Chemistry Reference
In-Depth Information
Fig. 19 Geometry of the water clusters under investigation. (a) Structure of the central dimer
containing the two BCPs of interest. (b) Cluster with all surrounding water molecules of the first
water shell. (c) Optimized structure of the whole (H
2
O)
11
cluster (first and second shell)
The decay of the contributions to the density of a given point in space across
hydrogen bonded networks was tested through computations of water clusters
(Fig.
19
). The common motif of all clusters is the central dimer of two molecules
of water forming a hydrogen bond (Fig.
19a
). As environment, this dimer is
surrounded by up to nine additional water molecules, arranged in such a way that
the number of hydrogen bonds toward the central dimer is maximized. Thereby, the
central dimer molecules form four hydrogen bonds, clearly more than the average
value found for liquid water. Nevertheless, this structure is ideally suited for the
intended investigations. The complete system (see Fig.
19c
) comprising 11 water
molecules was fully optimized at the B3LYP/TZVP level. The system including
only the first shell of water molecules around the dimer is shown in Fig.
19b
.
Starting from the structure in Fig.
19c
, 63 smaller clusters were obtained by
replacing more and more of the surrounding molecules. The structures were not
further optimized to avoid a bias due to a change in the geometry. To account for the
different approaches frequently used for investigations of protein-inhibitor sys-
tems, the EDs for all clusters were computed in three different ways. In a first
model, the EDs were determined in pure gas phase calculation, only considering the
atoms of the given truncated cluster. The second approach uses a polarizable
continuum model approximating surrounding liquid water with the standard
parameters provided by the GAUSSIAN03 Package [
139
]. The third system models
the surrounding water molecules by means of a QM/MM approach, using a field of
point charges to describe the electrostatic influence on the QM system. In these
calculations, the deleted atoms in the truncated clusters were replaced by the point
charges used in the DL_POLY code [
106
]. For all systems, the EDs were computed
at the B3 [
108
]-LYP [
109
,
110
]/TZVP [
111
] level, partitioned according to the
QTAIM theory and analyzed with the source function. The analysis was carried
out at two BCPs, one along the covalent OH bond between the oxygen atom O1
and the hydrogen atom H2 (BCP
A
), the second BCP (BCP
B
) along the hydrogen
bond linking the two molecules of the central dimer. These BCPs are shown in
Fig.
19a
.
