148
T. A. Zubatiuk et al.
DNTs, a clear difference is revealed between purine and pyrimidine nucleotides.
In the case of TMP and CMP, the C6–H…O5′ hydrogen bond is observed in all
conformers except the south/anti conformer of CMP where the C6–H atom interacts
with the oxygen of the phosphate group. An opposite situation is found for purine
nucleotides. The C8–H…O-P hydrogen bond is located in south/anti conformers of
AMP and GMP, while the C8–H…O5′ bond is formed in the north/anti conformer
of AMP. Unlike these conformers, interactions with the participation of the C8′–H
atom were not found in the north/anti conformer of GMP (Table 5.5).
The values of electron density and Laplacian of electron density at the BCP for all
of these hydrogen bonds meet Popelier′s criteria. The range of variation of the properties of the BCP for well-defined hydrogen bonds (ρ > 0.015 a.u., ∇
2
(ρ) > 0.044 a.u.)
may be used for further classification of other intramolecular interactions in DNTs.
An analysis of the ellipticity of these hydrogen bonds (ε < 0.09) and the distance between BCP and RCP (L RCP > 1.5 a.u.) does not indicate any instability of these interactions, and these values also may be used as a reference for further consideration.
Molecule Conformer D–H…A
H…A
(Å)
D–H…A
(deg.)
ρ
(Å/a.u.
3
)
∇ρ
(ε/a.u.
5
)
ε
L RCP
(a.u.)
AMP
S/anti
C8–H…O–P
2.028
177.6
0.0228 0.0610 0.0366 2.57
C2′–H…O5′
2.519
110.0
0.0110 0.0398 0.4462 0.82
AMP
N/anti
C8–H…O5′
2.200
154.8
0.0160 0.0472 0.0800 1.78
AMP
N/syn
N6–H…O–P
2.215
129.3
0.0148 0.0510 0.1760 3.92
C2′–H…N3
2.322
120.9
0.0157 0.0518 0.1158 1.46
GMP
S/anti
C2′–H…O–P
C8–H…O–P
2.262
2.030
153.7
162.1
0.0154
0.0223
0.0441
0.0640
0.0574
0.0396
1.93
2.14
GMP
N/anti
C3′–H…O–P
2.490
135.1
0.0108 0.0085 0.0795 1.40
O3′–H…O(H)–P 1.792
166.2
0.0357 0.0263 0.0620 2.37
GMP
S/syn
N10–H…O–P
C2′–H…N3
C2′–H…O5′
1.681
2.359
2.638
174.6
127.2
108.7
0.0457
0.0138
0.0081
0.1335
0.0456
0.0325
0.0262
0.0489
2.0929
2.82
1.32
0.31
GMP
N/syn
N10–H…O–P
C3′–H…N3
1.714
2.893
161.5
111.7
0.0426
0.0055
0.1248
0.0192
0.0427
0.4419
2.61
0.92
TMP
S/anti
C9–H…O–P
C1′–H…O7
C2′–H…O5
C6–H…O5′
2.331
2.211
2.495
2.161
166.3
110.7
109.4
160.5
0.0125
0.0198
0.0112
0.0182
0.0376
0.0785
0.0413
0.0512
0.0437
0.8871
0.2387
0.0670
1.89
0.46
1.03
1.73
TMP
N/anti
C9–H…O–P
C6–H…O5′
2.253
2.128
178.6
171.2
0.0143
0.0188
0.0424
0.0529
0.0317
0.0529
2.26
1.52
CMP
S/anti
C6–H…O–P
C1′–H…O7
C2′–H…O5′
2.195
2.238
2.513
149.4
104.0
111.0
0.0174
0.0197
0.0109
0.0477
0.0804
0.0393
0.294
0.9646
0.3163
2.69
0.44
0.93
CMP
N/anti
C5–H…O–P
C6–H…O5′
2.785
2.069
121.2
161.5
0.0052
0.0220
0.0201
0.0611
0.1969
0.0650
1.06
1.56
CMP
N/syn
N8–H…O–P
C6–H…O4′
C3′–H…O5′
C2′-H…O7
2.150
2.255
2.332
2.90
141.2
99.7
107.6
118.1
0.0169
0.0196
0.0144
0.0159
0.0523
0.0855
0.0609
0.0561
0.0861
1.6105
1.6211
0.2114
1.75
0.39
0.30
1.17
Table 5.5 Geometrical parameters, characteristics of (3, − 1) BCPs, and distances between BCP
and RCP for all potential intramolecular hydrogen bonds. True hydrogen bonds are underlined
T. A. Zubatiuk et al.
DNTs, a clear difference is revealed between purine and pyrimidine nucleotides.
In the case of TMP and CMP, the C6–H…O5′ hydrogen bond is observed in all
conformers except the south/anti conformer of CMP where the C6–H atom interacts
with the oxygen of the phosphate group. An opposite situation is found for purine
nucleotides. The C8–H…O-P hydrogen bond is located in south/anti conformers of
AMP and GMP, while the C8–H…O5′ bond is formed in the north/anti conformer
of AMP. Unlike these conformers, interactions with the participation of the C8′–H
atom were not found in the north/anti conformer of GMP (Table 5.5).
The values of electron density and Laplacian of electron density at the BCP for all
of these hydrogen bonds meet Popelier′s criteria. The range of variation of the properties of the BCP for well-defined hydrogen bonds (ρ > 0.015 a.u., ∇
2
(ρ) > 0.044 a.u.)
may be used for further classification of other intramolecular interactions in DNTs.
An analysis of the ellipticity of these hydrogen bonds (ε < 0.09) and the distance between BCP and RCP (L RCP > 1.5 a.u.) does not indicate any instability of these interactions, and these values also may be used as a reference for further consideration.
Molecule Conformer D–H…A
H…A
(Å)
D–H…A
(deg.)
ρ
(Å/a.u.
3
)
∇ρ
(ε/a.u.
5
)
ε
L RCP
(a.u.)
AMP
S/anti
C8–H…O–P
2.028
177.6
0.0228 0.0610 0.0366 2.57
C2′–H…O5′
2.519
110.0
0.0110 0.0398 0.4462 0.82
AMP
N/anti
C8–H…O5′
2.200
154.8
0.0160 0.0472 0.0800 1.78
AMP
N/syn
N6–H…O–P
2.215
129.3
0.0148 0.0510 0.1760 3.92
C2′–H…N3
2.322
120.9
0.0157 0.0518 0.1158 1.46
GMP
S/anti
C2′–H…O–P
C8–H…O–P
2.262
2.030
153.7
162.1
0.0154
0.0223
0.0441
0.0640
0.0574
0.0396
1.93
2.14
GMP
N/anti
C3′–H…O–P
2.490
135.1
0.0108 0.0085 0.0795 1.40
O3′–H…O(H)–P 1.792
166.2
0.0357 0.0263 0.0620 2.37
GMP
S/syn
N10–H…O–P
C2′–H…N3
C2′–H…O5′
1.681
2.359
2.638
174.6
127.2
108.7
0.0457
0.0138
0.0081
0.1335
0.0456
0.0325
0.0262
0.0489
2.0929
2.82
1.32
0.31
GMP
N/syn
N10–H…O–P
C3′–H…N3
1.714
2.893
161.5
111.7
0.0426
0.0055
0.1248
0.0192
0.0427
0.4419
2.61
0.92
TMP
S/anti
C9–H…O–P
C1′–H…O7
C2′–H…O5
C6–H…O5′
2.331
2.211
2.495
2.161
166.3
110.7
109.4
160.5
0.0125
0.0198
0.0112
0.0182
0.0376
0.0785
0.0413
0.0512
0.0437
0.8871
0.2387
0.0670
1.89
0.46
1.03
1.73
TMP
N/anti
C9–H…O–P
C6–H…O5′
2.253
2.128
178.6
171.2
0.0143
0.0188
0.0424
0.0529
0.0317
0.0529
2.26
1.52
CMP
S/anti
C6–H…O–P
C1′–H…O7
C2′–H…O5′
2.195
2.238
2.513
149.4
104.0
111.0
0.0174
0.0197
0.0109
0.0477
0.0804
0.0393
0.294
0.9646
0.3163
2.69
0.44
0.93
CMP
N/anti
C5–H…O–P
C6–H…O5′
2.785
2.069
121.2
161.5
0.0052
0.0220
0.0201
0.0611
0.1969
0.0650
1.06
1.56
CMP
N/syn
N8–H…O–P
C6–H…O4′
C3′–H…O5′
C2′-H…O7
2.150
2.255
2.332
2.90
141.2
99.7
107.6
118.1
0.0169
0.0196
0.0144
0.0159
0.0523
0.0855
0.0609
0.0561
0.0861
1.6105
1.6211
0.2114
1.75
0.39
0.30
1.17
Table 5.5 Geometrical parameters, characteristics of (3, − 1) BCPs, and distances between BCP
and RCP for all potential intramolecular hydrogen bonds. True hydrogen bonds are underlined