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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


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.



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



Method for predicting enzyme-catalyzed reactions  


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.



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.


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.


Biohydroxylation Reactions Catalyzed by Enzymes and Whole-Cell Systems  

Microsoft Academic Search

The biohydroxylation of a number of cyclic substrates (3–24) containing aromatic side chains was used to compare substrate specificity and selectivity of hydroxylation using microbial enzymes and whole-cell biocatalysts. In general, the regioselectivity of reaction was remarkably similar between the different catalysts in that little aromatic or benzylic, but significant aliphatic hydroxylation was observed. However, a more detailed investigation of

Sabine L. Flitsch; Suzanne J. Aitken; Cathy S.-Y. Chow; Gideon Grogan; Adam Staines



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


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



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)



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



Measurement of peroxidase activity in single neutrophils by combining catalyzed-enzyme reaction and epi-fluorescence microscopy  

Microsoft Academic Search

An epi-fluorescence microscopy for determination of peroxidase in individual neutrophils was developed by a combination of enzyme-catalyzed reaction and fluorescence detection. In this method, an individual cell was transferred into a microliter-volume vessel and lysed by freeze-thawing and ultrasonication. The peroxidases-catalyzed reaction was initiated by adding the buffer solution containing nonfluorescent substrates 10-acetyl-3,7-dihydroxyphenoxazine and H2O2 to the vessel. Peroxidase activity

Wenpeng Li; Wenrui Jin



Possibilities and Scope of the Double Isotope Effect Method in the Elucidation of Mechanisms of Enzyme Catalyzed Reactions  

Microsoft Academic Search

Kinetic isotope effects on enzyme catalyzed reactions are indicative for the first irreversible in a sequence of individual steps. Hints on the relative velocities of other steps can only be obtained from the partitioning factor R and its dependence on external reaction conditions. In general, the experimental data needed are obtained from isotope abundance measurements in a defined position of

H.-L. Schmidt; R. Medina



Decreases in molecularity promote conversion when reactions are catalyzed by enzymes immobilized in slab-shaped beads  

Microsoft Academic Search

Application of Fick's first law to substrate undergoing chemical reaction catalyzed by an enzyme immobilized in a porous slab-shaped bead leads to substrate concentration profiles that are flatter when the ratio of stoichiometric coefficients of product to reactant (x) is lower. Since the actual effectiveness factor decreases when x increases (at approximately the same rate irrespective of the value taken

R. M. Barros; F. X. Malcata



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)



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

SciTech Connect

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

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



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.



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.



Catalyzed enzyme electrodes  


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)



Dual-color fluorescence cross-correlation spectroscopy for monitoring the kinetics of enzyme-catalyzed reactions.  


Dual-color fluorescence correlation spectroscopy is a biophysical technique that enables precise and sensitive analyzes of molecular interactions. It is unique in its ability to analyze reactions in real time at nanomolar substrate concentrations and below, especially when applied to the monitoring of enzyme-catalyzed reactions. Furthermore, it offers a wide range of accessible reactions, restricted only by the prerequisite that a chemical bond or a physical interaction between two spectrally distinguishable fluorophores is established or broken. Recently, the optical setup of dual-color fluorescence correlation spectroscopy has been extended toward two-photon excitation, resulting in several advantages compared with standard excitation, such as lower fluorescence background, an even larger spectrum of potential fluorescence dyes to be used, as well as a more stable and simplified optical setup. So far, the method has been successfully employed to analyze the kinetics of nucleic acid and peptide modifications catalyzed by nucleases, polymerases, and proteases. PMID:11384186

Rarbach, M; Kettling, U; Koltermann, A; Eigen, M



Use of inhibitors to study reactions catalyzed by enzymes requiring pyridoxal phosphate as coenzyme  

Microsoft Academic Search

The stereochemistry of a variety of pyridoxal phosphate-mediated enzymic reactions has been studied using enzyme inhibitors that are stereospecifically labeled in the b-position with deuterium. A versatile synthesis has been developed to prepare a wide variety of stereospecifically labeled D- and L-amino acids and inhibitors. Investigation of the \\

Benjamin Adams; B. Svante Axelsson; Kenneth J. M. Beresford; Nicola J. Church; Philip A. Spencer; Sheena M. Whyte; Douglas W. Young



Enantioselective reactions catalyzed by synthetic enzymes. A model for chemical evolution  

Microsoft Academic Search

Polyleucines of various lengths act as enantioselective catalysts in the aldol condensation between cyclohexanone and various aromatic aldehydes. Polyleucine and other polyamino acids behave as synthetic enzymes in the epoxidation of chalcone and other electron-deficient alkenes. Both reactions are of considerable prebiotic significance.

Stefano Colonna; Dario Perdicchia; Ernesto Di Mauro



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

Microsoft Academic Search

For those enzymes that proceed via a stepwise reaction mechanism with a discrete chemical intermediate and where deuterium and ¹³C isotope effects are on separate steps, a new method has been developed to solve for the intrinsic deuterium and ¹³C kinetic isotope effects that relies on directly observing the partitioning of the intermediate between the forward and reverse directions. This

Charles B. Grissom; W. W. Cleland



A Procedure for the Joint Evaluation of Substrate Partitioning and Kinetic Parameters for Reactions Catalyzed by Enzymes in Reverse Micellar Solutions  

Microsoft Academic Search

A simple method useful for the joint evaluation of substrate partitioning and kinetic parameters for reactions catalyzed by enzymes entrapped in reverse micelles is proposed. The method is applied to the hydrolysis of 2-naphthyl acetate (2-NA) catalyzed by lipase in sodium 1,4-bis(2-ethylhexyl) sulfosuccinate (AOT)\\/buffer\\/heptane reverse micellar solutions. In the presence of micelles, the relationship between the initial reaction rate and

Luis Felipe Aguilar; Elsa Abuin; Eduardo Lissi



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.

School, Maryland V.


Diffusional and electrostatic effects on apparent kinetic parameters of reactions catalyzed by enzyme immobilized on the external surface of a support  

Microsoft Academic Search

Diffusional and electrostatic effects on the apparent maximum reaction rate Vmapp and the apparent Michaelis constant Kmapp were investigated theoretically for a system in which an enzyme immobilized on the external surface of a solid support catalyzes a reaction according to Michaelis-Menten kinetics. In such a system, the dependence of Vmapp and Kmapp on the substrate concentration can be expressed

Fumihide Shiraishi



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.



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


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



A paper-based surface-enhanced resonance Raman spectroscopic (SERRS) immunoassay using magnetic separation and enzyme-catalyzed reaction.  


In this study, a novel paper-based SERRS immunoassay based on magnetic separation and alkaline phosphatase (ALP) enzyme catalyzed hydrolysis reaction was developed. By using modified antibodies conjugated to magnetic beads, capture of mouse IgG followed by addition of ALP-labeled antibodies would form a sandwich-like immunoconjugate. After magnetic separation, 5-bromo-4-chloro-3-indolyl phosphate (BCIP), a low SERRS active compound, was added as the substrate for ALP to generate a high SERRS response. Detection was conducted on a silver colloid/PVP/filter paper SERS substrate by spotting a pre-aggregated silver colloid sol onto polyvinyl pyrrolidone (PVP) modified filter paper using a semi-automatic TLC sample applicator. The optimization of the highly SERS active paper-based substrate, dynamic hydrolysis process of BCIP, quantitative detection of IgG, and selectivity of the assay was studied in detail. By taking advantage of magnetic separation in order to decrease the background interference, the selective enzyme reaction involved in producing a highly SERRS active product could detect mouse IgG from 1 to 500 ng mL(-1) with a LOD of 0.33 ng mL(-1). PMID:23486763

Chen, Yuanyuan; Cheng, Hanwen; Tram, Kha; Zhang, Shengfeng; Zhao, Yanhua; Han, Liyang; Chen, Zengping; Huan, Shuangyan



Catalyzed enzyme electrodes  

Microsoft Academic Search

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

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



Catalyzed enzyme electrodes  

Microsoft Academic Search

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

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



Characterization of the oxidation reactions catalyzed by cyp2d enzyme in rat renal microsomes  

Microsoft Academic Search

Monooxygenase activities in rat renal microsomes were determined with the substrates of hepatic CYP2D enzymes. Seven kinds of CYP2D-mediated monooxygenase activities and immunochemically determined CYP2D contents in kidneys corresponded to approximately 3 % of those in livers. Debrisoquine 4-hydroxylase and bunitrolol 4-hydroxylase in renal microsomes were inhibited almost completely by the antibody against a CYP2D enzyme purified from rat liver.

Yasuhiro Masubuchi; Kyoko Yamamoto; Tokuji Suzuki; Toshiharu Hone; Shizuo Narimatsu



Ion sensitivity of the light reaction catalyzed by enzyme preparations from Photobacterium phosphoreum  

Microsoft Academic Search

Cations, especially divalent ones, increase the intensity of the light flash, obtained by adding FMNH to luciferase preparations containing palmital. Besides, they cause a more rapid decay of the light reaction. Probably, the effect is due to inhibition of the oxidation of FMNH independent of the light reaction by some oxidizing substance. This substance may oxidize free as well as

Willemke Terpstra; H. G. van Eijk



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

E-print Network

by the ordered release of arginino- succinate, PP. , and AiMP. Ghose and Raushel (1985) then proved the existence of the citrulline-adenylate intermediate in this reaction through static and dynamic quench experiments. This involved the quantitation of acid... to incubate in a 30 0 water bath with the pH bei~g adjusted to pH 6. 5 with acetic acid. at 5 minute intervals. After 25 minutes the remaining 0. 5 mL of KCNO solution was Scheme 8. Strategy for synthesis of ( - 08)ATP 18 (Cohn and Hu, 1980) ado- -0 + ado...

Hilscher, Larry Wayne



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



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

Microsoft Academic Search

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

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



Advances in lipase-catalyzed esterification reactions.  


Lipase-catalyzed esterification reactions are among the most significant chemical and biochemical processes of industrial relevance. Lipases catalyze hydrolysis as well as esterification reactions. Enzyme-catalyzed esterification has acquired increasing attention in many applications, due to the significance of the derived products. More specifically, the lipase-catalyzed esterification reactions attracted research interest during the past decade, due to an increased use of organic esters in biotechnology and the chemical industry. Lipases, as hydrolyzing agents are active in environments, which contain a minimum of two distinct phases, where all reactants are partitioned between these phases, although their distribution is not fixed and changes as the reaction proceeds. The kinetics of the lipase-catalyzed reactions is governed by a number of factors. This article presents a thorough and descriptive evaluation of the applied trends and perspectives concerning the enzymatic esterification, mainly for biofuel production; an emphasis is given on essential factors, which affect the lipase-catalyzed esterification reaction. Moreover, the art of using bacterial and/or fungal strains for whole cell biocatalysis purposes, as well as carrying out catalysis by various forms of purified lipases from bacterial and fungal sources is also reviewed. PMID:23954307

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



Mechanism of enzyme-catalyzed phospho group transfer  

SciTech Connect

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

Hansen, D.E.



Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2  

PubMed Central

S-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an ?-amino-?-carboxypropyl (“acp”) group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the “acp” group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNAPhe, and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this “acp” group has a significant role in preventing decoding frame shifts, the mechanism of the “acp” group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from Pyrococcus horikoshii and Methanococcus jannaschii. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the “acp” group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase. PMID:19717466

Umitsu, Masataka; Nishimasu, Hiroshi; Noma, Akiko; Suzuki, Tsutomu; Ishitani, Ryuichiro; Nureki, Osamu



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.



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

PubMed Central

The reason for secretion of nucleoside diphosphate kinase (NdK), an enzyme involved in maintaining the cellular pool of nucleoside triphosphates in both prokaryotes and eukaryotes, by Mycobacterium tuberculosis is intriguing. We recently observed that NdK from M.tuberculosis (mNdK) localizes within nuclei of HeLa and COS-1 cells and also nicks chromosomal DNA in situ (A. K. Saini, K. Maithal, P. Chand, S. Chowdhury, R. Vohra, A. Goyal, G. P. Dubey, P. Chopra, R. Chandra, A. K. Tyagi, Y. Singh and V. Tandon (2004) J. Biol. Chem., 279, 50142–50149). In the current study, using a molecular beacon approach, we demonstrate that the mNdK catalyzes the cleavage of single strand DNA. It displays Michaelis–Menten kinetics with a kcat/KM of 9.65 (±0.88) × 106 M?1 s?1. High affinity (Kd ? KM of ?66 nM) and sequence-specific binding to the sense strand of the nuclease hypersensitive region in the c-myc promoter was observed. This is the first study demonstrating that the cleavage reaction is also enzyme-catalyzed in addition to the enzymatic kinase activity of multifunctional NdK. Using our approach, we demonstrate that GDP competitively inhibits the nuclease activity with a KI of ?1.9 mM. Recent evidence implicates mNdK as a potent virulence factor in tuberculosis owing to its DNase-like activity. In this context, our results demonstrate a molecular mechanism that could be the basis for assessing in situ DNA damage by secretory mNdK. PMID:15888727

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



Stabilized enzymes in continuous gas phase reactions  

SciTech Connect

We are assessing the utility of enzymes to catalyze reactions in a continuous gas phase reactor. First, alcohol dehydrogenase has been used to oxidize an unsaturated alcohol, 3-methyl-2-buten-1-ol (UOL), to the corresponding unsaturated aldehyde, 3-methyl-2-butenal (UAL). Cofactor NAD{sup +} was regenerated by concomitant acetone reduction to isopropyl alcohol. Second, organophosphorus hydrolase (OPH) has been used to hydrolyze pesticide vapors. In order to control enzyme hydration level, enzyme water adsorption isotherms at different temperature have been studied. Huttig`s isotherm model has been found suitable to describe adsorption behavior. The influence of enzyme hydration level, enzyme loading on glass beads, reaction temperature and flow rate on enzymatic reaction rate and biocatalyst stability were investigated. Reaction kinetics were studied and a kinetic model was proposed. We will also report our attempts to further stabilize enzymes for use in gas reactions by incorporating them into polymer matrices.

Yang, Fangxiao; LeJeune, K.; Yang, Zhen [Univ. of Pittsburgh, PA (United States)] [and others



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



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.


Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase  

PubMed Central

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

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



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

PubMed Central

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

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



Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase  

E-print Network

enzymatic systems containing one or a few enzymes (we exclude complex natural systems like glycolysis). Waves and patterns in living systems are often driven by biochem- ical reactions with enzymes as catalysts and regulators. We present a reaction­diffusion system catalyzed by the enzyme glucose oxidase

Epstein, Irving R.


Unusual Cytochrome P450 Enzymes and Reactions*  

PubMed Central

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

Guengerich, F. Peter; Munro, Andrew W.



Palladium-catalyzed oxidative carbonylation reactions.  


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

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



An antibody-catalyzed bimolecular Diels-Alder reaction  

SciTech Connect

There exist over 1,500 known enzymes which carry out a vast array of chemical reactions with remarkable specificity and reaction rates. It is surprising then that there are no documented examples of enzyme-catalyzed pericyclic cycloaddition reactions, yet there are among the most powerful and commonly used reactions in synthetic organic chemistry. The most important of these is the Diels-Alder reaction of a diene with a dienophile, which provides a straightforward and highly stereospecific route to cyclohexene derivatives. Given the importance of this reaction in organic chemistry and its novel mechanism, it was of interest to ask whether a Diels-Alderase enzymatic catalyst could be evolved from an antibody combining site. Generation of antibodies to a structure that mimics the pericyclic transition state for a Diels-Alder reaction should result in an antibody combining site that lowers the entropy of activation {Delta}S{sup {double dagger}} by binding both the diene and the dienophile in a reactive conformation. The authors approach toward the design of a transition-state analogue involves incorporation of an ethano bridge, which locks the cyclohexene ring of hapten in a conformation that resembles the proposed pericyclic transition state for the Diels-Alder reaction of cisoid diene with dienophile. The authors now report that antibodies generated to the transition-state analogue catalyze the addition of the acyclic water-soluble diene to the maleimide derivative to give the cyclohexene product.

Braisted, A.C.; Schultz, P.G. (Lawrence Berkeley Laboratory, CA (USA))



Enzyme-catalyzed synthesis of aliphatic-aromatic oligoamides.  


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

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



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

SciTech Connect

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

Coates, Leighton [ORNL



Gold(I)-catalyzed enantioselective cycloaddition reactions  

PubMed Central

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



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


Activation and inactivation of an enzyme catalyzed by a single, bifunctional protein: a new example and why  

Microsoft Academic Search

Recent studies have shown that the light-dark mediated regulation of the leaf photosynthetic enzyme pyruvate, Pi dikinase results from interconversion between an active nonphosphorylated form of the enzyme and an inactive form phosphorylated on a threonine residue. These phosphorylation and dephosphorylation reactions are apparently catalyzed by a single protein termed the pyruvate, Pi dikinase regulatory protein and, notably, both reactions

J. N. Burnell; M. D. Hatch



Metal-Catalyzed Cross-Coupling Reactions for Indoles  

NASA Astrophysics Data System (ADS)

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

Li, Jie Jack; Gribble, Gordon W.


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

SciTech Connect

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

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



Time-dependent kinetic complexities in cholinesterase-catalyzed reactions.  


Cholinesterases (ChEs) display a hysteretic behavior with certain substrates and inhibitors. Kinetic cooperativity in hysteresis of ChE-catalyzed reactions is characterized by a lag or burst phase in the approach to steady state. With some substrates damped oscillations are shown to superimpose on hysteretic lags. These time dependent peculiarities are observed for both butyrylcholinesterase and acetylcholinesterase from different sources. Hysteresis in ChE-catalyzed reactions can be interpreted in terms of slow transitions between two enzyme conformers E and E'. Substrate can bind to E and/or E', both Michaelian complexes ES and ?'S can be catalytically competent, or only one of them can make products. The formal reaction pathway depends on both the chemical structure of the substrate and the type of enzyme. In particular, damped oscillations develop when substrate exists in different, slowly interconvertible, conformational, and/or micellar forms, of which only the minor form is capable of binding and reacting with the enzyme. Biphasic pseudo-first-order progressive inhibition of ChEs by certain carbamates and organophosphates also fits with a slow equilibrium between two reactive enzyme forms. Hysteresis can be modulated by medium parameters (pH, chaotropic and kosmotropic salts, organic solvents, temperature, osmotic pressure, and hydrostatic pressure). These studies showed that water structure plays a role in hysteretic behavior of ChEs. Attempts to provide a molecular mechanism for ChE hysteresis from mutagenesis studies or crystallographic studies failed so far. In fact, several lines of evidence suggest that hysteresis is controlled by the conformation of His438, a key residue in the catalytic triad of cholinesterases. Induction time may depend on the probability of His438 to adopt the operative conformation in the catalytic triad. The functional significance of ChE hysteresis is puzzling. However, the accepted view that proteins are in equilibrium between preexisting functional and non-functional conformers, and that binding of a ligand to the functional form shifts equilibrium towards the functional conformation, suggests that slow equilibrium between two conformational states of these enzymes may have a regulatory function in damping out the response to certain ligands and irreversible inhibitors. This is particularly true for immobilized (membrane bound) enzymes where the local substrate and/or inhibitor concentrations depend on influx in crowded organellar systems, e.g. cholinergic synaptic clefts. Therefore, physiological or toxicological relevance of the hysteretic behavior and damped oscillations in ChE-catalyzed reactions and inhibition cannot be ruled out. PMID:23157295

Masson, P



Enzyme-catalyzed regioselective transesterification of peracylated sophorolipids  

Microsoft Academic Search

Regioselective transesterifications and hydrolysis of peracylated sophorolipid (SL) derivatives catalyzed by lipases was investigated. This study is the first evaluation of the lipase-catalyzed reactions on the non-lactonic SL derivatives. Four lipases, namely from porcine pancreas (PPL, Type II), Candida rugosa (AYS, TypeVII), Pseudomonas cepacia (PS-30), and Candida antarctica (Novozym 435, carrier fixed lipase fraction B) were used in anhydrous THF

Jason A Carr; Kirpal S Bisht



Exploring Transition Metal Catalyzed Reactions via AB Initio Reaction Pathways  

NASA Astrophysics Data System (ADS)

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

Hratchian, Hrant P.



Detoxification of sulfur mustard by enzyme-catalyzed oxidation using chloroperoxidase.  


One of the most interesting methods for the detoxification of sulfur mustard is enzyme-catalyzed oxidation. This study examined the oxidative destruction of a sulfur mustard by the enzyme chloroperoxidase (EC Chloroperoxidase (CPO) belongs to a group of enzymes that catalyze the oxidation of various organic compounds by peroxide in the presence of a halide ion. The enzymatic oxidation reaction is affected by several factors: pH, presence or absence of chloride ion, temperature, the concentrations of hydrogen peroxide and enzyme and aqueous solubility of the substrate. The optimum reaction conditions were determined by analyzing the effects of all factors, and the following conditions were selected: solvent, Britton-Robinson buffer (pH=3) with tert-butanol (70:30 v/v); CPO concentration, 16U/mL; hydrogen peroxide concentration, 40mmol/L; sodium chloride concentration, 20mmol/L. Under these reaction conditions, the rate constant for the reaction is 0.006s(-1). The Michaelis constant, a measure of the affinity of an enzyme for a particular substrate, is 1.87×10(-3)M for this system. The Michaelis constant for enzymes with a high affinity for their substrate is in the range of 10(-5) to 10(-4)M, so this value indicates that CPO does not have a very high affinity for sulfur mustard. PMID:24034427

Popiel, S; Nawa?a, J



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

Microsoft Academic Search

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

Mateja Primoži?; Muzafera Paljevac; Željko Knez



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



Mammalian Tyrosinase Catalyzes Three Reactions in the Biosynthesis of Melanin  

Microsoft Academic Search

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

Ann Korner; John Pawelek



Copper-catalyzed coupling reaction of arylhydrazines and trialkylphosphites.  


A novel CuO-catalyzed coupling reaction of arylhydrazines with trialkyl phosphites to afford arylphosphonates is described. The reaction proceeded at 80 °C in air without external reductants, oxidants, and ligands. PMID:24467414

Chen, Sheng-Yan; Zeng, Run-Sheng; Zou, Jian-Ping; Asekun, Olayinka Taiwo



Isoprenoid biosynthesis: manifold chemistry catalyzed by similar enzymes  

Microsoft Academic Search

Isoprenoids comprise a family of more than 23,000 natural products, among them the precursors of cholesterol and taxol. The structures of three isoprenoid-cyclizing enzymes have recently been determined and here are placed in the greater context of isoprenoid biosynthesis. On the basis of reaction mechanisms, a subdivision into class I and class II enzymes is proposed. The chain folds of

K Ulrich Wendt; Georg E Schulz



Improved enzyme stability in lipase-catalyzed synthesis of fatty acid ethyl ester from soybean oil.  


In this work, we describe the optimization of the ethanolysis of soybean oil by the enzyme Lipozyme TL-IM in the lipase-catalyzed biodiesel synthesis and the improvement of the enzyme stability over repeated batches. The studied process variables were: reaction temperature, substrate molar ratio, enzyme content, and volume of added water. Fractional factorial design was used to analyze the variables so as to select those with higher influence on the reaction and then perform a central composite design to find the optimal reaction conditions. The optimal conditions found were: temperature, 26 degrees C; substrate molar ratio, 7.5:1 (ethanol/oil); enzyme content, 25% in relation to oil weight; and added water, 4% in relation to oil weight. Under these conditions, the yield conversion obtained was 69% in 12 h. The enzyme stability assessment in repeated batches was carried out by washing the immobilized enzyme with different solvents (n-hexane, water, ethanol, and propanol) after each batch. In the treatment with n-hexane, around 80% of the enzyme activity still remains after seven cycles of synthesis, suggesting its economical application on biodiesel production. PMID:18548204

Costa Rodrigues, Rafael; Volpato, Giandra; Wada, Keiko; Záchia Ayub, Marco Antônio



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


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



~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.


Mathematical Analysis of Activation Thresholds in EnzymeCatalyzed Positive Feedbacks: Application  

E-print Network

angiotensin is produced from angiotensinogen by the proteolytic enzyme renin; fibrinolysis, which providesMathematical Analysis of Activation Thresholds in Enzyme­Catalyzed Positive Feedbacks: Application A hierarchy of enzyme­catalyzed positive feedback loops is examined by mathematical and numerical analysis

New York at Stoney Brook, State University of


Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine.  


As the most active metabolite of heroin, 6-monoacetylmorphine (6-MAM) can penetrate into the brain for the rapid onset of heroin effects. The primary enzymes responsible for the metabolism of 6-MAM to the less potent morphine in humans are acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The detailed reaction pathways for AChE- and BChE-catalyzed hydrolysis of 6-MAM to morphine have been explored, for the first time, in the present study by performing first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the two enzymatic reaction processes follow similar catalytic reaction mechanisms, and the whole catalytic reaction pathway for each enzyme consists of four reaction steps. According to the calculated results, the second reaction step associated with the transition state TS2(a)/TS2(b) should be rate-determining for the AChE/BChE-catalyzed hydrolysis, and the free energy barrier calculated for the AChE-catalyzed hydrolysis (18.3 kcal mol(-1)) is 2.5 kcal mol(-1) lower than that for the BChE-catalyzed hydrolysis (20.8 kcal mol(-1)). The free energy barriers calculated for the AChE- and BChE-catalyzed reactions are in good agreement with the experimentally derived activation free energies (17.5 and 20.7 kcal mol(-1) for the AChE- and BChE-catalyzed reactions, respectively). Further structural analysis reveals that the aromatic residues Phe295 and Phe297 in the acyl pocket of AChE (corresponding to Leu286 and Val288 in BChE) contribute to the lower energy of TS2(a) relative to TS2(b). The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse. PMID:24595354

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



Glutaminase catalyzes reaction of glutamate to GABA.  


Here, for the first time, we report an NMR spectroscopy study of l-Glutamine (Gln) conversion by Glutaminase (Glnase), which shows that the reaction involves two distinct steps. In the first step, Glnase rapidly hydrolyzes Gln to Glutamate (Glu) (?16.87 ?mol of Gln/min/mg of Glnase) and in the second step, Glu generated in the first step is decarboxylated into gamma-amino butyric acid (GABA) with a much slower rate (?0.185 ?mol/min/mg). When Glnase was added to the sample containing l-Glu alone, it was also converted to GABA, at a similar rate as in the second step mentioned above. The rate of Glu decarboxylation into GABA by Glnase is about an order of magnitude lower than that by commonly known enzyme, Glutamate decarboxylase. Potential impact of these findings, on the mechanistic aspects of Gln-Glu shuttle in neuroscience and glutaminolysis in tumors, is discussed. PMID:24755074

Nanga, Ravi Prakash Reddy; DeBrosse, Catherine; Singh, Anup; D'Aquilla, Kevin; Hariharan, Hari; Reddy, Ravinder



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

Microsoft Academic Search

The removal of phenol by peroxidase-catalyzed polymerization was examined using the Coprinus cinereus peroxidases at different levels of impurity with respect to contamination. The phenol removal efficiency was improved by lowering the peroxidase purity. Acidic and high molecular weight proteins present as impurities in the peroxidase solution had some positive effect on the phenol-polymerizing reaction. The residual enzyme activity, either

M. Masuda; A. Sakurai; M. Sakakibara



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.



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 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)




Microsoft Academic Search

Bismuth (III) chloride effectively catalyzes aza-Diels-Alder reaction of N-aryl aldimines with nucleophilic olefins for the first time to afford quinoline derivatives in high yields at ambient temperature. IICT Communication No. 4499.

B. V. Subba Reddy; R. Srinivas; J. S. Yadav; T. Ramalingam



Bis(amino)cyclopropenylidene (BAC) Catalyzed Aza-Benzoin Reaction.  


A bis(amino)cyclopropenylidene (BAC) catalyzed aza-benzoin reaction between aldehydes and phosphinoyl imines has been developed. The reaction is general with a wide range of aromatic aldehydes and aromatic imines. The reaction displays excellent chemoselectivity favoring aza-benzoin products over homobenzoin products. PMID:25272948

Wilde, Myron M D; Gravel, Michel



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

SciTech Connect

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

Estabrook, Ronald W. [Virginia Lazenby O'Hara Professor of Biochemistry, Ida and Cecil Green Chair in the Biomedical Sciences, Department of Biochemistry, Room Y7.206B, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9038 (United States)]. E-mail:



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.



Enzyme catalyzed electricity-driven water softening system.  


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



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.



Enantioselective Diels-Alder reactions catalyzed by hydrogen bonding.  


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, alpha,alpha,alpha',alpha'-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 pi,pi-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



Adventures in Gold-Catalyzed Cascade Reactions and Rearrangements  

Microsoft Academic Search

Gold-catalyzed organic transformations have been a hot topic of research in synthetic organic community over the last few years. Amazingly, most of the reactions can be performed under mild conditions using a catalytic amount of gold complexes. One of the widely reported reactions using gold catalysts is heterocyclization that involves an activation of a pi-system followed by a nucleophilic attack

Dinesh Vinod Vidhani



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


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.



Enantioselective aldol reactions catalyzed by chiral phosphine oxides.  


The development of enantioselective aldol reactions catalyzed by chiral phosphine oxides is described. The aldol reactions presented herein do not require the prior preparation of the masked enol ethers from carbonyl compounds as aldol donors. The reactions proceed through a trichlorosilyl enol ether intermediate, formed in situ from carbonyl compounds, which then acts as the aldol donor. Phosphine oxides activate the trichlorosilyl enol ethers to afford the aldol adducts with high stereoselectivities. This procedure was used to realize a directed cross-aldol reaction between ketones and two types of double aldol reactions (a reaction at one/two ? position(s) of a carbonyl group) with high diastereo- and enantioselectivities. PMID:23828817

Kotani, Shunsuke; Sugiura, Masaharu; Nakajima, Makoto



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


One major problem in the lipase-catalyzed production of biodiesel or fatty acid methyl esters (FAME) is the high acidity of the product, mainly caused by water presence, which produces parallel hydrolysis and esterification reactions instead of transesterification to FAME. Therefore, the use of reaction medium in absence of water (anhydrous medium) was investigated in a lipase-catalyzed process to improve FAME yield and final product quality. FAME production catalyzed by Novozym 435 was carried out using waste frying oil (WFO) as raw material, methanol as acyl acceptor, and 3Å molecular sieves to extract the water. The anhydrous conditions allowed the esterification of free fatty acids (FFA) from feedstock at the initial reaction time. However, after the initial esterification process, water absence avoided the consecutives reactions of hydrolysis and esterification, producing FAME mainly by transesterification. Using this anhydrous medium, a decreasing in both the acid value and the diglycerides content in the product were observed, simultaneously improving FAME yield. Enzyme reuse in the anhydrous medium was also studied. The use of the moderate polar solvent tert-butanol as a co-solvent led to a stable catalysis using Novozym 435 even after 17 successive cycles of FAME production under anhydrous conditions. These results indicate that a lipase-catalyzed process in an anhydrous medium coupled with enzyme reuse would be suitable for biodiesel production, promoting the use of oils of different origin as raw materials. PMID:21889401

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



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.



Good vibrations in enzyme-catalysed reactions  

Microsoft Academic Search

Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute

Sam Hay; Nigel S. Scrutton



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



Palladium-Catalyzed Coupling Reactions of Aryl Chlorides  

Microsoft Academic Search

Collectively, palladium-catalyzed cou- pling reactions represent some of the most powerful and versatile tools avail- able to synthetic organic chemists. Their widespread popularity stems in part from the fact that they are gen- erally tolerant to a large number of functional groups, which allows them to be employed in a wide range of applications. However, for many years a major

Adam F. Littke; Gregory C. Fu



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



Cascade reactions catalyzed by metal organic frameworks.  


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



Enzyme Reactions in Nanoporous, Picoliter Volume Containers  

SciTech Connect

Advancements in nanoscale fabrication allow creation of small volume reaction containers that can facilitate the screening and characterization of enzymes. A porous, ~19 pL volume vessel has been used in this work to carry out enzyme reactions under varying substrate concentrations. Glucose oxidase and horseradish peroxidase can be contained in these structures and diffusively fed with a solution containing glucose and the fluorogenic substrate Amplex Red through the engineered nanoscale pore structure. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Kinetic characteristics of the enzyme were evaluated and compared with results from conventional scale reactions. These picoliter, nanoporous containers can facilitate quick determination of enzyme kinetics in microfluidic systems without the requirement of surface tethering and can be used for applications in drug discovery, clinical diagnostics and high-throughput screening.

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



The effectiveness of immobilized lipase Thermomyces lanuginosa in catalyzing interesterification of palm olein in batch reaction.  


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

Saw, Mei Huey; Siew, Wai Lin



Stau-catalyzed big-bang nucleosynthesis reactions  

SciTech Connect

We study the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a hypothetical long-lived negatively charged, massive leptonic particle (called X{sup -}) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X{sup -} particle has a lifetime of tau{sub X} > or approx. 10{sup 3} s, it can capture a light element previously synthesized in standard BBN and form a Coulombic bound state and induces various types of reactions in which X{sup -} acts as a catalyst. Some of these X{sup -} catalyzed reactions have significantly large cross sections so that the inclusion of the reactions into the BBN network calculation can markedly change the abundances of some elements. We use a high-accuracy three-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

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



Direct Detection and Kinetic Analysis of Covalent Intermediate Formation in the 4-Amino-4-deoxychorismate Synthase Catalyzed Reaction  

E-print Network

ReceiVed February 13, 2006 ABSTRACT: Chorismate-utilizing enzymes catalyze diverse reactions, providing activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH4 +-dependent activities, respectively. Lastly

Toney, Michael


Reversible H Atom Abstraction Catalyzed by the Radical S-Adenosylmethionine Enzyme HydG.  


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



Thermally Induced And Base Catalyzed Reactions Of Naphthoquinone Diazides  

NASA Astrophysics Data System (ADS)

Thermally induced and base catalyzed reactions of a phenol ester of 1,2-naphthoquinone-diazide-5-sulfonic acid (DAM) with p-cresol were investigated. In total seven reaction products were obtained for the thermally induced reaction. The three major products, TR--F4, TR-F6 and TR-F7, were isolated and their structures were determined by means of several advanced spectroscopic techniques like Fourier transform nuclear magnetic resonance (FTNMR) and field desorption mass spectroscopy (FD-MS). Besides a cresol ester of indenecarboxylic acid (TR-F6) and an azo compound which contains two DAM originated moieties and cresol (TR-F7), the formation of a novel compound was found; a phenol ester of 2-cresyl-l-naphthol-5-sulfonic acid. On the other hand, four reaction products were found in the base (a 2.38wt% tetramethylammonium hydroxide aq. solution) catalyzed reaction products of DAM with p-cresol, and two major products, BC-Fl and BC-F3, which appeared at the initial stage of the reaction were isolated. The structure determination of the two major products was carried out in the same manner as described above. It was discovered that BC-Fl was a cresol ester of 1-naphthol while BC-F3 was an azoxy compound. Brief discussions will be made on those reactions of naphthoquinone diazides with a matrix novolak resin with reference to the results obtained by the present study.

Koshiba, Mitsunobu; Murata, Makoto; Matsui, Mariko; Harita, Yoshiyuki



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


Sulfur-containing molecules such as thioethers are commonly found in chemical biology, organic synthesis, and materials chemistry. While many reliable methods have been developed for preparing these compounds, harsh reaction conditions are usually required in the traditional methods. The transition metals have been applied in this field, and the palladium-catalyzed coupling of thiols with aryl halides and pseudo halides is one of the most important methods in the synthesis of thioethers. Other metals have also been used for the same purpose. Here, we summarize recent efforts in metal-catalyzed C-S bond cross-coupling reactions, focusing especially on the coupling of thiols with aryl- and vinyl halides based on different metals. PMID:24443103

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



Enzyme-catalyzed hydrolysis of the supported phospholipid bilayers studied by atomic force microscopy.  


Atomic force microscopy (AFM) is employed to reveal the morphological changes of the supported phospholipid bilayers hydrolyzed by a phospholipase A(2) (PLA(2)) enzyme in a buffer solution at room temperature. Based on the high catalytic selectivity of PLA(2) toward l-enantiomer phospholipids, five kinds of supported bilayers made of l- and D-dipalmitoylphosphatidylcholines (DPPC), including l-DPPC (upper leaflet adjacent to solution)/l-DPPC (bottom leaflet) (or l/l in short), l/d, d/l, d/d, and racemic ld/ld, were prepared on a mica surface in gel-phase, to explicate the kinetics and mechanism of the enzyme-induced hydrolysis reaction in detail. AFM observations for the l/l bilayer show that the hydrolysis rate for l-DPPC is significantly increased by PLA(2) and most of the hydrolysis products desorb from substrate surface in 40 min. As d-enantiomers are included in the bilayer, the hydrolysis rate is largely decreased in comparison with the l/l bilayer. The time used to hydrolyze the as-prepared bilayers by PLA(2) increases in the sequence of l/l, l/d, ld/ld, and d/l (d/d is inert to the enzyme action). d-enantiomers in the enantiomer hybrid bilayers remain on the mica surface at the end of the hydrolysis reaction. It was confirmed that the hydrolysis reaction catalyzed by PLA(2) preferentially occurs at the edges of pits or defects on the bilayer surface. The bilayer structures are preserved during the hydrolysis process. Based on these observations, a novel kinetics model is proposed to quantitatively account for the PLA(2)-catalyzed hydrolysis of the supported phospholipid bilayers. The model simulation demonstrates that PLA(2) mainly binds with lipids at the perimeter of defects in the upper leaflet and leads to a hydrolysis reaction, yielding species soluble to the solution phase. The lipid molecules underneath subsequently flip up to the upper leaflet to maintain the hydrophilicity of the bilayer structure. Our analysis shows that d-enantiomers in the hybrid bilayers considerably reduce the hydrolysis rate by its ineffective binding with PLA(2). PMID:22995243

Wu, HengLiang; Yu, Le; Tong, Yujin; Ge, Aimin; Yau, Shuehlin; Osawa, Masatoshi; Ye, Shen



Cerium-catalyzed oxidative C–C bond forming reactions  

Microsoft Academic Search

With respect to economical and ecological considerations, molecular oxygen is the oxidant of choice for functionalization of organic substrates. On the basis of our cerium-catalyzed ?-hydroxylation of ?-dicarbonyl compounds, we have developed an oxidative process for C–C bond formation in the presence of simple olefins like styrene. Products of these reactions, which are isolated as endoperoxidic 1,2-dioxane derivatives with potential

Jens Christoffers; Thomas Werner; Michael Rössle



Involvement of free radicals in peroxidatic reactions catalyzed by chloroperoxidase  

Microsoft Academic Search

The mechanism of chloroperoxidase (CPO)-catalyzed peroxidatic reactions of several substituted hydroquinones was studied at various hydrogen peroxide concentrations. The pathway was studied using cytochrome c as the radical trapping agent. As the hydroquinones became more hindered there was a difference in the amount of radicals trapped. For hydroquinone, 59.3% radical pathway, and methylhydroquinone, 81.4% radical, the difference in radicals trapped

David P. Provencal



Native transfer RNA catalyzes Diels-Alder reaction.  


In this paper we show that transfer ribonucleic acids (tRNAs) catalyze the Diels-Alder cycloaddition reaction. A new DNA oxidative damage product, 6-furfuryladenine (kinetin) or its riboside (diene), was transformed with dimethyl acetylenedicarboxylate or maleic anhydride (dienophile). The reaction proceeds in the presence of tRNA at high pressure but not at ambient condition. If so tRNA in prebiotic conditions (RNA world) had at least two functions: catalytic and a carrier of genetic information. It means that tRNA at high pressure shows catalytic properties and is a true Diels-Alderase. PMID:12054754

Mielcarek, Michal; Barciszewska, Miroslawa Z; Sa?anski, Piotr; Stobiecki, Maciej; Jurczak, Janusz; Barciszewski, Jan



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.



Pd-catalyzed cross-coupling reactions of alkyl halides.  


Cross-coupling reactions have become indispensable tools for creating carbon-carbon (or heteroatom) bonds in organic synthesis. Like in other important transition metal catalyzed reactions, such as metathesis, addition, and polymerization, unsaturated compounds are usually employed as substrates for cross-coupling reactions. However during the past decade, a great deal of effort has been devoted to the use of alkyl halides as saturated compounds in cross-coupling reactions, which has resulted in significant progress in this undeveloped area by introducing new effective ligands. Many useful catalytic systems are now available for synthetic transformations based on C(sp(3))-C(sp(3)), C(sp(3))-C(sp(2)) and C(sp(3))-C(sp) bond formation as complementary methods to conventional C(sp(2))-C(sp(2)), C(sp(2))-C(sp) and C(sp)-C(sp) coupling. This tutorial review summarizes recent advances in cross-coupling reactions of alkyl halides and pseudohalides catalyzed by a palladium complex. PMID:21785791

Kambe, Nobuaki; Iwasaki, Takanori; Terao, Jun



The role of microemulsions in lipase-catalyzed hydrolysis reactions.  


The kinetics of the p-nitrophenyl butyrate hydrolysis reaction, catalyzed by Candida rugosa lipase in the water-in-oil microemulsion cetyltrimethylammonium bromide/water/pentanol/hexane, was investigated. The results described in the present manuscript reveal two peculiar characteristics of the reaction: (i) the initial rate of hydrolysis is very fast and (ii) by decreasing the water content of the microemulsion, the reaction rate approaches the typical behavior of reactions performed in aqueous solution. In particular, for microemulsion systems with a high water content, the end points of the reactions are dictated by the shape stability of the microemulsion. For these systems, our methodological approach shows that the process follows a second-order kinetics equation, indicative of the dual role played by water, which is involved both as a component of the microemulsion, i.e., relevant for the microemulsion stability and as a reagent of the hydrolysis reaction. In contrast, for microemulsions containing a small amount of water, after the hydrolysis reaction the system seems to fall in the no existence range of the microemulsion. Accordingly, the kinetics results are more complex: in the initial stage, the reaction follows a zero-order kinetics equation, while for longer reaction times a first-order kinetics equation fits the experimental data, as would be expected for an enzymatic reaction in a homogeneous system. PMID:24585724

Lopez, Francesco; Cinelli, Giuseppe; Colella, Matilde; De Leonardis, Antonella; Palazzo, Gerardo; Ambrosone, Luigi



A palladium-catalyzed reaction of aryl halides, potassium metabisulfite, and hydrazines.  


Aryl N-aminosulfonamides could be easily produced via a palladium-catalyzed coupling of aryl halides, potassium metabisulfite, and hydrazines. Potassium metabisulfite is an excellent equivalent of sulfur dioxide in the reaction of palladium-catalyzed aminosulfonylation. PMID:22945283

Ye, Shengqing; Wu, Jie



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


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


Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation. PMID:20300652

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



Gold-catalyzed cyclization reactions of allenol and alkynol derivatives.  


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

Alcaide, Benito; Almendros, Pedro



Solvent effects in Acid-catalyzed biomass conversion reactions.  


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

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



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

SciTech Connect

Crystalline (monomeric) soybean and (tetrameric) sweet potato {beta}-amylase were shown to catalyze the cis hydration of maltal ({alpha}-D-glucopyranosyl-2-deoxy-D-arabino-hex-1-enitol) to form {beta}-2-deoxymaltose. As reported earlier with the sweet potato enzyme, maltal hydration in D{sub 2}O by soybean {beta}-amylase was found to exhibit an unusually large solvent deuterium kinetic isotope effect (V{sub H}/V{sub D}=6.5), a reaction rate linearly dependent on the mole fraction of deuterium, and 2-deoxy-(2(a)-{sup 2}H)maltose as product. These results indicate (for each {beta}-amylase) that protonation is the rate-limiting step in a reaction involving a nearly symmetric one-proton transition state and that maltal is specifically protonated from above the double bond. That maltal undergoes cis hydration provides evidence in support of a general-acid-catalyzed, carbonium ion mediated reaction. Of fundamental significance is that {beta}-amylase protonates maltal from a direction opposite that assumed for protonating strach, yet creates products of the same anomeric configuration from both. Such stereochemical dichotomy argues for the overriding role of protein structures is dictating the steric outcome of reactions catalyzed by a glycosylase, by limiting the approach and orientation of water or other acceptors to the reaction center.

Kitahata, Sumio (Osaka Municipal Technical Research Inst. (Japan)); Chiba, S. (Hokkaido Univ. (Japan)); Brewer, C.F.; Hehre, E.J. (Albert Einstein Coll. of Medicine, Bronx, NY (United States))



The pyruvate-proton exchange reaction of malic enzyme from pigeon liver.  


Malic enzyme (L-malate:NADP+ oxidoreductase (decarboxylating) EC catalyzes the incorporation of proton from medium water into pyruvate present either as the initial substrate or as the enzyme-bound product of malate decarboxylation. In the later reaction a single proton is incorporated into the methyl group of pyruvate. The pyruvate-medium proton exchange reaction requires Mg2+, NADPH and CO2-HCO3- as cofactors. The apparent Michaelis constants of pyruvate, NADPH and CO2-HCO3- are 4.8 mM, 2 microM and approx. 9 microM, respectively. The experimentally determined incorporation of 2.5 tritium atoms from tritiated water into pyruvate indicates that all three methyl protons of this compound are stereochemically equivalent in the exchange reaction. These results are consistent with the postulated kinetic mechanism for the malate reaction (Hsu, R.Y., Lardy, H.A. and Cleland, W.W. (1967) J. Biol. Chem. 242, 5315--5322), which predicts the formation of an enolpyruvate intermediate during the reaction. The rate of malic enzyme-catalyzed detritiation of beta-tritiated pyruvate is unaffected by modification of an essential protein thiol group with 5,5'-dithiobis(2-nitrobenzoic acid) or KCN. Moreover, the native- and thiol-modified enzymes also catalyze the detritiation of beta-tritiated bromopyruvate at slower rates. PMID:7066344

Bratcher, S C; Hsu, R Y



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

E-print Network

nucleophilic substitution reactions of the phosphate diester, methyl 2,4-dinitrophenylphosphate monoanion4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate of Tetrahymena thermophila pre-rRNA catalyzes a guanosine-dependent endonuclease reaction that is analogous

Herschlag, Dan


Cold adaptation of enzyme reaction rates.  


A major issue for organisms living at extreme temperatures is to preserve both stability and activity of their enzymes. Cold-adapted enzymes generally have a reduced thermal stability, to counteract freezing, and show a lower enthalpy and a more negative entropy of activation compared to mesophilic and thermophilic homologues. Such a balance of thermodynamic activation parameters can make the reaction rate decrease more linearly, rather than exponentially, as the temperature is lowered, but the structural basis for rate optimization toward low working temperatures remains unclear. In order to computationally address this problem, it is clear that reaction simulations rather than standard molecular dynamics calculations are needed. We have thus carried out extensive computer simulations of the keto-enol(ate) isomerization steps in differently adapted citrate synthases to explore the structure-function relationships behind catalytic rate adaptation to different temperatures. The calculations reproduce the absolute rates of the psychrophilic and mesophilic enzymes at 300 K, as well as the lower enthalpy and more negative entropy of activation of the cold-adapted enzyme, where the latter simulation result is obtained from high-precision Arrhenius plots. The overall catalytic effect originates from electrostatic stabilization of the transition state and enolate and the reduction of reorganization free energy. The simulations, however, show psychrophilic, mesophilic, and hyperthermophilic citrate synthases to have increasingly stronger electrostatic stabilization of the transition state, while the energetic penalty in terms of internal protein interactions follows the reverse order with the cold-adapted enzyme having the most favorable energy term. The lower activation enthalpy and more negative activation entropy observed for cold-adapted enzymes are found to be associated with a decreased protein stiffness. The origin of this effect is, however, not localized to the active site but to other regions of the protein structure. PMID:18759500

Bjelic, Sinisa; Brandsdal, Bjørn O; Aqvist, Johan



Controllable Regioselective Acylation of Rutin Catalyzed by Enzymes in Nonaqueous Solvents  

Microsoft Academic Search

An efficient route to synthesize 3??- and 4???-vinyl rutin esters has been developed by enzyme-catalyzed regioselective acylation of rutin with divinyl dicarboxylates in organic media. Alkaline protease from Bacillus subtilis provided 3??-O-substituted vinyl rutin esters in pyridine, and Novozym 435 gave 4???-O-substituted vinyl rutin esters in tert-butanol.

Yong-mei Xiao; Qi Wu; Wei-bo Wu; Qing-yi Zhang; Xian-fu Lin



Theoretical study on the BF3-catalyzed Meinwald rearrangement reaction.  


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

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



Gold-catalyzed cyanosilylation reaction: homogeneous and heterogeneous pathways.  


Gold had been considered to be an extremely inert metal, but recently it was found that nanometer-sized gold particles on metal-oxide supports acted as catalysts for simple organic reactions, such as oxidation and hydrogenation, even at or below room temperature. Herein, we report that gold nanoparticles (AuNPs) of zero oxidation state (Au0) are catalytically active for a C--C bond-forming reaction, the cyanosilylation of aldehydes. The AuNP-catalyzed cyanosilylation proceeded smoothly at room temperature with 0.2 wt % loading of AuNPs. The reactions of aromatic aldehydes were almost quantitative, except for benzaldehyde derivatives containing the electron-withdrawing NO2 group, and alpha,beta-unsaturated aromatic aldehydes were the most reactive substrates. The reactions also went smoothly for aliphatic aldehydes. Mechanistic studies indicated that the reactions proceeded both homogeneously and heterogeneously: homogeneous catalysis by leached gold species and heterogeneous catalysis by the adsorption of the reactants (aldehydes and trimethylsilyl cyanide) onto AuNPs. The ratio of homogeneous and heterogeneous catalysis was estimated to be approximately 4:1. PMID:17492807

Cho, Woo Kyung; Lee, Jungkyu K; Kang, Sung Min; Chi, Young Shik; Lee, Hee-Seung; Choi, Insung S



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.



Ab initio study of ice catalyzation of HOCl + HCl reaction  

SciTech Connect

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

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



Sensitivity Analysis of Metabolic Cascades Catalyzed by Bifunctional Enzymes  

Microsoft Academic Search

Covalent modification\\/demodification cycles are common in metabolism. When the modification and demodification steps are carried out by two independent enzymes, the degree of modification can be ultrasensitive to the total concentration of either catalyst. We recently showed that the degree of modification of a target molecule cannot exhibit ultrasensitivity to the free concentrations of effectors that decide whether a bifunctional

Fernando Ortega; Måns Ehrenberg; Luis Acerenza; Hans V. Westerhoff; Francesc Mas; Marta Cascante



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



Electrostatic effects on the rates of DNA-catalyzed reactions  

NASA Astrophysics Data System (ADS)

Diol-epoxide metabolites of many genotoxic polycyclic aromatic hydrocarbons are hydrolyzed to tetraols in a detoxification reaction. The hydrolysis reaction has both spontaneous and acid-catalyzed components; moreover, the reaction rate increases in the presence of DNA. The best studied of these diol epoxide metabolites are the trans 7,8 diol-9,10 epoxides of benzo[a]pyrene: anti-BPDE, the proximate carcinogen, in which the oxirane ring is anti with respect to the 7-hydroxyl group, and its syn diastereomer, syn-BPDE. Jerina and coworkers have studied the kinetics of the hydrolysis of syn- and anti-BPDE as a function of pH and DNA concentration and have measured the equilibrium constant for the formation of a noncovalent complex with DNA. They constructed a two-state model in which the diol epoxide is either free or statically bound: the free fraction is hydrolyzed with the same kinetics as it exhibits in solution without DNA; the bound diol epoxide reacts at faster rates. In this model, the dependence of the observed hydrolysis rates on both DNA concentration and pH is explained by using the rate constants, k0 and kH, for reactions of the free diol epoxide, the rate constants, kcat0 and kcatH, for the bound molecule, and the binding constant, Keq. The present work uses an acidic-domain interpretation of the two-state model to explain the catalytic effect of DNA on the acid-catalyzed hydrolysis of syn- and anti-BPDE. Postulating that the rate enhancement is a result of acidic domains at the DNA surface, we assumed the relationship k catH = k H [H +] b, where [H +] b is the hydrogen ion concentration near the bound molecule. Using numerical solutions to the Poisson-Boltzmann equation, the pH dependence of acidic domains at the surface of the polyelectrolyte, DNA, was calculated. Energy-minimization calculations were used to estimate the conformations of diol epoxide-DNA intercalation complexes. Poisson-Boltzmann (PB) calculations on these structures yielded hydrogen-ion concentrations near the epoxide group consistent with the k catH/k H ratio over a range of added-salt concentrations. The results strongly suggest that DNA catalysis of diol-epoxide hydrolysis is a polyelectrolyte effect. The mechanisms and rate constants observed for the acid-catalyzed hydrolysis in the absence of DNA are consistent with the increase in the rate constant induced by DNA. It may be concluded that the catalysis is primarily an effect of the acidic domains in the surface grooves of the nucleic acid.

Pack, George R.; Wong, Linda



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



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


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



Understanding bistability in complex enzyme-driven reaction networks  

E-print Network

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

Craciun, Gheorghe


Palladium-catalyzed coupling reaction of perfluoroarenes with diarylzinc compounds.  


This report describes the first Pd(0)-catalyzed cross-coupling of hexafluorobenzene (C6F6) with diarylzinc compounds to give a variety of pentafluorophenyl arenes. This reaction could be applied to other perfluoroarenes, such as octafluorotoluene, pentafluoropyridine, and perfluoronaphthalene, to give the corresponding polyfluorinated coupling products. The optimal ligand in this catalytic reaction was PCy3 , and lithium iodide was indispensable as an additive for the coupling reaction. One of the roles of lithium iodide in this catalytic reaction was to promote the oxidative addition of one C-F bond of C6F6 to palladium. Stoichiometric reactions revealed that an expected oxidative-addition product, trans-[Pd(C6F5)I(PCy3)2], generated from the reaction of [Pd(PCy3)2] with C6F6 in the presence of lithium iodide, was not involved in the catalytic cycle. Instead, a transient three-coordinate, monophosphine-ligated species, [Pd(C6F5)I(PCy3)], emerged as a potential intermediate in the catalytic cycle. Therefore, we isolated a novel Pd(II) complex, [Pd(C6F5)I(PCy3)(py)], in which pyridine (py) acted as a labile ligand to generate the transient species. In fact, in the presence of lithium iodide, this Pd(II) complex was found to react smoothly with diphenylzinc to give the desired pentafluorophenyl benzene, whereas the same reaction conducted in the absence of lithium iodide resulted in a decreased yield of pentafluorophenyl benzene, which indicated that the other role of lithium iodide was to enhance the reactivity of the organozinc species during the transmetalation step. PMID:24431191

Ohashi, Masato; Doi, Ryohei; Ogoshi, Sensuke



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


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



A transient intermediate in the reaction catalyzed by (S)-mandelate dehydrogenase from Pseudomonas putida.  


(S)-Mandelate dehydrogenase from Pseudomonas putida is a member of a FMN-dependent enzyme family that oxidizes (S)-alpha-hydroxyacids to alpha-ketoacids. The reductive half-reaction consists of the steps involved in substrate oxidation and FMN reduction. In this study, we investigated the mechanism of this half-reaction in detail. At low temperatures, a transient intermediate was formed in the course of the FMN reduction reaction. This intermediate is characteristic of a charge-transfer complex of oxidized FMN and an electron-rich donor and is formed prior to full reduction of the flavin. The intermediate was not due to binding of anionic substrates or inhibitors. It was only observed with efficient substrates that have high k(cat) values. At higher temperatures, it was formed within the dead time of the stopped-flow instrument. The rate of formation of the intermediate was 3-4-fold faster than its rate of disappearance; the former had a larger isotope effect. This suggests that the charge-transfer donor is an electron-rich carbanion/enolate intermediate that is generated by the base-catalyzed abstraction of the substrate alpha-proton. This is consistent with the observation that the intermediate was not observed with the R277K and R277G mutants, which have been shown to destabilize the carbanion intermediate (Lehoux, I. E., and Mitra, B. (2000) Biochemistry 39, 10055-10065). Thus, the MDH reaction has two rate-limiting steps of similar activation energies: the formation and breakdown of a distinct intermediate, with the latter step being slightly more rate limiting. We also show that MDH is capable of catalyzing the reverse reaction, the reoxidation of reduced MDH by the product ketoacid, benzoylformate. The transient intermediate was observed during the reverse reaction as well, confirming that it is indeed a true intermediate in the MDH reaction pathway. PMID:14596603

Dewanti, Asteriani R; Mitra, Bharati



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

SciTech Connect

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

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



Acid-catalyzed reactions of epoxides for atmospheric nanoparticle growth.  


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



Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase (FDTS)  

PubMed Central

Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. Recently it has been shown that FDTS catalysis does not rely on an enzymatic nucleophile and the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist the efforts to rationally design inhibitors as leads for future antibiotics. PMID:22295882

Mishanina, Tatiana V.; Koehn, Eric M.; Conrad, John A.; Palfey, Bruce A.; Lesley, Scott A.



The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (?/?)8 barrel enzymes  

PubMed Central

The IMPDH/GMPR family of (?/?)8 enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMP dehydrogenase (IMPDH) and GMP reductase (GMPR) bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family. PMID:22332716

Hedstrom, Lizbeth



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 are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds into acidic aerosols. In the present study, we use the aerodyne aerosol mass spectrometer (AMS) to probe

Elrod, Matthew J.


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

Microsoft Academic Search

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

I. A. Butovich; C. Channa Reddy



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: Contact: Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23613486

Chang, Ivan; Baldi, Pierre



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


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



The Structural Basis for a Coordinated Reaction Catalyzed by a Bifunctional Glycosyltransferase in Chondroitin Biosynthesis*  

PubMed Central

Bifunctional chondroitin synthase K4CP catalyzes glucuronic acid and N-acetylgalactosamine transfer activities and polymerizes a chondroitin chain. Here we have determined that an N-terminal region (residues 58–134) coordinates two transfer reactions and enables K4CP to catalyze polymerization. When residues 58–107 are deleted, K4CP loses polymerase activity while retaining both transfer activities. Peptide 113DWPSDL118 within this N-terminal region interacts with C-terminal peptide 677YTWEKI682. The deletion of either sequence abolishes glucuronic acid but not N-acetylgalactosamine transfer activity in K4CP. Both donor bindings and transfer activities are lost by mutating 677YTWEKI682 to 677DAWEDI682. On the other hand, acceptor substrates retain their binding to K4CP mutants. The characteristics of these K4CP mutants highlight different states of the enzyme reaction, providing an underlying structural basis for how these peptides play essential roles in coordinating the two glycosyltransferase activities for K4CP to elongate the chondroitin chain. PMID:22936799

Sobhany, Mack; Kakuta, Yoshimitsu; Sugiura, Nobuo; Kimata, Koji; Negishi, Masahiko



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


[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



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


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



Large-scale ruthenium- and enzyme-catalyzed dynamic kinetic resolution of (rac)-1-phenylethanol.  


The scale-up of the ruthenium- and enzyme-catalyzed dynamic kinetic resolution (DKR) of (rac)-1-phenylethanol (2) is addressed. The immobilized lipase Candida antarctica lipase B (CALB) was employed for the resolution, which shows high enantioselectivity in the transesterification. The ruthenium catalyst used, (eta 5-C5Ph5)RuCl(CO)2 1, was shown to possess very high reactivity in the "in situ" redox racemization of 1-phenylethanol (2) in the presence of the immobilized enzyme, and could be used in 0.05 mol% with high efficiency. Commercially available isopropenyl acetate was employed as acylating agent in the lipase-catalyzed transesterifications, which makes the purification of the product very easy. In a successful large-scale DKR of 2, with 0.05 mol% of 1, (R)-1-phenylethanol acetate (3) was obtained in 159 g (97% yield) in excellent enantiomeric excess (99.8% ee). PMID:18096033

Bogár, Krisztián; Martín-Matute, Belén; Bäckvall, Jan-E



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



Difficult substrates in the R-hydroxynitrile lyase catalyzed hydrocyanation reaction: application of the mass transfer limitation principle in a two-phase system  

Microsoft Academic Search

The application of a number of new and\\/or difficult substrates in the catalyzed hydrocyanation reaction by R-hydroxynitrile lyase from almonds is described. By using an aqueous–organic two-phase system and increasing the rate of the enzymatic reaction relative to the mass transfer rate, the enantiomeric purity was improved. By fine tuning the reaction parameters (temperature, pH, and the amount of enzyme)

Pieter J. Gerrits; Jan Marcus; Lemonia Birikaki; Arne van der Gen



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

E-print Network

2,3-Migration in Rh(II)-Catalyzed Reactions of -Trifluoroacetamido r-Diazocarbonyl Compounds Feng(II)-catalyzed reactions of these diazo compounds gave 2,3-migration products in high yields. 1,2-Migration is one,2-migration reactions, the 1,2-hydride migration is generally predominant, but 1,2-alkyl, 1,2-aryl, 1,2-thio

Wang, Jianbo


Surprising effect of leaving group on the nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase  

SciTech Connect

We have begun our mechanistic studies of 4-chlorobenzoyl-CoA dehalogenase with a determination of the relative leaving group abilities for bromide, chloride, and fluoride in the dehalogenation reaction. Dehalogenation of 4-bromobenzoyl-CoA is twice as fast as dehalogenation of 4-chlorobenzoyl-CoA, while dehalogenation of 4-fluorobenzoyl-CoA is over 400-fold slower. These data are in striking contrast to the relative leaving group abilities observed for the glutathione-S-transferase-catalyzed dehalogenation of 4-halo-3-nitro-1-(trifluoromethyl)benzenes. Our data also differ from those observed for nonenzymic nucleophilic aromatic substitution reactions that occur by the S[sup N]Ar mechanism. The most reasonable mechanism for the enzymic dehalogenation reaction is probably the S[sub N]Ar mechanism. Nucleophilic aromatic substitution reactions that take place by this mechanism generally proceed fastest when the leaving group is fluoride, even though fluoride is the poorest leaving group among the halogens. The nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase shows leaving group abilities in the order opposite that expected on the basis of nonenzymic S[sub N]Ar reactions and the glutahione-S-transferase reaction. Two alternative explanations may account for these data. Our data do not permit a distinction between the various possible mechanisms for the dehalogenation reaction. 17 refs., 1 tab.

Crooks, G.P.; Copley, S.D. (Univ. of Colorado, Boulder (United States))



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

E-print Network

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

Naber, John R. (John Robert)



ENZYME: Enzyme Nomenclature Database  

NSDL National Science Digital Library

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


Oxygen Isotope Fractionation in Reactions Catalyzed by Enzymes  

Microsoft Academic Search

A study has been made of some of the enzymatic mechanisms responsible for the previously reported fractionation of oxygen isotopes by whole organisms. The data indicate that the fractionation occurs through the activity of metalloenzymes.

Daniel E. Feldman; Henry T. Yost Jr.; Bruce B. Benson



Hydroxylation and epoxidation reactions catalyzed by CYP153 enzymes  

Microsoft Academic Search

Several cytochrome P450 alkane hydroxylases of the CYP153 family were recently identified and functionally expressed in Pseudomonas putida GPo12 [van Beilen JB, Funhoff EG, van Loon A, Just A, Kaysser L, Bouza M, et al. Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases. Appl Environ Microbiol 2006;72:59–65]. Eight recombinants containing

Enrico G. Funhoff; Jenny Salzmann; Ulrich Bauer; Bernard Witholt; Jan B. van Beilen



Kinetics of reactions catalyzed by enzymes in solutions of surfactants  

Microsoft Academic Search

The effect of surfactants, both in water-in-oil microemulsions (hydrated reverse micelles) and aqueous solutions upon enzymatic processes is reviewed, with special emphasis on the effect of the surfactant upon the kinetic parameters of the process. Differences and similarities between processes taking place in aqueous and organic solvents are highlighted, and the main models currently employed to interpret the results are

María A. Biasutti; Elsa B. Abuin; Juana J. Silber; N. Mariano Correa; Eduardo A. Lissi



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

E-print Network

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

McCarren, P. R.



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...


Pd-Catalyzed Cross-Coupling Reactions of Amides and Aryl Mesylates  

E-print Network

A catalyst, based on a biarylphosphine ligand, for the Pd-catalyzed cross-coupling reactions of amides and aryl mesylates is described. This system allows an array of aryl and heteroaryl mesylates to be transformed into ...

Dooleweerdt, Karin


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

E-print Network

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

Teverovskiy, Georgiy



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

E-print Network

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

Strieter, Eric R



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



Efficient Pd-Catalyzed Amination Reactions for Heterocycle Functionalization  

E-print Network

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

Henderson, Jaclyn L.


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


The iron-catalyzed cross-coupling of aryl sulfamates and tosylates has been achieved with primary and secondary alkyl Grignards. This study of iron-catalyzed cross-coupling reactions also examines the isomerization and ?-hydride elimination problems that are associated with the use of isopropyl nucleophiles. While a variety of iron sources were competent in the reaction, the use of FeF(3)•3H(2)O was critical to minimize nucleophile isomerization. PMID:23244161

Agrawal, Toolika; Cook, Silas P



Oxalate Decarboxylase (OxDC) is an enzyme that catalyzes the manganese-dependent breakdown of the oxalate monoanion into  

E-print Network

Oxalate Decarboxylase (OxDC) is an enzyme that catalyzes the manganese-dependent breakdown of the oxalate monoanion into carbon dioxide and formate. Although the enzyme is found in many fungi and some subtilis Oxalate Decarboxylase Nigel G. J. Richards,1 Whitney F. Kellet,1 Ursula Rothlisberger,2 Pablo

McQuade, D. Tyler


Nonisothermal immobilized enzyme reaction in a packed-bed reactor  

Microsoft Academic Search

Summary This work investigates the reaction behavior of immobilized enzymes in a packed-bed reactor. The effect of heat generation due to exothermic enzyme reaction is considered. Conservations of substrate and energy constitute two coupled nonlinear partial differential equations which are simultaneously solved by a numerical method. It is found that substrate conversion is generally increased at higher temperature. However, the

Sheng Hsiung Lin



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


An unprecedented copper-catalyzed acylnitroso dearomatization reaction, which expands the traditional acylnitroso ene reaction and acylnitroso Diels-Alder reaction to a new type of transformation, has been developed under aerobic oxidation. Intermolecular and intra-/intermolecular reaction modes demonstrate an entirely different N- or O-acylnitroso selectivity. Hence, we can utilize this reaction as a highly diastereoselective access to a series of new pyrroloindoline derivatives, which are important structural motifs for natural-product synthesis. PMID:24590772

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



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


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

Liu, Yunyun; Wan, Jie-Ping



Synthesis of Pyridazinones through the Copper(I)-Catalyzed Multicomponent Reaction of Aldehydes, Hydrazines, and Alkynylesters.  


The copper-catalyzed multicomponent cyclization reaction, which combined aldehydes, hydrazines, and alkynylesters, was applied in the synthesis of pyridazinones. The reaction was regioselective and gave only six-membered pyridazinones in the complete absence of five-membered pyrazoles or a regioisomeric mixture. During this investigation, the use of 2-halobenzaldehyde as the starting material, under identical reaction conditions, gave 6-(2-ethoxyphenyl)pyridazinones after sequential Michael addition/1,2-addition/Ullmann cross-coupling reactions. PMID:25124722

Mantovani, Anderson C; Goulart, Tales A C; Back, Davi F; Zeni, Gilson



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.



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


[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



Molecular mechanics calculations as predictors of enantioselectivity for chiral nucleophile catalyzed reactions  

E-print Network

activated complexes for reactions catalyzed by chiral nucleophiles and to account for both the sense-lactam forming reaction5 by making the ketene nucleophilic (through generation of a zwitterionic intermediate),6Molecular mechanics calculations as predictors of enantioselectivity for chiral nucleophile

Lectka, Thomas


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

PubMed Central

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

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



Reaction intermediates discovered in crystal structures of enzymes.  


Crystal structures of enzymes have provided valuable information for the reaction mechanisms. Structures of the enzyme complex with different reaction intermediates are particularly valuable. In several cases, these structures of intermediates were discovered accidently, presumably by trapping in the crystal during freezing prior to X-ray data collection. High to atomic resolution structures reveal the detailed geometry of the reaction intermediate and its interactions within the enzyme active site. In other cases, the protein can be crystallized with its substrate, including examples of protease precursors that represent their own substrates. Examples are described of an FAD-dependent dehydrogenase, HIV protease and caspases, where the structures provide snapshots of steps in the reaction and the conformational changes occurring during the reaction. Complementary techniques such as computational chemistry, neutron crystallography, Laue crystallography, and time-resolved spectroscopy can give a more complete picture of the reaction. PMID:22607752

Weber, Irene T; Agniswamy, Johnson; Fu, Guoxing; Shen, Chen-Hsiang; Harrison, Robert W



Synthesis of heterocycles through transition-metal-catalyzed isomerization reactions.  


Metal-catalyzed isomerization of N- and O-allylic systems is emerging as an effective method to form synthetically useful iminium and oxocarbenium intermediates. In the presence of tethered nucleophiles, several recent examples illuminate this approach as a powerful strategy for the synthesis of structurally complex and diverse heterocycles. In this Concept article, we attempt to cover this area of research through a selection of recent versatile examples. PMID:24924616

Ishoey, Mette; Nielsen, Thomas E



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, Stephanie; Jakob, Ingrid; Sicard, Gilles; Chevalier, Joelle; Menetrier, Franck; Berdeaux, Olivier; Artur, Yves; Heydel, Jean-Marie; Le Bon, Anne-Marie



Enzyme catalysis in microgravity: steady-state kinetic analysis of the isocitrate lyase reaction.  


Two decades of research in microgravity have shown that certain biochemical processes can be altered by weightlessness. Approximately 10 years ago, our team, supported by the European Space Agency (ESA) and the Agenzia Spaziale Italiana, started the Effect of Microgravity on Enzyme Catalysis project to test the possibility that the microgravity effect observed at cellular level could be mediated by enzyme reactions. An experiment to study the cleavage reaction catalyzed by isocitrate lyase was flown on the sounding rocket MASER 7, and we found that the kinetic parameters were not altered by microgravity. During the 28th ESA parabolic flight campaign, we had the opportunity to replicate the MASER 7 experiment and to perform a complete steady-state analysis of the isocitrate lyase reaction. This study showed that both in microgravity and in standard g controls the enzyme reaction obeyed the same kinetic mechanism and none of the kinetic parameters, nor the equilibrium constant of the overall reaction were altered. Our results contrast with those of a similar experiment, which was performed during the same parabolic flight campaign, and showed that microgravity increased the affinity of lipoxygenase-1 for linoleic acid. The hypotheses suggested to explain this change effect of the latter were here tested by computer simulation, and appeared to be inconsistent with the experimental outcome. PMID:12568939

Ranaldi, Francesco; Vanni, Paolo; Giachetti, Eugenio



Global Conformational Change Associated with the Two-step Reaction Catalyzed by Escherichia coli Lipoate-Protein Ligase A*  

PubMed Central

Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645–33651). Here, we report two new LplA structures, LplA·lipoyl-5?-AMP and LplA·octyl-5?-AMP·apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5?-AMP reaction intermediate and rotation of the C-terminal domain by about 180°. These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys133 residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes. PMID:20089862

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



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.



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


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



Mild conditions for the synthesis of functionalized pyrrolidines via Pd-catalyzed carboamination reactions.  


[reaction: see text] The palladium-catalyzed carboamination of N-protected gamma-aminoalkenes with aryl bromides and triflates has been achieved under new, mild reaction conditions using the weak base Cs(2)CO(3) in dioxane solvent. These reactions tolerate a wide variety of functional groups, including enolizable ketones, nitro groups, methyl esters, and acetates, which are not compatible with previously described conditions. PMID:17249786

Bertrand, Myra Beaudoin; Leathen, Matthew L; Wolfe, John P



Efficient Biginelli Reaction Catalyzed by Sulfamic Acid or Silica Sulfuric Acid under Solvent?Free Conditions  

Microsoft Academic Search

Sulfamic acid efficiently catalyzes the three?component condensation reaction of aldehydes, 1,3?dicarbonyl compounds, and urea\\/thiourea under solvent?free conditions to afford the corresponding dihydropyrimidinones and thio?derivatives in high yields. Silica sulfuric acid is also found to be an efficient catalyst for the Biginelli reaction under solvent?free conditions. Compared to the classical Biginelli reaction conditions, this new method consistently has the advantage of



Phosphine oxide-catalyzed enantioselective intramolecular aldol reaction via regioselective enolization of unsymmetrical diketones with tetrachlorosilane.  


The phosphine oxide-catalyzed asymmetric intramolecular aldol reactions of diketones were investigated. The combination of tetrachlorosilane and a chiral phosphine oxide catalyst promoted the acetyl-selective enolization of diketones, and the subsequent intramolecular aldol reaction occurred in an enantioselective manner. The introduction of two trimethylsilyl groups at the 4- and 4'-positions in BINAP dioxide catalyst improved the enantioselectivity. This reaction provides an effective synthetic method to access ?-tertiary-hydroxy cyclohexanones in high yields and with high enantioselectivity. PMID:25192225

Kotani, Shunsuke; Aoki, Shohei; Sugiura, Masaharu; Ogasawara, Masamichi; Nakajima, Makoto



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


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. Biotechnol. Bioeng. 2014;111: 2446-2453. © 2014 Wiley Periodicals, Inc. PMID:24902824

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



Mercuracarborand-catalyzed Diels-Alder reactions of a thionoester with cyclopentadiene  

Microsoft Academic Search

The multidentate Lewis acids B-octamethyl [12]-mercuracarborand-4 (1) and B-hexamethyl [9]-mercuracarborand-3 (2) catalyze the Diels-Alder reaction of a thionoester 4 with cyclopentadiene. The reaction proceeds more rapidly when catalyzed with 1 and 2 than with monodentate bis(closo-9,12-dimethyl-1,2-carboran-1-yl)mercury (3). Mercury-199 NMR studies demonstrated the formation of a 1:1 complex of 1 with 4 in which the thio function of 4 is coordinated

Hans Lee; Martin Diaz; M. Frederick Hawthorne



Steady State Kinetics of Mannitol Phosphorylation Catalyzed by Enzyme IImtl of the Escherichia coli Phosphoenolpyruvate-dependent Phosphotransferase System  

Microsoft Academic Search

The kinetics of mannitol phosphorylation catalyzed by enzyme IImtl of the bacterial P-enolpyruvate-dependent phosphotransferase system are described for three different physical conditions of the enzyme, (i) embedded in the membrane of inside-out (ISO) oriented vesicles, (ii) solubilized and assayed above the critical micellular concentration (cmc) of the detergent, and (iii) solubilized and assayed below the cmc of the detergent. The

George T. Robillard; Ria H. ten Hoeve-Duurkens; Juke S. Lolkema



Ultrasound assisted enzyme catalyzed transesterification of waste cooking oil with dimethyl carbonate.  


This work reports the production of biodiesel with waste cooking oil and dimethyl carbonate in solvent free system through transesterification by immobilized enzyme (Novozym 435) under the influence of ultrasound irradiation. The experiments were conducted in an ultrasonic water bath under three different conditions i.e. ultrasonic irradiation (UI) without stirring, UI coupled with stirring and only stirring to compare their overall effects on fatty acid methyl esters (FAME) conversion. As compared with the conventional stirring method, where FAME conversion was 38.69% at 4h, the UI without stirring significantly enhanced the conversion of enzymatic transesterification to 57.68% for the same reaction time. However the reaction rate was further increased under the condition of ultrasonication coupled with stirring and resulted into higher conversion of 86.61% for the same reaction time. Effects of reaction parameters, such as temperature, ratio of DMC/oil, speed of agitation and enzyme loading on the conversion were investigated. Furthermore, repeated use of Novozym 435 showed gradual decline in both conversion as well as enzyme activity. PMID:23178034

Gharat, Nikhil; Rathod, Virendra K



Vanadium bromoperoxidase from Delisea pulchra: enzyme-catalyzed formation of bromofuranone and attendant disruption of quorum sensing.  


Vanadium bromoperoxidase was isolated and cloned from the marine red alga Delisea pulchra. This enzyme catalyzes the bromolactonization of 4-pentynoic acid forming 5E-bromo-methylidenetetrahydro-2-furanone, a compound which is shown herein to inhibit quorum sensing in the engineered reporter strain, Agrobacterium tumefaciens NTL4. PMID:22006105

Sandy, Moriah; Carter-Franklin, Jayme N; Martin, Jessica D; Butler, Alison



Enzymic mechanisms involving concomitant transfer and hydrolysis reactions  

PubMed Central

The kinetic parameters of ten different enzymic mechanisms in which bimolecular transfer reactions occur concomitantly with the hydrolysis of the donor molecule have been studied. The usefulness of these parameters for making a choice of mechanism is discussed. The analysis has been extended to the use of alternative substrates in bimolecular transfer reactions that proceed without the hydrolysis of the donor molecule. PMID:4772273

Frère, Jean-Marie



Gold-Catalyzed Transannular [4+3] Cycloaddition Reactions  

PubMed Central

Macrocyclic propargyl acetates containing a furan ring were prepared using the CrCl2-promoted reaction. In the presence of either a Au(I) or a Au(III) catalyst, a tandem 3,3-rearrangement-transannular [4+3] cycloaddition reaction occurred to provide multiple fused ring systems. The transannular [4+3] cycloaddition reactions of the macrocyclic propargyl acetates are regio- and diastereospecific. The regiochemistry of the product is controlled by the position of the acetoxy group in the starting material and the stereochemistry of the reaction depends on the ring size. PMID:19937623

Gung, Benjamin W.; Craft, Derek T.; Bailey, Lauren N.; Kirschbaum, Kristin



Solid Nanoparticles that Catalyze Biofuel Upgrade Reactions at the  

E-print Network

of the hybrid particles at the interface. I n phase-transfer catalysis, reactions are car- ried out), it would be desirable to perform sequential reactions under phase-transfer condi- tions in a single reactor nanoparticles, we demonstrate biphasic hydrodeoxygenation and condensation catalysis in three substrate classes

Resasco, Daniel


Barrier compression and tunneling in enzyme catalysed reactions  

Microsoft Academic Search

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

Nigel Scrutton



Purification of the two-enzyme system catalyzing the oxidation of the D-proline residue of pristinamycin IIB during the last step of pristinamycin IIA biosynthesis.  

PubMed Central

High levels of conversion of 14C-labelled pristinamycin IIB (PIIB) to pristinamycin IIA (PIIA) were obtained in vivo in Streptomyces pristinaespiralis and in some other streptogramin A producers. This established that PIIB was an intermediate on the pathway to PIIA. In addition, in vitro studies with cell-free protein preparations demonstrated that the oxidation of PIIB to PIIA is a complex process requiring NADH, riboflavin 5'-phosphate (FMN), and molecular oxygen. Two enzymes were shown to be necessary to catalyze this reaction. Both were purified to homogeneity from S. pristinaespiralis by a coupled enzyme assay based on the formation of PIIA and by requiring addition of the complementing enzyme. One enzyme was purified about 3,000-fold by a procedure including a decisive affinity chromatography step on FMN-agarose. It was shown to be a NADH:FMN oxidoreductase (E.C. (hereafter called FMN reductase), providing reduced FMN (FMNH2) to the more abundant second enzyme. The latter was purified only 160-fold and was called PIIA synthase. Our data strongly suggest that this enzyme catalyzes a transient hydroxylation of PIIB by molecular oxygen immediately followed by a dehydration leading to PIIA. The native PIIA synthase consists of two different subunits with Mrs of around 50,000 and 35,000, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, while the FMN reductase seems to be a monomer with a Mr of around 28,000 and containing one molecule of tightly bound FMN. Stepwise Edman degradation of the entire polypeptides or some of their trypsin-digested fragments provided amino acid sequences for the two isolated proteins. PMID:7665508

Thibaut, D; Ratet, N; Bisch, D; Faucher, D; Debussche, L; Blanche, F



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


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

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



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


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

Nguyen, Minh H; Smith, Amos B



9422 Stratospheric ice catalyzes chlorine reactions 9428 Fusing silk and silica  

E-print Network

of hydrochloric acid form a quasiliquid layer on the surface of stratospheric ice crystals. The quasiliquid layer deteriorates with age CHEMISTRY Stratospheric ice catalyzes chlorine reactions To explain how ice crystals can nitrate and promoted the adsorption of acetic acid onto the ice crystals. The effects were observed

McFadden, Geoff


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

E-print Network

(I) catalyzed Huisgen alkyne and azide reaction to generate a triazole, this approach has potential by reducing Alumina 50% 3 min NCS Isoxazole Trace 3 Alumina 50% 3 min Copper/ Acetate Triazole 90% yield by HPLC 4 Alumina 50% 9 min None Triazole Failed 5 None 40% 3 min NCS Isoxazole Failed 6 Alumina/ Carbonate 50% 3

Collins, Gary S.


Recent Developments in Pd-Catalyzed Alkene Aminoarylation Reactions for the Synthesis of Nitrogen Heterocycles  

PubMed Central

This short review describes new developments in Pd-catalyzed aminoarylation reactions between aryl halides and alkenes bearing pendant nitrogen nucleophiles. These transformations provide a novel and powerful method for accessing numerous 3-, 5-, 6-, and 7-membered nitrogen heterocycles. PMID:23243321

Schultz, Danielle M.; Wolfe, John P.



Heterogeneous Atmospheric Aerosol Production by Acid Catalyzed Particle-Phase Reactions  

Microsoft Academic Search

According to evidence from our laboratory, acidic surfaces on atmospheric aerosols lead to potentially multifold increases in secondary organic aerosol (SOA) mass. Experimental observations using a multichannel flow reactor, Teflon (polytetrafluoroethylene) film bag batch reactors, and outdoor Teflon-film smog chambers strongly confirm that inorganic acids, such as sulfuric acid, catalyze particle-phase heterogeneous reactions of atmospheric organic carbonyl species. The net

Myoseon Jang; Nadine M. Czoschke; Sangdon Lee; Richard M. Kamens



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.



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


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



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

Microsoft Academic Search

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




N-heterocyclic carbene-catalyzed internal redox reaction of alkynals: an efficient synthesis of allenoates.  


An efficient N-heterocyclic carbene (NHC)-catalyzed internal redox reaction of alkynals that bear a ? leaving group has been developed. This process provides a new access to a range of allenoates in good yields. Preliminary results demonstrate that the enantioselective variant can also be achieved. PMID:22352302

Zhao, Yu-Ming; Tam, Yik; Wang, Yu-Jie; Li, Zigang; Sun, Jianwei



Cobalt catalysis at the crossroads: cobalt-catalyzed Alder-ene reaction versus [2 + 2] cycloaddition.  


The application of bidentate phosphine ligands in cobalt-catalyzed transformations of cyclic alkenes such as cyclopentene and cycloheptene with internal alkynes led to a chemoselective Alder-ene or a [2 + 2] cycloaddition reaction depending on the electronic nature of the alkyne and the bite angle of the ligand used. PMID:20196545

Hilt, Gerhard; Paul, Anna; Treutwein, Jonas



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

PubMed Central

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

Nguyen, Minh H.; Smith, Amos B.



Enzymes in Analytical Chemistry.  

ERIC Educational Resources Information Center

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

Fishman, Myer M.



Development of transitional metal-catalyzed reactions for organic synthesis  

E-print Network

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

Rainka, Matthew P. (Matthew Paul)



Mineral catalyzed hydrothermal reactions as precursors to extant anabolic pathways  

NASA Astrophysics Data System (ADS)

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

Cody, G. D.


Consecutive Rh(I)-catalyzed Alder-ene\\/Diels–Alder\\/Diels–Alder reaction sequence affording rapid entry to polycyclic compounds  

Microsoft Academic Search

Conversion of acyclic allenynes to polycyclic compounds using consecutive transition metal catalyzed carbon–carbon bond forming reactions in a single chemical operation is described. Reaction of an allenyne with a Rh(I) catalyst affords a cross-conjugated triene via a formal Alder-ene reaction. The triene then participates in a Rh(I)-catalyzed intramolecular [4+2] cycloaddition reaction to generate a new conjugated diene. An external dienophile

Kay M. Brummond; Lingfeng You



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

Microsoft Academic Search

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

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



Synthesis of amides through the Cannizzaro-type reaction catalyzed by lanthanide chlorides  

Microsoft Academic Search

Amidation of aldehydes with lithium amides through the LnCl3-catalyzed Cannizzaro-type reactions afforded a variety of amides in high yields. The electronic and steric effects on the reaction were investigated. The features of the economical catalysts, high yields, tolerance of a wide range of lithium amides and aromatic aldehydes make this methodology an easy and valid contribution to the direct synthesis

Lijun Zhang; Shunpeng Su; Hongping Wu; Shaowu Wang



Convenient and Efficient Palladium-Catalyzed Coupling Reaction Between Ferroceneboronic Acid and Organic Triflates  

Microsoft Academic Search

A simple and efficient palladium (Pd)–catalyzed Suzuki cross-coupling reaction between ferroceneboronic acid and organic triflates for the preparation of monosubstituted ferrocene derivatives has been developed. A systematic study of various solvents, bases, and catalysts revealed that the combination of Pd(PPh3)4 (0.025 equiv) and K3PO4 (2 equiv) in refluxing dioxane gave reproducible and excellent yields of the coupling products. The reaction

Bohua Long; Yingbin Yang; Lanxiang Wang; Weimin He; Jiannan Xiang



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 descr...

Bothma, Jacques P; McKenzie, Ross H



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



Reaction dynamics of ATP hydrolysis catalyzed by P-glycoprotein.  


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

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



Experimental and theoretical methods in kinetic studies of heterogeneously catalyzed reactions.  


This review aims to illustrate the potential of kinetic analysis in general and microkinetic modeling in particular for rational catalyst design. Both ab initio calculations and experiments providing intrinsic kinetic data allow us to assess the effects of catalytic properties and reaction conditions on the activity and selectivity of the targeted reactions. Three complementary approaches for kinetic analysis of complex reaction networks are illustrated, using select examples of acid zeolite-catalyzed reactions from the authors' recent work. Challenges for future research aimed at defining targets for synthesis strategies that enable us to tune zeolite properties are identified. PMID:24910922

Reyniers, Marie-Françoise; Marin, Guy B



Theoretical revisit of a Fe(CO)(5)-catalyzed water-gas shift reaction.  


We have revisited the water-gas shift reaction catalyzed by iron pentacarbonyl at the DFT-B3LYP level. The reaction mechanism proposed by Rozanska and Vuilleumier (Inorg. Chem. 2008, 47, 8635-8640) has been followed and revised. The results show that transition states TS4/5 and TS5/2_a actually connect other intermediates rather than those suggested by Rozanska and Vuilleumier. Furthermore, the entire reaction has been proven to proceed with processes 1 --> 2 --> 3 --> 4 --> 6 --> 7 --> 2. It is the first time that species 6 and 7 are reported as intermediates for this reaction mechanism. PMID:20199050

Zhang, Fuli; Zhao, Liang; Xu, Chunming; Chen, Yu



Detoxification of substituted phenols by oxidoreductive enzymes through polymerization reactions  

Microsoft Academic Search

Laccases from the fungiRhizoctonia praticola andTrametes versicolor as well as horseradish peroxidase and tyrosinase were evaluated for their ability to polymerize phenolic contaminants. The removal of phenols through polymerization depended on the chemical structure and concentration of the substrate, pH of the reaction mixture, activity of the enzyme, length of incubation, and temperature. The enzymes retained their activity throughout a

J. Dec; J.-M. Bollag



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

E-print Network

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

Masayasu Kamimura; Yasushi Kino; Emiko Hiyama



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



Silver catalyzed zinc Barbier reaction of benzylic halides in water  

Microsoft Academic Search

Benzylic chlorides react in aqueous dibasic potassium phosphate under silver catalysis with aromatic aldehydes in the presence of zinc dust to give 1,2-diaryl alcohols in moderate to good yields. Dimerization to bibenzyls and reduction of the halide are important side reactions. A wide range of substituted aromatic and heteroaromatic aldehydes and of substituted benzylic chlorides can be used. Aliphatic aldehydes

Lothar W. Bieber; Elisabeth C. Storch; Ivani Malvestiti; Margarete F. da Silva



Chiral Counterions in Asymmetric Transition Metal-Catalyzed Reactions  

E-print Network

application of chiral anions to asymmetric catalysis is relatively recent ·classical resolution ·phase-transfer.2 kcal·mol-1 (in DCE) Ag #12;Chiral Cations in Phase Transfer Catalysis Asymmetric Enolate Alkylation Reactions ·classical resolution ·phase-transfer catalysis #12;Coulomb's Law and Ion Pairing in Solution

Stoltz, Brian M.


Theoretical study on the Diels-Alder reaction of cyclopentadiene with methacrolein catalyzed by diethylimidazolium cation  

NASA Astrophysics Data System (ADS)

The theoretical studies of how room temperature ionic liquids control desired reactions are very scarce in contrast with their increasing applications in many fields as recyclable solvents, catalysts, and reaction mediums. The present work considers the Diels-Alder (D-A) reaction of cyclopentadiene with methacrolein in the presence of diethylimidazolium salts as the first prototype of our systemic studies about important organic synthesis reactions catalyzed by room temperature ionic liquids. We show the mechanism details of the D-A reactions with and without the dialkylimidazolium cation and rationalize the experimental findings based on the results from the quantum chemistry calculations at the AM1, HF/6-31G(d), and B3PW91/6-31G(d,p) levels of theory, respectively. It is found that the diethylimidazolium cation acts as a Lewis acid center to catalyze the D-A reaction, which decreases the barrier and increases the asynchronicity of the D-A reaction, but does not change the potential energy surface profile of the reaction compared to the noncatalyzed process. The present results rationalize the early experimental findings well and provide the first prototype for theoretically understanding the D-A reaction in the presence of dialkylimidazolium salts.

Sun, Hui; Zhang, Dongju; Ma, Chen; Liu, Chengbu


Sucrose phosphorylases catalyze transglycosylation reactions on carboxylic acid compounds  

Microsoft Academic Search

Two sucrose phosphorylases were employed for glycosylation of carboxylic acid compounds. Streptococcus mutans sucrose phosphorylase showed remarkable transglycosylating activity, especially under acidic conditions. Leuconostoc mesenteroides sucrose phosphorylase exhibited very weak transglycosylating activity. Three main products were detected from the reaction\\u000a mixture using benzoic acid and sucrose as an acceptor and a donor molecule, respectively. These compounds were identified\\u000a as 1-O-benzoyl

Kazuhisa Sugimoto; Koji Nomura; Hiromi Nishiura; Kohji Ohdan; Takahisa Nishimura; Hideo Hayashi; Takashi Kuriki



Enzyme catalyzed cross-linking of spruce galactoglucomannan improves its applicability in barrier films.  


Hemicelluloses are one of the main constituents of plant cell walls and thereby one of the most abundant biopolymers on earth. They can be obtained as by-products from different wood based processes, most importantly from the mechanical pulping. Hemicelluloses have interesting properties in e.g. barrier film applications. However, their relatively low molecular weight after isolation and co-extraction with lignin has limited their use. In this work, we present a novel technique for increasing the molecular weight of different wood hemicelluloses from mechanical pulping process waters as well as from pre-hydrolysis extracts. This is achieved by enzyme-catalyzed cross-linking of aromatic moieties bound to the hemicelluloses. The cross-linking treatment resulted in significantly improved mechanical properties in barrier films made with spruce galactoglucomannan. To our knowledge, this is the first time that wood hemicelluloses have been cross-linked by utilizing the bound aromatic moieties and creates new possibilities for utilizing this raw material source. PMID:23648031

Oinonen, Petri; Areskogh, Dimitri; Henriksson, Gunnar



Bioinorganic Chemistry in Thyroid Gland: Effect of Antithyroid Drugs on Peroxidase-Catalyzed Oxidation and Iodination Reactions  

PubMed Central

Propylthiouracil (PTU) and methimazole (MMI) are the most commonly used antithyroid drugs. The available data suggest that these drugs may block the thyroid hormone synthesis by inhibiting the thyroid peroxidase (TPO) or diverting oxidized iodides away from thyroglobulin. It is also known that PTU inhibits the selenocysteine-containing enzyme ID-1 by reacting with the selenenyl iodide intermediate (E-SeI). In view of the current interest in antithyroid drugs, we have recently carried out biomimetic studies to understand the mechanism by which the antithyroid drugs inhibit the thyroid hormone synthesis and found that the replacement of sulfur with selenium in MMI leads to an interesting compound that may reversibly block the thyroid hormone synthesis. Our recent results on the inhibition of lactoperoxidase (LPO)-catalyzed oxidation and iodination reactions by antithyroid drugs are described. PMID:17497002

Roy, Gouriprasanna; Mugesh, G.



Bioinorganic chemistry in thyroid gland: effect of antithyroid drugs on peroxidase-catalyzed oxidation and iodination reactions.  


Propylthiouracil (PTU) and methimazole (MMI) are the most commonly used antithyroid drugs. The available data suggest that these drugs may block the thyroid hormone synthesis by inhibiting the thyroid peroxidase (TPO) or diverting oxidized iodides away from thyroglobulin. It is also known that PTU inhibits the selenocysteine-containing enzyme ID-1 by reacting with the selenenyl iodide intermediate (E-SeI). In view of the current interest in antithyroid drugs, we have recently carried out biomimetic studies to understand the mechanism by which the antithyroid drugs inhibit the thyroid hormone synthesis and found that the replacement of sulfur with selenium in MMI leads to an interesting compound that may reversibly block the thyroid hormone synthesis. Our recent results on the inhibition of lactoperoxidase (LPO)-catalyzed oxidation and iodination reactions by antithyroid drugs are described. PMID:17497002

Roy, Gouriprasanna; Mugesh, G



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

E-print Network

homoaldol equivalent reactions (Table 1.1). Scheme 1.7. Chromium-Mediated Coupling Reactions OMe OMe CrCl2, TMSI THF, ?30 ?C 88% H O Ph + OMe Ph OH O MeO Me Me OTBDMS I Me O OR ORRO OMe OR OHC CrCl2-NiCl2 (0.1%) DMSO,rt 81%, dr...), the [PyBoxi-Pr] ligand exhibited the highest enantioselectivity (11% ee). 27 Table 1.7. Asymmetric Homoaldol Equivalent Reactions Employing Carbazole and PyBox Ligandsa,b 1% ee 0% ee7% ee N N N N OO N PhPh N N OO N i-Pri-Pr 11...

Kang, Jun



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.


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



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


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

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



Enantioselective Henry reaction catalyzed by "ship in a bottle" complexes.  


Two chiral Schiff-base complexes of copper(II) have been successfully encapsulated inside the cavity of zeolite-NaY via a "ship in a bottle" synthesis method. The presence of the two complexes inside the cages of zeolite-Y has been confirmed based on various spectrochemical and physicochemical techniques, viz. FTIR, UV-vis/DRS, ESR, XPS, CV, EDX, SEM, and TGA. Zeolite-encapsulated chiral copper(II) Schiff-base complexes are found to give a high-enantioselective (84% ee, R conformation) nitro-aldol product at -20 °C. The encapsulated copper complexes are found to show higher catalytic efficiency than their homogeneous counterparts under identical conditions. Density functional theory (DFT) calculation has been implemented to understand the effect of the zeolite matrix on structural, electronic, and reactivity properties of the synthesized complexes. Theoretical calculation predicts that upon encapsulation into the zeolite matrix the Cu center becomes more susceptible to nucleophilic attack, favoring a nitro-aldol reaction. A plausible mechanism is suggested based on the experimental and theoretical results. The structures of reaction intermediates and transition state(s) involved in the catalytic cycle are derived using DFT. PMID:23848182

Bania, Kusum K; Karunakar, Galla V; Goutham, Kommuru; Deka, Ramesh C



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


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



Conjugation reactions catalyzed by bifunctional proteins related to beta-oxidation in bile acid biosynthesis.  


The conjugation reactions of hydration and dehydrogenation catalyzed by the dehydratase and dehydrogenase activities of D-3-hydroxyacyl-CoA dehydratase/D-3-hydroxyacyl-CoA dehydrogenase bifunctional protein (DBP) and enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase bifunctional protein (LBP) in the side chain degradation step of bile acid biosynthesis were investigated using chemically synthesized C27-bile acid CoA esters as substrates. The hydration catalyzed by DBP showed high diastereoselectivity for (24E)-3alpha,7alpha,12alpha-trihydroxy- and (24E)-3alpha,7alpha-dihydroxy-5beta-cholest-24-en-26-oyl CoA to give (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy- and (24R,25R)-3alpha,7alpha,24-trihydroxy-5beta-cholestan-26-oyl CoAs, respectively, and the dehydrogenation catalyzed by DBP also showed high stereospecificity for the above (24R,25R)-isomers to give 3alpha,7alpha,12alpha-trihydroxy- and 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestan-26-oyl CoAs, respectively. On the other hand, the dehydratase activity of LBP displayed a different diastereoselectivity producing the (24S,25S)-isomer, and dehydrogenase activity of LBP was stereospecific for the (24S,25R)-isomer to give the above 24-oxo-derivative. The hydration and dehydrogenation reactions catalyzed by DBP were effectively conjugated to convert (24E)-5beta-cholestenoyl CoA to 24-oxo-5beta-cholestanoyl CoA. However, the reactions catalyzed by LBP were not conjugated. These results indicate that DBP plays an important role in the biosynthesis of bile acid. PMID:11146090

Kurosawa, T; Sato, M; Nakano, H; Fujiwara, M; Murai, T; Yoshimura, T; Hashimoto, T



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

PubMed Central

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

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



Asymmetric copper-catalyzed Diels-Alder reaction revisited: control of the structure of bis(oxazoline) ligands.  

E-print Network

1 Asymmetric copper-catalyzed Diels-Alder reaction revisited: control of the structure of bis,R)-dihydroethano trans-dicarboxylic acid, a complete series of ligands was evaluated in the copper-catalyzed Diels-Alder[2.2.2] backbone; Diels-Alder catalysis; Copper; Enantioselectivity. * Corresponding author. E

Paris-Sud XI, Université de


Palladium-catalyzed coupling reactions for the functionalization of Si surfaces: superior stability of alkenyl monolayers.  


Palladium-catalyzed Suzuki, Heck, and Sonogashira coupling reactions were studied as reaction protocols for organic modification of Si surfaces. These synthetically useful protocols allow for surface modification of alkene, alkyne, and halide terminated surfaces. Surface oxidation and metal contamination were assessed by X-ray photoelectron spectroscopy. The nature of the primary passivation layer was an important factor in the oxidation resistance of the Si surface during the secondary functionalization. Specifically, the use of alkynes as the primary functionalization layer gave superior stability compared to alkene analogues. The ability to utilize Pd-catalyzed coupling chemistries on Si surfaces opens great versatility for potential molecular and nanoscale electronics and sensing/biosensing applications. PMID:23968278

Collins, Gillian; O'Dwyer, Colm; Morris, Michael; Holmes, Justin D



Measurement of the alpha-secondary kinetic isotope effect for the reaction catalyzed by mammalian protein farnesyltransferase.  


Protein farnesytransferase (FTase) catalyzes the transfer of a 15-carbon prenyl group from farnesyl diphosphate (FPP) to the cysteine residue of target proteins and is a member of the newest class of zinc metalloenzymes that catalyze sulfur alkylation. Common substrates of FTase include oncogenic Ras proteins, and therefore inhibitors are under development for the treatment of various cancers. An increased understanding of the salient features of the chemical transition state of FTase may aid in the design of potent inhibitors and enhance our understanding of the mechanism of this class of zinc enzymes. To investigate the transition state of FTase we have used transient kinetics to measure the alpha-secondary 3H kinetic isotope effect at the sensitive C1 position of FPP. The isotope effect for the FTase single turnover reaction using a peptide substrate that is farnesylated rapidly is near unity, indicating that a conformational change, rather than farnesylation, is the rate-limiting step. To look at the chemical step, the kinetic isotope effect was measured as 1.154 +/- 0.006 for a peptide that is farnesylated slowly, and these data suggest that FTase proceeds via a concerted mechanism with dissociative character. PMID:17117849

Pais, June E; Bowers, Katherine E; Fierke, Carol A



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


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

Yamada, Taro; Takusagawa, Fusao



A palladium-catalyzed addition reaction of aroyl/heteroaroyl acid anhydrides to norbornenes.  


A palladium complex derived from Pd2(dba)3 and dppp catalyzes the addition reaction of aroyl/heteroaroyl acid anhydrides to norbornenes, giving 2-aroyl/heteroaroyl-3-aroyloxy/heteroaroyloxy-bicyclo[2,2,1]heptanes. The C-O bond of acid anhydride is cleaved, and the aroyl/heteroaroyl and aroyloxy/heteroaroyloxy groups are added to alkenes. trans-Adducts are selectively obtained with the endo-benzoyl group and exo-benzoyloxy group. PMID:25347414

Arisawa, Mieko; Tanii, Saori; Yamaguchi, Masahiko



Kinetic isotope and thermodynamic analysis of the nornicotine-catalyzed aqueous aldol reaction  

Microsoft Academic Search

A series of kinetic isotope effects and thermodynamic studies were performed to test key predictions of a computationally derived model for a nornicotine-catalyzed aqueous aldol reaction. The relative energies of the two computationally-derived transition states were challenged using the proton inventory, which demonstrated that a single water molecule from the solvent is involved in, or before, the rate-limiting step. These

Claude J. Rogers; Tobin J. Dickerson; Kim D. Janda



Metal-Catalyzed Acyl Transfer Reactions of Enol Esters: Role of Y5(Oi  

E-print Network

Metal-Catalyzed Acyl Transfer Reactions of Enol Esters: Role of Y5(Oi Pr)13O and (thd)2Y(Oi Pr of catalytic amounts (0.05-1 mol %) of Y5(OiPr)13O to give the corresponding esters. In selected cases including the pentameric yttrium aggregate Y5- (µ5-O)(µ3-Oi Pr)4(µ2-(Oi Pr)4(Oi Pr)5, generally formulated

RajanBabu, T. V. "Babu"


Isotope Effects and Mechanism of the Asymmetric BOROX Br?nsted Acid Catalyzed Aziridination Reaction  

PubMed Central

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

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



Dinuclear Zinc-Prophenol-Catalyzed Enantioselective ?-Hydroxyacetate Aldol Reaction with Activated Ester Equivalents  

PubMed Central

An enantioselective ?-hydroxyacetate aldol reaction that employs N-acetyl pyrroles as activated ester equivalents and generates syn 1,2-diols in good yield and diastereoselectivity is reported. This dinuclear zinc Prophenol-catalyzed transformation proceeds with high enantioselectivity with a wide variety of substrates including aryl, alyl, and alkenyl aldehydes. The resulting ?,?-dihydroxy activated esters are versatile intermediates for the synthesis of a variety of carboxylic acid derivatives including amides, esters, and unsymmetrical ketones. PMID:23947595

Trost, Barry M.; Michaelis, David J.; Truica, Mihai I.



Dinuclear zinc-ProPhenol-catalyzed enantioselective ?-hydroxyacetate aldol reaction with activated ester equivalents.  


An enantioselective ?-hydroxyacetate aldol reaction that employs N-acetyl pyrroles as activated ester equivalents and generates syn 1,2-diols in good yield and diastereoselectivity is reported. This dinuclear zinc-ProPhenol-catalyzed transformation proceeds with high enantioselectivity with a wide variety of substrates including aryl, alyl, and alkenyl aldehydes. The resulting ?,?-dihydroxy activated esters are versatile intermediates for the synthesis of a variety of carboxylic acid derivatives including amides, esters, and unsymmetrical ketones. PMID:23947595

Trost, Barry M; Michaelis, David J; Truica, Mihai I



Dehydrogenative Meyer-Schuster-like rearrangement: a gold-catalyzed reaction generating an alkyne.  


Easily accessible propargylic esters are converted to the inverted alkynyl ketones in an oxidative gold-catalyzed reaction. Gagosz's catalyst in combination with PhI(OAc)2 is the best system for this conversion and 18 examples with yields up to 80?% are reported. The results indicate that the triple bond in the product is formed by elimination from a vinylgold intermediate. In a formal sense the new conversion overall is a dehydrogenative Meyer-Schuster rearrangement. PMID:24338996

Yu, Yang; Yang, Weibo; Pflästerer, Daniel; Hashmi, A Stephen K



A secondary kinetic isotope effect study of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase-catalyzed reaction: evidence for a retroaldol-aldol rearrangement.  


1-Deoxy-d-xylulose 5-phosphate (DXP) reductoisomerase (DXR, also known as methyl-d-erythritol 4-phosphate (MEP) synthase) is a NADPH-dependent enzyme, which catalyzes the conversion of DXP to MEP in the nonmevalonate pathway of isoprene biosynthesis. Two mechanisms have been proposed for the DXR-catalyzed reaction. In the alpha-ketol rearrangement mechanism, the reaction begins with deprotonation of the C-3 hydroxyl group followed by a 1,2-migration to give methylerythrose phosphate, which is then reduced to MEP by NADPH. In the retroaldol/aldol rearrangement mechanism, DXR first cleaves the C3-C4 bond of DXP in a retroaldol manner to generate a three-carbon and a two-carbon phosphate bimolecular intermediate. These two species are then reunited by an aldol reaction to form a new C-C bond, yielding an aldehyde intermediate. Subsequent reduction by NADPH affords MEP. To differentiate these mechanisms, we have prepared [3-(2)H]- and [4-(2)H]-DXP and carried out a competitive secondary kinetic isotope effect (KIE) study of the DXR reaction. The normal 2 degrees KIEs observed for [3-(2)H]- and [4-(2)H]-DXP provide compelling evidence supporting a retroaldol/aldol mechanism for the rearrangement catalyzed by DXR, with the rate-limiting step being cleavage of the C3-C4 bond of DXP. PMID:19159292

Munos, Jeffrey W; Pu, Xiaotao; Mansoorabadi, Steven O; Kim, Hak Joong; Liu, Hung-wen



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



A general method for palladium-catalyzed reactions of primary sulfonamides with aryl nonaflates.  


A general method for Pd-catalyzed sulfonamidation of aryl nonafluorobutanesulfonates (aryl nonaflates) is described. A biaryl phosphine ligand, t-BuXPhos, formed the most active catalyst, and K(3)PO(4) in tert-amyl alcohol was found to be the optimal base-solvent combination for the reaction. The reaction conditions were tolerant of various functional groups such as cyano, nitro, ester, aldehyde, ketone, chloride, carbamate, and phenol. Heterocyclic aryl nonaflates were found to be suitable coupling partners. High yields of the coupled products were obtained from the reactions between inherently disfavored substrates such as electron-rich nonaflates and electron-poor sulfonamides. Kinetic data suggest reductive elimination to be the rate-limiting step for the reaction. The only limitation of this methodology that we have identified is the inability of 2,6-disubstituted aryl nonaflates to efficiently participate in the reaction. PMID:21510695

Shekhar, Shashank; Dunn, Travis B; Kotecki, Brian J; Montavon, Donna K; Cullen, Steven C



Reactions of cysteamine and other amine metabolites with glyoxylate and oxygen catalyzed by mammalian D-amino acid oxidase.  

PubMed Central

Pig kidney D-amino acid oxidase [D-amino-acid:oxygen oxidoreductase (deaminating), EC] catalyzes a rapid uptake of oxygen when high concentrations (50-100 mM) of glyoxylate and the following amines are present under usual assay conditions (pH 8.3): cysteamine, 2-aminoethanol, putrescine, D,L-1-amino-2-propanol, D,L-2-amino-1-propanol, 3-amino-1-propanol, D,L-octopamine, ethylenediamine, and L-cysteine ethyl ester. Notable physiological amines that do not support a rapid O2 reaction under the above conditions include histamine, serotonin, epinephrine, norepinephrine, spermidine, spermine, and cadaverine. A more detailed kinetic investigation of the reactions involving the first four reactive amines listed above indicated that the cysteamine reaction proceeds at a rapid rate even when cysteamine and glyoxylate are present at less than millimolar concentrations, but greater than millimolar concentrations are needed in the other amine reactions in order to observe a reasonable rate. At low concentrations and pH 7.4, the cysteamine-glyoxylate substrate (presumably thiazolidine-2-carboxylic acid) reacts an order of magnitude faster than any other known D-amino acid oxidase substrate. Considerable circumstantial evidence suggests that the reaction involving cysteamine is occurring physiologically, but the reactions of other amines would be occurring in the cell at a very low rate, if at all. It is proposed that the product of the enzymic reaction may be a metabolic effector that can modify the reactivity of proteins or nucleic acids by covalent attachment. PMID:37501

Hamilton, G A; Buckthal, D J; Mortensen, R M; Zerby, K W



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

SciTech Connect

Carbon-neutral hydrogen gas is a compelling energy carrier, especially for the transportation section. Low-cost hydrogen can be produced from abundant renewable lignocellulosic biomass through a number of methods employing chemical catalysis, biocatalysis or a combination of both, but these technologies suffer from low hydrogen yields (well below the theoretical yield of 12 H2 per glucose), undesired side-products and/or required severe reaction conditions. Here we present a novel in vitro synthetic biology approach for producing near theoretical hydrogen yields from cellulosic materials (cellodextrins) and water at 32oC and 1 atm. These non-natural catabolic pathways containing up to 14 enzymes and one coenzyme degrade cellodextrins initially to glucose-1-phosphate and eventually to CO2, split water and finally release the chemical energy in the form of hydrogen gas. Up to 11.2 H2 per anhydroglucose was produced in a batch reaction. This spontaneous endothermic reaction is driven by entropy gain, suggesting that the thermal energy is adsorbed for generating more chemical energy (hydrogen gas) than that in cellodextrins, i.e., output/input of chemical energy > 1, with an input of ambient-temperature thermal energy.

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



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

E-print Network

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

Woodin, Katrina Sue



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

E-print Network

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

McAvoy, Camille Z



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


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



Catalytic activity of an encaged Verkade's superbase in a base-catalyzed Diels-Alder reaction.  


Organocatalysis in a confined space has been performed through encapsulation of a proazaphosphatrane superbase in a hemicryptophane host. The resulting catalyst displays good to high catalytic activity in the base-catalyzed Diels-Alder reactions investigated. A comparison with the model superbase, which lacks a cavity, shows much higher diastereomeric excess with the encaged proazaphosphatrane for the reaction of 3-hydroxy-2-pyrone with N-methylmaleimide. The use of an encaged superbase as organocatalyst is unprecedented and highlights how the confinement may impact the stereoselectivity. PMID:25132071

Chatelet, Bastien; Dufaud, Véronique; Dutasta, Jean-Pierre; Martinez, Alexandre



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

PubMed Central

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

Wolfe, John P.



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.



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

PubMed Central

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

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



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.



Regioselective cobalt-catalyzed alder-ene reaction toward silicon- and boron-functionalized building blocks.  


The cobalt-catalyzed formal Alder-ene reaction of functionalized alkenes and alkynes leads to bifunctionalized 1,4-dienes in high yields and excellent regio- and stereoselectivities. The silicon-functionalized building blocks are easily converted into iodo-functionalized derivatives and in combination with boron-functionalized building blocks polyenes can be generated utilizing a Suzuki cross-coupling. In addition, building blocks incorporating allylic silane functionalities can be used in Sakurai allylation or Prins-type cyclization reactions for the synthesis of heterocyclic products such as tetrahydrofuranes or tetrahydropyranes. PMID:21162547

Hilt, Gerhard; Erver, Florian; Harms, Klaus



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



Site-specific bioconjugation of a murine dihydrofolate reductase enzyme by copper(I)-catalyzed azide-alkyne cycloaddition with retained activity.  


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



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


Water soluble ZnS quantum dots (QDs) modified by mercaptoacetic acid (MAA) were used to determinate proton concentration in aqueous solutions by fluorescence spectroscopic technique. The results showed that the fluorescence of the water-soluble QDs could be quenched by proton concentration and the fluorescence intensity of the water-soluble QDs decreased linearly as the pH varied from 4.5 to 7.0. Based on this phenomenon, a convenient, rapid and specific method to determine of enzyme reaction kinetics was proposed. The modified ZnS QDs were successfully used as pH probes in monitoring the hydrolysis of glycidyl butyrate catalyzed by porcine pancreatic lipase (PPL). The proposed method was found to improve stability, sensitivity and a monitoring range for determination proton concentration as compared to the already described analytical methods based on p-Nitrophenoxide (PNP). PMID:22579390

Wu, Dudu; Chen, Zhi



Cu((i))/amino acid catalyzed coupling reactions of aryl halides and nucleophiles: applications in large-scale production.  


Amino acids can be used as ligands to promote Ullmann-type coupling reactions. This review briefly discusses how L-proline, 4-hydroxy-L-proline and N,N-dimethylglycine can serve as the ideal ligands for copper-catalyzed coupling of aryl halides with different nucleophiles. Seven examples of applications of copper/amino acid catalyzed reactions in large-scale preparations are described. PMID:22273372

Ma, Dawei; Jiang, Yongwen



Fundamental reaction pathway and free energy profile for hydrolysis of intracellular second messenger adenosine 3',5'-cyclic monophosphate (cAMP) catalyzed by phosphodiesterase-4.  


As important drug targets for a variety of human diseases, cyclic nucleotide phosphodiesterases (PDEs) are a superfamily of enzymes sharing a similar catalytic site. We have performed pseudobond first-principles quantum mechanical/molecular mechanical-free energy perturbation (QM/MM-FE) and QM/MM-Poisson-Boltzmann surface area (PBSA) calculations to uncover the detailed reaction mechanism for PDE4-catalyzed hydrolysis of adenosine 3',5'-cyclic monophosphate (cAMP). This is the first report on QM/MM reaction-coordinate calculations including the protein environment of any PDE-catalyzed reaction system, demonstrating a unique catalytic reaction mechanism. The QM/MM-FE and QM/MM-PBSA calculations revealed that the PDE4-catalyzed hydrolysis of cAMP consists of two reaction stages: cAMP hydrolysis (stage 1) and bridging hydroxide ion regeneration (stage 2). The stage 1 includes the binding of cAMP in the active site, nucleophilic attack of the bridging hydroxide ion on the phosphorus atom of cAMP, cleavage of O3'-P phosphoesteric bond of cAMP, protonation of the departing O3' atom, and dissociation of hydrolysis product (AMP). The stage 2 includes the binding of solvent water molecules with the metal ions in the active site and regeneration of the bridging hydroxide ion. The dissociation of the hydrolysis product is found to be rate-determining for the enzymatic reaction process. The calculated activation Gibbs free energy of ?16.0 and reaction free energy of -11.1 kcal/mol are in good agreement with the experimentally derived activation free energy of 16.6 kcal/mol and reaction free energy of -11.5 kcal/mol, suggesting that the catalytic mechanism obtained from this study is reliable and provides a solid base for future rational drug design. PMID:21973014

Chen, Xi; Zhao, Xinyun; Xiong, Ying; Liu, Junjun; Zhan, Chang-Guo



Simulating feedback and reversibility in substrate-enzyme reactions  

NASA Astrophysics Data System (ADS)

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

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



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


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



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

E-print Network

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

Lu, Zhe



Enantioselective TADMAP-catalyzed carboxyl migration reactions for the synthesis of stereogenic quaternary carbon.  


The chiral, nucleophilic catalyst TADMAP [1, 3-(2,2,2-triphenyl-1-acetoxyethyl)-4-(dimethylamino)pyridine] has been prepared from 3-lithio-4-(dimethylamino)pyridine (5) and triphenylacetaldehyde (3), followed by acylation and resolution. TADMAP catalyzes the carboxyl migration of oxazolyl, furanyl, and benzofuranyl enol carbonates with good to excellent levels of enantioselection. The oxazole reactions are especially efficient and are used to prepare chiral lactams (23) and lactones (30) containing a quaternary asymmetric carbon. TADMAP-catalyzed carboxyl migrations in the indole series are relatively slow and proceed with inconsistent enantioselectivity. Modeling studies (B3LYP/6-31G*) have been used in qualitative correlations of catalyst conformation, reactivity, and enantioselectivity. PMID:16417383

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



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)



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


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 (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This 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



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

NASA Astrophysics Data System (ADS)

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

Suga, Hiroyuki


Diastereoselectivity in Lewis-Acid Catalyzed Mukaiyama Aldol Reactions: A DFT Study  

PubMed Central

The basis for diastereoselectivity in Lewis acid-catalyzed Mukaiyama aldol reactions was studied using density functional theory. By exploring the conformations of the transition structures for the diastereodifferentiating step of seven different reactions, simple models were generated. The effects of varying the substituents on the enol carbon and the ?-carbon of the silyl enol ether from methyl to tert-butyl groups and the substituent on the aldehyde between methyl and phenyl groups were investigated by comparison of the transition structures for different reactions. Expanding on the previous qualitative models by Heathcock and Denmark, we found that while the pro-anti pathways takes place via antiperiplanar transition structures, the pro-syn pathways prefer synclinal transition structures. The relative steric effects of the Lewis acid and trimethyl silyl groups and the influence of E/Z isomerism on the aldol transition state were investigated. By calculating 36 transition structures at the M06/6-311G*//B3LYP/6-31G* level of theory and employing the IEFPCM polarizable continuum model for solvation effects, this study expands the mechanistic knowledge and provides a model for understanding the diastereoselectivity in Lewis acid-catalyzed Mukaiyama aldol reactions. PMID:22891640

Lee, Joshua M.; Helquist, Paul; Wiest, Olaf



Expeditious synthesis of a new hexasaccharide using transglycosylation reaction catalyzed by Bacillus (1-->3),(1-->4)-Beta-D-glucan 4-glucanohydrolase.  


Enzymatic hydrolysis of barley (1-->3),(1-->4)-beta-D-glucan using a recombinant (1-->3),(1-->4)-beta-glucanase from Bacillus licheniformis gives Glc beta 4Glc beta 3Glc isolated after acetylation in 49% yield. Conventional treatment produced the corresponding beta-fluoride which was carefully de-O-acetylated. A transglycosylation reaction with this substrate, catalyzed by the title enzyme, gave Glc beta 4Glc beta 3Glc beta 4Glc beta 4Glc beta 3Glc in 20% yield. PMID:9821269

Viladot, J L; Stone, B; Driguez, H; Planas, A



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


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



MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes  

PubMed Central

Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL: PMID:22730453

Braun, Andreas; Halwachs, Bettina; Geier, Martina; Weinhandl, Katrin; Guggemos, Michael; Marienhagen, Jan; Ruff, Anna J.; Schwaneberg, Ulrich; Rabin, Vincent; Torres Pazmino, Daniel E.; Thallinger, Gerhard G.; Glieder, Anton



Mesoscopic statistical properties of multistep enzyme-mediated reactions.  


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 study, the authors address this problem by solving the chemical master equations for various enzymatic reactions. A perturbation theory analogous to that used in quantum mechanics allows the determination of the first (n) and the second (?2) 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(n)/dt (or 'dose-response' curve) and the Fano factor F= ?2/(n) are both realistically measurable quantities, and whereas 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 the authors explore this possibility in the context of four sample multistep enzymatic reactions. 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. PMID:21028932

de Ronde, W H; Daniels, B C; Mugler, A; Sinitsyn, N A; Nemenman, I



Cobalamin- and Corrinoid-Dependent Enzymes  

PubMed Central

This chapter will review the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyltransfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations. PMID:20877792

Matthews, Rowena G.



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

NASA Astrophysics Data System (ADS)

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

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



Cyclones in the Diels-Alder reaction catalyzed by aluminum chloride  

SciTech Connect

A comparison was made of the kinetic parameters for the uncatalyzed and catalyzed (with aluminum chloride) Diels-Alder reaction between N-arylmaleimides and acrylic, methacrylic, and fumaric esters as dienophiles and phencyclone and tetracyclone as dienes. By thermochemical and spectrophotometric experiments it was shown that the aluminum chloride coordinates with the dienophile in a ratio of 1:1. With a larger concentration of the catalyst coordination also takes place at the carbonyl of the diene. For the complexes of N-arylmaleimides the rate constants for the reaction with free tetracyclone and phencyclone increase by not more than 60 times, those for the esters of the unsaturated acids increase by 300-600 times, whereas those in the reaction with anthracene increase by 10/sup 5/ times. The results are discussed form the standpoint of the change in the energy of the molecular orbitals of the reagents.

Kiselev, V.D.; Shakirov, I.M.; Konovalov, A.I.



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


A concise and effective three-step synthesis of 4a,8a-azaboranaphthalene (ABN) has been developed in gram scale. Electrophilic aromatic substitution reactions of ABN provide excellent functional-group-tolerant cross-coupling partners in various Pd-catalyzed cross-coupling reactions (e.g., Sonogashira, Suzuki-Miyaura, or Heck reaction). Photophysical, electrochemical, and DFT calculations all suggest a narrowed HOMO-LUMO gap with extended ?-conjugation characters in the cross-coupled molecules. The ABN moiety as a new fluorophore has a distinct and selective fluorescence response toward Zn(II) and Cd(II) ions, demonstrating great potential for the ABN structural motif in fluorescent chemosensors. PMID:25226093

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



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


Roles of the Redox-Active Disulfide and Histidine Residues Forming a Catalytic Dyad in Reactions Catalyzed by 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase?  

PubMed Central

NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC), an atypical member of the disulfide oxidoreductase (DSOR) family of enzymes, catalyzes the reductive cleavage and carboxylation of 2-ketopropyl-coenzyme M [2-(2-ketopropylthio)ethanesulfonate; 2-KPC] to form acetoacetate and coenzyme M (CoM) in the bacterial pathway of propylene metabolism. Structural studies of 2-KPCC from Xanthobacter autotrophicus strain Py2 have revealed a distinctive active-site architecture that includes a putative catalytic triad consisting of two histidine residues that are hydrogen bonded to an ordered water molecule proposed to stabilize enolacetone formed from dithiol-mediated 2-KPC thioether bond cleavage. Site-directed mutants of 2-KPCC were constructed to test the tenets of the mechanism proposed from studies of the native enzyme. Mutagenesis of the interchange thiol of 2-KPCC (C82A) abolished all redox-dependent reactions of 2-KPCC (2-KPC carboxylation or protonation). The air-oxidized C82A mutant, as well as wild-type 2-KPCC, exhibited the characteristic charge transfer absorbance seen in site-directed variants of other DSOR enzymes but with a pKa value for C87 (8.8) four units higher (i.e., four orders of magnitude less acidic) than that for the flavin thiol of canonical DSOR enzymes. The same higher pKa value was observed in native 2-KPCC when the interchange thiol was alkylated by the CoM analog 2-bromoethanesulfonate. Mutagenesis of the flavin thiol (C87A) also resulted in an inactive enzyme for steady-state redox-dependent reactions, but this variant catalyzed a single-turnover reaction producing a 0.8:1 ratio of product to enzyme. Mutagenesis of the histidine proximal to the ordered water (H137A) led to nearly complete loss of redox-dependent 2-KPCC reactions, while mutagenesis of the distal histidine (H84A) reduced these activities by 58 to 76%. A redox-independent reaction of 2-KPCC (acetoacetate decarboxylation) was not decreased for any of the aforementioned site-directed mutants. We interpreted and rationalized these results in terms of a mechanism of catalysis for 2-KPCC employing a unique hydrophobic active-site architecture promoting thioether bond cleavage and enolacetone formation not seen for other DSOR enzymes. PMID:21764916

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



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)



Calculation of a reaction path for KOH catalyzed ring-opening polymerization of hexamethylcyclotrisiloxane  

SciTech Connect

Polysiloxanes represent an important class of industrial polymers. Traditionally, poly(dimethylsiloxane) (PDMS) can be prepared by base-catalyzed ring-opening of cyclic dimethylsiloxanes. Ab initio electronic calculations were conducted to examine a reaction path for the KOH catalyzed ring-opening polymerization of hexamethylcyclotrisiloxane (D{sub 3}). The overall picture that emerges is initial side-on attack by KOH on a Si-O bond in the D{sub 3} ring leading to a stable addition complex with a 5-fold coordinated Si atom. The reaction path leads to a five-coordinate transition state, then to a stable insertion product (KOH inserts into the ring). The relative stability of a ring-opened product HO[Si(CH{sub 3}){sub 2}O]{sub 3}K is also considered. The energy along the reaction path was modeled both in the gas phase and in a moderately polar solvent (tetrahydrofuran, THF). The solvation energy was calculated using a recent implementation of an electrostatic model, where the solute molecule is placed in a non-spherical cavity in a dielectric continuum. The effect of basis set and electron correlation on the gas-phase energy and the effect of basis set on the solvation energy was studied. 34 refs., 5 figs., 4 tabs.

Kress, J.D.; Tawa, G.J.; Hay, P.J. [Los Alamos National Lab., NM (United States)] [Los Alamos National Lab., NM (United States); Leung, P.C. [3M Corporation, St. Paul, MN (United States)] [3M Corporation, St. Paul, MN (United States)



Highly sensitive electrochemical aptasensor based on a ligase-assisted exonuclease III-catalyzed degradation reaction.  


In this paper, we have proposed a new electrochemical aptasensor based on a novel ligase-assisted Exo III-catalyzed degradation reaction (LAECDR), which consists of DNA ligase-catalyzed ligation of thrombin-binding aptamer (TBA) with an extension strand (E-strand) and Exo III-catalyzed selective degradation of probe DNA, by using an improved target-induced strand displacement strategy. As a result of LAECDR, methylene blue (MB)-labeled mononucleotides can be released from the 3'-terminal of probe DNA and captured by cucurbit[7]uril-functionalized electrode to induce noticeable electrochemical response. Nevertheless, in the presence of the target protein, thrombin, the TBA that is partially complementary to probe DNA is preferentially binding with the target protein, thereby inhibiting LAECDR from taking place. The remaining intact probe DNA will prevent the terminal-attached MB from approaching to the electrode surface due to strong electrostatic repulsion, so the electrochemical response will be changed by thrombin. By tracing the electrochemical response of adsorbed MB, our aptasensor can exhibit high sensitivity for thrombin detection with a wide linear range from 100 fM to 1 nM and an extremely low detection limit of 33 fM, which can also easily distinguish thrombin in the complex serum samples with high specificity. Therefore, our aptasensor might have great potential in clinical applications in the future. PMID:24786305

Zhao, Jing; Hu, Suisui; Zhong, Weidong; Wu, Jiguang; Shen, Zhongming; Chen, Zhong; Li, Genxi



Metal-catalyzed reductive coupling reactions of organic halides with carbonyl-type compounds.  


Metal-catalyzed reductive coupling reactions of aryl halides and (pseudo)halides with carbonyl-type compounds have undergone an impressive development within the last years. These methodologies have shown to be a powerful alternate strategy, practicality aside, to the use of stoichiometric, well-defined, and, in some cases, air-sensitive organometallic species. In this Minireview, the recent findings in this field are summarized, with particular emphasis on the mechanistic interpretation of the results and future aspects of this area of expertise. PMID:24905555

Moragas, Toni; Correa, Arkaitz; Martin, Ruben



Computational perspective on Pd-catalyzed C-C cross-coupling reaction mechanisms.  


Palladium-catalyzed C-C cross-coupling reactions (Suzuki-Miyaura, Negishi, Stille, Sonogashira, etc.) are among the most useful reactions in modern organic synthesis because of their wide scope and selectivity under mild conditions. The many steps involved and the availability of competing pathways with similar energy barriers cause the mechanism to be quite complicated. In addition, the short-lived intermediates are difficult to detect, making it challenging to fully characterize the mechanism of these reactions using purely experimental techniques. Therefore, computational chemistry has proven crucial for elucidating the mechanism and shaping our current understanding of these processes. This mechanistic elucidation provides an opportunity to further expand these reactions to new substrates and to refine the selectivity of these reactions. During the past decade, we have applied computational chemistry, mostly using density functional theory (DFT), to the study of the mechanism of C-C cross-coupling reactions. This Account summarizes the results of our work, as well as significant contributions from others. Apart from a few studies on the general features of the catalytic cycles that have highlighted the existence of manifold competing pathways, most studies have focused on a specific reaction step, leading to the analysis of the oxidative addition, transmetalation, and reductive elimination steps of these processes. In oxidative addition, computational studies have clarified the connection between coordination number and selectivity. For transmetalation, computation has increased the understanding of different issues for the various named reactions: the role of the base in the Suzuki-Miyaura cross-coupling, the factors distinguishing the cyclic and open mechanisms in the Stille reaction, the identity of the active intermediates in the Negishi cross-coupling, and the different mechanistic alternatives in the Sonogashira reaction. We have also studied the closely related direct arylation process and highlighted the role of an external base as proton abstractor. Finally, we have also rationalized the effect of ligand substitution on the reductive elimination process. Computational chemistry has improved our understanding of palladium-catalyzed cross-coupling processes, allowing us to identify the mechanistic complexity of these reactions and, in a few selected cases, to fully clarify their mechanisms. Modern computational tools can deal with systems of the size and complexity involved in cross-coupling and have a continuing role in solving specific problems in this field. PMID:23848308

García-Melchor, Max; Braga, Ataualpa A C; Lledós, Agustí; Ujaque, Gregori; Maseras, Feliu



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


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. PMID:21090871

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



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


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

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



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


Poly(ethersulfone) (PES) can be modified in a flexible manner using mild, environmentally benign components such as 4-hydroxybenzoic acid and gallic acid, which can be attached to the surface via catalysis by the enzyme laccase. This leads to grafting of mostly linear polymeric chains (for 4-hydroxybenzoic acid, and for gallic acid at low concentration and short modification time) and of networks (for gallic acid at high concentration and long exposure time). The reaction is stopped at a specific time, and the modified surfaces are tested for adsorption of BSA, dextrin and tannin using in-situ reflectometry and AFM imaging. At short modification times, the adsorption of BSA, dextrin and tannin is significantly reduced. However, at longer modification times, the adsorption increases again for both substrates. As the contact angle on modified surfaces at short modification times is reduced (indicative of more hydrophilic surfaces), and keeps the same low values at longer modification times, hydrophilicity is not the only determining factor for the measured differences. At longer modification times, intra-layer reactivity will increase the amount of cross-linking (especially for gallic acid), branching (for 4-hydroxybenzoic acid) and/or collapse of the polymer chains. This leads to more compact layers, which leads to increased protein adsorption. The modifications were shown to have clear potential for reduction of fouling by proteins, polysaccharides, and polyphenols, which could be related to the surface morphology. PMID:22560487

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



Efficient and General Synthesis of 3-Aminoindolines and 3-Aminoindoles via Copper-Catalyzed Three Component Coupling Reaction  

PubMed Central

An efficient three component coupling (TCC) reaction toward a variety of 3-aminoindoline and 3-aminoindole derivatives has been developed. This cascade transformation proceeds via the copper-catalyzed coupling reaction between 2-aminobenzaldehyde, secondary amine, and alkyne leading to propargylamine intermediate, which, under the reaction conditions, undergoes cyclization into the indoline core. The latter, upon treatment with a base, smoothly isomerizes into indole. Alternatively, indole can directly be synthesized in a one-pot sequential reaction. PMID:23620715

Chernyak, Dmitri; Chernyak, Natalia



Efficient and General Synthesis of 3-Aminoindolines and 3-Aminoindoles via Copper-Catalyzed Three Component Coupling Reaction.  


An efficient three component coupling (TCC) reaction toward a variety of 3-aminoindoline and 3-aminoindole derivatives has been developed. This cascade transformation proceeds via the copper-catalyzed coupling reaction between 2-aminobenzaldehyde, secondary amine, and alkyne leading to propargylamine intermediate, which, under the reaction conditions, undergoes cyclization into the indoline core. The latter, upon treatment with a base, smoothly isomerizes into indole. Alternatively, indole can directly be synthesized in a one-pot sequential reaction. PMID:23620715

Chernyak, Dmitri; Chernyak, Natalia; Gevorgyan, Vladimir



MACiE: a database of enzyme reaction mechanisms  

E-print Network

’Boyle1, Peter Murray-Rust1, Janet M. Thornton2 and John B. O. Mitchell1,#1; 1Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK and 2EMBL-EBI, Wellcome Trust Genome... /) contain descriptions of the overall reactions performed by enzymes, accompanied in some cases by a textual or graphical description of the mechansim. MACiE is unique in combining detailed stepwise mechanistic information (including 2D anima- tions), a wide...

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



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


In the transition-metal-catalyzed cross-coupling reactions, the use of the first row transition metals as catalysts is much more appealing than the precious metals owing to the apparent advantages such as cheapness and earth abundance. Within the last two decades, particularly the last five years, explosive interests have been focused on the nickel-catalyzed Suzuki-Miyaura reactions. This has greatly advanced the chemistry of transition-metal-catalyzed cross-coupling reactions. Most notably, a broad range of aryl electrophiles such as phenols, aryl ethers, esters, carbonates, carbamates, sulfamates, phosphates, phosphoramides, phosphonium salts, and fluorides, as well as various alkyl electrophiles, which are conventionally challenging, by applying palladium catalysts can now be coupled efficiently with boron reagents in the presence of nickel catalysts. In this review, we would like to summarize the progress in this reaction. PMID:23460083

Han, Fu-She



Cobalt- versus ruthenium-catalyzed Alder-ene reaction for the synthesis of credneramide A and B.  


The first synthesis of the natural products credneramide A and B was accomplished by utilizing Alder-ene reactions between a terminal alkene and an internal alkyne to generate the rather uncommon 1,4-diene substructure of these compounds. Moreover, two different short linear sequences toward these targets are evaluated using either a cobalt-catalyzed Alder-ene reaction of 1-chloropent-1-yne or a ruthenium-catalyzed Alder-ene reaction of 1-trimethylsilyl-1-pentyne with 5-hexenoic acid derivatives in the key step transformation. In addition, saponification of the primary Alder-ene product derived from the cobalt-catalyzed Alder-ene reaction led to credneric acid, the biological precursor of both natural products. PMID:22568728

Erver, Florian; Hilt, Gerhard



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


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



Three dimensional mapping of the creatine kinase enzyme reaction rate in muscles of the lower leg  

PubMed Central

Phosphorous (31P) magnetization transfer (MT) techniques enable the non-invasive measurement of metabolic turnover rates of important enzyme catalyzed reactions, such as the creatine kinase reaction (CK), a major transducing reaction involving adenosine triphosphate and phosphocreatine. Alteration in the kinetics of the CK reaction rate appears to play a central role in many disease states. In this study, we developed and implemented at ultra-high field (7T), a novel three-dimensional 31P-MT imaging sequence that maps the kinetics of CK in the entire volume of the lower leg at relatively high resolution (0.52 mL voxel size), and within acquisition times that can be tolerated by patients (below 60 min). We tested the sequence on five healthy and two clinically diagnosed type 2-diabetic patients. Overall, we obtained measurements that are in close agreement with measurements reported previously using spectroscopic methods. Importantly, our spatially resolved method allowed us to measure local CK reaction rate constants and metabolic fluxes in individual muscles in healthy subjects. Furthermore, in the case of patients with diabetes, it allowed us to detect variations of the CK rate of different muscles, which would not have been possible using unlocalized MRS methods. The results of this work suggest that 3D-mapping of the CK reaction rates and metabolic fluxes can be achieved in the skeletal muscle in vivo at relatively high spatial resolution and with acquisition times well tolerated by patients. The ability to measure bioenergetics simultaneously in large areas of muscles will bring new insights into possible heterogeneous patterns of muscle metabolism associated with several diseases and serve as a valuable tool for monitoring the efficacy of interventions. PMID:23436474

Parasoglou, Prodromos; Xia, Ding; Chang, Gregory; Convit, Antonio; Regatte, Ravinder R.



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


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



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


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

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



The Palladium-Catalyzed Cross-Coupling Reaction of Phenylboronic Acid with Haloarenes in the Presence of Bases  

Microsoft Academic Search

The transition metal-catalyzed reactions of organometallics with organic halides have been extensively studied to prove a new approach to selective formation of carbon-carbon bonds. Recently, such coupling reactions of haloarenes with aryl magnesium and zinc compounds in the presence of palladium or nickel complexes have been reported for the synthesis of biaryls. Davidson and Triggs have previously reported that arylboronic

N. Miyaura; T. Yanagi; A. Suzuki



Use of isopropyl alcohol as a solvent in Ti(O- iPr) 4-catalyzed Knöevenagel reactions  

Microsoft Academic Search

Knöevenagel reactions of aldehydes and ketones with malononitrile, isopropyl cyanoacetate and diisopropyl malonate catalyzed by Ti(O-i-Pr)4 proceeded smoothly in i-PrOH to give the corresponding reaction products in good to high yield. 3-Substituted coumarins were prepared by the present method.

Kohei Yamashita; Takanori Tanaka; Masahiko Hayashi



Synthesis of functionalized chromans by PnBu3-catalyzed reactions of salicylaldimines and salicylaldehydes with allenic ester.  


P(n)Bu(3)-catalyzed cyclization reactions of salicylaldimines and salicylaldehydes with ethyl 2,3-butadienoate gave the corresponding functionalized chromans in moderate to good yields in THF under mild conditions. The new reaction provides a new method for the synthesis of biologically active chroman products. PMID:21070027

Sun, Yin-Wei; Guan, Xiao-Yang; Shi, Min




PubMed Central

The mechanism of enzyme-inhibitor-substrate reactions has been analyzed from a theoretical standpoint and illustrated by data from the system cholinesterase-physostigmine-acetylcholine. This treatment is by no means limited to a single system but should be generally applicable to others of similar type. Competitive enzyme-inhibitor-substrate systems show the same characteristic "zones of behavior" already demonstrated for non-competitive systems by Straus and Goldstein. These zones, three in number, determine the mathematical function which relates activity of an enzyme to concentration of an added substrate or inhibitor or both. The effects of suboptimal substrate concentration in such systems have been considered, and the errors arising from various common simplifications of the descriptive equations have been pointed out. The zone behavior phenomenon has been shown to be useful in determining the number of molecules of substrate or inhibitor combining reversibly with a single enzyme center. The kinetics of competitive inhibition, dilution effect, combination of inhibitor or substrate with enzyme, and destruction of inhibitor or substrate by enzyme have been analyzed and experimentally verified, and absolute velocity constants have been determined. Theoretical conclusions have been discussed from the standpoint of their physiological significance. Specifically, it has been shown that: 1. The inhibition of cholinesterase by physostigmine is competitive. A single molecule of physostigmine or acetylcholine combines with one center of cholinesterase—n = 1; and the mechanism n = 2 has been. excluded. Numerical values of the constants for this system are as follows: KI = 3.11 x 10–8 k1 (combination) = 8.3 x 105 k2 (dissociation) = 0.026 KS = 1.25 x 10–3 k3 (combination) = 260 k4 (dissociation) = 0.32 2. No definitive value can be assigned to E, the molar concentration of enzyme centers, but in 4.54 per cent dog serum, E < 1.8 x 10–8 (EI' < 0.58). The system therefore operates in (or nearly in) zone A at this concentration. 3. Competitive displacement of inhibitor by substrate and vice versa introduces considerable error in the usual 20 minute determination of the activity of an inhibited enzyme, unless properly corrected for. 4. Dissociation of the enzyme-inhibitor complex on dilution proceeds moderately slowly so that the full corrections for dilution cannot be applied unless time has been allowed for full dissociation. 5. Combination of physostigmine with cholinesterase is slow at all but large concentrations of inhibitor. 6. The destruction of physostigmine or acetylcholine by cholinesterase follows the predicted curve; kD for the destruction of physostigmine is found to be > 0.00182; kD for acetylcholine destruction is > 3500. There is no reason to assume inhibition of destruction by excess substrate or inhibitor. 7. The common assumption that enzymatic activity follows (or nearly follows) a monomolecular course is true only under limited conditions, which have been here defined. It is not valid, as a rule, for the enzymatic destruction of an inhibitor (e.g., physostigmine) and its application to such a case may lead to erroneous conclusions about the reaction mechanism. PMID:19873399

Goldstein, Avram



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



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

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

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



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


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

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



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.



Influence of electron transport proteins on the reactions catalyzed by Fusarium fujikuroi gibberellin monooxygenases.  


The multifunctional cytochrome P450 monooxygenases P450-1 and P450-2 from Fusarium fujikuroi catalyze the formation of GA14 and GA4, respectively, in the gibberellin (GA)-biosynthetic pathway. However, the activity of these enzymes is qualitatively and quantitatively different in mutants lacking the NADPH:cytochrome P450 oxidoreductase (CPR) compared to CPR-containing strains. 3beta-Hydroxylation, a major P450-1 activity in wild-type strains, was strongly decreased in the mutants relative to oxidation at C-6 and C-7, while synthesis of C19-GAs as a result of oxidative cleavage of C-20 by P450-2 was almost absent whereas the C-20 alcohol, aldehyde and carboxylic acid derivatives accumulated. Interaction of the monooxygenases with alternative electron transport proteins could account for these different product distributions. In the absence of CPR, P450-1 activities were NADH-dependent, and stimulated by cytochrome b5 or by added FAD. These properties as well as the decreased efficiency of P450-1 and P450-2 in the mutants are consistent with the participation of cytochrome b5:NADH cytochrome b5 reductase as redox partner of the gibberellin monooxygenases in the absence of CPR. We provide evidence, from either incubations of GA12 (C-20 methyl) with cultures of the mutant suspended in [18O]H2O or maintained under an atmosphere of [18O]O2:N2 (20:80), that GA15 (C-20 alcohol) and GA24 (C-20 aldehyde) are formed directly from dioxygen and not from hydrolysis of covalently enzyme-bound intermediates. Thus these partially oxidized GAs correspond to intermediates of the sequential oxidation of C-20 catalyzed by P450-2. PMID:17920091

Troncoso, Claudia; Cárcamo, José; Hedden, Peter; Tudzynski, Bettina; Rojas, M Cecilia



Rh(I)-catalyzed carbonylative cyclization reactions of alkynes with 2-bromophenylboronic acids leading to indenones.  


The Rh-catalyzed reaction of alkynes with 2-bromophenylboronic acids involves carbonylative cyclization to give indenones. The key steps in the reaction involve the addition of an arylrhodium(I) species to an alkyne and the oxidative addition of C-Br bonds on the adjacent phenyl ring to give vinylrhodium(I) species II. The regioselectivity depends on both the electronic and the steric nature of the substituents on the alkynes. A bulky group and an electron-withdrawing group favor the -position of indenones. In the case of silyl- or ester-substituted alkynes, the regioselectivity is extremely high. The selectivity increases in the order SiMe3 > COOR > aryl > alkyl. The reaction of norbornene with 2-bromophenylboronic acids under 1 atm of CO gives the corresponding indanone derivative. The reaction of alkynes with 2-bromophenylboronic acids under nitrogen gives naphthalene derivatives, in which two molecules of alkynes are incorporated. A vinylrhodium complex similar to II can also be generated by a different route by employing 2-bromophenyl(trimethylsilyl)acetylene and arylboronic acids in the presence of Rh(I) complex as the catalyst, resulting in the formation of indenones. The reaction of 1-(2-bromophenyl)-hept-2-yn-1-one with PhB(OH)2 in the presence of Rh(I) complex also resulted in carbonylative cyclization to give an indan-1,3-dione derivative. PMID:17417848

Harada, Yasuyuki; Nakanishi, Jun; Fujihara, Hirokazu; Tobisu, Mamoru; Fukumoto, Yoshiya; Chatani, Naoto



Alkyne-azide click reaction catalyzed by metallic copper under ultrasound.  


This protocol is for the ultrasound (US)-assisted 1,3-dipolar cycloaddition reaction of azides and alkynes using metallic copper (Cu) as the catalyst. The azido group is a willing participant in this kind of organic reaction and its coupling with alkynes is substantially improved in the presence of Cu(I). This protocol does not require additional ligands and proceeds with excellent yields. The Cu-catalyzed azide-alkyne cycloaddition (CuAAC) is generally recognized as the most striking example of 'click chemistry'. Reactions involving metals represent the favorite domain of sonochemistry because US favors mechanical depassivation and enhances both mass transfer and electron transfer from the metal to the organic acceptor. The reaction rate increases still further when simultaneous US and microwave irradiation are applied. The US-assisted click synthesis has been applied for the preparation of a wide range of 1,4-disubstituted 1,2,3-triazole derivatives starting both from small molecules and oligomers such as cyclodextrins (CDs). Using this efficient and greener protocol, all the adducts can be synthesized in 2-4 h (including work-up and excluding characterization). Click chemistry has been shown to be able to directly link chemistry to biology, thus becoming a true interdisciplinary reaction with extremely wide applicability. PMID:20203675

Cintas, Pedro; Barge, Alessandro; Tagliapietra, Silvia; Boffa, Luisa; Cravotto, Giancarlo



X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction.  


Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis (PPATMt) in the apo form and in complex with the substrate ATP were determined at 1.62 and 1.70?Å resolution, respectively, using crystals grown in microgravity by the counter-diffusion method. The ATP molecule of the PPATMt-ATP complex was located with full occupancy in the active-site cavity. Comparison of the solved structures with previously determined structures of PPATMt complexed with the reaction product dephosphocoenzyme A (dPCoA) and the feedback inhibitor coenzyme A (CoA) was performed using superposition on C(?) atoms. The peculiarities of the arrangement of the ligands in the active-site cavity of PPATMt are described. The conformational states of the PPAT molecule in the consequent steps of the catalyzed reaction in the apo enzyme and the enzyme-substrate and enzyme-product complexes are characterized. It is shown that the binding of ATP and dPCoA induces the rearrangement of a short part of the polypeptide chain restricting the active-site cavity in the subunits of the hexameric enzyme molecule. The changes in the quaternary structure caused by this rearrangement are accompanied by a variation of the size of the inner water-filled channel which crosses the PPAT molecule along the threefold axis of the hexamer. The molecular mechanism of the observed changes is described. PMID:23151631

Timofeev, Vladimir; Smirnova, Evgenia; Chupova, Larisa; Esipov, Roman; Kuranova, Inna



Palladium-Catalyzed Aryl Amination Reactions of 6-Bromo- and 6-Chloropurine Nucleosides  

PubMed Central

Palladium-catalyzed C–N bond forming reactions of 6-bromo- as well as 6-chloropurine ribonucleosides and the 2’-deoxy analogues with aryl amines are described. Efficient conversions were observed with Pd(OAc)2/Xantphos/Cs2CO3, in PhMe at 100 °C. Reactions of the bromo nucleoside derivatives could be conducted at a lowered catalytic loading (5 mol % Pd(OAc)2/7.5 mol % Xantphos), whereas good product yields were obtained with a higher catalyst load (10 mol % Pd(OAc)2/15 mol % Xantphos) when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxyls appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of aryl amines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6-chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates. PMID:21818182

Thomson, Paul F.; Lagisetty, Pallavi; Balzarini, Jan; De Clercq, Erik; Lakshman, Mahesh K.



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


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



Enzyme-Catalyzed modification of oilseed materials to produce eco-friendly products  

Microsoft Academic Search

Novel products produced from seed oil materials (TAG, phospholipids, and minor components such as tocopherols, sterols, stanols,\\u000a and fatty acyl esters of the latter two) by enzyme-mediated purification or chemical modification are reviewed. The primary\\u000a focus is on “value-added products” of current and potential use (particularly in the food, cosmetics, and pharmaceutical industries)\\u000a that require the selectivity of enzymes and

Douglas G. Hayes



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


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

Woehl, E; Dunn, M F



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))



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



Distinct Reactions Catalyzed by Bacterial and Yeast trans-Aconitate Methyltransferases  

E-print Network

-aconitate methyltransferase from the bacterium Escherichia coli catalyzes the monomethyl esterification of trans-aconitate methyltransferase also catalyzes the monomethyl esterification of trans-aconitate, we identify that the methylation

Clarke, Steven


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.



Structural Characterization of a 140 degrees 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 PPi, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140 to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

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



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.



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.



Negative Resist for i-Line Lithography Utilizing Acid Catalyzed Silanol-Condensation Reaction  

NASA Astrophysics Data System (ADS)

Negative resist systems composed of a novolak resin, diphenylsilanediol (Ph2Si(OH)2) and an acid generator are investigated for i-line lithography. The reaction in this resist system is based on an acid-catalyzed condensation reaction; the acid produced in the exposed area induces a condensation reaction of Ph2Si(OH)2 during post-exposure baking. The condensation product, siloxane, acts as an aqueous-base dissolution inhibitor, while silanol compounds in unexposed areas work as dissolution accelerators. The resist composed of a novolak resin, Ph2Si(OH)2 and 2-naphthoylmethyl-tetramethylenesulfonium hexafluoroantimonate (NMTMS-SbF6) shows a sensitivity of about 200 mJ/cm2 at 365 nm. This sensitivity is lower than that at 248 nm when triphenylsulfonium triflate (Ph3S+OTf-) is used as an acid generator, which can be ascribed to the low quantum yield of acid generation from NMTMS-SbF6. Using this resist, 0.3 ?m space patterns with 1 ?m film thickness were obtained by combining an i-line stepper with a phase-shifting mask.

Hayashi, Nobuaki; Tadano, Keiko; Tanaka, Toshihiko; Shiraishi, Hiroshi; Ueno, Takumi; Iwayanagi, Takao



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


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



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

SciTech Connect

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

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



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.



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....


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


The solid-phase version of the Pd-catalyzed Hiyama reaction between a variety of aryltriethoxysilanes and immobilized aryl halides was developed. Smooth cross-coupling was achieved to afford the corresponding biaryl products in moderate to excellent yields. The described protocol would be particularly useful for the construction of 4'-substituted 1,1'-biphenyl derivatives. PMID:24689507

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



Efficient synthesis of eight-membered nitrogen heterocycles from o-propargylic oximes by rhodium-catalyzed cascade reactions.  


Azocine derivatives were successfully synthesized from O-propargylic oximes by means of a Rh-catalyzed 2,3-rearrangement/heterocyclization cascade reaction. Moreover, the chirality of the substrate was maintained throughout the cascade process to afford the corresponding optically active azocines. PMID:25044489

Nakamura, Itaru; Sato, Yoshinori; Takeda, Keisuke; Terada, Masahiro



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: 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


Pd-Catalyzed Suzuki-Miyaura Cross-Coupling Reactions Between Sulfamates and Potassium Boc-Protected Aminomethyltrifluoroborates  

PubMed Central

Sulfamates were studied as the electrophilic partners in the palladium-catalyzed Suzuki–Miyaura cross-coupling reaction with potassium Boc-protected primary and secondary aminomethyltrifluoroborates. A broad range of substrates was successfully coupled to provide the desired products. Complex molecules containing a new carbon-carbon bond and an aminomethyl moiety could be prepared through this developed method. PMID:23646846

Molander, Gary A.; Shin, Inji



Pd-catalyzed Suzuki-Miyaura cross-coupling reactions between sulfamates and potassium Boc-protected aminomethyltrifluoroborates.  


Sulfamates were studied as the electrophilic partners in the palladium-catalyzed Suzuki-Miyaura cross-coupling reaction with potassium Boc-protected primary and secondary aminomethyltrifluoroborates. A broad range of substrates was successfully coupled to provide the desired products. Complex molecules containing a new carbon-carbon bond and an aminomethyl moiety could be prepared through this developed method. PMID:23646846

Molander, Gary A; Shin, Inji



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

E-print Network

on catalysis with cationic gold(I) complexes have been demon- strated, examples of ligand variation as a meansLigand-Controlled Access to [4 + 2] and [4 + 3] Cycloadditions in Gold-Catalyzed Reactions to LAu(I)X complexes as catalysts because of the potential of controlling reactivity2

Toste, Dean


N-Vinylpyridinium and -ammonium Tetrafluoroborate Salts: New Electrophilic Coupling Partners for Pd(0)-Catalyzed Suzuki Cross-Coupling Reactions  

PubMed Central

N-Vinylpyridinium and -trialkylammonium tetrafluoroborate salts represent a new class of electrophilic coupling partner for Pd(0)-catalyzed Suzuki cross-coupling reactions and give very good to excellent yields of products with a wide range of boronic acids. The salts are easily prepared from activated acetylenes and pyridinium or trialkylammonium tetrafluoroborates to form crystalline, air-stable, and nonhygroscopic crystals. PMID:17253706

Buszek, Keith R.; Brown, Neil



New Chiral Sulfoxide Ligands Possessing a Phosphano or Phosphanoamino Functionality in Palladium-Catalyzed Asymmetric Allylic Nucleophilic Substitution Reactions  

Microsoft Academic Search

New chiral sulfoxide ligands possessing a phosphano or phosphanoamino functionality as an alternative coordinating element were developed, and their usefulness was demonstrated by applying them to palladium-catalyzed asymmetric allylic nucleophilic substitution reactions. The structure of the catalyst precursor coordinated by the chiral phosphino sulfoxide was determined by X-ray crystallographic analysis. The possible mechanism for the asymmetric induction using these chiral

Kunio Hiroi; Yoshio Suzuki; Ikuko Abe; Ryoko Kawagishi



Clustering and optimal arrangement of enzymes in reaction-diffusion systems  

E-print Network

Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

Alexander Buchner; Filipe Tostevin; Ulrich Gerland



Choline Monooxygenase, an Unusual Iron-Sulfur Enzyme Catalyzing the First Step of Glycine Betaine Synthesis in Plants: Prosthetic Group Characterization and cDNA Cloning  

Microsoft Academic Search

Plants synthesize the osmoprotectant glycine betaine via the route choline --> betaine aldehyde --> glycine betaine. In spinach, the first step is catalyzed by choline monooxygenase (CMO), a ferredoxin-dependent stromal enzyme that has been hypothesized to be an oligomer of identical subunits and to be an Fe-S protein. Analysis by HPLC and matrix-assisted laser desorption ionization MS confirmed that native

Bala Rathinasabapathi; Michael Burnet; Brenda L. Russell; Douglas A. Gage; Pao-Chi Liao; Gordon J. Nye; Paul Scott; John H. Golbeck; Andrew D. Hanson



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


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



Critical role of DNA intercalation in enzyme-catalyzed nucleotide flipping  

PubMed Central

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.



Fluorogenic probes using 4-substituted-2-nitrobenzenesulfonyl derivatives as caging groups for the analysis of human glutathione transferase catalyzed reactions.  


We have synthesized a series of 4-substituted-2-nitrobenzene-sulfonyl compounds for caged fluorogenic probes and conducted a Hammett plot analysis using the steady-state kinetic parameters. The results revealed that the glutathione transferase (GST) alpha catalyzed reaction was dependent on the ? value in the same way as the non-enzymatic reaction, whereas the dependence of the ? value of the GST mu and pi was not as pronounced as that of GST alpha. PMID:24151635

Shibata, Aya; Nakano, Yukiko; Ito, Mika; Araki, Mika; Zhang, Jie; Yoshida, Yasuhiko; Shuto, Satoshi; Mannervik, Bengt; Morgenstern, Ralf; Mogenstern, Ralf; Ito, Yoshihiro; Abe, Hiroshi



Gold-catalyzed oxa-Povarov reactions for the synthesis of highly substituted dihydrobenzopyrans from diaryloxymethylarenes and olefins.  


Oxa-Povarov reactions involving readily available diaryloxymethylarenes and aryl-substituted alkenes are reported. Their [4+2] cycloadditions were efficiently catalyzed by IPrAuSbF6 (IPr=1,3-bis(diisopropylphenyl)imidazol-2-ylidene) with high diastereoselectivity. Product analysis revealed that the reactions likely proceed by a stepwise ionic mechanism, because both E- and Z-configured ?-methylstyrene gave the same cycloadducts in the same proportions. PMID:25042462

Pagar, Vinayak Vishnu; Tseng, Chang-Chin; Liu, Rai-Shung



The total synthesis of the crinine alkaloid hamayne via a Pd[0]-catalyzed intramolecular alder-ene reaction.  


The racemic form of the title alkaloid, 1, has been prepared in 13 steps from the ring-fused gem-dibromocyclopropane 7. Key transformations include the thermally induced electrocyclic ring-opening of compound 7, the Pd[0]-catalyzed intramolecular Alder-ene (IMAE) reaction of the derived sulfonamide (±)-12, and the conversion of the ensuing C-3a-arylhexahydroindole (±)-16 into (±)-hamayne via a Pictet-Spengler reaction. PMID:21970722

Petit, Laurent; Banwell, Martin G; Willis, Anthony C



Size exclusion chromatography for the quantitative profiling of the enzyme-catalyzed hydrolysis of Xylo-oligosaccharides.  


High-performance size exclusion chromatography (HPSEC) is a widely used method for the qualitative profiling of oligosaccharide mixtures, including, for example, enzymatic hydrolysates of plant biomass materials. A novel method employing HPSEC for the quantitative analytical profiling of the progress of enzymatic hydrolysis of different xylan substrates was developed. The method relies on dividing the HPSEC elution profiles into fixed time intervals and utilizing the linear refractive index response (area under the curve) of defined standard compounds. To obtain optimal HPSEC profiles, the method was designed using 0.1 M CH(3)COONa both in the mobile phase and as the sample solution matrix, after systematic evaluation of the influence of the mobile phase, including the type, ionic strength, and pH, on the refractive index detector response. A time study of the enzyme-catalyzed hydrolysis of birchwood xylan and wheat bran by a Bacillus subtilis XynA xylanase (GH 11) was used as an example to demonstrate the workability of the HPSEC method for obtaining progress curves describing the evolution in the product profile during enzyme catalysis. PMID:19994888

Rasmussen, Louise E; Meyer, Anne S



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



Lipase-catalyzed optical resolution of racemic naproxen in biphasic enzyme membrane reactors  

Microsoft Academic Search

A lipase-immobilized membrane reactor was applied for the optical resolution of racemic naproxen, and the effect of various operation conditions on reaction rate and enantio-selectivity was examined. The membrane reactor consisted of an organic phase dissolving naproxen ester, a lipase-immobilized polyamide membrane, and an aqueous phase to recover the reaction products. The lipase immobilized in the membrane reactor showed a

Keiji Sakaki; Lidietta Giorno; Enrico Drioli



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



Computational study of gold-catalyzed homo- and cross-coupling reactions.  


The role of gold as the organizing metal in homo- and cross-coupling reactions is explored in this paper combining DFT calculations with QTAIM, NBO, and the energetic span model analysis. For the gold(III) complex 7, a key intermediate in the experimental oxidative coupling scheme by Zhang et al., we describe the mechanisms corresponding to a cross-coupling after transmetalation with boron compounds and to a homocoupling after transmetalation with the original gold(I) complex 6, a new example of dual role of this metal in homogeneous catalysis. We predict for the first path a two-step transmetalation with a low energy rate-limiting step characterized by a four-center transition structure, where fluorine plays an essential role, followed by a reductive elimination where the C-C bond formation is coupled to the departure of fluorine from the gold center. The homocoupling path follows a similar mechanism, with a two-step transmetalation with interesting changes in bonding around the Au(I) center and a rate-limiting reductive elimination. Our findings on the competition between mechanisms, and the effect of ligands and solvent, agree with the experimental results and provide new insights into the mechanism of gold-catalyzed cross-coupling reactions. PMID:23597253

Nieto Faza, Olalla; Silva López, Carlos



Palladium-catalyzed ?-arylation of zinc enolates of esters: reaction conditions and substrate scope.  


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

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



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

PubMed Central

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

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



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

SciTech Connect

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

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



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; Bala, Piotr; Geller, Maciej; Grochowski, Pawel



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


Iodine was demonstrated to be an efficient catalyst for disproportionation of aryl-substituted ethers under solvent-free reaction conditions. Variously substituted 1,1,1',1'-tetraaryldimethyl ethers were transformed into the corresponding diarylketone and diarylmethane derivatives. I2-catalyzed transformation of 4-methoxyphenyl substituted ethers yielded mono- and dialkylated Friedel-Crafts products as well. Treatment of trityl alkyl and trityl benzyl ethers with a catalytic amount of iodine produced triphenylmethane and the corresponding aldehydes and ketones. The electron-donating substituents facilitated the reaction, while the electron-withdrawing groups retarded it; the difference in reactivity is not very high. Such an observation may be in favour of hydride transfer, predominantly from the less electron rich side of the ether with more stable carbocation formation. With the isotopic studies it was established that a substantial portion of the C-H bond scission took place in the rate-determining step, while the carbonyl oxygen atom originated from the starting ether, and not from the air. The transformation took place under air and under argon, and HI was not a functioning catalyst. PMID:23389585

Jereb, Marjan; Vraži?, Dejan



Palladium-catalyzed cascade reaction of alpha,beta-unsaturated sulfones with aryl iodides.  


Unlike traditionally used acyclic 1,2-disubstituted alkenes, the reaction of alpha,beta-unsaturated phenyl sulfones with aryl iodides under Heck reaction conditions (Pd(OAc)(2) as catalyst, Ag(2)CO(3) as base in DMF at 120 (0)C) takes place mainly by a cascade process, involving one unit of the alkene and three units of the aryl iodide, to afford a substituted 9-phenylsulfonyl-9,10-dihydrophenanthrene. The dominant formation of this 3:1 coupling product, instead of the Heck trisubstituted olefin, shows that aromatic C-H bond activation processes can compete with the usually fast syn beta-hydrogen elimination step in the Heck arylation of an acyclic olefin. The structural scope of this palladium-catalyzed cascade arylation of alpha,beta-unsaturated sulfones has proved to be wide with regard to substitution at the beta-position (alkyl, aryl, or alkenyl substitution), substitution at the sulfone unit (alkyl or phenyl sulfones), and configuration at the CdoublebondC bond (trans or cis). Moreover, although less favored than in the case of the arylation of alpha,beta-unsaturated sulfones, similarly substituted 9,10-dihydrophenanthrenes have also been obtained in the case of alpha,beta-unsaturated phosphine oxides and alpha,beta-unsaturated phosphonate esters. A Pd(0)-Pd(II)-Pd(IV) mechanistic pathway involving the successive formation of highly electrophilic sigma-alkylpalladium intermediates and palladacycles is proposed for this multicomponent arylation. PMID:12658648

Mauleón, Pablo; Núñez, Angel A; Alonso, Inés; Carretero, Juan C



Structural Insights into E1-Catalyzed Ubiquitin Activation and Transfer to Conjugating Enzymes  

SciTech Connect

Ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are conjugated to their targets by specific cascades involving three classes of enzymes, E1, E2, and E3. Each E1 adenylates the C terminus of its cognate Ubl, forms a E1{approx}Ubl thioester intermediate, and ultimately generates a thioester-linked E2{approx}Ubl product. We have determined the crystal structure of yeast Uba1, revealing a modular architecture with individual domains primarily mediating these specific activities. The negatively charged C-terminal ubiquitin-fold domain (UFD) is primed for binding of E2s and recognizes their positively charged first a helix via electrostatic interactions. In addition, a mobile loop from the domain harboring the E1 catalytic cysteine contributes to E2 binding. Significant, experimentally observed motions in the UFD around a hinge in the linker connecting this domain to the rest of the enzyme suggest a conformation-dependent mechanism for the transthioesterification function of Uba1; however, this mechanism clearly differs from that of other E1 enzymes.

Lee,I.; Schindelin, H.



Fundamental Reaction Pathways for Cytochrome P450-catalyzed 5?-Hydroxylation and N-Demethylation of Nicotine  

PubMed Central

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

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



Precipitation of enzyme-catalyzed phenol oxidative coupling products: Background ion and pH effects  

Microsoft Academic Search

The effects of solution pH and background ion types and concentrations on the precipitation of polymeric products generated in the catalytically facilitated oxidative coupling of phenol were investigated systematically. The coupling reactions mediated by horseradish peroxidase were carried out under a specific predetermined experimental condition. Acids, bases, and\\/or selected salts of ions having different valences were then added to the

Qingguo Huang; Jixin Tang; Walter J. Weber



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


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

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



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.  


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



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)




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.


Mechanism and stereochemical course at phosphorus of the reaction catalyzed by a bacterial phosphotriesterase  

SciTech Connect

The reaction mechanism for the phosphotriesterase from Pseudomonas diminuta has been examined. When paraoxon (diethyl 4-nitrophenyl phosphate) is hydrolyzed by this enzyme in oxygen-18-labeled water, the oxygen-18 label is found exclusively in the diethyl phosphate product. The absolute configurations for the (+) and (-) enantiomers of O-ethyl phenylphosphonothioic acid have been determined by X-ray diffraction structural determination of the individual crystalline 1-phenylethylamine salts. The (+) enantiomer of the free acid corresponds to the R/sub P/ configuration. The R/sub P/ enantiomer of O-ethyl phenylphosphonothioic acid has been converted to the S/sub P/ enantiomer of EPN (O-ethyl O-(4-nitrophenyl) phenylphosphonothioate). (S/sub P/)-EPN is hydrolyzed by the phosphotriesterase to the S/sub P/ enantiomer of O-ethyl phenylphosphonothioic acid. The enzymatic reaction therefore proceeds with inversion of configuration. These results have been interpreted as an indication of a single in-line displacement by an activated water molecule directly at the phosphorus center of the phosphotriester substrate. (R/sub P/)-EPN is not hydrolyzed by the enzyme at an appreciable rate.

Lewis, V.E.; Donarski, W.J.; Wild, J.R.; Raushel, F.M.



Relative rates of various steps of NO–CH 4–O 2 reaction catalyzed by Pd\\/H-ZSM-5  

Microsoft Academic Search

Reaction mechanism of the reduction of nitrogen monoxide by methane in an oxygen excess atmosphere (NO–CH4–O2 reaction) catalyzed by Pd\\/H-ZSM-5 has been studied at 623–703K in the absence of water vapor, in comparison with the mechanism for Co-ZSM-5. Kinetic isotope effect for the N2 formation in NO–CH4–O2 vs. NO–CD4–O2 reactions was 1.65 at 673K and decreased with a decrease in

Hidenaga Kato; Chikafumi Yokoyama; Makoto Misono



Enzyme catalyzed synthesis of structured phospholipids with conjugated linoleic acid and plant sterols  

E-print Network

. I would like to thank Dr. Huanbiao Mo for the study of cancer cells. I would like to thank Dr. Ronald MacFarlane and Dr. Zachlyn Farwig for mass spectroscopic analysis of samples and suggestions to identify my new reaction compounds. I also............................................................. 68 18 Suppression of murine B16 melanoma skin tumor cells by CLA-PL................... 87 19 Suppression of Caco-2 colon cancer cells by CLA isomers................................. 87 20 Examples of different dosage forms of plant sterols...

Hossen, Md Monjur



Ruthenium-catalyzed ?-(hetero)arylation of saturated cyclic amines: reaction scope and mechanism.  


Transition-metal-catalyzed sp(3) C-H activation has emerged as a powerful approach to functionalize saturated cyclic amines. Our group recently disclosed a direct catalytic arylation reaction of piperidines at the ? position to the nitrogen atom. 1-(Pyridin-2-yl)piperidine could be smoothly ?-arylated if treated with an arylboronic ester in the presence of a catalytic amount of [Ru3(CO)12] and one equivalent of 3-ethyl-3-pentanol. A systematic study on the substrate and reagent scope of this transformation is disclosed in this paper. The effect of substitution on both the piperidine ring and the arylboronic ester has been investigated. Smaller (pyrrolidine) and larger (azepane) saturated ring systems, as well as benzoannulated derivatives, were found to be compatible substrates with the ?-arylation protocol. The successful use of a variety of heteroarylboronic esters as coupling partners further proved the power of this direct functionalization method. Mechanistic studies have allowed for a better understanding of the catalytic cycle of this remarkable transformation featuring an unprecedented direct transmetalation on a Ru(II)-H species. PMID:23780756

Peschiulli, Aldo; Smout, Veerle; Storr, Thomas E; Mitchell, Emily A; Eliáš, Zden?k; Herrebout, Wouter; Berthelot, Didier; Meerpoel, Lieven; Maes, Bert U W



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


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



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

SciTech Connect

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

Bhushan, Bharat [Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Que., H4P 2R2 (Canada); Halasz, Annamaria [Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Que., H4P 2R2 (Canada); Hawari, Jalal [Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Que., H4P 2R2 (Canada)]. E-mail:



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


A dehydrogenase from Clostridium sp. EDB2 and a diaphorase from Clostridium kluyveri were reacted with CL-20 to gain insights into the enzyme-catalyzed hydride transfer to CL-20, and the enzyme's stereo-specificity for either pro-R or pro-S hydrogens of NAD(P)H. Both enzymes biotransformed CL-20 at rates of 18.5 and 24nmol/h/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated product with a molecular weight of 393Da. In enzyme kinetics studies using reduced deuterated pyridine nucleotides, we found a kinetic deuterium isotopic effect of 2-fold on CL-20 biotransformation rate using dehydrogenase enzyme against (R)NADD as a hydride-source compared to either (S)NADD or NADH. Whereas, in case of diaphorase, the kinetic deuterium isotopic effect of about 1.5-fold was observed on CL-20 biotransformation rate using (R)NADPD as hydride-source. In a comparative study with LC-MS, using deuterated and non-deuterated NAD(P)H, we found a positive mass-shift of 1Da in the N-denitrohydrogenated product suggesting the involvement of a deuteride (D(-)) transfer from NAD(P)D. The present study thus revealed that both dehydrogenase and diaphorase enzymes from the two Clostridium species catalyzed a hydride transfer to CL-20 and showed stereo-specificity for pro-R hydrogen of NAD(P)H. PMID:16225844

Bhushan, Bharat; Halasz, Annamaria; Hawari, Jalal



Rare earth perfluorooctanoate [RE(PFO) 3] catalyzed one-pot Mannich reaction: three component synthesis of ?-amino carbonyl compounds  

Microsoft Academic Search

Mannich reaction of acetophenone, aldehydes and aromatic amines catalyzed efficiently by RE(PFO)3 was described firstly, which carried out smoothly in high yields with three component one-pot method. Furthermore, it was found these catalysts were completely recovered and reused without loss of their catalytic activities and are thus environmentally conscious, and this procedure is a new choice to synthesis ?-aminocarbonyl compounds.

Limin Wang; Jianwei Han; Jia Sheng; He Tian; Zhaoyu Fan



The gilded edge in acetylenic scaffolding: pd-catalyzed cross-coupling reactions of phosphine-gold(I) oligoynyl complexes.  


Stable bis(gold(I) alkynyl) complexes of tetraethynylethene (TEE) derivatives were readily prepared and employed in Sonogashira-like palladium-catalyzed phosphine-gold(I) halide elimination reactions with aryl iodides and redox-active tetrathiafulvalene (TTF) mono- and bisiodides. This presents a particularly convenient method for the preparation of symmetrical and asymmetrical tetrathiafulvalene (TTF)-fused radiaannulenes in good yields. PMID:25007357

Mazzanti, Virginia; Jiang, Huixin; Gotfredsen, Henrik; Morsing, Thorbjørn J; Parker, Christian R; Nielsen, Mogens Brøndsted



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



Organic reactions catalyzed by insolubilized enzymes. Part III. Synthesis of peptides catalyzed by ?-chymotrypsin immobilized on graft copolymers  

Microsoft Academic Search

?-Chymotrypsin (?-CT) has been covalently immobilized on polyethylene\\/2-hydroxyethyl methacrylate (PE\\/HEMA) graft copolymers, with loadings of 33–87 mg of immobilized protein\\/g copolymer. These enzymatic derivatives have been used in the kinetically controlled synthesis of dipeptides. The influence of the enzymatic loading, grafting and hydrolysis degree of the supports on the synthesis of the model dipeptide Bz-l-Tyr-l-Leu-NH2 is discussed. Organic solvents with

Andres R. Alcantara; M. Helena Gil; A. Jorge Guiomar; M. Trinidad Lopez-Belmonte; Manuela C. M. Sobral; Carlos Torres; Jose V. Sinisterra



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


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



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.



Interfacial electric field effects on a carbene reaction catalyzed by Rh porphyrins.  


An intramolecular reaction catalyzed by Rh porphyrins was studied in the presence of interfacial electric fields. 1-Diazo-3,3-dimethyl-5-phenylhex-5-en-2-one (2) reacts with Rh porphyrins via a putative carbenoid intermediate to form cyclopropanation product 3,3-dimethyl-5-phenylbicyclo[3.1.0]hexan-2-one (3) and insertion product 3,3-dimethyl-2,3-dihydro-[1,1'-biphenyl]-4(1H)-one (4). To study this reaction in the presence of an interfacial electric field, Si electrodes coated with thin films of insulating dielectric layers were used as the opposing walls of a reaction vessel, and Rh porphyrin catalysts were localized to the dielectric-electrolyte interface. The charge density was varied at the interface by changing the voltage across the two electrodes. The product ratio was analyzed as a function of the applied voltage and the surface chemistry of the dielectric layer. In the absence of an applied voltage, the ratio of 3:4 was approximately 10:1. With a TiO2 surface, application of a voltage induced a Rh porphyrin-TiO2 interaction that resulted in an increase in the 3:4 ratio to a maximum in which 4 was nearly completely suppressed (>100:1). With an Al2O3 surface or an alkylphosphonate-coated surface, the voltage caused a decrease in the 3:4 ratio, with a maximum effect of lowering the ratio to 1:2. The voltage-induced decrease in the 3:4 ratio in the absence of TiO2 was consistent with a field-dipole effect that changed the difference in activation energies for the product-determining step to favor product 4. Effects were observed for porphyrin catalysts localized to the electrode-electrolyte interface either through covalent attachment or surface adsorption, enabling the selectivity to be controlled with unfunctionalized Rh porphyrins. The magnitude of the selectivity change was limited by the maximum interfacial charge density that could be attained before dielectric breakdown. PMID:23837635

Gorin, Craig F; Beh, Eugene S; Bui, Quan M; Dick, Graham R; Kanan, Matthew W



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


Fructosamines, also known as Amadori products, are formed by the condensation of glucose with the amino group of amino acids or proteins. These compounds are precursors of advanced glycation end products (AGEs) that can be formed either endogenously during aging and diabetes, and exogenously in heat-processed food. The negative effects of dietary AGEs on human health as well as their negative impact on the quality of dairy products have been widely described, therefore specific tools able to prevent the formation of glycation products are needed. Two fructosamine oxidase enzymes isolated from Aspergillus sp. namely, Faox I and Faox II catalyze the oxidative deglycation of Amadori products representing a potential tool for inhibiting the Maillard reaction in dairy products. In this paper, the ability of recombinant Faox I and II in limiting the formation of carboxy-methyl lysine (CML) and protein-bound hydroxymethyl furfurol (b-HMF) in a commercial UHT low lactose milk and a beta-lactoglobulin (?-LG) glucose model system was investigated. Results show a consistent reduction of CML and b-HMF under all conditions. Faox effects were particularly evident on b-HMF formation in low lactose commercial milk. Peptide analysis of the ?-LG glucose system identified some peptides, derived from cyanogen bromide hydrolysis, as suitable candidates to monitor Faox action in milk-based products. All in all data suggested that non-enzymatic reactions in dairy products might be strongly reduced by implementing Faox enzymes. PMID:23604465

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



Examining the importance of dynamics, barrier compression and hydrogen tunnelling in enzyme catalysed reactions  

Microsoft Academic Search

Nuclear quantum mechanical tunnelling 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 semiclassical limit. Other experimental evidence for tunnelling, and the potential role of promoting vibrations that transiently compress the reaction barrier, is more indirect, being derived from

Sam Hay; Nigel S. Scrutton



Stimulation of dihydroxyacetone and glycerol kinase activity in Streptococcus faecalis by phosphoenolpyruvate-dependent phosphorylation catalyzed by enzyme I and HPr of the phosphotransferase systems  

Microsoft Academic Search

Recently a report was given of the phosphoenolpyruvate (PEP)-dependent phosphorylation of a 55-kilodalton protein of Streptococus faecalis catalyzed by enzyme I and histidine-containing protein (HPr) of the phosphotransferase system. The purified 55-kilodalton protein was found to exhibit dihydroxyacetone kinase activity. Glycerol was six times more slowly phosphorylated than dihydroxyacetone. The K\\/sub m\\/s were found to 0.7 mM for ATP, 0.45

J. Deutscher; H. Sauerwald



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.


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.



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


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


Efficient Access to Substituted Silafluorenes by Nickel-Catalyzed Reactions of Biphenylenes with Et2 SiH2.  


The reaction of biphenylene (1) with Et2 SiH2 in the presence of [Ni(PPhMe2 )4 ] results in the formation of a mixture of 2-diethylhydrosilylbiphenyl [2(Et2 HSi)] and 9,9,-diethyl-9-silafluorene (3). Silafluorene 3 was isolated in 37.5?% and 2(Et2 HSi) 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 Et2 SiH2 and 1-methylbiphenylene. By contrast, no selectivity could be found in the Ni-catalyzed reaction between Et2 SiH2 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



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


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

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



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



Photoelectrochemical Biosensor Using Enzyme-Catalyzed in Situ Propagation of CdS Quantum Dots on Graphene Oxide.  


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



Pathway profiling in Mycobacterium tuberculosis: elucidation of cholesterol-derived catabolite and enzymes that catalyze its metabolism.  


Mycobacterium tuberculosis, the bacterium that causes tuberculosis, imports and metabolizes host cholesterol during infection. This ability is important in the chronic phase of infection. Here we investigate the role of the intracellular growth operon (igr), which has previously been identified as having a cholesterol-sensitive phenotype in vitro and which is important for intracellular growth of the mycobacteria. We have employed isotopically labeled low density lipoproteins containing either [1,7,15,22,26-(14)C]cholesterol or [1,7,15,22,26-(13)C]cholesterol and high resolution LC/MS as tools to profile the cholesterol-derived metabolome of an igr operon-disrupted mutant (?igr) of M. tuberculosis. A partially metabolized cholesterol species accumulated in the ?igr knock-out strain that was absent in the complemented and parental wild-type strains. Structural elucidation by multidimensional 1H and 13C NMR spectroscopy revealed the accumulated metabolite to be methyl 1?-(2'-propanoate)-3a?-H-4?-(3'-propanoic acid)-7a?-methylhexahydro-5-indanone. Heterologously expressed and purified FadE28-FadE29, an acyl-CoA dehydrogenase encoded by the igr operon, catalyzes the dehydrogenation of 2'-propanoyl-CoA ester side chains in substrates with structures analogous to the characterized metabolite. Based on the structure of the isolated metabolite, enzyme activity, and bioinformatic annotations, we assign the primary function of the igr operon to be degradation of the 2'-propanoate side chain. Therefore, the igr operon is necessary to completely metabolize the side chain of cholesterol metabolites. PMID:22045806

Thomas, Suzanne T; VanderVen, Brian C; Sherman, David R; Russell, David G; Sampson, Nicole S



Method of reduction of nitroaromatics by enzymatic reaction with redox enzymes  


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)



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


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)



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


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.



Nickel-Catalyzed Coupling Reactions of Alkyl Electrophiles, Including Unactivated Tertiary Halides, to Generate Carbon–Boron Bonds  

PubMed Central

Through the use of a catalyst formed in situ from NiBr2•diglyme and a pybox ligand (both of which are commercially available), we have achieved our first examples of coupling reactions of unactivated tertiary alkyl electrophiles, as well as our first success with nickel-catalyzed couplings that generate bonds other than C–C bonds. Specifically, we have determined that this catalyst accomplishes Miyaura-type borylations of unactivated tertiary, secondary, and primary alkyl halides with diboron reagents to furnish alkylboronates, a family of compounds with substantial (and expanding) utility, under mild conditions; indeed, the umpolung borylation of a tertiary alkyl bromide can be achieved at a temperature as low as ?10 °C. The method exhibits good functional-group compatibility and is regiospecific, both of which can be issues with traditional approaches to the synthesis of alkylboronates. In contrast to seemingly related nickel-catalyzed C–C bond-forming processes, tertiary halides are more reactive than secondary or primary halides in this nickel-catalyzed C–B bond-forming reaction; this divergence is particularly noteworthy in view of the likelihood that both transformations follow an inner-sphere electron-transfer pathway for oxidative addition. PMID:22668072

Dudnik, Alexander S.



Nickel-catalyzed coupling reactions of alkyl electrophiles, including unactivated tertiary halides, to generate carbon-boron bonds.  


Through the use of a catalyst formed in situ from NiBr(2)·diglyme and a pybox ligand (both of which are commercially available), we have achieved our first examples of coupling reactions of unactivated tertiary alkyl electrophiles, as well as our first success with nickel-catalyzed couplings that generate bonds other than C-C bonds. Specifically, we have determined that this catalyst accomplishes Miyaura-type borylations of unactivated tertiary, secondary, and primary alkyl halides with diboron reagents to furnish alkylboronates, a family of compounds with substantial (and expanding) utility, under mild conditions; indeed, the umpolung borylation of a tertiary alkyl bromide can be achieved at a temperature as low as -10 °C. The method exhibits good functional-group compatibility and is regiospecific, both of which can be issues with traditional approaches to the synthesis of alkylboronates. In contrast to seemingly related nickel-catalyzed C-C bond-forming processes, tertiary halides are more reactive than secondary or primary halides in this nickel-catalyzed C-B bond-forming reaction; this divergence is particularly noteworthy in view of the likelihood that both transformations follow an inner-sphere electron-transfer pathway for oxidative addition. PMID:22668072

Dudnik, Alexander S; Fu, Gregory C



Imino-oxy acetic acid dealkylation as evidence for an inner-sphere alcohol intermediate in the reaction catalyzed by peptidylglycine alpha-hydroxylating monooxygenase.  


Peptidylglycine alpha-hydroxylating monooxygenase (PHM, EC catalyzes the stereospecific hydroxylation of a glycyl alpha-carbon in a reaction that requires O(2) and ascorbate. Subsequent dealkylation of the alpha-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC, yields a bioactive amide and glyoxylate. PHM is a noncoupled, type II dicopper monooxygenase which activates O(2) at only a single copper atom, Cu(M). In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The (D)(V/K)(APPARENT, BIAA) decreased from 14.7 +/- 1.0 as [O(2)] --> 0 to 1.0 +/- 0.2 as [O(2)] --> infinity suggesting the dissociation rate constant from the PHM x BIAA complex decreases as [O(2)] increases; thereby, reducing the steady-state concentration of [PHM](free). BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked Cu(II)-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

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



Three-Component Ag-Catalyzed Enantioselective Vinylogous Mannich and Aza-Diels-Alder Reactions with Alkyl-Substituted Aldehydes  

PubMed Central

Efficient protocols for three-component catalytic enantioselective vinylogous Mannich (VM) reactions of alkyl-substituted aldimines (including those bearing heteroatom-containing substituents) and readily available siloxyfurans are presented. High efficiency and stereoselectivity is achieved through the use of o-thiomethyl-p-methoxyaniline-derived aldimines. Reactions, performed under an atmosphere of air and in undistilled THF, can be promoted in the presence of as little as 1 mol % of easily accessible amino acid-based chiral ligands and commercially available AgOAc. The desired products are obtained in 44% to 92% yield, and in up to >98:<2 diastereomer and >99:<1 enantiomer ratio (>98% ee). Removal of the N-activating group is performed through a one-vessel oxidation/hydrolysis operation, which proceeds via a stable aza-quinone (characterized by X-ray crystallography). Evidence is presented indicating that reactions with chiral non-racemic aldehydes are subject to catalyst control: both substrate enantiomers react to afford the desired product diastereomers in high stereoselectivity. Aryl- and alkynyl-substituted o-thiomethyl-p-methoxyaniline-derived aldimines undergo Ag-catalyzed enantioselective VM more efficiently and with higher selectivity than the corresponding o-anisidyl substrates. Additionally, Ag-catalyzed aza-Diels-Alder reactions of the alkyl-substituted aldimines bearing the structurally modified N-aryl unit afford enantiomerically enriched (up to 95% ee) products in up to 88% yield. PMID:19053434

Mandai, Hiroki; Mandai, Kyoko



Enantioselective Synthesis of anti- and syn-homopropargyl alcohols via Chiral Br?nsted Acid Catalyzed asymmetric Allenylboration reactions  

PubMed Central

Chiral Brønsted acid catalyzed asymmetric allenylboration reactions are described. Under optimized conditions, anti-homopropargyl alcohols 2 are obtained in high yields with excellent diastereo- and enantioselectivities from stereochemically matched aldehyde allenylboration reactions with (M)-1 catalyzed by the chiral phosphoric acid (S)-4. The syn-isomers 3 can also be obtained in good diastereoselectivities and excellent enantioselectivities from the mismatched allenylboration reactions of aromatic aldehydes using (M)-1 in the presence of the enantiomeric phosphoric acid (R)-4. The stereochemistry of the methyl group introduced into 2 and 3 is controlled by the chirality of the allenylboronate (M)-1, whereas the configuration of the new hydroxyl stereocenter is controlled by the enantioselectivity of the chiral phosphoric acid catalyst used in these reactions. The synthetic utility of this methodology was further demonstrated in triple asymmetric syntheses of a variety of anti,anti-stereotriads, the direct synthesis of which has constituted a significant challenge using previous generations of aldol and crotylmetal reagents. PMID:22731887

Chen, Ming; Roush, William R.



A Novel Glucosylation Reaction on Anthocyanins Catalyzed by Acyl-Glucose-Dependent Glucosyltransferase in the Petals of Carnation and Delphinium[C][W  

PubMed Central

Glucosylation of anthocyanin in carnations (Dianthus caryophyllus) and delphiniums (Delphinium grandiflorum) involves novel sugar donors, aromatic acyl-glucoses, in a reaction catalyzed by the enzymes acyl-glucose–dependent anthocyanin 5(7)-O-glucosyltransferase (AA5GT and AA7GT). The AA5GT enzyme was purified from carnation petals, and cDNAs encoding carnation Dc AA5GT and the delphinium homolog Dg AA7GT were isolated. Recombinant Dc AA5GT and Dg AA7GT proteins showed AA5GT and AA7GT activities in vitro. Although expression of Dc AA5GT in developing carnation petals was highest at early stages, AA5GT activity and anthocyanin accumulation continued to increase during later stages. Neither Dc AA5GT expression nor AA5GT activity was observed in the petals of mutant carnations; these petals accumulated anthocyanin lacking the glucosyl moiety at the 5 position. Transient expression of Dc AA5GT in petal cells of mutant carnations is expected to result in the transfer of a glucose moiety to the 5 position of anthocyanin. The amino acid sequences of Dc AA5GT and Dg AA7GT showed high similarity to glycoside hydrolase family 1 proteins, which typically act as ?-glycosidases. A phylogenetic analysis of the amino acid sequences suggested that other plant species are likely to have similar acyl-glucose–dependent glucosyltransferases. PMID:20971893

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



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


Aminoglycoside Antibiotic-Inactivating Enzymes in Actinomycetes Similar to those Present in Clinical Isolates of Antibiotic-Resistant Bacteria  

Microsoft Academic Search

Various species of Streptomyces possess aminoglycoside-modifying enzymes. Streptomyces kanamyceticus contains an enzyme that acetylates the 6'-amino group of kanamycin A and B, gentamicin C1a, and neomycin. Streptomyces spectabilis produces an enzyme that acetylates the 2'-amino group of the hexose ring of gentamicin C1a. These enzymes catalyze reactions identical to those catalyzed by enzymes found in gram-negative bacteria containing R (antibiotic

Raoul Benveniste; Julian Davies



Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions  

PubMed Central

Combined quantum mechanics/molecular mechanics (QM/MM) modelling has the potential to answer fundamental questions about enzyme mechanisms and catalysis. Calculations using QM/MM methods can now predict barriers for enzyme-catalysed reactions with unprecedented, near chemical accuracy, i.e. to within 1 kcal/mol in the best cases. Quantitative predictions from first-principles calculations were only previously possible for very small molecules. At this level, quantitative, reliable predictions can be made about the mechanisms of enzyme-catalysed reactions. This development signals a new era of computational biochemistry. PMID:17880750

Mulholland, Adrian J



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


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

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



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

E-print Network

the synthesis of those two enantiomers, the enzymatic resolution of glycerol acetonide was investigated via the stereoselective hydrolysis of racemic ester derivatives. In a first attempt, simple resolutions were studied using isopropylidene glycerol acetate.... . . . . . . . . . . . . 32 III. Solvent effect on the hydrolysis of isopropylidene and cyclohexylidene glycerol acetate 34 IV. Comparison of the hydrolysis of isopropylidene glycerol esters. 35 V. Hydrolysis of N-CBz-1-ala glycerol acetonide. . . . . . 47 VI...

Chauvet, Christine Jeanne



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


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



Syntheses of Functionalized Benzylic Compounds: Development of Palladium-Catalyzed Decarboxylative Benzylation Reactions  

E-print Network

thought that it would be feasible and ideal to perform decarboxylative benzylation (DcB) based from well-explored decarboxylative allylation (DcA) methodology. Indeed, we were able to show that Pd-catalyzed DcB was an indispensable tool in synthesizing...

Torregrosa, Robert Ryan P.



A Computational Study of the Origin of Stereoinduction in NHC-Catalyzed Annulation Reactions of ?,?-Unsaturated Acyl Azoliums  

PubMed Central

The origin of stereoselectivity of NHC-catalyzed annulation reactions of ynals and stable enols was studied with Density Functional Theory. The data suggest that the C-C bond formation is the stereo-determining step. Only the deprotonated pathway (containing an oxy anion and overall neutral species) was found to give rise to discrimination of the competing stereoisomers. This is due predominantly to electrostatic repulsion of the ?-stabilizing enolate functionality with the ?-cloud of the aryl group in the NHC-catalyst. PMID:23687566

Lyngvi, Eirik; Bode, Jeffrey W.; Schoenebeck, Franziska



Total synthesis of resveratrol-based natural products using a palladium-catalyzed decarboxylative arylation and an oxidative Heck reaction.  


Controlled access to resveratrol-based natural products is offered by a novel, modular concept. A common building block readily available on a large scale serves as the starting material for the introduction of structurally important aryl groups by a Pd-catalyzed decarboxylative arylation and an oxidative Heck reaction with good yields and high stereoselectivity. The modular approach is convincingly documented by the successful synthesis of three racemic resveratrol-based natural products (quadrangularin?A, ampelopsin?D, and pallidol). PMID:24500870

Klotter, Felix; Studer, Armido



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



Short communication Phylogeny of Calvin cycle enzymes supports Plantae monophyly  

E-print Network

enzymes involved in glycolysis and gluceoneogenesis that catalyze reactions similar to those in the CCShort communication Phylogeny of Calvin cycle enzymes supports Plantae monophyly Adrian Reyes), takes place in the plastid stroma. The eukaryotic CC involves 11 different enzymes (Table 1

Bhattacharya, Debashish


Medical treatments, fuel sources from studying elusive enzyme  

E-print Network

- 1 - Medical treatments, fuel sources from studying elusive enzyme April 3, 2012 Neutrons are used in the transfer of protons during enzyme-catalyzed reactions. Prior to this research, no one has ever directly, in macromolecular catalysts-- the catalytic mechanisms of enzymes. #12;- 2 - Researchers took an interest




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 ...


Galacto-oligosaccharide production from lactose by an enzymic batch reaction using ?-galactosidase  

Microsoft Academic Search

Enzymic reaction of lactose was carried out to produce galacto-oligosaccharide with a high degree of conversion. The reaction process was analysed with a simple model. The reaction involved a batch process operated with initial lactose concentrations ranging from 0·139 to 1·67 mol litre?1 at 40°C and pH 4·5 with ?-galactosidase from Aspergillus oryzae. A maximum oligosaccharide conversion of over 30%

Ken-ichi Iwasaki; Mitsutoshi Nakajima; Shin-ichi Nakao



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.


Oxidative half-reaction of arabidopsis thaliana sulfite oxidase: generation of superoxide by a peroxisomal enzyme.  


Vertebrate forms of the molybdenum-containing enzyme sulfite oxidase possess a b-type cytochrome prosthetic group that accepts reducing equivalents from the molybdenum center and passes them on to cytochrome c. The plant form of the enzyme, on the other hand, lacks a prosthetic group other than its molybdenum center and utilizes molecular oxygen as the physiological oxidant. Hydrogen peroxide is the ultimate product of the reaction. Here, we present data demonstrating that superoxide is produced essentially quantitatively both in the course of the reaction of reduced enzyme with O(2) and during steady-state turnover and only subsequently decays (presumably noncatalytically) to form hydrogen peroxide. Rapid-reaction kinetic studies directly following the reoxidation of reduced enzyme demonstrate a linear dependence of the rate constant for the reaction on [O(2)] with a second-order rate constant of k(ox) = 8.7 x 10(4) +/- 0.5 x 10(4) m(-1)s(-1). When the reaction is carried out in the presence of cytochrome c to follow superoxide generation, biphasic time courses are observed, indicating that a first equivalent of superoxide is generated in the oxidation of the fully reduced Mo(IV) state of the enzyme to Mo(V), followed by a slower oxidation of the Mo(V) state to Mo(VI). The physiological implications of plant sulfite oxidase as a copious generator of superoxide are discussed. PMID:19875441

Byrne, Robert S; Hänsch, Robert; Mendel, Ralf R; Hille, Russ



Performance of DFT methods and origin of stereoselectivity in bipyridine N,N'-dioxide catalyzed allylation and propargylation reactions.  


Enantioselectivities for the allylation and propargylation of benzaldehyde catalyzed by bipyridine N,N'-dioxides were predicted using popular DFT methods. The results reveal deficiencies of several DFT methods while also providing a new explanation for the stereoselectivity of these reactions. In particular, even though many DFT methods provide accurate predictions of experimental ee's for these reactions, these predictions sometimes stem from qualitatively incorrect transition states. Overall, B97-D/TZV(2d,2p) provides the best compromise between accurate predictions of low-lying transition states and stereoselectivities for these reactions. The origin of stereoselectivity in these reactions was also examined, and arises from electrostatic interactions within the chiral electrostatic environment of a hexacoordinate silicon intermediate; the previously published transition state model for these reactions is flawed. Ultimately, these results suggest two strategies for the design of highly stereoselective catalysts for the propargylation of aromatic aldehydes, and pave the way for the computational design of novel catalysts for these reactions. PMID:25216295

Sepúlveda, Diana; Lu, Tongxiang; Wheeler, Steven E



Initial reaction(s) in biotransformation of CL-20 is catalyzed by salicylate 1-monooxygenase from Pseudomonas sp. strain ATCC 29352.  


CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) (C(6)H(6)N(12)O(12)), a future-generation high-energy explosive, is biodegradable by Pseudomonas sp. strain FA1 and Agrobacterium sp. strain JS71; however, the nature of the enzyme(s) involved in the process was not understood. In the present study, salicylate 1-monooxygenase, a flavin adenine dinucleotide (FAD)-containing purified enzyme from Pseudomonas sp. strain ATCC 29352, biotransformed CL-20 at rates of 0.256 +/- 0.011 and 0.043 +/- 0.003 nmol min(-1) mg of protein(-1) under anaerobic and aerobic conditions, respectively. The disappearance of CL-20 was accompanied by the release of nitrite ions. Using liquid chromatography/mass spectrometry in the negative electrospray ionization mode, we detected a metabolite with a deprotonated mass ion [M - H](-) at 345 Da, corresponding to an empirical formula of C(6)H(6)N(10)O(8), produced as a result of two sequential N denitration steps on the CL- 20 molecule. We also detected two isomeric metabolites with [M - H](-) at 381 Da corresponding to an empirical formula of C(6)H(10)N(10)O(10). The latter was a hydrated product of the metabolite C(6)H(6)N(10)O(8) with addition of two H(2)O molecules, as confirmed by tests using (18)O-labeled water. The product stoichiometry showed that each reacted CL-20 molecule produced about 1.7 nitrite ions, 3.2 molecules of nitrous oxide, 1.5 molecules of formic acid, and 0.6 ammonium ion. Diphenyliodonium-mediated inhibition of salicylate 1-monooxygenase and a comparative study between native, deflavo, and reconstituted enzyme(s) showed that FAD site of the enzyme was involved in the biotransformation of CL-20 catalyzed by salicylate 1-monooxygenase. The data suggested that salicylate 1-monooxygenase catalyzed two oxygen-sensitive single-electron transfer steps necessary to release two nitrite ions from CL-20 and that this was followed by the secondary decomposition of this energetic chemical. PMID:15240281

Bhushan, Bharat; Halasz, Annamaria; Spain, Jim C; Hawari, Jalal



Initial Reaction(s) in Biotransformation of CL-20 Is Catalyzed by Salicylate 1-Monooxygenase from Pseudomonas sp. Strain ATCC 29352  

PubMed Central

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) (C6H6N12O12), a future-generation high-energy explosive, is biodegradable by Pseudomonas sp. strain FA1 and Agrobacterium sp. strain JS71; however, the nature of the enzyme(s) involved in the process was not understood. In the present study, salicylate 1-monooxygenase, a flavin adenine dinucleotide (FAD)-containing purified enzyme from Pseudomonas sp. strain ATCC 29352, biotransformed CL-20 at rates of 0.256 ± 0.011 and 0.043 ± 0.003 nmol min?1 mg of protein?1 under anaerobic and aerobic conditions, respectively. The disappearance of CL-20 was accompanied by the release of nitrite ions. Using liquid chromatography/mass spectrometry in the negative electrospray ionization mode, we detected a metabolite with a deprotonated mass ion [M ? H]? at 345 Da, corresponding to an empirical formula of C6H6N10O8, produced as a result of two sequential N denitration steps on the CL- 20 molecule. We also detected two isomeric metabolites with [M ? H]? at 381 Da corresponding to an empirical formula of C6H10N10O10. The latter was a hydrated product of the metabolite C6H6N10O8 with addition of two H2O molecules, as confirmed by tests using 18O-labeled water. The product stoichiometry showed that each reacted CL-20 molecule produced about 1.7 nitrite ions, 3.2 molecules of nitrous oxide, 1.5 molecules of formic acid, and 0.6 ammonium ion. Diphenyliodonium-mediated inhibition of salicylate 1-monooxygenase and a comparative study between native, deflavo, and reconstituted enzyme(s) showed that FAD site of the enzyme was involved in the biotransformation of CL-20 catalyzed by salicylate 1-monooxygenase. The data suggested that salicylate 1-monooxygenase catalyzed two oxygen-sensitive single-electron transfer steps necessary to release two nitrite ions from CL-20 and that this was followed by the secondary decomposition of this energetic chemical. PMID:15240281

Bhushan, Bharat; Halasz, Annamaria; Spain, Jim C.; Hawari, Jalal



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

SciTech Connect

Past activities have resulted in a legacy of contaminated soil and groundwater at Department of Energy facilities nationwide. Uranium and chromium are among the most frequently encountered and highest-priority metal and radionuclide contaminants at DOE installations. Abiotic chemical reduction of uranium and chromium at contaminated DOE sites can be beneficial because the reduced metal species are less soluble in water, less mobile in the environment, and less toxic to humans and ecosystems. Although direct biological reduction has been reported for U(VI) and Cr(VI) in laboratory studies and at some field sites, the reactions can sometimes be slow or even inhibited due to unfavorable environmental conditions. One promising approach for the in-situ remediation of DOE contaminants is to develop electron shuttle catalysts that can be delivered precisely to the specific subsurface locations where contaminants reside. Previous research has shown that reduction of oxidized organic and inorganic contaminants often can be catalyzed by electron shuttle systems. Metalloporphyrins and their derivatives are well known electron shuttles for many biogeochemical systems, and thus were selected to study their catalytic capabilities for the reduction of chromium and uranium in the presence of reducing agents. Zero valent iron (ZVI) was chosen as the primary electron donor in most experimental systems. Research proceeded in three phases and the key findings of each phase are reported here. Phase I examined Cr(VI) reduction and utilized micro- and nano-sized ZVI as the electron donors. Electron shuttle catalysts tested were cobalt- and iron-containing metalloporphyrins and Vitamin B12. To aid in the recycle and reuse of the nano-sized ZVI and soluble catalysts, sol-gels and calcium-alginate gel beads were tested as immobilization/support matrices. Although the nano-sized ZVI could be incorporated within the alginate gel beads, preliminary attempts to trap it in sol-gels were not successful. Conversely, the water-soluble catalysts could be trapped within sol-gel matrices but they tended to leach out of the alginate gel beads during use. In general, immobilization of the nano-sized ZVI in gel beads and of the catalysts in sol-gels tended to result in slower rates of Cr(VI) reduction, but these effects could be overcome to some extent by using higher reactant/catalyst concentrations. In addition, the lowering of their effectiveness would likely be offset by the benefits obtained when recycling and reusing the materials because they were immobilized. Addition of the catalytic electron shuttles will be most useful when the micro-sized or nano-sized ZVI becomes less reactive with reaction time. Continued work in Phase II in the area of nano-sized ZVI immobilization led to procedures that were successful in incorporating the iron particles in sol-gel matrices. The water-soluble reductants sodium dithionite and L-ascorbic acid were also tested, but their use appeared to lead to formation of complexes with the uranyl cation which limited their effectiveness. Also, although the sol-gel supported nano-sized ZVI showed some promise at reducing uranium, the fluoride used in the sol-gel synthesis protocol appeared to lead to formation of uranyl-fluoride complexes that were less reactive. Because hexavalent chromium is an anion which does not form complexes with fluoride, it was used to demonstrate the intrinsic reactivity of the sol-gel immobilized nano-sized ZVI. Consistent with our observations in Phase I, the sol-gel matrix once again slowed down the reduction reaction but the expected benefits of recycle/reuse should outweigh this adverse effect. The major emphasis in Phase III of this study was to simultaneously incorporate nano-sized ZVI and water-soluble catalysts in the same sol-gel matrix. The catalysts utilized were cobalt complexes of uroporphyrin and protoporphyrin and Cr(VI) reduction was used to test the efficacy of the combined "catalyst + reductant" sol-gel matrix. When enough catalyst was added to the sol-gels, enhancement of the Cr(VI)

Schlautman, Mark A. [Clemson University, Clemson, SC (United States)



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.



Friedel–Crafts Acylation and Related Reactions Catalyzed by Heteropoly Acids  

Microsoft Academic Search

The Friedel–Crafts acylation of anisole (AN) with acetic anhydride (AA) and the Fries rearrangement of phenyl acetate in the liquid phase catalyzed by bulk and silica-supported heteropoly acids (HPA), mainly H3PW12O40 (PW), have been studied. In anisole acylation, PW exhibits very high activity, yielding up to 98% para and 2–4% ortho isomer of methoxyacetophenone (MOAP) at 90-110°C and an AN\\/AA

J. Kaur; E. F. Kozhevnikova; K. Griffin; B. Harrison; I. V. Kozhevnikov



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

Naray-Szabo, Gabor; Olah, Julianna; Kramos, Balazs



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.



Synthesis of alkenyl sulfides through the iron-catalyzed cross-coupling reaction of vinyl halides with thiols.  


We report here the iron-catalyzed cross-coupling reaction of alkyl vinyl halides with thiols. While many works are devoted to the coupling of thiols with alkyl vinyl iodides, interestingly, the known S-vinylation of vinyl bromides and chlorides is limited to 1-(2-bromovinyl)benzene and 1-(2-chlorovinyl)benzene. Investigation on the coupling reaction of challenging alkyl vinyl bromides and chlorides with thiols is rare. Since the coupling of 1-(2-bromovinyl)benzene and 1-(2-chlorovinyl)benzene with thiols can be performed in the absence of any catalyst, here we focus on the coupling of thiols with alkyl vinyl halides. This system is generally reactive for alkyl vinyl iodides and bromides to provide the products in good yields. 1-(Chloromethylidene)-4-tert-butyl-cyclohexane was also coupled with thiols, giving the targets in moderate yields. PMID:22708836

Lin, Yun-Yung; Wang, Yu-Jen; Lin, Che-Hung; Cheng, Jun-Hao; Lee, Chin-Fa



Reaction dynamics and transition-state structures for acetylcholinesterase-catalyzed hydrolysis of aryl esters and anilides  

SciTech Connect

The acylation and deacylation stages of acetylcholinesterase-catalyzed hydrolysis of various aryl ester and anilide substrates were investigated. For the natural substrate of acetylcholinesterase (AChE), acetylcholine, diffusion or enzyme conformational processes limit the acylation rate. Several anilides and aryl esters have been synthesized and found to be substrates of AChE. The acylation and deacylation reactivities of o-nitroformanilide, p-methoxyphenyl formate and o-nitrophenyl acetate were characterized by measuring substrate secondary and solvent isotope effects and by determining pL(L = H,D)-rate profiles and Eyring plots. Substrate secondary deuterium kinetic isotope effects are consistent with decreasing nucleophilic interaction at the carbonyl carbon of the scissle bond of the substrate in the rate-determining transition state with increasing V/K. These results lend quantitative support to a model for acylation rate determination involving a virtual transition state that contains contributions from the transition states of sequential physical and chemical steps.

Acheson, S.A.



Novel Optical Resolution of Phenylalanine Racemate Utilizing Enzyme Reaction and Membrane Extraction  

Microsoft Academic Search

A novel optical resolution method for d,l-phenylalanine in which an enzyme reaction and a membrane extraction are combined has been designed. In the first stage only the l-isomer of the racemic phenylalanine methyl ester was selectively hydrolyzed by the enzyme ?-chymotrypsin. Further, the unreacted ester was selectively recovered from the mixture of the transferred amino acid and the ester form

K. Abe; M. Goto; F. Nakashio



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


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



Rh-Catalyzed Intermolecular Reactions of Cyclic ?-Diazocarbonyl Compounds with Selectivity Over Tertiary C-H Bond Migration  

PubMed Central

Intermolecular Rh-catalyzed reactions of cyclic ?-diazocarbonyl compounds with chemoselectivity over ?-hydride elimination are described. These methods represent the first general intermolecular reactions of Rh-carbenoids that are selective over tertiary ?-C?H bond migration. Successful transformations include cyclopropanation, cyclopropenation, and various X–H insertion reactions with a broad scope of substrates. We propose that the intermolecular approach of substrates to carbenes from acyclic diazo precursors may be relatively slow due to a steric interaction with the ester function, which is perpendicular to the ?-system of the carbene. For carbenes derived from 5- and 6-membered cyclic ?-diazocarbonyls, it is proposed that the carbene is constrained to be more conjugated with the carbonyl, thereby relieving the steric interaction for intermolecular reactions, and accelerating the rate of intermolecular reactivity relative to intramolecular ?-hydride migration. However, attempts to use ?-diazo-?-ethylcaprolactone in intermolecular cyclopropanation with styrene were unsuccessful. It is proposed that the conformational flexibility of the 7-membered ring allows the carbonyl to be oriented perpendicular to Rh-carbene. The significant intermolecular interaction between the carbonyl and approaching substrate is in agreement with the poor ability of ?-diazo-?-ethylcaprolactone to participate in intermolecular cyclopropanation reactions. DFT calculations provide support for the mechanistic proposals that are described. PMID:22676258

DeAngelis, Andrew; Dmitrenko, Olga; Fox, Joseph M.



27. Size exclusion chromatography data show the enzyme forms a dimer (fig. S4).  

E-print Network

this paper. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction N. Houk,4 Forrest E. Michael,3 David Baker1,2,7 The Diels-Alder reaction is a cornerstone. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe

Gelb, Michael


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



L-myo-inosose-1 as a probable intermediate in the reaction catalyzed by myo-inositol oxygenase  

SciTech Connect

In previous investigations, it was necessary to have Fe(II) and cysteine present in order to assay the catalytic activity of purified hog kidney myo-inositol oxygenase. In the present study it was found that, if this purified nonheme iron enzyme is slowly frozen in solution with glutathione and stored at -20 degrees C, it is fully active in the absence of activators if catalase is present to remove adventitious H/sub 2/O/sub 2/. With this simpler assay system it was possible to clarify the effects of several variables on the enzymic reaction. Thus, the maximum velocity is pH-dependent with a maximum around pH 9.5, but the apparent Km for myo-inositol (air atmosphere) remains constant at 5.0 mM throughout a broad pH range. The enzyme is quite specific for its substrate myo-inositol, is very sensitive to oxidants and reductants, but is not affected by a variety of complexing agents, nucleotides, sulfhydryl reagents, etc. In other experiments it was found that L-myo-inosose-1, a potential intermediate in the enzymic reaction, is a potent competitive inhibitor (Ki = 62 microM), while other inososes and a solution thought to contain D-glucodialdehyde, another potential intermediate, are weak inhibitors. Also, both a kinetic deuterium isotope effect (kH/kD = 2.1) and a tritium isotope effect (kH/kT = 7.5) are observed for the enzymic reaction when (1-2H)- and (1-3H)-myo-inositol are used as reactants. These latter results are considered strong evidence that the oxygenase reaction proceeds by a pathway involving L-myo-inosose-1 as an intermediate rather than by an alternative pathway that would have D-glucodialdehyde as the intermediate.

Naber, N.I.; Swan, J.S.; Hamilton, G.A.



Modeling the Role of G12V and G13V Ras Mutations in the Ras-GAP-Catalyzed Hydrolysis Reaction of Guanosine Triphosphate.  


Cancer-associated point mutations in Ras, in particular, at glycine 12 and glycine 13, affect the normal cycle between inactive GDP-bound and active GTP-bound states. In this work, the role of G12V and G13V replacements in the GAP-stimulated intrinsic GTP hydrolysis reaction in Ras is studied using molecular dynamics (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. A model molecular system was constructed by motifs of the relevant crystal structure (Protein Data Bank entry 1WQ1 ). QM/MM optimization of geometry parameters in the Ras-GAP-GTP complex and QM/MM-MD simulations were performed with a quantum subsystem comprising a large fraction of the enzyme active site. For the system with wild-type Ras, the conformations fluctuated near the structure ready to be involved in the efficient chemical reaction leading to the cleavage of the phosphorus-oxygen bond in GTP upon approach of the properly aligned catalytic water molecule. Dynamics of the system with the G13V mutant is characterized by an enhanced flexibility in the area occupied by the ?-phosphate group of GTP, catalytic water, and the side chains of Arg789 and Gln61, which should somewhat hinder fast chemical steps. Conformational dynamics of the system with the G12V mutant shows considerable displacement of the Gln61 side chain and catalytic water from their favorable arrangement in the active site that may lead to a marked reduction in the reaction rate. The obtained computational results correlate well with the recent kinetic measurements of the Ras-GAP-catalyzed hydrolysis of GTP. PMID:25339142

Khrenova, Maria G; Mironov, Vladimir A; Grigorenko, Bella L; Nemukhin, Alexander V



Recent progress in lanthanide-catalyzed organic reactions in protic media  

Microsoft Academic Search

Lanthanide triflates are stable in water. It is possible for lanthanides to undergo many organic reactions in environmentally\\u000a friendly solvents. This makes lanthanides very promising in the field of green chemistry. This review describes the recent\\u000a development of the lanthanidecatalyzed organic reactions in protic solvents. Those reactions include Diels-Alder, Aldol, Allylation,\\u000a acetalization, pericyclization, radical reactions as well as some newlydeveloped

Luo Sanzhong; Zhang Baolian; Xian Ming; Adam JaÑczuk; Xie Wenhua; Cheng Jinpei; Peng George Wang



Direct enantioselective aldol-Tishchenko reaction catalyzed by chiral lithium diphenylbinaphtholate.  


Chiral lithium diphenylbinaphtholate is an effective catalyst for the enantioselective aldol-Tishchenko reaction, affording 1,3-diol derivatives with three contiguous chiral centers and high stereoselectivities. Successive aldol-aldol-Tishchenko reactions gave a triol derivative with five consecutive chiral centers. The present reaction was applicable to highly enantioselective Evans-Tishchenko reduction. PMID:21355567

Ichibakase, Tomonori; Nakajima, Makoto



Redox Reactions of Metalloporphyrins and their Role in Catalyzed Reduction of Carbon Dioxide  

SciTech Connect

Pulse radiolysis and laser photolysis are used to study redox processes of metalloporphyrins and related complexes in order to evaluate these light absorbing molecules as sensitizers and intermediates in solar energy conversion schemes. The main thrust of the current studies is to investigate the role of reduced metalloporphyrins as intermediates in the catalyzed reduction of carbon dioxide. Studies involve cobalt and iron porphyrins, phthalocyanines, corroles, and corrins as homogeneous catalysts for reduction of carbon dioxide in solution. The main aim is to understand the mechanisms of these photochemical schemes in order to facilitate their potential utilization.

Neta, P.



Mechanism of the reaction catalyzed by mandelate racemase. 1. Chemical and kinetic evidence for a two-base mechanism  

SciTech Connect

The fate of the {alpha}-hydrogen of mandelate in the reaction catalyzed by mandelate racemase has been investigated by a mass spectroscopic method. The method entails the incubation of (R)- or (S)-({alpha}-{sup 1}H) mandelate in buffered D{sub 2}O to a low extent of turnover (about 5-8%), esterification of the resulting mixture of mandelates with diazomethane, derivatization of the methyl esters with a chiral derivatizing agent, and quantitation of the isotope content of the {alpha}-hydrogen of both substrate and product by gas chromatography/mass spectrometric analysis. No significant substrate-derived {alpha}-protium was found in the product for racemization in either direction. In addition, in the (R) to (S) direction almost no exchange of the {alpha}-hydrogen in the remaining (R) substrate pool occurred, but in the (S) to (R) direction 3.5-5.1% exchange of the {alpha}-hydrogen in the remaining substrate (after 5.1-7.2% net turnover) was found. Qualitatively similar results were obtained in the (S) to (R) direction in H{sub 2}O when (S)-({alpha}-{sup 2}H)mandelate was used as substrate. In other experiments, an overshoot in the progress curve was observed when the racemization of either enantiomer of ({alpha}-{sup 1}H) mandelate in D{sub 2}O was monitored by following the change in ellipticity of the reaction mixture; the magnitude of the overshoot was greater in the (R) to (S) than in the (S) to (R) direction. All of the available data indicate that the reaction catalyzed by mandelate racemase proceeds by a two-base mechanism, in contrast to earlier proposals.

Powers, V.M.; Koo, C.W.; Kenyon, G.L. (Univ. of California, San Francisco (United States)); Gerlt, J.A.; Kozarich, J.W. (Univ. of Maryland, College Park (United States))



First Application of An Efficient and Versatile Ligand for Copper-Catalyzed Cross-Coupling Reactions of Vinyl Halides with N-Heterocycles and Phenols  

PubMed Central

2-Pyridin-2-yl-1H-benzoimidazole L3 is presented as a new, efficient, and versatile bidentate N-donor ligand suitable for the copper-catalyzed formation of vinyl C-N and C-O bonds. This inexpensive and easily prepared ligand facilitates copper-catalyzed cross-coupling reactions of alkenyl bromides and iodides with N-heterocycles and phenols to afford the desired cross-coupled products in good to excellent yields with full retention of stereochemistry. This method is particularly noteworthy given its efficiency i.e., mild reaction conditions, low catalyst loading, simplicity, versatility, and exceptional level of functional group tolerance. PMID:20039699

Kabir, M. Shahjahan; Lorenz, Michael; Namjoshi, Ojas A.; Cook, James M.



First application of an efficient and versatile ligand for copper-catalyzed cross-coupling reactions of vinyl halides with N-heterocycles and phenols.  


2-Pyridin-2-yl-1H-benzoimidazole L3 is presented as a new, efficient, and versatile bidentate N-donor ligand suitable for the copper-catalyzed formation of vinyl C-N and C-O bonds. This inexpensive and easily prepared ligand facilitates copper-catalyzed cross-coupling reactions of alkenyl bromides and iodides with N-heterocycles and phenols to afford the desired cross-coupled products in good to excellent yields with full retention of stereochemistry. This method is particularly noteworthy given its efficiency, that is, mild reaction conditions, low catalyst loading, simplicity, versatility, and exceptional level of functional group tolerance. PMID:20039699

Kabir, M Shahjahan; Lorenz, Michael; Namjoshi, Ojas A; Cook, James M



Asymmetric Glyoxylate-Ene Reactions Catalyzed by Chiral Pd(II) Complexes in the Ionic Liquid [bmim][PF6  

PubMed Central

The room temperature ionic liquid [bmim][PF6] was employed as the reaction medium in the asymmetric glyoxylate-ene reaction of ?-methyl styrene (4a) with ethyl glyoxylate using chiral palladium(II) complexes as the catalysts. [Pd(S-BINAP)(3,5-CF3-PhCN)2](SbF6)2 (1b) showed the highest catalytic activity. Under the reaction conditions of 40 °C, 0.5 h, and 1b/4a molar ratio of 0.05, ethyl ?-hydroxy-4-phenyl-4-pentenoate was obtained in excellent chemical yield (94 %) with high enantioselectivity (70 %). Other ?-hydroxy esters can also be obtained in high chemical yields and enantioselectities through the glyoxylate-ene reactions of alkenes with glyoxylates catalyzed by 1b in [bmim][PF6]. Moreover, the ionic liquid [bmim][PF6] which contained the palladium(II) complex could be recycled and reused several times without significant loss of the catalytic activity.

He, Xi Jun; Shen, Zhen Lu; Mo, Wei Min; Hu, Bao Xiang; Sun, Nan



Mechanistic studies of the rhodium-catalyzed direct C-H amination reaction using azides as the nitrogen source.  


Direct C-H amination of arenes offers a straightforward route to aniline compounds without necessitating aryl (pseudo)halides as the starting materials. The recent development in this area, in particular in the metal-mediated transformations, is significant with regard to substrate scope and reaction conditions. Described herein are the mechanistic details on the Rh-catalyzed direct C-H amination reaction using organic azides as the amino source. The most important two stages were investigated especially in detail: (i) the formation of metal nitrenoid species and its subsequent insertion into a rhodacycle intermediate, and (ii) the regeneration of catalyst with concomitant release of products. It was revealed that a stepwise pathway involving a key Rh(V)-nitrenoid species that subsequently undergoes amido insertion is favored over a concerted C-N bond formation pathway. DFT calculations and kinetic studies suggest that the rate-limiting step in the current C-H amination reaction is more closely related to the formation of Rh-nitrenoid intermediate rather than the presupposed C-H activation process. The present study provides mechanistic details of the direct C-H amination reaction, which bears both aspects of the inner- and outer-sphere paths within a catalytic cycle. PMID:24450395

Park, Sae Hume; Kwak, Jaesung; Shin, Kwangmin; Ryu, Jaeyune; Park, Yoonsu; Chang, Sukbok



Mechanistic studies on iridium catalyzed allylic substitution.  

E-print Network

??Mechanistic studies on iridium catalyzed allylic substitution reactions catalyzed by iridium phosphoramidite complexes revealed that the active catalyst is generated through a base assisted cyclometalation… (more)

Madrahimov, Sherzod



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.



Development of asymmetric reactions catalyzed by chiral organotin-alkoxide reagents.  


Asymmetric catalysis under almost-neutral reaction conditions is key for the efficient synthesis of optically active polar molecules. We have developed catalytic enantioselective reactions of acyclic or cyclic alkenyl esters by using an (S)-BINOL-derived chiral tin-dibromide reagent that possesses a bulky aryl group at the 3 or 3' position as the chiral pre-catalyst in the presence of a sodium alkoxide and an alcohol, in which a chiral tin alkoxide bromide is generated in situ and recycled with the assistance of an alcohol. In this Personal Account, we describe three types of asymmetric transformation that proceed through a chiral tin enolate: 1) The asymmetric aldol reaction of alkenyl esters or unsaturated lactones with aldehydes or isatins; 2) the asymmetric three-component Mannich-type reaction of alkenyl esters and related cycloaddition reactions; and 3) the asymmetric N-nitroso aldol reaction of unsaturated lactones with nitrosoarenes. PMID:23424074

Yanagisawa, Akira; Yoshida, Kazuhiro



Functionalized graphene oxide as a nanocatalyst in dephosphorylation reactions: pursuing artificial enzymes.  


The present study reports for the first time the use of a thiol-functionalized graphene oxide nanocatalyst with impressive activity (>10(5)-fold) in dephosphorylation reactions. The innovative and recyclable nanocatalyst has potential in designing artificial enzymes with targeted multifunctionalities and in detoxification of organophosphorus agents. PMID:25026937

Orth, Elisa S; Fonsaca, Jéssica E S; Almeida, Thomas Golin; Domingues, Sergio H; Ferreira, José G L; Zarbin, Aldo J G



Hetero-cope rearrangements of nitrosobutenes. DFT studies of thermal and acid-catalyzed reactions.  


[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



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



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 l