A study of the atmospherically relevant reaction between molecular chlorine and dimethylsulfide (DMS): establishing the reaction intermediate and measurement of absolute photoionization cross-sections

In a study using UV photoelectron spectroscopy (PES) of the atmospherically relevant reaction CH3SCH3 + Cl2 → CH3SCH2Cl + HCl bands associated with a reaction intermediate have been observed. These have been assigned to ionization of the covalently bound molecule (CH3)2SCl2 on the basis of the intensity of the observed bands as a function of reaction time, molecular orbital calculations of vertical ionization energies and evidence from infrared spectroscopy. A method has also been developed, with the flow-tube/PE spectrometer combination used, to measure photoionization cross-sections of the reagents and products at the photon energy utilized and this has allowed the photoionization cross-section of the intermediate to be estimated. This work augments an earlier study in which the rate constant of the reaction between CH3SCH3 (DMS) and Cl2 has been measured at room temperature.

A pentacyclic reaction intermediate of riboflavin synthase

The S41A mutant of riboflavin synthase from Escherichia coli catalyzes the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a very low rate. Quenching of presteady-state reaction mixtures with trifluoroacetic acid afforded a compound with an absorption maximum at 412 nm (pH 1.0) that can be converted to a mixture of riboflavin and 6,7-dimethyl-8-ribityllumazine by treatment with wild-type riboflavin synthase. The compound was shown to qualify as a kinetically competent intermediate of the riboflavin synthase-catalyzed reaction. Multinuclear NMR spectroscopy, using various 13C- and 15N-labeled samples, revealed a pentacyclic structure arising by dimerization of 6,7-dimethyl-8-ribityllumazine. Enzyme-catalyzed fragmentation of this compound under formation of riboflavin can occur easily by a sequence of two elimination reactions.

Enzymology, structure, and dynamics of acetohydroxy acid isomeroreductase

Acetohydroxy acid isomeroreductase is a key enzyme involved in the biosynthetic pathway of the amino acids isoleucine, valine, and leucine. This enzyme is of great interest in agrochemical research because it is present only in plants and microorganisms, making it a potential target for specific herbicides and fungicides. Moreover, it catalyzes an unusual two-step reaction that is of great fundamental interest. With a view to characterizing both the mechanism of inhibition by potential herbicides and the complex reaction mechanism, various techniques of enzymology, molecular biology, mass spectrometry, X-ray crystallography, and theoretical simulation have been used. The results and conclusions of these studies are described briefly in this paper.

Facile crystallization of Escherichia coli ketol-acid reductoisomerase

Ketol-acid reductoisomerase (EC 1.1.1.86) catalyses the second reaction in the biosynthesis of branched-chain amino acids. The reaction involves an Mg2+-dependent alkyl migration followed by an NADPH-dependent reduction of the 2-keto group. Here, the crystallization of the Escherichia coli enzyme is reported. A form with a C-terminal hexahistidine tag could be crystallized under 18 different conditions in the absence of NADPH or Mg2+ and a further six crystallization conditions were identified with one or both ligands. With the hexahistidine tag on the N-terminus, 20 crystallization conditions were found, some of which required the presence of NADPH, NADP(+), Mg2+ or a combination of ligands. Finally, the selenomethionine-substituted enzyme with the N-terminal tag crystallized under 15 conditions. Thus, the enzyme is remarkably easy to crystallize. Most of the crystals diffract poorly but several data sets were collected at better than 3.2 Angstrom resolution; attempts to phase them are currently in progress.

Cyclopropane-1,1-dicarboxylate is a slow-, tight-binding inhibitor of rice ketol-acid reductoisomerase

Ketol-acid reductoisomerase (EC 1.1.1.86) catalyses the second reaction in the biosynthesis of the branched-chain amino acids. The reaction catalyzed consists of two stages, the first of which is an alkyl migration from one carbon atom to its neighbour. The likely transition state is therefore a cyclopropane derivative, and cyclopropane-1,1-dicarboxylate(CPD) has been reported to inhibit the Escherichia coli enzyme. In addition, this compound causes the accumulation of the substrate of ketol-acid reductoisomerase in plants. Here, we investigate the inhibition of the purified rice enzyme. The cDNA was cloned, and the recombinant protein was expressed in E. coli, purified and characterized kinetically. The purified enzyme is strongly inhibited by cyclopropane-1,1-dicarboxylate, with an inhibition constant of 90 nM. The inhibition is time-dependent and this is due to the low rate constants for formation (2.63 X 10(5) M-1 min(-1)) and dissociation (2.37 x 10(-2) min(-1)) of the enzyme-inhibitor complex. Other cyclopropane derivatives are much weaker inhibitors while dimethylmalonate is moderately effective. (c) 2004 Elsevier Ireland Ltd. All rights reserved.

Time-resolved gas-phase kinetic study of the germylene addition reaction, GeH2 + C2D2

Time-resolved studies of germylene, GeH2, generated by laser. ash photolysis of 3,4-dimethyl-1-germacyclopent-3-ene, have been carried out to obtain rate coefficients for its bimolecular reaction with C2D2. The reaction was studied in the gas phase, mainly at a total pressure of 1.3 kPa (in SF6 bath gas) at five temperatures in the range 298-558 K. Pressure variation measurements over the range 0.13-13 kPa ( SF6) at 298, 397 and 558 K revealed a small pressure dependence but only at 558 K. After correction for this, the second-order rate coefficients gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.96 +/- 0.05) + ( 6.16 +/- 0.37 kJ mol(-1))/RT ln 10 Comparison with the reaction of GeH2 + C2H2 (studied earlier) showed a similar behaviour with almost identical rate coefficients. The lack of a significant isotope effect is consistent with a rate-determining addition process and is explained by irreversible decomposition of the reaction intermediate to give Ge(P-3) + C2H4. This result contrasts with that for GeH2 + C2H4/C2D4 and those for the analogous silylene reactions. The underlying reasons for this are discussed.

In Situ Infrared (FTIR) Study of the Mechanism of the Borohydride Oxidation Reaction on Smooth Pt Electrode

Although Pt has been thoroughly studied regarding its activity for the borohydride oxidation reaction (BOR), the BOR mechanism at Pt remains unclear: Depending on the applied potential, spontaneous BH(4)(-) hydrolysis can compete with the direct BOR. The goal of the present work is to provide more insight into the behavior of smooth Pt electrodes toward the BOR, by coupling in situ infrared reflectance spectroscopy with electrochemistry. The measurements were performed on a Pt electrode in 1 M NaOH/1 M NaBH(4), so as to detect the reaction intermediate species generated as a function of the applied potential. Several bands were monitored in the B-H ((v) over bar approximate to 1180, 1080, and 972 cm(-1)) and B-O ((v) over bar = 1325 and similar to 1425 cm(-1)) bond regions upon increased electrode polarization. These absorption bands, which appear sequentially and were already detected for similar measurements on Au electrodes, are assigned to BH(3), BH(2), and BO(2)(-) species. In light of these experimental data and previous results obtained in our group for Pt- or Au-based electrodes, possible initial elementary steps of the BOR on platinum electrodes are proposed and discussed according to the relevant literature data.

Reaction of Copper(II) Chloroacetate with Pyrazole. Synthesis of a One-Dimensional Coordination Polymer and Unexpected Dehydrochlorination Reaction

The reaction of copper(II) chloroacetate (1d) with pyrazole (Hpz) mainly yielded the mononuclear compound [Cu(μ-ClCH2COO)2(Hpz)2] (2m), which self-assembled generating a one-dimensional coordination polymer. Moreover, the concomitant isolation of the tetranuclear [{Cu2(μ-pz)(μ-OCH2COO)(Hpz)(MeOH)}2(μ-ClCH2COO)2] (3t) and hexanuclear [{Cu3(μ3-OH)(μ-pz)3(Hpz)2}2(μ-ClCH2COO)2](Cl)2 (4h) species evidenced the occurrence of a peculiar, previously unreported, dehydrochlorination reaction and the formation of the trinuclear triangular moiety [Cu3(μ3-OH)(μ-pz)3]. Theoretical calculations based on density functional theory including solvation effects indicate a possible pathway for the formation of 3t. Interestingly, besides the energy minimum corresponding to 3t, a further relative energy minimum is found for a species which can be considered a possible reaction intermediate.

The crystal structures of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate

Acetohydroxyacid synthase (AHAS) and acetolactate synthase (ALS) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the decarboxylation of pyruvate to give a cofactor-bound hydroxyethyl group, which is transferred to a second molecule of pyruvate to give 2-acetolactate. AHAS is found in plants, fungi, and bacteria, is involved in the biosynthesis of the branched-chain amino acids, and contains non-catalytic FAD. ALS is found only in some bacteria, is a catabolic enzyme required for the butanediol fermentation, and does not contain FAD. Here we report the 2.3-Angstrom crystal structure of Klebsiella pneumoniae ALS. The overall structure is similar to AHAS except for a groove that accommodates FAD in AHAS, which is filled with amino acid side chains in ALS. The ThDP cofactor has an unusual conformation that is unprecedented among the 26 known three-dimensional structures of nine ThDP-dependent enzymes, including AHAS. This conformation suggests a novel mechanism for ALS. A second structure, at 2.0 Angstrom, is described in which the enzyme is trapped halfway through the catalytic cycle so that it contains the hydroxyethyl intermediate bound to ThDP. The cofactor has a tricyclic structure that has not been observed previously in any ThDP-dependent enzyme, although similar structures are well known for free thiamine. This structure is consistent with our proposed mechanism and probably results from an intramolecular proton transfer within a tricyclic carbanion that is the true reaction intermediate. Modeling of the second molecule of pyruvate into the active site of the enzyme with the bound intermediate is consistent with the stereochemistry and specificity of ALS.

Low-Spin Heme b3 in the Catalytic Center of Nitric Oxide Reductase from Pseudomonas nautica

Biochemistry, 2011, 50 (20), pp 4251–4262 DOI: 10.1021/bi101605p

Frequent nitric oxide synthase-2 expression in human colon adenomas: implication for tumor angiogenesis and colon cancer progression.

An increased expression of nitric oxide synthase (NOS) has been observed in human colon carcinoma cell lines as well as in human gynecological, breast, and central nervous system tumors. This observation suggests a pathobiological role of tumor-associated NO production. Hence, we investigated NOS expression in human colon cancer in respect to tumor staging, NOS-expressing cell type(s), nitrotyrosine formation, inflammation, and vascular endothelial growth factor expression. Ca2+-dependent NOS activity was found in normal colon and in tumors but was significantly decreased in adenomas (P < 0.001) and carcinomas (Dukes' stages A-D: P < 0.002). Ca2+-independent NOS activity, indicating inducible NOS (NOS2), is markedly expressed in approximately 60% of human colon adenomas (P < 0.001 versus normal tissues) and in 20-25% of colon carcinomas (P < 0.01 versus normal tissues). Only low levels were found in the surrounding normal tissue. NOS2 activity decreased with increasing tumor stage (Dukes' A-D) and was lowest in colon metastases to liver and lung. NOS2 was detected in tissue mononuclear cells (TMCs), endothelium, and tumor epithelium. There was a statistically significant correlation between NOS2 enzymatic activity and the level of NOS2 protein detected by immunohistochemistry (P < 0.01). Western blot analysis of tumor extracts with Ca2+-independent NOS activity showed up to three distinct NOS2 protein bands at Mr 125,000-Mr 138,000. The same protein bands were heavily tyrosine-phosphorylated in some tumor tissues. TMCs, but not the tumor epithelium, were immunopositive using a polyclonal anti-nitrotyrosine antibody. However, only a subset of the NOS2-expressing TMCs stained positively for 3-nitrotyrosine, which is a marker for peroxynitrite formation. Furthermore, vascular endothelial growth factor expression was detected in adenomas expressing NOS2. These data are consistent with the hypothesis that excessive NO production by NOS2 may contribute to the pathogenesis of colon cancer progression at the transition of colon adenoma to carcinoma in situ.

UDP-N-acetilglicosamina enolpiruvil transferase: determinação dos estados de protonação de resíduos de aminoácidos do sítio ativo pelo método PM6

UDP-N-acetylglucosamine-enolpyruvyl transferase (MurA) catalyzes the reaction between phosphoenol pyruvate and UDP-N-acetylglucosamine. We present a theoretical approach using the semiempirical PM6 method for defining protonation state of three active site residues, K22, H125, and K160. Prior comparison with neutron diffraction data showed that PM6 accurately predicted protonation states of active site residues of b-trypsin and D-xylose isomerase. Using the same methodology with MurA crystallographic data, we conclude that when reaction intermediate is located at the active site, H125 and K22 are in protonated form and K160 in neutral form.

Avaliação da atividade antimicrobiana de soluções de flumequina submetidas aos processos eletroquímico e foto-eletroquímico

Flumequine degradation by electrochemical and photo-electrochemical processes was evaluated in this study. The antimicrobial activity of the solutions subjected to the electrochemical processes was monitored during the assays. The experiments were carried out using DSA® (dimensionally stable anode) electrode. The influence of current density was investigated for the 7.5 to 45 mA cm-2 range. The photo-electrochemical process was more efficient for degrading flumequine (85%) and reducing solution antimicrobial activity. For both processes, the residual antimicrobial activity decreased as flumequine degradation increased. The reaction intermediate m/z 244 (5-methyl-1-oxo-6,7-dihydro-1H,5H-pyrido[3,2,1-ij]quinoline-2-carboxylic acid) was identified.

Elementary steps in aqueous proton transfer reactions : a first principles molecular dynamics study

La nature des acides dans un environnement aqueux est primordiale dans de nombreux aspects de la chimie et de la biologie. La caractéristique principale d'un acide est sa capacité à transférer un proton vers une molécule d'eau ou vers n'importe quelle base, mais ce procédé n'est pas aussi simple qu'il y paraît. Il peut au contraire être extrêmement complexe et dépendre de manière cruciale de la solvatation des différents intermédiaires de réaction impliqués. Cette thèse décrit les études computationnelles basées sur des simulations de dynamique moléculaire ab initio qui ont pour but d'obtenir une description à l'échelle moléculaire des divers procédés de transferts de proton entre acide et bases dans un milieu aqueux. Pour cela, nous avons étudié une serie de système, dont l'acide hydrofluorique aqueux, l'acide trifluoroacétique aqueux, et un système modèle constitué d'un phénol et d'une entité carboxylate reliés entre eux par une molécule d'eau en solution aqueuse. Deux états intermédiaires ont été identifiés pour le transfert d'un proton depuis un acide. Ces intermédiaires apparaissent stabilisés par un motif local de solvatation via des ponts H. Leurs signatures spectroscopiques ont été caractérisées au moyen de la spectroscopie infrarouge, en utilisant le formalisme de la dynamique moléculaire ab initio, qui inclut l'effet quantique nucléaire de manière explicite. Cette étude a aussi identifié trois chemins de réaction élémentaire, qui sont responsable pour le transfert d'un proton d'un acide à une base, ainsi que leurs échelles de temps caractéristiques. Les conclusions tirées de ces études sont discutées dans les détails, au niveau moléculaire, avec une emphase sur les comparaisons entre les résultats théoriques et les mesures expérimentales obtenues dans a littérature ou via des collaborateurs.

Caracterización de las reacciones adversas a medicamentos como causa de ingreso a una unidad de cuidado intermedio en un hospital de tercer nivel de atención

Objetivo: Determinar la ocurrencia de reacciones adversas a medicamentos (RAM) como causa de ingreso a una unidad de cuidado intermedio de un hospital universitario. Materiales y Métodos: Se revisaron las historias clínicas de los pacientes admitidos a la Sala de Emergencias – Cuidado Intermedio (SALEM) entre septiembre y diciembre de 2012 que cumplieron los criterios de inclusión y se detectaron los casos sospechosos de reacción adversa a medicamento (RAM) que posteriormente fueron evaluados por cuatro investigadores respecto a la causalidad a través del Algoritmo de Naranjo, prevenibilidad usando los criterios de Shumock y Thornton y la clasificación clínica mediante el empleo del sistema DoTS. Resultados: Se encontraron 96 pacientes que presentaron 108 casos de RAM. Las RAM más frecuentes fueron las arritmias y la hemorragia de vías digestivas altas (12.04%), 20.3% de los casos correspondieron a fallos terapéuticos, y, los medicamentos mayormente asociados fueron el ácido acetil salicílico (15.74%) y el losartán (10.19%). 46 casos fueron catalogados como posibles y uno solo como definitivo. Usando la clasificación DoTS se estableció que en el 82.4% de los casos la dosis era colateral (dentro del rango de dosis terapéutica), 89.8% fueron independientes del tiempo, y entre los factores mayormente asociados a susceptibilidad a la RAM estuvieron las comorbilidades (41.7%) y la edad (49%). 44% de las RAM fueron prevenibles. Conclusión: Las RAM son una causa de ingreso no despreciable en una unidad de cuidado intermedio para las cuales existen diferentes sistemas de evaluación, y una cantidad significativa de ellas es prevenible. Se requieren más estudios a nivel nacional para evaluar la incidencia de estas y establecer estándares de clasificación y medidas para mitigar su efecto.