Tunneling and Conformational Flexibility Play Critical Roles in the Isomerization Mechanism of Vitamin D

The thermal isomerization reaction converting previtamin D to vitamin D is an intramolecular [1,7]-sigmatropic hydrogen shift with antarafacial stereochemistry. We have studied the dynamics of this reaction by means of the variational transition-state theory with multidimensional corrections for tunneling in both gas-phase and <i>n</i>-hexane environments. Two issues that may have important effects on the dynamics were analyzed in depth, i.e., the conformations of previtamin D and the quantum effects associated with the hydrogen-transfer reaction. Of the large number of conformers of previtamin D that were located, there are 16 that have the right disposition to react. The transition-state structures associated with these reaction paths are very close in energy, so all of them should be taken into account for an accurate calculation of both the thermal rate constants and the kinetic isotope effects. This issue is particularly important because the contribution of each of the reaction paths to the total thermal rate constant is quite sensitive to the environment. The dynamics results confirm that tunneling plays an important role and that model systems that were considered previously to study the hydrogen shift reaction cannot mimic the complexity introduced by the flexibility of the rings of previtamin D. Finally, the characterization of the conformers of both previtamin D and vitamin D allowed the calculation of the thermal equilibrium constants of the isomerization process

Correction to Tunneling and Conformational Flexibility Play Critical Roles in the Isomerization Mechanism of Vitamin D

Correction to Tunneling and Conformational Flexibility Play Critical Roles in the Isomerization Mechanism of Vitamin

A Convergent Approach to the Dioxaadamantane Core of (±)-Tetrodotoxin

A fully stereocontrolled 1,3-diol orthoesterification and a water-promoted intramolecular Henry addition, combined with the previously reported formal (3 + 3) annulation of α-nitro-α,β-enals and 2,2-dimethyl-1,3-dioxan-5-one, provided for a short convergent pathway to the dioxaadamantane core of (±)-tetrodotoxin

Prediction of Experimentally Unavailable Product Branching Ratios for Biofuel Combustion: The Role of Anharmonicity in the Reaction of Isobutanol with OH

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

Computational Kinetics by Variational Transition-State Theory with Semiclassical Multidimensional Tunneling: Direct Dynamics Rate Constants for the Abstraction of H from CH₃OH by Triplet Oxygen Atoms

Rate constants and the product branching ratio for hydrogen abstraction from CH₃OH by O­(³P) were computed with multistructural variational transition-state theory including microcanonically optimized multidimensional tunneling. Benchmark calculations of the forward and reverse classical barrier heights and the reaction energetics have been carried out by using coupled cluster theory and multireference calculations to select the most reliable density functional method for direct dynamics computations of the rate constants. The dynamics calculations included the anharmonicity of the zero-point energies and partition functions, with specific-reaction-parameter scaling factors for reactants and transition states, and multistructural torsional anharmonicity was included for the torsion around the C–O bond in methanol and in the transition states. The resulting rate constants are presented over a wider range than they are available from experiment, but in the temperature range where experiments are available, they agree well with experimental values, which is encouraging for their reliability over the wider temperature range and for future computations of oxygen atom reaction rates. In contrast to a previous computational prediction, the branching ratio predicted by the present work shows that the formation of CH₂OH + OH is the dominant channel over the whole range of temperature from 250 to 2000 K

Atomic Oxygen Recombination at Surface Defects on Reconstructed (0001) α‑Quartz Exposed to Atomic and Molecular Oxygen

The surface chemistry of silica is strongly affected by the nature of chemically active sites (or defects) occurring on the surface. Here, we employ quantum mechanical electronic structure calculations to study an uncoordinated silicon defect, a non-bridging oxygen defect, and a peroxyl defect on the reconstructed (0001) surface of α-quartz. We characterized the spin states and energies of the defects, and calculated the reaction profiles for atomic oxygen recombination at the defects. We elucidated the diradical character by analyzing the low-lying excited states using multireference wave function methods. We show that the diradical defects consist of weakly coupled doublet radicals, and the atomic oxygen recombination can take place through a barrierless process at defects. We have delineated the recombination mechanism and computed the formation energy of the peroxyl and non-bridging oxygen defects. We found that key recombination reaction paths are barrierless. In addition, we characterize the electronically excited states that may play a role in the chemical and physical processes that occur during recombination on these surface defect sites

The Structure of Silica Surfaces Exposed to Atomic Oxygen

In this work we use molecular dynamics (MD) simulations with the ReaxFF_SiO^GSI potential to model the structure of quartz and amorphous silica surfaces exposed to atomic oxygen. The ReaxFF_SiO^GSI potential is a reactive force field that was specifically parametrized to describe gas surface interactions in silica–oxygen systems (Kulkarni, A. D.; et al. <i>J. Phys. Chem. C</i> <b>2012</b>, <i>117</i>, 258–269). We show that the ReaxFF_SiO^GSI potential accurately describes the experimentally measured bulk structure of quartz and amorphous silica, as well as experimentally and computationally characterized surface features for these materials. A flux boundary condition is implemented in molecular dynamics simulations to model the exposure of silica surfaces to atomic oxygen. We find that the types of defects occurring on silica surfaces under vacuum and exposed to atomic oxygen at high temperatures are in agreement with previous MD simulations and experimental measurements of silica surfaces. The ReaxFF_SiO^GSI potential predicts a peroxyl defect that has not been observed in previous MD simulations of silica surfaces, but has been experimentally identified. Density functional theory (DFT) calculations are used to validate the extent to which the ReaxFF_SiO^GSI potential predicts the structure and binding energy of the oxygen molecule on this defect. Through MD simulation and comparison with experiment, we identify the chemical surface defects that exist on real silica surfaces exposed to atomic oxygen at high temperatures and discuss their role in the catalytic recombination of atomic oxygen

New Pathways for Formation of Acids and Carbonyl Products in Low-Temperature Oxidation: The Korcek Decomposition of γ‑Ketohydroperoxides

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 <i>ab initio</i> 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

New Pathways for Formation of Acids and Carbonyl Products in Low-Temperature Oxidation: The Korcek Decomposition of γ‑Ketohydroperoxides

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 <i>ab initio</i> 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

Chloroform as a Hydrogen Atom Donor in Barton Reductive Decarboxylation Reactions

The utility of chloroform as both a solvent and a hydrogen atom donor in Barton reductive decarboxylation of a range of carboxylic acids was recently demonstrated (Ko, E. J. et al. <i>Org. Lett</i>. <b>2011</b>, <i>13</i>, 1944). In the present work, a combination of electronic structure calculations, direct dynamics calculations, and experimental studies was carried out to investigate how chloroform acts as a hydrogen atom donor in Barton reductive decarboxylations and to determine the scope of this process. The results from this study show that hydrogen atom transfer from chloroform occurs directly under kinetic control and is aided by a combination of polar effects and quantum mechanical tunneling. Chloroform acts as an effective hydrogen atom donor for primary, secondary, and tertiary alkyl radicals, although significant chlorination was also observed with unstrained tertiary carboxylic acids