156
T. A. Zubatiuk et al.
confirm the earlier suggested assumptions [19, 20, 52] that the SU plays a role of
a soft buffer, changing the conformation according to the interactions between the
BB and the BU.
Based on the analysis of the electron density distribution it was demonstrated that conformers with anti orientation of the base are characterized by the C6/
C8–H…O5′, or the C6/C8–H…O-P hydrogen bond (Table 5.12). However, in the
case of some conformations of backbone such reference hydrogen bond converts to
another form. Thus, in BII-form of DNA in case of all nucleotides, the C6/C8–H…
O3′ (n − 1) hydrogen bond is observed. In the case of mGMP in BI-form of DNA
this hydrogen bond is weaker and it can be classified as rather strong electrostatic
interaction rather than an intramolecular hydrogen bond. An absence of such reference H-bonds for anti-conformers of purine nucleotides in case of ZI–ZII-form
of DNA (Table 5.13) is observed. Presence of all these reference hydrogen bonds
(C6/C8–H…O5′, C6/C8–H…O–P, and C6/C8–H…O3′ (n − 1)) can be summarized
Table 5.10 Selected geometrical parameters of methyl ethers of 2′-deoxyribonucleotides in equilibrium, A-DNA and B-DNA like conformations calculated at the B3LYP/ aug-cc-pvdz level
Nucleotide Parameter
Equilibrium
DNA-like conformation
S/anti
N/anti
A
a
BI
b
BII
b
mGMP
C1′–O4′ (Å)
1.426
1.413
1.415
1.416
1.419
C4′–O4′ (Å)
1.447
1.449
1.445
1.447
1.446
χ (deg.)
− 95.1
− 133.7
− 146.6
− 120.9
− 133.2
P
183.4
6.3
16.7
146.3
165.4
mAMP
C1′–O4′ (Å)
1.426
1.415
1.416
1.416
1.419
C4′–O4′ (Å)
1.446
1.449
1.446
1.447
1.447
χ (deg.)
− 99.0
− 138.5
− 147.5
− 119.5
− 137.4
P
183.2
3.8
11.3
162.3
166.0
a
N/anti conformers
b
S/anti conformers
Table 5.11 Selected geometrical parameters of methyl ethers of 2′-deoxyribonucleotides in equilibrium and DNA-Z like conformations, calculated at the B3LYP/ aug-cc-pvdz level
Nucleotide Parameter
Equilibrium
DNA-like conformation
S/anti
N/anti
ZI
a
ZII
a
ZI
b
, ZII
b
ZI
c
, ZII
c
mGMP
C1′–O4′ (Å)
1.426
1.413
1.412
1.404 1.406
1.414
C4′–O4′ (Å)
1.447
1.449
1.460
1.457 1.457
1.464
χ (deg).
− 95.1
− 133.7
− 140.6
− 161.0
44.9
69.1
P
183.4
6.3
167.6
17.6
6.8
177.8
mAMP
C1′–O4′ (Å)
1.426
1.415
1.411
1.403 1.410
1.414
C4′–O4′ (Å)
(Å)
1.446
1.449
1.460
1.460 1.453
1.459
Χ (deg.)
− 99.0
− 138.5
− 150.0
− 169.4
79.1
81.4
P
183.2
3.8
171.0
2.1
36.0
169.3
a
N/anti conformers
b
N/syn conformers
c
S/syn conformers
T. A. Zubatiuk et al.
confirm the earlier suggested assumptions [19, 20, 52] that the SU plays a role of
a soft buffer, changing the conformation according to the interactions between the
BB and the BU.
Based on the analysis of the electron density distribution it was demonstrated that conformers with anti orientation of the base are characterized by the C6/
C8–H…O5′, or the C6/C8–H…O-P hydrogen bond (Table 5.12). However, in the
case of some conformations of backbone such reference hydrogen bond converts to
another form. Thus, in BII-form of DNA in case of all nucleotides, the C6/C8–H…
O3′ (n − 1) hydrogen bond is observed. In the case of mGMP in BI-form of DNA
this hydrogen bond is weaker and it can be classified as rather strong electrostatic
interaction rather than an intramolecular hydrogen bond. An absence of such reference H-bonds for anti-conformers of purine nucleotides in case of ZI–ZII-form
of DNA (Table 5.13) is observed. Presence of all these reference hydrogen bonds
(C6/C8–H…O5′, C6/C8–H…O–P, and C6/C8–H…O3′ (n − 1)) can be summarized
Table 5.10 Selected geometrical parameters of methyl ethers of 2′-deoxyribonucleotides in equilibrium, A-DNA and B-DNA like conformations calculated at the B3LYP/ aug-cc-pvdz level
Nucleotide Parameter
Equilibrium
DNA-like conformation
S/anti
N/anti
A
a
BI
b
BII
b
mGMP
C1′–O4′ (Å)
1.426
1.413
1.415
1.416
1.419
C4′–O4′ (Å)
1.447
1.449
1.445
1.447
1.446
χ (deg.)
− 95.1
− 133.7
− 146.6
− 120.9
− 133.2
P
183.4
6.3
16.7
146.3
165.4
mAMP
C1′–O4′ (Å)
1.426
1.415
1.416
1.416
1.419
C4′–O4′ (Å)
1.446
1.449
1.446
1.447
1.447
χ (deg.)
− 99.0
− 138.5
− 147.5
− 119.5
− 137.4
P
183.2
3.8
11.3
162.3
166.0
a
N/anti conformers
b
S/anti conformers
Table 5.11 Selected geometrical parameters of methyl ethers of 2′-deoxyribonucleotides in equilibrium and DNA-Z like conformations, calculated at the B3LYP/ aug-cc-pvdz level
Nucleotide Parameter
Equilibrium
DNA-like conformation
S/anti
N/anti
ZI
a
ZII
a
ZI
b
, ZII
b
ZI
c
, ZII
c
mGMP
C1′–O4′ (Å)
1.426
1.413
1.412
1.404 1.406
1.414
C4′–O4′ (Å)
1.447
1.449
1.460
1.457 1.457
1.464
χ (deg).
− 95.1
− 133.7
− 140.6
− 161.0
44.9
69.1
P
183.4
6.3
167.6
17.6
6.8
177.8
mAMP
C1′–O4′ (Å)
1.426
1.415
1.411
1.403 1.410
1.414
C4′–O4′ (Å)
(Å)
1.446
1.449
1.460
1.460 1.453
1.459
Χ (deg.)
− 99.0
− 138.5
− 150.0
− 169.4
79.1
81.4
P
183.2
3.8
171.0
2.1
36.0
169.3
a
N/anti conformers
b
N/syn conformers
c
S/syn conformers