Building Blocks for Oligonucleotides with 3Ј-C-Methylenephosphonate Linkages
FULL PAPER
135.8, 141.1 (C-6), 145.2, 151.5, 160.0, 164.3. MS (ESϩ/TOF) [M SiC(CH3)3], 2.57 (m, 1 H, 3Ј-H), 3.48 (dd, J5Јb,4Ј ϭ 3.4 Hz, 1 H,
ϩ Na]ϩ calcd. for C36H43BrN2O6SiNa 729.1971; found 729.1943. 5Јb-H), 3.53 (dd, J5Јa,5Јb ϭ 11.3 Hz, J5Јa,4Ј ϭ 2.4 Hz, 1 H, 5Јa-H),
C36H43BrN2O6Si: calcd. C 61.10, H 6.12, N 3.96; found C 61.30,
H 6.17, N 3.83.
3.56 (dd, 3J ϭ 6.1 Hz, 2J ϭ 10.7 Hz, 1 H, CH2OH), 3.72 (dd, 3J ϭ
6.9, J ϭ 10.7 Hz, 1 H, CH2OH), 3.78 (s, 3 H, OCH3), 4.18 (m, 1
2
H, 4Ј-H), 4.53 (d, J2Ј,3Ј ϭ 4.5 Hz, 1 H, 2Ј-H), 5.26 (d, 1 H, H-5),
5.62 (s, 1 H, 1Ј-H), 6.92 (2 H, MMT), 7.26Ϫ7.51 (12 H, MMT),
7.57 (2 H, Bz), 7.75 (1 H, Bz), 7.99 (2 H, Bz), 8.17 (d, J5,6 ϭ 8.2
Hz, 1 H, 6-H). 13C NMR (CD3CN, 20 °C): δ ϭ Ϫ5.12 (SiCH3),
Ϫ4.24 (SiCH3), 18.7 [SiC(CH3)3], 26.2 [SiC(CH3)3], 45.1 (C-3Ј),
56.0 (OCH3), 58.9 (CH2OH), 63.8 (C-5Ј), 78.6 (C-2Ј), 83.6 (C-4Ј),
88.0, 92.9 (C-1Ј), 101.6 (C-5), 114.2, 128.2, 128.3, 129.06, 129.08,
129.5, 130.5, 131.4, 131.6, 132.6, 136.0, 136.5, 142.0 (C-6), 145.2,
145.5, 150.5, 159.9, 163.4, 170.8. MS (ESϩ/TOF) [M ϩ Na]ϩ calcd.
for C43H48N2O8SiNa 771.3078; found 771.3059. C43H48N2O8Si:
calcd. C 68.96, H 6.46, N 3.74; found C 68.85, H 6.60, N 3.62.
1-[2-O-(tert-Butyldimethylsilyl)-3-deoxy-3-C-(iodomethyl)-5-O-(4-
methoxytriphenylmethyl)-β-D-ribo-pentofuranosyl]uracil (4): A solu-
tion of compound 1[21,22] (400 mg, 0.620 mmol) in dry acetonitrile/
pyridine (95:5 v/v, 8 mL) under nitrogen was cooled to 0Ϫ2 °C.
Triphenylphosphane (228 mg, 0.87 mmol, 1.4 equiv.) and iodine
(158 mg, 0.68 mmol, 1.1 equiv.) were added, and the mixture was
left on a melting ice-water bath and then stirred at room temper-
ature for 40 h. The reaction mixture was diluted with CH2Cl2 (50
mL) and then washed with 0.5 Na2S2O3 in saturated aqueous
NaHCO3 (50 mL). The water layer was extracted with CH2Cl2
(2ϫ20 mL). The combined organic layers were dried (Na2SO4), and
activated carbon (DARCO G-60, 100 mesh, powder) was added.
3-N-Benzoyl-1-[2-O-(tert-butyldimethylsilyl)-3-deoxy-5-O-(4-
The solution was filtered through Celite, and remaining product methoxytriphenylmethyl)-3-C-(trifluoromethanesulfonylmethyl)-β-D-
was extracted with dichloromethane (50 mL). The filtrate was di-
luted with toluene (10 mL) and concentrated. The residue was puri-
ribo-pentofuranosyl]uracil (8): A solution of compound 7 (160 mg,
0.21 mmol) and 2,6-di-tert-butylpyridine (115 µL, 0.51 mmol, 2.4
fied by silica gel column chromatography (toluene/ethyl acetate, equiv.) in dry CH2Cl2 (6 mL) under nitrogen was cooled to Ϫ78
1
5:1, v/v) to give 4 (422 mg, 90%). H NMR (CD3CN, 20 °C): δ ϭ °C (dry ice-acetone), and a solution of trifluoromethanesulfonic
0.24 (s, 3 H, SiCH3), 0.25 (s, 3 H, SiCH3), 0.91 [s, 9 H, SiC(CH3)3], anhydride (43 µL, 0.26 mmol, 1.2 equiv.) in dry CH2Cl2 (0.5 mL)
2.63 (m, 1 H, 3Ј-H), 2.84 (dd, 3J ϭ 4.0 Hz, 2J ϭ 9.9 Hz, 1 H, was added dropwise over 30 min. The reaction mixture was stirred
3
2
CH2I), 3.10 (t, J ϭ J ϭ 9.9 Hz, 1 H, CH2I), 3.36 (dd, J5Јb,4Ј
ϭ
at Ϫ78 °C for an additional 3 h, and was then allowed to reach
0Ϫ2 °C (ice-water bath). The mixture was diluted with CH2Cl2 (15
3.4 Hz, 1 H, 5Јb-H), 3.58 (dd, J5Јa,5Јb ϭ 11.7 Hz, J5Јa,4Ј ϭ 1.7 Hz,
1 H, 5Јa-H), 3.78 (s, 3 H, OCH3), 3.98 (m, 1 H, 4Ј-H), 4.41 (d, mL) and washed with aqueous NaHCO3 (15 mL). The water layer
J2Ј,3Ј ϭ 3.9 Hz, 1 H, 2Ј-H), 5.24 (d, 1 H, 5-H), 5.61 (s, 1 H, 1Ј-H), was washed with CH2Cl2 (2 ϫ 15 mL) and the combined organic
6.91 and 7.26Ϫ7.46 (14 H, MMT), 7.92 (d, J5,6 ϭ 8.1 Hz, 1 H, 6-
layers were dried (Na2SO4). The organic phase was concentrated
H), 9.19 (br. s, 1 H, NH). 13C NMR (CD3CN, 20 °C): δ ϭ Ϫ4.80 under reduced pressure (Ͻ25 °C) and the residue was immediately
(SiCH3), Ϫ3.74 (SiCH3), Ϫ0.93 (CH2I), 18.8 [SiC(CH3)3], 26.4 purified by silica gel column chromatography (stepwise gradient of
[SiC(CH3)3], 46.7 (C-3Ј), 56.0 (OCH3), 62.8 (C-5Ј), 79.5 (C-2Ј), 83.3 0.5Ϫ2% ethyl acetate in CH2Cl2). If the product (8) was obtained
(C-4Ј), 88.1, 91.9 (C-1Ј), 101.9 (C-5), 114.3, 128.3, 129.09, 129.11,
129.27, 129.31, 129.35, 131.5, 135.7, 141.1 (C-6), 145.2, 151.5,
160.0, 164.4. MS (ESϩ/TOF) [M ϩ Na]ϩ calcd. for C36H43IN2O6-
as an oil, it readily turned orange in colour (probably due to detri-
tylation). The product (8) was more stable in a solid form, which
was obtained by lyophilization from benzene immediately after
SiNa 777.1833; found 777.1812. C36H43IN2O6Si: calcd. C 57.29, H concentration of the pure fractions. This procedure gave 8 as a
5.74, N 3.71; found C 57.40, H 5.80, N 3.59.
white powder (160 mg, 85%). The product was stored at Ϫ80 °C
(it slowly decomposed if stored in room temperature). 1H NMR
(CD3CN, 20 °C): δ ϭ 0.06 (s, 3 H, SiCH3), 0.11 (s, 3 H, SiCH3),
3-N-Benzoyl-1-[2-O-(tert-butyldimethylsilyl)-3-deoxy-3-C-(hydroxy-
methyl)-5-O-(4-methoxytriphenylmethyl)-β-D-ribo-pentofurano-
0.85 [s, 9 H, SiC(CH3)3], 3.01 (m, 1 H, 3Ј-H), 3.43 (dd, J5Јb,4Ј
ϭ
syl]uracil (7): Compound 1[21,22] (230 mg, 0.357 mmol), Na2CO3
(302 mg, 2.85 mmol, 8 equiv.) and tetra-n-butylammonium brom-
ide (6 mg, 0.019 mmol, 0.05 equiv.) were dissolved in a two-phase
system of CH2Cl2 (8 mL) and H2O (15 mL). The mixture was co-
oled on an ice-water bath and vigorously stirred while a solution
of benzoyl chloride (54 µL, 0.46 mmol, 1.3 equiv.) in dry CH2Cl2 (2
mL) was added dropwise over 30 minutes. The reaction was stirred
vigorously at 0Ϫ2 °C (ice-water bath) for an additional 2.5 h. TLC
analysis showed remaining starting material, and therefore more
benzoyl chloride (17 µL, 0.15 mmol, 0.4 equiv.) dissolved in dry
CH2Cl2 (0.5 mL) was added dropwise over 10 minutes. The reaction
mixture was kept on an ice-water bath, and vigorous stirring was
continued for an additional 2 hours. TLC analysis showed complete
conversion into one product (the O4-benzoylated product[27]). The
ice-water bath was removed, and the mixture was stirred for an
additional 17 hours at room temperature in order to effect O4ǞN3
benzoyl migration[27] to give the N3-benzoylated product 7. The
3.2 Hz, 1 H, 5Јb-H), 3.55 (dd, J5Јa,5Јb ϭ 11.5 Hz, J5Јa,4Ј ϭ 2.3 Hz,
1 H, 5Јa-H), 3.76 (s, 3 H, OCH3), 4.06 (m, 1 H, 4Ј-H), 4.53 (d,
3
2
J2Ј,3Ј ϭ 4.9 Hz, 1 H, 2Ј-H), 4.64 (dd, J ϭ 6.0, J ϭ 10.0 Hz, 1 H,
CH2OTf), 4.77 (dd, 3J ϭ 7.9 Hz, 2J ϭ 10.0 Hz, 1 H, CH2OTf),
5.31 (d, 1 H, H-5), 5.63 (s, 1 H, 1Ј-H), 6.92 (2 H, MMT), 7.25Ϫ7.46
(12 H, MMT), 7.54 (2 H, Bz), 7.73 (1 H, Bz), 7.97 (2 H, Bz), 8.00
(d, J5,6 ϭ 8.3 Hz, 1 H, 6-H). 13C NMR (CD3CN, 20 °C): δ ϭ
Ϫ5.45 (SiCH3), Ϫ4.08 (SiCH3), 18.7 [SiC(CH3)3], 26.1 [SiC(CH3)3],
42.9 (C-3Ј), 56.0 (OCH3), 63.0 (C-5Ј), 65.4 (CH2OTf), 77.8 (C-2Ј),
1
82.1 (C-4Ј), 88.2, 92.9 (C-1Ј), 101.9 (C-5), 114.3, 119.0 (q, JC,F
ϭ
319 Hz, CF3), 128.4, 129.1, 129.2, 129.3, 130.5, 131.4, 131.6, 132.5,
135.7, 136.6, 141.7 (C-6), 144.9, 145.3, 150.5, 160.1, 163.3, 170.7.
MS (ESϩ/TOF) [M ϩ Na]ϩ calcd. for C44H47F3N2O10SSiNa
903.2571; found 903.2592. C44H47F3N2O10SSi: calcd. C 59.99, H
5.38, N 3.18, S 3.64; found C 60.12, H 5.48, N 3.02, S 3.40.
Triethylammonium 2Ј-O-(tert-Butyldimethylsilyl)-3Ј-deoxy-5Ј-O-(4-
reaction mixture was transferred to a separation funnel, and the methoxytriphenylmethyl)uridine 3Ј-C-Methylenephosphinate (5).
layers were separated. The water layer was washed with CH2Cl2 Method A: A solution of compound 3 (260 mg, 0.344 mmol) in dry
(2 ϫ 15 mL). The combined organic layers were dried (Na2SO4)
and concentrated, and the residue was purified by silica gel column
acetonitrile (14 mL, nitrogen-purged), under nitrogen in a flask fit-
ted with a septum, was cooled to Ϫ42 °C (dry ice/acetonitrile), and
Hünig’s base (360 µL, 2.07 mmol, 6 equiv.) was added by syringe.
chromatography (stepwise gradient of 1Ϫ2% methanol in CH2Cl2)
1
to obtain compound 7 (244 mg, 91%). H NMR (CD3CN, 20 °C): BTSP (4 reagent solution prepared as described above, 1.0 mL,
δ ϭ 0.08 (s, 3 H, SiCH3), 0.11 (s, 3 H, SiCH3), 0.87 [s, 9 H,
Eur. J. Org. Chem. 2002, 1509Ϫ1515
4 mmol, 12 equiv.) was added dropwise by syringe (concentrated
1513