Chemistry Reference
In-Depth Information
TABLE 4.2
Free Valence of Heavy Atoms in Guanine Isomers
Free Valence
Heavy Atom
in Figure 4.5
Type
Guanine A
Guanine B
Difference
1
C
+0.192
+0.133
+0.059
2
N
−0.164
+0.127
−0.291
3
C
+0.126
+0.122
+0.004
4
N
+0.071
+0.072
−0.001
5
C
+0.072
+0.079
−0.007
6
C
+0.173
+0.156
+0.017
7
N
−0.526
−0.480
−0.046
8
C
+0.091
+0.094
−0.003
9
N
+0.006
+0.010
−0.004
10
O
−0.025
−0.103
+0.078
11
N
−0.134
−0.204
+0.070
10
O
1
7
6
N
2
N
8
N
N
N
3
5
9
11
4
FIGURE 4.5
Indices of heavy atoms in guanine isomers.
guanine from
Figure 4.4
. The heavy atoms are indexed as in Figure 4.5. The biggest
differences are calculated for the heavy atoms in isomers A, 1, 2, and 10, which are
part of the amide group.
4.3.3 d
escriptors
oF
M
olecular
F
ragMents
In order to calculate descriptors for the molecular fragments, the term
fragment
must be defined mathematically so as to be consistent with the computer program
algorithm. Fragments can be defined by comparing groups of atoms that are identi-
fied on the molecular map with groups included in previous lists, created empirically
(Satoh et al. 1997; Japertas et al. 2002). Another method is based on the idea that
each fragment contains only nonrotatable bonds and the fragments are connected
by rotatable bonds (Terwillinger et al. 2006; Choi 2006; Zhu and Agrafiotis 2007).
However, mathematical definition of a rotatable bond is itself difficult (Tarko 2011a).
The identification of fragments can be done considering the value of the bond order
and the types of atoms that are connected, in an attempt to define fragments that are
as similar to classical chemical groups as possible (Tarko 2004a). A much simpler
method takes into account only the value of the bond order for the chemical bonds
of the heavy atoms (Tarko 2004b). Each fragment contains only multiple bonds
