157
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
as C–H…O hydrogen bond between C6/C8–H group of base and oxygen atom of
backbone. In anti-conformers of purine nucleotides in ZI–ZII-forms of DNA an
absence of such H-bonds may be explained by some screening of the oxygen atoms
of backbone by hydrogen atoms of the C5′–H2 methyl groups, which in our investigations, corresponds to the C3′ atom of previous nucleotide.
Two other reference hydrogen bonds are observed in syn-conformers of nucleotides in equilibrium and Z-forms of DNA (Table 5.14). First of them is the N10–
H…O–P hydrogen bond. This H-bond occurs in all syn-conformers of mGMP. This
hydrogen bond is also found in case of north/syn conformer of mAMP. This reference H-bonds are also responsible for the stabilization of the syn-conformers of
mCMP, mAMP, and mGMP. Other reference hydrogen bond is the C2′–H…N3 hydrogen bond. In case of north/syn conformer of mGMP in equilibrium, and north/
syn conformers in Z-forms of DNA such bond is weaken. Therefore, it is possible to
conclude that it corresponds to rather strong electrostatic interaction rather than to
intramolecular hydrogen bond. These H-bonds stabilize syn-conformers when formation of the N–H…O–P hydrogen bond between the amino and phosphate groups
is impossible. Interestingly, in some cases an existence of two such reference hydrogen bonds (C2′–H…N3 and N–H…O–P) at the same time is observed.
There are three specific hydrogen bonds in the structure of methyl ethers of
DNTs. These are the C–H…O–P bonds between the methyl and phosphate groups
Table 5.12 B3LYP/aug-cc-pvdz intramolecular interaction in methyl ethers of 2′-deoxyribonucleotides in equilibrium and DNA like conformations. True hydrogen bonds are underlined
Interaction Nucleotide
А-DNA
ВI-DNA
BII-DNA
H…A (Å)
D–H…A
(deg.)
H…A (Å)
D–H…A
(deg.)
H…A (Å)
D–H…A
(deg.)
mTMP
C6–H…O3′
(n − 1)
3.84
150.0
3.54
132.4
2.48
127.8
C6–H…O5′ 2.14
173.0
2.23
163.4
2.50
159.2
C9–H…O–P 2.38
176.2
2.48
173.4
2.53
167.6
mCMP
C6–H…O3′
(n − 1)
3.75
149.8
3.39
139.6
2.16
155.2
C6–H…O5′ 2.09
168.3
2.23
165.7
2.78
141.5
mAMP
C8–H…
O3′(n − 1)
3.97
149.6
3.51
141.3
2.20
168.4
C8–H…O5′ 2.36
155.8
2.55
144.2
3.02
132.8
C8–H…O–P 3.35
154.8
3.14
163.6
3.32
138.9
mGMP
C8–H…O3′
(n − 1)
4.13
148.6
3.98
146.2
2.26
164.2
C8–H…O5′ 2.53
153.5
3.07
138.8
3.04
133.7
C8–H…O–P 3.53
160.2
3.76
174.2
3.31
143.3
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
as C–H…O hydrogen bond between C6/C8–H group of base and oxygen atom of
backbone. In anti-conformers of purine nucleotides in ZI–ZII-forms of DNA an
absence of such H-bonds may be explained by some screening of the oxygen atoms
of backbone by hydrogen atoms of the C5′–H2 methyl groups, which in our investigations, corresponds to the C3′ atom of previous nucleotide.
Two other reference hydrogen bonds are observed in syn-conformers of nucleotides in equilibrium and Z-forms of DNA (Table 5.14). First of them is the N10–
H…O–P hydrogen bond. This H-bond occurs in all syn-conformers of mGMP. This
hydrogen bond is also found in case of north/syn conformer of mAMP. This reference H-bonds are also responsible for the stabilization of the syn-conformers of
mCMP, mAMP, and mGMP. Other reference hydrogen bond is the C2′–H…N3 hydrogen bond. In case of north/syn conformer of mGMP in equilibrium, and north/
syn conformers in Z-forms of DNA such bond is weaken. Therefore, it is possible to
conclude that it corresponds to rather strong electrostatic interaction rather than to
intramolecular hydrogen bond. These H-bonds stabilize syn-conformers when formation of the N–H…O–P hydrogen bond between the amino and phosphate groups
is impossible. Interestingly, in some cases an existence of two such reference hydrogen bonds (C2′–H…N3 and N–H…O–P) at the same time is observed.
There are three specific hydrogen bonds in the structure of methyl ethers of
DNTs. These are the C–H…O–P bonds between the methyl and phosphate groups
Table 5.12 B3LYP/aug-cc-pvdz intramolecular interaction in methyl ethers of 2′-deoxyribonucleotides in equilibrium and DNA like conformations. True hydrogen bonds are underlined
Interaction Nucleotide
А-DNA
ВI-DNA
BII-DNA
H…A (Å)
D–H…A
(deg.)
H…A (Å)
D–H…A
(deg.)
H…A (Å)
D–H…A
(deg.)
mTMP
C6–H…O3′
(n − 1)
3.84
150.0
3.54
132.4
2.48
127.8
C6–H…O5′ 2.14
173.0
2.23
163.4
2.50
159.2
C9–H…O–P 2.38
176.2
2.48
173.4
2.53
167.6
mCMP
C6–H…O3′
(n − 1)
3.75
149.8
3.39
139.6
2.16
155.2
C6–H…O5′ 2.09
168.3
2.23
165.7
2.78
141.5
mAMP
C8–H…
O3′(n − 1)
3.97
149.6
3.51
141.3
2.20
168.4
C8–H…O5′ 2.36
155.8
2.55
144.2
3.02
132.8
C8–H…O–P 3.35
154.8
3.14
163.6
3.32
138.9
mGMP
C8–H…O3′
(n − 1)
4.13
148.6
3.98
146.2
2.26
164.2
C8–H…O5′ 2.53
153.5
3.07
138.8
3.04
133.7
C8–H…O–P 3.53
160.2
3.76
174.2
3.31
143.3