enolates with methanol at 65?°C. An oxygen atmosphere accelerates the process, and when combined with the use of a bulky monodentate phosphine ligand, interrupts the catalytic cycle by preventing enone reduction. Subsequent addition of pro-nucleophiles to the reaction mixture allowed a one-pot methylenation/conjugate addition protocol to be developed, which greatly expands the range of products that can be made by this methodology. PMID:25491653

  20. Hydrogen-Borrowing and Interrupted-Hydrogen-Borrowing Reactions of Ketones and Methanol Catalyzed by Iridium**

    PubMed Central

    Shen, Di; Poole, Darren L; Shotton, Camilla C; Kornahrens, Anne F; Healy, Mark P; Donohoe, Timothy J

    2015-01-01

    Reported herein is the use of catalytic [{Ir(cod)Cl}2] to facilitate hydrogen-borrowing reactions of ketone enolates with methanol at 65 °C. An oxygen atmosphere accelerates the process, and when combined with the use of a bulky monodentate phosphine ligand, interrupts the catalytic cycle by preventing enone reduction. Subsequent addition of pro-nucleophiles to the reaction mixture allowed a one-pot methylenation/conjugate addition protocol to be developed, which greatly expands the range of products that can be made by this methodology. PMID:25491653