Chemistry Reference
In-Depth Information
reaction occurs and the QM/MM scheme is easily implemented. However, there are
many chemical systems in which a priori knowledge about where the reactive
region will be during the course of the simulation is not predictable by chemical
intuition. Within our group we have had success employing a simplistic approach to
a QM/MM-MD algorithm that is applicable to chemical systems where a priori
knowledge is largely unavailable as to which atoms should be considered as part of
the reactive region [
28
,
29
]. This is specifically the case when gaseous atoms collide
with an amorphous surface that can readily diffuse over time. For example, in our
studies with squalane we even found that the incident atom was not always confined
within a ~20
˚
20
˚
(height) cylindrical box that contains over 2,000
atoms comprising the liquid. This is not the situation that is observed with crystal-
line solids or self-assembled monolayers. When modeling those surfaces, one can
predefine atoms into a QM region because the incident atoms would rarely interact
with more than the first or second monolayer.
In order to circumvent the limitation of predefining which atoms are to be
treated with QM, we allow atoms to be redefined dynamically as “in” or “out” of
the reactive region depending on their location relative to radical species that are
capable of undergoing a reaction. Specifically, the reactive regions are centered
around “seed atoms”, which are defined as all of the open-shell/radical atoms. In
the case of our studies involving atomic radicals reacting with squalane, the seed
atoms were defined as the initial gaseous incident atom plus, over the course of the
simulation, any atom that loses one of its originally bonded atoms. For example
(see Fig.
1
), if the F(
2
P) atom abstracts a H from squalane, then the carbon radical
(radius)
Fig. 1 Pictorial representation of the dynamic partitioning using the “seed atom” method for the
F(
2
P)
þ
squalane reaction
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