Electronic
structure and direct dynamics calculations were used
to study the potential energy surface and atomic-level dynamics for
the OH– + CH3I reactions. The results
are compared with crossed molecular beam, ion imaging experiments.
The DFT/B97-1/ECP/d level of theory gives reaction energetics in good
agreement with experiment and higher level calculations, and it was
used for the direct dynamics simulations that were performed for reactant
collision energies of 2.0, 1.0, 0.5, and 0.05 eV. Five different pathways
are observed in the simulations, forming CH3OH + I–, CH2I– + H2O, CH2 + I– + H2O, IOH– + CH3, and [CH3--I--OH]−. The SN2 first pathway and the proton-transfer
second pathway dominate the reaction dynamics. Though the reaction
energetics favor the SN2 pathway, the proton-transfer pathway is more
important except for the lowest collision energy. The relative ion
yield determined from the simulations is in overall good agreement
with experiment. Both the SN2 and proton-transfer pathways
occur via direct rebound, direct stripping, and indirect mechanisms.
Except for the highest collision energy, 70–90% of the indirect
reaction for the SN2 pathway occurs via formation of the
hydrogen-bonded OH–---HCH2I prereaction
complex. For the proton-transfer pathway the indirect reaction is
more complex with the roundabout mechanism and formation of the OH–---HCH2I and CH2I–---HOH complexes contributing to the reaction. The majority of the
SN2 reaction is direct at 2.0, 1.0, and 0.5 eV, dominated
by stripping. At 0.05 eV the two direct mechanisms and the indirect
mechanisms have nearly equal contributions. The majority of the proton-transfer
pathway is direct stripping at 2.0, 1.0, and 0.5 eV, but the majority
of the reaction is indirect at 0.05 eV. The product relative translational
energy distributions are in good agreement with experiment for both
the SN2 and proton-transfer pathways. For both, direct
reaction preferentially transfers the product energy to relative translation,
whereas transfer to product vibration is more important for the indirect
reactions. For the proton-transfer reactions the velocity scattering
angle distribution is peaked in the forward direction and in quite
good agreement with experiment. However, for the SN2 reaction,
the experimental scattering is isotropic in nature whereas forward
scattering dominates the simulation distributions. The implication
is that the simulations give too much stripping, which leads to forward
scattering. The dynamics for the OH– + CH3I SN2 pathway are similar to those found previously for
the F– + CH3I SN2 reaction.
We present a study of the different product channels in the reactions of OH and OH-(H2O) with methyl iodide over a range of collision energies. Direct dynamics classical trajectory simulations are employed to obtain an atomistic comparison with the experimental results. For the experiments we have combined a crossed beam ion imaging setup with a multipole rf ion trap. The trap allows us to prepare the molecular and cluster ions with a controlled internal temperature and thus provides well-defined initial conditions for reaction experiments at low collision energy. Changing the internal temperature of the cluster ions was found to have a profound effect on their reactivity.
Abietic acid, a constituent of pine resin, is naturally derived from abietadiene --a process that requires four enzymes: one (abietadiene synthase) for conversion of the acyclic, achiral geranylgeranyl diphosphate to the polycyclic, chiral abietadiene (a complex process involving the copalyl diphosphate intermediate) and then three to oxidize a single methyl group of abietadiene to the corresponding carboxylic acid. In previous work (Nature Chem.2009, 1, 384), electronic structure calculations on carbocation rearrangements leading to abietadienyl cation revealed an interesting potential energy surface with a bifurcating reaction pathway (two transition-state structures connected directly with no intervening minimum), which links two products--one natural and one not yet isolated from Nature. Herein we describe direct dynamics simulations of the key step in the formation of abietadiene (in the gas phase and in the absence of the enzyme). The simulations reveal that abietadiene synthase must intervene in order to produce abietadiene selectively, in essence steering this reaction to avoid the generation of byproducts with different molecular architectures.
We describe accommodations that we have made to our applied
computational–theoretical
chemistry laboratory to provide access for blind and visually impaired
students interested in independent investigation of structure–function
relationships. Our approach utilizes tactile drawings, molecular model
kits, existing software, Bash and Perl scripts written in-house, and
three-dimensional printing in a process that allows a blind or visually
impaired student to satisfy her or his curiosity about structure–function
relationships with minimal assistance from sighted co-workers.
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