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Ammonium Hydroxide → 5-methylseleno-3'-t-butyldimethylsilyl-5'-O-(4,4-dimethoxytrityl)-2'-deoxycytidine

HRID 2406285
Notes
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Reaction equation

HRID 2406285 reaction equation
[CH3:1][Se:2][C:3]1[C:4](=O)[NH:5][C:6](=[O:47])[N:7]([CH:46]=1)[C@@H:8]1[O:38][C@H:12]([CH2:13][O:14][C:15]([C:32]2[CH:37]=[CH:36][CH:35]=[CH:34][CH:33]=2)([C:26]2[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=2)[C:16]2[CH:21]=[CH:20][C:19]([O:24][CH3:25])([O:22][CH3:23])[CH2:18][CH:17]=2)[C@@:10]([Si:39]([C:42]([CH3:45])([CH3:44])[CH3:43])([CH3:41])[CH3:40])([OH:11])[CH2:9]1.C([N:52](C(C)C)CC)(C)C.C(C1C=CC(S(Cl)(=O)=O)=C(C(C)C)C=1C(C)C)(C)C.[OH-].[NH4+]>C(#N)C.CN(C)C1C=CN=CC=1.C(Cl)Cl.CO.C(OCC)(=O)C.CCCCCC>[CH3:1][Se:2][C:3]1[C:4]([NH2:52])=[N:5][C:6](=[O:47])[N:7]([CH:46]=1)[C@@H:8]1[O:38][C@H:12]([CH2:13][O:14][C:15]([C:26]2[CH:27]=[CH:28][CH:29]=[CH:30][CH:31]=2)([C:32]2[CH:33]=[CH:34][CH:35]=[CH:36][CH:37]=2)[C:16]2[CH:21]=[CH:20][C:19]([O:22][CH3:23])([O:24][CH3:25])[CH2:18][CH:17]=2)[C@@:10]([Si:39]([C:42]([CH3:43])([CH3:45])[CH3:44])([CH3:40])[CH3:41])([OH:11])[CH2:9]1
ParticipantsProcedureWorkupSources & evidenceReaction notes

Participants

10

Reactant 4

HCID 14923Ammonium HydroxideHCID 81531DiisopropylethylamineHCID 11514985Triisopropylbenzenesulfonyl chlorideHCID 1317317735-methylseleno-3'-t-butyldimethylsilyl-5'-O-(4,4-dimethoxytrityl)-2'-deoxyuridine

Product 1

HCID 1317317725-methylseleno-3'-t-butyldimethylsilyl-5'-O-(4,4-dimethoxytrityl)-2'-deoxycytidine
Yield 64.9%

Reagents, catalysts & solvents 5

HCID 142844-(Dimethylamino)pyridineCatalystHCID 887MethanolSolventHCID 6342AcetonitrileSolventHCID 6344DichloromethaneSolventHCID 21226206Ethyl acetate hexaneSolvent

Procedure

After 5-methylseleno-3′-t-butyldimethylsilyl-5′-O-(4,4-dimethoxytrityl)-2′-deoxyuridine 480 mg (MW 752.2, 0.64 mmol) was dissolved in acetonitrile 10 ml, diisopropylethyl amine (0.67 ml, 3.19 mmol, 5 eq.), triisopropylbenzenesulfonyl chloride (576 mg, 1.59 mmol, 2.5 eq.) and p-dimethylamino pyridine (96 mg, 0.64 mmol, 1 eq.) were added sequentially. The reaction mixture was stirred for 16 hours and monitored on TLC (ethyl acetate/hexane, 3:7). After completion, excessive concentrated ammonium hydroxide solution was added dropwise and the reaction was stirred under room temperature for 1 hour. After the reaction was completed (monitored on TLC, 5% MeOH in CH2Cl2, Rf=5), the organic solvent and ammonium hydroxide were evaporated under reduced pressure. A silica gel column was equilibrated with CH2Cl2 before the crude product was loaded and purified on the column. The product was eluded by MeOH in CH2Cl2 (1-7%). The fractions containing the product were combined, evaporated and dried on high vacuum overnight to yield yellow solid 307 mg. (yield=64%). 1H-NMR (400 MHz, DMSO) δ: 0.05 (s, 6H, SiCH3), 0.87 (s, 9H, t-butyl), 1.95 (s, 3H, SeCH3), 2.18-2.25 and 2.58-2.62 (2×m, 2H, H-2′), 3.30-3.33 and 3.46-3.49 (2×m, 2H, H-5′), 3.84 (s, 6H, 2×OMe), 4.03-4.08 (m, 1H, H-3′), 4.42-4.46 (m, 1H, H-4′), 6.11 (s, 1H, NH2), 6.28-631 (t, J=5.6 Hz, 1H, H-1′), 6.50 (s, 1H, NH2), 6.86-7.48 (m, 13H, arom-H), 8.30 (s, 1H, H-6). 13C NMR (100 MHz, DMSO) δ: −4.86 and −4.69 [Si(CH3)2], 7.31 (SeCH3), 17.96 [SiC(CH3)], 25.74 [SiC(CH3)], 41.74 (C-2′), 55.26 (OMe), 62.88 (C-5′), 72.23 (C-3′), 85.55 (C-4′), 87.05 (arom-C), 87.16 (C-1′), 103.45 (C-5), 113.23 (arom-C), 126.94 Carom-C), 128.15 (arom-C), 130.11 (arom-C), 135.50 (arom-C), 141.74 (C-6), 144.41 (arom-C), 149.89 (C-2), 155.46 (arom-C), 158.66 (C-4), 161.46 (arom-C), 165.55 (arom-C). HR-MS (ESI-TOF, positive ion mode): molecular formula, C32H47N3O6SeSi: [M+H]−: 738.2468 (calc. 738.2478).

Workup

  1. stirringthe reaction was stirred under room temperature for 1 hour
  2. customthe organic solvent and ammonium hydroxide were evaporated under reduced pressure
  3. custompurified on the column
  4. additionThe fractions containing the product
  5. customevaporated
  6. customdried on high vacuum overnight

Sources & evidence

ORD record
ord-369b37c9c2e34c3fb2a1b88155b460f8
Source dataset
uspto-grants-2014_08
DOI
10.6084/m9.figshare.5104873.v1
Patent number
US08809357B2

Reaction notes

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