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.     

Electron diffraction studies of the molecular structures of iron(II) chloride and iron(II) bromide. Evidence on the structure of dimeric species Fe2Br4

An expression for the extreme values of mean-square amplitudes of vibrations in polyatomic molecules has been derived which permits estimation of the mean-square amplitude without solving the vibrational problem. This expression can be improved for the stretching and scissoring modes when the assignment of frequencies is known. In turn, the corresponding vibrational frequency may be estimated from the experimental value of the mean-square amplitude. The mean-square amplitudes of the butadiene-1,3 molecule are considered as an example.     

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.     

Study of 7-azaindole in its first four singlet states

The molecular structure and properties of 7-azaindole in its first four singlet states were studied with a view to improving current understanding of the photophysical behavior of its C(2h) dimer. This dimer, which exhibits a double proton transfer via its two hydrogen bonds upon electronic excitation, has for 35 years been used as a model for the photophysical behavior of DNA base pairs. Electronic excitation of 7-azaindole simultaneously increases its acidity and basicity; these changes facilitate a concerted mechanism for the double proton transfer in the dimer. In this work, we found the acidity and basicity changes to occur only in its first pi,pi(*) excited singlet state.     

Polarization of the Electrical Double Layer. Time Evolution after Application of an Electric Field

Electrophoresis is one of the electrokinetic phenomena most widely investigated, both from a fundamental point of view and as a research tool in academia and industry. However, the dependence between electrophoretic mobility and zeta potential is, in a general case, far from simple, because of the many physical processes involved. In this work, we first describe qualitatively and (in some cases) quantitatively the time behavior of the dipole moment induced in the electrical double layer by an applied electric field. Further, a simple relationship is deduced between the dipole moment and the electrophoretic mobility. Through the analysis of the time dependence of the former, it is possible to resolve the different contributions to the stationary values of the mobility. Three characteristic relaxation times are distinguished in the time evolution of the dipole moment: tau(H) (the time needed for hydrodynamic flows to be established), tau(MW) (time for ionic electromigration to develop), and tau(VD) (after this time, diffusion flows are established in the system, and the double layer polarization is complete). This means that different mechanisms are operating on the double layer for different times after the application of the field, and that computing the mobility at such different times is equivalent to calculating the steady-state electrophoretic mobility under different approximations. A comparison is shown between estimated and computed mobility values as functions of time and of zeta potential, confirming the validity of the asymptotic calculations. Copyright 2000 Academic Press.     

Analytische Aspekte der Oxydation organischer Stickstoffverbindungen mit Chromsäure. XXVIII

Zusammenfassung Die schon früher beschriebene gasvolumetrische Methode zur N-N-Gruppenbestimmung durch Oxydationsaufschluß mit Chromsäure wurde zur Bestimmung des heterocyklischen Stickstoffes in Indazolinonderivaten mit Erfolg benützt und dadurch weiter die allgemeine Anwendbarkeit der Methode bestätigt. Enthält die Substanz gleichzeitig Amino- oder Nitrogruppen, können diese aus derselben Einwaage als Ammoniak bzw. Salpetersäure bestimmt werden.

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Analytical aspects of the oxidation of organic nitrogen compounds with chromic acid

Summary The gas volumetric method for determining N-N groups by oxidative fusion with chromic acid (which has already been described previously) was successfully employed to determine the heterocyclic nitrogen in indazolinone derivatives. The general applicability of the method was thereby confirmed. If the substance contains amino or nitro groups at the same time, these can be determined in the same sample as ammonia or nitric acid.

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XXVII. Mitteilung, siehe¹.     

Application of partial least-squares regression to the resolution of highly correlated spectra. Simultaneous spectrofluorimetric determination of Al(3+), Ga(3+) and In(3+)

The simultaneous spectrofluorimetric determination of mixtures of aluminium, gallium and indium as their 8-hydroxyquinoline complexes following extraction into chloroform is studied. The high collinearity of the spectra hindered their resolution by multiple linear regression (MLR) methodology; therefore, experimental data were processed by partial least-squares regression (PLSR) methodology. A previous step in the study of three-dimensional fluorescence spectrum is possible to select the best information to quantify this system with high collinearity. Finally the optimal conditions for quantitation, the best data preprocessing procedure and the most suitable spectral mode for calibration were established. Using an external set allowed the three analytes to be determined simultaineously at concentrations below 1 mug ml(-1) with errors less than 10% for aluminium and indium, and 15% for gallium.     

Synthesis and acid-base properties of (1H-benzimidazol-2-yl-methyl)phosphonate (Bimp2-). Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N-1)H and the phosphonate group

The synthesis of (1H-benzimidazol-2-yl-methyl)phosphonic acid, H2(Bimp)+/-, is described: 2-chloromethylbenzimidazole was reacted with ethylchloroformate to give 1-carboethoxy-2-chloromethylbenzimidazole which was treated with trimethyl phosphite and after hydrolysis with aqueous HBr H2(Bimp)+/- was obtained. In H2(Bimp)+/- one proton is at the N-3 site and the other at the phosphonate group; both acidity constants were determined in aqueous solution by potentiometric pH titrations (25 degrees C; I = 0.1 M, NaNO3) and this furnished the pKa values of 5.37 +/- 0.02 and 7.41 +/- 0.02, respectively. The acidity constant for the release of the primary proton from the P(O)(OH)2 group of H3(Bimp)+ was estimated: pKa = 1.5 +/- 0.2. Moreover, Bimp2- can be further deprotonated at its neutral (N-1/N-3)H site to give the benzimidazolate residue, but this reaction occurs only in strongly alkaline solution (KOH); application of the H_ scale developed by G. Yagil (J. Phys. Chem., 1967, 71, 1034) together with UV spectrophotometric measurements gave pKa = 14.65 +/- 0.12. Comparisons with acidity constants taken from the literature show that this latter pKa value is far too large and this allows the conclusion that an intramolecular hydrogen bond is formed between the (N-1/N-3)H site and the phosphonate group of Bimp2-; the formation degree of this hydrogen-bonded isomer is estimated to be 98 +/- 2%. The general relevance of this and the other results are shortly discussed and the species distribution for the Bimp system in dependence on pH is provided.     

Synthesis of vinca alkaloids and related compounds. 100. Stereoselective oxidation reactions of compounds with the aspidospermane and quebrachamine ring system. First synthesis of some alkaloids containing the epoxy ring

The first syntheses of the alkaloids (-)-mehranine (3), (+)-voaphylline/conoflorine (4), (+)-N(a)-methylvoaphylline/hecubine (5), and (-)-lochnericine (2) were achieved by stereoselective epoxidation starting from (-)-tabersonine (1), through intermediates with the aspidospermane and quebrachamine skeleton.