This article shows how to evaluate rotational symmetry numbers for different molecular configurations and how to apply them to transition state theory. In general, the symmetry number is given by the ratio of the reactant and transition state rotational symmetry numbers. However, special care is advised in the evaluation of symmetry numbers in the following situations: (i) if the reaction is symmetric, (ii) if reactants and/or transition states are chiral, (iii) if the reaction has multiple conformers for reactants and/or transition states and, (iv) if there is an internal rotation of part of the molecular system. All these four situations are treated systematically and analyzed in detail in the present article. We also include a large number of examples to clarify some complicated situations, and in the last section we discuss an example involving an achiral diasteroisomer.

We present new reaction pathways relevant to low-temperature oxidation in gaseous and condensed phases. The new pathways originate from γ-ketohydroperoxides (KHP), which are well-known products in low-temperature oxidation and are assumed to react only via homolytic O-O dissociation in existing kinetic models. Our ab initio calculations identify new exothermic reactions of KHP forming a cyclic peroxide isomer, which decomposes via novel concerted reactions into carbonyl and carboxylic acid products. Geometries and frequencies of all stationary points are obtained using the M06-2X/MG3S DFT model chemistry, and energies are refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. Thermal rate coefficients are computed using variational transition-state theory (VTST) calculations with multidimensional tunneling contributions based on small-curvature tunneling (SCT). These are combined with multistructural partition functions (Q(MS-T)) to obtain direct dynamics multipath (MP-VTST/SCT) gas-phase rate coefficients. For comparison with liquid-phase measurements, solvent effects are included using continuum dielectric solvation models. The predicted rate coefficients are found to be in excellent agreement with experiment when due consideration is made for acid-catalyzed isomerization. This work provides theoretical confirmation of the 30-year-old hypothesis of Korcek and co-workers that KHPs are precursors to carboxylic acid formation, resolving an open problem in the kinetics of liquid-phase autoxidation. The significance of the new pathways in atmospheric chemistry, low-temperature combustion, and oxidation of biological lipids are discussed.

Isobutanol is a prototype biofuel, and sorting out the mechanism of its combustion is an important objective where theoretical modeling can provide information that is unavailable and not easily obtained by experiment. In the present work the rate constants and branching ratios for the hydrogen abstraction reactions from isobutanol by hydroxyl radical have been calculated using multi-path variational transition-state theory with small-curvature tunneling. We use hybrid degeneracy-corrected vibrational perturbation theory to show that it is critical to consider the anharmonicity difference of high-frequency modes between reactants and transition states. To obtain accurate rate constants, we must apply different scaling factors to the calculated harmonic vibrational frequencies at the reactants and at the transition states. The factors determining the reaction rate constants have been analyzed in detail, including variational effects, tunneling contributions, the effect of multiple reaction paths on transmission coefficients, and anharmonicities of low- and high-frequency vibrational modes. The analysis quantifies the uncertainties in the rate calculations. A key result of the paper is a prediction for the site dependence of hydrogen abstraction from isobutanol by hydroxyl radical. This is very hard to measure experimentally, although it is critical for combustion mechanism modeling. The present prediction differs considerably from previous theoretical work.

No abstract

Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose’s ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not only rare but also have a different topology and geometry. We further show that the canonical geometry is not dictated by a physical constraint—geometries found in noncanonical interactions have similar calculated bond energies. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes, with different cofactors and catalytic chemistries, from a common pre-LUCA (last universal common ancestor) ancestor that possessed the β2-Asp/Glu motif.

A hydrogen bond at the transition state can lower the enthalpy of activation, but raise the free energy of activation.

We present a new least-action variational approximation for tunneling in polyatomic reactions based on the procedure developed by Garrett and Truhlar for atom-diatom reactions. (63) The method calculates the semiclassical ground-state tunneling probability at every tunneling energy by minimizing the value of imaginary action integral along a family of paths ranging from the minimum energy path to the straight path. The method is illustrated by applications to two hydrogen-atom abstraction reactions from methane using analytical potential energy surfaces.

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.