Chemistry Reference
In-Depth Information
The ammonium group forms two salt bridges to the residue of Asp56 (through the
H3 center) and Asp54 (through the H1 center). The third proton (H2), however,
only builds up a hydrogen bond to a solvent water molecule. The O1 center of the
carboxylate group forms two salt bridges with the positively charged guanidinium
groups of Arg70 and of Arg34, i.e., its environment is very similar to the one
within crystals of the pure compound. As in the crystal, the O2 center is only
involved in one salt bridge to the guanidinium group of Arg34. However, a
second contact exists to the phenol group of Tyr63. Due to the differences in
the networks in crystals of the pure compound and in the enzyme-inhibitor
complex, one would expect stronger differences for O2 and H2. On the basis of
the numbers of salt bridges and hydrogen bonds, the data for O1, H1, and H3
should be very similar.
Tables
8
-
14
show the influence of the environments on the bonding properties
for the different bonds in AMCHA. The abbreviation
geom
/
prop
indicates in which
environment the geometry was computed and which environment was simulated for
the calculation of the property, respectively (g
gas phase, s
solvent, p
protein,
c
crystal). For example, p/s means that the geometry was taken from the protein
environment but for the computation of the properties a polar solvent surrounding was
modeled. The abbreviation p/p stands for the results taken from the AMCHA-K1
Pg
complex, while c/c denotes results obtained for the crystal of pure AMCHA. Figure
7
gives contour plot representations of
2
(r) of AMCHA in the plane spanned by the
carboxylate group. The geometries are optimized in the respective environment.
Figure
8
shows the corresponding Laplacians where the geometry is fixed to the
r
r
Table 8 Influence of the environment on topological properties of the density at the bond critical
point (BCP) of the C-O2 bond of AMCHA
Geom/prop
a
r
l
l
l
1
2
3
g/g
2.53
22.31
20.65
29.09
s/s
2.50
22.05
20.93
29.58
p/p
2.43
20.95
20.30
25.30
p/g
2.45
21.18
19.21
23.04
p/s
2.43
20.96
19.82
24.84
c/c
2.49
21.97
20.70
29.71
Max:min
b,c
4.3
6.5
7.5
29.0
p/p:c/c
c
2.5
4.6
1.9
14.8
p/p:p/g
c
0.8
1.1
5.7
9.8
p/p:p/s
c
0.1
0.0
2.4
1.9
p/p:g/g
c
6.6
10.4
4.2
19.1
p/p:s/s
c
2.7
4.5
1.4
9.2
r
i
denotes the eigenvalues of the Hessian of the ED at the BCP. EDs
are given in e/
˚
3
, and Laplacians in e/
˚
5
. The numbering of the centers can be taken from Fig.
6
a
The abbreviation geom/prop indicates in which environment the geometry was computed and
which environment was simulated in the calculation of the property, respectively (g
is the ED at the BCP, while
l
gas phase;
s
crystal). For example, p/s means that the geometry was taken from
the protein environment but for the computation of the properties a polar solvent surrounding was
modeled
b
[(maximal value
solvent; p
protein; c
minimal value)/minimal value]*100
c
Change with respect to p/p in percent
