154
T. A. Zubatiuk et al.
the case of A-DNA does not correspond to real deformation of nucleotides due to
incorporation into macromolecule. Nevertheless, taking into account rather small
differences in values of torsion angles for equilibrium conformation of DNTs and
average values for A-DNA it is possible to suggest that deformation energy in this
case should be the smallest. The largest increase of energy is found for the Z-forms
of DNA (Table 5.8).
The obtained data demonstrate that the polarization effect of environment results
in considerable decrease of deformation energy of nucleotides during incorporation
into all types of DNA (Table 5.8). Only for A-DNA notable decrease of deformation
energy is not found.
In the case of A-DNA amount of energy for the deformation of the geometry of
nucleotides is practically equal for all molecules. However, for BI, BII, ZI, and ZIIforms of DNA (south/anti conformation of nucleotides) a difference between purine
Table 5.7 B3LYP/aug-cc-pvdz geometrical parameters (deg.) of conformers of methyl ethers of
2′-deoxyribonucleotides
Nucleotide Conformer Backbone torsion angles
α
β
γ
δ
ζ
χ
P
υ max
mTMP
S/anti
− 87.7 −105.6
63.1 141.6 −71.6 − 113.5 171.8
30.1
N/anti
− 70.7 − 166.6
57.6 87.6 − 73.5 − 144.7 11.6
28.1
mCMP
S/anti
− 85.1 − 107.9
60.7 141.5 − 72.0 − 124.3 171.1
30.5
N/anti
− 65.8 − 177.0
59.0 85.9 − 73.8 − 153.3
6.2
30.8
N/syn
− 65.3 − 160.9
58.8 95.5 − 75.4
161.0 330.6
33.1
mAMP
S/anti
− 102.3 − 101.0
61.3 144.7 − 70.9
− 99.0 183.2
29.8
N/anti
− 75.8 − 161.9
54.1 89.5 − 73.8 − 138.5
3.8
27.7
S/syn
74.2
157.4 − 172.0 115.4 73.0
79.8 120.0
40.3
N/syn
− 66.9 − 169.5
58.9 99.2 − 77.1
121.0 322.5
35.2
mGMP
S/anti
− 105.3
− 99.6
60.0 145.3 − 71.1
− 95.1 183.4
30.4
N/anti
− 80.3 − 155.4
52.6 92.7 − 73.8 − 133.7
6.3
23.7
S/syn
− 68.2 − 110.7
58.2 134.2 − 70.0
72.7 155.0
31.8
N/syn
− 90.0 − 139.9
53.4 85.7 − 67.8
65.8 40.6
27.3
Table 5.8 B3LYP/aug-cc-pvdz deformation energies (kcal/mol) of isolated and hydrated (within
parentheses) methyl ethers of 2′-deoxyribonucleotides resulted from incorporation into DNA
DNA form
Nucleotide
mTMP
mCMP
mAMP
mGMP
A
a
− 1.8(− 0.1)
− 1.6(− 0.1)
− 1.8(− 0.6)
− 2.0(− 0.2)
BI
b
5.1(− 0.1)
4.4(0.2)
6.6(− 0.4)
6.3(0.2)
BII
b
12.0(0.5)
4.2(0.5)
6.7(0.4)
5.9(0.4)
ZI
b
5.8(1.1)
5.0(1.3)
10.8(0.6)
10.8(− 0.3)
ZII
b
6.4(0.8)
5.1(0.6)
10.8(0.6)
10.8(− 0.3)
ZI
a
, ZII
a
9.7(0.0)
9.8(0.9)
ZI
c
, ZII
c
0.5(2.8)
10.1(− 10.6)
ZI
d
, ZII
d
1.0(1.1)
13.0(0.2)
a
N/anti-conformers
b
S/anti-conformers
c
N/syn-conformers
d
S/syn-conformers
T. A. Zubatiuk et al.
the case of A-DNA does not correspond to real deformation of nucleotides due to
incorporation into macromolecule. Nevertheless, taking into account rather small
differences in values of torsion angles for equilibrium conformation of DNTs and
average values for A-DNA it is possible to suggest that deformation energy in this
case should be the smallest. The largest increase of energy is found for the Z-forms
of DNA (Table 5.8).
The obtained data demonstrate that the polarization effect of environment results
in considerable decrease of deformation energy of nucleotides during incorporation
into all types of DNA (Table 5.8). Only for A-DNA notable decrease of deformation
energy is not found.
In the case of A-DNA amount of energy for the deformation of the geometry of
nucleotides is practically equal for all molecules. However, for BI, BII, ZI, and ZIIforms of DNA (south/anti conformation of nucleotides) a difference between purine
Table 5.7 B3LYP/aug-cc-pvdz geometrical parameters (deg.) of conformers of methyl ethers of
2′-deoxyribonucleotides
Nucleotide Conformer Backbone torsion angles
α
β
γ
δ
ζ
χ
P
υ max
mTMP
S/anti
− 87.7 −105.6
63.1 141.6 −71.6 − 113.5 171.8
30.1
N/anti
− 70.7 − 166.6
57.6 87.6 − 73.5 − 144.7 11.6
28.1
mCMP
S/anti
− 85.1 − 107.9
60.7 141.5 − 72.0 − 124.3 171.1
30.5
N/anti
− 65.8 − 177.0
59.0 85.9 − 73.8 − 153.3
6.2
30.8
N/syn
− 65.3 − 160.9
58.8 95.5 − 75.4
161.0 330.6
33.1
mAMP
S/anti
− 102.3 − 101.0
61.3 144.7 − 70.9
− 99.0 183.2
29.8
N/anti
− 75.8 − 161.9
54.1 89.5 − 73.8 − 138.5
3.8
27.7
S/syn
74.2
157.4 − 172.0 115.4 73.0
79.8 120.0
40.3
N/syn
− 66.9 − 169.5
58.9 99.2 − 77.1
121.0 322.5
35.2
mGMP
S/anti
− 105.3
− 99.6
60.0 145.3 − 71.1
− 95.1 183.4
30.4
N/anti
− 80.3 − 155.4
52.6 92.7 − 73.8 − 133.7
6.3
23.7
S/syn
− 68.2 − 110.7
58.2 134.2 − 70.0
72.7 155.0
31.8
N/syn
− 90.0 − 139.9
53.4 85.7 − 67.8
65.8 40.6
27.3
Table 5.8 B3LYP/aug-cc-pvdz deformation energies (kcal/mol) of isolated and hydrated (within
parentheses) methyl ethers of 2′-deoxyribonucleotides resulted from incorporation into DNA
DNA form
Nucleotide
mTMP
mCMP
mAMP
mGMP
A
a
− 1.8(− 0.1)
− 1.6(− 0.1)
− 1.8(− 0.6)
− 2.0(− 0.2)
BI
b
5.1(− 0.1)
4.4(0.2)
6.6(− 0.4)
6.3(0.2)
BII
b
12.0(0.5)
4.2(0.5)
6.7(0.4)
5.9(0.4)
ZI
b
5.8(1.1)
5.0(1.3)
10.8(0.6)
10.8(− 0.3)
ZII
b
6.4(0.8)
5.1(0.6)
10.8(0.6)
10.8(− 0.3)
ZI
a
, ZII
a
9.7(0.0)
9.8(0.9)
ZI
c
, ZII
c
0.5(2.8)
10.1(− 10.6)
ZI
d
, ZII
d
1.0(1.1)
13.0(0.2)
a
N/anti-conformers
b
S/anti-conformers
c
N/syn-conformers
d
S/syn-conformers