Double Sugar and Phosphate Backbone-Constrained Nucleotides
3.74 (d, Jgem ) 12.1 Hz, 1H, H5′′a), 3.23 (d, JH2′a,H7′a ) 4.9 Hz,
1H, H2′a), 3.04 (m, 1H, H7′a), 2.32 (m, 1H, H2′b), 2.07 (m, 1H,
H2′′b). 1.89 (s, 3H, T-Me), 1.34 (d, JH7′a,7′Me ) 7.6 Hz, 3H, 7′-
4.10 (ddd, JH5′′b,H4′b ) 2.7 Hz, JH5′b,H5′′b ) JH5′′b,p ) 11.9 Hz,1H,
H5′′b), 4.01 (d, JH6′a,p ) 24.6 Hz, 1H, H6′a), 3.91 (d, JH5′a,H5′′a
)
11.3 Hz, 1H, H5′a), 3.86 (d, JH5′a,H5′′a ) 11.3 Hz, 1H, H5′′a),
3.78-3.79 (m, 7H, H4′b, OMe), 3.27 (m, 2H, H2′a, H7′a), 2.37
(m, 1H, H2′b), 2.06 (m, 1H, H2′′b), 1.74 (s, 3H, T-Me), 1.43
(d, JH7′a, 7′Me ) 6.4 Hz, 3H, 7′-Me), 1.25(s, 3H, T-Me). 13C NMR
(125 MHz, CDCl3): δ 163.9(C4), 163.6 (C4), 158.9, 158.8, 150.1
(C2), 149.8 (C2), 143.9, 135.5, 134.8, 134.7, 134.5, 130.4, 130.3,
128.1, 128.0, 127.5, 113.5, 113.4, 110.8 (C5), 87.3, 84.5 (C1′b),
84.2 (d, J ) 2.2 Hz, C4′b), 84.0 (d, J ) 4.9 Hz, C6′a), 83.4 (C1′a),
83.3 (d, J ) 6.9 Hz, C4′a), 81.0 (d, J ) 9.7 Hz, C3′a), 69.6 (C3′b),
67.4 (d, J ) 6.2 Hz, C5′b), 58.7 (C5′a), 55.3 (OMe), 49.4 (C2′a),
39.6 (C2′b), 39.3 (C7′a), 13.4 (7′-Me), 12.3 (T-Me), 11.7 (T-Me).
MALDI-TOF M/S: [M + Na]+ found 909.345, calcd 909.2725.
(Sp)-D2-CNA-dT (17a). 16a (20 mg) was dissolved in 2 mL of
2% TFA in CH2Cl2 and stirred at room temperature for 3 min. Ten
milliliters of double-distilled water was added to the reaction
mixture and the organic phase was removed. The aqueous phase
was washed with CH2Cl2 twice. The crude product in the aqueous
phase was purified by RP-HPLC (Kromasil 100, C18, 5 µm, 250
× 8 mm. 0f40′, CfC/D ) 60/40, v/v; flow rate 1.5 mL/min at
room temperature; Buffer C: 5% MeOH in H2O; Buffer D: pure
MeCN) to give 17a (10 mg, tR ) 28.8 min). 17a. 31P NMR (202.5
Me), 1.30 (s, 3H, T-Me), 0.90 (s, 9H, tert-butyl), 0.12 (s, 6H). 13
C
NMR (125 MHz, CDCl3): δ 163.9(C4), 163.8 (C4), 158.8, 158.7,
150.2 (C2), 145.0 (C2), 143.9, 135.4, 135.1, 134.7, 134.6, 130.1,
130.0, 128.2, 128.1, 127.3, 113.5, 113.4, 111.1 (C5), 110.8 (C5),
87.4, 85.6 (C1′b), 85.1 (d, J ) 6.4 Hz, C4′b), 83.9 (d, J ) 6.4 Hz,
C6′a), 83.7(d, J ) 7.3 Hz, C4′a), 83.4(C1′a), 81.2 (d, J ) 9.2 Hz,
C3′a), 71.6 (C3′b), 67.9 (d, J ) 4.4 Hz, C5′b), 58.4 (C5′a), 55.2
(OMe), 49.2 (C2′a), 40.6 (C2′b), 37.9 (C7′a), 25.7 (tBDMS), 17.9
(tBDMS), 13.4 (7′-Me), 12.5 (T-Me), 11.9 (T-Me), -4.7(tBDMS),
-4.8 (tBDMS). MALDI-TOF M/S: [M + Na]+ found 1023.36,
1
calcd 1023.36. 15b. 31P NMR (202.5 MHz, CDCl3): δ -7.1. H
NMR (500 MHz, CDCl3): δ 9.01 (broad, 1H, H3), 8.82 (broad,
1H, H3), 7.85 (s, 1H, H6), 7.45-6.83 (m, 15H), 6.25 (dd, JH1′b,H2′b
) 5.8 Hz, JH1′b,H2′′b ) 7.6 Hz, 1H, H1′b), 5.61 (s, 1H, H1′a), 5.07
(d, JH3′a,p ) 17.9 Hz, 1H, H3′a), 4.28 (m, 1H, H3′b), 4.02-3.78
(m, 11H, H5′b, H6′a, H5′′b, H5′a, H5′′a, H4′b, OMe), 3.29 (m,
1H, H7′a), 3.24 (d, JH2′a,H7′a ) 5 Hz, 1H, H2′a), 2.24 (m, 1H, H2′b),
2.00 (m, 1H, H2′′b), 1.88 (s, 3H, T-Me), 1.43 (d, JH7′a,7′Me ) 7.5
Hz, 3H, 7′-Me), 1.22(s, 3H, T-Me), 0.90 (s, 9H, tert-butyl), 0.12
(s, 6H). 13C NMR (125 MHz, CDCl3): δ 163.7(C4), 163.6 (C4),
158.9, 150.2 (C2), 149.8 (C2), 143.7, 135.6, 134.8, 134.7, 134.6,
130.3, 130.2, 128.3, 128.1, 127.5, 113.4, 113.3, 111.1 (C5), 110.8
(C5), 87.4, 85.2 (C1′b), 84.9 (d, J ) 4.6 Hz, C4′b), 83.9 (d, J )
5.5 Hz, C6′a), 83.4 (C1′a), 83.2 (d, J ) 5.5 Hz, C4′a), 81.2 (d, J
) 10.1 Hz, C3′a), 71.8 (C3′b), 67.9 (d, J ) 5.5 Hz, C5′b), 58.6
(C5′a), 55.3 (OMe), 49.3 (C2′a), 40.4 (C2′b), 39.0 (C7′a), 25.7
(tBDMS), 17.9 (tBDMS), 13.4 (7′-Me), 12.3 (T-Me), 11.7 (T-Me),
-4.7(tBDMS), -4.8 (tBDMS). MALDI-TOF M/S: [M + Na]+
found 1023.36, calcd 1023.366.
1
MHz, D2O): δ -6.4. H NMR (500 MHz, D2O): δ7.78 (s, 1H,
H6), 7.75 (s, 1H, H6), 6.23 (dd, JH1′b,H2′b ) 6.4 Hz, JH1′b,H2′′b ) 7.0
Hz, 1H, H1′b), 5.61 (s, 1H, H1′a), 4.89 (d, JH3′a,p ) 17.0 Hz, 1H,
H3′a), 4.44 (m, 1H, H3′b), 4.36 (ddd, JH5′b, H4′b ) 2.7 Hz, JH5′b, p
)
6.5 Hz, JH5′b, H5′′b ) 11.6 Hz, 1H, H5′b), 4.31-4.25 (m, 2H, H5′′b,
H6′a), 4.24 (d, Jgem ) 14.0 Hz, 1H, H5′a), 4.18 (d, Jgem ) 14.0 Hz,
1H, H5′′a), 4.13 (m, 1H, H4′b), 3.03 (d, JH2′a,H7′a ) 4.9 Hz, 1H,
H2′a), 2.95 (m, 1H, H7′a), 2.40-2.28 (m, 2H, H2′b, H2′′b), 1.82
(s, 3H, T-Me), 1.79 (s, 3H, T-Me), 1.24 (d, JH7′a,7′Me ) 7.4 Hz, 3H,
7′-Me). 13C NMR (125 MHz, D2O): δ 166.6, 166.3(C4), 151.6,
150.8 (C2), 137.4, 136.5, 110.3, 110.4 (C5), 85.5 (C1’b), 84.5 (d,
J ) 6.9 Hz, C6′a), 84.1 (d, J ) 6.9 Hz, C4′b), 84.0(d, J ) 6.9 Hz,
C4′a), 83.5(C1′a), 81.6 (d, J ) 8.3 Hz, C3′a), 70.1 (C3′b), 68.1 (d,
J ) 5.5 Hz, C5′b), 56.4 (C5′a), 48.6 (C2′a), 38.2 (C2′b), 37.6 (C7′a),
12.3 (7′-Me), 11.7 (T-Me), 11.5 (T-Me). MALDI-TOF M/S: [M
+ Na]+ found 607.070, calcd 607.1417.
5′a-O-Dimethoxytrityl-(Sp)-D2-CNA-dT (16a) and 5′a-O-
Dimethoxytrityl-(Rp)-D2-CNA-dT (16b). 15a (150 mg, 0.15 mmol)
was dissolved in 3 mL dry THF, to which 0.25 mL of 1 M TBAF/
THF was added. The mixture was allowed to stir at room
temperature for 20 min. After evaporation of solvent on vacuum,
the residue was subjected to short column chromatography on silica
gel (EtOAc/MeCN ) 7/3 containing 1% pyridine, methanol from
1% to 3%) to give 16a (99 mg, 74.5%) and 16b (19 mg, 14.3%).
16a and 16b can also be obtained from 15b, thus 15b (60 mg,
0.06 mmol) was dissolved in 2 mL dry THF, to which 0.12 mL of
1 M TBAF/THF was added. The mixture was allowed to stir at
room temperature for 20 min. After evaporation of solvent on
vacuum, the residue was subjected to short column chromatography
on silica gel (EtOAc/MeCN ) 7/3 containing 1% pyridine,
methanol from 1% to 3%) to give 16a (17 mg, 32%) and 16b (31
mg, 58%). 16a. 31P NMR (202.5 MHz, CDCl3): δ -6.5. 1H NMR
(500 MHz, CDCl3): δ7.59 (s, 1H, H6), 7.45-6.84 (m, 14H), 6.24
(Sp)-D2-CNA-dT (17b). 16b (17 mg) was dissolved in 2 mL of
2% TFA in CH2Cl2 and stirred at room temperature for 3 min. Ten
milliliters of double distilled water was added to the reaction
mixture, and the organic phase was removed. The aqueous phase
was washed with CH2Cl2 twice. The crude product in the aqueous
phase was purified by RP-HPLC (Kromasil 100, C18, 5 µm, 250
× 8 mm. 0f40′, CfC/D ) 60/40, v/v; flow rate 1.5 mL/min at
room temperature; Buffer C: 5% MeOH in H2O; Buffer D: pure
MeCN) to give 17b (10 mg, tR ) 29.07 min). 17b. 31P NMR (202.5
1
MHz, D2O): δ -4.6. H NMR (500 MHz, D2O): δ7.81 (s, 1H,
H6), 7.44 (s, 1H, H6), 6.20 (dd, JH1′b,H2′b ) 6.7 Hz, JH1′b,H2′′b ) 6.4
Hz, 1H, H1′b), 5.63 (s, 1H, H1′a), 4. 09 (d, JH3′a, p ) 16.1 Hz, 1H,
H3′a), 4.47 (m, 1H, H3′b), 4.39-4.27 (m, 2H, H5′b, H5′′b), 4.23
(d, 1H, JH5′b,p ) 25.2 Hz, H6′a), 4.15 (d, Jgem ) 13.9 Hz, 1H, H5′a),
4.08 (m, 2H, H5′′a, H4′b), 3.21 (d, JH2′a,H7′a ) 4.7 Hz, 1H, H2′a),
2.92 (m, 1H, H7′a), 2.37-2.34 (m, 2H, H2′b, H2′′b), 1.82 (s, 3H,
T-Me), 1.81 (s, 3H, T-Me), 1.31 (d, JH7′a,7′Me ) 7.3 Hz, 3H, 7′-
Me). 13C NMR (125 MHz, D2O): δ 166.6, 166.4 (C4), 151.7, 151.0
(C2), 137.3, 136.6, 111.2, 110.4 (C5), 85.4 (C1′b), 84.2 (d, J )
6.1 Hz, C6′a), 83.9 (d, J ) 6.9 Hz, C4′b), 83.8 (d, J ) 6.9 Hz,
C4′a), 83.2(C1′a), 81.4 (d, J ) 9.4 Hz, C3′a), 69.7 (C3′b), 67.8 (d,
J ) 5.4 Hz, C5′b), 56.5 (C5′a), 48.7 (C2′a), 39.7 (C2′b), 37.9 (C7′a),
12.3 (7′-Me), 11.7 (T-Me), 11.5 (T-Me). MALDI-TOF M/S: [M
+ H]+ found 585.105, calcd 585.1598.
(t, J ) 5.5 Hz, 1H, H1′b), 5.50 (s, 1H, H1′a), 5.05 (d, JH3′a,p
)
17.0 Hz, 1H, H3′a), 4.45 (m, 1H, H3′b), 4.37 (dd, JH5′b,H4′b ) 3.4
Hz, JH5′b,p ) 9.0 Hz, 2H, H5′b, H5′′b), 4.10 (m, 2H, H5′a, H4′b),
3.98 (d, JH6′a,p ) 24.9 Hz, 1H, H6′a), 3.78 (s, 6H, OMe), 3.74 (d,
Jgem ) 12.1 Hz, 1H, H5′′a), 3.26 (d, JH2′a,H7′a ) 4.9 Hz, 1H, H2′a),
3.05 (m, 1H, H7′a), 2.44 (m, 1H, H2′b), 2.12 (m, 1H, H2′′b), 1.88
(s, 3H, T-Me), 1.32 (d, JH7′a,7′Me ) 7.2 Hz, 3H, 7′-Me), 1.30 (s,
3H, T-Me). 13C NMR (1250 MHz, CDCl3): δ 163.9(C4), 158.8,
158.7, 150.5 (C2), 150.2 (C2), 143.9, 135.5, 135.1, 134.8, 134.6,
130.1, 128.2, 128.1, 127.3, 113.5, 111.2 (C5), 110.9 (C5), 87.5,
85.4 (C1′b), 84.6 (d, J ) 5.5 Hz, C4′b), 84.1 (d, J ) 4.6 Hz, C6′a),
83.7(d, J ) 7.3 Hz, C4′a), 83.5(C1′a), 81.4 (d, J ) 8.2 Hz, C3′a),
70.7 (C3′b), 68.0 (d, J ) 3.7 Hz, C5′b), 58.4 (C5′a), 55.2 (OMe),
49.1 (C2′a), 39.9 (C2′b), 37.7 (C7′a), 13.4 (7′-Me), 12.5 (T-Me),
11.9 (T-Me). MALDI-TOF M/S: [M + Na]+ found 909.305, calcd
3′b-(2-(Cyanoethoxy(diisopropylamino)phosphinoxy))-5′a-
(4,4′-dimethoxytrityloxymethyl)- (Sp)-D2-CNA-dT (18). Com-
pound 17a (75 mg, 0.085 mmol) was dissolved in dry THF (3 mL),
and DIPEA (0.057 mL, 0.34 mmol) was added. The mixture was
cooled with ice, and 2-cynoethyl-N,N-diisopropylphosphorami-
dochloridite (0.037 mL, 0.17 mmol) was added dropwise to the
1
909.2725. 16b. 31P NMR (202.5 MHz, CDCl3): δ -5.0. H NMR
(500 MHz, CDCl3): δ7.78 (s, 1H, H6), 7.41-6.83 (m, 14H), 6.22
(dd, JH1′b,H2′b ) 6.4 Hz, JH1′b,H2′′b ) 5.5 Hz, 1H, H1′b), 5.63 (s, 1H,
H1′a), 5.10 (d, JH3′a,p ) 17.4 Hz, 1H, H3′a), 4.24 (m, 1H, H3′b),
4.13 (ddd, JH5′b, H4′b ) 5.4 Hz, JH5′b,H5′′b ) JH5′b,p) 11.9 Hz,1H, H5′b),
J. Org. Chem. Vol. 74, No. 9, 2009 3263