Rate constants and (12)C/(13)C kinetic isotope effects are calculated by direct dynamics for the OH + CH(4) --> H(2)O + CH(3) reaction. The electronic structure calculations required to generate the implicit potential energy surface were carried out by the high-level multicoefficient Gaussian-3/version-3 (MCG3) method and compared to two other multilevel methods, MC3BB and MC3MPW, and three density functional methods, M06-2X, BB1K, and MPW1K. The rate constants and (12)C/(13)C kinetic isotope effects are shown to depend strongly on the coordinate system used to calculate the frequencies as well as on the method used to account for the torsional anharmonicity of the lowest-frequency vibrational mode of the generalized transition states.
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http://dx.doi.org/10.1021/jp072843j | DOI Listing |
Phys Chem Chem Phys
August 2018
Departamento de Química Física and Instituto de Computacion Cientifica Avanzada, Universidad de Extremadura, 06071 Badajoz, Spain.
An exhaustive kinetics study was performed for the title reaction using two theoretical approaches: variational transition-state theory and quasi-classical trajectory calculations, based on an original new analytical full-dimensional potential energy surface, named PES-2018, which has been fitted to high-level ab initio calculations. The theoretical results were compared with the available experimental data in the temperature range 189-350 K, a difficult comparison because of experimental controversies about the final rate constants (factor of about two) and on the activation energy (positive and negative values have been reported). There is agreement between the two theoretical approaches, with differences of less than 20%, and with the most recent experiments, with differences of less than 30%.
View Article and Find Full Text PDFPlant Cell Environ
September 2013
Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud, 91405 Orsay Cedex, France.
Although ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was discovered nearly 60 years ago, the associated chemical mechanism of the reaction is still incompletely understood. The catalytic cycle consists of four major steps: ribulose-1,5-bisphosphate binding, enolization, CO₂ or O₂ addition and hydration, and cleavage of the intermediate. The use of individual rate constants for these elemental steps yields mathematical expressions for usual kinetic constants (k(cat), K(m)), CO₂ versus O₂ specificity (S(c/o)) as well as other chemical parameters such as the ¹²C/¹³C isotope effect.
View Article and Find Full Text PDFJ Am Chem Soc
September 2010
Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA.
The intramolecular (13)C kinetic isotope effects for the ring-opening of cyclopropylcarbinyl radical were determined over a broad temperature range. The observed isotope effects are unprecedentedly large, ranging from 1.062 at 80 degrees C to 1.
View Article and Find Full Text PDFJ Am Chem Soc
August 2009
Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
It has been proposed that the decarboxylation of mandelylthiamin, the adduct of benzoylformate and thiamin, is uniquely catalyzed by protonated pyridines through a preassociation mechanism in which proton transfer competes with the internal return of carbon dioxide. Application of this mechanism suggests that the observed primary (12)C/(13)C kinetic isotope effect in the absence of catalyst is reduced in magnitude because diffusion of carbon dioxide is partially rate-determining. Where proton transfer blocks the internal return of carbon dioxide, the separation of carbon dioxide is facilitated, and the observed isotope effect increases toward the intrinsic value for carbon-carbon bond breaking.
View Article and Find Full Text PDFRapid Commun Mass Spectrom
August 2009
Plateforme Métabolisme Métabolome, IFR87 La Plante et son Environnement, Institut de Biotechnologie des Plantes, Université Paris-Sud XI, 91405 Orsay cedex, France.
The natural (13)C/(12)C isotope composition (delta(13)C) of plants and organic compounds within plant organs is a powerful tool to understand carbon allocation patterns and the regulation of photosynthetic or respiratory metabolism. However, many enzymatic fractionations are currently unknown, thus impeding our understanding of carbon trafficking pathways within plant cells. One of them is the (12)C/(13)C isotope effect associated with invertases (EC 3.
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