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.     

Effect of particle geometry on phase transitions in two-dimensional liquid crystals

Using a version of density-functional theory which combines Onsager approximation and fundamental-measure theory for spatially nonuniform phases, we have studied the phase diagram of freely rotating hard rectangles and hard discorectangles. We find profound differences in the phase behavior of these models, which can be attributed to their different packing properties. Interestingly, bimodal orientational distribution functions are found in the nematic phase of hard rectangles, which cause a certain degree of biaxial order, albeit metastable with respect to spatially ordered phases. This feature is absent in discorectangles, which always show unimodal behavior. This result may be relevant in the light of recent experimental results which have confirmed the existence of biaxial phases. We expect that some perturbation of the particle shapes (either a certain degree of polydispersity or even bimodal dispersity in the aspect ratios) may actually destabilize spatially ordered phases thereby stabilizing the biaxial phase.     

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.     

Further studies on the chemistry and structure of n-oxides of sparteine and its derivatives—V: Synthesis and structure of 2-phenylsparteine-n16-oxide,a new case of “sponge” proton

The synthesis of 2-phenylsparteine-N₁₆-oxide (7) and its perchlorate salt (7-H⁺) was carried out. On the basis of spectral data, and by comparison with appropriate sparteine-N-oxides, the mechanism of formation and the structures of the two new compounds were proposed. It was found, the basicity of the new N-oxide is unexpectedly high and comparable to the basicity of quaternary ammonium hydroxides. The structure and the strength of intramolecular H-bond in 7-H⁺ makes 7 an excellent “catcher” proton or specific ”sponge” proton.     

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.     

Synthesis of different chiral amino gamma-butyrolactones and amino gamma-butenolides

Different transformations of chiral epoxy esters 1 afford two different amino gamma-butyrolactones 2 and 6, and amino gamma-butenolides 8, by different nucleophilic opening-closing processes. [reaction: see text]     

Electrochemical behaviour of an indium electrode in concentrated KOH solutions at different temperatures

Summary The electrochemical behaviour of pure indium in KOH solutions (1–4M) was studied at different temperatures (25–70°C) by potentiostatic techniques. Two anodic peaks corresponding to the formation of In(OH)₃ and In₂O₃ were observed. The heights of the two peaks increased with the increase of alkali concentration. An increase of temperature increased the peak currents and shifted their corresponding potentials to more negative values. The variation of the peak currents and peak potentials with scan rate suggested that the anodic dissolution of indium was a diffusion controlled process. In cyclic voltammetry, the reverse scan consistently showed one peak which was attributed to the reduction of anodic oxidation products into indium. X-ray diffraction analysis confirmed the presence of In(OH)₃ at the first anodic peak, In(OH)₃ and In₂O₃ at the second anodic peak and In₂O₃ in the permanent passive region.

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Zum elektrochemischen Verhalten einer Indium-Elektrode in konzentrierter Kalilauge bei verschiedenen Temperaturen

Zusammenfassung Es wurde das Verhalten von reinem Indium in 1 – 4M KOH-Lösungen bei Temperaturen zwischen 25 und 70°C mittels potentiostatischer Methoden untersucht. Zwei anodische Peaks, entsprechend der Bildung von In(OH)₃ und In₂O₃, traten auf. Die Höhe der beiden Peaks wurde mit zunehmender Alkalikonzentration gesteigert. Eine Temperaturerhöhung verstärkte die Peakströme und verschob die entsprechenden Potentiale zu negativeren Werten. Die Abhängigkeit der Peakströme und Peakpotentiale von der Scangeschwindigkeit legte den Schluß nahe, daß die anodische Lösung von Indium in einem diffusionskontrollierten Prozeß stattfindet. Bei der cyclischen Voltammetrie zeigte der reverse Scan einheitlich einen Peak, der der Reduktion der anodischen Oxidationsprodukte zu Indium zugeschrieben wurde. Röntgendiffraktionsanalyse bestätigte die Präsenz von In(OH)₃ beim ersten anodischen Peak, In(OH)₃ beim zweiten Peak und In₂O₃ im permanent passiven Bereich.

     

Calculation of cross sections for positron-Ar collisions

The three-body classical trajectory Monte-Carlo (CTMC) method is used to investigate positron-argon atom collisions. The total ionization cross sections are presented along with singly and doubly differential cross sections. The existence of the cusp-like peak in the triply differential electron and positron spectra at positron impact is predicted.     

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.