158
T. A. Zubatiuk et al.
in north/anti conformer of mTMP. However, it should be noted that these H-bonds
are rather weak and probably do not influence significantly the properties of DNTs.
In syn conformer of mGMP in Z-forms of DNA the C–H…N hydrogen bond between the H5′ hydrogen atom of sugar and the N3 nitrogen atom of base is revealed.
On the other hand, in south/syn conformer of mGMP the C3′–H…O–P hydrogen
bond (Table 5.14) is found.
The results of calculations demonstrate that a general pattern of reference intramolecular hydrogen bonds in methyl esters of DNTs is almost the same as in
species containing P–OH fragment. Only in the case of C3′-endo/anti conformer of
Table 5.13 B3LYP/aug-cc-pvdz intramolecular interaction in anti-conformers of methyl ethers
of 2′-deoxyribonucleotides in Z-DNA like conformations. True hydrogen bonds are underlined
Interaction
Nucleotide
ZI-DNA
ZII-DNA
H…A (Å)
D–H…A (deg.)
H…A (Å)
D–H…A (deg.)
mTMP
C6–H…O3′ (n − 1) 3.67
137.6
3.72
125.5
C6-H…O5′
2.26
159.7
2.43
144.9
C9–H…O–P
–
–
2.46
164.7
mCMP
C6–H…O3′ (n − 1) 3.69
135.7
3.78
117.9
C6–H…O5′
2.28
156.0
2.48
135.4
mAMP
C8–H…O3′ (n − 1) 3.31
165.4
3.31
165.4
C8–H…O5′
3.47
143.9
3.47
143.9
C8–H…O–P
-----mGMP
C8–H…O3′(n − 1) 3.39
178.2
3.39
178.2
C8–H…O5′
3.67
137.4
3.67
137.4
C8–H…O–P
-----Table 5.14 B3LYP/aug-cc-pvdz intramolecular interaction in syn-conformers of methyl ethers
of 2′-deoxyribonucleotides in Z-DNA like conformations. True hydrogen bonds are underlined
Interaction
Nucleotide
ZI-DNA
ZII-DNA
H…A (Å)
D–H…A (deg.)
H…A (Å)
D–H…A (deg.)
mAMP
C2′–H…N3
2.67
107.0
2.36
129.3
C5′–H…N3
3.74
125.1
3.32
139.6
N10–H…O–P
–
–
–
–
mGMP
C2′–H…N3
3.06
108.9
2.44
125.0
C5′–H…N3
2.35
140.8
2.56
141.6
N10–H…O–P
1.93
154.0
2.01
144.3
C3′–H…O–P
4.93
100.3
4.96
102.9
T. A. Zubatiuk et al.
in north/anti conformer of mTMP. However, it should be noted that these H-bonds
are rather weak and probably do not influence significantly the properties of DNTs.
In syn conformer of mGMP in Z-forms of DNA the C–H…N hydrogen bond between the H5′ hydrogen atom of sugar and the N3 nitrogen atom of base is revealed.
On the other hand, in south/syn conformer of mGMP the C3′–H…O–P hydrogen
bond (Table 5.14) is found.
The results of calculations demonstrate that a general pattern of reference intramolecular hydrogen bonds in methyl esters of DNTs is almost the same as in
species containing P–OH fragment. Only in the case of C3′-endo/anti conformer of
Table 5.13 B3LYP/aug-cc-pvdz intramolecular interaction in anti-conformers of methyl ethers
of 2′-deoxyribonucleotides in Z-DNA like conformations. True hydrogen bonds are underlined
Interaction
Nucleotide
ZI-DNA
ZII-DNA
H…A (Å)
D–H…A (deg.)
H…A (Å)
D–H…A (deg.)
mTMP
C6–H…O3′ (n − 1) 3.67
137.6
3.72
125.5
C6-H…O5′
2.26
159.7
2.43
144.9
C9–H…O–P
–
–
2.46
164.7
mCMP
C6–H…O3′ (n − 1) 3.69
135.7
3.78
117.9
C6–H…O5′
2.28
156.0
2.48
135.4
mAMP
C8–H…O3′ (n − 1) 3.31
165.4
3.31
165.4
C8–H…O5′
3.47
143.9
3.47
143.9
C8–H…O–P
-----mGMP
C8–H…O3′(n − 1) 3.39
178.2
3.39
178.2
C8–H…O5′
3.67
137.4
3.67
137.4
C8–H…O–P
-----Table 5.14 B3LYP/aug-cc-pvdz intramolecular interaction in syn-conformers of methyl ethers
of 2′-deoxyribonucleotides in Z-DNA like conformations. True hydrogen bonds are underlined
Interaction
Nucleotide
ZI-DNA
ZII-DNA
H…A (Å)
D–H…A (deg.)
H…A (Å)
D–H…A (deg.)
mAMP
C2′–H…N3
2.67
107.0
2.36
129.3
C5′–H…N3
3.74
125.1
3.32
139.6
N10–H…O–P
–
–
–
–
mGMP
C2′–H…N3
3.06
108.9
2.44
125.0
C5′–H…N3
2.35
140.8
2.56
141.6
N10–H…O–P
1.93
154.0
2.01
144.3
C3′–H…O–P
4.93
100.3
4.96
102.9