161
5 Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides
(5.1)
G
GP
av
i i
i
M
=
=
∑
1
Table 5.15  B3LYP/aug-cc-pvdz relative Gibbs free energy (kcal/mol), 298 K and population (%)
Nucleotide
Tautomer
Conformer
ΔG
P
Conformers of non-protonated 2′-deoxyribonucleotides
mTMP
S/anti
N/anti
0
4.85
100
0
mCMP
S/anti
N/anti
N/ort
0
3.22
8.22
99.96
0.04
0
mAMP
S/anti
N/anti
N/ort
0
6.95
12.00
100
0
0
mGMP
S/anti
N/anti
S/syn
N/syn
8.11
16.28
0
4.18
0
0
100
0
Conformers of protonated tautomers of 2′-deoxyribonucleotides a
mTMP-H
H7cis
H7cis
H7trans
H8cis
H8cis
H8trans
H8trans
S/ort
N/anti
C4′-endo/syn
S/ort
S/anti
S/anti
N/anti
11.67
19.61
0
5.65
6.11
0
1.09
0
0
100
0
0
86.2
13.8
mCMP-H
H3
H3
H3
H7cis
H7cis
H7cis
H7trans
H7trans
H7trans
S/anti
N/anti
C2′-exo/ort
S/anti
N/anti
C2′-exo/ort
N/anti
C4′-endo/syn
C2′-exo/ort
4.06
5.35
0
1.04
3.55
2.06
10.36
0
9.37
0.1
0
99.9
14.3
0.2
2.6
0
82.9
0
mGMP-H
H3
H7
H7
H10
H11
H11
S/syn
C3′-exo/ort
S/syn
C3′-exo/ort
C3′-exo/ort
S/syn
0
0
2.50
0
16.13
0
100
97.5
2.5
100
0
100
mAMP-H
H1
H1
H3
H7
H10
S/syn
S/ort
C3′-exo/ort
C3′-exo/ort
C3′-exo/ort
9.24
0
0
0
0
0
100
100
100
100
a
Energies for non-protonated molecules are taken from ref [53]