The Journal of Organic Chemistry
Article
1HII, H2′), 5.15 (s, 1HI, H2′), 4.63 (d, 1HI, J = 12.0, CH2PhA), 4.62
(d, 1HII, J = 12.0, CH2PhA), 4.58 (d, 1H, J = 12.0, CH2PhB), 4.50 (s,
1H, H3′), 3.744 (s, 3HI, OCH3), 3.741 (s, 3HII, OCH3), 3.733 (s, 3HI,
OCH3), 3.729 (s, 3HII, OCH3), 3.64−3.73 (m, 1H, H5″A), 3.46−3.55
(m, 3H, H5′A+B, H5″B), 1.733 (s, 3HI, 5-CH3), 1.725 (s, 3HII, 5-CH3).
61.2 (C2′I), 59.6 (C2′II), 58.5 (C5′I), 58.4 (C5′II), 55.0 (OCH3), 52.9
(C5″I), 52.7 (C5″II), 24.90 (COCH3,I), 24.87 (COCH3,II), 14.2 (5-
CH3). 19F NMR (DMSO-d6) δ −70.0 (CF3,I), −71.6 (CF3,II). ESI-
+
HRMS m/z 799.2947 ([M + H]+, C43H42F3N4O8 Calcd 799.2949).
(1R,3R,4R,7S)-1-(4,4′-Dimethoxytrityloxymethyl)-5-(hexadecano-
yl)-7-hydroxy-3-(4-N-benzoyl-5-methyl-cytosine-1-yl)-2-oxa-5-
azabicyclo[2.2.1]heptane (22). 5-Methylcytosine intermediate 20
(2.00 g, 3.50 mmol) was coevaporated with anhydrous pyridine (2 ×
10 mL) and then dissolved in anhydrous DCM (35 mL) and
anhydrous pyridine (1.4 mL, 17.3 mmol) under stirring at 0 °C.
Palmitoyl chloride (1.05 mL, 3.46 mmol) was added dropwise and the
resulting mixture stirred at 0 °C for 3 h. DCM (35 mL) was added and
the resulting mixture was washed consecutively with satd aq NaHCO3
(2 × 40 mL) and water (2 × 40 mL). The aqueous phases were back-
extracted with DCM (150 mL in total). The combined organic phase
was dried over Na2SO4, filtered and evaporated to dryness under
reduced pressure. The resulting residue was purified by silica gel
column chromatography (0−7% MeOH in DCM, v/v) to afford a
white foam (1.56 g, Rf = 0.5 (10% MeOH in DCM, v/v)), tentatively
assigned as (1R,3R,4R,7S)-1-(4,4′-Dimethoxytrityloxymethyl)-5-(hex-
adecanoyl)-7-hydroxy-3-(5-methyl-cytosine-1-yl)-2-oxa-5-azabicyclo-
[2.2.1]heptane (N2′-palmitoyl,5′-O-dimethoxytrityl-5-methylcytosine-
amino-LNA). A portion of this intermediate (78 mg, 5% of the total
amount) was dissolved in anhydrous DMF (2.0 mL). Anhydrous
pyridine (24 μL, 0.30 mmol) and benzoic anhydride (25 mg, 0.11
mmol) were added and the reaction mixture stirred at rt for 20 h.
Additional anhydrous pyridine (24 μL, 0.30 mmol) and benzoic
anhydride (29 mg, 0.13 mmol) were added, and the reaction mixture
stirred for another 78 h. The reaction mixture was diluted with EtOAc
(30 mL) and then successively washed with satd aq NaHCO3 (2 × 20
mL) and water (2 × 20 mL). The aqueous phases were back-extracted
with EtOAc (30 mL in total). The combined organic phase was dried
over Na2SO4, filtered and evaporated to dryness under reduced
pressure. The resulting residue was purified by silica gel column
chromatography (0−2% MeOH and 0.1% pyridine in DCM, v/v/v) to
afford a rotameric mixture of desired nucleoside 22 (71 mg, 45% from
20, 7:3 ratio according to 1H NMR) as a white foam. TLC (5%
MeOH in DCM, v/v): Rf = 0.4; 1H NMR (CDCl3) δ 13.43 (br s, 1H,
4-NH), 8.32−8.25 (m, 2HI, H2Bz, H6Bz), 8.17−8.23 (m, 2HII, H2Bz,
H6Bz), 7.84 (s, 1HI, H6), 7.77 (s, 1HII, H6), 7.55−7.22 (m, 12H,
13C NMR (DMSO-d6) δ 178.2 (COPh), 159.2 (C4), 158.3 (C4DMT
/
C4′DMT), 158.2 (C4DMT/C4′DMT), 155.0 (q, J = 36.5, COCF3,I), 154.8
(q, J = 37.0, COCF3,II), 146.9 (C2), 144.4 (C1″DMT), 137.1 (C1Bn,II),
137.0 (C1Bn,I), 136.7 (C6, C1Bz), 134.84 (C1DMT,I/C1′DMT,I), 134.83
(C1DMT,II/C1′DMT,II), 134.75 (C1DMT,II/C1′DMT,II), 134.73 (C1DMT,I
/
C1′DMT,I), 132.6 (C4Bz), 129.72 (C2DMT,II, C6DMT,II, C2′DMT,II
C6′DMT,II), 129.69 (C2DMT,I, C6DMT,I, C2′DMT,I, C6′DMT,I), 129.4
(C2Bz, C6Bz), 128.33 (C3Bz, C5Bz, C3Bn,I, C5Bn,I), 128.29 (C3Bn,II
,
,
C5Bn,II), 128.1 (C3″DMT, C5″DMT), 127.9 (C4Bn,I), 127.8 (C4Bn,II),
127.5 (C2″DMT, C6″DMT), 127.4 (C2Bn, C6Bn), 126.9 (C4″DMT), 115.8
(q, J = 288.5, CF3,II), 115.7 (q, J = 287.7, CF3,I), 113.40 (C3DMT,I
C5DMT,I/C3′DMT,I, C5′DMT,I), 113.38 (C3DMT,II, C5DMT,II/C3′DMT,II
,
,
C5′DMT,II), 113.36 (C3DMT,I, C5DMT,I/C3′DMT,I, C5′DMT,I), 113.35
(C3DMT,II, C5DMT,II/C3′DMT,II, C5′DMT,II), 109.4 (C5), 87.4 (C4′II),
86.3 (C1′II), 86.06 (CAr3,II), 86.03 (CAr3,I), 85.98 (C4′I), 75.8 (C3′I),
74.3 (C3′II), 71.4 (CH2PhII), 71.3 (CH2PhI), 61.3 (C2′I), 59.8 (C2′II),
58.5 (C5′I), 58.4 (C5′II), 55.0 (OCH3), 52.9 (C5″I), 52.8 (C5″II), 13.4
(5-CH3).52 19F NMR (DMSO-d6) δ −70.1 (CF3,II), −71.5 (CF3,I).
+
ESI-HRMS m/z 861.3104 ([M + H]+, C48H44F3N4O8 Calcd
861.3106).
(1R,3R,4R,7S)-7-Benzyloxy-1-(4,4′-dimethoxytrityl)oxymethyl-3-
(4-N-acetyl-5-methylcytosin-1-yl)-5-trifluoroacetyl-2-oxa-5-
azabicyclo[2.2.1]heptane (21b). Nucleoside 19 (1.00 g, 1.32 mmol)
was coevaporated with pyridine (3 mL) and then dissolved in a
mixture of anhydrous pyridine (7 mL) and anhydrous DCM (7 mL).
Ac2O (0.14 mL, 1.48 mmol) was added. The reaction mixture stirred
at rt for 24 h, whereafter Ac2O (0.07 mL, 0.74 mmol) and DMAP (79
mg, 0.65 mmol) were added, and the reaction mixture stirred for
additional 72 h. Ac2O (0.07 mL, 0.74 mmol) was added, and the
reaction mixture stirred for additional 24 h, whereafter the reaction
mixture was evaporated to dryness and the residue coevaporated with
toluene (3 × 10 mL). To the resulting residue was added DCM (50
mL) whereupon washing was performed with satd aq NaHCO3 (50
mL) and brine (50 mL). The combined aq phase was extracted with
DCM (25 mL), and the combined organic phase dried over MgSO4
and evaporated to dryness. The resulting residue was purified by
DCVC (0−6% MeOH in DCM, v/v) to afford a rotameric mixture of
the desired nucleoside 21b (868 mg, 82%, 2:3 ratio of rotamers
H2DMT, H6DMT, H2′DMT, H6′DMT, H2″DMT, H3″DMT, H4″DMT
H5″DMT, H6″DMT, H3Bz, H4Bz, H5Bz), 6.90−6.83 (m, 4H, H3DMT
,
,
H5DMT, H3′DMT, H5′DMT), 5.49 (s, 1H, H1′), 5.12 (s, 1HII, H2′), 4.52
(s, 1HI, H2′), 4.37 (s, 1HII, H3′), 4.29 (s, 1HI, H3′), 3.81−3.78 (m,
6H, 2 × OCH3), 3.73 (d, J = 11.0, 1HII, H5′A), 3.67 (d, J = 11.2, 1HI,
H5′A), 3.58−3.37 (m, 3H, H5′B, H5″A+B), 2.55−2.34 (m, 2HI,
COCH2), 2.12−2.19 (m, 2HII, COCH2), 1.82 (s, 3HI, 5-CH3), 1.76 (s,
3HII, 5-CH3), 1.72−1.49 (m, 2H, COCH2CH2), 1.38−1.12 (m, 24H,
(CH2)12CH3), 0.87 (t, J = 6.8, 3H, (CH2)14CH3). 13C NMR (CDCl3)
δ 179.7 (COPh), 173.3 (CO(CH2)14,I), 173.2 (CO(CH2)14,II), 159.9
(C4), 158.93 (C4DMT/C4′DMT), 158.87 (C4DMT/C4′DMT), 148.0 (C2),
1
according to H NMR) as a white foam. TLC (5% MeOH in EtOAc,
1
v/v): Rf (19) = 0.1, Rf (21b) = 0.6. H NMR (DMSO-d6) δ 9.90 (s,
1H, ex, 4-NH), 7.85−7.88 (m, 1H, H6), 7.36−7.40 (m, 2H, H2″DMT
H6″DMT), 7.23−7.43 (m, 10H, H3Bn, H4Bn, H5Bn, H2DMT, H6DMT
,
,
H2′DMT, H6′DMT, H3″DMT, H4″DMT, H5″DMT), 7.14−7.19 (m, 2H,
H2Bn, H6Bn), 6.85−6.91 (m, 4H, H3DMT, H5DMT, H3′DMT, H5′DMT),
5.75 (s, 1H, H1′), 5.30 (s, 1HII, H2′), 5.14 (s, 1HI, H2′), 4.61 (d, J =
11.8, 1HI, CH2PhA), 4.60 (d, J = 11.8, 1HII, CH2PhA), 4.54 (d, J = 11.8,
1H, CH2PhB), 4.45 (s, 1H, H3′), 3.74 (s, 3HI, OCH3), 3.733 (s, 3HII,
OCH3), 3.729 (s, 3HI, OCH3), 3.726 (s, 3HII, OCH3), 3.63−3.72 (m,
1H, H5″A), 3.45−3.55 (m, 3H, H5′A+B, H5″B), 2.30 (s, 3H, COCH3),
1.69 (s, 3H, 5-CH3). 13C NMR (DMSO-d6) δ 170.6 (COCH3,I), 170.5
144.5 (C1″DMT), 137.0 (C1Bz), 136.0 (C6), 135.6 (C1DMT,II
C1′DMT,II), 135.43 (C1DMT/C1′DMT), 135.40 (C1DMT,I/C1′DMT,I),
132.7 (C4Bz,I), 132.5 (C4Bz,II), 130.3 (C2DMT,I/II, C6DMT,I/II/C2′DMT,I/II
/
,
C6′DMT,I/II), 130.2 (C2DMT,I/II, C6DMT,I/II/C2′DMT,I/II, C6′DMT,I/II),
130.1 (C2Bz, C6Bz), 128.29 (C2″DMT,I/II, C3″DMT,I/II, C5″DMT,I/II
C6″DMT,I/II, C3Bz,I/II, C5Bz,I/II), 128.24 (C2″DMT,I/II, C3″DMT,I/II
C5″DMT,I/II, C6″DMT,I/II, C3Bz,I/II, C5Bz,I/II), 128.19 (C2″DMT,I/II
,
,
,
(COCH3,II), 162.7 (C4), 158.24 (C4DMT,I, C4′DMT,I), 158.20 (C4DMT,II
,
C4′DMT,II), 155.0 (q, J = 36.4, COCF3,I), 154.9 (q, J = 37.3, COCF3,II),
153.6 (C2I), 153.5 (C2II), 144.3 (C1″DMT), 140.7 (C6), 137.04
(C1Bn,II), 136.94 (C1Bn,I), 134.92 (C1DMT,I/C1′DMT,I), 134.83
C3″DMT,I/II, C5″DMT,I/II, C6″DMT,I/II, C3Bz,I/II, C5Bz,I/II), 127.4
(C4″DMT,I), 127.3 (C4″DMT,II), 113.58 (C3DMT,I, C5DMT,I/C3′DMT,I,
(C1DMT,II/C1′DMT,II), 134.82 (C1DMT,II/C1′DMT,II), 134.77 (C1DMT,I
/
C1′DMT,I), 129.7 (C2DMT, C6DMT, C2′DMT, C6′DMT), 128.31 (C3Bn,I
C5Bn,I), 128.28 (C3Bn,II, C5Bn,II), 128.0 (C3″DMT, C5″DMT), 127.9
(C4Bn,I), 127.8 (C4Bn,II), 127.6 (C2″DMT, C6″DMT), 127.51 (C2Bn,II
C6Bn,II), 127.50 (C2Bn,I, C6Bn,I), 126.9 (C4″DMT), 115.82 (q, J = 288.3,
CF3,II), 115.76 (q, J = 287.8, CF3,I), 113.40 (C3DMT,I, C5DMT,I
C3′DMT,I, C5′DMT,I), 113.38 (C3DMT,II, C5DMT,II/C3′DMT,II, C5′DMT,II),
,
C5′DMT,I), 113.56 (C3DMT, C5DMT/C3′DMT, C5′DMT), 113.52
(C3DMT,II, C5DMT.,II/C3′DMT,II, C5′DMT,II), 111.8 (C5), 89.1 (C4′II),
88.3 (C4′I), 87.7 (C1′I), 87.5 (C1′II), 87.1 (CAr3,I), 87.0 (CAr3,II),
70.3 (C3′I), 69.0 (C3′II), 63.5 (C2′I), 61.4 (C2′II), 59.6 (C5′II), 59.1
(C5′I), 55.4 (OCH3), 52.4 (C5″II), 51.1 (C5″I), 34.4 (COCH2,I), 34.1
(COCH2,II), 32.1 (CH2CH2CH3), 29.9, 29.8, 29.7, 29.63, 29.57, 29.5,
25.3 (COCH2CH2,I), 24.8 (COCH2CH2,II), 22.8 (CH2CH3), 14.3
((CH2)14CH3), 13.8 (5-CH3);53 HRMS-ESI m/z: 913.5085 ([M +
H]+, C55H68N4O8−H+ calcd 913.5110). When the benzoylation
reaction was run on 1.83 mmol scale, the overall yield from 20 to
,
/
113.36 (C3DMT,I, C5DMT,I/C3′DMT,I, C5′DMT,I), 113.35 (C3DMT,II
,
C5DMT,II/C3′DMT,II, C5′DMT,II), 105.5 (C5II), 105.4 (C5I), 87.3
(C4′II), 86.8 (C1′I), 86.4 (C1′II), 86.03 (CAr3,II), 85.99 (CAr3,I),
85.9 (C4′I), 75.6 (C3′I), 74.0 (C3′II), 71.4 (CH2PhII), 71.3 (CH2PhI),
10726
dx.doi.org/10.1021/jo302036h | J. Org. Chem. 2012, 77, 10718−10728