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Proposed Reaction Mechanism (proposed + reaction_mechanism)
Selected AbstractsThe allene oxide cyclase family of Arabidopsis thaliana , localization and cyclizationFEBS JOURNAL, Issue 10 2008Florian Schaller Jasmonates are derived from oxygenated fatty acids (oxylipins) via the octadecanoid pathway and are characterized by a pentacyclic ring structure. They have regulatory functions as signaling molecules in plant development and adaptation to environmental stress. Recently, we solved the structure of allene oxide cyclase 2 (AOC2) of Arabidopsis thaliana, which is, together with the other three AOCs, a key enzyme in the biosynthesis of jasmonates, in that it releases the first cyclic and biologically active metabolite , 12-oxo-phytodienoic acid (OPDA). On the basis of models for the bound substrate, 12,13(S)-epoxy-9(Z),11,15(Z)-octadecatrienoic acid, and the product, OPDA, we proposed that a conserved Glu promotes the reaction by anchimeric assistance. According to this hypothesis, the transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable ,,, interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein environment. Here, site-directed mutagenesis was used to explore and verify the proposed reaction mechanism. In a comparative analysis of the AOC family from A. thaliana involving enzymatic characterization, in vitro import, and transient expression of AOC,enhanced green fluorescent protein fusion proteins for analysis of subcellular targeting, we demonstrate that all four AOC isoenzymes may contribute to jasmonate biosynthesis, as they are all located in chloroplasts and, in concert with the allene oxide synthase, they are all able to convert 13(S)-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid into enantiomerically pure cis(+)-OPDA. [source] Kinetics of cellulose conversion at 25 MPa in sub- and supercritical waterAICHE JOURNAL, Issue 1 2004Mitsuru Sasaki Abstract Experiments of microcrystalline cellulose conversion in subcritical and supercritical water were conducted at temperatures between 290 and 400°C, a pressure of 25 MPa, and residence times of 0.02,13.1 s using a continuous-flow-type microreactor. First, the reaction mechanism of microcrystalline cellulose in subcritical and supercritical water was proposed on the basis of detailed product analyses. Next, the kinetic description of this reaction in subcritical and supercritical water using a grain model was carried out to verify the proposed reaction mechanism and consequently found that the reaction-rate models were able to express the reaction of microcrystalline cellulose at identical conditions. © 2004 American Institute of Chemical Engineers AIChE J, 50: 192,202, 2004 [source] Systematic conformational search analysis of the SRR and RRR epimers of 7-hydroxymatairesinolJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 2 2010Giovanni Li Manni Abstract An extensive and systematic conformational search was performed on the two epimers of the natural lignan 7-hydroxymatairesinol (HMR), by means of a home-made Systematic Conformational Search Analysis (SCSA) code, designed to select more and more stable conformers through sequential geometry optimization of trial structures at increasing levels of calculation theory. In the present case, the starting molecular structures were selected by the semi-empirical AM1 method and filtered , i.e. decreased in number by choosing the more stable species , on the basis of their energy calculated by the HF method and the 6-31G(d) basis set. The geometries obtained were further refined by performing density functional theory (DFT) optimizations, using the B3LYP functional and the 6-31G(d,p) basis set, both in vacuo and in ethanol solution. This procedure allowed us to isolate, at a high level of theory, three groups of epimer conformers characterized by open, semi-folded, and folded conformations. Moreover, the SCSA allowed us to describe a conformational space made-up by about 20 species for each of the two epimers. The corresponding energy content of these species was within 27,kJ,mol,1 from the absolute minimum found, both in vacuo and in ethanol solution. The conformational analysis, followed by the inspection of the stereochemistry of the two most stable conformers of both epimers, provides support in rationalizing the proposed reaction mechanism of the catalytic hydrogenolysis of the HMR to matairesinol (MAT). Copyright © 2009 John Wiley & Sons, Ltd. [source] Joint theoretical and experimental study of the gas-phase elimination kinetics of tert -butyl ester of carbamic, N, N -dimethylcarbamic, N -hydroxycarbamic acids and 1-(tert -butoxycarbonyl)-imidazoleJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2007Jose R Mora Abstract The gas-phase elimination kinetics of the title compounds were carried out in a static reaction system and seasoned with allyl bromide. The working temperature and pressure ranges were 200,280,°C and 22,201.5,Torr, respectively. The reactions are homogeneous, unimolecular, and follow a first-order rate law. These substrates produce isobutene and corresponding carbamic acid in the rate-determining step. The unstable carbamic acid intermediate rapidly decarboxylates through a four-membered cyclic transition state (TS) to give the corresponding organic nitrogen compound. The temperature dependence of the rate coefficients is expressed by the following Arrhenius equations: for tert -butyl carbamate logk1 (s,1),=,(13.02,±,0.46),,,(161.6,±,4.7) kJ/mol(2.303,RT),1, for tert -butyl N -hydroxycarbamate logk1 (s,1),=,(12.52,±,0.11),,,(147.8,±,1.1) kJ/mol(2.303,RT),1, and for 1-(tert -butoxycarbonyl)-imidazole logk1 (s,1),= (11.63,±,0.21),(134.9,±,2.0) kJ/mol(2.303,RT),1. Theoretical studies of these elimination were performed at Møller,Plesset MP2/6-31G and DFT B3LYP/6-31G(d), B3LYP/6-31G(d,p) levels of theory. The calculated bond orders, NBO charges, and synchronicity (Sy) indicate that these reactions are concerted, slightly asynchronous, and proceed through a six-membered cyclic TS type. Results for estimated kinetic and thermodynamic parameters are discussed in terms of the proposed reaction mechanism and TS structure. Copyright © 2007 John Wiley & Sons, Ltd. [source] Vitamin B2 -sensitized Photo-oxidation of DopaminePHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 5 2008Walter A. Massad Kinetics and mechanism of the photo-oxidation of the natural catecholamine-type neurotransmitter dopamine (DA) has been studied in aqueous solution, under aerobic conditions, in the presence of riboflavin (Rf, vitamin B2) as a photosensitizer. Results indicate the formation of a weak dark complex Rf,DA, with a mean apparent association constant Kass = 30 m,1, only detectable at DA concentrations much higher than those employed in photochemical experiments. An intricate mechanism of competitive reactions operates upon photoirradiation. DA quenches excited singlet and triplet states of Rf, with rate constants of 4.2 × 109 and 2.2 × 109 m,1 s,1, respectively. With the catecholamine in a concentration similar to that of dissolved molecular oxygen in air-saturated water, DA and oxygen competitively quench the triplet excited state of Rf, generating superoxide radical anion (O2,,) and singlet molecular oxygen (O2(1,g)) by processes initiated by electron and energy-transfer mechanisms, respectively. Rate constants values of 1.9 × 108 and 6.6 × 106 m,1 s,1 have been obtained for the overall and reactive (chemical) interaction of DA with O2(1,g). The presence of superoxide dismutase increases both the observed rates of aerobic DA photo-oxidation and oxygen uptake, due to its known catalytic scavenging of O2,,, a species that could revert the overall photo-oxidation effect, according to the proposed reaction mechanism. As in most of the catecholamine oxidative processes described in the literature, aminochrome is the DA oxidation product upon visible light irradiation in the presence of Rf. It is generated with a quantum yield of 0.05. [source] Synthesis of 4,5-Dihydroisoxazoles by Condensation of Primary Nitro Compounds with Alkenes by Using a Copper/Base Catalytic SystemCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2008Luca Cecchi Dr. Abstract A new procedure for the synthesis of 4.5-dihydroisoxazoles by condensation of primary nitro compounds with olefins by using a copper/base catalytic system is described. The catalytic effect of copper(II) salts is evidenced by comparison of the reaction rates. Thus, activated nitro compounds react faster than with organic catalysis by tertiary amines, whereas nitroalkanes, unable to condense with dipolarophiles in the presence of the base alone, undergo the reaction on addition of a copper(II) catalyst. The observed occurrence of induction periods in most reactions is ascribed to an equilibrium preceding the rate-determining step, and gives a hint as to the proposed reaction mechanism. The results indicate that this method might be of practical and general utility for synthetic practice. E, descritta una nuova procedura sintetica per la preparazione di 4,5-diidroisossazoli attraverso la condensazione di nitrocomposti primari con olefine. Il metodo si basa sull,utilizzo di un sistema catalitico costituito da rame(II) accompagnato da una base organica. L,effetto catalitico dei sali di rame(II) è stato evidenziato confrontando le velocità di conversione per alcune reazioni modello. Infatti, i nitrocomposti attivati reagiscono più velocemente che non in sola presenza di ammine terziarie mentre i nitroalcani, i quali non condensano con i dipolarofili in presenza della sola base, reagiscono per aggiunta di rame(II). Queste reazioni di condensazione hanno mostrato la presenza di tempi d,induzione variabili in funzione dei substrati e della tipologia di rame utilizzata. Il tempo d,induzione è imputabile a pre-equilibri che precedono lo stadio lento della reazione e sono in accordo con il meccanismo di reazione proposto. I risultati ottenuti mostrano che questo metodo è pratico e di utilità generale per la sintesi organica. [source] Re-examining the role of Lys67 in class C ,-lactamase catalysisPROTEIN SCIENCE, Issue 3 2009Yu Chen Abstract Lys67 is essential for the hydrolysis reaction mediated by class C ,-lactamases. Its exact catalytic role lies at the center of several different proposed reaction mechanisms, particularly for the deacylation step, and has been intensely debated. Whereas a conjugate base hypothesis postulates that a neutral Lys67 and Tyr150 act together to deprotonate the deacylating water, previous experiments on the K67R mutants of class C ,-lactamases suggested that the role of Lys67 in deacylation is mainly electrostatic, with only a 2- to 3-fold decrease in the rate of the mutant vs the wild type enzyme. Using the Class C ,-lactamase AmpC, we have reinvestigated the activity of this K67R mutant enzyme, using biochemical and structural studies. Both the rates of acylation and deacylation were affected in the AmpC K67R mutant, with a 61-fold decrease in kcat, the deacylation rate. We have determined the structure of the K67R mutant by X-ray crystallography both in apo and transition state-analog complexed forms, and observed only minimal conformational changes in the catalytic residues relative to the wild type. These results suggest that the arginine side chain is unable to play the same catalytic role as Lys67 in either the acylation or deacylation reactions catalyzed by AmpC. Therefore, the activity of this mutant can not be used to discredit the conjugate base hypothesis as previously concluded, although the reaction catalyzed by the K67R mutant itself likely proceeds by an alternative mechanism. Indeed, a manifold of mechanisms may contribute to hydrolysis in class C ,-lactamases, depending on the enzyme (wt or mutant) and the substrate, explaining why different mutants and substrates seem to support different pathways. For the WT enzyme itself, the conjugate base mechanism may be well favored. [source] | ||||||||||