150
T. A. Zubatiuk et al.
At least the characteristics of two interactions (C3′–H…O–P in the north/anti
conformer and C2′–H…N3 in the south/syn conformer of GMP) are very similar to
the characteristics of well-defined hydrogen bonds. Only the H…O distance in the
C3′–H…O–P bond (2.490 Å) is considerably longer, compared to other hydrogen
bonds (Table 5.5). However, this probably is compensated by a higher value of the
C–H…O angle (135.1°). Therefore, these interactions undoubtedly should be considered as true hydrogen bonds.
The most interesting situation is observed for the C2′–H…O7 interaction in the
north/syn conformer of CMP. The geometrical parameters of this potential hydrogen
bond are almost appropriate for hydrogen bonding. The C–H…O angle is slightly
smaller than 120° (Table 5.5). The values of ellipticity and L RCP are also close to
suitable ranges, but are slightly outside the normal values. Therefore, it is possible
to consider this interaction as a hydrogen bond, but it represents a borderline case
for the classification of such interactions.
The remaining interactions (C2′–H…O5′ in the south/anti conformer of TMP,
CMP, and AMP) are characterized by unsuitable geometrical parameters, a shorter
distance between the BCP and RCP, and considerably higher ellipticity at the BCP
(Table 5.5). Therefore these interactions also should be considered as electrostatic
interactions, rather than the hydrogen bonds.
In summary, a topological analysis of the electron density distribution in DNTs
reveals numerous intramolecular D–H…A interactions that may be considered as
potential hydrogen bonds. However, a more detailed analysis of the properties of
BCP for these interactions allows a clear enough distinction between true hydrogen
bonds and strong electrostatic interactions of atoms with opposite charges to be
made. On the basis of data presented in [52] it is demonstrated that geometrical
parameters and values of the electron density and the Laplacian of electron density
cannot be used for classification of such interactions. Only the values of the bond
ellipticity (ε) and distance between BCP and ring critical points (RCP) allow a distinction between true hydrogen bonds and strong electrostatic interactions to be
made. According to the analysis true hydrogen bonds should be characterized by
the following values of BCP properties: ε < 0.1 and L RCP > 1.4 a.u. for well-defined
hydrogen bonds and ε < 0.22 and L RCP > 1.1 a.u. for all hydrogen bonds, including
very weak hydrogen bonds.
5.5 Deformation of 2′-Deoxyribonucleotides Inside DNA
Macromolecule
As was previously shown, investigation of structure of canonical 2′-deoxyribonucleosides and 2′-deoxyribonucleotides [12, 15, 18–20, 48, 52] revealed existence
of numerous N–H…O and C–H…X (where X = O, N) intramolecular hydrogen
bonds. Purine and pyrimidine nucleotides are characterized by the unique set of
intramolecular interactions defined by the nature of the base and conformation of
SU and BU. Formation of intramolecular hydrogen bonds significantly influences
conformations of molecules [15, 19, 48, 52]. In particular, they are responsible for
T. A. Zubatiuk et al.
At least the characteristics of two interactions (C3′–H…O–P in the north/anti
conformer and C2′–H…N3 in the south/syn conformer of GMP) are very similar to
the characteristics of well-defined hydrogen bonds. Only the H…O distance in the
C3′–H…O–P bond (2.490 Å) is considerably longer, compared to other hydrogen
bonds (Table 5.5). However, this probably is compensated by a higher value of the
C–H…O angle (135.1°). Therefore, these interactions undoubtedly should be considered as true hydrogen bonds.
The most interesting situation is observed for the C2′–H…O7 interaction in the
north/syn conformer of CMP. The geometrical parameters of this potential hydrogen
bond are almost appropriate for hydrogen bonding. The C–H…O angle is slightly
smaller than 120° (Table 5.5). The values of ellipticity and L RCP are also close to
suitable ranges, but are slightly outside the normal values. Therefore, it is possible
to consider this interaction as a hydrogen bond, but it represents a borderline case
for the classification of such interactions.
The remaining interactions (C2′–H…O5′ in the south/anti conformer of TMP,
CMP, and AMP) are characterized by unsuitable geometrical parameters, a shorter
distance between the BCP and RCP, and considerably higher ellipticity at the BCP
(Table 5.5). Therefore these interactions also should be considered as electrostatic
interactions, rather than the hydrogen bonds.
In summary, a topological analysis of the electron density distribution in DNTs
reveals numerous intramolecular D–H…A interactions that may be considered as
potential hydrogen bonds. However, a more detailed analysis of the properties of
BCP for these interactions allows a clear enough distinction between true hydrogen
bonds and strong electrostatic interactions of atoms with opposite charges to be
made. On the basis of data presented in [52] it is demonstrated that geometrical
parameters and values of the electron density and the Laplacian of electron density
cannot be used for classification of such interactions. Only the values of the bond
ellipticity (ε) and distance between BCP and ring critical points (RCP) allow a distinction between true hydrogen bonds and strong electrostatic interactions to be
made. According to the analysis true hydrogen bonds should be characterized by
the following values of BCP properties: ε < 0.1 and L RCP > 1.4 a.u. for well-defined
hydrogen bonds and ε < 0.22 and L RCP > 1.1 a.u. for all hydrogen bonds, including
very weak hydrogen bonds.
5.5 Deformation of 2′-Deoxyribonucleotides Inside DNA
Macromolecule
As was previously shown, investigation of structure of canonical 2′-deoxyribonucleosides and 2′-deoxyribonucleotides [12, 15, 18–20, 48, 52] revealed existence
of numerous N–H…O and C–H…X (where X = O, N) intramolecular hydrogen
bonds. Purine and pyrimidine nucleotides are characterized by the unique set of
intramolecular interactions defined by the nature of the base and conformation of
SU and BU. Formation of intramolecular hydrogen bonds significantly influences
conformations of molecules [15, 19, 48, 52]. In particular, they are responsible for