4 research outputs found
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
Kinetics of the Methanol Reaction with OH at Interstellar, Atmospheric, and Combustion Temperatures
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
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