4 research outputs found

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

    No full text
    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

    No full text
    Correction to Tunneling and Conformational Flexibility Play Critical Roles in the Isomerization Mechanism of Vitamin

    Kinetics of the Methanol Reaction with OH at Interstellar, Atmospheric, and Combustion Temperatures

    Get PDF
    The OH radical is the most important radical in combustion and in the atmosphere, and methanol is a fuel and antifreeze additive, model biofuel, and trace atmospheric constituent. These reagents are also present in interstellar space. Here we calculate the rate constants, branching ratios, and kinetic isotope effects (KIEs) of the hydrogen abstraction reaction of methanol by OH radical in a broad temperature range of 30–2000 K, covering interstellar space, the atmosphere, and combustion by using the competitive canonical unified statistical (CCUS) model in both the low-pressure and high-pressure limits and, for comparison, the pre-equilibrium model. Coupled cluster CCSD­(T)-F12a theory and multi-reference CASPT2 theory were used to carry out benchmark calculations of the stationary points on the potential energy surface to select the most appropriate density functional method for direct dynamics calculations of rate constants. We find a significant effect of the anharmonicity of high-frequency modes of transition states on the low-temperature rate constant, and we show how tunneling leads to an unusual negative temperature dependence of the rate constants in the range 200 K > <i>T</i> > 100 K. The calculations also demonstrate the importance of the extent of stabilization of the pre-reactive complex. The capture rate for the formation of the complex is the dominant dynamical bottleneck for <i>T</i> < 100 K, and it leads to weak temperature dependence of the rate below 100 K in the high-pressure-limit of the CCUS model. We also report the pressure dependence of branching ratios (which are hard to measure so theory is essential) and the KIEs, and we report an unusual nonmonotonic variation of the KIE in the high-pressure limit at low temperatures

    Unraveling the Factors That Control Soft Landing of Small Silyl Ions on Fluorinated Self-Assembled Monolayers

    No full text
    Dynamics simulations were performed to study soft landing of SiNCS<sup>+</sup> and (CH<sub>3</sub>)<sub>2</sub>SiNCS<sup>+</sup> ions on a self-assembled monolayer of perfluorinated alkanethiols on gold (F-SAM). Using classical trajectories, the short-time collision dynamics (picosecond scale) were investigated to analyze trapping probabilities for these silyl ions. Thermal desorption of trapped ions was simulated by using “boxed molecular dynamics” (BXD). The simulations predict substantial ion trapping in the collisions of these ions with the F-SAM, especially when the projectile’s incident direction is normal to the surface. Desorption of the SiNCS<sup>+</sup> ion occurs significantly faster than desorption of the methylated ion, which may explain why soft landing was experimentally observed for the latter ion only [Miller, S. A.; Luo, H.; Pachuta, S. J.; Cooks, R. G. <i>Science</i> <b>1997</b>, <i>275</i>, 1447–1450; Luo, H.; Miller, S. A.; Cooks, R. G.; Pachuta, S. J. <i>Int. J. Mass. Spectrom. Ion Processes</i> <b>1998</b>, <i>174</i>, 193–217]. The free energy profiles for desorption of these ions show minima at 15 Å above the gold slab, indicating that the silyl ion has a preference to reside on top of the monolayer. Deep penetration of the ion into the monolayer is prevented by a large free energy barrier. However, according to DFT calculations, if this process occurred, the SiNCS<sup>+</sup> ion could strongly bind to the Au(111) surface that supports the perfluorinated alkanethiol chains
    corecore