Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change

High-level ab initio mapping of the multiple H-abstraction pathways of the OH + glycine reaction

We perform a systematic search in the transition-state (TS) and product-channel complex (MIN) regions of the multi-channel OH + glycine → H₂O + H₂N-CH-COOH (CH)/HN-CH₂-COOH (NH)/H₂N-CH₂-COO (COOH) reactions. Geometry optimizations reveal {7, 3, 3} CH-TS, {2, 2, 2} CH-MIN, {17, 10, 5} NH-TS, {35, 19, 19} NH-MIN, and {6, 5, 5} COOH-TS conformers at the {MP2/3-21G, MP2/aug-cc-pVDZ, CCSD(T)-F12b/aug-cc-pVDZ} levels of theory as well as 2 additional CH-TSs based on chemical intuition. The benchmark relative energies of the TS, MIN, and product conformers are obtained by considering basis set effects up to aug-cc-pVQZ using the explicitly-correlated CCSD(T)-F12b method, post-(T) correlation up to CCSDT(Q), core correlation, scalar relativistic effects, spin-orbit coupling, and zero-point energy corrections. All the CH [ΔE_e(ΔH₀) = -38.54(-38.61) kcal mol^-1], NH [ΔE_e(ΔH₀) = -16.72(-17.98) kcal mol^-1], and COOH [ΔE_e = -4.98 kcal mol^-1] reactions are exothermic and proceed via shallow, usually negative, classical(adiabatic) barriers of -0.37(-0.95), -1.91(-2.48), and 1.02(-0.57) kcal mol^-1, respectively. In the entrance channel MRCI/aug-cc-pVTZ computations reveal several complexes with reactive(non-reactive) arrangements and binding energies of 1.0, 1.6, 3.3, (5.2 and 5.9) kcal mol^-1, stabilized by CH⋯OH, NH⋯OH, COOH⋯OH, (OH⋯OC and OH⋯N) hydrogen bonds, respectively.

Benchmark ab initio characterization of the abstraction and substitution pathways of the OH + CH4/C2H6 reactions

We report benchmark ab initio stationary-point properties for the hydrogen-abstraction, hydrogen-substitution, and methyl-substitution pathways of the OH + CH₄/C₂H₆ reactions.

Kinetics and dynamics study of the OH + C2H6 → H2O + C2H5 reaction based on an analytical global potential energy surface

To describe the gas-phase hydrogen abstraction reaction between the hydroxyl radical and the ethane molecule, an analytical full-dimensional potential energy surface was developed within the Born-Oppenheimer approximation. This reactive process is a ten-body system with 24 degrees of freedom, which represents a theoretical challenge. The new surface, named PES-2020, presents low barrier, 3.76 kcal mol-1, high exothermicity, -16.20 kcal mol-1, and intermediate complexes in the entrance and exit channels. To test the quality and accuracy of the analytical surface several stringent tests were performed and, in general, PES-2020 reasonably simulates the theoretical information used as input, it is a continuous and smooth potential, without spurious minima, it presents great versatility and a reasonable description of this ten-body reaction. Based on this surface, an exhaustive kinetics and dynamics study was performed with a double objective: to analyze the capacity of the new surface to simulate the experimental evidence, and to help understand the mechanism of reaction and the role of the ethyl group in the reaction. In the kinetics study, three approaches were used: variational transition-state theory with multidimensional tunnelling (VTST/MT), ring polymer molecular dynamics (RPMD) and quasi-classical trajectory (QCT) results, in the temperature range 200-2000 K. There is general agreement between the three approaches and they reasonably simulate the experimental behaviour, which gives confidence to the fitness of the new surface to describe the system. In the dynamics study, QCT calculations were performed at 298 K for a direct comparison with the only experimental result reported. We found that ethyl fragment presents a noticeable internal energy (∼20%) and so cannot be considered as a spectator. The water product vibrational energy is reasonably reproduced, though when a level-by-level distribution is analyzed the agreement is only qualitative.

Variational transition state theory: theoretical framework and recent developments

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.

Quantum tunneling in testosterone 6beta-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces

Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6beta-hydrogen abstraction and the 6beta-d(1)-testosterone 6beta-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

Transition-state geometry measurements from (13)c isotope effects. The experimental transition state for the epoxidation of alkenes with oxaziridines

We here suggest and evaluate a methodology for the measurement of specific interatomic distances from a combination of theoretical calculations and experimentally measured (13)C kinetic isotope effects. This process takes advantage of a broad diversity of transition structures available for the epoxidation of 2-methyl-2-butene with oxaziridines. From the isotope effects calculated for these transition structures, a theory-independent relationship between the C-O bond distances of the newly forming bonds and the isotope effects is established. Within the precision of the measurement, this relationship in combination with the experimental isotope effects provides a highly accurate picture of the C-O bonds forming at the transition state. The diversity of transition structures also allows an evaluation of the Schramm process for defining transition-state geometries on the basis of calculations at nonstationary points, and the methodology is found to be reasonably accurate.

Hybrid density functional theory with a specific reaction parameter: hydrogen abstraction reaction of difluoromethane by the hydroxyl radical

Accurate potential energy surfaces for the OH + CH2F2 --> H2O + CHF2 reaction are constructed using hybrid and hybrid meta density functional theory methods (mPW1PW91, B1B95, and mPW1B95) with specific reaction parameters in conjunction with the 6-31 + G(d,p) basis set. The accuracy of a surface is examined by comparing the calculated rate constants with the experimental ones. The rate constants are calculated over the temperature range 200-1,500 K using variational transition state theory with multidimensional tunneling contributions. The hybrid density functional theory methods with specific-reaction-parameter Hartree-Fock exchange contributions (39.2-41.0% for mPW1PW91, 41.0-42.2% for B1B95, and 44.9-46.3% for mPW1B95, respectively) provide accurate rate constants over an extended temperature range. The classical barrier height for the hydrogen abstraction reaction on these potential energy surfaces is determined to be 5.0-5.3 kcal mol(-1), and the best estimate value is 5.14 kcal mol(-1).

Viewpoint: Isotopic fractionation by plant nitrate reductase, twenty years later

Plant nitrate reductase, the enzyme that reduces nitrate (NO₃^-) to nitrite (NO₂^-), is known to fractionate N isotopes, depleting nitrite in ¹⁵N compared with substrate nitrate. Nearly 20 years ago, the nitrogen isotope effect associated with this reaction was found to be around 1.015. However, the relationships between the isotope effect and the mechanism of the reaction have not yet been examined in the light of recent advances regarding the catalytic cycle and enzyme structure. We thus give here the mathematical bases of the ¹⁴N / ¹⁵N and also the ¹⁶O / ¹⁸O isotope effects as a function of reaction rates. Enzymatic nitrate reduction involves steps other than NO₃^- reduction itself, in which the oxidation number of N changes from +V (nitrate) to +III (nitrite). Using some approximations, we give numerical estimates of the intrinsic N and O isotope effects and this leads us to challenge the assumptions of nitrate reduction itself as being a rate-limiting step within the nitrate reductase reaction, and of the formation of a bridging oxygen as a reaction intermediate.

Hybrid Density Functional Theory with Specific Reaction Parameter: Hydrogen Abstraction Reaction of Fluoromethane by the Hydroxyl Radical

Three potential energy surfaces with specific reaction parameters are developed and tested for the OH + CH(3)F --> H(2)O + CH(2)F reaction. The goal of this work is to determine surfaces that provide calculated reaction rate constants that are comparable to the experimental data. The potential energy surfaces are constructed using hybrid and hybrid meta density functional theory methods, and the levels of electronic structure theory used in this study are mPW1PW91, B1B95, and mPW1B95 in conjunction with the 6-31+G(d,p) basis set. The reaction rate constants are calculated over the range 200-1,500 K using variational transition state theory with multidimensional tunneling contributions. New specific-reaction-parameter Hartree-Fock contributions are determined, and the hybrid density functional theory methods with these new contributions (35.5 +/- 1.2% for mPW1PW91, 36.6 +/- 1.2% for B1B95, and 40.7 +/- 1.2% for mPW1B95, respectively) reproduce accurate rate constants over an extended temperature range. On these potential energy surfaces, the classical barrier height for the hydrogen abstraction reaction is determined to be 3.4-3.8 kcal/mol, with a best estimate value of 3.6 kcal/mol.

Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H+C2H6 reaction

This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy surface is a combined valence bond molecular mechanics (CVBMM) surface. Rate constants calculated with the CVBMM surface agree with the MPW54 rate constants within 12% for 534-2000 K and within 23% for 200-491 K. The full CVBMM potential-energy surface is now available for use in variety of dynamics calculations, and it provides a prototype for developing CVBMM potential-energy surfaces for other reactions.

Study of the Carbon-13 and Deuterium Kinetic Isotope Effects in the Cl and OH Reactions of CH4 and CH3Cl

Relative rate experiments have been carried out for three isotopologues of chloromethane and their reactions with Cl atoms and OH radicals. The OH and Cl reaction rates of CH2DCl and CHD2Cl were measured by long-path FTIR spectroscopy relative to CH3Cl at 298+/-2 K and 1013+/-10 hPa in purified air. The FTIR spectra were fitted using a nonlinear least squares spectral fitting method including measured high-resolution infrared spectra as references. The relative reaction rates defined by alpha=klight/kheavy were determined to be kOH+CH3Cl/kOH+CH2DCl=1.41+/-0.05, kOH+CH3Cl/kOH+CHD2Cl=2.03+/-0.05, kCl+CH3Cl/kCl+CH2DCl=1.42+/-0.04, and kCl+CH3Cl/kCl+CHD2Cl=2.27+/-0.04. The carbon-13 and deuterium kinetic isotope effects in the OH and Cl reactions of CH3Cl were investigated further using variational transition state theory, and the results were compared to similar calculations performed for the CH4+OH/Cl reaction systems. The calculations show that the order of magnitude difference for the carbon-13 kinetic isotope effect in the OH reaction of CH3Cl compared to CH4 reported by Gola et al. (Atmos. Chem. Phys. 2005, 5, 2395) can be explained by the lower barrier to internal rotation of the OH radical in the transition state of the CH4+OH reaction than in the CH3Cl+OH reaction. The deuterium kinetic isotope effects can be explained in terms of combined variational effects and tunneling.