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.     

Derivative spectrophotometric resolution of mixtures of the food colourants Tartrazine, Amaranth and Curcumin in a micellar medium

A study of the absorption spectra of the food colourants Tartrazine (E-102), Amaranth (E-123) and Curcumin (E-100) in various organic solvents and pH media, have been carried out. In addition, the spectral behaviour in aqueous micellar systems of anionic, cationic and non-ionic surfactants, as well as beta-cyclodextrin, was investigated. Analytical methods are proposed for the determination of the three dyes in mixtures without any prior separation step, by the application of the derivative technique to the normal absorption spectra, based on the use of cetyltrimethylammonium bromide (CTAB) in 0.1 M NaOH, over the concentration range 2-50 mug ml(-1). The methods are applied for determining the three dyes in commercial food products.     

Computing the Fukui function from ab initio quantum chemistry: approaches based on the extended Koopmans’ theorem

The extended Koopmans’ theorem is related to Fukui function, which measures the change in electron density that accompanies electron attachment and removal. Two approaches are used, one based on the extended Koopmans’ theorem differential equation and the other based directly on the expression of the ionized wave function from the extended Koopmans’ theorem. It is observed that the Fukui function for electron removal can be modeled as the square of the first Dyson orbital, plus corrections. The possibility of useful generalizations to the extended Koopmans’ theorem is considered; some of these extensions give approximations, or even exact expressions, for the Fukui function for electron attachment.