Chemistry Reference
In-Depth Information
3 Simulating Gas-Liquid Interactions
3.1 Building a Model Liquid Surface
Prior to the scattering of a gaseous atom off of a liquid surface, a properly
equilibrated surface must be created. Initially, we have created a bulk model of
the desired liquid with the TINKER program by using the OPLS all-atom force field
[
47
] and the isobaric-isothermal (NPT) ensemble for ~1.0 ns at 400 K with periodic
boundary conditions applied. This ensures that the fluctuations in bulk density have
reached a minimum. Afterward, the final structure of this simulation is used as the
initial structure for an additional NPT simulation which is cooled to 298 K (or some
arbitrary experimental temperature) for ~0.5 ns at which the average bulk density is
measured in comparison with physical property values. In our work with squalane
(C
30
H
62
) the density was found to be 0.769 g/cm
3
, compared to the observed value
of 0.815 g/cm
3
. To create a liquid surface, at this point the periodic boundaries in
one direction are extended by a factor of three so that two empty vacuum regions
are present on top and bottom of a slab of the equilibrated bulk liquid. This system
is then run for ~1.0 ns with the NVT ensemble to allow for surface relaxation of the
bulk liquid. After the surface density has equilibrated, random snapshots of the
surface are used as the starting surface for the reactive scattering simulations. It is
these surfaces that are used to compute the average surface density profiles, which
enables us to analyze the types, locations, and orientations of different molecules
(or parts of the molecule, like functional groups) within the liquid.
In our previous work, we were able to show that, even though the bulk squalane
contains twice as many secondary carbons as primary or tertiary, at the surface the
majority of the carbons are primary and stick up out of the surface (see Fig.
1
). It is
important to understand what types of atoms are on the surface as their reactivity is
what drives the surface chemistry. Additionally, with our [emim][NO
3
] surface we
found that the anion is more abundant at the surface than the cation and that the
ethyl-chains that lie on the surface tend to stick up towards the vacuum [
37
].
However, we found that there exists a slightly different surface topology for
[emim][NTf
2
], which includes a larger anion that keeps the ethyl chain from
protruding out of the surface [
36
]. In contrast, the surface of [C
12
mim][NTf
2
] has
long hydrocarbon chains sticking up into the vacuum, causing a noticeable differ-
ence in the reaction profile that occurs upon gaseous atom collision.
3.2 Gas-Liquid Scattering Model
In order to simulate gaseous atoms scattering from a liquid surface that represents a
realistic sampling of the various chemical and surface features, various input
conditions should be considered to enable a connection to the experimental con-
ditions. The following conditions are what we have chosen for our models. After an
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