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  • 1
    Electronic Resource
    Electronic Resource
    Effect of Solvation on Ozonolysis Reaction Intermediates and Transition States (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 608-617 
    Details
    ISSN: 0948-5023
    Keywords: Ozonolysis ; Ozone ; Reaction mechanisms ; Solvent effects ; Theoretical calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Electrostatic solvent effects on the ozonolysis of ethylene have been investigated using correlated ab initio and density functional approaches. We use a simple polarizable continuum model for the solvent. It allows us to evaluate the medium effect on both the electronic and nuclear structure of the chemical species involved in the reaction. The computations confirm that basically the reaction proceeds through the Criegee mechanism. However, formation of the van der Waals complexes ethyl-ene/ozone and carbonyl oxide/formaldehyde also appears to play a role. All the calculated species are stabilized with respect to the reactants except the transition state corresponding to the primary ozonide formation. In general, electrostatic solvent effects are relatively small for activation barriers of single reaction steps and more substantial for the corresponding reaction energies. Moreover, the medium significantly modifies the structure of some species for which polarization effects are crucial.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060608
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  • 2
    Electronic Resource
    Electronic Resource
    Insights in the Peptide Hydrolysis Mechanism by Thermolysin: A Theoretical QM/MM study (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 527-538 
    Details
    ISSN: 0948-5023
    Keywords: Hybrid methods ; QM/MM ; LSCF ; Zinc metalloproteases ; Thermolysin ; Peptide hydrolysis ; Enzymatic mechanism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The hydrolysis by thermolysin of a Gly-Phe-Leu peptide, considered as a model substrate of the enkephalin family, has been studied with a mixed QM/MM method with the AM1/AMBER parameterization. This study is based on the mechanism proposed by Matthews in which the Glu-143 residue plays the role of a proton shuttle in the course of the reaction. The study focused on the description of every step of the process, reaction intermediates and transition states, and on the influence, both energetical and structural, of the whole protein on these stationary points. The overall mechanism appears to be quite realistic, but the study shows that some reaction steps that were assumed to be concerted should occur in two phases. Analysis of the role of the amino-acids surrounding the active site has shown their important participation in the fluctuations of the energy. In particular, the major role of His-231 on the overall mechanism has been confirmed. This study shows that modeling reaction mechanisms for enzymes is quite feasible and opens the way for computer experiments that may be helpful in devising and interpreting detailed experimental investigations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060527
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  • 3
    Electronic Resource
    Electronic Resource
    The reaction field of a water molecule in liquid water: Comparison of different quantum/classical models (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 5220-5227 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reaction field of a water molecule in liquid water has been computed with the help of continuum, discrete-continuum, and discrete models, using density functional theory calculations. In the continuum model, the liquid is simply described by a polarizable dielectric medium. The solute is placed in a cavity defined by a scaled van der Waals surface. Two different sets of van der Waals radii have been used for the atomic spheres. The discrete-continuum model consists of a quantum molecule surrounded by four classical molecules, the resulting aggregate being embedded in a dielectric continuum. Finally, in the discrete model, a molecular dynamics simulation is carried out for a quantum molecule in a box containing 215 classical molecules with periodic boundary conditions. The reaction field and the induced dipole moment in the standard continuum model are substantially underestimated. However, the use of optimized van der Waals radii for the atomic spheres produces a notable improvement. The discrete-continuum and discrete models lead to close results that are in good agreement with experimental data and previous theoretical estimations. For instance, the induced dipole moment (0.80 and 0.82 D for discrete-continuum and discrete models, respectively) compares well with the experimental estimate (0.75 D) and with Car–Parrinello simulations (1.08 D). The reaction field potential is analyzed in terms of multipole moment contributions. The role of the first shell and bulk solvent are also examined. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1389094
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  • 4
    Electronic Resource
    Electronic Resource
    Antiarrhythmic actions of clemizole as pharmacologic evidence for a circus movement mechanism in atrial flutter (1969)
    Springer
    Naunyn-Schmiedeberg's archives of pharmacology 262 (1969), S. 325-336 
    Details
    ISSN: 1432-1912
    Keywords: Clemizole ; Arrhythmia ; Antihistaminics ; Cell Membrane
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The antihistaminic clemizole was studied as an antiarrhythmic in a preparation in which two arrhythmias of different nature and mechanism were produced in the right atrium of anesthetized dogs. One of the arrhythmias was a circus movement flutter induced by the method of Rosenblueth and García Ramos; the other, an ectopic focus induced by local application of aconitine in the auricular appendage, electrically isolated from the rest of the atrium. Clemizole selectively converted the flutter to sinus rhythm with little action on the coexistent aconitine dysrhythmia. It did not modify arterial pressure. In effective doses the wave length of the impulse was increased by prolongation of the refractory period without significant reduction in conduction velocity. Similarly, in subendocardial cells of isolated rat atria, clemizole in appropriate concentrations retards repolarization with little effect on the rate of depolarization. These results afford pharmacological evidence for the existence of atrial circus movement arrhythmias which can respond to prolongation of the refractory period unaccompanied by effects on other properties of the tissue. Other arrhythmias, self-sustained by the discharge of an ectopic focus, such as the tachysystole produced by aconitine, are not suppressed by similar increase in the refractory period.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00538434
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  • 5
    Electronic Resource
    Electronic Resource
    Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics (2000)
    Springer
    Theoretical chemistry accounts 104 (2000), S. 89-95 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Proton transfer – Serine – Continuum solvent model – Nonequilibrium effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-point-energy contributions are added. Our calculations allow the dynamic aspects of the ionization mechanism to be discussed by incorporating nonequilibrium effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002149900109
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