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1

Stochastic Simulation of Enzyme-Catalyzed Reactions with Disparate Timescales  

E-print Network

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

Paul, Mark

2

Microorganisms detected by enzyme-catalyzed reaction  

NASA Technical Reports Server (NTRS)

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

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

1966-01-01

3

Representing Rate Equations for Enzyme-Catalyzed Reactions  

ERIC Educational Resources Information Center

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…

Ault, Addison

2011-01-01

4

Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes.  

PubMed

The intermolecular asymmetric Stetter reaction is an almost unexplored transformation for biocatalysts. Previously reported thiamine diphosphate (ThDP)-dependent PigD from Serratia marcescens is the first enzyme identified to catalyze the Stetter reaction of ?,?-unsaturated ketones (Michael acceptor substrates) and ?-keto acids. PigD is involved in the biosynthesis of the potent cytotoxic agent prodigiosin. Here, we describe the investigation of two new ThDP-dependent enzymes, SeAAS from Saccharopolyspora erythraea and HapD from Hahella chejuensis. Both show a high degree of homology to the amino acid sequence of PigD (39 and 51 %, respectively). The new enzymes were heterologously overproduced in Escherichia coli, and the yield of soluble protein was enhanced by co-expression of the chaperone genes groEL/ES. SeAAS and HapD catalyze intermolecular Stetter reactions in vitro with high enantioselectivity. The enzymes possess a characteristic substrate range with respect to Michael acceptor substrates. This provides support for a new type of ThDP-dependent enzymatic activity, which is abundant in various species and not restricted to prodigiosin biosynthesis in different strains. Moreover, PigD, SeAAS, and HapD are also able to catalyze asymmetric carbon-carbon bond formation reactions of aldehydes and ?-keto acids, resulting in 2-hydroxy ketones. PMID:24957249

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

2014-12-01

5

Method for predicting enzyme-catalyzed reactions  

DOEpatents

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.

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

2013-03-19

6

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

E-print Network

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

Magee, Joseph W.

7

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

E-print Network

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

van Vliet, Lucas J.

8

Helical polymer as mimetic enzyme catalyzing asymmetric aldol reaction.  

PubMed

This Communication reports optically active helical substituted polyacetylenes which solely catalyzed asymmetric Aldol reaction between cyclohexanone and p-nitrobenzaldehyde; more importantly the helical structures are found to play crucial roles in the asymmetric catalysis, with a remarkable yield and ee (both up to 80%). A synergic effect is observed between the helical structures in the polymer main chains and the pendent prolinamide moieties for successfully catalyzing the asymmetric reaction. The role of the helical polymer backbones is further verified by tuning the relative helical structure content. PMID:22318956

Zhang, Dongyue; Ren, Chonglei; Yang, Wantai; Deng, Jianping

2012-04-23

9

Measurement of positional isotope exchange rates in enzyme catalyzed reactions by fast atom bombardment mass spectrometry  

E-print Network

MEASUREMENT OF POSITIONAL ISOTOPE EXCHANGE RATES IN ENZYME CATALYZED REACTIONS BY FAST ATOM BOMBARDMENT MASS SPECTROMETRY A Thesis by LARRY NAYNE HILSCHER Submitted to the Gradu te College of Texas A&M University in partial fulfil" mert... of the requiremer ts for the degree of MASTEP. QF SCIENCE August 1985 Major Subject: Chemistry MEASUREMENT OF POSITIONAL ISOTOPE EXCHANGE RATES IN ENZYME CATALYZED REACTIONS BY FAST ATOM BOMBARDMENT MASS SPECTROMETRY A Thesis LARRY NAYNE HILSCHER Approved...

Hilscher, Larry Wayne

1985-01-01

10

Stereoselective synthesis of caffeic acid amides via enzyme-catalyzed asymmetric aminolysis reaction.  

PubMed

In this study, a new method was developed to prepare enantiopure caffeic acid amides by enzyme-catalyzed asymmetric aminolysis reaction. Methoxymethyl chloride (MOMCl) was first introduced as a protective and esterified reagent to obtain the MOM-protected caffeic acid MOM ester 1d. Aminolysis reaction occurred between 1d and (R, S)-?-phenylethylamine in the presence of an immobilized lipase (Novozym 435) from Candida antarctica. Compared with the methyl-protected caffeic acid methyl ester 1c, 1d as substrate improved the lipase-catalyzed reaction rate by 5.5-fold. After Novozym 435-catalyzed aminolysis reaction was established, we evaluated the effects of synthesis parameters on the catalytic activity and enantioselectivity of Novozym 435. A reaction conversion rate of 25.5% and an E value of >100 were achieved under the following optimum conditions: reaction solvent, anhydrous isooctane; reaction temperature, 70°C; reaction time, 24h; ester-to-amine substrate molar ratio, 1:40; and enzyme additive amount, 40 mg. Kinetic and thermodynamic analyses were conducted to determine the main factors affecting enantiomeric discrimination. Novozym 435 still showed 80% of its initial activity after recycling five times. Highly optically pure caffeic acid amides with an enantiomeric excess of 98.5% were finally obtained by HCl deprotection. The established enzyme-catalyzed asymmetric aminolysis method in this study might be used to prepare other caffeic acid amides. PMID:24056082

Xiao, Peiliang; Zhang, Suoqin; Ma, Huayu; Zhang, Aijun; Lv, Xiaoli; Zheng, Liangyu

2013-12-01

11

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

SciTech Connect

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

Massey, I.J.; Aitken, M.D.; Ball, L.M.; Heck, P.E. (Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Environmental Sciences and Engineering)

1994-11-01

12

Energy Diagrams for Enzyme-Catalyzed Reactions: Concepts and Misconcepts  

ERIC Educational Resources Information Center

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

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

2003-01-01

13

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

SciTech Connect

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

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

1988-08-17

14

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

15

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

SciTech Connect

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.

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

2010-10-28

16

Enzyme-catalyzed polymerization to functional polymers  

Microsoft Academic Search

In this article, described are our recent advances in enzymatic polymerization, defined as chemical polymer syntheses in vitro (in test tubes) via non-biosynthetic pathways catalyzed by an isolated enzyme. The major target macromolecules formed via the enzymatic polymerizations in this article are polyesters and polyphenols. For synthesis of polyesters, hydrolases are used as catalyst; hydrolases, enzymes catalyzing a bond-cleavage reaction

Hiroshi Uyama; Shiro Kobayashi

2002-01-01

17

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

ERIC Educational Resources Information Center

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

Bozlee, Brian J.

2007-01-01

18

Enzyme Reactions  

NSDL National Science Digital Library

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.

School, Minerva D.

2011-10-03

19

Catalyzed enzyme electrodes  

DOEpatents

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.

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

20

The study of the stereospecificity in enzyme-catalyzed reactions of glyceryl acetonide derivatives  

E-print Network

, valerate and octanoate, or cyclohexylidene glycerol acetate in the presence of Porcine Pancreatic Lipase or Pig Liver Esterase. However, only very low enantiomeric excess was found. Double resolution techniques were then investigated with glycerol... and esters used as intermediates in chiral building block synthesis. ~ The reverse reaction, esterification or even transesterification, carried out with the same enzymes in organic solvents has also been developed as a complementary strategy. a Lipases...

Chauvet, Christine Jeanne

1987-01-01

21

Assembly of zinc finger motif-fused enzymes on a dsDNA scaffold for catalyzing consecutive reactions with a proximity effect.  

PubMed

The feasibility of assembling enzymes, catalyzing consecutive reactions, on to a double-stranded DNA (dsDNA) scaffold utilizing zinc finger motifs is described. The catalytic activities of two zinc finger motif-fused enzymes catalyzing a bioluminescence reaction with energy recycling, namely pyruvate phosphate dikinase and firefly luciferase, have been evaluated. Bioluminescence measurements with dsDNA scaffolds coding a different distance between the binding sites for each zinc finger motif-fused enzyme confirmed the effect of the distance, proving the proximity effect of ATP recycling presumed to be the result of efficient intermediate diffusion. Thus, fusion to zinc finger motifs offers a promising option for the assembly of bi-enzymes, catalyzing a consecutive reaction, onto a dsDNA scaffold with a proximity effect. PMID:25216646

Funabashi, Hisakage; Yanagi, Satoshi; Suzuki, Shigeya; Mie, Masayasu; Kobatake, Eiry

2015-01-01

22

Enzyme Reactions  

NSDL National Science Digital Library

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.

Maryland Virtual High School

23

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

ERIC Educational Resources Information Center

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…

Sims, Paul A.

2009-01-01

24

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

PubMed

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

Natsume, Tomotaka; Yoshimoto, Makoto

2014-03-12

25

Stoichiometry of the Redox Neutral Deamination and Oxidative Dehydrogenation Reactions Catalyzed by the Radical SAM Enzyme DesII  

PubMed Central

DesII from Streptomyces venezuelae is a radical SAM (S-adenosyl-l-methionine) enzyme that catalyzes the deamination of TDP-4-amino-4,6-dideoxy-d-glucose to form TDP-3-keto-4,6-dideoxy-d-glucose in the biosynthesis of TDP-d-desosamine. DesII also catalyzes the dehydrogenation of the non-physiological substrate TDP-d-quinovose to TDP-3-keto-6-deoxy-d-glucose. These properties prompted an investigation of how DesII handles SAM in the redox neutral deamination versus the oxidative dehydrogenation reactions. This work was facilitated by the development of an enzymatic synthesis of TDP-4-amino-4,6-dideoxy-d-glucose that couples a transamination equilibrium to the thermodynamically favorable oxidation of formate. In this study, DesII is found to consume SAM versus TDP-sugar with stoichiometries of 0.96 ± 0.05 and 1.01 ± 0.05 in the deamination and dehydrogenation reactions, respectively, using Na2S2O4 as the reductant. Importantly, no significant change in stoichiometry is observed when the flavodoxin/flavodoxin NADP+ oxidoreductase/NADPH reducing system is used in place of Na2S2O4. Moreover, there is no evidence of an uncoupled or abortive process in the deamination reaction, as indicated by the observation that dehydrogenation can take place in the absence of an external source of reductant whereas deamination cannot. Mechanistic and biochemical implications of these results are discussed. PMID:20121093

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

2010-01-01

26

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

Microsoft Academic Search

The green plant enzyme chlorophyllase (EC 3.1.1.14, chlorophyll chlorophyllido-hydroase) has been used for the synthesis of a variety of primary alcohol and diol esters of chlorophyll a, bacteriochlorophyll a, and pyrobacteriochlorophyll a. Green plant chlorophyllase accepts a much larger range of alcohol and chlorophyll substrates than had previously been realized. Thus, chlorophyllide and bacteriochlorophyllide esters of primary alcohols such as

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

1988-01-01

27

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

ERIC Educational Resources Information Center

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…

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

2010-01-01

28

Enzyme-Catalyzed Processes in Organic Solvents  

Microsoft Academic Search

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,

Aleksey Zaks; Alexander M. Klibanov

1985-01-01

29

Visualization of enzyme-catalyzed reactions using pH indicators: rapid screening of hydrolase libraries and estimation of the enantioselectivity  

Microsoft Academic Search

The use of pH indicators to monitor hydrolase-catalyzed reactions is described. The formation of acid following an enzyme-mediated hydrolysis causes a drop in the pH that can be visualized by a change in the color of the indicator-containing solution. The best indicators are those showing a color transition within the operational pH range of the hydrolases, like bromothymol blue and

Francisco Mor??s-Varas; Amit Shah; John Aikens; Neelesh P Nadkarni; J. David Rozzell; David C Demirjian

1999-01-01

30

Fatty acid synthetase. A steady state kinetic analysis of the reaction catalyzed by the enzyme from pigeon liver.  

PubMed

The kinetic mechanism of pigeon liver fatty acid synthetase action has been studied using steady state kinetic analysis. Initial velocity studies are consistent with an earlier suggestion that the enzyme catalyzes this reaction by a seven-site ping-pong mechanism. Although the range of substrate concentrations that could be used was limited by several factors, the initial velocity patterns showing the relationship between the substrates acetyl coenzyme CoA, malonyl-CoA, and NADPH appear to be a series of parallel lines, regardless of which substrate is varied at fixed levels of a second substrate. However, two of the substrates, acetyl-CoA and malonly-CoA, apparently exhibit a competitive substrate inhibition with respect to each other, but NADPH shows no inhibition of any kind. Product inhibition patterns suggest that free CoA is competitive versus acetyl-CoA and malonyl-CoA and is uncompetitive versus NADPH, and that NADP+ is competitive versus NADPH and uncompetitive versus acetyl-CoA or malonyl-CoA. These results are consistent with a seven-site ping-pong mechanism with intermediates covalently bound to 4'-phosphopantetheine (part of acyl carrier protein). Double competitive substrate inhibition by acetyl-CoA and malonyl-CoA is consistent with the rate equation derived for the over-all mechanism. The kinetic mechanism developed from these results is capable of explaining the formation of fatty acids from malonyl-CoA and NADPH alone (Katiyar, S. S., Briedis, A. V., and Porter, J. W. (1974) Arch. Biochem. Biophys. 162, 412-420) and also the formation of triacetic acid lactone from either malonyl-CoA alone or acetyl-CoA plus malonyl-CoA. PMID:235526

Katiyar, S S; Cleland, W W; Porter, J W

1975-04-10

31

Gold-Catalyzed Multi-Component Reactions  

NASA Astrophysics Data System (ADS)

The following sections are included: * Introduction * Gold-Catalyzed Three-Component Reactions * Gold-Catalyzed Three-Component Reactions/Tandem Cyclization * Concluding Remarks * Acknowledgments * References

Skouta, Rachid; Li, Chao-Jun

2014-04-01

32

Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination  

PubMed Central

The kinetics of the glucose oxidase-catalyzed reaction of glucose with O2, which produces gluconic acid and hydrogen peroxide, and the catalase-assisted breakdown of hydrogen peroxide to generate oxygen, have been measured via the rate of O2 depletion or production. The O2 concentrations in air-saturated phosphate-buffered salt solutions were monitored by measuring the decay of phosphorescence from a Pd phosphor in solution; the decay rate was obtained by fitting the tail of the phosphorescence intensity profile to an exponential. For glucose oxidation in the presence of glucose oxidase, the rate constant determined for the rate-limiting step was k = (3.0 ± 0.7) ×104 M?1s?1 at 37°C. For catalase-catalyzed H2O2 breakdown, the reaction order in [H2O2] was somewhat greater than unity at 37°C and well above unity at 25°C, suggesting different temperature dependences of the rate constants for various steps in the reaction. The two reactions were combined in a single experiment: addition of glucose oxidase to glucose-rich cell-free media caused a rapid drop in [O2], and subsequent addition of catalase caused [O2] to rise and then decrease to zero. The best fit of [O2] to a kinetic model is obtained with the rate constants for glucose oxidation and peroxide decomposition equal to 0.116 s?1 and 0.090 s?1 respectively. Cellular respiration in the presence of glucose was found to be three times as rapid as that in glucose-deprived cells. Added NaCN inhibited O2 consumption completely, confirming that oxidation occurred in the cellular mitochondrial respiratory chain. PMID:19348778

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

2009-01-01

33

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

SciTech Connect

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

Kool, E.T.

1988-01-01

34

Strictosidine Synthase: Mechanism of a Pictet–Spengler Catalyzing Enzyme  

PubMed Central

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

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

2010-01-01

35

Isotope effects in the transient phases of the reaction catalyzed by ethanolamine ammonia-lyase: determination of the number of exchangeable hydrogens in the enzyme-cofactor complex.  

PubMed

Transient phases of the reaction catalyzed by ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been investigated by stopped-flow visible spectrophotometry and deuterium kinetic isotope effects. The cleavage of adenosylcobalamin (coenzyme B(12)) to form cob(II)alamin (B(12r)) with ethanolamine as the substrate occurred within the dead time of the instrument whenever coenzyme B(12) was preincubated with enzyme prior to mixing with substrate. The rate was, however, slowed sufficiently to be measured with perdeutero ethanolamine as the substrate. Optical spectra indicate that, during the steady states of the reactions with ethanolamine and with S-2-aminopropanol as substrates, approximately 90% of the active sites contain B(12r). Reformation of the carbon-cobalt bond of the cofactor occurs following depletion of substrate in the reaction mixtures, and the rate constant for this process reflects k(cat) of the respective substrates. This late phase of the reaction also exhibits (2)H isotope effects similar to those measured for the overall reaction with (2)H-labeled substrates. With unlabeled substrates, the rate of cofactor reassembly is independent of the number of substrate molecules turned over in the steady-state phase. However, with (2)H-labeled substrates, kinetic isotope effects appear in the reassembly phase, and these isotope effects are maximal after only approximately 2 equiv of substrate/active site are processed. With 5'-deuterated coenzyme B(12) and deuterated substrate, the isotope effect on reassembly is independent of the number of substrate molecules that are turned over. These results indicate that the pool of exchangeable hydrogens in the enzyme-cofactor complex is two-a finding consistent with the hydrogens in the C5' methylene of coenzyme B(12). PMID:11009622

Bandarian, V; Reed, G H

2000-10-01

36

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

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

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

2015-01-01

37

Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme.  

PubMed

The Pictet-Spengler reaction, which yields either a beta-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 beta-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 beta-carboline product is proposed from these data. PMID:18081287

Maresh, Justin J; Giddings, Lesley-Ann; Friedrich, Anne; Loris, Elke A; Panjikar, Santosh; Trout, Bernhardt L; Stöckigt, Joachim; Peters, Baron; O'Connor, Sarah E

2008-01-16

38

Enzyme Reaction Annotation Using Cloud Techniques  

PubMed Central

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

Huang, Chuan-Ching

2013-01-01

39

Controlling reaction specificity in pyridoxal phosphate enzymes  

PubMed Central

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

Toney, Michael D.

2012-01-01

40

Enzyme-catalyzed degradation of carbon nanomaterials  

NASA Astrophysics Data System (ADS)

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

Kotchey, Gregg P.

41

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

PubMed

Malic enzyme prepared and purified from Brevundimonas diminuta IFO13182 catalyzed the decarboxylation reaction of malate to pyruvate and CO2 using NAD+ as the coenzyme, and the reverse reaction was used in the present study for L-malic acid production with fixation of HCO3(-) as a model compound for carbon source. The L-malic acid production was based on electrochemical regeneration of NADH on a carbon plate electrode modified by layer-by-layer adsorption of polymer-bound mediator (Alginic acid bound viologen derivative, Alg-V), polymer-bound coenzyme (Alginic acid bound NAD+, Alg-NAD+), and lipoamide dehydrogenase (LipDH). Electrochemical reduction of immobilized NAD+ catalyzed by LipDH in a multilayer film was achieved, and the L-malic acid production with HCO3(-) fixation system with layer-by-layer immobilization of Alg-V/LipDH/Alg-NAD+/malic enzyme multilayer film on the electrode gave an L-malic acid production of nearly 11.9 mmol and an HCO3(-) fixation rate of nearly 47.4% in a buffer containing only KHCO3 and pyruvic acid potassium salt, using a cation exchange membrane. The total turnover number of NADH within 48 h was about 19,000, which suggests that efficient NADH regeneration and fast electron transfer were achieved within the multilayer film, and that the modified electrode is a potential method for the fixation of HCO3(-) without addition of free coenzyme. PMID:19147103

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

2009-01-01

42

Ruthenium-catalyzed regioselective allylic trifluoromethylthiolation reaction.  

PubMed

An efficient Ru-catalyzed regioselective allylic trifluoromethylthiolation reaction of allylic carbonates was developed. The linear allylic trifluoromethyl thioethers were obtained in 52-91% yields. Mechanistic investigation revealed that this reaction proceeds via a double allylic trifluoromethylthiolation sequence. PMID:25203498

Ye, Ke-Yin; Zhang, Xiao; Dai, Li-Xin; You, Shu-Li

2014-12-19

43

Surface catalyzed mercury transformation reactions  

NASA Astrophysics Data System (ADS)

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).

Varanasi, Patanjali

44

A model study of sequential enzyme reactions and electrostatic channeling  

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

45

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

Microsoft Academic Search

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

Diana Lindberg; Mario de la Fuente Revenga; Mikael Widersten

2010-01-01

46

Biginelli Reaction Catalyzed by Copper Nanoparticles  

PubMed Central

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

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

2012-01-01

47

Firefly bioluminescence: a mechanistic approach of luciferase catalyzed reactions.  

PubMed

Luciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two-step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH(2)), with ATP-Mg(2+) generating inorganic pyrophosphate and an intermediate luciferyl-adenylate (LH(2)-AMP); the second is the oxidation and decarboxylation of LH(2)-AMP to oxyluciferin, the light emitter, producing CO(2), AMP, and photons of yellow-green light (550- 570 nm). In a dark reaction LH(2)-AMP is oxidized to dehydroluciferyl-adenylate (L-AMP). Luciferase also shows acyl-coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl-coenzyme A (L-CoA), luciferyl-coenzyme A (LH(2)-CoA), and fatty acyl-CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3'-phosphate chain plus an intact terminal pyrophosphate moiety. The LH(2) stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D-LH(2) or L-LH(2), has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging. PMID:18949818

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

2009-01-01

48

Internal friction in enzyme reactions.  

PubMed

The empirical concept of internal friction was introduced 20 years ago. This review summarizes the results of experimental and theoretical studies that help to uncover the nature of internal friction. After the history of the concept, we describe the experimental challenges in measuring and interpreting internal friction based on the viscosity dependence of enzyme reactions. We also present speculations about the structural background of this viscosity dependence. Finally, some models about the relationship between the energy landscape and internal friction are outlined. Alternative concepts regarding the viscosity dependence of enzyme reactions are also discussed. PMID:23281036

Rauscher, Anna; Derényi, Imre; Gráf, László; Málnási-Csizmadia, András

2013-01-01

49

Polymerization of humic substances by an enzyme-catalyzed oxidative coupling  

NASA Astrophysics Data System (ADS)

A novel understanding of the structural features of humic substances supports the self-assembly supramolecular association of relatively small molecules rather than their polymeric nature. An increase in the conformational stability of humus may thus be achieved through promotion of intermolecular covalent bondings between heterogeneous humic molecules by an enzyme-catalyzed oxidative reaction. We present evidence from high performance size exclusion chromatography (HPSEC) and diffuse reflectance infrared spectrometry (DRIFT) that oxidation of a humic material catalyzed by horseradish peroxidase stabilizes the humic structure by the formation of aryl and alkyl ethers and permanently enhances its molecular size.

Piccolo, A.; Cozzolino, A.; Conte, P.; Spaccini, R.

2000-10-01

50

Kinetic Determination of Drug Particles Concentration via Enzyme-Catalyzed Decomposition of Hydrogen Peroxide  

Microsoft Academic Search

The inhibition effect of blood pressure control drug particles, metoprolol (C34H56N2O12), and atenolol (C14H22N2O3), on the enzyme catalyzed decomposition of hydrogen peroxide reaction has been investigated by ultraviolet spectrophotometry. The results obtained when hydrogen peroxide was spectrophotometrically monitored were compared with those previously obtained from electrochemical measurements. As expected, the two series of measurements were shown to be consistent with

F. Pogacean; I. Baldea; L. Olenic; S. Pruneanu; A. S. Biris

2011-01-01

51

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

PubMed Central

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

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

2012-01-01

52

Methanogen Homoaconitase Catalyzes Both Hydrolyase Reactions in Coenzyme B Biosynthesis*S?  

PubMed Central

Homoaconitase enzymes catalyze hydrolyase reactions in the ?-aminoadipate pathway for lysine biosynthesis or the 2-oxosuberate pathway for methanogenic coenzyme B biosynthesis. Despite the homology of this iron-sulfur protein to aconitase, previously studied homoaconitases catalyze only the hydration of cis-homoaconitate to form homoisocitrate rather than the complete isomerization of homocitrate to homoisocitrate. The MJ1003 and MJ1271 proteins from the methanogen Methanocaldococcus jannaschii formed the first homoaconitase shown to catalyze both the dehydration of (R)-homocitrate to form cis-homoaconitate, and its hydration is shown to produce homoisocitrate. This heterotetrameric enzyme also used the analogous longer chain substrates cis-(homo)2aconitate, cis-(homo)3aconitate, and cis-(homo)4aconitate, all with similar specificities. A combination of the homoaconitase with the M. jannaschii homoisocitrate dehydrogenase catalyzed all of the isomerization and oxidative decarboxylation reactions required to form 2-oxoadipate, 2-oxopimelate, and 2-oxosuberate, completing three iterations of the 2-oxoacid elongation pathway. Methanogenic archaeal homoaconitases and fungal homoaconitases evolved in parallel in the aconitase superfamily. The archaeal homoaconitases share a common ancestor with isopropylmalate isomerases, and both enzymes catalyzed the hydration of the minimal substrate maleate to form d-malate. The variation in substrate specificity among these enzymes correlated with the amino acid sequences of a flexible loop in the small subunits. PMID:18765671

Drevland, Randy M.; Jia, Yunhua; Palmer, David R. J.; Graham, David E.

2008-01-01

53

Enzyme-catalyzed synthesis of hydrophobically modified starch  

Microsoft Academic Search

The reaction of starch and alkyl or alkenyl ketene dimer and starch gave a novel type of hydrophobically modified starch. The reaction was facilitated with the use of an enzyme, which gave products with higher degrees of substitution (DS) at lower temperatures. The starch used included maltodextrin, amylose, cationic starch, and pre-gelatinised starch, with molecular weights ranging from several hundreds

Lei Qiao; Qu-Ming Gu; H. N. Cheng

2006-01-01

54

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

PubMed

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

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

2014-08-01

55

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.  

PubMed

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry. PMID:20647463

Siegel, Justin B; Zanghellini, Alexandre; Lovick, Helena M; Kiss, Gert; Lambert, Abigail R; St Clair, Jennifer L; Gallaher, Jasmine L; Hilvert, Donald; Gelb, Michael H; Stoddard, Barry L; Houk, Kendall N; Michael, Forrest E; Baker, David

2010-07-16

56

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

PubMed Central

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

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

2013-01-01

57

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

E-print Network

Figure 8-1 ~ristalsof bovine chyrnotrypsin. 1 Enzymes are proteins specialized to catalyze of biochemistry is the history of en- zyme research. The name enzyme ("in yeast") was not used until 1877- furic acid. Although Louis Pasteur recognized that fermentation is catalyzed by enzymes, he postulated

Vallino, Joseph J.

58

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

NASA Astrophysics Data System (ADS)

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.

Masterson, Jean E.; Schwartz, Steven D.

2014-10-01

59

Vanadium-Catalyzed C(sp3 )H Fluorination Reactions  

E-print Network

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

Chen, Chuo

60

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

PubMed

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

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

2015-01-01

61

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

PubMed

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

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

2010-02-01

62

Influencing Enzymes: A Lesson on Enzyme Reactions  

NSDL National Science Digital Library

This teaching resource was developed by a K-12 science teacher in the American Physiological SocietyÃÂs 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.

Camia Steinmann (Clear Creek High School)

2007-08-01

63

Stau-catalyzed big-bang nucleosynthesis reactions  

NASA Astrophysics Data System (ADS)

We study the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a hypothetical long-lived negatively charged, massive leptonic particle (called X-) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X- particle has a lifetime of ?X>~103 s, it can capture a light element previously synthesized in standard BBN and form a Coulombic bound state and induces various types of reactions in which X- acts as a catalyst. Some of these X- catalyzed reactions have significantly large cross sections so that the inclusion of the reactions into the BBN network calculation can markedly change the abundances of some elements. We use a high-accuracy three-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

Kamimura, Masayasu; Kino, Yasushi; Hiyama, Emiko

2010-06-01

64

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

65

Enzyme catalyzed electricity-driven water softening system.  

PubMed

Hardness in water, which is caused by divalent cations such as calcium and magnesium ions, presents a major water quality problem. Because hard water must be softened before use in residential applications, there is great interest in the saltless water softening process because, unlike ion exchange softeners, it does not introduce additional ions into water. In this study, a saltless hardness removal driven by bioelectrochemical energy produced through enzymatic oxidation of glucose was proposed and investigated. Glucose dehydrogenase was coated on a carbon electrode to catalyze glucose oxidation in the presence of NAD? as a cofactor/mediator and methylene green as an electrocatalyst. The results showed that electricity generation stimulated hardness removal compared with non-electricity conditions. The enzymatic water softener worked upon a 6h batch operation per day for eight days, and achieved an average hardness removal of 46% at a high initial concentration of 800 mg/L as CaCO?. More hardness was removed at a lower initial concentration. For instance, at 200mg/L as CaCO? the enzymatic water softener removed 76.4±4.6% of total hardness. The presence of magnesium ions decreased hardness removal because of its larger hydrated radius than calcium ions. The enzymatic water softener removed 70-80% of total hardness from three actual hard water samples. These results demonstrated a proof-of-concept that enzyme catalyzed electricity generation can be used to soften hard water. PMID:23040397

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

2012-12-10

66

Copper-Catalyzed Oxidative Heck Reactions between Alkyltrifluoroborates and Vinylarenes  

PubMed Central

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

Liwosz, Timothy W.; Chemler, Sherry R.

2013-01-01

67

Enantioselective Diels–Alder reactions catalyzed by hydrogen bonding  

PubMed Central

Like molecules of life (e.g., proteins and DNA), many pharmaceutical drugs are also asymmetric (chiral); they are not superimposable on their mirror images. One mirror image form (enantiomer) of a drug can have desirable activity, the other not. Consequently, the development of methods for the selective synthesis of one enantiomer is of great scientific and economic importance. We report here that a simple, commercially available chiral alcohol, ?,?,??,??-tetraaryl-1,3-dioxolane-4,5-dimethanol (TADDOL), catalyzes the all-carbon Diels–Alder reactions of aminosiloxydienes and substituted acroleins to afford the products in good yields and high enantioselectivities (up to 92% enantiomeric excess). It is remarkable that the reactions are promoted by hydrogen bonding, the ubiquitous “glue” that helps to keep water molecules together and holds up the 3D structures of proteins. Hydrogen bond catalysis is little used in chemical synthesis, wherein most reactions are promoted by complexes of Lewis acidic metal salts coordinated to chiral ligands. As it does for enzymes, hydrogen bonding not only organizes TADDOL into a well defined conformation, but, functioning as a Brønsted acid catalyst, it also activates the dienophile toward reaction with the diene. The gross structure of the TADDOL has been found to have a profound influence on both the rate and the enantioselectivity of the cycloadditions. These structure–function effects are rationalized by evaluating the conformation adopted by the TADDOLs in the crystal state. It is suggested that ?,?-stacking plays an central role in the overall catalytic cycle, in particular, the enantioselective step. PMID:15069185

Thadani, Avinash N.; Stankovic, Ana R.; Rawal, Viresh H.

2004-01-01

68

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

PubMed

The intermolecular asymmetric Stetter reaction is a rarely found biocatalysts transformation. MenD, the second enzyme of the menaquinone biosynthetic pathway, catalyzes as a physiological reaction a Stetter-like addition of ?-ketoglutarate to isochorismate. The substrate range of MenD for similar 1,4-additions is highly restricted. All other thiamine diphosphate dependent enzymes known to act as stetterases are members of the PigD enzyme subfamily, which accept aliphatic and aromatic ?,?-unsaturated ketones and thioesters as Michael acceptor substrates. Here, we describe the unexpected activity of MenD with short-chain ?,?-unsaturated acids and derivatives as substrates in Stetter reactions. MenD possesses a characteristic substrate range with respect to Michael acceptor substrates which is distinctly different from the classical stetterases. This provides biocatalytic access to new types of products which are not related to the products currently accessible by thiamine diphosphate dependent enzyme catalysis. PMID:25111035

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

2014-12-10

69

Endo-selective pd-catalyzed silyl methyl heck reaction.  

PubMed

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

Parasram, Marvin; Iaroshenko, Viktor O; Gevorgyan, Vladimir

2014-12-31

70

Ti-Catalyzed Reactions of Hindered Isocyanates with Alcohols  

E-print Network

Ti-Catalyzed Reactions of Hindered Isocyanates with Alcohols Claude Spino,* Marc-Andre´ Joly, Ce with an alcohol or an amine to produce a carbamate or a urea, respectively, with water to produce a primary amine. The reactions between many unhindered isocy- anates and primary alcohols proceed without catalysis

Spino, Claude

71

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

PubMed

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

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

2014-04-01

72

In Vitro Analysis of RNA Degradation Catalyzed by Deadenylase Enzymes  

PubMed Central

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

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

2014-01-01

73

Chiral bicyclic guanidine-catalyzed enantioselective reactions of anthrones.  

PubMed

Chiral bicyclic guanidine 1 was found to be an excellent catalyst for reactions between anthrones and various dienophiles. The catalyst can tolerate a range of substituents and substitution patterns, making several anthrone derivatives suitable for this reaction. Both Diels-Alder and Michael adducts were obtained in excellent yields, high regioselectivities, and high enantioselectivities. This is the first case of a highly enantioselective base-catalyzed anthrone Diels-Alder reaction. PMID:17044689

Shen, Juan; Nguyen, Thanh Truc; Goh, Yong-Peng; Ye, Weiping; Fu, Xiao; Xu, Junye; Tan, Choon-Hong

2006-10-25

74

Adenosyl radical: reagent and catalyst in enzyme reactions  

PubMed Central

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

Patterson, Dustin P.

2010-01-01

75

Imidazolidinone intermediates in prolinamide-catalyzed aldol reactions.  

PubMed

The reaction between acetone and 4-nitrobenzaldehyde catalyzed by aniline prolinamide 1 was studied in depth. Working in different solvents with equimolar amounts of reagents and monitoring the reaction by 1H NMR, we detected and identified several imidazolidinones, such as those of the acetone 4, the aldol products 5a and 5b, and aldehydes 10a and 10b. According to our results, these compounds could influence the reaction rate and diminish product enantioselectivity. Furthermore, acetone imidazolidinone 4 was seen to react with 4-nitrobenzaldehyde to furnish the aldol product 3. This reaction can be catalyzed by different nucleophiles and acids. In fact, strong acids such as camphorsulfonic or trifluoroacetic acid, convert imidazolidinones into iminium salts and afford more enantioselective aldol reactions when different aromatic prolinamides are used. Enantiomeric excesses of ca. 82% are reached. PMID:20461270

Fuentes de Arriba, Angel L; Simón, Luis; Raposo, César; Alcázar, Victoria; Sanz, Francisca; Muñiz, Francisco M; Morán, Joaquín R

2010-06-28

76

Stereochemical course of enzyme-catalyzed aminopropyl transfer: spermidine synthase  

SciTech Connect

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

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

1986-05-01

77

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

SciTech Connect

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.

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

2009-01-01

78

Development of a Lewis Base Catalyzed Selenocyclization Reaction  

ERIC Educational Resources Information Center

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,…

Collins, William

2009-01-01

79

A common topology of proteins catalyzing ATP-triggered reactions  

Microsoft Academic Search

A protein fold, six parallel ? strands surrounding the central ? helix, is likely to be a common structure in protein families known to have a typical set of nucleotide binding consensus sequenced motifs A and B and to catalyze ATP-triggered reactions. According to this ATP-triggered protein fold, the conserved Glu (or Asp), which acts as a general base to

Masasuke Yoshida; Toyoki Amano

1995-01-01

80

Au-catalyzed reaction of propargylic sulfides and dithioacetals.  

PubMed

Propargylic sulfides and dithioacetals are found to undergo similar transformations as propargylic carboxylates when catalyzed by AuCl or AuCl3, affording indene derivatives through pentannulation of aromatic rings. The reaction presumably involves Au carbene as the reactive intermediate. PMID:17288372

Peng, Lingling; Zhang, Xiu; Zhang, Shiwei; Wang, Jianbo

2007-02-16

81

Calcium(II)-catalyzed aza-Piancatelli reaction.  

PubMed

The first examples of calcium-catalyzed aza-Piancatelli reactions between substituted 2-furylcarbinols and aniline derivatives are described. A variety of 4-aminocyclopentenones have been synthesized stereoselectively in high yields. The experimental procedure utilizes simple salts and does not require specific precautions. PMID:25485996

Lebœuf, David; Schulz, Emmanuelle; Gandon, Vincent

2014-12-19

82

Cascade reactions catalyzed by metal organic frameworks.  

PubMed

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

Dhakshinamoorthy, Amarajothi; Garcia, Hermenegildo

2014-09-01

83

The Development of the First Catalyzed Reaction of Ketenes and Imines: Catalytic, Asymmetric Synthesis of -Lactams  

E-print Network

The Development of the First Catalyzed Reaction of Ketenes and Imines: Catalytic, Asymmetric for the catalytic, asymmetric synthesis of -lactams resulting from the development of a catalyzed reaction resistance pressures,1 recently -lactams (especially nonnatural ones) have achieved many important

Lectka, Thomas

84

Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI60 cell lines  

Microsoft Academic Search

BACKGROUND: Drugs can influence the whole metabolic system by targeting enzymes which catalyze metabolic reactions. The existence of interactions between drugs and metabolic reactions suggests a potential way to discover drug targets. RESULTS: In this paper, we present a computational method to predict new targets for approved anti-cancer drugs by exploring drug-reaction interactions. We construct a Drug-Reaction Network to provide

Limin Li; Xiaobo Zhou; Wai-Ki Ching; Ping Wang

2010-01-01

85

Mild and efficient cyanuric chloride catalyzed Pictet–Spengler reaction  

PubMed Central

Summary A practical, mild and efficient protocol for the Pictet–Spengler reaction catalyzed by cyanuric chloride (trichloro-1,3,5-triazine, TCT) is described. The 6-endo cyclization of tryptophan/tryptamine and modified Pictet–Spengler substrates with both electron-withdrawing and electron-donating aldehydes was carried out by using a catalytic amount of TCT (10 mol %) in DMSO under a nitrogen atmosphere. TCT catalyzed the Pictet–Spengler reaction involving electron-donating aldehydes in excellent yield. Thus, it has a distinct advantage over the existing methodologies where electron-donating aldehydes failed to undergo 6-endo cyclization. Our methodology provided broad substrate scope and diversity. This is indeed the first report of the use of TCT as a catalyst for the Pictet–Spengler reaction. PMID:23843919

Sharma, Ashish; Singh, Mrityunjay; Rai, Nitya Nand

2013-01-01

86

Silver and gold-catalyzed multicomponent reactions  

PubMed Central

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

Abbiati, Giorgio

2014-01-01

87

An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation  

PubMed Central

Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions. PMID:23382649

Shi, Ke; Huang, Wai Mun; Aihara, Hideki

2013-01-01

88

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

SciTech Connect

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

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

1986-08-12

89

Electron nuclear double resonance determined structures of enzyme reaction intermediates: structural evidence for substrate destabilization  

NASA Astrophysics Data System (ADS)

Angle selective ENDOR of nitroxyl spin-labels is briefly reviewed to illustrate the methodology of structure analysis developed in our laboratory for characterizing catalytically competent intermediates of enzyme catalyzed reactions. ENDOR structure determination of a reaction intermediate of ?-chymotrypsin formed with a kinetically specific spin-labeled substrate and of an enzyme-inhibitor complex formed with a spin-labeled transition-state inhibitor analog is briefly described. Both spin-labeled molecules bound in the active site of the enzyme are found in torsionally distorted conformations. It is suggested that this torsionally distorted state in which the bound ligand is of higher potential energy than in the ground state conformation reflects substrate destabilization in the course of the enzyme catalyzed reaction.

Makinen, Marvin W.

1998-12-01

90

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

PubMed

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

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

2014-09-24

91

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

PubMed

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

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

2014-11-15

92

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

PubMed

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

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

2014-11-01

93

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

PubMed

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

Al-Huniti, Mohammed H; Lepore, Salvatore D

2013-10-11

94

Stereoretentive Copper (II) Catalyzed Ritter Reactions of Secondary Cycloalkanols  

PubMed Central

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

Al-huniti, Mohammed H.

2013-01-01

95

Using Reaction Mechanism to Measure Enzyme Similarity  

PubMed Central

Summary The concept of reaction similarity has been well-studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach which incorporates relevant information on each mechanistic step, and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanism. In many cases mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC. PMID:17400244

O’Boyle, Noel M.; Holliday, Gemma L.; Almonacid, Daniel E.; Mitchell, John B.O.

2012-01-01

96

Retention of anomeric form in lysozyme-catalyzed reaction.  

PubMed

A lysozyme-catalyzed reaction is initiated by a cleavage of the beta-1, 4-glucosaminide linkage, followed by hydration and transglycosylation. Since all glycosides produced by transglycosylation have beta-glycosidic linkages between the sugar and the acceptor moieties, the lysozyme-catalyzed reaction has been classified as an anomer-retention reaction. However, there is no experimental evidence on the anomer retention of the new reducing residue produced by the hydrolysis of the substrate. In the present study, an attempt was made to determine the anomeric form of the GlcNAc residue at the reducing end in nascent hydrolytic products. The anomeric forms of the enzymatic products were separated and quantitatively analyzed by high-performance liquid chromatography. The amounts of alpha- and beta-anomers in the product were plotted against the reaction time. Computer analysis of the experimental data indicated that the nascent hydrolytic product takes only the beta-anomeric form and that the alpha-anomer is formed from beta-anomer by mutarotation. PMID:3813561

Yanase, Y; Fukamizo, T; Hayashi, K; Goto, S

1987-02-15

97

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

ERIC Educational Resources Information Center

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…

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

2011-01-01

98

Enzyme catalysis Enzyme catalysis is the catalysis of chemical reactions by  

E-print Network

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

Cavanagh, John

99

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

100

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

ERIC Educational Resources Information Center

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)

Lombardo, Anthony

1982-01-01

101

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

PubMed

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

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

2010-06-01

102

Palladium-catalyzed coupling reactions of tetrafluoroethylene with arylzinc compounds.  

PubMed

Organofluorine compounds are widely used in all aspects of the chemical industry. Although tetrafluoroethylene (TFE) is an example of an economical bulk organofluorine feedstock, the use of TFE is mostly limited to the production of poly(tetrafluoroethylene) and copolymers with other alkenes. Furthermore, no catalytic transformation of TFE that involves carbon-fluorine bond activation has been reported to date. We herein report the first example of a palladium-catalyzed coupling reaction of TFE with arylzinc reagents in the presence of lithium iodide, giving ?,?,?-trifluorostyrene derivatives in excellent yields. PMID:21322557

Ohashi, Masato; Kambara, Tadashi; Hatanaka, Tsubasa; Saijo, Hiroki; Doi, Ryohei; Ogoshi, Sensuke

2011-03-16

103

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

PubMed

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

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

2013-11-20

104

Synthesis of acylphosphonates by a palladium-catalyzed phosphonocarbonylation reaction of aryl iodides with phosphites.  

PubMed

Acylphosphonates are conveniently synthesized from aryl iodides by a palladium-catalyzed reaction with dialkyl phosphites under an atmospheric pressure of carbon monoxide. The reaction demonstrates the first example of the use of phosphorus nucleophiles in related metal-catalyzed carbonylation reactions. PMID:25414042

Masuda, Yusuke; Ishida, Naoki; Murakami, Masahiro

2015-02-01

105

Mechanistic origin of chemoselectivity in thiolate-catalyzed Tishchenko reactions.  

PubMed

The thiolate-catalyzed Tishchenko reaction has shown high chemoselectivity for the formation of double aromatic-substituted esters. In the present study, the detailed reaction mechanism and, in particular, the origin of the observed high chemoselectivity, have been studied with DFT calculations. The catalytic cycle mainly consisted of three steps: 1,2-addition, hydride transfer, and acyl transfer steps. The calculation results reproduce the experimental observations that 4-chlorobenzaldehyde acts as the hydrogen donor (carbonyl part in the ester product), while 2-methoxybenzaldehyde acts as the hydrogen acceptor (alcohol part in the product). The two main factors are responsible for such chemoselectivity: 1) in the rate-determining hydride transfer step, the para-chloride substituent facilitates the hydride-donating process by weakening the steric hindrance, and 2) the ortho-methoxy substituent facilitates the hydride-accepting process by stabilizing the magnesium center (by compensating for the electron deficiency). PMID:25213329

Yu, Hai-Zhu; Tian, Xue-Jiao; Lin, Xiang; Hu, Guo-Hua; Dang, Zhi-Min

2014-12-01

106

Clay-catalyzed reactions of coagulant polymers during water chlorination.  

PubMed

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. PMID:14697704

Lee, Jiunn-Fwu; Liao, Pao-Mei; Lee, Chung-Kung; Chao, Huan-Ping; Peng, Chin-Luen; Chiou, Cary T

2004-02-15

107

Clay-catalyzed reactions of coagulant polymers during water chlorination  

USGS Publications Warehouse

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.

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

2004-01-01

108

Ultrasound assisted enzyme catalyzed degradation of Cetirizine dihydrochloride.  

PubMed

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

Sutar, Rahul S; Rathod, Virendra K

2015-05-01

109

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

Microsoft Academic Search

While it is well established that organics compose a large fraction of the atmospheric aerosol mass, the mechanisms through which organics are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds with carbonyl groups have recently been suggested as important pathways for transfer of volatile organics into acidic aerosols. In the present study, we use the aerodyne

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

2006-01-01

110

Gold-catalyzed tandem reactions of methylenecyclopropanes and vinylidenecyclopropanes.  

PubMed

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

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

2014-03-18

111

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

E-print Network

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 ...

Ng, Sze-Sze

2008-01-01

112

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

PubMed Central

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

Czekster, Clarissa M.; Blanchard, John S.

2012-01-01

113

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

PubMed

Tetrahydrofolate cofactors are required for one carbon transfer reaction 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 products, 24% to the epimerase product and 25% to the oxygenase products. The aldolase reaction is strongly pH dependent, and apparent pK(a) 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

Czekster, Clarissa M; Blanchard, John S

2012-12-01

114

Red seaweed enzyme-catalyzed bromination of bromophenol red: An inquiry-based kinetics laboratory experiment for undergraduates.  

PubMed

Haloperoxidase enzymes are of interest for basic and applied bioscientists because of their increasing importance in pharmaceutical industry and environmental cleanups. In a guided inquiry-based laboratory experiment for life-science, agricultural science, and health science undergraduates, the bromoperoxidase from a red seaweed was used to brominate bromophenol red, a novel starting substrate. Substrate and enzyme concentration dependence of this enzyme-catalyzed reaction as followed colorimetrically yielded initial rates of reaction that the students compared with those of their peers. The students worked as collaborative groups partially designing their own experiments and carrying them out. In performing the laboratory experiment, they were minimally guided by the instructor and teaching assistants. To engage the students before the laboratory, a short activity involving the enzyme-induced color change was carried out. At the end of the laboratory session, student groups discussed their results in front of the class and reached their own conclusions. Most students had better understanding of important concepts in enzyme kinetics and showed good attitude toward the overall student-centered laboratory exercise. PMID:21567713

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

2009-03-01

115

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

PubMed

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

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

2014-01-15

116

Acid-catalyzed reactions of epoxides for atmospheric nanoparticle growth.  

PubMed

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

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

2014-11-01

117

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

SciTech Connect

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

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

2009-06-03

118

Enantioselective Carbonyl-Ene Reactions Catalyzed by Chiral Cationic Dirhodium(II,III) Carboxamidates.  

PubMed

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

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

2014-12-19

119

Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants  

PubMed Central

Triacylglycerol (TAG) is known to be synthesized in a reaction that uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol acyltransferase. We have found that some plants and yeast also have an acyl-CoA-independent mechanism for TAG synthesis, which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:diacylglycerol acyltransferase, or PDAT. PDAT was characterized in microsomal preparations from three different oil seeds: sunflower, castor bean, and Crepis palaestina. We found that the specificity of the enzyme for the acyl group in the phospholipid varies between these species. Thus, C. palaestina PDAT preferentially incorporates vernoloyl groups into TAG, whereas PDAT from castor bean incorporates both ricinoleoyl and vernoloyl groups. We further found that PDAT activity also is present in yeast microsomes. The substrate specificity of this PDAT depends on the head group of the acyl donor, the acyl group transferred, and the acyl chains of the acceptor DAG. The gene encoding the enzyme was identified. The encoded PDAT protein is related to lecithin:cholesterol acyltransferase, which catalyzes the acyl-CoA-independent synthesis of cholesterol esters. However, budding yeast PDAT and its relatives in fission yeast and Arabidopsis form a distinct branch within this protein superfamily, indicating that a separate PDAT enzyme arose at an early point in evolution. PMID:10829075

Dahlqvist, Anders; Ståhl, Ulf; Lenman, Marit; Banas, Antoni; Lee, Michael; Sandager, Line; Ronne, Hans; Stymne, Sten

2000-01-01

120

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions  

PubMed Central

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

Chang, Ivan; Baldi, Pierre

2013-01-01

121

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

ERIC Educational Resources Information Center

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)

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

1985-01-01

122

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

PubMed

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

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

123

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

PubMed

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

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

2005-03-18

124

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

E-print Network

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 ...

Moslin, Ryan Thomas McLeod

2007-01-01

125

Entropy is Key to the Formation of Pentacyclic Terpenoids by Enzyme-Catalyzed Polycyclization.  

PubMed

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

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

2014-05-01

126

Absolute configurations of monoesters produced by enzyme catalyzed hydrolysis of diethyl 3-hydroxyglutarate  

Microsoft Academic Search

Biocatalytic asymmetrizations of diethyl 3-hydroxyglutarate furnish a route to the enantiomers of ethyl 4-cyano-3-hydroxybutanoate. The enantiopreference of different enzymes has been established by chiral chromatography. Conclusive evidence for absolute configurations has been provided by X-ray crystallographic structure determination of co-crystals of the predominant monoester with (R)-phenylethylamine. The predominant enantiopure monoester produced by ammonolysis of diethyl 3-hydroxyglutarate catalyzed by immobilized lipase

Anders Riise Moen; Bård Helge Hoff; Lars Kristian Hansen; Thorleif Anthonsen; Elisabeth Egholm Jacobsen

2004-01-01

127

Enzyme reactions in a multicompartment electrolyzer with isoelectrically trapped enzymes  

Microsoft Academic Search

The possibility of performing bioconversions under an electric field is here reported. A system is described by which the enzyme is trapped by an isoelectric mechanism between two zwitterionic membranes having pI values encompassing the isoelectric point of the enzyme. The enzyme is loaded into a multicompartment electrolyzer and kept operating under an electric field, which will continuously harvest the

Marcella Chiari; Norma Dell'Orto; Monica Mendozza; Giacomo Carrea; Pier Giorgio Righetti

1996-01-01

128

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

PubMed

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

Jarrett, Joseph T

2014-12-01

129

Mechanism of the Reaction Catalyzed by Isoaspartyl Dipeptidase from Escherichia coli,  

E-print Network

superfamily and catalyzes the hydrolytic cleavage of -aspartyl dipeptides. Structural studies of the wild-type enzyme have demonstrated that the active site consists of a binuclear metal center positioned at the C with the free R-amino group of the dipeptide substrate. Kinetic constants were obtained for the mutant enzymes

Holden, Hazel

130

Trisoxazoline\\/Cu(II)-catalyzed asymmetric intramolecular Friedel–Crafts alkylation reaction of indoles  

Microsoft Academic Search

Intramolecular Friedel–Crafts alkylation reaction of indoles catalyzed by trisoxazoline\\/copper(II) is described. This annulation provides an easy access to polycyclic indole derivatives with up to 90% ee in up to 99% yield.

Jiao-Long Zhou; Meng-Chun Ye; Xiu-Li Sun; Yong Tang

2009-01-01

131

2-Halogenoimidazolium Salt Catalyzed Aza-Diels-Alder Reaction through Halogen-Bond Formation.  

PubMed

2-Halogenoimidazolium salts are found to catalyze aza-Diels-Alder reaction of aldimines with Danishefsky diene in an efficient manner. Comparative studies and titration experiments support the formation of halogen bonding between imines and catalysts. PMID:25551775

Takeda, Youhei; Hisakuni, Daichi; Lin, Chun-Hsuan; Minakata, Satoshi

2015-01-16

132

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

EPA Science Inventory

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

133

Synthesis of 3-indole derivatives by copper sulfonato Salen catalyzed three-component reactions in water.  

PubMed

An efficient three-component reaction of indole, aldehyde, and malononitrile in water catalyzed by a copper(II) sulfonato Salen complex afforded 3-indole derivatives in good to excellent yields up to 97%. PMID:21340052

Qu, Yanyang; Ke, Fang; Zhou, Li; Li, Zhengkai; Xiang, Haifeng; Wu, Di; Zhou, Xiangge

2011-04-01

134

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

PubMed Central

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

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

2013-01-01

135

Mechanism for folate-independent aldolase reaction catalyzed by serine hydroxymethyltransferase.  

PubMed

Serine hydroxymethyltransferase catalyzes the cleavage of ?-hydroxyamino acids into glycine and aldehydes in the absence of tetrahydrofolate. The enzyme accepts various ?-hydroxyamino acids as the substrate of this reaction. The reaction rate varies depending on the substituent and stereochemistry at the C? atom: the erythro forms and the ?-phenyl substituent are preferred over the threo forms and the ?-methyl substituent, respectively. Although several mechanisms have been proposed, what determines the substrate preference remains unclear. We first performed quantum mechanical calculations to assess the validity of the reaction mechanisms. The results indicate that the retro-aldol mechanism starting with abstraction of the proton from the ?-hydroxyl group is plausible. This also suggests that C?-C? bond cleavage is the rate-limiting step. We next measured the dependence of the rate constants on temperature with four representative substrates and calculated the activation energies and pre-exponential factors from the Arrhenius plots. The activation energies of the erythro forms were lower than those of the threo forms. The ?-phenyl substituent lowered the activation energy in the threo form, whereas it did not alter the activation energy but increased the pre-exponential factor in the erythro form. We present a unified model to explain the origin of the substituent and stereochemical preferences by combining the theoretical and experimental results. A possible biological role of the tetrahydrofolate-independent activity in thermophiles is also discussed. PMID:22141341

Chiba, Yoko; Terada, Tohru; Kameya, Masafumi; Shimizu, Kentaro; Arai, Hiroyuki; Ishii, Masaharu; Igarashi, Yasuo

2012-02-01

136

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

E-print Network

COPPER-CATALYZED CROSS-COUPLING REACTIONS: THE FORMATION OF CARBON-CARBON AND CARBON-SULFUR BONDS Chemistry #12;© Copyright by Craig G. Bates 2005 All Rights Reserved #12;COPPER-CATALYZED CROSS without her. Thank You January 24, 2005 #12;vi ABSTRACT COPPER-CATALYZED CROSS-COUPLING REACTIONS

Venkataraman, Dhandapani "DV"

137

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

PubMed

An efficient three-component coupling reaction toward a variety of furan derivatives has been developed. This cascade transformation proceeds via the gold-catalyzed coupling reaction of phenylglyoxal derivatives, secondary amines, and terminal alkynes, under the reaction conditions, that undergoes cyclization into the furan core. PMID:23687935

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

2013-06-01

138

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

NASA Astrophysics Data System (ADS)

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

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

139

Glutathione-dependent one-electron transfer reactions catalyzed by a B?? trafficking protein.  

PubMed

CblC is involved in an early step in cytoplasmic cobalamin processing following entry of the cofactor into the cytoplasm. CblC converts the cobalamin cargo arriving from the lysosome to a common cob(II)alamin intermediate, which can be subsequently converted to the biologically active forms. Human CblC exhibits glutathione (GSH)-dependent alkyltransferase activity and flavin-dependent reductive decyanation activity with cyanocobalamin (CNCbl). In this study, we discovered two new GSH-dependent activities associated with the Caenorhabditis elegans CblC for generating cob(II)alamin: decyanation of CNCbl and reduction of aquocobalamin (OH2Cbl). We subsequently found that human CblC also catalyzes GSH-dependent decyanation of CNCbl and reduction of OH2Cbl, albeit efficiently only under anaerobic conditions. The air sensitivity of the human enzyme suggests interception by oxygen during the single-electron transfer step from GSH to CNCbl. These newly discovered GSH-dependent single-electron transfer reactions expand the repertoire of catalytic activities supported by CblC, a versatile B12-processing enzyme. PMID:24742678

Li, Zhu; Gherasim, Carmen; Lesniak, Nicholas A; Banerjee, Ruma

2014-06-01

140

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

NASA Astrophysics Data System (ADS)

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.

Yao, Yuan; Li, Ze-Sheng

2012-01-01

141

Transition state and rate-limiting step of the reaction catalyzed by the human dual-specificity phosphatase, VHR.  

PubMed

The dual-specificity phosphatases are unusual catalysts in that they can utilize protein substrates containing phosphotyrosine as well as phosphoserine/threonine. The dual-specificity phosphatases and the protein-tyrosine phosphatases (PTPases) share the active site motif (H/V)C(X)5R(S/T), but display little amino acid sequence identity outside of the active site. Although the dual-specificity phosphatases and the PTPases appear to bring about phosphate monoester hydrolysis through a similar mechanism, it is not clear what causes the difference in the active-site specificity between the two groups of enzymes. In this paper, we show that the human dual-specificity phosphatase, VHR [for VH1-Related; Ishibashi et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 12170-12174], is rather promiscuous toward small phosphate monoesters (including both aryl and alkyl phosphates of primary alcohols) with effectively identical kcat/Km and kcat values while the pKa values of the leaving groups (phenols or alcohols) varied from 7 to 16. Linear free-energy relationship analysis of kcat and kcat/Km of the enzyme-catalyzed hydrolysis reaction suggests that a uniform mechanism is utilized for both the aryl and alkyl substrates. The very small dependency of kcat/Km on the leaving group pKa can be accounted for by the protonation of the leaving group. Pre-steady-state burst kinetic analysis of the VHR-catalyzed hydrolysis of p-nitrophenyl phosphate provides direct kinetic evidence for the involvement of a phosphoenzyme intermediate in the dual specificity phosphatase-catalyzed reaction. The rate-limiting step for the VHR-catalyzed hydrolysis of p-nitrophenyl phosphate corresponds to the decomposition of the phosphoenzyme intermediate.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8519766

Zhang, Z Y; Wu, L; Chen, L

1995-12-12

142

Mass spectrum patterns of 18O-tagged peptides labeled by enzyme-catalyzed oxygen exchange.  

PubMed

(18)O-labeling of peptides is a technique widely and routinely applied in the protein chemistry laboratories. The rate of (18)O incorporation at the carboxyl terminus of peptides via enzyme-catalyzed oxygen exchange fluctuates from peptide to peptide. This fluctuation is mostly attributed to enzyme-substrate different affinity. The final distributions of the (18)O(0)-, (18)O(1)-, and (18)O(2)-tagged peptides remain unpredictable though usually constrained to binomial proportions. It is proved here that this constraint can sometimes be a poor model. A more general model is then derived which predicts linear paths for digestion in H(2)(18)O-enriched water while confining binomial proportions to postdigestion labeling. Both subderived models are simple in structure and relevant for the current software development in the analysis of quantitative shotgun proteomics data. Accuracy and time dependency are examined and compared with actual labeled-digest data. PMID:21417365

Fernandez-de-Cossio, Jorge

2011-04-15

143

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

PubMed Central

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

2014-01-01

144

Recent developments in gold-catalyzed cycloaddition reactions  

PubMed Central

Summary In the last years there have been extraordinary advances in the development of gold-catalyzed cycloaddition processes. In this review we will summarize some of the most remarkable examples, and present the mechanistic rational underlying the transformations. PMID:21915211

2011-01-01

145

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

PubMed Central

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

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

2012-01-01

146

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

PubMed

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

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

2014-12-01

147

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

SciTech Connect

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

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

2012-01-26

148

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

PubMed

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

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

2010-04-01

149

Palladium-catalyzed cross-coupling reactions of 2-iodo-4-(phenylchalcogenyl)-1-butenes.  

PubMed

[reaction: see text] 2-Iodo-4-(phenylchalcogenyl)-1-butenes 2 or 3, which are derived from the ring-opening reaction of methylenecyclopropanes (MCPs) 1 by iodine, can be applied to some palladium-catalyzed cross-coupling reactions such as the Sonogashira, Heck, Kumada, Suzuki, and Negishi reactions under mild conditions to give the corresponding coupling products in good yields. These reactions proceeded smoothly at room temperature (20 degrees C) in most cases without any phosphine ligand and additive. The phenylchalcogenyl group plays an important role in the reactions and a plausible reaction mechanism has been proposed. PMID:16323852

Shi, Min; Liu, Le-Ping; Tang, Jie

2005-12-01

150

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

E-print Network

4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate Received March I , 1991 ABSTRACT: The L-21 ScaI ribozyme derived from the intervening sequence of cleavage, that test aspects of a kinetic model proposed for the ribozyme reaction (Herschlag, D., & Cech, T

Herschlag, Dan

151

Ag/ThioClickFerrophos-catalyzed enantioselective Mannich reaction and amination of glycine Schiff base.  

PubMed

The AgOAc/ThioClickFerrophos complex catalyzed the asymmetric Mannich reaction of glycine Schiff base with N-tosylimines effectively to give a mixture of syn and anti adducts (syn/anti = 60/40-70/30) at high yields with high enantioselectivities (up to 98% ee). The complex also catalyzed the asymmetric amination of glycine Schiff base with di-tert-butyl azodicarboxylate with high enantioselectivity. PMID:21410238

Imae, Kazumi; Shimizu, Kenta; Ogata, Kenichi; Fukuzawa, Shin-ichi

2011-05-01

152

A bifunctional enzyme in a single gene catalyzes the incorporation of GlcN into the Aeromonas core lipopolysaccharide.  

PubMed

The core lipopolysaccharide (LPS) of Aeromonas hydrophila AH-3 and Aeromonas salmonicida A450 is characterized by the presence of the pentasaccharide alpha-d-GlcN-(1-->7)-l-alpha-d-Hep-(1-->2)-l-alpha-d-Hep-(1-->3)-l-alpha-d-Hep-(1-->5)-alpha-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

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

2009-11-27

153

Distinct Reactions Catalyzed by Bacterial and Yeast trans Aconitate Methyltransferases †  

Microsoft Academic Search

The trans-aconitate methyltransferase from the bacterium Escherichia coli catalyzes the monomethyl esterification of trans-aconitate and related compounds. Using two-dimensional 1H\\/13C nuclear magnetic resonance spectroscopy, we show that the methylation is specific to one of the three carboxyl groups and further demonstrate that the product is the 6-methyl ester of trans-aconitate (E-3-carboxy-2- pentenedioate 6-methyl ester). A similar enzymatic activity is present

Hui Cai; Jane Strouse; Darren Dumlao; Michael E. Jung; Steven Clarke

2001-01-01

154

Expression and purification of pheophorbidase, an enzyme catalyzing the formation of pyropheophorbide during chlorophyll degradation: comparison with the native enzyme.  

PubMed

Formation of pyropheophorbide (PyroPheid) during chlorophyll metabolism in some higher plants has been shown to involve the enzyme pheophorbidase (PPD). This enzyme catalyzes the conversion of pheophorbide (Pheid) a to a precursor of PyroPheid, C-13(2)-carboxylPyroPheid a, by demethylation, and then the precursor is decarboxylated non-enzymatically to yield PyroPheid a. In this study, expression, purification, and biochemical characterization of recombinant PPD from radish (Raphanus sativus L.) were performed, and its properties were compared with those of highly purified native PPD. Recombinant PPD was produced using a glutathione S-transferase (GST) fusion system. The PPD and GST genes were fused to a pGEX-2T vector and expressed in Escherichia coli under the control of a T7 promoter as a fusion protein. The recombinant PPD-GST was expressed as a 55 kDa protein as measured by SDS-PAGE and purified by single-step affinity chromatography through a GSTrap FF column. PPD-GST was purified to homogeneity with a yield of 0.42 mg L(-1) of culture. The protein purified by this method was confirmed to be PPD by measuring its activity. The purified PPD-GST fusion protein revealed potent catalytic activity for demethylation of the methoxycarbonyl group of Pheid a and showed a pH optimum, substrate specificity, and thermal stability quite similar to the native enzyme purified from radish, except for the Km values toward Pheid a: 95.5 microM for PPD-GST and about 15 microM for native PPDs. PMID:18846292

Suzuki, Yasuyo; Soga, Keiko; Yoshimatsu, Katsuhiko; Shioi, Yuzo

2008-10-01

155

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

PubMed

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

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

1989-01-01

156

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

PubMed

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

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

2013-08-01

157

Continuous In Vitro Evolution of a Ribozyme that Catalyzes Three Successive Nucleotidyl Addition Reactions  

NASA Technical Reports Server (NTRS)

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.

McGinness, Kathleen E.; Wright, Martin C.; Joyce, Gerald F.

2002-01-01

158

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

PubMed Central

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

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

159

Ionic Liquid Catalyzed the Internal Redox Esterification Reaction  

Microsoft Academic Search

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

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

2012-01-01

160

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

SciTech Connect

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

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

1987-06-30

161

Bound Lac repressor protein differentially inhibits the unwinding reactions catalyzed by DNA helicases.  

PubMed Central

A partial duplex DNA substrate containing the Lac repressor binding site, within the duplex region, was constructed to examine the effect of bound Lac repressor on the unwinding reaction catalyzed by several DNA helicases. The substrate contained 90 base pairs of double-stranded DNA and, in the absence of Lac repressor, was effectively unwound by each of the seven helicases tested. The unwinding reactions catalyzed by Escherichia coli Rep protein, bacteriophage T4 Dda protein and E. coli DNA helicase I were not inhibited by the presence of bound Lac repressor. Both SV40 T antigen and E. coli helicase II were partially inhibited by bound repressor at the highest repressor concentrations tested. The helicase reactions catalyzed by E. coli DnaB protein and helicase IV were substantially inhibited by the presence of bound protein. When the length of the duplex region was increased to 323 base pairs the inhibition spectrum caused by bound Lac repressor on the unwinding reactions catalyzed by DnaB protein, helicase I and helicase II was essentially the same as that observed using the shorter partial duplex molecule. Inhibition of the unwinding reaction was due to the presence of bound Lac repressor as evidenced by the substantially weaker inhibition of helicase IV by Lac repressor in the presence of IPTG. In addition, we have shown that Rep protein displaces the bound repressor protein during the course of an unwinding reaction. Images PMID:1336182

Yancey-Wrona, J E; Matson, S W

1992-01-01

162

Synthesis of oligonucleotides carrying 5'-5' linkages using copper-catalyzed cycloaddition reactions.  

PubMed

There is considerable interest in coupling oligonucleotides to molecules and surfaces. Although amino- and thiol-containing oligonucleotides are being successfully used for this purpose, cycloaddition reactions may offer greater advantages due to their higher chemoselectivity and speed. In this study, copper-catalyzed 1,3-dipolar cycloaddition reactions between oligonucleotides carrying azido and alkyne groups are examined. For this purpose, several protocols for the preparation of oligonucleotides carrying these two groups are described. The non-templated chemical ligation of two oligonucleotides via copper-catalyzed [3+2] cycloaddition is described. By solid-phase methodology, oligonucleotides carrying 5'-5' linkages can be obtained in good yields. PMID:18081090

Alvira, Margarita; Eritja, Ramon

2007-12-01

163

The DNA unwinding reaction catalyzed by Rep protein is facilitated by an RHSP-DNA interaction.  

PubMed Central

The unwinding reaction catalyzed by the Escherichia coli Rep protein is stimulated by a small 15 kDa protein called Rep helicase stimulatory protein (RHSP)(1). The RHSP-stimulated unwinding reaction catalyzed by Rep protein proceeded at a rapid rate after a time lag of 1-2 min at 37 degrees C. This time lag was eliminated by preincubating RHSP with the DNA substrate, indicating that stimulation resulted from an interaction between RHSP and DNA. RHSP was shown to increase the rate as well as the extent of the unwinding reaction catalyzed by Rep protein. RHSP bound both single- and double-stranded DNA with apparent equal affinity, forming an unusually stable complex. Electron microscopy illustrated that the RHSP-DNA complex consisted of large protein aggregates bound to DNA forming a highly condensed, aggregated DNA-protein complex. The protein aggregates were not observed in the absence of DNA and appeared to form cooperatively in the presence of DNA. NH2-terminal amino acid sequence analysis suggested that RHSP was identical to E. coli ribosomal-protein L14. Binding assays showed that the interaction between RHSP and rRNA was similar to the RHSP-DNA interaction. Several models are put forth to explain the stimulation of the unwinding reaction catalyzed by Rep protein. In addition, the potential physiological significance of the RHSP-stimulated Rep protein unwinding reaction is discussed. Images PMID:1650456

Yancey, J E; Matson, S W

1991-01-01

164

Transition metal catalyzed carbon-silicon bond forming reactions using chlorosilanes promoted by Grignard reagents.  

PubMed

New catalytic C--Si bond-forming reactions using chlorosilanes are described. These reactions proceed efficiently under mild conditions by the combined use of Grignard reagents and transition metal catalysts, such as Ti, Zr, Ni, and Pd. It is proposed that ate complex intermediates formed by the reaction of transition metals with Grignard reagents play important roles as the active catalytic species. The present study demonstrates the practical use of chlorosilanes in transition metal catalyzed silylation reactions providing convenient methods for allyl- or vinylsilane synthesis. The reaction pathways of these transformations as well as the scope and limitations are discussed. PMID:17318829

Terao, Jun; Kambe, Nobuaki

2007-01-01

165

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

PubMed

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

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

2015-01-18

166

Ultrasensitive electrochemical detection of breast cancer cells based on DNA-rolling-circle-amplification-directed enzyme-catalyzed polymerization.  

PubMed

An ultrasensitive cytosensor based on DNA-rolling-circle-amplification-directed enzyme-catalyzed polymerization is demonstrated. As a proof of concept, the cytosensor shows excellent sensitivity for MCF-7 cell detection with a lower detection limit of 12 cells per mL. PMID:25536491

Sheng, Qinglin; Cheng, Ni; Bai, Wushuang; Zheng, Jianbin

2015-02-01

167

Using Simple Donors to Drive the Equilibria of Glycosyltransferase-Catalyzed Reactions  

PubMed Central

We report the ability of simple glycoside donors to drastically shift the equilibria of glycosyltransferase-catalyzed reactions, transforming NDP-sugar formation from an endo- to an exothermic process. To demonstrate the utility of this thermodynamic adaptability, we highlight the glycosyltransferase-catalyzed synthesis of 22 sugar nucleotides from simple aromatic sugar donors as well as the corresponding in situ formation of sugar nucleotides as a driving force in context of glycosyltransferase-catalyzed reactions for small molecule glycodiversification. These simple aromatic donors also enabled the first general colorimetric assay for glycosyltransfer, applicable to drug discovery, protein engineering, and other fundamental sugar nucleotide-dependent investigations. This study directly challenges the general notion that NDP-sugars are ‘high-energy’ sugar donors when taken out of their traditional biological context. PMID:21857660

Gantt, Richard W.; Peltier-Pain, Pauline; Cournoyer, William J.; Thorson, Jon S.

2011-01-01

168

Using simple donors to drive the equilibria of glycosyltransferase-catalyzed reactions.  

PubMed

We report that simple glycoside donors can drastically shift the equilibria of glycosyltransferase-catalyzed reactions, transforming NDP-sugar formation from an endothermic to an exothermic process. To demonstrate the utility of this thermodynamic adaptability, we highlight the glycosyltransferase-catalyzed synthesis of 22 sugar nucleotides from simple aromatic sugar donors, as well as the corresponding in situ formation of sugar nucleotides as a driving force in the context of glycosyltransferase-catalyzed reactions for small-molecule glycodiversification. These simple aromatic donors also enabled a general colorimetric assay for glycosyltransfer, applicable to drug discovery, protein engineering and other fundamental sugar nucleotide-dependent investigations. This study directly challenges the general notion that NDP-sugars are 'high-energy' sugar donors when taken out of their traditional biological context. PMID:21857660

Gantt, Richard W; Peltier-Pain, Pauline; Cournoyer, William J; Thorson, Jon S

2011-10-01

169

Enantioselective Direct Mannich Reactions of Cyclic ?-Ketoesters Catalyzed by Chiral Phosphine via a Novel Dual-Reagent Catalysis.  

PubMed

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

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

2015-02-01

170

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

PubMed Central

Splicing of nuclear pre-mRNA occurs via two steps of the transesterification reaction, forming a lariat intermediate and product. The reactions are catalyzed by the spliceosome, a large ribonucleoprotein complex composed of five small nuclear RNAs and numerous protein factors. The spliceosome shares a similar catalytic core structure with that of fungal group II introns, which can self-splice using the same chemical mechanism. Like group II introns, both catalytic steps of pre-mRNA splicing can efficiently reverse on the affinity-purified spliceosome. The spliceosome also catalyzes a hydrolytic spliced-exon reopening reaction as observed in group II introns, indicating a strong link in their evolutionary relationship. We show here that, by arresting splicing after the first catalytic step, the purified spliceosome can catalyze debranching of lariat-intron-exon 2. The debranching reaction, although not observed in group II introns, has similar monovalent cation preferences as those for splicing catalysis of group II introns. The debranching reaction is in competition with the reverse Step 1 reaction influenced by the ionic environment and the structure of components binding near the catalytic center, suggesting that the catalytic center of the spliceosome can switch between different conformations to direct different chemical reactions. PMID:23681507

Tseng, Chi-Kang; Cheng, Soo-Chen

2013-01-01

171

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

PubMed

Splicing of nuclear pre-mRNA occurs via two steps of the transesterification reaction, forming a lariat intermediate and product. The reactions are catalyzed by the spliceosome, a large ribonucleoprotein complex composed of five small nuclear RNAs and numerous protein factors. The spliceosome shares a similar catalytic core structure with that of fungal group II introns, which can self-splice using the same chemical mechanism. Like group II introns, both catalytic steps of pre-mRNA splicing can efficiently reverse on the affinity-purified spliceosome. The spliceosome also catalyzes a hydrolytic spliced-exon reopening reaction as observed in group II introns, indicating a strong link in their evolutionary relationship. We show here that, by arresting splicing after the first catalytic step, the purified spliceosome can catalyze debranching of lariat-intron-exon 2. The debranching reaction, although not observed in group II introns, has similar monovalent cation preferences as those for splicing catalysis of group II introns. The debranching reaction is in competition with the reverse Step 1 reaction influenced by the ionic environment and the structure of components binding near the catalytic center, suggesting that the catalytic center of the spliceosome can switch between different conformations to direct different chemical reactions. PMID:23681507

Tseng, Chi-Kang; Cheng, Soo-Chen

2013-07-01

172

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

PubMed

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

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

2003-09-01

173

Toward the ideal synthesis. New transition metal-catalyzed reactions inspired by novel medicinal leads  

Microsoft Academic Search

Studies in our laboratory are directed at the advancement of synthesis, biology, and medicine. This lecture will focus on new transition metal-catalyzed reactions that have been inspired by biologically potent targets such as phorbol and Taxol ® and by the more general interest in producing syntheses that are concise, efficient, cost- and resource-effective, envi- ronmentally benign, quick, and simple to

Paul A. Wender; F. Christopher Bi; Gabriel G. Gamber; Francis Gosselin; Robert D. Hubbard; Marc J. C. Scanio; Robert Sun; Travis J. Williams; Lei Zhang

2002-01-01

174

Asymmetric Dearomatization of ?-Naphthols through an Amination Reaction Catalyzed by a Chiral Phosphoric Acid.  

PubMed

A highly efficient catalytic asymmetric dearomatization of naphthols by means of an electrophilic amination reaction catalyzed by chiral phosphoric acid is presented. This protocol provides a facile access to functionalized ?-naphthalenone compounds with a chiral quaternary carbon center in excellent yields and enantioselectivity (up to 99?% yield, up to 96?%?ee). PMID:25414091

Wang, Shou-Guo; Yin, Qin; Zhuo, Chun-Xiang; You, Shu-Li

2015-01-01

175

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

E-print Network

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

Elrod, Matthew J.

176

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

PubMed

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

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

2013-05-01

177

Examples of acid-catalyzed mineral dissolution reactions resulting in pH  

E-print Network

Examples of acid-catalyzed mineral dissolution reactions resulting in pH buffering: The goal and analyzed by the Alberta Geological Survey. Percent mineral composition for each sample is presented sample was assumed to have a porosity of 20% and a total rock mass of 12 kg. 4.61 Calcite(78), Quartz(18

Peters, Catherine A.

178

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

NASA Technical Reports Server (NTRS)

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.

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

1973-01-01

179

Oscillating photoluminescence in the cerium ion catalyzed Belousov-Zhabotinsky reaction  

Microsoft Academic Search

Oscillating photoluminescence in the Ce(III)\\/Ce(IV) catalyzed Belousov-Zhabotinsky reaction is described. No quantitative data can be obtained from luminescence intensity measurements, due to quenching and inner filter effects. From lifetime measurements, it is possible to evaluate the quenching effect, which is attributed to bromate ions that oxidize the excited Ce(III) species. Some consequences are discussed.

F. Bolletta; L. Prodi; N. Zaccheroni

1995-01-01

180

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

PubMed

?,?-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

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

2015-02-16

181

From vinyl pyranoses to carbasugars by an iron-catalyzed reaction complementary to classical Ferrier carbocyclization.  

PubMed

Starting from vinyl pyranoses an iron-catalyzed tandem isomerization-intramolecular aldolization reaction was developed to prepare cyclohexenone derivatives bearing substituents on the double bond, and it has been applied in a short synthesis of 4-epi-gabosines A and B, from d-glucose. PMID:19641820

Mac, Dinh Hung; Samineni, Ramesh; Petrignet, Julien; Srihari, Pabbaraja; Chandrasekhar, Srivari; Yadav, Jhillu Singh; Grée, René

2009-08-21

182

Distinct Reactions Catalyzed by Bacterial and Yeast trans-Aconitate Methyltransferases  

E-print Network

, suggesting that methylation occurs on a specific site in trans-aconitate (11). Tandem mass spectrometry didDistinct Reactions Catalyzed by Bacterial and Yeast trans-Aconitate Methyltransferases Hui Cai-1569 ReceiVed September 29, 2000; ReVised Manuscript ReceiVed December 14, 2000 ABSTRACT: The trans-aconitate

Clarke, Steven

183

Rhodium-complex-catalyzed addition reactions of chloroacetyl chlorides to alkynes.  

PubMed

The addition reaction of chloroacetyl chloride derivatives with terminal alkynes was found to be catalyzed by Rh(acac)(CO)(AsPh(3)) to afford (Z)-1,4-dichloro-3-buten-2-one derivatives, which displayed diverse reactivities in synthetic elaboration. PMID:18991444

Kashiwabara, Taigo; Fuse, Kouichiro; Hua, Ruimao; Tanaka, Masato

2008-12-01

184

Development of the Pictet-Spengler reaction catalyzed by AuCl3/AgOTf.  

PubMed

Mild and efficient AuCl3/AgOTf-catalyzed Pictet-Spengler reactions were developed to afford in good yields a variety of tetrahydroisoquinoline and tetrahydro-beta-carboline ring systems, which constitute important motifs in biologically active natural and synthetic organic compounds. PMID:16526809

Youn, So Won

2006-03-17

185

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

DOEpatents

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.

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

2003-12-30

186

9422 Stratospheric ice catalyzes chlorine reactions 9428 Fusing silk and silica  

E-print Network

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

McFadden, Geoff

187

Palladium(II)-catalyzed dehydrogenative alkenylation of cyclic enaminones via the Fujiwara-Moritani reaction.  

PubMed

A new Pd(II)-catalyzed dehydrogenative alkenylation reaction involving two alkenes was developed. A variety of nonaromatic, cyclic enaminones were successfully coupled to primary and secondary alkenes yielding a series of unique 1,3-dienes. The generality of this transformation presents a useful strategy for directly cross-coupling alkenes and offers an attractive new approach to functionalize enaminones. PMID:21995751

Yu, Yi-Yun; Niphakis, Micah J; Georg, Gunda I

2011-11-01

188

Estimation of rate constants in lysozyme-catalyzed reaction of chitooligosaccharides.  

PubMed

The rate constants of the cleavage of glycoside linkage, hydration (hydrolysis) and transglycosylation in a lysozyme-catalyzed reaction of substrate chitooligosaccharides were evaluated by computer analysis of the experimentally obtained reaction time-courses. In the computer analysis, the rate equation was numerically solved by use of the known binding constants for each subsite. Because of the complexity of the lysozyme-catalyzed reaction, optimal values of rate constants were determined by checking the sensitivity of each rate constant to the computed time-courses. It was not possible to estimate uniquely the rate constants for transglycosylation and hydration, owing to the nature of the enzymatic reaction, but it was possible to estimate accurately their ratio. The estimated values were 0.94 s-1 for the rate constant for the cleavage of glycosidic linkage and 133 for the ratio of rate constants of transglycosylation and hydration. PMID:7309713

Masaki, A; Fukamizo, T; Otakara, A; Torikata, T; Hayashi, K; Imoto, T

1981-10-01

189

Metal-Catalyzed Cascade Reactions: Useful Synthetic Tools for the Preparation of Polycyclic Arenes.  

PubMed

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

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

2014-11-01

190

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

E-print Network

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

Kang, Jun

2011-10-21

191

Reaction Dynamics of ATP Hydrolysis Catalyzed by P-Glycoprotein  

PubMed Central

P-glycoprotein (P-gp) is a member of the ABC transporter family that confers drug resistance to many tumors by catalyzing their efflux, and it is a major component of drug–drug interactions. P-gp couples drug efflux with ATP hydrolysis by coordinating conformational changes in the drug binding sites with the hydrolysis of ATP and release of ADP. To understand the relative rates of the chemical step for hydrolysis and the conformational changes that follow it, we exploited isotope exchange methods to determine the extent to which the ATP hydrolysis step is reversible. With ?18O4-labeled ATP, no positional isotope exchange is detectable at the bridging ?-phosphorus–O??-phosphorus bond. Furthermore, the phosphate derived from hydrolysis includes a constant ratio of three 18O/two 18O/one 18O that reflects the isotopic composition of the starting ATP in multiple experiments. Thus, H2O-exchange with HPO42– (Pi) was negligible, suggesting that a [P-gp·ADP·Pi] is not long-lived. This further demonstrates that the hydrolysis is essentially irreversible in the active site. These mechanistic details of ATP hydrolysis are consistent with a very fast conformational change immediately following, or concomitant with, hydrolysis of the ?-phosphate linkage that ensures a high commitment to catalysis in both drug-free and drug-bound states. PMID:24506763

2015-01-01

192

Graphene cover-promoted metal-catalyzed reactions.  

PubMed

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

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

2014-12-01

193

Eutectic salt catalyzed environmentally benign and highly efficient Biginelli reaction.  

PubMed

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

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

2012-01-01

194

Eutectic Salt Catalyzed Environmentally Benign and Highly Efficient Biginelli Reaction  

PubMed Central

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

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

2012-01-01

195

The Studies of the Phosphine-Initiated General Base-Catalyzed Double-Michael Reaction and the Nitro-Nazarov Reaction.  

E-print Network

??General base-catalyzed double-Michael reactions of allenes with various dinucleophiles are described. The reactions are facilitated most efficiently by a catalytic amount of trimethylphosphine, affording six… (more)

Szeto, Judy

2014-01-01

196

Barrier compression and tunneling in enzyme catalysed reactions  

NASA Astrophysics Data System (ADS)

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.

Scrutton, Nigel

2011-03-01

197

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

NASA Astrophysics Data System (ADS)

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.

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

2014-08-01

198

Thiourea-catalyzed enantioselective iso-Pictet-Spengler reactions.  

PubMed

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

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

2011-10-21

199

Enantioselective direct aldol reactions catalyzed by L-prolinamide derivatives.  

PubMed

l-Prolinamides 2, prepared from l-proline and simple aliphatic and aromatic amines, have been found to be active catalysts for the direct aldol reaction of 4-nitrobenzaldehyde with neat acetone at room temperature. They give moderate enantioselectivities of up to 46% enantiomeric excess (ee). The enantioselectivity increases as the amide N-H becomes a better hydrogen bond donor. l-Prolinamides 3, derived from the reaction of l-proline with alpha,beta-hydroxyamines such that there is a terminal hydroxyl group, show more efficient catalysis and higher enantioselectivities. In particular, catalyst 3h, prepared from l-proline and (1S,2S)-diphenyl-2-aminoethanol, exhibits high enantioselectivities of up to 93% ee for aromatic aldehydes and up to >99% ee for aliphatic aldehydes under -25 degrees C. Model reactions of benzaldehyde with three enamines derived from the condensation of prolinamides with acetone have been studied by quantum mechanics calculations. The calculations reveal that the amide N-H and the terminal hydroxyl groups form hydrogen bonds with the benzaldehyde substrate. These hydrogen bonds reduce the activation energy and cause high enantioselectivity. Our results suggest a new strategy in the design of new organic catalysts for direct asymmetric aldol reactions and related transformations. PMID:15079057

Tang, Zhuo; Jiang, Fan; Cui, Xin; Gong, Liu-Zhu; Mi, Ai-Qiao; Jiang, Yao-Zhong; Wu, Yun-Dong

2004-04-20

200

The GenK-catalyzed C-6? Methylation in the Biosynthesis of Gentamicin: Isolation and Characterization of a Cobalamin-dependent Radical SAM Enzyme  

PubMed Central

The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-L-methionine (SAM) superfamily was previously predicted based on bioinformatic analysis. A number of these are Cbl-dependent methyltransferases but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp3 carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that one equivalent each of 5?-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. Based on these results, one mechanistic possibility for the GenK reaction can be ruled out and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed. PMID:23679096

Kim, Hak Joong; McCarty, Reid M.; Ogasawara, Yasushi; Liu, Yung-nan; Mansoorabadi, Steven O.; LeVieux, Jake; Liu, Hung-wen

2013-01-01

201

Enzyme Catalysis and the Gibbs Energy  

ERIC Educational Resources Information Center

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.)

Ault, Addison

2009-01-01

202

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

PubMed

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

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

1991-06-01

203

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

PubMed

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

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

2013-01-01

204

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

PubMed Central

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

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

2013-01-01

205

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

PubMed Central

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

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

206

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

PubMed

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

Dubbaka, Srinivas Reddy; Vogel, Pierre

2005-12-01

207

Extracellular Enzymes Lab Biochemistry  

E-print Network

Extracellular Enzymes Lab Biochemistry · All organisms convert small organic compounds shown here: All of these reactions, of which there are more than 1000, are catalyzed by enzymes. Glucose Phosphate PathwayEMP Pathway #12;Amino Acids #12;More Complete Metabolic Network TOP #12;#12;Enzymes

Vallino, Joseph J.

208

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

PubMed

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

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

2014-06-16

209

Iron-catalyzed cross-coupling reactions. A scalable synthesis of the immunosuppressive agent FTY720.  

PubMed

A chemo- and regioselective cross-coupling reaction of the functionalized aryl triflate 5 with octylmagnesium bromide catalyzed by cheap, nontoxic, and environmentally benign Fe(acac)(3) sets the basis for a practical and scaleable synthesis of the octylbenzene derivative 6, which serves as a key building block for the preparation of FTY720 (1). This 2-amino-1,3-propanediol derivative shows highly promising immunosuppressive properties and is currently in human clinical phase III trials. PMID:15153030

Seidel, Günter; Laurich, Daniel; Fürstner, Alois

2004-05-28

210

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

PubMed

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

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

2015-01-01

211

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

PubMed Central

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

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

2015-01-01

212

EzCatDB: the enzyme reaction database, 2015 update.  

PubMed

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

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

2015-01-28

213

Quantum Transition State Theory for proton transfer reactions in enzymes  

E-print Network

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.

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

2009-10-07

214

Studies Pertaining to the Diastereoselective Fischer Indolization and Exploration of Aryl Carbamates in Nickel-Catalyzed Reactions.  

E-print Network

??Chapter one provides a concise review of nickel- and iron-catalyzed cross-couplings of unconventional phenolic derivatives. The review summarizes carbon-carbon, carbon¬-nitrogen, and carbon-hydrogen bond forming reactions… (more)

Mesganaw, Tehetena

2012-01-01

215

Palladium- and Ruthenium-Catalyzed Decarboxylative Allylations and Michael Addition-Allylation Reactions. Applications in Nitrogen Heterocycle Synthesis  

E-print Network

Our group has a long-standing interest in Pd or Ru-catalyzed decarboxylative coupling reactions. It has been shown that allyl ?-ketoesters, upon treatment with palladium or ruthenium, generate freely diffusing enolates and ?-allyl electrophiles...

Wang, Chao

2008-08-21

216

Enantioselective synthesis of beta-trifluoromethyl-beta-lactones via NHC-catalyzed ketene-ketone cycloaddition reactions.  

PubMed

The highly diastereo- and enantioselective synthesis of beta-trifluoromethyl-beta-lactones bearing two contiguous stereocenters was realized by chiral N-heterocyclic carbene-catalyzed formal cycloaddition reaction of alkyl(aryl)ketenes and trifluoromethyl ketones. PMID:19681591

Wang, Xiao-Na; Shao, Pan-Lin; Lv, Hui; Ye, Song

2009-09-17

217

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

PubMed Central

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

Qian, Deyun

2011-01-01

218

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

PubMed Central

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

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

2010-01-01

219

Computational analysis of cyclophane-based bisthiourea-catalyzed Henry reactions.  

PubMed

The Henry reaction between benzaldehyde and nitromethane catalyzed by a cyclophane-based bisthiourea has been studied with density functional theory [M06-2X-D3/def2-TZVPP/IEFPCM//TPSS-D2/6-31G(d)/IEFPCM]. The results of our study reveal that the transformation involves the reaction of a thiourea-nitronate complex with the uncoordinated aldehyde. On the basis of our calculations, the formation of the major stereoisomer is kinetically preferred. Employing smaller model systems, we show that the observed stereoselectivity arises primarily from differences in hydrogen bonding in diastereomeric transition states. PMID:24927014

Breugst, Martin; Houk, K N

2014-07-01

220

Transition-Metal-Catalyzed Laboratory-Scale Carbon–Carbon Bond-Forming Reactions of Ethylene  

PubMed Central

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

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

2014-01-01

221

Transition-metal-catalyzed laboratory-scale carbon-carbon bond-forming reactions of ethylene.  

PubMed

Ethylene, the simplest alkene, is the most abundantly synthesized organic molecule by volume. It is readily incorporated into transition-metal-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

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

2013-10-18

222

Cyclopropenimine-Catalyzed Enantioselective Mannich Reactions of t-Butyl Glycinates with N-Boc-Imines  

PubMed Central

Cyclopropenimine 1 is shown to catalyze Mannich reactions between glycine imines and N-Boc-aldimines with high levels of enantio- and diastereocontrol. The reactivity of 1 is shown to be substantially greater than a widely used thiourea cinchona alkaloid derived catalyst. A variety of aryl and aliphatic N-Boc-aldimines are effective substrates for this transformation. A preparative scale reaction to deliver >90 mmol of product is shown using 1 mol% catalyst. The product of this transformation is converted into several useful derivatives. PMID:23906087

Bandar, Jeffrey S.; Lambert, Tristan H.

2013-01-01

223

Phase-Transfer-Catalyzed Asymmetric SN Ar Reaction of ?-Amino Acid Derivatives with Arene Chromium Complexes.  

PubMed

Although phase-transfer-catalyzed asymmetric SN Ar reactions provide unique contribution to the catalytic asymmetric ?-arylations of carbonyl compounds to produce biologically active ?-aryl carbonyl compounds, the electrophiles were limited to arenes bearing strong electron-withdrawing groups, such as a nitro group. To overcome this limitation, we examined the asymmetric SN Ar reactions of ?-amino acid derivatives with arene chromium complexes derived from fluoroarenes, including those containing electron-donating substituents. The arylation was efficiently promoted by binaphthyl-modified chiral phase-transfer catalysts to give the corresponding ?,?-disubstituted ?-amino acids containing various aromatic substituents with high enantioselectivities. PMID:25413360

Shirakawa, Seiji; Yamamoto, Kenichiro; Maruoka, Keiji

2015-01-12

224

Masked 3-aminoindan-1-ones by a palladium-catalyzed three-component annulation reaction.  

PubMed

A new palladium(0)-catalyzed three-component reaction involving a set of salicylic aldehyde triflates, ethylene glycol vinyl ether, and various secondary nucleophilic amines has been developed. Through systematic optimization experiments using multivariate design, the conditions effecting robust and convenient one-pot generation of protected 3-aminoindan-1-ones were identified. A reaction route involving an initial internal Heck arylation of the hydroxyalkyl vinyl ether, iminium ion formation, and subsequent tandem cyclization is invoked to explain the selective formation of the isolated tertiary 3-aminoindan acetals. Hydrogenolysis of orthogonally blocked 3-aminoindan-1-ones delivered primary or secondary amines after 10-20 min of microwave heating. PMID:15675852

Arefalk, Anna; Larhed, Mats; Hallberg, Anders

2005-02-01

225

Copper-catalyzed intramolecular tandem reaction of (2-halogenphenyl)(3-phenyloxiran-2-yl)methanones: synthesis of (Z)-aurones.  

PubMed

A convenient and efficient method for the copper-catalyzed synthesis of (Z)-aurones via intramolecular tandem reaction of (2-halogenphenyl)(3-phenyloxiran-2-yl)methanones is reported. Moreover, a plausible mechanism for the formation of (Z)-aurones is proposed. This is the first report on the synthesis of (Z)-aurones through copper-catalyzed Ullmann coupling reaction employing epoxides as substrates. PMID:24735197

Weng, Yiyi; Chen, Qixu; Su, Weike

2014-05-01

226

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

PubMed

The first examples of metal-catalyzed extended Pummerer reactions through the activation of sulfoxides are described. The copper-catalyzed reactions of ketene dithioacetal monoxides with alkynyl sulfides and ynamides provided a wide variety of ?,?-disulfanyl-?,?-unsaturated carbonyl compounds with an accompanying oxygen rearrangement. The products can be easily converted into 1,4-dicarbonyl compounds and substituted heteroaromatics. DFT calculations and mechanistic experiments revealed a new interesting stepwise addition/oxygen rearrangement mechanism. PMID:23463458

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

2013-04-26

227

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

Microsoft Academic Search

The hammerhead ribozyme is generally accepted as a well characterized metalloenzyme. However, the precise nature of the interactions of the RNA with metal ions remains to be fully defined. Examination of metal ion-catalyzed hammerhead reactions at limited concentrations of metal ions is useful for evaluation of the role of metal ions, as demonstrated in this study. At concentrations of Mn2+

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

2002-01-01

228

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

PubMed Central

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

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

2014-01-01

229

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

PubMed

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

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

2001-12-12

230

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

PubMed

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

Kumar, Pradeep; Dwivedi, Namrata

2013-02-19

231

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

SciTech Connect

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

Tasayco, M.L.; Prestwich, G.D. (State Univ. of New York, Stony Brook (USA))

1990-02-25

232

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

PubMed

An efficient palladium-catalyzed Heck-type reaction of fluoroalkyl halides, including perfluoroalkyl bromides, trifluoromethyl iodides, and difluoroalkyl bromides, has been developed. The reaction proceeds under mild reaction conditions with high efficiency and broad substrate scope, and provides a general and straightforward access to fluoroalkylated alkenes which are of interest in life and material sciences. PMID:25469665

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

2015-01-19

233

Superacid-catalyzed intramolecular cyclization reaction of arylcyanopropionate: geminal substitution effect on superelectrophilicity.  

PubMed

We present superacid-catalyzed intramolecular cyclization reactions of arylcyanopropionates to give cyclized five- and six-membered beta-enamino esters in moderate to high yields. Known intramolecular ring-closing reactions of protonated nitrile to aromatic carbon atom are limited to the 6-membered case. Interestingly, a significant synergistic increase of reactivity of the cyano functionality was observed, and the cyano nitrogen atom was converted into an amino group, when an ester group was present in a geminal arrangement. Deuterium exchange experiments excluded the involvement of deprotonation of the alpha-proton in the cyclization process. The acidity dependence of the cyclization reactions and (13)C NMR studies of a model compound, methyl cyanoacetate, in various acidic media were consistent with the involvement of the O, N-diprotonated dication of methyl cyanoacetate, a distonic dication, in strong acid, and this is considered to be the de facto electrophile in the present cyclization reaction of arylcyanopropionates. PMID:18476746

Nakamura, Satoshi; Sugimoto, Hiromichi; Ohwada, Tomohiko

2008-06-01

234

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

E-print Network

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 ...

Colby Davie, Elizabeth A. (Elizabeth Anne)

2005-01-01

235

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

PubMed Central

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

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

2014-01-01

236

Palladium-catalyzed cyclization reactions of allenes in the presence of unsaturated carbon-carbon bonds.  

PubMed

Modern synthetic chemists have looked for rapid and efficient ways to construct complex molecules while minimizing synthetic manipulation and maximizing atom-economy. Over the last few decades, researchers have made considerable progress toward these goals by taking full advantage of transition metal catalysis and the diverse reactivities of allenes, functional groups which include two cumulative carbon-carbon double bonds. This Account describes our efforts toward the development of Pd-catalyzed cyclization reactions of allenes in the presence of compounds that contain unsaturated carbon-carbon bonds such as alkenyl halides, simple alkenes, allenes, electron-deficient alkynes, or propargylic carbonates. First, we discuss the coupling-cyclization reactions of allenes bearing a nucleophilic functionality in the presence of alkenyl halides, simple alkenes, functionalized and nonfunctionalized allenes, or electron-deficient alkynes. These processes generally involve a Pd(II)-catalyzed sequence: cyclic nucleopalladation, insertion or nucleopalladation, and ?-elimination, reductive elimination, cyclic allylation or protonation. We then focus on Pd(0)-catalyzed cyclization reactions of allenes in the presence of propargylic carbonates. In these transformations, oxidative addition of propargylic carbonates with Pd(0) affords allenylpalladium(II) species, which then react with allenes via insertion or nucleopalladation. These transformations provide easy access to a variety of synthetically versatile monocyclic, dumbbell-type bicyclic, and fused multicyclic compounds. We have also prepared a series of highly enantioenriched products using an axial-to-central chirality transfer strategy. A range of allenes are now readily available, including optically active ones with central and/or axial chirality. Expansion of these reactions to include other types of functionalized allenes, such as allenyl thiols, allenyl hydroxyl amines, and other structures with differing steric and electronic character, could allow access to cyclic skeletons that previously were difficult to prepare. We anticipate that other studies will continue to explore this promising area of synthetic organic chemistry. PMID:24479609

Ye, Juntao; Ma, Shengming

2014-04-15

237

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

PubMed

The peptidoglycan of Staphylococcus aureus is characterized by a high degree of crosslinking and almost completely lacks free carboxyl groups, due to amidation of the D-glutamic acid in the stem peptide. Amidation of peptidoglycan has been proposed to play a decisive role in polymerization of cell wall building blocks, correlating with the crosslinking of neighboring peptidoglycan stem peptides. Mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin. We identified the enzymes catalyzing the formation of D-glutamine in position 2 of the stem peptide. We provide biochemical evidence that the reaction is catalyzed by a glutamine amidotransferase-like protein and a Mur ligase homologue, encoded by SA1707 and SA1708, respectively. Both proteins, for which we propose the designation GatD and MurT, are required for amidation and appear to form a physically stable bi-enzyme complex. To investigate the reaction in vitro we purified recombinant GatD and MurT His-tag fusion proteins and their potential substrates, i.e. UDP-MurNAc-pentapeptide, as well as the membrane-bound cell wall precursors lipid I, lipid II and lipid II-Gly?. In vitro amidation occurred with all bactoprenol-bound intermediates, suggesting that in vivo lipid II and/or lipid II-Gly? may be substrates for GatD/MurT. Inactivation of the GatD active site abolished lipid II amidation. Both, murT and gatD are organized in an operon and are essential genes of S. aureus. BLAST analysis revealed the presence of homologous transcriptional units in a number of gram-positive pathogens, e.g. Mycobacterium tuberculosis, Streptococcus pneumonia and Clostridium perfringens, all known to have a D-iso-glutamine containing PG. A less negatively charged PG reduces susceptibility towards defensins and may play a general role in innate immune signaling. PMID:22291598

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

2012-01-01

238

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

NASA Astrophysics Data System (ADS)

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

Abideen, Saqib Ul

239

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

PubMed Central

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

Vora, Harit U.; Wheeler, Philip

2013-01-01

240

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

SciTech Connect

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

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

2010-11-03

241

Statistical properties of multistep enzyme-mediated reactions  

SciTech Connect

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.

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

242

High performance catalyzed-reaction layer for medium temperature operating solid oxide fuel cells  

SciTech Connect

New concepts for a high performance catalyzed-reaction layer for medium temperature operating solid oxide fuel cells were proposed. Mixed conducting oxide particles, samaria-doped ceria (SDC), were employed as the anode material utilizing highly dispersed noble metal catalysts on their surface. As the cathode material, Sr-doped LaMnO[sub 3] (LSM) particles catalyzed with microcrystalline Pt were employed. Performances of the anode or cathode were examined in the cell using yttria-stabilized zirconia electrolyte at a series of operating temperatures. It was found that the anodic polarization resistance and its activation energy were greatly decreased by loading only a small amount of the catalysts (such as Ru, Rh, and Pt) onto the SDC particles. The polarization loss at the anode showed a minimum value by using the SDC particles with a mean diameter of 1.5 to 2.0 [mu]m. A large depolarizing effect was also observed with a Pt-catalyzed LSM cathode, especially at high current densities.

Watanabe, M.; Uchida, H.; Shibata, M.; Mochizuki, N.; Amikura, K. (Yamanashi Univ., Kofu (Japan). Lab. of Electrochemical Energy Conversion)

1994-02-01

243

Reaction mechanism of the bicopper enzyme peptidylglycine ?-hydroxylating monooxygenase.  

PubMed

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

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

2014-05-16

244

Asymmetric one-pot sequential Friedel–Crafts-type alkylation and ?-oxyamination catalyzed by a peptide and an enzyme  

PubMed Central

Summary In the presence of a peptide catalyst and the oxidative enzyme laccase, a one-pot sequential reaction including a Friedel–Crafts-type alkylation of ?,?-unsaturated aldehydes followed by an ?-oxyamination was realized. The reaction in aqueous solvent to promote the enzymatic oxidation, and the use of a peptide catalyst compatible with such conditions, were essential. The present sequential reaction afforded oxygen-functionalized indole or pyrrole derivatives in a highly enantioselective manner. PMID:23019467

Akagawa, Kengo; Umezawa, Ryota

2012-01-01

245

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

NASA Astrophysics Data System (ADS)

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

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

2010-11-01

246

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

PubMed

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

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

2014-06-20

247

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

PubMed

The mechanism of M(II)-PNP-pincer catalyzed reaction between (i) ethene, (ii) trans-butene with 2-methylbut-2-ene, 2,3-dimethylbut-2-ene and tert-butylbutene is examined by using density functional theory methods (where M = Pt or Pd). All key intermediates and transition states involved in the reaction are precisely located on the respective potential energy surfaces using the popular DFT functionals such as mPW1K, M06-2X, and B3LYP in conjunction with the 6-31+G** basis set. The reaction between these olefins can lead to a linear coupling product or a substituted cyclopropane. The energetic comparison between coupling as well as cyclopropanation pathways involving four pairs of olefins for both platinum (1-4) and palladium (5-8) catalyzed reactions is performed. The key events in the lower energy pathway in the mechanistic course involves (i) a C-C bond formation between the metal bound olefin (ethene or trans-butene) and a free olefin, and (ii) two successive [1,2] hydrogen migrations in the ensuing carbocationic intermediates (1c-4c, and 1d-4d), toward the formation of the coupling product. The computed barriers for these steps in the reaction of metal bound ethene to free tert-butylbutene (or other butenes) are found to be much lower than the corresponding steps when trans-butene is bound to the metal pincer. The Gibbs free energy differences between the transition states leading to the coupling product (TS(d-e)) and that responsible for cyclopropanated product (TS(d-g)) are found to be diminishingly closer in the case of the platinum pincer as compared to that in the palladium system. The computed energetics indicate that the coupled product prefers to remain as a metal olefin complex, consistent with the earlier experimental reports. PMID:22648566

Rajeev, Ramanan; Sunoj, Raghavan B

2012-07-21

248

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

E-print Network

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

Epstein, Irving R.

249

Role of homogeneous formate complexes in the water gas shift reaction catalyzed by the group 6 metal carbonyls  

Microsoft Academic Search

The mechanism of the homogeneous water gas shift reaction catalyzed by the group 6 metal carbonyls involves the intermediacy of a formate complex. Catalytic pressure reactions as well as stoichiometric photolysis and pyrolysis experiments provide support for this mechanism. 10 references, 1 table.

William A. R. Slegeir; Richard S. Sapienza; Richard Rayford; Lillian Lam

1982-01-01

250

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

PubMed Central

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

Liao, Yuan-Xi; Hu, Qiao-Sheng

2010-01-01

251

Aryl ketone synthesis via tandem orthoplatinated triarylphosphite-catalyzed addition reactions of arylboronic acids with aldehydes followed by oxidation.  

PubMed

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

Liao, Yuan-Xi; Hu, Qiao-Sheng

2010-10-15

252

Rapid access to spirocyclized indolenines via palladium-catalyzed cascade reactions of tryptamine derivatives and propargyl carbonate.  

PubMed

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

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

2014-07-01

253

Hydrolase-catalyzed biotransformations in deep eutectic solvents.  

PubMed

Hydrolases show good catalytic activity in deep eutectic solvents, despite the presence of urea, which can denature enzymes, or alcohols, which can interfere with hydrolase-catalyzed reactions. PMID:18309428

Gorke, Johnathan T; Srienc, Friedrich; Kazlauskas, Romas J

2008-03-14

254

Chemoselective Chromium(II)-Catalyzed Cross-Coupling Reactions of Dichlorinated Heteroaromatics with Functionalized Aryl Grignard Reagents.  

PubMed

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

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

2015-01-26

255

Vomilenine reductase--a novel enzyme catalyzing a crucial step in the biosynthesis of the therapeutically applied antiarrhythmic alkaloid ajmaline.  

PubMed

Delineation of the biochemical pathway leading to the antiarrhythmic Rauvolfia alkaloid ajmaline has been an important target in biosynthetic research for many years. The biosynthetic sequence starting with tryptamine and the monoterpene secologanin consists of about 10 different steps. Most of the participating enzymes have been detected and characterized previously, except those catalyzing the reduction of the intermediate vomilenine. A novel NADPH-dependent enzyme that reduces the intermediate has been isolated from Rauvolfia serpentina cell suspension cultures. Vomilenine reductase (M(r )43 kDa, temp opt 30 degrees C, pH opt 5.7-6.2), saturates the indolenine double bond of vomilenine with stereospecific formation of 2beta(R)-1,2-dihydrovomilenine. The described detection, enrichment and properties of the reductase not only closes a gap in ajmaline biosynthesis but is also a prerequisite for overexpressing the protein heterologously for final clarification of its molecular properties. PMID:11937349

von Schumann, Gerald; Gao, Shujuan; Stöckigt, Joachim

2002-06-01

256

LOCATING THE RATE-DETERMINING STEP(S) FOR THREE-STEP HYDROLASE-CATALYZED REACTIONS WITH DYNAFIT  

PubMed Central

Summary Hydrolytic reactions of oligopeptide 4-nitroanilides catalyzed by human-?-thrombin, human activated protein C and human factor Xa were studied at pH 8.0–8.4 and 25.0 ± 0.1 °C by the progress curve method and individual rate constants were calculated mostly within 10% internal error using DYNAFITV. A systematic strategy has been developed for fitting a three-step consecutive mechanism to eighteen hundred to six thousand time-course data points polled from two to four independent kinetic experiments. Enzyme and substrate concentrations were also calculated. Individual rate constants well reproduce published values obtained under comparable conditions and the Michaelis-Menten kinetic parameters calculated from these elementary rate constants are also within reasonable limits of published values. For comparison, the integrated Michaelis-Menten equation was also fitted to data from twelve sets. Both the kcat and kcat/Km values are within 15% agreement with those calculated using the elementary rate constants obtained with DYNAFITV. Rate constants for the second and third consecutive steps are within 3–4 fold indicating that both determine the overall rate. The Factor Xa-catalyzed hydrolysis of N?-Z-D-Arg-Gly-Arg-pNA·2HCl at pH 8.4 in a series of buffers containing increasing fractions of deuterium at 25.0 ± 0.1 °C shows a very strong dependence of k3 and a moderate dependence of k2 on D content in the buffer: the fractionation factors are: 0.49 ± 0.03 for K1, 0.70 ± 0.05 for k2, and (0.32 ± 0.03)2 for k3. PMID:18342021

Zhang, Daoning; Kovach, Ildiko M.; Sheehy, John Paul

2008-01-01

257

Adenylate-forming enzymes  

PubMed Central

Thioesters, amides and esters are common chemical building blocks in a wide array of natural products. The formation of these bonds can be catalyzed in a variety of ways. For chemists, the use of an activating group is a common strategy and adenylate enzymes are exemplars of this approach. Adenylating enzymes activate the otherwise unreactive carboxylic acid by transforming the normal hydroxyl leaving group into adenosine monophosphate. Recently there have been a number of studies of such enzymes and in this review we suggest a new classification scheme. The review highlights the diversity in enzyme fold, active site architecture and metal coordination that has evolved to catalyze this particular reaction. PMID:19836944

Schmelz, Stefan; Naismith, James H.

2012-01-01

258

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

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

259

Lewis acid catalyzed reactions of chiral imidazolidinones and oxazolidinones: insights on the role of the catalyst.  

PubMed

The mechanism proposed by Evans to justify the selectivity obtained in Lewis acid catalyzed Diels-Alder reactions of cyclopentadiene with acyloxazolidinones has been generalized and used in the rationalization of selectivities obtained in many other systems. However, we recently proposed an alternative mechanism, on the basis of open-chain mono- and bicomplexes, that avoids the need for chelates and explains the selectivity obtained by Evans. In this manuscript we apply our proposal to the catalyzed conjugated addition of amines to acylimidazolidinones, reported by Cardillo, and we clearly show that aluminum chelates are not involved in the reaction, as they induce no selectivity, while Cardillo observed high experimental selectivities. Our data equally show that bicomplexes with carbonyl parallel orientation, proposed by Cardillo to justify the experimental selectivity with nonchelating Lewis acids, indeed induce the opposite selectivity and have also to be dismissed. On the other hand, our mechanistic proposal allows for the full rationalization of the data obtained by Cardillo with aluminum, boron, or zinc Lewis acids and supports our previous proposal on DA cycloadditions of dienes to Evans chiral auxiliary derivatives. PMID:21786834

Duarte, Filipe J S; Bakalova, Snezhana M; Cabrita, Eurico J; Santos, A Gil

2011-09-01

260

Synthesis of Highly Substituted ?-Butyrolactones by a Gold-Catalyzed Cascade Reaction of Benzyl Esters.  

PubMed

Easily accessible benzylic esters of 3-butynoic acids in a gold-catalyzed cyclization/rearrangement cascade reaction provided 3-propargyl ?-butyrolactones with the alkene and the carbonyl group not being conjugated. Crossover experiments showed that the formation of the new C?C bond is an intermolecular process. Initially propargylic-benzylic esters were used, but alkyl-substituted benzylic esters worked equally well. In the case of the propargylic-benzylic products, a simple treatment of the products with aluminum oxide initiated a twofold tautomerization to the allenyl-substituted ?-butyrolactones with conjugation of the carbonyl group, the olefin, and the allene. The synthetic sequence can be conducted stepwise or as a one-pot cascade reaction with similar yields. Even in the presence of the gold catalyst the new allene remains intact. PMID:25352382

Blanco Jaimes, Maria Camila; Ahrens, Alexander; Pflästerer, Daniel; Rudolph, Matthias; Hashmi, A Stephen K

2015-01-01

261

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

SciTech Connect

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

Mazighi, K.; Carroll, P.J.; Sneddon, L.G. (Univ. of Pennsylvania, Philadelphia (United States))

1993-05-12

262

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

NASA Technical Reports Server (NTRS)

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

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

1988-01-01

263

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

PubMed

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

Hopkins, B A; Wolfe, J P

2014-12-01

264

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

PubMed

Catalytic reactions promoted by N-heterocyclic carbenes (NHCs) have exploded in popularity since 2004 when several reports described new fundamental reactions that extended beyond the long-studied generation of acyl anion equivalents. These new NHC-catalyzed reactions allow chemists to generate unique reactive species from otherwise inert starting materials, all under simple, mild reaction conditions and with exceptional selectivities. In analogy to transition metal catalysis, the use of NHCs has introduced a new set of elementary steps that operate via discrete reactive species, including acyl anion, homoenolate, and enolate equivalents, usually generated by oxidation state reorganization ("redox neutral" reactions). Nearly all NHC-catalyzed reactions offer operationally simple reactions, proceed at room temperature without the need for stringent exclusion of air, and do not generate reaction byproducts. Variation of the catalyst or reaction conditions can profoundly influence reaction outcomes, and researchers can tune the desired selectivities through careful choice of NHC precursor and base. The catalytically generated homoenolate and enolate equivalents are nucleophilic species. In contrast, the catalytically generated acyl azolium and ?,?-unsaturated acyl azoliums are electrophilic cationic species with unique and unprecedented chemistry. For example, when generated catalytically, these species transformed an ?-functionalized aldehyde to an ester under redox neutral conditions without coupling reagents or waste. In addition to providing new approaches to catalytic esterifications, acyl azoliums offer unique reactivities that chemists can exploit for selective reactions. This Account focuses on the discovery and mechanistic investigation of the catalytic generation of acyl azoliums and ?,?-unsaturated acyl azoliums. These chemical species are fascinating, and their catalytic generation is an important development. Studies of their unusual chemistry, however, date back to the intense investigation of thiamine-dependent enzymatic processes in the 1960s. Acyl azoliums are remarkably reactive in acylation chemistry and are unusually chemoselective. These two properties have led to a new wave of reactions such as redox esterification reaction (1) and the catalytic kinetic resolution of challenging substrates (i.e., 3). Our group and others have also developed methods to generate and exploit ?,?-unsaturated acyl azoliums, which have facilitated new C-C bond-forming annulations, including a catalytic, enantioselective variant of the Claisen rearrangement (2). From essentially one class of catalysts, the N-mesityl derived triazolium salts, researchers can easily prepare highly enantioenriched dihydropyranones and dihydropyridinones. Although this field is now one of the most explored areas of enantioselective C-C bond forming reactions, many mechanistic details remained unsolved and in dispute. In this Account, we address the mechanistic inquiries about the characterization of the unsaturated acyl triazolium species and its kinetic profile under catalytically relevant conditions. We also provide explanations for the requirement and effect of the N-mesityl group in NHC catalysis based on detailed experimental data within given specific reactions or conditions. We hope that our studies provide a roadmap for catalyst design/selection and new reaction discovery based on a fundamental understanding of the mechanistic course of NHC reactions. PMID:24410291

Mahatthananchai, Jessada; Bode, Jeffrey W

2014-02-18

265

Assay, purification, and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans.  

PubMed Central

Hydrogenobyrinic acid a,c-diamide was shown to be the substrate of cobaltochelatase, an enzyme that catalyzes cobalt insertion in the corrin ring during the biosynthesis of coenzyme B12 in Pseudomonas denitrificans. Cobaltochelatase was demonstrated to be a complex enzyme composed of two different components of M(r) 140,000 and 450,000, which were purified to homogeneity. The 140,000-M(r) component was shown to be coded by cobN, whereas the 450,000-M(r) component was composed of two polypeptides specified by cobS and cobT. Each component was inactive by itself, but cobaltochelatase activity was reconstituted upon mixing CobN and CobST. The reaction was ATP dependent, and the Km values for hydrogenobyrinic acid a,c-diamide, Co2+, and ATP were 0.085 +/- 0.015, 4.2 +/- 0.2, and 220 +/- 36 microM, respectively. Spectroscopic data revealed that the reaction product was cob(II)yrinic acid a,c-diamide, and experiments with a coupled-enzyme incubation system containing both cobaltochelatase and cob(II)yrinic acid a,c-diamide reductase (F. Blanche, L. Maton, L. Debussche, and D. Thibaut, J. Bacteriol. 174:7452-7454, 1992) confirmed this result. This report not only provides the first evidence that hydrogenobyrinic acid and its a,c-diamide derivative are indeed precursors of adenosylcobalamin but also demonstrates that precorrin-6x, precorrin-6y, and precorrin-8x, three established precursors of hydrogenobyrinic acid (D. Thibaut, M. Couder, A. Famechon, L. Debussche, B. Cameron, J. Crouzet, and F. Blanche, J. Bacteriol. 174:1043-1049, 1992), are also on the pathway to cobalamin. Images PMID:1429466

Debussche, L; Couder, M; Thibaut, D; Cameron, B; Crouzet, J; Blanche, F

1992-01-01

266

Development of new palladium(0)-catalyzed reactions based on novel oxidative addition mode.  

PubMed

We have developed palladium(0)/monophosphine-catalyzed trans-selective arylative, alkenylative, alkylative, and alkynylative cyclization reactions of alkyne-aldehydes and -ketones with organoboron reagents. These reactions afford six-membered allylic alcohols with endo tri- or tetra-substituted olefin groups and/or five-membered counterparts with exo olefin groups. The ratios of these products are dramatically affected by alkyne substituents as well as the phosphine ligand. The remarkable trans selectivity of the process results from the novel reaction mechanism involving 'anti-Wacker'-type oxidative addition. Although the cyclization reactions are influenced by the length of the tether between the alkyne and carbonyl group, they can be applied to a multi-component synthesis of biologically important indenes bearing three substituent groups at 1, 2, 3-positions from available o-ethynylbenzaldehyde derivatives. A two-component coupling reaction in methanol provides 1H-indenols, while a three-component reaction involving secondary aliphatic amines as the third component in DMF affords 1H-indenamines. This method allows combinatorial preparation of unsymmetrically substituted 1H-indenes that cannot be prepared via previous synthetic routes. The same catalytic system can also transform allene-carbonyl compounds into 3-cyclohexenols and -cyclopentenols with alkyl, aryl, alkenyl, alkynyl, and boryl groups at C-3. Microwave irradiation efficiently increases not only the reaction rate but also the product yield by suppressing formation of hydroarylation byproducts. Cyclization of optically active 1,3-disubstituted allene-aldehyde reveals that the reaction proceeds through not carbopalladation but 'anti-Wacker'-type oxidative addition. PMID:18758139

Tsukamoto, Hirokazu

2008-09-01

267

Temperature-dependent change in the rate-determining step in a reaction catalyzed by a hammerhead ribozyme  

Microsoft Academic Search

To characterize the reaction catalyzed by a hammerhead ribozyme, the dependence on temperature of the reaction was examined. An Arrhenius plot revealed a transition that indicated a temperature-dependent change in the activation energy at around 25°C. Thermodynamic parameters of the reaction were estimated at 10 and 35°C. The analyses led to the following conclusions. At 25–50°C. the chemical cleavage step

Yasuomi Takagi; Kazunari Taira

1995-01-01

268

Small peptides catalyze highly enantioselective direct aldol reactions of aldehydes with hydroxyacetone: unprecedented regiocontrol in aqueous media.  

PubMed

[reaction: see text] L-Proline-based small peptides have been developed as efficient catalysts for the asymmetric direct aldol reactions of hydroxyacetone with aldehydes. Chiral 1,4-diols 7, which are disfavored products in similar aldol reactions catalyzed by either aldolases or L-proline, were obtained in high yields and enantioselectivities of up to 96% ee with peptides 3 and 4 in aqueous media. PMID:15200341

Tang, Zhuo; Yang, Zhi-Hua; Cun, Lin-Feng; Gong, Liu-Zhu; Mi, Ai-Qiao; Jiang, Yao-Zhong

2004-06-24

269

Formal carbene insertion into C-C bond: Rh(I)-catalyzed reaction of benzocyclobutenols with diazoesters.  

PubMed

A Rh(I)-catalyzed formal carbene insertion into C-C bond of benzocyclobutenols has been realized by employing diazoesters as carbene precursors. The product indanol derivatives were obtained in good yields and in diastereoselective manner under mild reaction conditions. All-carbon quaternary center is constructed at the carbenic carbon. This catalytic reaction involves selective cleavage of C-C bond, Rh(I) carbene insertion, and intramolecular aldol reaction. PMID:24512084

Xia, Ying; Liu, Zhenxing; Liu, Zhen; Ge, Rui; Ye, Fei; Hossain, Mohammad; Zhang, Yan; Wang, Jianbo

2014-02-26

270

The Contribution of Electrostatic and van der Waals Interactions to the Stereospecificity of the Reaction Catalyzed by Lactate Dehydrogenase  

PubMed Central

Continuum electrostatic calculations in conjunction with molecular dynamics simulations have been used to investigate the source of the stereospecificity in the hydride transfer reaction catalyzed by lactate dehydrogenase (LDH). These studies show that favorable electrostatic interactions between the carboxamide group of the reduced nicotinamide adenine dinucleotide coenzyme and protein residues of the active site of LDH can account for much if not all of the stereospecificity of the LDH-catalyzed reaction, with A-side hydride transfer more than 107 times greater than B-side transfer. Unfavorable steric interactions within the binding complex for B-side transfer are not found. ImagesFIGURE 2 PMID:9017191

van Beek, Jeroen; Callender, Robert; Gunner, M. R.

1997-01-01

271

Bioluminescence reaction catalyzed by membrane-bound luciferase in the "firefly squid," Watasenia scintillans.  

PubMed

The small Japanese "firefly squid," Watasenia scintillans, emits a bluish luminescence from dermal photogenic organs distributed along the ventral aspects of the head, mantle, funnel, arms and eyes. The brightest light is emitted by a cluster of three tiny organs located at the tip of each of the fourth pair of arms. Studies of extracts of the arm organs show that the light is due to a luciferin-luciferase reaction in which the luciferase is membrane-bound. The other components of the reaction are coelenterazine disulfate (luciferin), ATP, Mg(2+), and molecular oxygen. Based on the results, a reaction scheme is proposed which involves a rapid base/luciferase-catalyzed enolization of the keto group of the C-3 carbon of luciferin, followed by an adenylation of the enol group by ATP. The AMP serves as a recognition moiety for docking the substrate molecule to a luciferase bound to membrane, after which AMP is cleaved and a four-membered dioxetanone intermediate is formed by the addition of molecular oxygen. The intermediate then spontaneously decomposes to yield CO(2) and coelenteramide disulfate (oxyluciferin) in the excited state, which serves as the light emitter in the reaction. PMID:12101012

Tsuji, Frederick I

2002-08-19

272

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

PubMed Central

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

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

2011-01-01

273

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

PubMed

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

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

2014-09-12

274

Regioselective Dihalohydration Reactions of Propargylic Alcohols: Gold-Catalyzed and Noncatalyzed Reactions**  

PubMed Central

The regioselective conversion of propargylic alcohols into previously unreported ?,?-diiodo-?-hydroxyketones was achieved by treatment with N-iodosuccinimide in the presence of a gold catalyst. The corresponding ?,?-dichloro-?-hydroxyketones were obtained by treatment with trichloroisocyanuric acid in the absence of a catalyst. The latter reaction can be extended to other alkynols. These transformations can be used to prepare potentially useful halogenated building blocks. Preliminary mechanistic studies suggest that the reaction involves participation of the acetonitrile solvent in the formation of a 5-halo-1,3-oxazine intermediate. PMID:25147077

D’Oyley, Jarryl M; Aliev, Abil E; Sheppard, Tom D

2014-01-01

275

Palladium-Catalyzed Suzuki-Miyaura Cross-coupling Reactions Employing Dialkylbiaryl Phosphine Ligands  

PubMed Central

Conspectus The cores of many types of polymers, ligands, natural products, and pharmaceuticals contain biaryl or substituted aromatic structures, and efficient methods of synthesizing these structures are crucial to the work of a broad spectrum of organic chemists. Recently, Pd-catalyzed carbon-carbon bond-forming processes, particularly the Suzuki–Miyaura cross-coupling reaction (SMC), have risen in popularity for this purpose. The SMC has many advantages over other methods for constructing these moieties, including mild conditions, high tolerance toward functional groups, the commercial availability and stability of its reagents, and the ease of handling and separating byproducts from its reaction mixtures. Until 1998, most catalysts for the SMC employed triarylphosphine ligands. More recently, new bulky and electron-rich phosphine ligands, which can dramatically improve the efficiency and selectivity of such cross-coupling reactions, have been introduced. In the course of our studies on carbon-nitrogen bond-forming reactions, we found that the use of electron-rich and bulky phosphines enhanced the rate of both the oxidative addition and reductive elimination processes; this was the beginning of our development of a new family of ligands, the dialkylbiarylphosphines L1–L12. These ligands can be used for a wide variety of palladium-catalyzed carbon–carbon, carbon–nitrogen, and carbon–oxygen bond-forming processes as well as serving as supporting ligands for a number of other reactions. The enhanced reactivity of these catalysts has expanded the scope of cross-coupling partners that can be employed in the SMC. Using such dialkylbiarylphosphine ligands, the coupling of unactivated aryl chlorides, aryl tosylates, heteroaryl systems, and very hindered substrate combinations have become routine. The utility of these ligands has been successfully demonstrated in a wide number of synthetic applications, including industrially relevant processes. In this account, we provide an overview of the use and impact of dialkylbiarylphosphine ligands in the SMC. We discuss our studies on the mechanistic framework of the reaction, which have allowed us to rationally modify the ligand structures in order to tune their properties. We also describe selected applications in the synthesis of natural products and new materials to illustrate the utility of these dialkylbiarylphosphine ligands in various “real-world” synthetic applications. PMID:18620434

Martin, Ruben; Buchwald, Stephen L.

2008-01-01

276

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

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.

Nguyen, T.; Fedorov, A; Williams, L; Fedorov, E; Li, Y; Xu, C; Almo, S; Raushel, F

2009-01-01

277

Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.  

PubMed Central

The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases. PMID:7751268

Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

1995-01-01

278

Water-catalyzed excited-state proton-transfer reactions in 7-azaindole and its analogues.  

PubMed

The mechanism of the water-catalyzed excited-state proton-transfer (ESPT) reaction for 7-azaindole (7AI) has long been investigated, but there are some controversial viewpoints. Recently, owing to the superiority of sensing biowaters in proteins by a 7AI analogue, 2,7-diazatryptophan, it is timely to reinvestigate water-catalyzed ESPT in 7AI and its analogues in an attempt to unify the mechanism. Herein, a series of 7AI analogues and their methylated derivatives were synthesized to carry out a systematic study on pKa, pKa*, and the associated fluorescence spectroscopy and dynamics. The results conclude that all 7AI derivatives undergo water-catalyzed ESPT in neutral water. However, for those derivatives with -H (7AI) and a electron-donating substituent at C(3), they follow water-catalyzed ESPT to form an excited N(7)-H proton-transfer tautomer, T*. T* is rapidly protonated to generate an excited cationic (TC*) species. TC* then undergoes a fast deactivation to the N(1)-H normal species in the ground state. Conversely, protonation in T* is prohibited for those derivatives with an electron-withdrawing group at the C(2) or C(3) or with the C(2) atom replaced by an electron-withdrawing nitrogen atom (N(2) in, e.g., 2,7-diazatryptophan), giving a prominent green T* emission. Additional support is given by the synthesis of the corresponding N(7)-CH3 tautomer species, for which pKa* of the cationic form, that is, the N(7)-CH3N(1)-H(+) species, is measured to be much greater than 7.0 for those with electron-donating C(3) substituents, whereas it is lower than 7.0 upon anchoring electron-withdrawing groups. For 7AI, the previously missing T* emission is clearly resolved with a peak wavelength at 530 nm in the pH interval of 13.0-14.3 (H- 14.2). PMID:25225896

Wu, Yu-Sin; Huang, Huai-Ching; Shen, Jiun-Yi; Tseng, Huan-Wei; Ho, Jr-Wei; Chen, You-Hua; Chou, Pi-Tai

2015-02-12

279

Quantum Mechanical\\/Molecular Mechanical Studies of the Triosephosphate Isomerase-Catalyzed Reaction:  Verification of Methodology and Analysis of Reaction Mechanisms  

Microsoft Academic Search

Three possible mechanisms for the reactions catalyzed by triosephosphate isomerase (TIM) have been studied by the combined quantum mechanical\\/molecular mechanical (QM\\/MM) approach at a number of QM levels including AM1, AM1 with specific reaction parameters (SRP), and B3LYP\\/6-31+G(d,p). The comparison of the various QM levels is used to verify the adequacy of our recent B3LYP\\/MM analysis of the reaction mechanism

Qiang Cui; Martin Karplus

2002-01-01

280

The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?  

NASA Astrophysics Data System (ADS)

We consider the role of quantum effects in the transfer of hydrogen-like species in enzyme-catalyzed reactions. This review is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects (KIEs) implies that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We review the path integral approach and the Caldeira-Leggett model, which provides a general framework to describe and understand tunneling in a quantum system that interacts with a noisy environment at nonzero temperature. Here the quantum system is the active site of the enzyme, and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature T0, which is determined by the curvature of the potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. We review typical values for the parameters in the Caldeira-Leggett Hamiltonian, including the frequency-dependent friction and noise due to the environment. For physically reasonable parameters, we show that quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of KIEs for two classes of enzymes that have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction and noise due to the environment are weak and only slightly modify the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental fluctuations with frequencies much less than 1000 cm-1 do not have a significant effect on quantum corrections to the reaction rate. This is essentially because the time scales associated with the dynamics of proton transfer are faster than much of the low-frequency noise associated with the protein and solvent.

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

2010-05-01

281

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

SciTech Connect

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.

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

1989-08-18

282

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

SciTech Connect

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.

Andrews, Mark

1997-01-08

283

NMR analysis of enzyme-catalyzed and free-equilibrium mutarotation kinetics of monosaccharides.  

PubMed

We have exploited the saturation difference (SD) NMR technique to investigate the mutarotations of two sugars, l-fucose and d-ribose, at equilibrium. The KM and kcat values of Escherichia coli FucU-catalyzed mutarotation of l-fucose have been determined by this technique, and the values of KM for alpha- and beta-forms are shown to be the same. Similarly, the spontaneous mutarotation of d-ribose was investigated by using the same method, and it was found that d-ribose has an exceptionally high spontaneous alpha-to-beta conversion rate only between the furan forms. PMID:15281797

Ryu, Kyoung-Seok; Kim, Changhoon; Park, Chankyu; Choi, Byong-Seok

2004-08-01

284

Transition-metal-catalyzed carbonylation reactions of olefins and alkynes: a personal account.  

PubMed

Carbon monoxide was discovered and identified in the 18th century. Since the first applications in industry 80 years ago, academic and industrial laboratories have broadly explored CO's use in chemical reactions. Today organic chemists routinely employ CO in organic chemistry to synthesize all kinds of carbonyl compounds. Despite all these achievements and a century of carbonylation catalysis, many important research questions and challenges remain. Notably, apart from academic developments, industry applies carbonylation reactions with CO on bulk scale. In fact, today the largest applications of homogeneous catalysis (regarding scale) are carbonylation reactions, especially hydroformylations. In addition, the vast majority of acetic acid is produced via carbonylation of methanol (Monsanto or Cativa process). The carbonylation of olefins/alkynes with nucleophiles, such as alcohols and amines, represent another important type of such reactions. In this Account, we discuss our work on various carbonylations of unsaturated compounds and related reactions. Rhodium-catalyzed isomerization and hydroformylation reactions of internal olefins provide straightforward access to higher value aldehydes. Catalytic hydroaminomethylations offer an ideal way to synthesize substituted amines and even heterocycles directly. More recently, our group has also developed so-called alternative metal catalysts based on iridium, ruthenium, and iron. What about the future of carbonylation reactions? CO is already one of the most versatile C1 building blocks for organic synthesis and is widely used in industry. However, because of CO's high toxicity and gaseous nature, organic chemists are often reluctant to apply carbonylations more frequently. In addition, new regulations have recently made the transportation of carbon monoxide more difficult. Hence, researchers will need to develop and more frequently use practical and benign CO-generating reagents. Apart from formates, alcohols, and metal carbonyls, carbon dioxide also offers interesting options. Industrial chemists seek easy to prepare catalysts and patent-free ligands/complexes. In addition, non-noble metal complexes will interest both academic and industrial researchers. The novel Lucite process for methyl methacrylate is an important example of an improved catalyst. This reaction makes use of a specific palladium/bisphosphine catalyst, which led to the successful implementation of the technology. More active and productive catalysts for related carbonylations of less reactive olefins would allow for other large scale applications of this methodology. From an academic point of view, researchers continue to look for selective reactions with more functionalized olefins. Finally, because of the volatility of simple metal carbonyl complexes, carbonylation reactions today remain a domain of homogeneous catalysis. The invention of more stable and recyclable heterogeneous catalysts or metal-free carbonylations (radical carbonylations) will be difficult, but could offer interesting challenges for young chemists. PMID:24564478

Wu, Xiao-Feng; Fang, Xianjie; Wu, Lipeng; Jackstell, Ralf; Neumann, Helfried; Beller, Matthias

2014-04-15

285

[Conformation aspects of peptide interaction with proteolytic enzymes. Alpha-chymotrypsin catalyzed hydrolysis of the cyclopeptides containing leucyltyrosyl fragments].  

PubMed

The studies were made on the interaction of alpha-chymotrypsin with a series of cyclopeptides cyclo(-L-leucyl-L-tyrosyl-glycyln-), n=4, 6 and 8 (I, II and III respectively), and cyclo(-L-leucyl-L-tryosyl-beta-aminovalero-yl2-) (IV). Compounds I and IV are resistant to enzyme action whereas cyclopeptides II and III proved to be the substrates, their kinetic constants being Km=15.4 and 13.2 mM and kcat=0.54 and 9.53 sec-1 respectively. The binding capacity of cyclopeptides I-IV is evaluated by their competitive inhibition of alpha-chymotrypsin catalyzed hydrolysis of N-acetyl-L-tyrosine methyl ester. PMID:1203366

Tsetlin, M M; Ivanov, V T; Ovchinnikov, Y A; Klyosov, A A

1975-01-01

286

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

SciTech Connect

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.

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

2009-05-21

287

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

SciTech Connect

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.

Netzel, D.A.

1991-04-01

288

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

SciTech Connect

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.

Netzel, D.A.

1991-04-01

289

Imidazolium hydrogen carbonates versus imidazolium carboxylates as organic precatalysts for N-heterocyclic carbene catalyzed reactions.  

PubMed

Imidazolium-2-carboxylates (NHC-CO(2) adducts, 3) and (benz)imidazolium hydrogen carbonates ([NHC(H)][HCO(3)], 4) were independently employed as organic precatalysts for various molecular N-heterocyclic carbene (NHC) catalyzed reactions. NHC-CO(2) adducts were obtained by carboxylation in THF of related free NHCs (2), while the synthesis of [NHC(H)][HCO(3)] precursors was directly achieved by anion metathesis of imidazolium halides (1) using potassium hydrogen carbonate (KHCO(3)) in methanolic solution, without the need for the prior preparation of free carbenes. Thermogravimetric analysis (TGA) and TGA coupled with mass spectrometry (TGA-MS) of most [NHC(H)][HCO(3)] precursors 4 showed a degradation profile in stages, with either a concomitant or a stepwise release of H(2)O and CO(2), between 108 and 280 °C, depending on the nature of the azolium and substituents. In solution, NHC generation from both [NHC(H)][HCO(3)] salts and NHC-CO(2) adducts could be achieved at room temperature, most likely by a simple solvation effect. Both types of precursors proved efficient for organocatalyzed molecular reactions, including cyanosilylation, benzoin condensation, and transesterification reactions. The catalytic efficiencies of NHC-CO(2) adducts 3 were found to be approximately 3 times higher than those of their [NHC(H)][HCO(3)] counterparts 4. PMID:23092332

Fèvre, Maréva; Coupillaud, Paul; Miqueu, Karinne; Sotiropoulos, Jean-Marc; Vignolle, Joan; Taton, Daniel

2012-11-16

290

Gold atoms stabilized on various supports catalyze the water-gas shift reaction.  

PubMed

For important chemical reactions that are catalyzed by single-site metal centers, such as the water-gas shift (WGS) reaction that converts carbon monoxide and water to hydrogen and carbon dioxide, atomically dispersed supported metal catalysts offer maximum atom efficiency. Researchers have found that for platinum metal supported on ceria and doped ceria in the automobile exhaust catalyst, atomic Pt-Ox-Ce species are the active WGS reaction sites. More recently, preparations of gold at the nanoscale have shown that this relatively "new material" is an active and often more selective catalyst than platinum for a variety of reactions, including the WGS reaction. The activity of gold is typically attributed to a size effect, while the interface of gold with the support has also been reported as important for oxidation reactions, but exactly how this comes about has not been probed satisfactorily. Typical supported metal catalysts prepared by traditional techniques have a heterogeneous population of particles, nanoclusters, subnanometer species, and isolated atoms/ions on the support surfaces, making the identification of the active sites difficult. Both we and other researchers have clearly shown that gold nanoparticles are spectator species in the WGS reaction. Evidence has now amassed that the gold active site for the WGS reaction is atomic, that is, Au-Ox species catalyze the reaction, similar to Pt-Ox. In this Account, we review the relevant literature to conclude that the intrinsic activity of the Au-Ox(OH)-S site, where S is a support, is the same for any S. The support effect is indirect, through its carrying (or binding) capacity for the active sites. Destabilization of the gold under reducing conditions through the formation of clusters and nanoparticles is accompanied by a measurable activity loss. Therefore, it is necessary to investigate the destabilizing effect of different reaction gas mixtures on the gold atom sites and to consider regeneration methods that effectively redisperse the gold clusters into atoms. For gold catalysts, we can remove weakly bound clusters and nanoparticles from certain supports by leaching techniques. Because of this, we can prepare a uniform dispersion of gold atoms/ions strongly bound to the support surface by this two-step (loading followed by leaching) approach. Presently, one-step preparation methods to maximize the number of the single atom sites on various supports need to be developed, specific to the type of the selected support. Often, it will be beneficial to alter the surface properties of the support to enhance metal ion anchoring, for example, by shape and size control of the support or by the use of light-assisted deposition and anchoring of the metal on photoresponsive supports. Because of their importance for practical catalyst development, synthesis methods are discussed at some length in this Account. PMID:24266870

Flytzani-Stephanopoulos, Maria

2014-03-18

291

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

292

Diazo compounds and N-tosylhydrazones: novel cross-coupling partners in transition-metal-catalyzed reactions.  

PubMed

Transition-metal-catalyzed carbene transformations and cross-couplings represent two major reaction types in organometallic chemistry and organic synthesis. However, for a long period of time, these two important areas have evolved separately, with essentially no overlap or integration. Thus, an intriguing question has emerged: can cross-coupling and metal carbene transformations be merged into a single reaction cycle? Such a combination could facilitate the development of novel carbon-carbon bond-forming methodologies. Although this concept was first explored about 10 years ago, rapid developments inthis area have been achieved recently. Palladium catalysts can be used to couple diazo compounds with a wide variety of organic halides. Under oxidative coupling conditions, diazo compounds can also react with arylboronic acids and terminal alkynes. Both of these coupling reactions form carbon-carbon double bonds. As the key step in these catalytic processes, Pd carbene migratory insertion plays a vital role in merging the elementary steps of Pd intermediates, leading to novel carbon-carbon bond formations. Because the diazo substrates can be generated in situ from N-tosylhydrazones in the presence of base, the N-tosylhydrazones can be used as reaction partners, making this type of cross-coupling reaction practical in organic synthesis. N-Tosylhydrazones are easily derived from the corresponding aldehydes or ketones. The Pd-catalyzed cross-coupling of N-tosylhydrazones is considered a complementary reaction to the classic Shapiro reaction for converting carbonyl functionalities into carbon-carbon double bonds. It can also serve as an alternative approach for the Pd-catalyzed cross-coupling of carbonyl compounds, which is usually achieved via triflates. The combination of carbene formation and cross-coupling in a single catalytic cycle is not limited to Pd-catalyzed reactions. Recent studies of Cu-, Rh-, Ni-, and Co-catalyzed cross-coupling reactions with diazo compounds or N-tosylhydrazones show that these transformations also work with other transition metals, demonstrating the generality of the diazo compounds as new cross-coupling partners in transition-metal-catalyzed coupling reactions. PMID:23013153

Xiao, Qing; Zhang, Yan; Wang, Jianbo

2013-02-19

293

Highly enantioselective synthesis of tetrahydrocarbolines via iridium-catalyzed intramolecular Friedel-Crafts type allylic alkylation reactions.  

PubMed

A highly enantioselective synthesis of substituted tetrahydrocarbolines via Ir-catalyzed Friedel-Crafts type intramolecular asymmetric allylic alkylation of 2-indolyl allyl carbonates has been developed. This strategy features excellent chemoselectivity and enantioselectivity, mild reaction conditions, and an easily accessed chiral ligand. PMID:24215126

Xu, Qing-Long; Zhuo, Chun-Xiang; Dai, Li-Xin; You, Shu-Li

2013-12-01

294

Asymmetric catalytic Mannich reactions catalyzed by urea derivatives: enantioselective synthesis of beta-aryl-beta-amino acids.  

PubMed

Highly enantioselective addition reactions between silyl ketene acetals and N-Boc aldimines are catalyzed by the thiourea-based catalyst 1c. Extraordinary scope is observed in this methodology with regard to the imine substrate, with aryl and heteroaromatic derivatives generally affording nearly quantitative yields of beta-amino ester product in up to 98% enantioselectivity. PMID:12405820

Wenzel, Anna G; Jacobsen, Eric N

2002-11-01

295

Metal-ligand binding affinity vs reactivity: qualitative studies in Rh(I)-catalyzed asymmetric ring-opening reactions.  

PubMed

Rh(I)-catalyzed asymmetric ring opening (ARO) of oxabenzonorbornadiene is used as a model system to qualitatively study reactions involving multiple metal-ligand interactions. The key feature of this approach is the use of product ee as an indicator to quickly gain important information such as the relative ligand binding affinity and relative reactivity of catalysts. PMID:23683143

Tsui, Gavin Chit; Dougan, Patrick; Lautens, Mark

2013-06-01

296

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

E-print Network

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

Toste, Dean

297

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....

298

Gene Cloning and Molecular Characterization of a Two-Enzyme System Catalyzing the Oxidative Detoxification of ?-Endosulfan  

PubMed Central

The gram-positive bacterium Mycobacterium sp. strain ESD is able to use the cyclodiene insecticide endosulfan as a source of sulfur for growth. This activity is dependent on the absence of sulfite or sulfate in the growth medium. A cosmid library of strain ESD DNA was constructed in a Mycobacterium-Escherichia coli shuttle vector and screened for endosulfan-degrading activity in Mycobacterium smegmatis, a species that does not degrade endosulfan. Using this method, we identified a single cosmid that conferred sulfur-dependent endosulfan-degrading activity on the host strain. An open reading frame (esd) was identified within this cosmid that, when expressed behind a constitutive promoter in a mycobacterial expression vector, conferred sulfite- and sulfate-independent ?-endosulfan degradation activity on the recombinant strain. The translation product of this gene (Esd) had up to 50% sequence identity with an unusual family of monooxygenase enzymes that use reduced flavins, provided by a separate flavin reductase enzyme, as cosubstrates. An additional partial open reading frame was located upstream of the Esd gene that had sequence homology to the same monooxygenase family. A flavin reductase gene, identified in the M. smegmatis genome, was cloned, expressed, and used to provide reduced flavin mononucleotide for Esd in enzyme assays. Thin-layer chromatography and gas chromatography analyses of the enzyme assay mixtures revealed the disappearance of ?-endosulfan and the appearance of the endosulfan metabolites, endosulfan monoaldehyde and endosulfan hydroxyether. This suggests that Esd catalyzes the oxygenation of ?-endosulfan to endosulfan monoaldehyde and endosulfan hydroxyether. Esd did not degrade either ?-endosulfan or the metabolite of endosulfan, endosulfan sulfate. PMID:12450848

Sutherland, Tara D.; Horne, Irene; Russell, Robyn J.; Oakeshott, John G.

2002-01-01

299

Enantioselective synthesis of ( R)- and ( S)- N-Boc-morpholine-2-carboxylic acids by enzyme-catalyzed kinetic resolution: application to the synthesis of reboxetine analogs  

Microsoft Academic Search

The (R)- and (S)-N-Boc-morpholine-2-carboxylic acids 9 and 10 were prepared using an enantioselective synthesis employing a highly selective enzyme-catalyzed kinetic resolution of racemic n-butyl 4-benzylmorpholine-2-carboxylate (11) as the key step. Acids 9 and 10 were then converted efficiently and stereoselectively to reboxetine analogs 3 and 4.

Paul V. Fish; Malcolm Mackenny; Gerwyn Bish; Timothy Buxton; Russell Cave; David Drouard; David Hoople; Alan Jessiman; Duncan Miller; Christelle Pasquinet; Bhairavi Patel; Keith Reeves; Thomas Ryckmans; Melanie Skerten; Florian Wakenhut

2009-01-01

300

Enantioselective synthesis of fluorene derivatives by chiral N-triflyl phosphoramide catalyzed double Friedel-Crafts alkylation reaction.  

PubMed

A highly efficient tandem double Friedel-Crafts reaction between indoles and 2-formylbiphenyl derivatives by chiral N-triflyl phosphoramide was realized. Under mild conditions, various 9-(3-indolyl) fluorene derivatives have been obtained in good yield and up to 94% ee. Comparing to their corresponding chiral phosphoric acids, chiral N-triflyl phosphoramides catalyzed reactions led to products with opposite absolute configuration. PMID:22411157

Wang, Shou-Guo; Han, Long; Zeng, Mi; Sun, Feng-Lai; Zhang, Wei; You, Shu-Li

2012-04-28

301

Ab initio calculations concerning the reaction mechanism of the copper(II) catalyzed glycine condensation in aqueous sodium chloride solution  

NASA Astrophysics Data System (ADS)

Starting from results of detailed experimental work concerning the copper(II) catalyzed glycine condensation, quantum-mechanical studies of species which should be relevant for the reaction mechanism are presented. This reaction is of special interest because it could be important in explaining the formation of the first peptides on prebiotic earth. SCF geometry optimizations of aquo-chloro-glycinato—copper(II) complexes at Hartree—Fock level were performed especially to study the necessity of chlorine for the reaction. In that way a hypothetical reaction mechanism could be confirmed. Structural distortions as expected from the Jahn—Teller effect resulted from optimizations of copper complexes in C1 geometry.

Liedl, Klaus R.; Rode, Bernd M.

1992-09-01

302

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

PubMed

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

Hendershot, Jenna M; O'Brien, Patrick J

2014-11-10

303

Development of the ReaxFF Reactive Force Field for Describing Transition Metal Catalyzed Reactions, with Application to the Initial Stages of the Catalytic Formation of Carbon Nanotubes  

Microsoft Academic Search

With the aim of developing a computationally inexpensive method for modeling the high-temperature reaction dynamics of transition metal catalyzed reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial quantum mechanics (QM) training set, containing full reaction pathways for relevant reactions. In this paper we apply this approach to reactions involving carbon

Kevin D. Nielson; Jonas Oxgaard; Wei-Qiao Deng; William A. Goddard III; William A. Goddard

2005-01-01

304

In vivo identification of intermediate stages of the DNA inversion reaction catalyzed by the Salmonella Hin recombinase.  

PubMed Central

The Hin recombinase catalyzes a site-specific recombination reaction that results in the reversible inversion of a 1-kbp segment of the Salmonella chromosome. The DNA inversion reaction catalyzed by the Salmonella Hin recombinase is a dynamic process proceeding through many intermediate stages, requiring multiple DNA sites and the Fis accessory protein. Biochemical analysis of this reaction has identified intermediate steps in the inversion reaction but has not yet revealed the process by which transition from one step to another occurs. Because transition from one reaction step to another proceeds through interactions between specific amino acids, and between amino acids and DNA bases, it is possible to study these transitions through mutational analysis of the proteins involved. We isolated a large number of mutants in the Hin recombinase that failed to carry out the DNA exchange reaction. We generated genetic tools that allowed the assignment of these mutants to specific transition steps in the recombination reaction. This genetic analysis, combined with further biochemical analysis, allowed us to define contributions by specific amino acids to individual steps in the DNA inversion reaction. Evidence is also presented in support of a model that Fis protein enhances the binding of Hin to the hixR recombination site. These studies identified regions within the Hin recombinase involved in specific transition steps of the reaction and provided new insights into the molecular details of the reaction mechanism. PMID:9691026

Nanassy, O Z; Hughes, K T

1998-01-01

305

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

SciTech Connect

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.

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

2009-01-01

306

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

PubMed Central

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

Kawamura, Takashi; Kobayashi, Tomoki; Watanabe, Nobuhisa

2015-01-01

307

Low temperature iron- and nickel-catalyzed reactions leading to coalbed gas formation  

NASA Astrophysics Data System (ADS)

Hydrocarbon hydrogenolysis and CO 2 hydrogenation in the presence of Fe/SiO 2 and Ni/SiO 2 catalysts were evaluated as potential mechanisms contributing to natural gas formation in coalbeds. The hydrocarbons used as reactants in hydrogenolysis included butane, octane, 1-octene, and 1-dodecene. The reactions carried out in a laboratory batch reactor produced gas that contained methane concentrations greater than 90%, which resembles the composition of natural gas. Reaction temperatures were selected to resemble natural coalbed conditions. Evidence is presented to show that iron and nickel minerals, which can be present in coals at levels of 2000 and 10 ppm, respectively, can become active under geologic conditions. The oxides (Fe 2O 3 and NiO) used as precursors of the active catalysts (Fe and Ni metals) were reduced at 200°C under a hydrogen atmosphere. Mössbauer spectroscopy showed that ca. 6% of the iron oxide was converted to the metal; in the case of nickel, oxygen titration showed that the extent of reduction to the metal was ca. 29%. The resultant fractions of the active metals in coals are adequate to catalyze generation of appreciable amounts of methane over geologic time.

Medina, Juan Carlos; Butala, Steven J.; Bartholomew, Calvin H.; Lee, Milton L.

2000-02-01

308

Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease.  

PubMed Central

The mechanism of the first steps of the reaction catalyzed by HIV-1 protease was studied through molecular dynamics simulations. The potential energy surface in the active site was generated using the approximate valence bond method. The approximate valence bond (AVB) method was parameterized based on density functional calculations. The surrounding protein and explicit water environment was modeled with conventional, classical force field. The calculations were performed based on HIV-1 protease complexed with the MVT-101 inhibitor that was modified to a model substrate. The protonation state of the catalytic aspartates was determined theoretically. Possible reaction mechanisms involving the lytic water molecule are accounted for in this study. The modeled steps include the dissociation of the lytic water molecule and proton transfer onto Asp-125, the nucleophilic attack followed by a proton transfer onto peptide nitrogen. The simulations show that in the active site most preferable energetically are structures consisting of ionized or polarized molecular fragments that are not accounted for in conventional molecular dynamics. The mobility of the lytic water molecule, the dynamics of the hydrogen bond network, and the conformation of the aspartates in the active center were analyzed. PMID:12124265

Trylska, Joanna; Ba?a, Piotr; Geller, Maciej; Grochowski, Pawe?

2002-01-01

309

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

PubMed

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

Kawamura, Takashi; Kobayashi, Tomoki; Watanabe, Nobuhisa

2015-02-01

310

Understanding the mechanisms of cobalt-catalyzed hydrogenation and dehydrogenation reactions.  

PubMed

Cobalt(II) alkyl complexes of aliphatic PNP pincer ligands have been synthesized and characterized. The cationic cobalt(II) alkyl complex [(PNHP(Cy))Co(CH2SiMe3)]BAr(F)4 (4) (PNHP(Cy) = bis[(2-dicyclohexylphosphino)ethyl]amine) is an active precatalyst for the hydrogenation of olefins and ketones and the acceptorless dehydrogenation of alcohols. To elucidate the possible involvement of the N-H group on the pincer ligand in the catalysis via a metal-ligand cooperative interaction, the reactivities of 4 and [(PNMeP(Cy))Co(CH2SiMe3)]BAr(F)4 (7) were compared. Complex 7 was found to be an active precatalyst for the hydrogenation of olefins. In contrast, no catalytic activity was observed using 7 as a precatalyst for the hydrogenation of acetophenone under mild conditions. For the acceptorless dehydrogenation of 1-phenylethanol, complex 7 displayed similar activity to complex 4, affording acetophenone in high yield. When the acceptorless dehydrogenation of 1-phenylethanol with precatalyst 4 was monitored by NMR spectroscopy, the formation of the cobalt(III) acetylphenyl hydride complex [(PNHP(Cy))Co(III)(?(2)-O,C-C6H4C(O)CH3)(H)]BAr(F)4 (13) was detected. Isolated complex 13 was found to be an effective catalyst for the acceptorless dehydrogenation of alcohols, implicating 13 as a catalyst resting state during the alcohol dehydrogenation reaction. Complex 13 catalyzed the hydrogenation of styrene but showed no catalytic activity for the room temperature hydrogenation of acetophenone. These results support the involvement of metal-ligand cooperativity in the room temperature hydrogenation of ketones but not the hydrogenation of olefins or the acceptorless dehydrogenation of alcohols. Mechanisms consistent with these observations are presented for the cobalt-catalyzed hydrogenation of olefins and ketones and the acceptorless dehydrogenation of alcohols. PMID:23713752

Zhang, Guoqi; Vasudevan, Kalyan V; Scott, Brian L; Hanson, Susan K

2013-06-12

311

Direct asymmetric aldol reaction of aryl ketones with aryl aldehydes catalyzed by chiral BINOL-derived zincate catalyst.  

PubMed

Direct asymmetric aldol reaction of aryl ketones with aryl aldehydes catalyzed by chiral metal complex is reported for the first time herein. Two novel semicrown chiral ligands 1a and 1b were synthesized from (S)- and (R)-BINOL, respectively, and then employed to catalyze the direct asymmetric aldol addition of aryl ketones to aryl aldehydes. Introduced with 2.0 equiv of diethylzinc, 1b had higher enantioselectivity than 1a. Up to 97% yield and up to 80% enantioselectivity were achieved. PMID:18700798

Li, Hong; Da, Chao-Shan; Xiao, Yu-Hua; Li, Xiao; Su, Ya-Ning

2008-09-19

312

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)

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.

Cicero, Giancarlo; Carbonera, Chiara; Valegård, Karin; Hajdu, Janos; Andersson, Inger; Ranghino, Graziella

313

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

PubMed

(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

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

2004-10-01

314

Acid-Catalyzed Reactions of Tetrahydropyranyl-Protected Polyvinylphenol in a Novolak-Resin-Based Positive Resist  

NASA Astrophysics Data System (ADS)

This paper deals with an acid-catalyzed reaction mechanism of a polymeric dissolution inhibitor of a novolak-resin-based positive chemical amplification resist system. This resist system consists of a novolak matrix resin, tri(methanesulfonyloxy)benzene as an acid generator, and tetrahydropyranyl-protected polyvinylphenol (THP-M) as a polymeric dissolution inhibitor. The acid-catalyzed deprotection products of THP-M in the resist film are detected and their subsequent acid-catalyzed reactivities are evaluated. It is found that tetrahydropyranyl group are exchanged between THP-M and the matrix to yield a strong dissolution inhibitor, causing negative tone behavior at the overexposure dose. High-resolution patterns (0.3-?m contact holes) are achieved with high sensitivity (2.4 ?C/cm2 at 50 kV).

Sakamizu, Toshio; Shiraishi, Hiroshi; Yamaguchi, Hidenori; Ueno, Takumi; Hayashi, Nobuaki

1992-12-01

315

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

PubMed

First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to examine the catalytic mechanism for cocaine esterase (CocE)-catalyzed hydrolysis of (+)-cocaine in comparison with CocE-catalyzed hydrolysis of (-)-cocaine. It has been shown that the acylation of (+)-cocaine consists of nucleophilic attack of the hydroxyl group of Ser117 on the carbonyl carbon of (+)-cocaine benzoyl ester and the dissociation of (+)-cocaine benzoyl ester. The first reaction step of deacylation of (+)-cocaine, which is identical to that of (-)-cocaine, is rate-determining, indicating that CocE-catalyzed hydrolyses of (+)- and (-)-cocaine have a common rate-determining step. The computational results predict that the catalytic rate constant of CocE against (+)-cocaine should be the same as that of CocE against (-)-cocaine, in contrast with the remarkable difference between human butyrylcholinesterase-catalyzed hydrolyses of (+)- and (-)-cocaine. The prediction has been confirmed by experimental kinetic analysis on CocE-catalyzed hydrolysis of (+)-cocaine in comparison with CocE-catalyzed hydrolysis of (-)-cocaine. The determined common rate-determining step indicates that rational design of a high-activity mutant of CocE should be focused on the first reaction step of the deacylation. Furthermore, the obtained mechanistic insights into the detailed differences in the acylation between the (+)- and (-)-cocaine hydrolyses provide indirect clues for rational design of amino acid mutations that could more favorably stabilize the rate-determining transition state in the deacylation and, thus, improve the catalytic activity of CocE. This study provides a valuable mechanistic base for rational design of an improved esterase for therapeutic treatment of cocaine abuse. PMID:21486046

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

2011-05-01

316

An acyl group makes a difference in the reactivity patterns of cytochrome P450 catalyzed N-demethylation of substituted N,N-dimethylbenzamides-high spin selective reactions.  

PubMed

This paper addresses the experimentally observed mechanistic differences between the cytochrome P450-catalyzed N-demethylation of substituted N,N-dimethylanilines (DMA) and of N,N-dimethylbenzamides (DMBA). The two reactions of these substrates are initiated by C-H activation of the methyl groups on the nitrogen. Thus, the DMA reactions exhibit small deuterium kinetic isotope effects (KIEs), and these KIEs and the corresponding reaction rates exhibit a linear response to the electronic nature of the para substituent. By contrast, the DMBA reactions exhibit large KIEs; the KIEs and reaction rates do not at all respond to the nature of the para substituent. Accordingly, the present paper uses density functional theoretical calculations to address these reactivity patterns in para-substituted DMBA and compare these results to those obtained for the DMA reactions previously (Wang, Y.; Kumar, D.; Yang, C. L.; Han, K. L.; Shaik, S. J. Phys. Chem. B 2007, 111, 7700). The theoretical calculations reproduce the experimental trends of narrow variations in rates and KIEs. It is shown that the above mechanistic differences between the two reaction series of DMA and DMBA are caused by the ability of the para substituent to maintain a conjugation path between the C-H reaction center and the aryl moiety. Furthermore, the computational results show a new feature of reactivity, namely, that the N-demethylation of DMBA proceeds by a spin-selective reaction via the high spin state of the active species of the enzyme. This conclusion is reinforced by the match of the calculated and experimental KIE values. PMID:20146528

Wang, Yong; Li, Dongmei; Han, Keli; Shaik, Sason

2010-03-01

317

Factors That Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase  

SciTech Connect

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

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

2009-10-21

318

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

PubMed Central

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

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

2009-01-01

319

MODEL FOR ENZYME KINETICS USING PETRI NETWORKS  

Microsoft Academic Search

In this paper we propose a model for single substrate enzyme kinetics based on the differential Petri network formalism. Metabolic signaling pathways imply biochemical reactions in which substrates are enzyme catalyzed and turn them into active biochemical products. The enzymatic reactions are described quantitatively through ordinary differential equations (ODEs) in the proposed Petri network model. The specificity of the biochemical

RADU DOBRESCU; A. POPA; VICTOR PURCAREA

2009-01-01

320

PURIFICATION AND ISOLATION OF THE PHOSPHOGLYCERATE KINASE ENZYME  

E-print Network

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

Collins, Gary S.

321

New insights into atrazine degradation by cobalt catalyzed peroxymonosulfate oxidation: Kinetics, reaction products and transformation mechanisms.  

PubMed

The widespread occurrence of atrazine in waters poses potential risk to ecosystem and human health. In this study, we investigated the underlying mechanisms and transformation pathways of atrazine degradation by cobalt catalyzed peroxymonosulfate (Co(II)/PMS). Co(II)/PMS was found to be more efficient for ATZ elimination in aqueous solution than Fe(II)/PMS process. ATZ oxidation by Co(II)/PMS followed pseudo-first-order kinetics, and the reaction rate constant (kobs) increased appreciably with increasing Co(II) concentration. Increasing initial PMS concentration favored the decomposition of ATZ, however, no linear relationship between kobs and PMS concentration was observed. Higher efficiency of ATZ oxidation was observed around neutral pH, implying the possibility of applying Co(II)/PMS process under environmental realistic conditions. Natural organic matter (NOM), chloride (Cl(-)) and bicarbonate (HCO3(-)) showed detrimental effects on ATZ degradation, particularly at higher concentrations. Eleven products were identified by applying solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC/MS) techniques. Major transformation pathways of ATZ included dealkylation, dechlorination-hydroxylation, and alkyl chain oxidation. Detailed mechanisms responsible for these transformation pathways were discussed. Our results reveal that Co(II)/PMS process might be an efficient technique for remediation of groundwater contaminated by ATZ and structurally related s-triazine herbicides. PMID:25544494

Ji, Yuefei; Dong, Changxun; Kong, Deyang; Lu, Junhe

2015-03-21

322

Reaction mechanism of the direct gas phase synthesis of H2O2 catalyzed by Au3  

NASA Astrophysics Data System (ADS)

The gas phase reaction of molecular oxygen and hydrogen catalyzed by a Au3 cluster to yield H2O2 was investigated theoretically using second order Z-averaged perturbation theory, with the final energies obtained with the fully size extensive completely renormalized CR-CC(2,3) coupled cluster theory. The proposed reaction mechanism is initiated by adsorption and activation of O2 on the Au3 cluster. Molecular hydrogen then binds to the Au3O2 global minimum without an energy barrier. The reaction between the activated oxygen and hydrogen molecules proceeds through formation of hydroperoxide (HO2) and a hydrogen atom, which subsequently react to form the product hydrogen peroxide. All reactants, intermediates, and product remain bound to the gold cluster throughout the course of the reaction. The steps in the proposed reaction mechanism have low activation energy barriers below 15kcal/mol. The overall reaction is highly exothermic by ˜30kcal/mol.

Njegic, Bosiljka; Gordon, Mark S.

2008-09-01

323

The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease  

PubMed Central

The hydrogen-bond network in various stages of the enzymatic reaction catalyzed by HIV-1 protease was studied through quantum-classical molecular dynamics simulations. The approximate valence bond method was applied to the active site atoms participating directly in the rearrangement of chemical bonds. The rest of the protein with explicit solvent was treated with a classical molecular mechanics model. Two possible mechanisms were studied, general-acid/general-base (GA/GB) with Asp 25 protonated at the inner oxygen, and a direct nucleophilic attack by Asp 25. Strong hydrogen bonds leading to spontaneous proton transfers were observed in both reaction paths. A single-well hydrogen bond was formed between the peptide nitrogen and outer oxygen of Asp 125. The proton was diffusely distributed with an average central position and transferred back and forth on a picosecond scale. In both mechanisms, this interaction helped change the peptide-bond hybridization, increased the partial charge on peptidyl carbon, and in the GA/GB mechanism, helped deprotonate the water molecule. The inner oxygens of the aspartic dyad formed a low-barrier, but asymmetric hydrogen bond; the proton was not positioned midway and made a slightly elongated covalent bond, transferring from one to the other aspartate. In the GA/GB mechanism both aspartates may help deprotonate the water molecule. We observed the breakage of the peptide bond and found that the protonation of the peptidyl amine group was essential for the peptide-bond cleavage. In studies of the direct nucleophilic mechanism, the peptide carbon of the substrate and oxygen of Asp 25 approached as close as 2.3 ?. PMID:14739332

Trylska, Joanna; Grochowski, Pawe?; McCammon, J. Andrew

2004-01-01

324

A coumarin-specific prenyltransferase catalyzes the crucial biosynthetic reaction for furanocoumarin formation in parsley.  

PubMed

Furanocoumarins constitute a sub-family of coumarin compounds with important defense properties against pathogens and insects, as well as allelopathic functions in plants. Furanocoumarins are divided into two sub-groups according to the alignment of the furan ring with the lactone structure: linear psoralen and angular angelicin derivatives. Determination of furanocoumarin type is based on the prenylation position of the common precursor of all furanocoumarins, umbelliferone, at C6 or C8, which gives rise to the psoralen or angelicin derivatives, respectively. Here, we identified a membrane-bound prenyltransferase PcPT from parsley (Petroselinum crispum), and characterized the properties of the gene product. PcPT expression in various parsley tissues is increased by UV irradiation, with a concomitant increase in furanocoumarin production. This enzyme has strict substrate specificity towards umbelliferone and dimethylallyl diphosphate, and a strong preference for the C6 position of the prenylated product (demethylsuberosin), leading to linear furanocoumarins. The C8-prenylated derivative (osthenol) is also formed, but to a much lesser extent. The PcPT protein is targeted to the plastids in planta. Introduction of this PcPT into the coumarin-producing plant Ruta graveolens showed increased consumption of endogenous umbelliferone. Expression of PcPT and a 4-coumaroyl CoA 2'-hydroxylase gene in Nicotiana benthamiana, which does not produce furanocoumarins, resulted in formation of demethylsuberosin, indicating that furanocoumarin production may be reconstructed by a metabolic engineering approach. The results demonstrate that a single prenyltransferase, such as PcPT, opens the pathway to linear furanocoumarins in parsley, but may also catalyze the synthesis of osthenol, the first intermediate committed to the angular furanocoumarin pathway, in other plants. PMID:24354545

Karamat, Fazeelat; Olry, Alexandre; Munakata, Ryosuke; Koeduka, Takao; Sugiyama, Akifumi; Paris, Cedric; Hehn, Alain; Bourgaud, Frédéric; Yazaki, Kazufumi

2014-02-01

325

NADH Enzyme-Dependent Fluorescence Recovery after Photobleaching (ED-FRAP): Applications to Enzyme and Mitochondrial Reaction Kinetics, In Vitro  

Microsoft Academic Search

NADH enzyme-dependent fluorescence recovery after photobleaching (ED-FRAP) was evaluated for studying enzyme kinetics in vitro and in isolated mitochondria. Mass, optical, and nuclear magnetic resonance spectroscopy data were consistent with the UV NADH photolysis reaction being NADH?NAD·+H++e?. The overall net reaction was O2+2NADH+2H+?2NAD++2H2O, or in the presence of other competing electron acceptors such as cytochrome c, NADH+2Cytox?NAD++H++2Cytred. Solution pH could

Frederic Joubert; Henry M. Fales; Han Wen; Christian A. Combs; Robert S. Balaban

2004-01-01

326

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

PubMed

MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k(cat)/K(M) of 520 M(-1) s(-1), was far slower than the normal reaction, and 3 x 10(5)-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new "staged" MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA.ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA.UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA. PMID:19899805

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

2009-12-15

327

Enzymatic synthesis of L-DOPA alpha-glycosides by reaction with sucrose catalyzed by four different glucansucrases from four strains of Leuconostoc mesenteroides.  

PubMed

L-DOPA alpha-glycosides were synthesized by reaction of L-DOPA with sucrose, catalyzed by four different glucansucrases from Leuconostoc mesenteroides B-512FMC, B-742CB, B-1299A, and B-1355C. The glucansucrases catalyzed the transfer of d-glucose from sucrose to the phenolic hydroxyl position-3 and -4 of L-DOPA. The glycosides were fractionated and purified by Bio-Gel P-2 column chromatography, and the structures were determined by (1)H NMR spectroscopy. The major glycoside was 4-O-alpha-d-glucopyranosyl L-DOPA, and the minor glycoside was 3-O-alpha-D-glucopyranosyl L-DOPA. The two glycosides were formed by all four of the glucansucrases. The ratio of the 4-O-alpha-glycoside to the 3-O-alpha-glycoside produced by the B-512FMC dextransucrase was higher than that for the other three glucansucrases. The glycosylation of L-DOPA significantly reduced the oxidation of the phenolic hydroxyl groups, which prevents their methylation, potentially increasing the use of L-DOPA in the treatment of Parkinson's disease. The use of one enzyme, glucansucrase, and sucrose as the D-glucosyl donor makes the synthesis considerably simpler and cheaper than the formerly published procedure using cyclomaltodextrin and cyclomaltodextrin glucanyltransferase, followed by glucoamylase, and beta-amylase hydrolysis. PMID:20579635

Yoon, Seung-Heon; Fulton, D Bruce; Robyt, John F

2010-08-16

328

Unified mechanism of alkali and alkaline earth catalyzed gasification reactions of carbon by CO2 and H2O  

USGS Publications Warehouse

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.

Chen, S.G.; Yang, R.T.

1997-01-01

329

N-heterocyclic carbene catalyzed reactions of ?-bromo-?,?-unsaturated aldehydes/?,?-dibromoaldehydes with 1,3-dinucleophilic reagents.  

PubMed

Carbenes ring true: N-Heterocyclic carbene (NHC) catalyzed reactions of ?-bromo-?,?-unsaturated aldehydes/?,?-dibromoaldehydes with 1,3-dinucleophilic reagents, such as 1,3-dicarbonyl compounds, ?-enamino ketones, and ?-enamino esters through umpolung processes gave functionalized 3,4-dihydropyranones and 3,4-dihydropyridinones. The availability of the starting materials, lack of external oxidant, and usefulness of the products make this strategy attractive. PMID:22259126

Yao, Changsheng; Wang, Donglin; Lu, Jun; Li, Tuanjie; Jiao, Weihui; Yu, Chenxia

2012-02-13

330

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

E-print Network

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...

Gomez Ruiz, Alejandro

1998-01-01

331

Accelerated Search Kinetics Mediated by Redox Reactions of DNA Repair Enzymes  

NASA Astrophysics Data System (ADS)

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.

Fok, Pak-Wing; Chou, Tom

2009-05-01

332

Accelerated search kinetics mediated by redox reactions of DNA repair enzymes  

E-print Network

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.

Pak-Wing Fok; Tom Chou

2009-05-20

333

A single PLP-dependent enzyme PctV catalyzes the transformation of 3-dehydroshikimate into 3-aminobenzoate in the biosynthesis of pactamycin.  

PubMed

Natural amino donation: A PLP-dependent aminotransferase PctV, encoded in the pactamycin biosynthetic gene cluster, was found to catalyze the formation of 3-aminobenzoate from 3-dehydroshikimate with L-glutamate as the amino donor. The PctV reaction comprises a transamination and two dehydration reactions. This is the first report of a simple 3-ABA synthase in nature. PMID:23744829

Hirayama, Akane; Eguchi, Tadashi; Kudo, Fumitaka

2013-07-01

334

Rapid-Equilibrium Enzyme Kinetics  

ERIC Educational Resources Information Center

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…

Alberty, Robert A.

2008-01-01

335

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...

336

Highly enantioselective Friedel-Crafts alkylation reaction catalyzed by rosin-derived tertiary amine-thiourea: synthesis of modified chromanes with anticancer potency.  

PubMed

We present herein for the first time the synthesis and preliminary biological evaluation of various modified chromanes via a rosin-derived tertiary amine-thiourea-catalyzed highly enantioselective Friedel-Crafts alkylation reaction. PMID:22080190

Jiang, Xianxing; Wu, Lipeng; Xing, Yanhong; Wang, Long; Wang, Shoulei; Chen, Zongyao; Wang, Rui

2012-01-11

337

Aerobic oxidation reactions catalyzed by vanadium complexes of bis(phenolate) ligands.  

PubMed

Vanadium(V) complexes of the tridentate bis(phenolate)pyridine ligand H(2)BPP (H(2)BPP = 2,6-(HOC(6)H(2)-2,4-(t)Bu(2))(2)NC(5)H(3)) and the bis(phenolate)amine ligand H(2)BPA (H(2)BPA = N,N-bis(2-hydroxy-4,5-dimethylbenzyl)propylamine) have been synthesized and characterized. The ability of the complexes to mediate the oxidative C-C bond cleavage of pinacol was tested. Reaction of the complex (BPP)V(V)(O)(O(i)Pr) (4) with pinacol afforded the monomeric vanadium(IV) product (BPP)V(IV)(O)(HO(i)Pr) (6) and acetone. Vanadium(IV) complex 6 was oxidized rapidly by air at room temperature in the presence of NEt(3), yielding the vanadium(V) cis-dioxo complex [(BPP)V(V)(O)(2)]HNEt(3). Complex (BPA)V(V)(O)(O(i)Pr) (5) reacted with pinacol at room temperature, to afford acetone and the vanadium(IV) dimer [(BPA)V(IV)(O)(HO(i)Pr)](2). Complexes 4 and 5 were evaluated as catalysts for the aerobic oxidation of 4-methoxybenzyl alcohol and arylglycerol ?-aryl ether lignin model compounds. Although both 4 and 5 catalyzed the aerobic oxidation of 4-methoxybenzyl alcohol, complex 4 was found to be a more active and robust catalyst for oxidation of the lignin model compounds. The catalytic activities and selectivities of the bis(phenolate) complexes are compared to previously reported catalysts. PMID:22708725

Zhang, Guoqi; Scott, Brian L; Wu, Ruilian; Silks, L A Pete; Hanson, Susan K

2012-07-01

338

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

E-print Network

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

Matsubara, Ryosuke

339

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

E-print Network

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

Breitler, Simon

340

Parallel iterative reaction path optimization in ab initio quantum mechanical\\/molecular mechanical modeling of enzyme reactions  

Microsoft Academic Search

The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical\\/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in

Haiyan Liu; Zhenyu Lu; G. Andrés Cisneros; Weitao Yang

2004-01-01

341

Efficient access to substituted silafluorenes by nickel-catalyzed reactions of biphenylenes with Et?SiH?.  

PubMed

The reaction of biphenylene (1) with Et2SiH2 in the presence of [Ni(PPhMe2)4] results in the formation of a mixture of 2-diethylhydrosilylbiphenyl [2(Et2HSi)] and 9,9,-diethyl-9-silafluorene (3). Silafluorene 3 was isolated in 37.5% and 2(Et2HSi) in 36.9% yield. The underlying reaction mechanism was elucidated by DFT calculations. 4-Methyl-9,9-diethyl-9-silafluorene (7) was obtained selectively from the [Ni(PPhMe2)4]-catalyzed reaction of Et2SiH2 and 1-methylbiphenylene. By contrast, no selectivity could be found in the Ni-catalyzed reaction between Et2SiH2 and the biphenylene derivative that bears tBu substituents in the 2- and 7-positions. Therefore, two pairs of isomers of tBu-substituted silafluorenes and of the related diethylhydrosilylbiphenyls were formed in this reaction. However, a subsequent dehydrogenation of the diethylhydrosilylbiphenyls with Wilkinson's catalyst yielded a mixture of 2,7-di-tert-butyl-9,9-diethyl-9-silafluorene (8) and 3,6-di-tert-butyl-9,9-diethyl-9-silafluorene (9). Silafluorenes 8 and 9 were separated by column chromatography. PMID:25205601

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

2014-11-01

342

Industrial Enzymes and Biocatalysis  

NASA Astrophysics Data System (ADS)

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.

McAuliffe, Joseph C.; Aehle, Wolfgang; Whited, Gregory M.; Ward, Donald E.

343

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

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

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

2014-01-01

344

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

SciTech Connect

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.

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

2011-07-13

345

Photoelectrochemical biosensor using enzyme-catalyzed in situ propagation of CdS quantum dots on graphene oxide.  

PubMed

An innovative photoelectrochemical (PEC) biosensor platform was designed based on the in situ generation of CdS quantum dots (QDs) on graphene oxide (GO) using an enzymatic reaction. Horseradish peroxidase catalyzed the reduction of sodium thiosulfate with hydrogen peroxide to generate H2S, which reacted with Cd(2+) to form CdS QDs. CdS QDs could be photoexcited to generate an elevated photocurrent as a readout signal. This strategy offered a "green" alternative to inconvenient presynthesis procedures for the fabrication of semiconducting nanoparticles. The nanomaterials and assembly procedures were characterized by microscopy and spectroscopy techniques. Combined with immune recognition and on the basis of the PEC activity of CdS QDs on GO, the strategy was successfully applied to a PEC assay to detect carcinoembryonic antigen and displayed a wide linear range from 2.5 ng mL(-1) to 50 ?g mL(-1) and a detection limit of 0.72 ng mL(-1) at a signal-to-noise ratio of 3. The PEC biosensor showed satisfactory performance for clinical sample detection and was convenient for determining high concentrations of solute without dilution. This effort offers a new opportunity for the development of numerous rapid and convenient analytical techniques using the PEC method that may be applied in the design and preparation of various solar-energy-driven applications. PMID:25154012

Zeng, Xianxiang; Tu, Wenwen; Li, Jing; Bao, Jianchun; Dai, Zhihui

2014-09-24

346

Enzyme catalytic efficiency: a function of bio-nano interface reactions.  

PubMed

Biocatalyst immobilization onto carbon-based nanosupports has been implemented in a variety of applications ranging from biosensing to biotransformation and from decontamination to energy storage. However, retaining enzyme functionality at carbon-based nanosupports was challenged by the non-specific attachment of the enzyme as well as by the enzyme-enzyme interactions at this interface shown to lead to loss of enzyme activity. Herein, we present a systematic study of the interplay reactions that take place upon immobilization of three pure enzymes namely soybean peroxidase, chloroperoxidase, and glucose oxidase at carbon-based nanosupport interfaces. The immobilization conditions involved both single and multipoint single-type enzyme attachment onto single and multi-walled carbon nanotubes and graphene oxide nanomaterials with properties determined by Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray analysis (EDX), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Our analysis showed that the different surface properties of the enzymes as determined by their molecular mapping and size work synergistically with the carbon-based nanosupports physico-chemical properties (i.e., surface chemistry, charge and aspect ratios) to influence enzyme catalytic behavior and activity at nanointerfaces. Knowledge gained from these studies can be used to optimize enzyme-nanosupport symbiotic reactions to provide robust enzyme-based systems with optimum functionality to be used for fermentation, biosensors, or biofuel applications. PMID:24666280

Campbell, Alan S; Dong, Chenbo; Meng, Fanke; Hardinger, Jeremy; Perhinschi, Gabriela; Wu, Nianqiang; Dinu, Cerasela Zoica

2014-04-23

347

Probing the specificity of gamma-glutamylamine cyclotransferase: an enzyme involved in the metabolism of transglutaminase-catalyzed protein crosslinks.  

PubMed

?-Glutamylamine cyclotransferase (gGACT) catalyzes the intramolecular cyclization of a variety of L-?-glutamylamines producing 5-oxo-L-proline and free amines. Its substrate specificity implicates it in the downstream metabolism of transglutaminase products, and is distinct from that of ?-glutamyl cyclotransferase which acts on L-?-glutamyl amino acids. To elucidate the mechanism by which gGACT distinguishes between L-?-glutamylamine and amino acid substrates, the specificity of the rabbit kidney enzyme for the amide region of substrates was probed through the kinetic analysis of a series of L-?-glutamylamines. The isodipeptide N(?)-(L-?-glutamyl)-L-lysine 1 was used as a reference. The kinetic constants of the L-?-glutamyl derivative of n-butylamine 7, were nearly identical to those of 1. Introduction of a methyl or carboxylate group on the carbon adjacent to the side-chain amide nitrogen in L-?-glutamylamine substrates resulted in a dramatic decrease in substrate properties for gGACT thus providing an explanation of why gGACT does not act on L-?-glutamyl amino acids except for L-?-glutamylglycine. Placement of substituents on carbons further removed from the side-chain amide nitrogen in L-?-glutamylamines restored activity for gGACT, and L-?-glutamylneohexylamine 19 had a higher specificity constant (k(cat) /K(m)) than 1. gGACT did not exhibit any stereospecificity in the amide region of L-?-glutamylamine substrates. In addition, analogues (26-30) with heteroatom substitutions for the ? methylene position of the L-?-glutamyl moiety were examined. Several thiocarbamoyl derivatives of L-cysteine (28-30) were excellent substrates for gGACT. PMID:22120669

Bowser, Todd E; Trawick, Mary Lynn

2013-01-01

348

Method of reduction of nitroaromatics by enzymatic reaction with redox enzymes  

DOEpatents

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).

Shah, Manish M. (Richland, WA)

2000-01-01

349

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

DOEpatents

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.

Shah, M.M.; Campbell, J.A.

1998-07-07

350

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

DOEpatents

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.

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

1998-01-01

351

Study on the kinetics of homogeneous enzyme reactions in a micro/nanofluidics device.  

PubMed

In this paper, a micro/nanofluidic preconcentration device integrated with an electrochemical detector has been used to study the enrichment of enzymes and homogeneous enzyme reaction kinetics. The enzymes are first concentrated in front of a nanochannel via an exclusion-enrichment effect (EEE) mechanism of the nanochannel integrated in a microfluidics device. If a substrate is electrokinetically transported to the concentrated enzymes, homogeneous enzymatic reaction occurs. The enzymatic reaction product can penetrate through the nanochannel to be detected electrochemically. In this device, the enriched enzymes can be well retained and repeatedly used, thus, the enzymatic reaction occurs in a continuous-flow mode. For demonstration, Glucose oxidase (GOx) was chosen as the model enzyme to study the influence of enzyme concentration on its reaction kinetics. The different concentration of GOx in front of the nanochannel was simply achieved by using different enrichment time. When substrate glucose was introduced electrokinetically, a rapid electrochemical steady-state response could be obtained. It was found that the electrochemical response to a constant glucose concentration increased with the increase of enzyme enrichment time, which is expected for homogeneous enzymatic reactions. Under proper conditions, the electrochemical responds linearly to the glucose concentration ranging from 0 to 15 mM, and the Michaelis constants (K(m)) are relatively low, which indicates a more efficient complex formation between enzyme and substrate. These results suggest that the present micro/nanofluidics device is promising for the study of enzymatic reaction kinetics and other bioassays such as cell assays, drug discovery, and clinical diagnosis. PMID:20162240

Wang, Chen; Li, Su-Juan; Wu, Zeng-Qiang; Xu, Jing-Juan; Chen, Hong-Yuan; Xia, Xing-Hua

2010-03-01

352

Sequential Reactions of Surface-Tethered Glycolytic Enzymes  

PubMed Central

SUMMARY The development of complex hybrid organic-inorganic devices faces several challenges, including how they can generate energy. Cells face similar challenges regarding local energy production. Mammalian sperm solve this problem by generating ATP down the flagellar principal piece by means of glycolytic enzymes, several of which are tethered to a cytoskeletal support via germ cell-specific targeting domains. Inspired by this design, we have produced recombinant hexokinase type 1 and glucose-6-phosphate isomerase capable of oriented immobilization on a nickel-nitrilotriacetic acid modified surface. Specific activities of enzymes tethered via this strategy were substantially higher than when randomly adsorbed. Furthermore, these enzymes showed sequential activities when tethered onto the same surface. This is the first demonstration of surface-tethered pathway components showing sequential enzymatic activities, and it provides a first step toward reconstitution of glycolysis on engineered hybrid devices. PMID:19778729

Mukai, Chinatsu; Bergkvist, Magnus; Nelson, Jacquelyn L.; Travis, Alexander J.

2014-01-01

353

Efficient Boron-Copper Additions to Aryl-Substituted Alkenes Promoted by NHC–Based Catalysts. Enantioselective Cu-Catalyzed Hydroboration Reactions  

PubMed Central

A Cu-catalyzed method for efficient boron-copper addition processes involving acyclic and cyclic disubstituted aryl olefins are reported. Reactions are promoted with 0.5–5 mol % of a readily available N-heterocyclic carbene (NHC) complex; the presence of MeOH promotes in situ protonation of the C–Cu bond and leads to efficient catalyst turnover, constituting a net Cu-catalyzed hydroboration process. Reactions proceed in >98:<2 site-selectivity, and furnish secondary organoborane isomers that complement those obtained through reactions of boron-hydride reagents or by Rh- or Ir-catalyzed hydroborations (benzylic secondary C–B bonds). Initial observations regarding processes catalyzed by chiral NHC complexes, delivering products in up to 99:1 enantiomeric ratio, are disclosed. PMID:19256564

Lee, Yunmi; Hoveyda, Amir H.

2009-01-01

354

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

E-print Network

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

Tas, A. Cuneyt

355

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

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

Nielsen, John Strikart; Møller, Birger Lindberg

2000-01-01

356

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

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

Nielsen, J S; Møller, B L

2000-04-01

357

Promiscuous protease-catalyzed aldol reactions: a facile biocatalytic protocol for carbon-carbon bond formation in aqueous media.  

PubMed

Several proteases, especially pepsin, were observed to directly catalyze asymmetric aldol reactions. Pepsin, which displays well-documented proteolytic activity under acidic conditions, exhibited distinct catalytic activity in a crossed aldol reaction between acetone and 4-nitrobenzaldehyde with high yield and moderate enantioselectivity. Fluorescence experiments indicated that under neutral pH conditions, pepsin maintains its native conformation and that the natural structure plays an important role in biocatalytic promiscuity. Moreover, no significant loss of enantioselectivity was found even after four cycles of catalyst recycling, showing the high stability of pepsin under the selected aqueous reaction conditions. This case of biocatalytic promiscuity not only expands the application of proteases to new chemical transformations, but also could be developed into a potentially valuable method for green organic synthesis. PMID:20959128

Li, Chao; Zhou, Yu-Jie; Wang, Na; Feng, Xing-Wen; Li, Kun; Yu, Xiao-Qi

2010-12-01

358

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...

359

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

Technology Transfer Automated Retrieval System (TEKTRAN)

Beta-D-xylosidase from Selenomonas ruminantium is the best catalyst known for promoting hydrolysis of 1,4-beta-D-xylooligosaccharides and it has potential utility in industrial saccharification processes. Kinetic parameters, kcat and kcat/Km, are more than 10-fold larger than those reported for the...

360

TfOH-catalyzed synthesis of 3-aryl isoindolinones via a tandem reaction.  

PubMed

A convenient metal-free method for the synthesis of 3-aryl isoindolinones via TfOH catalyzed aromatic C-H functionalization of electron-rich arenes with 2-formylbenzonitriles is developed. This process provided a new efficient strategy for the synthesis of isoindolinone derivatives in good to high yields and regioselectivities by forming two bonds. PMID:25370938

Hu, Jiaxing; Qin, Hua-Li; Xu, Wengang; Li, Junli; Zhang, Fanglin; Zheng, Hua

2014-12-25

361

Gold(I)-Catalyzed 1,4- and/or 1,5-Heteroaryl Migration Reactions through Regiocontrolled Cyclizations.  

PubMed

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

Wang, Chengyu; Xie, Xin; Liu, Jun; Liu, Yuanhong; Li, Yuxue

2015-01-01

362

Rapid and Efficient Copper-Catalyzed Finkelstein Reaction of (Hetero)Aromatics under Continuous-Flow Conditions.  

PubMed

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

Chen, Mao; Ichikawa, Saki; Buchwald, Stephen L

2015-01-01

363

Antibody-catalyzed decarboxylation and aldol reactions using a primary amine molecule as a functionalized small nonprotein component.  

PubMed

Catalytic antibody 27C1 bears binding sites for both a substrate- and a functionalized small nonprotein component in the active site. We investigated the possibility of exploiting imine and enamine intermediates using a primary amine molecule into the active site of antibody 27C1. The antibody catalyzed ?-keto acid decarboxylation with a rate enhancement (kcat/Km/kuncat) of 140,000, as well as highly regioselective cross-aldol reactions of ketones and p-nitrobenzaldehyde. These studies provide new strategies for the generation of catalytic antibodies possessing binding sites for functionalized components. PMID:24094435

Ishikawa, Fumihiro; Uno, Kouki; Nishikawa, Masao; Tsumuraya, Takeshi; Fujii, Ikuo

2013-11-15

364

Bulk gold catalyzed oxidation reactions of amines and isocyanides and iron porphyrin catalyzed N-H and O-H bond insertion/cyclization reactions of diamines and aminoalcohols  

SciTech Connect

This work involves two projects. The first project entails the study of bulk gold as a catalyst in oxidation reactions of isocyanides and amines. The main goal of this project was to study the activation and reactions of molecules at metal surfaces in order to assess how organometallic principles for homogeneous processes apply to heterogeneous catalysis. Since previous work had used oxygen as an oxidant in bulk gold catalyzed reactions, the generality of gold catalysis with other oxidants was examined. Amine N-oxides were chosen for study, due to their properties and use in the oxidation of carbonyl ligands in organometallic complexes. When amine N-oxides were used as an oxidant in the reaction of isocyanides with amines, the system was able to produce ureas from a variety of isocyanides, amines, and amine N-oxides. In addition, the rate was found to generally increase as the amine N-oxide concentration increased, and decrease with increased concentrations of the amine. Mechanistic studies revealed that the reaction likely involves transfer of an oxygen atom from the amine N-oxide to the adsorbed isocyanide to generate an isocyanate intermediate. Subsequent nucleophilic attack by the amine yields the urea. This is in contrast to the bulk gold-catalyzed reaction mechanism of isocyanides with amines and oxygen. Formation of urea in this case was proposed to proceed through a diaminocarbene intermediate. Moreover, formation of the proposed isocyanate intermediate is consistent with the reactions of metal carbonyl ligands, which are isoelectronic to isocyanides. Nucleophilic attack at coordinated CO by amine N-oxides produces CO{sub 2} and is analogous to the production of an isocyanate in this gold system. When the bulk gold-catalyzed oxidative dehydrogenation of amines was examined with amine N-oxides, the same products were afforded as when O{sub 2} was used as the oxidant. When the two types of oxidants were directly compared using the same reaction system and conditions, it was found that the oxidative dehydrogenation of dibenzylamine to Nbenzylidenebenzylamine, with N-methylmorpholine N-oxide (NMMO), was nearly quantitative (96%) within 24 h. However, the reaction with oxygen was much slower, with only a 52% yield of imine product over the same time period. Moreover, the rate of reaction was found to be influenced by the nature of the amine N-oxide. For example, the use of the weakly basic pyridine N-oxide (PyNO) led to an imine yield of only 6% after 24 h. A comparison of amine N-oxide and O2 was also examined in the oxidation of PhCH{sub 2}OH to PhCHO catalyzed by bulk gold. In this reaction, a 52% yield of the aldehyde was achieved when NMMO was used, while only a 7% product yield was afforded when O{sub 2} was the oxidant after 48 h. The bulk gold-catalyzed oxidative dehydrogenation of cyclic amines generates amidines, which upon treatment with Aerosil and water were found to undergo hydrolysis to produce lactams. Moreover, 5-, 6-, and 7-membered lactams could be prepared through a one-pot reaction of cyclic amines by treatment with oxygen, water, bulk gold, and Aerosil. This method is much more atom economical than industrial processes, does not require corrosive acids, and does not generate undesired byproducts. Additionally, the gold and Aerosil catalysts can be readily separated from the reaction mixture. The second project involved studying iron(III) tetraphenylporphyrin chloride, Fe(TPP)Cl, as a homogeneous catalyst for the generation of carbenes from diazo reagents and their reaction with heteroatom compounds. Fe(TPP)Cl, efficiently catalyzed the insertion of carbenes derived from methyl 2-phenyldiazoacetates into O-H bonds of aliphatic and aromatic alcohols. Fe(TPP)Cl was also found to be an effective catalyst for tandem N-H and O-H insertion/cyclization reactions when 1,2-diamines and 1,2-alcoholamines were treated with diazo reagents. This approach provides a one-pot process for synthesizing piperazinones and morpholinones and related analogues such as quinoxalinones and benzoxazin-2-ones.

Klobukowski, Erik

2011-12-29

365

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

E-print Network

Chemistry of Stable and Unstable Species, Peking University, Beijing 100871, China Received June 20, 2001 of enzyme. The molar reaction heat was calculated from the titration peak area divided by substrate moles change the reaction curve, it can be used as a probe to dig out other useful information. In this paper

Luhua, Lai

366

Positional Assembly of Enzymes on Bacterial Outer Membrane Vesicles for Cascade Reactions  

PubMed Central

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

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

2014-01-01

367

Studies on the oxidation reaction of tyrosine (Tyr) with H 2O 2 catalyzed by horseradish peroxidase (HRP) in alcohol-water medium by spectrofluorimetry and differential spectrophotometry  

NASA Astrophysics Data System (ADS)

An oxidation reaction of tyrosine (Tyr) with H 2O 2 catalyzed by horseradish peroxidase (HRP) was studied by spectrofluorimetry and differential spectrophotometry in the alcohol(methanol, ethanol, 1-propanol and isopropanol)-water mutual solubility system. Compared with the enzymatic-catalyzed reaction in the water medium, the fluorescence intensities of the product weakened, even extinguished. Because the addition of alcohols made the conformation of HRP change, the catalytic reaction shifted to the side of polymerization and the polymer (A nH 2, n ? 3) exhibited no fluorescence. The four alcohols cannot deactivate HRP. Moreover isopropanol activated HRP remarkably.

Tang, Bo; Wang, Yan; Liang, Huiling; Chen, Zhenzhen; He, Xiwen; Shen, Hanxi

2006-03-01

368

Development of the ReaxFF Reactive Force Field for Describing Transition Metal Catalyzed Reactions, with Application to the Initial Stages of the Catalytic Formation of Carbon  

E-print Network

Development of the ReaxFF Reactive Force Field for Describing Transition Metal Catalyzed Reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial that ReaxFF reproduces the QM reaction data with good accuracy while also reproducing the binding

Goddard III, William A.

369

Stereoselective synthesis of 2,6-trans-tetrahydropyran via primary diamine-catalyzed oxa-conjugate addition reaction of ?,?-unsaturated ketone: total synthesis of psymberin.  

PubMed

The total synthesis of psymberin was achieved employing a readily available chiral epoxide to prepare two of the three subunits in the natural product. The key reaction was a highly stereoselective organocatalytic oxa-conjugate addition reaction of ?,?-unsaturated ketone catalyzed by primary diamine for the synthesis of the 2,6-trans-tetrahydropyran embedded in psymberin. PMID:21988493

Byeon, Seong Rim; Park, Heekwang; Kim, Hyoungsu; Hong, Jiyong

2011-11-01

370

Efficient synthesis of ?- and ?-carbolines by sequential Pd-catalyzed site-selective C-C and twofold C-N coupling reactions.  

PubMed

Two concise and efficient approaches were developed for the synthesis of ?- and ?-carboline derivatives. The success of the synthesis relies on site-selective Suzuki-Miyaura reactions of 1-chloro-2-bromopyridine or 2,3-dibromopyridine with 2-bromophenylboronic acid and subsequent cyclization with amines which proceeds by twofold Pd-catalyzed C-N coupling reactions. PMID:25464277

Hung, Tran Quang; Dang, Tuan Thanh; Janke, Julia; Villinger, Alexander; Langer, Peter

2015-01-21

371

Efficient Lewis acid-assisted Brønsted acid (LBA) catalysis in the iron-catalyzed Friedel-Crafts alkylation reaction of indoles  

Microsoft Academic Search

Lewis acid-assisted Brønsted acid (LBA) catalysis was proposed for the iron-catalyzed Friedel-Crafts alkylation of indoles\\u000a with chalcones. This proposal was supported by the ESI-MS and cyclic voltammetry. The addition of acac to the iron-catalyzed\\u000a Friedel-Crafts alkylation of indoles with chalcones created a powerful catalytic system, which makes the alkylation reactions\\u000a occur easily under mild conditions.

Zhen-Yu Jiang; Ji-Rong Wu; Li Li; Xi-Huai Chen; Guo-Qiao Lai; Jian-Xiong Jiang; Yixin Lu; Li-Wen Xu

2010-01-01

372

Enzymatic synthesis of l-DOPA ?-glycosides by reaction with sucrose catalyzed by four different glucansucrases from four strains of Leuconostoc mesenteroides  

Microsoft Academic Search

l-DOPA ?-glycosides were synthesized by reaction of l-DOPA with sucrose, catalyzed by four different glucansucrases from Leuconostoc mesenteroides B-512FMC, B-742CB, B-1299A, and B-1355C. The glucansucrases catalyzed the transfer of d-glucose from sucrose to the phenolic hydroxyl position-3 and -4 of l-DOPA. The glycosides were fractionated and purified by Bio-Gel P-2 column chromatography, and the structures were determined by 1H NMR

Seung-Heon Yoon; D. Bruce Fulton; John F. Robyt

2010-01-01

373

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 ...

374

Bacterial Cyanide Oxygenase Is a Suite of Enzymes Catalyzing the Scavenging and Adventitious Utilization of Cyanide as a Nitrogenous Growth Substrate  

PubMed Central

Cyanide oxygenase (CNO) from Pseudomonas fluorescens NCIMB 11764 catalyzes the pterin-dependent oxygenolytic cleavage of cyanide (CN) to formic acid and ammonia. CNO was resolved into four protein components (P1 to P4), each of which along with a source of pterin cofactor was obligately required for CNO activity. Component P1 was characterized as a multimeric 230-kDa flavoprotein exhibiting the properties of a peroxide-forming NADH oxidase (oxidoreductase) (Nox). P2 consisted of a 49.7-kDa homodimer that showed 100% amino acid identity at its N terminus to NADH peroxidase (Npx) from Enterococcus faecalis. Enzyme assays further confirmed the identities of both Nox and Npx enzymes (specific activity, 1 U/mg). P3 was characterized as a large oligomeric protein (?300 kDa) that exhibited cyanide dihydratase (CynD) activity (specific activity, 100 U/mg). Two polypeptides of 38 kDa and 43 kDa were each detected in the isolated enzyme, the former believed to confer catalytic activity based on its similar size to other CynD enzymes. The amino acid sequence of an internal peptide of the 43-kDa protein was 100% identical to bacterial elongation factor Tu, suggesting a role as a possible chaperone in the assembly of CynD or a multienzyme CNO complex. The remaining P4 component consisted of a 28.9-kDa homodimer and was identified as carbonic anhydrase (specific activity, 2,000 U/mg). While the function of participating pterin and the roles of Nox, Npx, CynD, and CA in the CNO-catalyzed scavenging of CN remain to be determined, this is the first report describing the collective involvement of these four enzymes in the metabolic detoxification and utilization of CN as a bacterial nitrogenous growth substrate. PMID:16159773

Fernandez, Ruby F.; Kunz, Daniel A.

2005-01-01

375

On the mechanism of Lewis base catalyzed aldol addition reactions: kinetic and spectroscopic investigations using rapid-injection NMR.  

PubMed

The mechanistic foundations of the Lewis base catalyzed aldol addition reactions have been investigated. From a combination of low-temperature spectroscopic studies ((29)Si and (31)P NMR) and kinetic analyses using a rapid-injection NMR apparatus (RINMR), a correlation of the ground states and transition structures for the aldolization reactions has been formulated. The aldol addition of the tert-butylsilyl ketene acetal of tert-butyl propanoate with 1-naphthaldehyde is efficiently catalyzed by a combination of silicon tetrachloride and chiral phosphoramide Lewis bases. The rates and selectivities of the aldol additions are highly dependent on the structure of the Lewis bases: bisphosphoramides give the highest rate and selectivity, whereas a related monophosphoramide reacts slowly and with low selectivity. The monophosphoramide shows no nonlinear behavior. All of the additions show a first-order kinetic dependence on silyl ketene acetal and 1-naphthaldehyde and a zeroth-order dependence on silicon tetrachloride. The kinetic order in catalyst is structure dependent and is either half-, two-thirds-, or first-order. All of the phosphoramides are saturated with silicon tetrachloride in some form, and the resting-state species are mixtures of monomeric and dimeric, pentacoordinate cationic, or hexacoordinate neutral complexes. These data allow the formulation of a unified mechanistic scheme based on the postulate of a common reactive intermediate for all catalysts. PMID:19642696

Denmark, Scott E; Eklov, Brian M; Yao, Peter J; Eastgate, Martin D

2009-08-26

376

Acid-catalyzed Reactions in Model Secondary Organic Aerosol (SOA): Insights using Desorption-electrospray Ionization (DESI) Tandem Mass Spectrometry  

NASA Astrophysics Data System (ADS)

Atmospheric aerosols are presently little understood in terms of their sources, formation, and effect on climate forcing, despite their significant impacts on climate change and respiratory health. Secondary organic aerosols (SOA), which were thought to arise entirely from simple gas-particle partitioning, have recently been found to contain oligomeric species which result from the condensed-phase reactions of volatile organic compounds (VOCs). The non-methane VOC with the greatest emission flux, isoprene, is known to produce aerosols through chemistry involving its oxidation products. We selected one of its major oxidation product, methacrolein, to assess its role in oligomeric SOA formation in response to the acidic conditions found in cloud water. Since it has been found that acidified aerosol produces oligomeric species with greater molecular weight and yield, acid-catalyzed oligomerization is likely a significant process in the formation of SOA. Aqueous solutions of methacrolein were acidified with sulfuric acid, and studied using linear ion trap mass spectrometry (LIT-MS) with a home-built desorption-electrospray ionization (DESI) source. An extremely heterogeneous mixture of products was produced in this system, resulting from hydrolysis, acid- catalyzed oxidation, reduction, and organosulfate formation. Evidence for disproportionation and heterocycle formation are proposed as reaction mechanisms hitherto unrecognized in the production of SOA. The proposed structure and formation mechanism for several species, based upon their MS/MS spectra, will also be presented.

Fiddler, M. N.; Cooks, R. G.; Shepson, P.

2008-12-01

377

Facile surface PEGylation via tyrosinase-catalyzed oxidative reaction for the preparation of non-fouling surfaces.  

PubMed

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

Lee, Yunki; Park, Kyung Min; Bae, Jin Woo; Park, Ki Dong

2013-02-01

378

Synthesis of (±)-cis-clavicipitic acid by a Rh(I)-catalyzed intramolecular imine reaction.  

PubMed

A new and short synthesis of racemic cis-clavicipitic acid was achieved by taking advantage of the double nucleophilic character of indole-4-pinacolboronic ester. Key to the success of the synthesis were an efficient and selective C-3 indole Friedel-Crafts alkylation and the development of an unprecedented intramolecular rhodium-catalyzed 1,2-addition of an aryl pinacolboronic ester to an unactivated imine. PMID:24605802

Bartoccini, Francesca; Casoli, Mariangela; Mari, Michele; Piersanti, Giovanni

2014-04-01

379

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

E-print Network

Alumina 50% 3 min NCS Isoxazole Trace 3 Alumina 50% 3 min Copper/ Acetate Triazole 90% yield by HPLC 4 8 1:1 H2O:t- BuOH - 24 hours Copper/ Acetate Isoxazole Success! (New 2) Representative HPLC Trace catalyzed triazole formation A B C Combined HPLC traces of 1, 2, and 3. ~ 7.58, 9.05, and 8.94, respectively

Collins, Gary S.

380

DFT study of the spin-forbidden reaction of N 2O and CO catalyzed by Pt +  

NASA Astrophysics Data System (ADS)

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.

Wang, Yong-Cheng; Wang, Qing-Yun; Geng, Zhi-Yuan; Si, Yu-Bing; Zhang, Jian-Hui; Li, Hui-Zhen; Zhang, Qing-Li

2008-07-01

381

Poor enantioselectivity of the direct aldol reaction catalyzed by (S,S)-proline dipeptide: A density functional study  

NASA Astrophysics Data System (ADS)

Density functional theory calculations were performed to study the stereo-controlling step of the direct aldol reaction between acetone and 4-nitrobenzaldehyde catalyzed by (S,S)-proline dipeptide. Four transition state structures have been determined using B3LYP functional with the 6-31G* basis set, corresponding to the anti and syn arrangements of the methylene moiety with respect to the carbonyl group in enamine intermediate, and to the si and re attacks to the aldehyde carbonyl carbon, respectively. Solvent effects of DMSO on the stereo-controlling step were investigated with Onsager model. The energy results of the transition states reveal the origin of poor enantioselectivity for the reaction.0

Fan, Jian-Fen; Wu, Li-Fen; Tao, Fu-Ming

382

Functional Group Tolerant Nickel-Catalyzed Cross-Coupling Reaction for Enantioselective Construction of 30 Methyl-Bearing Stereocenters  

PubMed Central

The first Negishi nickel-catalyzed stereospecific cross-coupling reaction of secondary benzylic esters is reported. A series of traceless directing groups are evaluated for ability to promote cross-coupling with dimethylzinc. Esters with a chelating thioether derived from commercially-available 2-(methylthio)acetic acid are most effective. The products are formed in high yield and with excellent stereospecificity. A variety of functional groups are tolerated in the reaction including alkenes, alkynes, esters, amines, imides, and O-, S-, and N-heterocycles. The utility of this transformation is highlighted in the enantioselective synthesis of a retinoic acid receptor (RAR) agonist and a fatty acid amide hydrolase (FAAH) inhibitor. PMID:23751004

Wisniewska, Hanna M.; Swift, Elizabeth C.; Jarvo, Elizabeth R.

2013-01-01

383

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions  

PubMed Central

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

Náray-Szabó, Gábor; Oláh, Julianna; Krámos, Balázs

2013-01-01

384

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations.  

PubMed

AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N(1)-methyl adenine (1-meA) catalyzed by AlkB after the formation of Fe(IV)-oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH(-) has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH(-) ligand on the hydrogen abstraction by the Fe(IV)-oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH(-) ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe-O-C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme Fe(II) and ?-ketoglutarate (?-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB. PMID:25400523

Fang, Dong; Cisneros, G Andrés

2014-11-11

385

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

PubMed

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

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

2014-06-01

386

Theoretical studies on the regioselectivity of iridium-catalyzed 1,3-dipolar azide-alkyne cycloaddition reactions.  

PubMed

Iridium-catalyzed cycloaddition of thioalkynes and bromoalkynes with azides have been investigated with the aid of density functional theory (DFT) calculations at the M06 level of theory. Our investigation focused on the different regioselectivity observed for the reactions of the two classes of alkynes. The DFT results have shown that the mechanisms of cycloaddition reactions using thioalkynes and bromoalkynes as substrates are similar yet different. The reactions of thioalkynes occur via a metallabicyclic Ir-carbene intermediate formed through alkyne-azide oxidative coupling via attack of the azide terminal nitrogen toward the ? alkyne carbon, whose carbene ligand is stabilized by an alkylthio/arylthio substituent. Reductive elimination from the intermediate leads to the formation of the experimentally observed 5-sulfenyltriazole. In the reactions of bromoalkynes RC?CBr, the reaction mechanism involves the initial formation of a six-membered-ring metallacycle intermediate in the oxidative coupling step. The six-membered-ring intermediate then undergoes isomerization via migrating the terminal azide nitrogen from the ? carbon to the ? carbon to form a much less stable metallabicyclic Ir-carbene species from which reductive elimination gives 4-bromotriazole. PMID:25222638

Luo, Qiong; Jia, Guochen; Sun, Jianwei; Lin, Zhenyang

2014-12-19

387

Transformation pathways of MeO-PBDEs catalyzed by active center of P450 enzymes: A DFT investigation employing 6-MeO-BDE-47 as a case.  

PubMed

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

Wang, Xingbao; Chen, Jingwen; Wang, Yong; Xie, Hongbin; Fu, Zhiqiang

2015-02-01

388

Unusual origins of isotope effects in enzyme-catalysed reactions  

PubMed Central

High hydrostatic pressure is a neglected tool for probing the origins of isotope effects. In chemical reactions, normal primary deuterium isotope effects (DIEs) arising solely from differences in zero point energies are unaffected by pressure; but some anomalous isotope effects in which hydrogen tunnelling is suspected are partially suppressed. In some enzymatic reactions, high pressure completely suppresses the DIE. We have now measured the effects of high pressure on the parallel 13C heavy atom isotope effect of yeast alcohol dehydrogenase and found that it is also suppressed by high pressure and, similarly, suppressed in its entirety. Moreover, the volume changes associated with the suppression of both deuterium and heavy atom isotope effects are virtually identical. The equivalent decrease in activation volumes for hydride transfer, when one mass unit is added to the carbon end of a scissile C–H bond as when one mass unit is added to the hydrogen end, suggests a common origin. Given that carbon is highly unlikely to undergo tunnelling, it follows that hydrogen is not doing so either. The origin of these isotope effects must lie elsewhere. We offer protein domain motions as a possibility. PMID:16873122

Northrop, Dexter B

2006-01-01

389

Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes.  

PubMed

Tocopherols are lipid-soluble compounds synthesized only by photosynthetic eukaryotes and oxygenic cyanobacteria. The pathway and enzymes for tocopherol synthesis are homologous in cyanobacteria and plants except for 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ/MSBQ MT), which catalyzes a key methylation step in both tocopherol and plastoquinone (PQ) synthesis. Using a combined genomic, genetic, and biochemical approach, we isolated and characterized the VTE3 (vitamin E defective) locus, which encodes MPBQ/MSBQ MT in Arabidopsis. The phenotypes of vte3 mutants are consistent with the disruption of MPBQ/MSBQ MT activity to varying extents. The ethyl methanesulfonate-derived vte3-1 allele alters tocopherol composition but has little impact on PQ levels, whereas the null vte3-2 allele is deficient in PQ and alpha- and gamma-tocopherols. In vitro enzyme assays confirmed that VTE3 is the plant functional equivalent of the previously characterized MPBQ/MSBQ MT (Sll0418) from Synechocystis sp PCC6803, although the two proteins are highly divergent in primary sequence. Sll0418 orthologs are present in all fully sequenced cyanobacterial genomes, Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana but absent from vascular and nonvascular plant databases. VTE3 orthologs are present in all vascular and nonvascular plant databases and in C. reinhardtii but absent from cyanobacterial genomes. Intriguingly, the only prokaryotic genomes that contain VTE3-like sequences are those of two species of archea, suggesting that, in contrast to all other enzymes of the plant tocopherol pathway, the evolutionary origin of VTE3 may have been archeal rather than cyanobacterial. In vivo analyses of vte3 mutants and the corresponding homozygous Synechocystis sp PCC6803 sll0418::aphII mutant revealed important differences in enzyme redundancy, the regulation of tocopherol synthesis, and the integration of tocopherol and PQ biosynthesis in cyanobacteria and plants. PMID:14508009

Cheng, Zigang; Sattler, Scott; Maeda, Hiroshi; Sakuragi, Yumiko; Bryant, Donald A; DellaPenna, Dean

2003-10-01

390

Non-conventional hydrolase chemistry: amide and carbamate bond formation catalyzed by lipases  

Microsoft Academic Search

Biocatalysis in nonaqueous media is becoming increasingly important in organic synthesis. Lipases are the most used enzymes, especially in transesterification reactions. However, in the last years the amidation reaction catalyzed by lipases has also been shown to be a useful tool for the organic chemists. In this review, we discuss the possibilities of the enzymatic aminolysis and ammonolysis reactions for

Vicente Gotor

1999-01-01

391

Scope and limitations of aliphatic Friedel-Crafts alkylations. Lewis acid catalyzed addition reactions of alkyl chlorides to carbon-carbon double bonds  

SciTech Connect

Lewis acid catalyzed addition reactions of alkyl halides with unsaturated hydrocarbons have been studied. 1:1 addition products are formed if the addends dissociate faster than the corresponding products; otherwise, polymerization takes place. For reaction conditions under which these compounds exist mainly undissociated, solvolysis constants of model compounds can be used to predict the outcome of any such addition reactions if systems with considerable steric hindrance are excluded.

Mayr, H.; Striepe, W.

1983-04-22

392

Synthesis of tetrahydroisoquinolines and isochromans via Pictet–Spengler reactions catalyzed by Brønsted acid–surfactant-combined catalyst in aqueous media  

Microsoft Academic Search

Perfluorooctanesulfonic acid (PFOSA), Brønsted acid–surfactant-combined catalyst, efficiently catalyzes the Pictet–Spengler reactions of ?-arylethyl carbamate derivatives with aldehydes in water. The present reaction is accelerated by the addition of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). PFOSA in HFIP–water (10v\\/v%) is also successfully applied to the oxa-Pictet–Spengler reactions of ?-arylethyl alcohol compounds.

Akio Saito; Masaki Takayama; Aru Yamazaki; Junko Numaguchi; Yuji Hanzawa

2007-01-01

393

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

NASA Astrophysics Data System (ADS)

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.

Zhao, Haiying; Dou, Xiaoming

2005-01-01

394

Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305.  

PubMed

Flp provides a unique opportunity to apply the tools of chemical biology to phosphoryl transfer reactions. Flp and other tyrosine recombinases catalyze site-specific DNA rearrangements via a phosphotyrosine intermediate. Unlike most related enzymes, Flp's nucleophilic tyrosine derives from a different protomer than the remainder of its active site. Because the tyrosine can be supplied exogenously, nonnatural synthetic analogs can be used. Here we examine the catalytic role of Flp's conserved H305. DNA cleavage was studied using a peptide containing either tyrosine (pKa congruent with 10) or 3-fluoro-tyrosine (pKa congruent with 8.4). Religation was studied using DNA substrates with 3'-phospho-cresol (pKa congruent with 10) or 3'-para-nitro-phenol (pKa congruent with 7.1). In both cases, the tyrosine analog with the lower pKa specifically restored the activity of an H305 mutant. These results provide experimental evidence that this conserved histidine functions as a general acid/base catalyst in tyrosine recombinases. PMID:17317566

Whiteson, Katrine L; Chen, Yu; Chopra, Neeraj; Raymond, Amy C; Rice, Phoebe A

2007-02-01

395

New adaptive chiral thiophene ligands for copper-catalyzed asymmetric Henry reaction.  

PubMed

A new type of adaptive chiral thiophene-based ligands 3 has been designed and developed. The synthetic flexibility of the thienyl ring allowed for the preparation of polydendate C2-symmetric ligands in good yields, carrying simultaneously "hard" as well as "soft" coordinating atoms (i.e., N, S). The coordination attitude of 3 was then tested in the enantioselective base-free Cu(OAc)(2)-catalyzed addition of nitromethane to aromatic aldehydes, leading to the corresponding beta-nitro alcohols in excellent yields and enantiomeric excesses up to 86%. PMID:18830973

Bandini, Marco; Cabiddu, Salvatore; Cadoni, Enzo; Olivelli, Pasquale; Sinisi, Riccardo; Umani-Ronchi, Achille; Usai, Michele

2009-01-01

396

Selective iron-catalyzed cross-coupling reactions of grignard reagents with enol triflates, acid chlorides, and dichloroarenes.  

PubMed

Cheap, readily available, air stable, nontoxic, and environmentally benign iron salts such as Fe(acac)(3) are excellent precatalysts for the cross-coupling of Grignard reagents with alkenyl triflates and acid chlorides. Moreover, it is shown that dichloroarene and -heteroarene derivatives as the substrates can be selectively monoalkylated by this method. All cross-coupling reactions proceed very rapidly under notably mild conditions and turned out to be compatible with a variety of functional groups in both reaction partners. A detailed analysis of the preparative results suggests that iron-catalyzed C-C bond formations can occur via different pathways. Thus, it is likely that reactions of methylmagnesium halides involve iron-ate complexes as the active components, whereas reactions of Grignard reagents with two or more carbon atoms are effected by highly reduced iron-clusters of the formal composition [Fe(MgX)(2)](n) generated in situ. Control experiments using the ate-complex [Me(4)Fe]Li(2) corroborate this interpretation. PMID:15153029

Scheiper, Bodo; Bonnekessel, Melanie; Krause, Helga; Fürstner, Alois

2004-05-28

397

Mechanism of the EPSP synthase catalyzed reaction: evidence for the lack of a covalent carboxyvinyl intermediate in catalysis  

SciTech Connect

In order to detect covalent reaction intermediates in the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase reaction, we have investigated the interaction of EPSP synthase with the reaction product EPSP. An exchange of EPSP-methylene protons could be demonstrated by incubating EPSPS with EPSP in D/sub 2/O. Since trace amounts of contaminating Pi would lead to reversal of EPSPS reaction and hence methylene proton exchange, we added pyruvate kinase, ADP, Mg++ and K+. Under these conditions, any contaminating Pi that is converted to PEP is trapped as ATP. No exchange of EPSP protons with those of the solvent could be detected in the presence of this trap system, suggesting that enzyme-bound EPSP is unable to form a covalent tetrahedral complex. Incorporation of (/sup 14/C) from (/sup 14/C)-S3P and (/sup 14/C)-PEP into EPSP could be detected, but only in the absence of a PEP (or Pi) trap system. This indicates that for the exchange reaction, Pi is required, and also indicates the absence of a covalent intermediate, unless the carboxyvinyl-enzyme-bound S3P is completely restricted from exchange.

Wibbenmeyer, J.; Brundage, L.; Padgette, S.R.; Likos, J.J.; Kishore, G.M.

1988-06-16

398

The roles of counterion and water in a stereoselective cysteine-catalyzed Rauhut-Currier reaction: a challenge for computational chemistry.  

PubMed

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

Osuna, Sílvia; Dermenci, Alpay; Miller, Scott J; Houk, K N

2013-10-11

399

Highly enantioselective [4 + 2] cycloaddition reactions catalyzed by a chiral N-methyl-oxazaborolidinium cation.  

PubMed

The reaction of lithium aryl borohydrides with salts of beta-amino alcohols provides a new route for the synthesis of oxazaborolidines. This method also leads to the first synthesis of hitherto elusive N-methyl oxazaborolidine cations, specifically the cationic proline derivative 3. Compound 3 is a strong chiral Lewis acid which is very effective for catalysis of [4 + 2]-cycloaddition reactions in good yield and with high enantioselectivity. Several diverse examples illustrate the scope of these catalytic reactions. PMID:18582066

Canales, Eda; Corey, E J

2008-08-01

400

Hetero-cope rearrangements of nitrosobutenes. DFT studies of thermal and acid-catalyzed reactions.  

PubMed

[Structure: see text] Density functional theory studies of the hetero-Cope reactions of 4-nitroso-1-butenes and nitrosobicyclo[2.2.2]hexenes are reported. The reactions proceed via concerted mechanisms. The electron-withdrawing methoxycarbonyl group alpha- to the nitroso group decreases the activation barrier. Lewis acids such as SbF5 and TiCl4 accelerate the reactions, as has been found experimentally by Zakarian and Lu. PMID:17165908

Jabbari, Arash; Houk, K N

2006-12-21

401

Synergistic effect of two E2 ubiquitin conjugating enzymes in SCF(hFBH1) catalyzed polyubiquitination.  

PubMed

Ubiquitination is a post translational modification which mostly links with proteasome dependent protein degradation. This process has been known to play pivotal roles in the number of biological events including apoptosis, cell signaling, transcription and translation. Although the process of ubiquitination has been studied extensively, the mechanism of polyubiquitination by multi protein E3 ubiquitin ligase, SCF complex remains elusive. In the present study, we identified UbcH5a as a novel stimulating factor for poly-ubiquitination catalyzed by SCF(hFBH1) using biochemical fractionations and MALDI-TOF. Moreover, we showed that recombinant UbcH5a and Cdc34 synergistically stimulate SCF(hFBH1) catalyzed polyubiquitination in vitro. These data may provide an important cue to understand the mechanism how the SCF complex efficiently polyubiquitinates target substrates. [BMB Reports 2015; 48(1): 025-029]. PMID:24667174

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

2015-01-01

402

Biodegradation of Chlorinated Solvents: Reactions near DNAPL and Enzyme Function  

SciTech Connect

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.

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

2003-12-11

403

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

PubMed

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

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

2010-09-24

404

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

PubMed Central

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

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

2013-01-01

405

A Reactivity-Driven Approach to the Discovery and Development of Gold-Catalyzed Organic Reactions  

PubMed Central

Approaches to research in organic chemistry are as numerous as the reactions they describe. In this account, we describe our reactivity-based approach. Using our work in the area of gold-catalysis as a background, we discuss how a focus on reaction mechanism and reactivity paradigms can lead to the rapid discovery of new synthetic tools. PMID:21135915

Shapiro, Nathan D.; Toste, F. Dean

2010-01-01

406

Aldol reactions catalyzed by L-proline functionalized polymeric nanoreactors in water.  

PubMed

The use of functional core-shell micelles as asymmetric catalytic nanoreactors for organic reactions in water is presented. An unprecedented increase in rate of reaction was achieved, which is proposed to be associated with the ability of the nanostructures to effectively concentrate the reagents in the catalytically active micelle core. PMID:22911135

Lu, Annhelen; Cotanda, Pepa; Patterson, Joseph P; Longbottom, Deborah A; O'Reilly, Rachel K

2012-10-01

407

Construction of indole- and isoquinoline-fused nitrogen-containing heterocycles through copper-catalyzed multi-component reaction.  

PubMed

A copper-catalyzed synthesis of 2-(aminomethyl)indole through domino three-component coupling-cyclization has been developed. This reaction proceeds through Mannich-type coupling of 2-ethynylanilines, aldehydes, and secondary amines, followed by hydroamination. This indole formation was applicable to the synthesis of 4-methylene-2,3,4,9-tetrahyro-1H-pyrido[3,4-b]indoles and 5,6,7,8-tetrahydrobenzo[e]indolo[2,3-c]azepines via palladium-catalyzed C-H functionalization at the 3-position of indole. A combination of the three-component indole formation with nucleophilic cyclization promoted by t-BuOK or MsOH provides an effective access to beta-carboline scaffolds. Indole-fused 1,4-diazepines were also synthesized through deprotection/N-arylation at the nitrogen atom of indole by one-pot addition of MeONa after the formation of 2-(aminomethyl)indoles. In relation to the three-component indole formation, a novel four-component synthesis of isoquinolines has been developed. This isoquinoline formation includes Mannich-type reaction of 2-ethynylbenzaldehyde with (HCHO)(n) and secondary amine, imine formation with t-BuNH(2), isoquinoline formation, and elimination of t-butyl group to directly afford 3-(aminomethyl)isoquinolines in good yields. By the use of an alkane diamine instead of t-BuNH(2), fused 3-(aminomethyl)isoquinoline derivatives were obtained by cascade cyclization and oxidation. PMID:20606372

Ohta, Yusuke

2010-07-01

408

Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde‡, ¶  

PubMed Central

D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D2O was monitored by 1H NMR spectroscopy and kcat/Km = 0.034 M?1 s?1 was determined for this isomerization at pD 7.0. This is similar to kcat/Km = 0.017 M?1 s?1 for the TIM-catalyzed carbon deprotonation reaction of DGA in D2O at pD 7.0 [Amyes, T. L.; O’Donoghue, A. C. and Richard J. P. (2001) J. Am. Chem. Soc. 123, 11325–11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (kcat/Km = 490 M?1 s?1) than for the TIM-catalyzed isomerization of DGAP (kcat/Km = 9.6 x 106 M?1 s?1) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219–410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI-catalyzed isomerization of DGA in D2O at pD 7.0 gives a 90% yield of [1-1H]-DHA and a 10% yield of [1-2H]-DHA, the product of isomerization with deuterium incorporation from solvent D2O. By comparison, the transfer of 3H from labeled hexose substrate to solvent is observed only once in every 109 turnovers for the XI-catalyzed isomerization of [2-3H]-glucose in H2O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), Biochemistry 33, 1481–1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI•sugar complexes. PMID:21995300

Toteva, Maria M.; Silvaggi, Nicholas R.; Allen, Karen N.; Richard, John P.

2011-01-01

409

Specificity of Carica papaya latex in lipase-catalyzed interesterification reactions  

Microsoft Academic Search

Enzymatic interesterification of the chiral triacylglycerol, 1-butyroyl-2-stearoyl-3-palmitoyl-sn-glycerol (sn-BSP) with trimyristin indicated that the lipase present in Carica papaya latex exhibits an sn3 stereoselectivity. Other interesterification experiments with homogeneous triacylglycerols of varying chain length with tricaprylin showed that this enzyme also has a typoselectivity for short chain fatty acids.

P. Villeneuve; M. Pina; A. Skarbek; J. Graille; T. A. Foglia

1997-01-01

410

Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase  

PubMed Central

Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates. PMID:24584240

Inoue, Kengo; Usami, Yusuke; Ashikawa, Yuji; Noguchi, Haruko; Umeda, Takashi; Yamagami-Ashikawa, Aiko; Horisaki, Tadafumi; Uchimura, Hiromasa; Terada, Tohru; Nakamura, Shugo; Shimizu, Kentaro; Habe, Hiroshi; Yamane, Hisakazu; Fujimoto, Zui

2014-01-01

411

Mechanisms of Enzyme-Catalyzed Reduction of Two Carcinogenic Nitro-Aromatics, 3-Nitrobenzanthrone and Aristolochic Acid I: Experimental and Theoretical Approaches  

PubMed Central

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

Stiborová, Marie; Frei, Eva; Schmeiser, Heinz H.; Arlt, Volker M.; Martínek, Václav

2014-01-01

412

Rapid and efficient functionalized ionic liquid-catalyzed aldol condensation reactions associated with microwave irradiation.  

PubMed

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

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

2014-01-01

413

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

PubMed Central

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

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

2014-01-01

414

13C NMR Characterization of an Exchange Reaction between CO and CO2 Catalyzed by Carbon Monoxide Dehydrogenase†  

PubMed Central

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

2008-01-01

415

Cu(OTf)2-catalyzed asymmetric Friedel-Crafts alkylation reaction of indoles with arylidene malonates using bis(sulfonamide)-diamine ligands.  

PubMed

A highly efficient Cu-catalyzed asymmetric Friedel-Crafts alkylation reaction of indoles with arylidene malonates using simple, stable, and easily prepared bis-sulfonamide diamine ligands was developed. The desired products were obtained in up to 99% yield with 96% ee. PMID:23642187

Wu, Jing; Wang, Dongping; Wu, Fan; Wan, Boshun

2013-06-01

416

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

PubMed Central

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

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

2014-01-01

417

Cross-Couplings of Unactivated Secondary Alkyl Halides: Room-Temperature Nickel-Catalyzed Negishi Reactions of Alkyl Bromides and Iodides  

E-print Network

@mit.edu Palladium- and nickel-catalyzed cross-coupling reactions are widely used tools for constructing carbon-carbon bonds.1 To date, most studies of these processes have focused on forming Csp2-Csp2 (particularly biaryl-Bu-Pybox leads to a decrease in the efficiency of carbon-carbon bond formation (entries 1, 14, and 15). Finally

Fu, Gregory C.

418

Evolution of function in the crotonase superfamily: the stereochemical course of the reaction catalyzed by 2-ketocyclohexanecarboxyl-CoA hydrolase.  

PubMed

Members of the mechanistically diverse enoyl-CoA hydratase (crotonase) superfamily catalyze reactions that involve stabilization of an enolate anion derived from an acyl thioester of coenzyme A. 2-Ketocyclohexanecarboxyl-CoA hydrolase (BadI), found in a pathway for anaerobic degradation of benzoate by Rhodopseudomonas palustris, is a member of the crotonase superfamily that catalyzes a reverse Dieckmann reaction in which the substrate is hydrolyzed to pimelyl-CoA. The substrate is the configurationally labile 2S-ketocyclohexanecarboxyl-CoA, and in 2H2O solvent hydrogen is incorporated into the 2-proS position of the pimelyl-CoA product. Therefore, the stereochemical course of the BadI-catalyzed reaction is inversion. This information is important for understanding the roles of active-site functional groups in the active site of BadI as well as in the active sites of the homologous 1,4-dihydroxynaphthoyl-CoA synthases that catalyze a forward Dieckmann reaction. PMID:15186151

Eberhard, Ellen D; Gerlt, John A

2004-06-16

419

TaBr 5-catalyzed Biginelli reaction: one-pot synthesis of 3,4-dihydropyrimidin-2-(1 H)-ones\\/thiones under solvent-free conditions  

Microsoft Academic Search

An efficient TaBr5 (5–10mol%)-catalyzed Biginelli reaction under solvent-free conditions for one-pot syntheses of 3,4-dihydropyrimidin-2-(1H)-ones (DHPMs) and their thione analogs is reported. The catalyst is stable at room temperature and employed under mild and environmentally friendly conditions.

Naseem Ahmed; Johan E. van Lier

2007-01-01

420

Cross-coupling reaction of alpha-chloroketones and organotin enolates catalyzed by zinc halides for synthesis of gamma-diketones.  

PubMed

The reaction of tin enolates 1 with alpha-chloro- or bromoketones 2 gave gamma-diketones (1,4-diketones) 3 catalyzed by zinc halides. In contrast to the exclusive formation of 1,4-diketones 3 under catalytic conditions, uncatalyzed reaction of 1 with 2 gave aldol-type products 4 through carbonyl attack. NMR study indicates that the catalyzed reaction includes precondensation between tin enolates and alpha-haloketones providing an aldol-type species and their rearrangement of the oxoalkyl group with leaving halogen to produce 1,4-diketones. The catalyst, zinc halides, plays an important role in each step. The carbonyl attack for precondensation is accelerated by the catalyst as Lewis acid and the intermediate zincate promotes the rearrangement by releasing oxygen and bonding with halogen. Various types of tin enolates and alpha-chloro- and bromoketones were applied to the zinc-catalyzed cross-coupling. On the other hand, the allylic halides, which have no carbonyl moiety, were inert to the zinc-catalyzed coupling with tin enolates. The copper halides showed high catalytic activity for the coupling between tin enolates 1 and organic halides 7 to give gamma,delta-unsaturated ketones 8 and/or 9. The reaction with even chlorides proceeded effectively by the catalytic system. PMID:12071753

Yasuda, Makoto; Tsuji, Shoki; Shigeyoshi, Yusuke; Baba, Akio

2002-06-26

421

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

E-print Network

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

Toste, Dean

422

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 ...

423

[Pyrophosphate analogs in the pyrophosphorolysis reaction catalyzed by Escherichia coli RNA polymerase].  

PubMed

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

Rozovskaia, T A; Chenchik, A A; Tarusova, N B; Bibilashvili, R Sh; Khomutov, R M

1981-01-01

424

Epoxidation reactions catalyzed by rat liver cytochromes P-450 and P-448 occur at different faces of the 8,9-double bond of 8-methylbenz[a]anthracene.  

PubMed Central

8-Methylbenz[a]anthracene (8-MeBaA) transdihydrodiol metabolites were isolated by reversed-phase and normal-phase HPLCs from incubations of 8-MeBaA with liver microsomes or a reconstituted system containing purified cytochrome P-448 and epoxide hydrolase. Regardless of the enzyme source, the metabolically formed 8-MeBaA trans-3,4- and -5,6-dihydrodiols were found to be enriched in one enantiomeric isomer and differed only in the degree of optical purity. The 8-MeBaA trans-8,9-dihydrodiol formed by liver microsomes from either untreated or phenobarbital-treated rats was enriched with the (+)-enantiomer. In contrast, the 8-MeBaA trans-8,9-dihydrodiol formed either by liver microsomes from 3-methylcholanthrene-treated rats or by the reconstituted rat liver enzyme system containing cytochrome P-448 and epoxide hydrolase was enriched with the (-)enantiomer. These results indicate that, in catalyzing the formation of 3,4- and 5,6-epoxide intermediates, the interaction with the unsubstituted 3,4- and 5,6-double bonds of 8-MeBaA by the different forms of cytochrome P-450 occur preferentially on the same face of the aromatic plane and they differ only in the degree of stereoselectivity. However, different forms of cytochrome P-450 may interact with different faces of the aromatic plane at the methyl-substituted 8,9-double bond of 8-MeBaA, resulting in the formation of trans-8,9-dihydrodiols enriched in different enantiomeric forms. This demonstrates that different forms of cytochrome P-450 may catalyze the epoxidation reaction preferentially at different sides of the methyl-substituted double bond of a planar polycyclic hydrocarbon molecule. These properties may be used to further classify and to understand the enzyme-substrate interactions of the different forms of cytochrome P-450 in the drug-metabolizing enzyme systems. PMID:6960350

Yang, S K; Chou, M W; Fu, P P; Wislocki, P G; Lu, A H

1982-01-01

425

A new approach to carbon-carbon bond formation: Development of aerobic Pd-catalyzed reductive coupling reactions of organometallic reagents and styrenes  

PubMed Central

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

Gligorich, Keith M.; Iwai, Yasumasa; Cummings, Sarah A.; Sigman, Matthew S.

2009-01-01

426

anti-selective direct asymmetric Mannich reactions catalyzed by axially chiral amino sulfonamide as an organocatalyst.  

PubMed

A direct asymmetric Mannich reaction using a novel axially chiral amino trifluoromethanesulfonamide (S)-3 has been developed in highly anti-selective and enantioselective manners. Thus, in the presence of a catalytic amount of (S)-3, the reactions between aldehydes and the alpha-imino ester 4 proceed smoothly to give the functional beta-amino aldehydes with significantly higher anti/syn ratio and enantioselectivity than previously possible. PMID:16305223

Kano, Taichi; Yamaguchi, Yukako; Tokuda, Osamu; Maruoka, Keiji

2005-11-30

427

Aluminum triflate catalyzed tandem reactions of D-galactal: toward chiral benzopyrans, chromenes, and chromans.  

PubMed

3,4,6-Tri-O-acetyl-D-galactal is selectively converted into 1-O-aryl-2-deoxy derivatives or chiral bridged benzopyrans under Al(OTf)3 catalysis, depending on reaction conditions. The benzopyrans react with Al(OTf)3/acetic anhydride in ring-opening reactions in the absence or presence of acetic acid to selectively produce chiral chromenes or chromans, respectively, in high yields. PMID:25162834

Simelane, Sandile B; Kinfe, Henok H; Muller, Alfred; Williams, D Bradley G

2014-09-01

428

Asymmetric Dual-Reagent Catalysis: Mannich-type Reactions Catalyzed by Ion Pair.  

PubMed

The combination of a new bifunctional phosphine and an acrylate generate a zwitterion in?situ and it serves as an efficient catalyst for asymmetric reactions through a homogeneous ion-pairing mode. This new catalytic system has been successfully applied to Mannich-type reactions to give excellent results and it demonstrates a broad substrate scope. Such reactivity is not accessible with general organophosphine catalytic modes. Preliminary investigations into the mechanism are also presented. PMID:25515428

Wang, Hong-Yu; Zhang, Kai; Zheng, Chang-Wu; Chai, Zhuo; Cao, Dong-Dong; Zhang, Jia-Xing; Zhao, Gang

2015-02-01

429

Molecular diversity of acid-catalyzed one-pot reaction of arylamines, methyl propiolate, and isatins.  

PubMed

Under the catalysis of p-TsOH, ß-enamino esters, generated in situ from the reaction of arylamines and propiolate, were reacted with isatins to afford isatinylidene bis(3-arylamino)acrylates in moderate yields. When BF3·OEt2 was used as catalyst, similar reactions of the in situ generated ß-enamino esters resulted in the corresponding spiro[indoline-3,4'-pyridine] derivatives in good yields. PMID:24664284

Gao, Hong; Sun, Jing; Yan, Chao-Guo

2014-08-01

430

Reaction Mechanism of the Dinuclear Zinc Enzyme N-Acyl-L-homoserine Lactone Hydrolase: A Quantum Chemical Study  

E-print Network

-acyl-L-homoserine lactone hydrolase (AHL lactonase) is a dinuclear zinc enzyme responsible for the hydrolytic ring openingReaction Mechanism of the Dinuclear Zinc Enzyme N-Acyl-L-homoserine Lactone Hydrolase: A Quantum for the signaling specificity of AHLs.3 There are two different types of enzymes that can impede AHL activity. One

Liao, Rongzhen

431

Expanding P450 catalytic reaction space through evolution and engineering.  

PubMed

Advances in protein and metabolic engineering have led to wider use of enzymes to synthesize important molecules. However, many desirable transformations are not catalyzed by any known enzyme, driving interest in understanding how new enzymes can be created. The cytochrome P450 enzyme family, whose members participate in xenobiotic metabolism and natural products biosynthesis, catalyzes an impressive range of difficult chemical reactions that continues to grow as new enzymes are characterized. Recent work has revealed that P450-derived enzymes can also catalyze useful reactions previously accessible only to synthetic chemistry. The evolution and engineering of these enzymes provides an excellent case study for how to genetically encode new chemistry and expand biology's reaction space. PMID:24658056

McIntosh, John A; Farwell, Christopher C; Arnold, Frances H

2014-04-01

432

Physiological aspects of free-radical reactions.  

PubMed Central

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

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

1985-01-01