On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.     

Reactions of thiosemicarbazones derived from beta-keto amides and beta-keto esters with Zn(II) and Cd(II) acetates: influence of metal, substitution, reagent ratio and temperature on metal-induced cyclization

Zinc(II) and cadmium(II) acetates were reacted in methanol under various experimental conditions with thiosemicarbazones derived from beta-keto amides or beta-keto esters (HTSC). Some of these reactions afforded thiosemicarbazonate complexes [M(TSC)2] with IR and NMR spectra compatible with N,S-coordination, but most gave complexes [ML2], where HL is a substituted 2,5-dihydro-5-oxo-1H-pyrazole-1-carbothioamide resulting from cyclization of the HTSC. Some of these pyrazolonates and two of the HL ligands were studied by X-ray diffractometry, and their structures are discussed. Surprisingly, the reactions of zinc(II) acetate with HTSC in 1:1 mol ratio usually gave a third, previously unreported type of complex with a dideprotonated ligand, [Zn(L-H)], which was also formed when [ZnL2] and Zn(OAc)2 interacted at room temperature in 1:1 mol ratio. These L-H complexes are highly insoluble in all common solvents, which hinders their characterization but suggests that they are polymeric in nature.     

Evolution of the structural stability of large Cu,Ni, Pd,and Ag clusters with size: An analysis within the embedded atom method

A study of the structural stability of clusters made up of a single component has been carried out within the Embedded Atom Method. Perfect icosahedral and cuboctahedral Cu, Ni, Pd, and Ag clusters with up to 5083 atoms have been compared. The icosahedron is found to be the stable structure for small clusters, and a change of structure from icosahedral to cuboctahedral is found as the cluster size increases. A contraction of the interatomic distances results when the cluster size decreases.     

Sample stacking with matrix removal for the determination of paraquat, diquat and difenzoquat in water by capillary electrophoresis

Conditions for the simultaneous determination of paraquat, diquat and difenzoquat by capillary zone electrophoresis using a stacking technique in a chemically modified capillary have been established. To apply the stacking method with sample matrix removal for the analysis of cations, an anodic electroosmotic flow is mandatory. For quats, 50 mM acetic acid-ammonium acetate (pH 4.0) with 5% (v/v) methanol as electrophoretic buffer and the addition of 0.8 mM cetyltrimethylammonium bromide as wall capillary organic modifier was proposed. Field polarity reversal time was optimised for several sample matrices. Detection was carried out at 220 and 255 nm. Detection limits, based on a signal-to-noise ratio of 3:1, were lower than 15 microg l(-1) for standards in Milli-Q water and two to ten times higher for drinking water samples. Run-to-run and day-to-day reproducibility have been established. The method was successfully applied to the determination of the three herbicides in spiked drinking water.     

Cellulose microfibrils from banana farming residues: isolation and characterization

Cellulose microfibrils have been prepared from banana rachis using a combination of chemical and mechanical treatments. The morphology and structure of the samples were characterized using transmission electron microscopy, atomic force microscopy, and X-ray diffraction. Fourier-transformed infrared spectroscopy (FTIR) was used to characterize the chemical modifications of the samples after each treatment. Suspensions of bundled or individualized 5-nm-wide microfibrils were obtained after homogenization (PH) whereas an organosolv (PO) treatment resulted in shorter aggregates of parallel cellulose microcrystallites. The sharper rings in the X-ray diffraction pattern of the PO-treated sample suggest a higher crystallinity due to a more efficient removal of hemicelluloses and dissolution of amorphous zones by the acid treatment. Both microfibrils and microcrystals prepared by both methods can be used as reinforcing filler in nanocomposite materials.     

Use of highly efficient Draper-Lin small composite designs in the formal optimisation of both operational and chemical crucial variables affecting a FIA-chemiluminescence detection system

A new formal strategy in the multidimensional optimisation of the experimental variables affecting the chemiluminescence (CL) detection in flow injection analysis (FIA) is proposed here. The strategy implies several steps, being the most significant: selection of the variables to be studied and their experimental domain; use of a screening design to detect significant variables and interactions into the experimental region; study of the main effect of variables and second-order interactions; and finally application of a Draper-Lin small composite design (orthogonal) to obtain the optimum values of the significant variables. The methodology is applied to the determination of methylamine by FIA based on the use of the peroxyoxalate CL (PO-CL) reaction. Considering the high number of experiments required due to the different chemical and instrumental variables to be taken account and their adequate compatibility to obtain maximum sensitivity, the methodology offers a rigorous study of the main effects and interactions, achieving a reduction of experimental work.     

Application of principal component regression to luminescence data for the screening of ciprofloxacin and enrofloxacin in animal tissues

A new screening method for the analysis of enrofloxacin and ciprofloxacin in edible animal tissues is described. The method is based on the application of principal component regression to luminescence measurements after reaction of quinolones with terbium(III) in a micellar medium. The method was used, first, to discriminate between quinolone-containing or quinolone-not-containing samples (concentration below the detection limit) and, then, to quantify the sum of both analytes. Standards in a pure-water matrix, using the first three principal components, were used for the determination. RRMSE range from 4 to 10% depending on the analyte. Calibration was successfully applied to the analysis of spiked chicken and trout muscle at concentrations between 10 and 50 micrograms kg-1.     

Synthesis of bridgehead nitrogen heterocycles from pyrylium salts and β-functionalized amines

β-Functionalized primary amines are converted by the 2-ethoxycarbonyl-4,6-diphenylpyrylium cation into the corresponding bicyclic salts 2 . The N-substituted 4,6-diphenylpyridine-2-thiones 6 undergo cyclization to the byciclic compounds 8 by action of methyl iodide.     

Algebraic study of chiral anomalies

The algebraic structure of chiral anomalies is made globally valid on non-trivial bundles by the introduction of a fixed background connection. Some of the techniques used in the study of the anomaly are improved or generalized, including a systematic way of generating towers of descent equations.This work was supported in part by the Director, Office of Energy Research, Office of High Energy and Nuclear Physics, Division of High Energy Physics of the U.S. Department of Energy under contract DE-AC03-76SF00098 and in part by the National Science Foundation under research grant PHY81-18547