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  • 1
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The realization of molecule-based miniature devices with advanced functions requires the development of new and efficient approaches for combining molecular building blocks into desired functional structures, ideally with these structures supported on suitable substrates. Supramolecular ...
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  • 3
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An extension of transition-state theory for liquid-phase chemical reactions is presented. The effect of adding a second solvent water molecule on the proton-transfer reaction in a formamidine–water (FW) cluster was studied. Ab initio molecular-orbital calculations were performed for the formamidine–water–water (FWW) system to obtain the adiabatic potential-energy surface. It was expressed in two coordinate systems: (i) the total normal-coordinate system of the FWW system, and (ii) the composite normal-coordinate system consisting of two normal-coordinate systems of the isolated FW system and the isolated medium-water molecule. In either of these two systems, the solvent effect can be categorized as either (i) an equilibrium solvation effect or (ii) a frictional effect. In this article, the former effect was investigated in detail and, in the total normal-coordinate system, a frequency diagram was obtained by diagonalizing the Hessian matrix at successive geometries along intrinsic reaction coordinate and then, within the Rice–Ramsperger–Kassel–Marcus (RRkM) formalism, the rate constant was evaluated with the vibrational frequencies assigned in this manner. In the composite normal-coordinate system, the off-diagonal elements found in the Hessian matrix are due to the interaction between the FW system and the medium-water molecule at equilibrium separation. The rate constant was evaluated within the diagonal approximation. As a result, both treatments work well and yield similar conclusions about the role of the solvent to those drawn from chemical-reaction molecular-dynamics simulations. The reaction is found to be enhanced considerably by the assistance of an additional medium-water molecule. The second treatment is concluded to be reasonably applicable in the estimation of reaction rates for liquid-phase chemical reactions.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Chemistry - A European Journal 3 (1997), S. 210-218 
    ISSN: 0947-6539
    Keywords: ab initio calculations ; Baeyer-Villiger reactions ; migrations ; peroxyacids ; substituent effects ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Baeyer-Villiger reaction of p-anisaldehyde with peroxyacetic acid in nonpolar solvents to give p-anisylformate was examined on the basis of ab initio molecular orbital calculations. To explain the experimental observations, the free-energy change was evaluated for each case in the absence and in the presence of an acid catalyst. It was found that, without catalysts, the rate-determining step corresponds to the carbonyl addition of peroxyacetic acid to p-anisaldehyde and the reaction hardly occurs. Acetic acid was found to catalyze the carbonyl addition and change the rate-determining step from the carbonyl addition to the migration of the carbonyl-adduct intermediate. Trifluoroacetic acid was observed to catalyze both the carbonyl addition and migration, and the carbonyl addition was demonstrated to be a rate-determining step. The results provided a convincing explanation of the complex kinetics seen experimentally. Further calculations were performed for the reaction of benzaldehyde with peroxyacetic acid to give phenylformate. Migratory aptitude was found to depend on the catalyst. Isotope effects were also investigated, and the exceptional isotope effect observed experimentally was shown to be due to the rate-determining carbonyl addition caused by autocatalysis. It is concluded that the mechanism of the reaction varies with catalysis or substituent effects.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present for a polyatomic reaction system a reaction-path Hamiltonian described with a reaction coordinate and quasirectilinear vibrational coordinates that are constructed from a nonlinear combination of curvilinear internal coordinates. To determine the vibrational coordinates we use a quasipotential-energy expression in which, in a Taylor-series expansion of the potential energy around the reaction path, the usual derivatives with respect to the internal coordinates are replaced by the corresponding covariant derivatives. The vibrational coordinates are determined so that (1) when the angular momentum is assumed to be zero, the respective expressions for the quasipotential energy and the kinetic energy have diagonal forms in the second-order terms and the first-order terms with respect to the vibrational coordinates in the internal configuration subspace perpendicular to the reaction path, and (2) the covariant second derivatives of the potential energy with respect to the vibrational coordinates coincide with the usual second derivatives. The reaction and vibrational coordinates determined presently not only are separated from rotations but are also invariant under the transformation of the original internal coordinates. The present reaction-path Hamiltonian is expected to be of advantage for obtaining an appropriate picture of the reaction-path dynamics under the zero-angular momentum assumption. © 2000 American Institute of Physics.
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  • 7
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reaction-path Hamiltonian formulation reported in the preceding paper, where the Hamiltonian is described with quasirectilinear vibrational coordinates related nonlinearly to curvilinear internal coordinates, was applied to the examination of the reaction CH4+F→CH3+HF. For this reaction we made ab initio calculations and determined the harmonic vibrational frequencies along the reaction path by each of (1) a method using the new formulation, (2) the method of Miller et al. [J. Chem. Phys. 72, 99 (1980)], and (3) that of Truhlar et al. [J. Chem. Phys. 102, 3188 (1995)]. We found that the harmonic vibrational frequencies determined by the new method differ significantly from those determined by the other two methods in the region away from the stationary states. This difference is attributed to the limitations of the latter two methods. We concluded that the reaction-path Hamiltonian determined by the new method should be used to obtain an accurate picture of the reaction-path dynamics under the zero-angular-momentum assumption. © 2000 American Institute of Physics.
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  • 8
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The microscopic formulation of the solute and solvent reactive coordinates is reported. This formulation enables us to reduce the solution reaction to a simple barrier-crossing reaction on a potential-energy contour surface in the two-dimensional configuration space determined by these coordinates. We applied this formalism to the examination of the title reaction.© 1999 American Institute of Physics.
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  • 9
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A statistical calculation method is proposed for a classical reaction rate constant expressed as the equilibrium flux of systems through a dividing surface that corresponds to the hypersurface at the transition state perpendicular to the reactive normal coordinate. In this method, an efficient microcanonical Monte Carlo sampling method is employed to approximately compute the flux integral for the classical rate constant expression. To determine whether or not each configuration generated by a Markov walk in the Monte Carlo sampling lies on the dividing surface, we present a method to evaluate the value of the reactive normal coordinate at the configuration by means of a transformation of internal coordinates into normal coordinates. We applied the present statistical calculation method to the unimolecular dissociation of HFCO. It was found that the calculated rate constant is much more correct than the rate constant evaluated as the equilibrium flux through an intuitive dividing surface specified by an HCF angle. In addition, a separable and harmonic approximation for vibrational–rotational modes on a rate constant was found to overestimate the rate constant for the dissociation. © 1999 American Institute of Physics.
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  • 10
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A microscopic theory was presented for each of the nonadiabatic- and equilibrium-solvation regimes in microsolvated cluster reactions to examine nonequilibrium-solvation effects, and applied to the SN2 reactions: (H2O)nCl−+CH3Cl→ClCH3+Cl−(H2O)n for n=0–4. To have pictures for nonadiabatic and equilibrium solvations, the potential-energy surface of the reacting system on the transition-state region was described with effective normal coordinates defined in each of these solvation limits. The solute dynamics in each of these solvation limits was considered to be determined by the effective frequencies characterizing the motions along the corresponding normal coordinates, and a rate-constant expression was approximately derived. Ab initio molecular-orbital calculations were carried out for the microsolvated SN2 reactions, and the ratio of nonadiabatic- to equilibrium-solvation rate constants was evaluated. It was found that the ratio provides a better approximate value of a transmission coefficient that corresponds to the ratio of the nonequilibrium- to equilibrium-solvation rate constants, for the larger values of number of microsolvated waters. It was supported that the nonadiabatic-solvation picture appropriately characterizes the dynamics on the transition-state region in such a reaction that the time scale of the reaction is very short compared to the motions of solvent reorganization. Furthermore, the finding that the transmission coefficients were quite small gave us a new understanding of the importance of the nonequilibrium-solvation effect. In addition, the activation free energy for the microsolvated reaction in the case of n=4 was found unexpectedly to give most of the activation free energy for the corresponding solution reactions. © 1996 American Institute of Physics.
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