149
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
The second group of hydrogen bonds includes interactions that do not meet BCP
criteria. The value of the Laplacian of the electron density at the BCP is smaller than
0.024 a.u. for the C5–H…O–P bond in the north/anti conformer of CMP and the
C3′–H…N3 bond in the north/syn conformer of GMP (Table 5.5). Therefore these
interactions should be considered to be electrostatic interactions rather than real
hydrogen bonds. They are characterized by the longest H…O distances (more than
2.7 Å), small values of the C–H…O angles (less than 122°), and the electron density
at BCP (ρ < 0.006). In addition, these interactions have relatively high ellipticity at
the BCP (ε > 0.19) and a shorter distance to the RCP (L RCP < 1.1 a.u.).
The remaining interactions belong to the third group, and they require additional careful consideration. Using characteristics of the two groups of interactions
mentioned above, we can classify these potential intramolecular hydrogen bonds
in DNTs. First of all we should consider the N–H…O interaction in the north/syn
conformer of AMP (Table 5.5). This interaction demonstrates all properties of the
inherent hydrogen bond, namely, clear directionality and influence on the conformation of the molecule. The formation of this hydrogen bond results in out-ofplane deformation of the pyrimidine ring of adenine and stabilization of an unusual
conformer with orthogonal orientation of the base with respect to sugar. All BCP
properties of this hydrogen bond (Table 5.5) are within the ranges typical for welldefined hydrogen bonds mentioned above, except the N–H…O angle that is only
129.3° and the value of ellipticity at BCP that is too high for normal hydrogen bonds
(Table 5.5). Therefore, this interaction undoubtedly should be classified as a real
hydrogen bond. The high value of ellipticity probably reflects the weak character
of this bond, which is in agreement with the relatively long H…O distance and the
small value of the N–H…O angle. Consideration of the N–H…O interaction as a
true hydrogen bond allows the criteria for the existence of hydrogen bonds to be
refined. In particular, this concerns the value of ellipticity at the BCP that should be
less than 0.18.
An analysis of the BCP properties of the remaining potential intramolecular hydrogen bonds demonstrates that all values of ρ and ∇2(ρ) meet Popelier’s criteria
(Table 5.5). Therefore, these parameters cannot be used for the classification of the
interactions under consideration. The values of bond ellipticity and the distance
between the BCP and the RCP are much more informative for this purpose. The
C1′–H…O7 interaction in the south/anti conformer of TMP and CMP, the C6–H…
O4′ and the C3′–H…O5′ interactions in the north/syn conformer of CMP, and the
C2′–H…O5′ interaction in the south/syn conformer of GMP are characterized by
extremely large values of ellipticity (ε > 0.8) and very short distances between the
BCP and the RCP (L RCP < 0.5 a.u.). This indicates that the topology of the electron
density distribution at these BCPs is very unusual and lies out of range for normal
hydrogen bonds. Therefore, these interactions cannot be considered as hydrogen
bonds and should be treated as strong electrostatic interactions. It should be noted
that the H…O distances for some of these interactions are relatively short (2.21–
2.33 Å), but the values of the C–H…O angle are considerably smaller than 120°
(99.7–110.7°). This demonstrates that the H…O distance cannot be a good indicator
for the existence of hydrogen bonds. It should be combined with the value of the
C–H…O angle that is normally larger than 120°.
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
The second group of hydrogen bonds includes interactions that do not meet BCP
criteria. The value of the Laplacian of the electron density at the BCP is smaller than
0.024 a.u. for the C5–H…O–P bond in the north/anti conformer of CMP and the
C3′–H…N3 bond in the north/syn conformer of GMP (Table 5.5). Therefore these
interactions should be considered to be electrostatic interactions rather than real
hydrogen bonds. They are characterized by the longest H…O distances (more than
2.7 Å), small values of the C–H…O angles (less than 122°), and the electron density
at BCP (ρ < 0.006). In addition, these interactions have relatively high ellipticity at
the BCP (ε > 0.19) and a shorter distance to the RCP (L RCP < 1.1 a.u.).
The remaining interactions belong to the third group, and they require additional careful consideration. Using characteristics of the two groups of interactions
mentioned above, we can classify these potential intramolecular hydrogen bonds
in DNTs. First of all we should consider the N–H…O interaction in the north/syn
conformer of AMP (Table 5.5). This interaction demonstrates all properties of the
inherent hydrogen bond, namely, clear directionality and influence on the conformation of the molecule. The formation of this hydrogen bond results in out-ofplane deformation of the pyrimidine ring of adenine and stabilization of an unusual
conformer with orthogonal orientation of the base with respect to sugar. All BCP
properties of this hydrogen bond (Table 5.5) are within the ranges typical for welldefined hydrogen bonds mentioned above, except the N–H…O angle that is only
129.3° and the value of ellipticity at BCP that is too high for normal hydrogen bonds
(Table 5.5). Therefore, this interaction undoubtedly should be classified as a real
hydrogen bond. The high value of ellipticity probably reflects the weak character
of this bond, which is in agreement with the relatively long H…O distance and the
small value of the N–H…O angle. Consideration of the N–H…O interaction as a
true hydrogen bond allows the criteria for the existence of hydrogen bonds to be
refined. In particular, this concerns the value of ellipticity at the BCP that should be
less than 0.18.
An analysis of the BCP properties of the remaining potential intramolecular hydrogen bonds demonstrates that all values of ρ and ∇2(ρ) meet Popelier’s criteria
(Table 5.5). Therefore, these parameters cannot be used for the classification of the
interactions under consideration. The values of bond ellipticity and the distance
between the BCP and the RCP are much more informative for this purpose. The
C1′–H…O7 interaction in the south/anti conformer of TMP and CMP, the C6–H…
O4′ and the C3′–H…O5′ interactions in the north/syn conformer of CMP, and the
C2′–H…O5′ interaction in the south/syn conformer of GMP are characterized by
extremely large values of ellipticity (ε > 0.8) and very short distances between the
BCP and the RCP (L RCP < 0.5 a.u.). This indicates that the topology of the electron
density distribution at these BCPs is very unusual and lies out of range for normal
hydrogen bonds. Therefore, these interactions cannot be considered as hydrogen
bonds and should be treated as strong electrostatic interactions. It should be noted
that the H…O distances for some of these interactions are relatively short (2.21–
2.33 Å), but the values of the C–H…O angle are considerably smaller than 120°
(99.7–110.7°). This demonstrates that the H…O distance cannot be a good indicator
for the existence of hydrogen bonds. It should be combined with the value of the
C–H…O angle that is normally larger than 120°.