144
T. A. Zubatiuk et al.
in south conformers of CMP and AMP because of the equatorial orientation of the
phosphate group. The absence of an amino group makes the presence of any synconformers of TMP impossible, unlike the previously reported case [19].
Table 5.2 Selected geometrical parameters of the pyrimidine 2′-deoxyribonucleotides calculated
at the B3LYP/6-31++G(d,p) level
Parameters
Nucleotide, conformation
TMP
TMP
CMP
CMP
CMP
S/anti
N/anti
S/anti
N/anti
N/syn
C2(C4)–N10(N8)H2 (Å)
1.377
1.376
1.373
N9(N1)–C1′ (Å)
1.468
1.488
1.473
1.487
1.493
C1′–O4′ (Å)
1.429
1.412
1.423
1.416
1.418
C4′–O4′ (Å)
1.449
1.443
1.450
1.444
1.457
C3′–O3′ (Å)
1.438
1.425
1.438
1.426
1.437
O5′–P (Å)
1.687
1.689
1.680
1.694
1.676
Σ(NH2) (deg.)
–
–
349.4
350.8
335.8
OH–P–O5′–C5′ (deg.)
83.5
76.6
61.2
93.2
69.0
β (deg.)
180.0
178.4
142.6
155.3
159.3
γ (deg.)
10.6
55.3
40.1
53.0
42.2
δ (deg.)
143.5
86.6
142.3
85.9
98.2
χ (deg.)
− 115.7
− 148.5
− 144.1
− 155.8
162.1
P
181.4
12.9
184.9
5.1
330.7
νmax
33.3
28.9
34.3
30.9
34.5
Sugar conformation
3T2
3T2
3T2
3T2
2T1
Table 5.3 Selected geometrical parameters of the purine 2′-deoxyribonucleotides calculated at the
B3LYP/6-31++G(d,p) level
Parameters
Nucleotide, conformation
AMP
AMP
AMP
GMP
GMP
GMP
GMP
S/anti
N/anti
N/syn
S/anti
N/anti
S/syn
N/syn
C2(C4)–
N10(N8)H2 (Å)
1.367
1.365
1.367
1.393
1.389
1.353
1.355
N9(N1)–C1′ (Å)
1.456
1.470
1.473
1.451
1.477
1.451
1.454
C1′–O4′ (Å)
1.423
1.414
1.420
1.425
1.414
1.425
1.421
C4′-O4′ (Å)
1.452
1.446
1.454
1.445
1.457
1.447
1.437
C3′-O3′ (Å)
1.439
1.425
1.429
1.446
1.415
1.445
1.427
O5′-P (Å)
1.684
1.692
1.691
1.689
1.679
1.661
1.657
Σ(NH2) (deg.)
354.0
353.8
335.1
338.7
340.7
349.4
346.1
OH–P–O5′–C5′
(deg.)
68.4
−72.7
73.4
150.3
− 106.5
66.4
65.1
β (deg.)
132.9
− 163.2
174.2
101.0
96.7
174.0
−166.8
γ (deg.)
30.6
53.2
51.2
30.6
−66.9
42.7
47.4
δ (deg.)
142.9
90.1
100.2
134.3
99.7
139.1
86.5
χ (deg.)
− 130.2
− 139.6
122.4
− 110.7
− 117.3
70.9
62.0
P
171.9
3.3
320.9
146.5
358.7
158.2
44.0
νmax
36.5
27.3
35.1
40.2
28.6
36.4
26.8
Sugar
conformation
2T3
3T2
1T2
2T1
2T3
2T1
4T3
T. A. Zubatiuk et al.
in south conformers of CMP and AMP because of the equatorial orientation of the
phosphate group. The absence of an amino group makes the presence of any synconformers of TMP impossible, unlike the previously reported case [19].
Table 5.2 Selected geometrical parameters of the pyrimidine 2′-deoxyribonucleotides calculated
at the B3LYP/6-31++G(d,p) level
Parameters
Nucleotide, conformation
TMP
TMP
CMP
CMP
CMP
S/anti
N/anti
S/anti
N/anti
N/syn
C2(C4)–N10(N8)H2 (Å)
1.377
1.376
1.373
N9(N1)–C1′ (Å)
1.468
1.488
1.473
1.487
1.493
C1′–O4′ (Å)
1.429
1.412
1.423
1.416
1.418
C4′–O4′ (Å)
1.449
1.443
1.450
1.444
1.457
C3′–O3′ (Å)
1.438
1.425
1.438
1.426
1.437
O5′–P (Å)
1.687
1.689
1.680
1.694
1.676
Σ(NH2) (deg.)
–
–
349.4
350.8
335.8
OH–P–O5′–C5′ (deg.)
83.5
76.6
61.2
93.2
69.0
β (deg.)
180.0
178.4
142.6
155.3
159.3
γ (deg.)
10.6
55.3
40.1
53.0
42.2
δ (deg.)
143.5
86.6
142.3
85.9
98.2
χ (deg.)
− 115.7
− 148.5
− 144.1
− 155.8
162.1
P
181.4
12.9
184.9
5.1
330.7
νmax
33.3
28.9
34.3
30.9
34.5
Sugar conformation
3T2
3T2
3T2
3T2
2T1
Table 5.3 Selected geometrical parameters of the purine 2′-deoxyribonucleotides calculated at the
B3LYP/6-31++G(d,p) level
Parameters
Nucleotide, conformation
AMP
AMP
AMP
GMP
GMP
GMP
GMP
S/anti
N/anti
N/syn
S/anti
N/anti
S/syn
N/syn
C2(C4)–
N10(N8)H2 (Å)
1.367
1.365
1.367
1.393
1.389
1.353
1.355
N9(N1)–C1′ (Å)
1.456
1.470
1.473
1.451
1.477
1.451
1.454
C1′–O4′ (Å)
1.423
1.414
1.420
1.425
1.414
1.425
1.421
C4′-O4′ (Å)
1.452
1.446
1.454
1.445
1.457
1.447
1.437
C3′-O3′ (Å)
1.439
1.425
1.429
1.446
1.415
1.445
1.427
O5′-P (Å)
1.684
1.692
1.691
1.689
1.679
1.661
1.657
Σ(NH2) (deg.)
354.0
353.8
335.1
338.7
340.7
349.4
346.1
OH–P–O5′–C5′
(deg.)
68.4
−72.7
73.4
150.3
− 106.5
66.4
65.1
β (deg.)
132.9
− 163.2
174.2
101.0
96.7
174.0
−166.8
γ (deg.)
30.6
53.2
51.2
30.6
−66.9
42.7
47.4
δ (deg.)
142.9
90.1
100.2
134.3
99.7
139.1
86.5
χ (deg.)
− 130.2
− 139.6
122.4
− 110.7
− 117.3
70.9
62.0
P
171.9
3.3
320.9
146.5
358.7
158.2
44.0
νmax
36.5
27.3
35.1
40.2
28.6
36.4
26.8
Sugar
conformation
2T3
3T2
1T2
2T1
2T3
2T1
4T3