Atomistic simulations of reactive processes from gas to condensed phase

In this thesis, we use advance computational methods to explore molecular reaction dynamics
in gas and condensed phase. The molecular reactions that we describe in here have been
studied for the last 25 years, using computational methods, from stratospheric chemistry
to biochemistry.
We will first describe the vibrationally induced dissociation of H2SO4 to H2O and SO3 in
stratospheric conditions, which is one of the important reactive steps in the Earth's
atmosphere. Although this reaction has great significance in atmospheric chemistry, the
exact mechanism whereby the reaction happens is still unknown. It has been postulated that
the photodissociation of H2SO4 to form sulfur trioxide and water, can explain the anomalous
enhancement of the polar stratospheric sulfate aerosol layer in the springtime. This
photodissociation process was previously assumed to take place via absorption ultraviolet
(UV) radiation, to produce a dissociative electronically excited state. However, the
electronic absorption spectrum of H2SO4 up to 140 nm could not be found experimentally.
Alternative mechanisms, including vibrationally induced dissociation, were proposed. Using
adiabatic reactive molecular dynamics (ARMD) simulations with validated force fields for
the product and reactant channels, it is shown through explicit atomistic simulation that
by exciting the v9 OH-stretching mode, photodissociation can occur on the picosecond time
scale. With the potential energy surfaces used in the present work, v9 = 4 is sufficient
for this process. Because ARMD simulations allow multiple and long-time simulations, both
nonstatistical, impulsive H-transfer and statistical, intramolecular vibration energy
redistribution (IVR) regimes of the decomposition were found.
Another exciting reaction that we studied, this time in the condense phase, is the
[3,3]-sigmatropic rearrangement of allyl vinyl ethers. This is an important reaction due to
its special synthetic relevance, which allows the preparation of gamma, delta-unsaturated
carbonyl compounds. The intramolecular cyclic character (six-membered ring) of the
rearrangement is generally accepted. However, an understanding of the precise nature and
geometry of the transition state and the exact mechanism is still controversial. It is
generally accepted, evidenced by ab initio calculations using implicit solvent, that the
reaction proceed through chair-like intermediates. In this investigation, using high level
ab initio calculations, and ab initio Molecular Dynamics, we found that the reaction
proceeds via boat-like transition state. This finding allows to initiate new studies about
the real characterization of the transition state and hence its reaction mechanism.
Finally, we will describe the initial mechanism whereby the activation of the diguanylate
cyclase the PleD protein in Caulobacter crescentus is taking place. PleD is widely studied
since it participate in the formation of the ubiquitous second messenger, cyclic-di-GMP,
involved in bacterial biofilm formation and persistence.
PleD protein has an import role during the cell cycle of "C. cresentus". The active form of
diguanylate cyclase PleD localizes to the stalked pole of differentiating C. crescentus
cells. Pled is responsible for turning off flagellum rotations and inhibiting motility
before genome replication begins and also for regenerating motility after differentiation
has completed. Here we describe the coupling between the Phe102 and Thr83, in the active
form of the protein. This coupling is highly influenced by phosphorylation, and the
mechanisms seem to be key to form active dimers.