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[ CAS No. 68892-41-1 ] {[proInfo.proName]}

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Chemical Structure| 68892-41-1
Chemical Structure| 68892-41-1
Structure of 68892-41-1 * Storage: {[proInfo.prStorage]}
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Product Details of [ 68892-41-1 ]

CAS No. :68892-41-1 MDL No. :MFCD00010059
Formula : C35H37N5O7 Boiling Point : -
Linear Structure Formula :- InChI Key :RMQXDNUKLIDXOS-ZGIBFIJWSA-N
M.W : 639.70 Pubchem ID :135445746
Synonyms :
5'-O-DMT-N2-ibu-dG;N2-Isobutyryl-5′-O-(4,4′-dimethoxytrityl)-2′-deoxyguanosine;iBu-DMT-dG;5'-O-DMT-N2-Isobutyryl-2'-Deoxyguanosine
Chemical Name :N2-Isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyguanosine

Calculated chemistry of [ 68892-41-1 ]

Physicochemical Properties

Num. heavy atoms : 47
Num. arom. heavy atoms : 27
Fraction Csp3 : 0.31
Num. rotatable bonds : 12
Num. H-bond acceptors : 9.0
Num. H-bond donors : 3.0
Molar Refractivity : 174.92
TPSA : 149.82 Ų

Pharmacokinetics

GI absorption : Low
BBB permeant : No
P-gp substrate : Yes
CYP1A2 inhibitor : No
CYP2C19 inhibitor : Yes
CYP2C9 inhibitor : Yes
CYP2D6 inhibitor : Yes
CYP3A4 inhibitor : Yes
Log Kp (skin permeation) : -7.17 cm/s

Lipophilicity

Log Po/w (iLOGP) : 3.59
Log Po/w (XLOGP3) : 4.27
Log Po/w (WLOGP) : 3.76
Log Po/w (MLOGP) : 1.08
Log Po/w (SILICOS-IT) : 4.2
Consensus Log Po/w : 3.38

Druglikeness

Lipinski : 2.0
Ghose : None
Veber : 2.0
Egan : 1.0
Muegge : 1.0
Bioavailability Score : 0.17

Water Solubility

Log S (ESOL) : -6.13
Solubility : 0.000475 mg/ml ; 0.000000742 mol/l
Class : Poorly soluble
Log S (Ali) : -7.13
Solubility : 0.0000476 mg/ml ; 0.0000000744 mol/l
Class : Poorly soluble
Log S (SILICOS-IT) : -9.3
Solubility : 0.000000322 mg/ml ; 0.0000000005 mol/l
Class : Poorly soluble

Medicinal Chemistry

PAINS : 0.0 alert
Brenk : 0.0 alert
Leadlikeness : 3.0
Synthetic accessibility : 5.77

Safety of [ 68892-41-1 ]

Signal Word:Warning Class:N/A
Precautionary Statements:P280-P305+P351+P338 UN#:N/A
Hazard Statements:H302 Packing Group:N/A
GHS Pictogram:

Application In Synthesis of [ 68892-41-1 ]

* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.

  • Downstream synthetic route of [ 68892-41-1 ]

[ 68892-41-1 ] Synthesis Path-Downstream   1~88

  • 1
  • [ 108-30-5 ]
  • [ 68892-41-1 ]
  • [ 74405-46-2 ]
YieldReaction ConditionsOperation in experiment
65% With dmap In pyridine
With pyridine; dmap; triethylamine In dichloromethane for 4h; Ambient temperature;
  • 2
  • [ 68892-42-2 ]
  • [ 40615-36-9 ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
75% With pyridine; at 20℃; for 5h; Step 2-2N-Isobutyryl-5'O-Dimetoxytrityl deoxyguanosine (B5-II)2N-Isobutyryl deoxyguanosine (B5-I) was dried by co-evaporation with dry pyridine three times. To a stirred suspension of dry (B5-I) (14.15 mmol) in pyridine (100 mL), a solution of dimetoxytrityl chloride (14.8 mmol) in pyridine (30 mL) was added dropwise over a period of 60 min. The reaction mixture was left for 4 h at room temperature, cooled to 0 C. by immersion in an ice water bath, quenched with 5% NaHCO3 (100 mL), and extracted with ethyl acetate (3×100 mL). The organic fractions were pooled, dried over magnesium sulfate, concentrated in vacuum and the residue was co-evaporated with toluene. The gum oil residue was dissolved in a minimum amount of methylenechloride and added dropwise to a mixture of ethyl ether and petroleum ether (2000 mL 75/25) with stirring. After 20 min, pure 2N-Isobutyryl-5'O-Dimetoxytrityl deoxyguanosine precipitated from the solution and was filtered off and dried.Yield: 75%
  • 3
  • [ 5666-12-6 ]
  • [ 68892-41-1 ]
  • [ 1055040-37-3 ]
  • 4
  • [ 13154-24-0 ]
  • [ 68892-41-1 ]
  • [ 136198-19-1 ]
YieldReaction ConditionsOperation in experiment
78.8% With 1H-imidazole In N,N-dimethyl-formamide for 24h; Ambient temperature;
  • 5
  • [ 3348-44-5 ]
  • [ 68892-41-1 ]
  • C39H48N7O7P [ No CAS ]
YieldReaction ConditionsOperation in experiment
With triethylamine In acetonitrile
  • 6
  • [ 59274-18-9 ]
  • [ 68892-41-1 ]
  • [ 84432-75-7 ]
YieldReaction ConditionsOperation in experiment
With N-ethyl-N,N-diisopropylamine In tetrahydrofuran Ambient temperature;
  • 7
  • [ 66470-81-3 ]
  • [ 68892-41-1 ]
  • [ 120942-92-9 ]
YieldReaction ConditionsOperation in experiment
81% With pyridine In dichloromethane for 0.25h;
  • 8
  • [ 70063-12-6 ]
  • [ 68892-41-1 ]
  • [ 78635-94-6 ]
YieldReaction ConditionsOperation in experiment
With N-ethyl-N,N-diisopropylamine In tetrahydrofuran Ambient temperature;
  • 9
  • [ 63135-66-0 ]
  • [ 68892-41-1 ]
  • [ 1055040-37-3 ]
YieldReaction ConditionsOperation in experiment
With triethylamine In acetonitrile
  • 10
  • [ 68892-41-1 ]
  • [ 124482-92-4 ]
  • 5'-O-dimethoxytrityl-N2-isobutyryl-2'-deoxyguanosine-3'-O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite [ No CAS ]
YieldReaction ConditionsOperation in experiment
70% With N-ethyl-N,N-diisopropylamine In dichloromethane at 65℃; for 0.25h; Inert atmosphere; Microwave irradiation; Sealed tube;
In tetrahydrofuran according to ref 3) with modifications;
  • 11
  • [ 68892-41-1 ]
  • [ 86030-43-5 ]
  • [ 84416-84-2 ]
YieldReaction ConditionsOperation in experiment
With N-ethyl-N,N-diisopropylamine In tetrahydrofuran Ambient temperature;
  • 12
  • [ 68892-41-1 ]
  • [ 75302-66-8 ]
  • [ 114360-61-1 ]
YieldReaction ConditionsOperation in experiment
70% With N-ethyl-N,N-diisopropylamine In dichloromethane for 0.5h;
  • 13
  • [ 68892-41-1 ]
  • [ 91876-63-0 ]
  • [ 125190-10-5 ]
YieldReaction ConditionsOperation in experiment
87% With N-ethyl-N,N-diisopropylamine In dichloromethane for 0.25h;
  • 14
  • [ 68892-41-1 ]
  • [ 96404-99-8 ]
  • [ 80817-36-3 ]
YieldReaction ConditionsOperation in experiment
84% With 1-methyl-1H-imidazole; 2,4,6-triisopropylphenylsulfonyl chloride In pyridine for 0.5h;
  • 15
  • [ 68892-41-1 ]
  • [ 86979-44-4 ]
  • [ 86979-49-9 ]
YieldReaction ConditionsOperation in experiment
67% With 1-(mesitylene-2-sulfonyl)-3-nitro-1H-1,2,4-triazole In pyridine for 1h; Ambient temperature;
  • 16
  • [ 68892-41-1 ]
  • [ 108787-34-4 ]
  • [ 136340-78-8 ]
YieldReaction ConditionsOperation in experiment
91% With 1H-tetrazole In 1,4-dioxane; acetonitrile at 20℃; for 1h;
  • 17
  • [ 68892-41-1 ]
  • [ 93636-01-2 ]
  • [ 98293-12-0 ]
YieldReaction ConditionsOperation in experiment
81% With 1-methyl-1H-imidazole In tetrahydrofuran for 0.75h;
  • 18
  • [ 68892-41-1 ]
  • [ 139063-18-6 ]
  • [ 142721-39-9 ]
YieldReaction ConditionsOperation in experiment
76% With triethylamine In dichloromethane
  • 19
  • [ 68892-41-1 ]
  • [ 81087-19-6 ]
  • [ 84354-71-2 ]
YieldReaction ConditionsOperation in experiment
88% With 1-methyl-1H-imidazole In acetonitrile at 25℃; for 4.5h;
  • 20
  • [ 68892-41-1 ]
  • [ 88734-01-4 ]
  • Isopropyl-methyl-phosphoramidous acid (2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(2-isobutyrylamino-6-oxo-1,6-dihydro-purin-9-yl)-tetrahydro-furan-3-yl ester methyl ester [ No CAS ]
YieldReaction ConditionsOperation in experiment
With N-ethyl-N,N-diisopropylamine In tetrahydrofuran Ambient temperature;
  • 21
  • [ 68892-41-1 ]
  • [ 68892-42-2 ]
YieldReaction ConditionsOperation in experiment
With sodium carbonate; In methanol; dichloromethane; at 0℃; for 1h; Compound 48, N-[9-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenyl- methoxy]methyl]-4-hydroxy-tetrahydrofuran-2-yl]-6-oxo-lH-purin-2-yl]-2 -methyl-propanamide (50.0 g, 78.2 mmol) was dissolved in DCM/Methanol (1560 mL) and cooled to 0C. Sodium carbonate (9.94 g, 93.8 mmol) was added and the orange reaction mixture was stirred at 0C. After 60 minutes sodium carbonate (9.94 g, 93.8 mmol) was added at 0C and stirred until the orange color disappeared. The solvents were removed under reduced pressure. Dichloromethane was added to the crude reaction and the white precipitate was isolated and dried under high vacuum. The crude desired product was isolated as a white solid. (28.7 g, 85.1 mmol, yield: 109 %)
  • 22
  • [ 68892-41-1 ]
  • [ 81144-43-6 ]
YieldReaction ConditionsOperation in experiment
98% With ammonium hydroxide In 1,4-dioxane for 72h;
94% With methanol; 1,8-diaza[5.4.0]undec-7-ene In 1,4-dioxane at 50℃; for 5h;
  • 23
  • [ 68892-41-1 ]
  • [ 115131-08-3 ]
YieldReaction ConditionsOperation in experiment
90% With N-ethyl-N,N-diisopropylamine In dichloromethane for 0.333333h; Ambient temperature;
  • 24
  • [ 68892-41-1 ]
  • [ 100205-38-7 ]
YieldReaction ConditionsOperation in experiment
85% With triphenylphosphine; diethylazodicarboxylate In 1,4-dioxane for 0.5h;
  • 25
  • [ 68892-41-1 ]
  • N-(9-{(2R,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-hydroxy-tetrahydro-furan-2-yl}-8-bromo-6-oxo-6,9-dihydro-1H-purin-2-yl)-isobutyramide [ No CAS ]
YieldReaction ConditionsOperation in experiment
67% With bromine; sodium acetate In 1,4-dioxane
  • 27
  • [ 68892-41-1 ]
  • [ 123-76-2 ]
  • [ 86710-51-2 ]
YieldReaction ConditionsOperation in experiment
With dmap; dicyclohexyl-carbodiimide In 1,4-dioxane for 1h;
With dmap; dicyclohexyl-carbodiimide In 1,4-dioxane at 25℃; for 3h;
  • 28
  • [ 68892-41-1 ]
  • [ 93-97-0 ]
  • [ 93966-65-5 ]
YieldReaction ConditionsOperation in experiment
92% With dmap; triethylamine In dichloromethane for 3h; Ambient temperature;
  • 29
  • 5'-dimethoxytrityl N2-isobutyryl deoxyguanosine 3'-methylphosphinate [ No CAS ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
89% With tetrabutyl ammonium fluoride In tetrahydrofuran; water for 3h; Ambient temperature;
  • 30
  • [ 160107-22-2 ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
73% With 1H-imidazole In methanol for 72h; Ambient temperature;
  • 31
  • [ 68892-41-1 ]
  • [ 18162-48-6 ]
  • [ 152343-98-1 ]
YieldReaction ConditionsOperation in experiment
With n-butyllithium 1.) THF, -20 deg C, 20 min, 2.) THF, RT, 2 h; Multistep reaction;
With pyridine; silver nitrate In tetrahydrofuran at 20℃;
110 g With pyridine; 1H-imidazole for 18h; To dry 5’-O-(4,4’dimethoxytrityl)- N2- (isobutyryl)deoxyguanosine (100 g, 156 mM) was added imidazole (40 g, 0.588 M) in 1200 mL dry pyridine and 100 g (0.666 M) tertbutyldiinethylsilyl chloride. The solution was stirred for 18 hrs, the pyridine was removed by rotary evaporation, and the residue was dissolved in 700 mL of ethyl acetate. The organic phase was washed with 500 ml of 0.5 M K2HPO4 followed by 500 mL saturated NaHCO3. Drying produced 110 g (145 mM) of product 5’-O-(4,4’dimethoxytrityl)- N2- (isobutyryl)-3’-O-tert- butyldimethylsilyl-deoxyguanosine. A solution of the product in 1500 mL of methanol was prepared, and to this was added 150 mL of conc. aqueous ammonia. After brief swirling, the solution was allowed to stand overnight. The solvents were removed by rotary evaporation, and the dried solid was re-dissolved in 1400 mL of THF and 40 g of dry K2C03 were added. After 10 mm of stirring, 100 g di-tert-butyl pyrocarbonate was added. The solution was stirred for 3 hrs. TLC showed partial conversion (silica, 2 % MeOH, 2% pyridine in DCM, if starting material 0.3, rf product 0.7, visualized with 10 % H2S04 and heating). Longer reaction times gave less desired product and more side reaction materials. The K2C03 was removed by filtration and 400 mL of 0.5 M KH2PO4 was added. The THF was removed by rotary evaporation and the residue was mixed with 700 mL DCM. The organic phase was added to a silica column, 10 X 35 cm, packed with 2% methanol and 2% pyridine in DMF. A gradient to 10 % methanol was applied to the column over 14 L of solvent, and fractions containing pure 5’-O-DMT-3’-O- tertbutyldimethylsilyl- N2-(tert-butyloxycarbonyl)-deoxyguanosine were pooled and reduced by rotory evaporation. The yield was 25 g (34 mM, 22% yield from DMT dG(iBu)). The TBDMS group was removed by adding a solution of 60 mL 1 M TBAF in THF and 10 mL of HOAc in 500 mL of THF. After 18 hrs, saturated NaHCO3, 50 mL, was added and the THF was removed by rotary evaporation. The residue was dissolved in 600 mL DCM and washed with 400 mL saturated NaHCO3. The organic phase was reduced to a foam by rotary evaporation to give 5’-O- DMT-N2--(tert-butyloxycarbonyl)-deoxyguanosine (19.5 g, 29.1 mM, 86 % from 5’-O-DMT-3’- 0- tert-butyldimethylsilyl- N2 -(tert-butyloxycarbonyl)-deoxyguanosine). The material was pure enough for the next step. An analytical sample was prepared by column chromatography as above on a silica column, 10 X 35 cM, packed with 2% methanol and 2% pyridine in DCM. A gradient to 10% methanol was applied to the column over 10 L of solvent, and fractions containing pure product were pooled and evaporated. ‘H NMR (400 mHz, CDC13, PPM) 7.7 (m, 1H), 7.2- 7.4 (m, 1OH), 6.8 (d, 4H), 6.2 (t, 1H), 5.7 (s, 2H), 4.65 (m, 1H), 4.15 (m, 1H), 3.8 (s, 6H), 3.35 (m, 2H), 2.7 (m, 1H), 2.45 (m, 1H), 1.6 (s, 18Ff).
With 1H-imidazole In N,N-dimethyl-formamide at 20℃; for 20h; 30 First, from Compound 73 (Nucleoside & Nucleotide, 1985, 4, 641-649)Compound 74(9 - (3 - O - tert - butyldimethylsilyl - 2 - O - deoxy - β - D - ribofuranosyl) - 1 - hydro - 2 - isobutyrylamino - 6 H - purin - 6 -Was synthesized. That is, after dissolving the compound 73 (8.33 g, 13 mmol) in N, N-dimethylformamide (65 mL), imidazole (2.83 g, 42 mmol) and tert-butyldimethylsilyl chloride (5.89 g, 39 mmol) Sequentially,And the mixture was stirred at room temperature for 20 hours. After completion of the reaction, quenching was carried out with a saturated aqueous solution of sodium bicarbonate, followed by extraction with ethyl acetate.Subsequently, the organic layer was dried with magnesium sulfate and the solvent was distilled off under reduced pressure,A crude 3 'hydroxyl group protected compound (13 mmol) was obtained.The roughly purified 3 'hydroxyl protected product (13 mmol) was dissolved in chloroform (87 mL), and then p-toluenesulfonic acid monohydrate (7.42 g, 39 mmol) dissolved in methanol (37 mL) was heated at -15 ° C. , And the mixture was stirred at the same temperature for 1.5 hours.After completion of the reaction, saturated sodium bicarbonate water was added until the reaction solution became colorless from orange,Extraction with chloroform was performed.After drying the organic layer with magnesium sulfate and distilling off the solvent under reduced pressure,The residue was purified by silica gel column chromatography (ethyl acetate / n-hexane = 1/1 → ethyl acetate → methanol / chloroform = 1/20) to give compound 74 (5.44 g, 12 mmol, 2 stepsAbout 93%).
With 1H-imidazole In N,N-dimethyl-formamide at 0 - 20℃; for 72h;

  • 32
  • [ 68892-41-1 ]
  • [ 121-44-8 ]
  • [ 118352-76-4 ]
YieldReaction ConditionsOperation in experiment
33.8% With bis(trichloromethyl) carbonate; phosphonic acid In acetonitrile at 0℃; for 4h;
  • 33
  • [ 68892-41-1 ]
  • monochloro-N,N-isopropylamino-octylphosphine [ No CAS ]
  • [RP/SP]-5'-O-(4,4'-dimethoxytrityl)-N2-isobutanoyl-2'-deoxyguanosine-3'-O-(N,N-diisopropylamino,n-octyl)-phosphine [ No CAS ]
YieldReaction ConditionsOperation in experiment
75% With N-ethyl-N,N-diisopropylamine In dichloromethane for 2h; Ambient temperature;
  • 34
  • [ 68892-41-1 ]
  • [ 198637-74-0 ]
  • [ 212575-01-4 ]
YieldReaction ConditionsOperation in experiment
With N-ethyl-N,N-diisopropylamine In acetonitrile for 0.0833333h; Ambient temperature;
With N-ethyl-N,N-diisopropylamine In acetonitrile for 0.0833333h; Ambient temperature;
With N-ethyl-N,N-diisopropylamine In dichloromethane at 20℃; for 0.25h;
  • 35
  • [ 56183-63-2 ]
  • [ 68892-41-1 ]
  • [ 133728-85-5 ]
YieldReaction ConditionsOperation in experiment
With pyridine In acetonitrile at 20℃; for 0.5h;
With triethylamine In acetonitrile at 20℃; for 0.333333h;
With triethylamine In dichloromethane at 20℃; for 1h; Inert atmosphere;
  • 36
  • [ 68892-41-1 ]
  • [ 153120-90-2 ]
  • [ 136340-78-8 ]
YieldReaction ConditionsOperation in experiment
85% With N-ethyl-N,N-diisopropylamine In dichloromethane at 20℃; for 0.5h;
  • 37
  • [ 108-30-5 ]
  • [ 68892-41-1 ]
  • 3-[(2R,3S,5R)-2-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(2-isobutyrylamino-6-oxo-1,6-dihydro-purin-9-yl)-tetrahydro-furan-3-yloxycarbonyl]-propionic acid anion [ No CAS ]
YieldReaction ConditionsOperation in experiment
96% With triethylamine In dichloromethane at 20℃; for 3h;
  • 38
  • [ 68892-41-1 ]
  • [ 370596-60-4 ]
  • Diisopropyl-phosphoramidous acid (2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(2-isobutyrylamino-6-oxo-1,6-dihydro-purin-9-yl)-tetrahydro-furan-3-yl ester 4-oxo-pentyl ester [ No CAS ]
YieldReaction ConditionsOperation in experiment
68% With 1H-tetrazole In dichloromethane; acetonitrile
  • 39
  • [ 68892-41-1 ]
  • [ 411234-03-2 ]
  • 3'-O-(diisopropylamino)phosphinoacetic acid α,α-dimethyl-β-cyanoethyl ester 5'-O-(4,4'-dimethoxytrityl)-N-2-isobutyryl-2'-deoxyguanosine [ No CAS ]
YieldReaction ConditionsOperation in experiment
89% With 1H-tetrazole In dichloromethane at 20℃; for 24h;
  • 40
  • [ 68892-41-1 ]
  • [ 121-44-8 ]
  • O-phenyl H-phosphonothioate (p-chlorobenzyl)thiouronium salt [ No CAS ]
  • 5'-O-dimethoxytrityl-N2-isobutyryl-2'-deoxyadenosine 3'-H-phosphonothioate triethylammonium salt [ No CAS ]
YieldReaction ConditionsOperation in experiment
76% With pyridine; tert-butylchlorodiphenylsilane In toluene
  • 41
  • C14H13O2PSe*C8H9ClN2S [ No CAS ]
  • [ 68892-41-1 ]
  • C49H48N5O8PSe [ No CAS ]
YieldReaction ConditionsOperation in experiment
98% With pyridine; chlorophosphoric acid diphenyl ester In acetonitrile for 0.166667h;
  • 42
  • [ 68892-41-1 ]
  • [ 40615-39-2 ]
  • N2-isobutyryl-5'-O-(4,4'-dimethoxytrityl)-3'-O-(N,N-diisopropylamino)[2-[(N-formyl-N-methyl)amino]ethoxy]phosphinyl-2'-deoxyguanosine [ No CAS ]
YieldReaction ConditionsOperation in experiment
With 1H-tetrazole In acetonitrile at 25℃; for 12h;
  • 43
  • [ 68892-41-1 ]
  • [ 137348-88-0 ]
  • 5'-O-(4,4'-dimethoxytrityl)-N2-isobutyryl-2'-deoxyguanosine 3'-O-[(tert-butyl)-N,N-diisopropylphosphoramidite] [ No CAS ]
YieldReaction ConditionsOperation in experiment
79% With N,N-diisopropylamine tetrazolide In dichloromethane at 20℃;
  • 44
  • [ 64350-24-9 ]
  • [ 68892-41-1 ]
  • 45
  • [ 68892-41-1 ]
  • [ 93134-41-9 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: 1,3-dicyclohexylcarbodiimide; (N,N-dimethylamino)pyridine / dioxane / 3 h / 25 °C 2: acetic acid / 2 h / 25 °C
Multi-step reaction with 2 steps 1: 5 h / 20 °C 2: p-toluenesulfonic acid / ethyl acetate; methanol / 20 °C
Multi-step reaction with 2 steps 1: (N,N-dimethylamino)pyridine, dicyclohexylcarbodiimide / dioxane / 1 h 2: 80 percent acetic acid / 0.5 h
  • 46
  • [ 68892-41-1 ]
  • [ 753456-27-8 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 4 steps 1.1: 1,3-dicyclohexylcarbodiimide; (N,N-dimethylamino)pyridine / dioxane / 3 h / 25 °C 2.1: acetic acid / 2 h / 25 °C 3.1: triethylamine; thionyl chloride / acetonitrile / 0.17 h / 5 °C 3.2: 83 percent / acetonitrile / 2 h / 25 °C 4.1: 48 percent / hydrazine hydrate; pyridine; acetic acid / 0.05 h / 25 °C
  • 47
  • [ 68892-41-1 ]
  • [ 753456-23-4 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1.1: 1,3-dicyclohexylcarbodiimide; (N,N-dimethylamino)pyridine / dioxane / 3 h / 25 °C 2.1: acetic acid / 2 h / 25 °C 3.1: triethylamine; thionyl chloride / acetonitrile / 0.17 h / 5 °C 3.2: 83 percent / acetonitrile / 2 h / 25 °C
  • 48
  • [ 68892-41-1 ]
  • [ 753456-31-4 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 5 steps 1.1: 1,3-dicyclohexylcarbodiimide; (N,N-dimethylamino)pyridine / dioxane / 3 h / 25 °C 2.1: acetic acid / 2 h / 25 °C 3.1: triethylamine; thionyl chloride / acetonitrile / 0.17 h / 5 °C 3.2: 83 percent / acetonitrile / 2 h / 25 °C 4.1: 48 percent / hydrazine hydrate; pyridine; acetic acid / 0.05 h / 25 °C 5.1: 54 percent / triethylamine / acetonitrile / 1 h / 25 °C
  • 49
  • [ 68892-41-1 ]
  • N-{9-[(2R,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-(2-oxo-3-oxa-1-thia-2λ5-phospha-spiro[4.5]dec-2-yloxy)-tetrahydro-furan-2-yl]-6-oxo-6,9-dihydro-1H-purin-2-yl}-isobutyramide [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: iPr2NEt / acetonitrile / 0.08 h / Ambient temperature 2: SeO2 / acetonitrile / 3 h / Ambient temperature
Multi-step reaction with 2 steps 1: diisopropylethylamine / acetonitrile / 0.08 h / Ambient temperature 2: 54 percent / SeO2 / acetonitrile / 3 h / Ambient temperature
  • 50
  • [ 68892-41-1 ]
  • [ 883716-66-3 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: diisopropylethylamine / acetonitrile / 0.08 h / Ambient temperature 2: sulfur / acetonitrile / 12 h
  • 51
  • [ 68892-41-1 ]
  • 5’-O-DMT-O6-diphenylcarbamoyl-N2-isobutyryl-2’-deoxyguanosine-3’-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: diisopropylethylamine / acetonitrile / 0.08 h / Ambient temperature 2: sulfur / acetonitrile / 12 h 3: 95 percent / pyridine, diisopropylethylamine / 1 h / Ambient temperature
  • 52
  • [ 68892-41-1 ]
  • O6-[2-(methylnitrosamino)ethyl]-2'-deoxyguanosine [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 5 steps 1: dioxane / 0.25 h 2: diethylazodicarboxylate, triphenylphosphine / dioxane / 1 h / Ambient temperature 3: 1M HF/pyridine / 0.25 h 4: aq. NH3 / methanol / 10 h / 80 °C 5: 80percent aq. AcOH / 0.5 h / Ambient temperature
  • 53
  • [ 68892-41-1 ]
  • C34H37N7O7 [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 4 steps 1: dioxane / 0.25 h 2: diethylazodicarboxylate, triphenylphosphine / dioxane / 1 h / Ambient temperature 3: 1M HF/pyridine / 0.25 h 4: aq. NH3 / methanol / 10 h / 80 °C
  • 54
  • [ 68892-41-1 ]
  • 5'-O-(dimethoxytrityl)-N2-isobutyryl-O6-[2-(nitrosaminomethyl)ethyl]-2'-deoxyguanosine [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: dioxane / 0.25 h 2: diethylazodicarboxylate, triphenylphosphine / dioxane / 1 h / Ambient temperature 3: 1M HF/pyridine / 0.25 h
  • 55
  • [ 68892-41-1 ]
  • [ 184224-53-1 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: dioxane / 0.25 h 2: diethylazodicarboxylate, triphenylphosphine / dioxane / 1 h / Ambient temperature
  • 56
  • [ 68892-41-1 ]
  • [ 99540-94-0 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: 1.) BuLi / 1.) THF, -20 deg C, 20 min, 2.) THF, RT, 2 h 2: 80percent aq. AcOH / 0.5 h / Ambient temperature
Multi-step reaction with 2 steps 1: pyridine; silver nitrate / tetrahydrofuran / 20 °C 2: trichloroacetic acid / dichloromethane / 0.17 h / 20 °C
Multi-step reaction with 2 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 20 h / 20 °C 2: toluene-4-sulfonic acid / methanol; chloroform / 1.5 h / -15 °C
Multi-step reaction with 2 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 72 h / 0 - 20 °C 2: toluene-4-sulfonic acid / dichloromethane; methanol / 0.5 h / 0 °C

  • 57
  • [ 961-07-9 ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 4 steps 1: pyridine / 0.5 h / 0 °C 2: pyridine / 2 h 3: aq. NH4OH / pyridine / 0.5 h 4: 72 percent / DMAP, TEA / pyridine / 1 h
Multi-step reaction with 3 steps 1: pyridine; methanol / 5 h / 20 °C 2: NaOH / ethanol; H2O / 0.67 h / 0 - 3 °C 3: 84 percent / 1.) pyridine, 0 deg C, 16 h, 2.) pyridine, CH3OH, 20 deg C, 1 h
Multi-step reaction with 2 steps 1: 1.) 1,1,1,3,3,3-hexamethyldisilazane / 1.) DMF, 5 h, 2.) pyridine, 16 h 2: 87 percent / 4-dimethylaminopyridine / pyridine; dioxane / 2 h
Multi-step reaction with 3 steps 1: 90 percent / pyridine / CHCl3 / 2 h / Ambient temperature 2: 77 percent / aq. NaOH / ethanol / 0.25 h / 0 °C 3: 85 percent / pyridine / 2 h / Ambient temperature
Multi-step reaction with 2 steps 1.1: pyridine; chloro-trimethyl-silane / 0.5 h / Cooling with ice 1.2: 2 h / 20 °C 2.1: pyridine; dmap; triethylamine / 4 h / 20 °C
Multi-step reaction with 2 steps 1.1: pyridine; chloro-trimethyl-silane / 0.5 h / Cooling with ice bath 1.2: 2.5 h / 20 °C 1.3: 0.5 h / Cooling with ice 2.1: pyridine / 5 h / 20 °C

  • 58
  • [ 68892-41-1 ]
  • [ 119595-55-0 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: Et3N / acetonitrile 2: acetonitrile
Multi-step reaction with 2 steps 1: tetrazole / CH2Cl2; acetonitrile / 0.25 h / Ambient temperature 2: CH2Cl2; acetonitrile / 0.5 h / Ambient temperature
  • 59
  • [ 68892-41-1 ]
  • [ 119595-57-2 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: Et3N / acetonitrile 2: acetonitrile
  • 60
  • [ 68892-41-1 ]
  • [ 119595-58-3 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: Et3N / acetonitrile 2: acetonitrile
  • 61
  • [ 68892-41-1 ]
  • [ 119595-56-1 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: Et3N / acetonitrile 2: acetonitrile
  • 62
  • [ 68892-42-2 ]
  • [ 40615-36-9 ]
  • N2-isobutyryl-2',5'-O-bis(4,4'-dimethoxytrityl)-2'-deoxyguanosine [ No CAS ]
  • [ 68892-41-1 ]
  • 63
  • [ 68892-41-1 ]
  • [ 102691-36-1 ]
  • 5'-O-dimethoxytrityl-N2-isobutyryl-2'-deoxyguanosine-3'-O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite [ No CAS ]
YieldReaction ConditionsOperation in experiment
92% With N-ethyl-N,N-diisopropylamine; trifluoroacetic acid In tetrahydrofuran at 20℃; for 12h; 8 Examples 1-11 Examples 1-11; These Examples illustrate the phosphitylation of several protected nucleoside reagents with 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite in the presence of several activators according to the present invention. Eleven phosphitylation reactions (1-11) comprising reacting a protected nucleoside reagent with 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite in the presence of an acid-base activator according to the present invention were conducted, and the product yields of each calculated, as described in the General Procedure, below. The various combinations of protected nucleoside, activator base, activator acid, solvent, and yield for each of the 11 reactions are listed in Table 1. General Procedure: The activator base (1.1 to 1.2 equivalents) is added to the solvent and 0.95 to 1.1 equivalents of activator acid is subsequently added thereto at ambient temperature to form the activator solution. About 1 equivalent of the protected nucleoside is dissolved in about 10 equivalents of the solvent in a separate vessel and about 3 equivalents of the solvent is then distilled off under reduced pressure. About 1 to 1.2 equivalents of 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite is added to the nucleoside mixture at ambient temperature, and the activator solution prepared previously is then added to the nucleoside mixture at ambient temperature with vigorous stirring. After 12 hours, the reaction mixture is diluted with toluene and washed with water. The organic layer is separated, dried over sodium sulfate if necessary, and concentrated under reduced pressure. The yield of the desired amidite is then calculated using HPLC techniques, that is, the resulting product mixture is run through an HPLC column using an appropriate eluent, and the area under the HPLC peaks used to determine the %yield of product in the mixture.
67% With α-picoline; trifluoroacetic acid In tetrahydrofuran at 20℃; for 12h; 7 Examples 1-11 Examples 1-11; These Examples illustrate the phosphitylation of several protected nucleoside reagents with 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite in the presence of several activators according to the present invention. Eleven phosphitylation reactions (1-11) comprising reacting a protected nucleoside reagent with 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite in the presence of an acid-base activator according to the present invention were conducted, and the product yields of each calculated, as described in the General Procedure, below. The various combinations of protected nucleoside, activator base, activator acid, solvent, and yield for each of the 11 reactions are listed in Table 1. General Procedure: The activator base (1.1 to 1.2 equivalents) is added to the solvent and 0.95 to 1.1 equivalents of activator acid is subsequently added thereto at ambient temperature to form the activator solution. About 1 equivalent of the protected nucleoside is dissolved in about 10 equivalents of the solvent in a separate vessel and about 3 equivalents of the solvent is then distilled off under reduced pressure. About 1 to 1.2 equivalents of 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite is added to the nucleoside mixture at ambient temperature, and the activator solution prepared previously is then added to the nucleoside mixture at ambient temperature with vigorous stirring. After 12 hours, the reaction mixture is diluted with toluene and washed with water. The organic layer is separated, dried over sodium sulfate if necessary, and concentrated under reduced pressure. The yield of the desired amidite is then calculated using HPLC techniques, that is, the resulting product mixture is run through an HPLC column using an appropriate eluent, and the area under the HPLC peaks used to determine the %yield of product in the mixture.
  • 64
  • [ 64325-78-6 ]
  • [ 4546-72-9 ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
This compound was prepared from N6 -benzoyl-2'-deoxyadenosine by the same procedure used for the preparation of N2 -isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyguanosine.
  • 65
  • [ 68892-42-2 ]
  • [ 40615-36-9 ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
In pyridine; N2 -Isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyguanosine (2) The tritylation procedure of Jones45 was modified such that no DMAP was used. To 3.37 g (10.0 mmol) of N2 -isobutyryl-2'-deoxyguanosine (that was first concentrated from dry pyridine) in 50 mL of dry pyridine, was added 4.06 g (12.0 mmol, 1.20 equiv.) of 4,4'-dimethoxytrityl chloride. The reaction was stirred for 15 h, and then concentrated. The residue was partitioned between CH2 Cl2 and 0.5% aq. NaHCO3, shaken, and separated. The organic layer was washed with 0.5% aq. NaHCO3 and dried. The crude product was purified by flash chromatography.
  • 66
  • [ 68892-41-1 ]
  • [ 124-63-0 ]
  • [ 1187644-19-4 ]
YieldReaction ConditionsOperation in experiment
With pyridine at 0℃; for 15.25h; Cooling with ice; B.3 Step 3-3'-O(R)-(methylsulfonyl)2N-Isobutyryl-5'O-Dimetoxytrityl deoxyguanosine (B5-III)Methanesulfonyl chloride (0.12 mol) was added dropwise over a period of 15 min to a cooled (ice-water-bath) solution of (B5-II) (0.06 mol) in dry pyridine (80 mL). The cooled reactants were then stirred at 0° C. for 15 h. The products were then poured into a vigorously stirred ice water mixture (1500 g). The precipitated solid was collected by filtration, washed with water (4×100 mL) and dried in vacuo over P2O5
  • 67
  • [ 68892-41-1 ]
  • [ 170236-39-2 ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 2 steps 1: Dess-Martin periodane / dichloromethane / 5.17 h / 0 - 20 °C / Inert atmosphere 2: sodium tetrahydroborate / dichloromethane; isopropyl alcohol / -60 °C / Inert atmosphere
Multi-step reaction with 3 steps 1: pyridine / 15.25 h / 0 °C / Cooling with ice 2: dimethyl sulfoxide / 90 °C 3: methanol; potassium carbonate / 1 h / 20 °C
Multi-step reaction with 5 steps 1: sodium carbonate / methanol; dichloromethane / 1 h / 0 °C 2: pyridine / 1 h / 20 °C / Inert atmosphere 3: trifluoromethylsulfonic anhydride; pyridine / dichloromethane / 0.75 h / 0 °C / Inert atmosphere 4: pyridine / 2 h / 20 °C 5: sodium hydroxide / 1,4-dioxane; tetrahydrofuran; methanol / 2 h / 0 °C
Multi-step reaction with 5 steps 1: toluene-4-sulfonic acid / methanol; dichloromethane / 1 h / 0 °C 2: pyridine / 1 h / 20 °C / Inert atmosphere 3: pyridine; trifluoromethylsulfonic anhydride / dichloromethane / 0.75 h / -35 - 0 °C / Inert atmosphere 4: pyridine / 2 h / 20 °C 5: methanol; sodium hydroxide / tetrahydrofuran; 1,4-dioxane / 2 h / 0 °C

  • 68
  • [ 68892-41-1 ]
  • [ 109-78-4 ]
  • [ 160107-22-2 ]
YieldReaction ConditionsOperation in experiment
Stage #1: 5'-O-dimethoxytrityl-N-isobutyryldeoxyguanosine With pyridine; diphenyl hydrogen phosphite for 2h; Inert atmosphere; Stage #2: 3-Hydroxypropionitrile for 2h; A.1.1 Step 1-2N-Isobutyryl-3'-O-(2-Cyanoethyl)H-Phosphonate-5'O-Dimetoxytrityl deoxyguanosine (A4-I)2N-Isobutyryl-50-Dimetoxytrityl deoxyguanosine (0.5 g, 0.78 mmol) was dried by co-evaporation with dry toluene and suspended in dry pyridine (10 mL) under inert atmosphere. Diphenyl phosphite (250 μL, 1.3 mmol) was added and stirred for 2 h. 3-hydroxypropionitrile (150 μL, 2.16 mmol) was added. After stirring for 2 hr, the solvent was evaporated. The oily crude was used without further purification.
  • 69
  • [ 85272-30-6 ]
  • [ 68892-41-1 ]
  • [ 152685-42-2 ]
YieldReaction ConditionsOperation in experiment
With 2,6-di-tert-butyl-4-methylpyridine In N,N-dimethyl-formamide; acetonitrile at -40℃; for 1h; Inert atmosphere; 4.2. General procedure for preparation of intermediates (taking intermediate T as an example) General procedure: Bis(trifluoromethanesulfony1)diisopropylsilane (2.47 g, 5.99 mmol, 1 equiv) was added via syringe to a solution of 2,6-di-tert-butyl-4-methylpyridine (1.23 g, 5.99 mmol, 1 equiv) in CH3CN (15 mL) in a 200-mL round-bottom flask under N2 atmosphere. The resulted clear solution was cooled to -40 °C, followed by addition of a solution of 5'-O-(4,4'-dimethoxytrityl)thymidine (DMT-T) (3.00 g, 5.51 mmol, 0.92 equiv) and 2,6-di-tert-butyl-4-methylpyridine (295 mg, 1.44 mmol, 0.24 equiv) in DMF (25 mL) dropwise via syringe over 10 min. The reaction mixture was stirred at -40 °C for further 1 h, and the intermediate T was obtained, which was directly used for the next step without purification.refPreviewPlaceHolder8d
  • 70
  • [ 68892-41-1 ]
  • [ 530-62-1 ]
  • [ 1357928-20-1 ]
YieldReaction ConditionsOperation in experiment
92.7% In dichloromethane at 20℃; for 4h; 3.2.2.5 (2R,3S,5R)-2-((Bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-5-(2-isobutyramido-6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-3-yl-1H-imidazole-1-carboxylate (3) 2-Isobutyryl-5′-DMT-2′-deoxyguanosine (10.6g, 16.5mmol) was dissolved in 140mL dry DCM and carbonyldiimidazole (13.4g, 82.5mmol) was added. The mixture was stirred at room temperature for four hours and washed with water. After drying and evaporating the organic phase, the desired compound was obtained as a yellowish foam. No further purification was required. Yield: 11.2g, 92.7% (15.3mmol). (0054) ESI-MS: calc: 733.29. Found [M+H+]: 734.04. (0055) 1H NMR (DMSO-d6): 8.34 (s, 1H, Imidazole), 8.18 (s, 1H, H-8), 7.69 (s, 1H, Imidazole), 7.31 (d, J=7.4Hz, 2H, DMT), 7.18 (d, J=8.4Hz, 8H, DMT), 7.09 (s, 1H, Imidazole), 6.77 (t, J=17.7Hz, 3H, DMT), 6.37 (t, J=14.3Hz, 1H, H-1′), 5.5 (d, J=5.9Hz, 1H, H-3′), 4.45 (m, 1H, H-4′), 3.7 (s, 6H, OCH3), 3.41 (t, J=18Hz, 1H, H-5′), 3.19 (m, 2H, H-5′ and H-2′), 2.84-2.7 (m, 2H, H-2′ and CH (iBu)), 1.1 (d, J=6.74Hz, 6H, CH3 (iBu)).
In dichloromethane at 20℃; for 4h; 1.A.1 5'-DMT-2-isobutyryl-2'-deoxyguanosine was dissolved in dichloromethane (DCM) and treated with 4 equivalents of carbonyl diimidazole (CDI). After four hours at room temperature, the reaction mix was washed with water, dried and evaporated to afford compound 2.
With dmap In dichloromethane at 20℃; for 14h;
  • 71
  • N,N,N',N'-tetraisopropyl-O-[3-(N,N-dimethylamino)prop-1-yl]phosphordiamidite [ No CAS ]
  • [ 68892-41-1 ]
  • N2-isobutyryl-5'-O-(4,4'-dimethoxytrityl)-3'-O-[(N,N-diisopropylamino)(3-[N,N-dimethylamino]prop-1-yl)oxy]phosphinyl-2'-deoxyguanosine [ No CAS ]
YieldReaction ConditionsOperation in experiment
With 1H-tetrazole In acetonitrile at 25℃; for 10h; General procedure for the preparation of deoxyribonucleoside phosphoramidites (3a-c) General procedure: To a stirred solution of 1 (401 mg, 1.20 mmol) in MeCN (20 ml) was added the appropriately protected deoxyribonucleoside (2a-c, 1.0 mmol) along with 0.45 M 1H-tetrazole in MeCN (2.2 ml, 1.0 mmol). The reaction mixture was stirred for 3 h (2a-b) or 10 h (2c) at ~25 C. The reaction mixture was then concentrated under reduced pressure to a gummy material; the crude phosphoramidite was purified by chromatography on silica gel (~25 g), which was equilibrated in a solution of hexane:Et3N (95:5 v/v). The product was eluted from the column using a gradient of CH2Cl2 (0 → 95%) in hexane: Et3N (95:5 v/v). Fractions containing the pure phosphoramidite, as indicated by TLC, were pooled together and were evaporated to dryness under low pressure. The foamy material was dissolved in dry benzene (5 ml) and the resulting solution was manually stirred in a dry ice-acetone bath. The frozen material was then lyophilized under high vacuum to give the phosphoramidite 3a-c, as a white powder, the yield of which was in the range of 62-75%.
  • 72
  • [ 80817-46-5 ]
  • [ 68892-41-1 ]
  • C47H44ClN8O10P [ No CAS ]
YieldReaction ConditionsOperation in experiment
With pyridine In 1,4-dioxane
With pyridine In 1,4-dioxane at 20℃; for 3h; General procedure: Thecouplings were carried out essentially as described previously[8]. A solution of 2-chlorophenyl phosphorodichloridate(7.6 mmol, 1.88 g) in anhydrous dioxane (5.75 mL) was addedin one portion to a suspension of 1-hydroxybenzotriazole(15.2 mmol, 2.06 g; dried in vacuo over P2O5 at 55 °C for 3 d)and pyridine (15 mmol, 1.2 mL) in anhydrous dioxane (30 mL).The reaction mixture was stirred for 2 h, and the precipitate wasfiltered off under anhydrous conditions to give a stock solutionof bis(benzotriazol-1-yl) 2-chlorophenyl phosphate(0.2 mol L-1) as a clear colorless liquid. The solution(ρ = 1.057 g L-1) could be stored for several weeks at -20 °C.
With pyridine In 1,4-dioxane
  • 73
  • [ 68892-41-1 ]
  • [ 108-24-7 ]
  • 5'-(4,4'-dimethoxytrityl)-2'-deoxy-N<SUP>2</SUP>-acetyl-N<SUP>2</SUP>,N<SUP>6</SUP>-diaminopurine riboside [ No CAS ]
  • [ 161786-58-9 ]
YieldReaction ConditionsOperation in experiment
Stage #1: 5'-O-dimethoxytrityl-N-isobutyryldeoxyguanosine; acetic anhydride With pyridine; 1-methyl-1H-imidazole In toluene at 20℃; for 96h; Stage #2: With ammonium hydroxide In methanol at 55℃; for 16h; 5′-(4,4′-dimethoxytrityl)-2′-deoxy-N2-acetyl-N2,N6-diaminopurine riboside (5a) To 5′-(2,2′-dimethoxytrityl)-2′-deoxy-N2-isobutyryl guanosine (3a, 6.40 g, 10 mmol) in a 1 L bottle was added 400 mL of a 2:3:5 v/v/v solution ofN-methylimidazole, pyridine, toluene. The bottle was capped, and the solution was mixed until homogeneous. A 1:4 v/v solution of acetic anhydride and toluene (400 mL) was added. The bottle was capped, and the solution was mixed thoroughly. The solution sat at room temperature for 4 days. The solution was diluted with 500 mL of ethyl acetate and washed twice with 600 mL portions of saturated aqueous sodium bicarbonate solution. The organic layer was dried with sodium sulfate, filtered, and concentrated under vacuum to ~10 mL of a heterogeneous brown mixture. MeOH (40 mL) was added to dissolve the residue. Concentrated ammonium hydroxide (30% w/w, 400 mL) was added. The solution was mixed and transferred to a 500 mL Pyrex media bottle. The bottle was capped and heated to 55 °C for 16 h. The solution was cooled to room temperature. The crude mixture was analyzed by RP-HPLC-MS, and it was determined to contain 8% of compound 5a by UV quantification. A portion of the crude was purified by the chromatography procedure written below to yield a white solid:1H NMR (300MHz, DMSO-d6) δ 9.86 (s, 1H), 8.21 (s, 1H), 7.46 - 7.37 (m, 2H), 7.37 - 7.21 (m, 11H), 6.88 (t,J=9.1 Hz, 5H), 6.37 (t,J=6.5 Hz, 1H), 5.41 (d,J=4.5 Hz, 1H), 4.60 - 4.50 (m, 1H), 4.08 - 3.98 (m, 1H), 3.81 (d,J=1.0 Hz, 8H), 3.59 (s, 2H), 3.37 - 3.25 (m, 1H), 3.24 - 3.14 (m, 1H), 2.91 (quin,J=6.4 Hz, 1H), 2.47 - 2.33 (m, 1H), 2.25 (s, 3H);13C NMR 125MHz, DMSO-d6) δ 169.1, 157.9, 156.0, 152.8, 149.9, 144.8, 138.4, 135.6, 135.5, 129.6, 127.6, 126.5, 116.1, 113.0, 85.8, 85.4, 82.9, 70.6, 69.7, 64.2, 54.9, 24.4. HRMSm/zcalculated for C33H34N6O6[M - H]-609.2467, found 609.2472
  • 74
  • N,N,N',N'-tetraisopropyl-[1-(2-nitrophenyl) ethyl]phosphorodiamidite [ No CAS ]
  • [ 68892-41-1 ]
  • 5'-O-(4,4'-dimethoxytrityl)-N2-isobutyrylguanosine-3'-{O-[1-(2-nitrophenyl)ethyl]-N,N'-diisopropyl-amino}phosphoramidite [ No CAS ]
YieldReaction ConditionsOperation in experiment
50% With 1H-tetrazole; bis(diisopropylamino)chlorophosphine In dichloromethane at 20℃; for 4h;
  • 75
  • [ 68892-42-2 ]
  • C23H19F3O4 [ No CAS ]
  • [ 68892-41-1 ]
YieldReaction ConditionsOperation in experiment
74% With N-ethyl-N,N-diisopropylamine; In tetrahydrofuran; at 0 - 20℃; for 2h;Inert atmosphere; Schlenk technique; General procedure: To a solution of trityl alcohol (0.6 mmol, 1.2 equiv.) in dry CH2Cl2 (5 mL) in a round-bottomed flask was added trifluoroacetic anhydride (0.21 mL, 1.5 mmol, 3 equiv.) at rt under argon from a Schlenk line. A deep red solution was formed immediately (with 1a, the color was slightly lighter). After stirring for 2 h, the mixture was concentrated to dryness on a rotary evaporator under reduced pressure provided by a water aspirator. The flask was reattached to the Schlenk line and flushed with argon. The intermediate trityl cation was re-dissolved in dry THF (5 mL), and added via a cannula to a solution of alcohol substrate (0.5 mmol, 1 equiv.) and DIEA (0.175 mL, 1 mmol, 2 equiv.) in dry THF (5 mL) at rt (5-8) or 0 C (3, 9-11). After stirring for 2 h (while warming to rt slowly if applicable), the reaction mixture was poured into a separatory funnel containing 5% NaHCO3 (15 mL), and extracted with EtOAc (10 mL×2). The extracts were dried over anhydrous Na2SO4, filtered, and concentrated.
  • 76
  • [ 1528733-82-5 ]
  • [ 68892-41-1 ]
  • C54H59N6O8PSi [ No CAS ]
YieldReaction ConditionsOperation in experiment
73% With chloro-trimethyl-silane; triethylamine In tetrahydrofuran at 20℃; Cooling; General procedure: The nucleoside 109-112 (178.5 mmol) was dried in a single neck 2000 mL round bottom flask by azeotropic evaporation by anhydrous toluene (250 mL) and dried under vacuum for 18 h. This dried compound was dissolved in dry THF (375 ~ 600 mL) and transferred into three neck 2000 mL round bottom flask with magnetic stir bar. Then, triethylamine (125 mL, 898 mmol), dried over CaH2, was added into the reaction mixture, then cooled to -10 ~ -20 °C. Chlorotrimethylsilane (22.6 mL, 179 mmol) was added dropwise over 10 min. A THF solution (215 mL) of the crude chlorooxazaphospholidine (253 mmol) was added through cannula over ~ 15 min then, gradually warmed to room temperature about 1 h. LCMS showed that the starting material was consumed. Then, the reaction mixture was treated with water (2.4 mL, 0.13 mol) and the reaction mixture was further stirred less than 5 min then, 25 g of MgS04 was added followed by stirring the reaction mixture for another 10 min. Then, it was filtered carefully under vacuum/argon and the resulting filtrate was reduced to yellow foam by rotary evaporation then dried under high vacuum overnight. Crude mixture was purified by silica column (which was pre-deactivated with acetonitrile) chromatography using ethyl acetate (5% TEA) and acetonitrile (5% TEA) as eluents.
  • 77
  • N,N,N’,N’-tetraisopropyl-1-(3-methoxypropyl)phosphanediamine [ No CAS ]
  • [ 68892-41-1 ]
  • 5'-O-(4,4'-dimethoxytrityl)-3'-O-[3-methoxypropyl(diisopropylamino)phosphanyl]-2'-deoxy-(2-N-isobutyryl)guanosine [ No CAS ]
YieldReaction ConditionsOperation in experiment
76% With 1-methyl-1H-imidazole; 1H-tetrazole In N,N-dimethyl-formamide at 20℃; Inert atmosphere;
  • 78
  • (2R,3aR,6S,7aR)-3a-methyl-2-((perfluorophenyl)thio)-6-(prop-1-en-2-yl)hexahydrobenzo[d][1,3,2]oxathiaphosphole 2-sulfide [ No CAS ]
  • [ 68892-41-1 ]
  • N-(9-((2R,4S,5R)-5-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-(((2S,3aR,6S,7aR)-3a-methyl-6-(prop-1-en-2-yl)-2-sulfidohexahydrobenzo[d][1,3,2]oxathiaphosphol-2-yl)oxy)tetrahydrofuran-2-yl)-6-oxo-6,9-dihydro-1H-purin-2-yl)isobutyramide [ No CAS ]
YieldReaction ConditionsOperation in experiment
47.1% With 1,8-diazabicyclo[5.4.0]undec-7-ene In N,N-dimethyl-formamide at 0 - 20℃; for 0.166667h; Inert atmosphere; 16.2.19 2.19. Compound 3-130 A dry 250 mL round bottom flask was charged with (2R,3aR,6S,7aR)-3a-methyl- (1119) 2-((perfluorophenyl)thio)-6-(prop-1-en-2-yl)hexahydrobenzo[d][ 1,3,2]oxathiaphosphole 2-sulfide(5.8 g, 12.99 mmol) and N-(9-((2R,4S,5R)-5-((bis(4- methoxyphenyl)(phenyl)methoxy)methyl)-4-hydroxytetrahydrofuran-2-yl)-6-oxo-6,9-dihydro-lH-purin-2-yl)isobutyramide (8.9g, l3.9mmol) under a stream of nitrogen. N,N-dimethylformamide (50 mL) was added to the mixture which was allowed to stir at room temperature until it became homogeneous. The mixture was cooled to 0 °C. 1,8-diazabicyclo[5.4.0]undec-7-ene (2.081 mL, 13.91 mmol) was then added to the mixture drop-wise. The mixture was stirred at 0 °C for 10 minutes. (1120) [0343] The cold reaction mixture was diluted with ~200mL toluene. The mixture was transferred to a separatory funnel where it was washed twice with 1M pH 7.4 phosphate buffer solution (Aldrich P3619). Organics were dried with Na2S04. The mixture was filtered and the filtrate was concentrated to dryness. 9.25g. Evaporate onto celite (toluene) The mixture was purified via Biotage medium pressure liquid chromatography (Silica; Isco RediSep l20g; 70% EtOAc-Hex 1% triethylamine to 100% Ethyl acetate 1% triethylamine over 6 CV, hold at 100% for 10CV). Major peak was isolated. N-(9- ((2R,4S,5R)-5-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-(((2S,3aR,6S,7aR)- 3a-methyl-6-(prop-l-en-2-yl)-2-sulfidohexahydrobenzo[d][l,3,2]oxathiaphosphol-2-yl)oxy)tetrahydrofuran-2-yl)-6-oxo-6,9-dihydro-lH-purin-2-yl)isobutyramide (5.8g, 6.55 mmol, 47.1 % yield). . 1H NMR (500 MHz, ACETONITRILE-d3) d 12.06 - 11.78 (m, 1H), 9.22 (br s, 1H), 7.82 (s, 1H), 7.46 - 7.34 (m, 2H), 7.34- 7.16 (m, 8H), 6.90 - 6.72 (m, 4H), 6.26 (t, =6.8 Hz, 1H),5.54-5.42 (m, 1H), 4.99 (d, =l .2 Hz, 1H), 4.87 (s, 1H), 4.43 (dt, =l2.7, 3.2 Hz, 1H), 4.30 (dt, J=5.8, 3.1 Hz, 1H), 4.09 (q, J=1.1 Hz, 1H), 3.76 (d, J=2.9 Hz, 6H), 3.45 (dd, =l0.5,5.9 Hz, 1H), 3.29 (dd, =l0.4, 3.5 Hz, 1H), 3.15- 3.02 (m, 1H), 2.70 - 2.53 (m, 3H), 2.20 (s, 8H), 2.03- 1.91 (m, 7H), 1.76 (s, 3H), 1.67 (s, 3H), 1.17 (t, J=7.2 Hz, 6H).
  • 79
  • [ 4712-55-4 ]
  • [ 68892-41-1 ]
  • bicarbonate salt of 1,8-diazabicyclo[5.4.0]undec-7-ene [ No CAS ]
  • 1,8-diazabicyclo[5.4.0]undec-7-enium 5′-O-dimethoxytrityl-N2-isobutyryldeoxyguanosine 3′-H-phosphonate [ No CAS ]
YieldReaction ConditionsOperation in experiment
80% Stage #1: diphenyl hydrogen phosphite; 5'-O-dimethoxytrityl-N-isobutyryldeoxyguanosine With pyridine In water at 0 - 20℃; for 1h; Inert atmosphere; Stage #2: With triethylamine In water at 20℃; for 1h; Inert atmosphere; Stage #3: bicarbonate salt of 1,8-diazabicyclo[5.4.0]undec-7-ene With pyridine In chloroform; water Inert atmosphere;
  • 80
  • [ 68892-41-1 ]
  • C52H66N7O13PSi [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 72 h / 0 - 20 °C 2: toluene-4-sulfonic acid / dichloromethane; methanol / 0.5 h / 0 °C 3: 1,8-diazabicyclo[5.4.0]undec-7-ene; lithium chloride / N,N-dimethyl-formamide / 16 h / 25 °C / Inert atmosphere; Sealed tube
  • 81
  • [ 68892-41-1 ]
  • C59H69N10O12PSi [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 72 h / 0 - 20 °C 2: toluene-4-sulfonic acid / dichloromethane; methanol / 0.5 h / 0 °C 3: 1,8-diazabicyclo[5.4.0]undec-7-ene; lithium chloride / N,N-dimethyl-formamide / 16 h / 25 °C / Inert atmosphere; Sealed tube
  • 82
  • [ 68892-41-1 ]
  • C58H69N8O13PSi [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 72 h / 0 - 20 °C 2: toluene-4-sulfonic acid / dichloromethane; methanol / 0.5 h / 0 °C 3: 1,8-diazabicyclo[5.4.0]undec-7-ene; lithium chloride / N,N-dimethyl-formamide / 16 h / 25 °C / Inert atmosphere; Sealed tube
  • 83
  • [ 68892-41-1 ]
  • C56H71N10O13PSi [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 72 h / 0 - 20 °C 2: toluene-4-sulfonic acid / dichloromethane; methanol / 0.5 h / 0 °C 3: 1,8-diazabicyclo[5.4.0]undec-7-ene; lithium chloride / N,N-dimethyl-formamide / 16 h / 25 °C / Inert atmosphere; Sealed tube
  • 84
  • [ 68892-41-1 ]
  • C58H69N8O13PSi [ No CAS ]
YieldReaction ConditionsOperation in experiment
Multi-step reaction with 3 steps 1: 1H-imidazole / N,N-dimethyl-formamide / 72 h / 0 - 20 °C 2: toluene-4-sulfonic acid / dichloromethane; methanol / 0.5 h / 0 °C 3: 1,8-diazabicyclo[5.4.0]undec-7-ene; lithium chloride / N,N-dimethyl-formamide / 16 h / 25 °C / Inert atmosphere; Sealed tube
  • 85
  • [ 68892-41-1 ]
  • C11H19OPS2 [ No CAS ]
  • [ 74-88-4 ]
  • (S)-Methyl-phosphonothioic acid O-[(2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(2-isobutyrylamino-6-oxo-1,6-dihydro-purin-9-yl)-tetrahydro-furan-3-yl] ester S-methyl ester [ No CAS ]
YieldReaction ConditionsOperation in experiment
46% Stage #1: 5'-O-dimethoxytrityl-N-isobutyryldeoxyguanosine; C11H19OPS2 With 1,8-diazabicyclo[5.4.0]undec-7-ene In tetrahydrofuran at 20℃; for 12h; Inert atmosphere; Stage #2: methyl iodide With triethylamine In tetrahydrofuran at 20℃; for 1h; stereospecific reaction;
  • 86
  • [ 68892-41-1 ]
  • C11H19OPS2 [ No CAS ]
  • [ 74-88-4 ]
  • (R)-Methyl-phosphonothioic acid O-[(2R,3S,5R)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(2-isobutyrylamino-6-oxo-1,6-dihydro-purin-9-yl)-tetrahydro-furan-3-yl] ester S-methyl ester [ No CAS ]
YieldReaction ConditionsOperation in experiment
59% Stage #1: 5'-O-dimethoxytrityl-N-isobutyryldeoxyguanosine; C11H19OPS2 With 1,8-diazabicyclo[5.4.0]undec-7-ene In tetrahydrofuran at 20℃; for 12h; Inert atmosphere; Stage #2: methyl iodide With triethylamine In tetrahydrofuran at 20℃; for 1h; stereospecific reaction;
  • 87
  • [ 68892-41-1 ]
  • C75H100N19O30P5S4 [ No CAS ]
  • C104H122N23O37P5S5 [ No CAS ]
YieldReaction ConditionsOperation in experiment
98% Stage #1: 5'-O-dimethoxytrityl-N-isobutyryldeoxyguanosine; C75H100N19O30P5S4 With 4,5-dicyano-1H-imidazole In acetonitrile Stage #2: With 3-((N,N-dimethylaminomethylidene)amino)-3H-1,2,4-dithiazole In acetonitrile Stage #3: With 1H-imidazole; pyridine hydrogenfluoride In tetrahydrofuran at 0℃; for 2h; 2.2 General procedure for preparation of 5' DMT-MOE CCGU-OH General procedure: Compound 4-8 (153 g, 92.8 mmol) and compound 4-6 (89.9 g, 97.5 mmol) were co- evaporated with ACN (400 mL x 3) under Ar2 in a 3000 mL single-necked round bottle, and 3A molecular sieve (45.0 g) were added to the single-necked bottle, under Ar2 pressure ACN (928 mL) was added. The mixture was stirred at 25oC for an hour, and then Py-TFA (1 M, 139 mL) was added to the mixture. HPLC showed the starting material was consumed completely. [0406] After the coupling reaction finished DDTT (20.0 g, 97.5 mmol) was added to the mixture. The reaction mixture was stirred at 25oC for 0.5 hr and changed from yellow cloudy to yellow homogenous solution which suggested the reaction went to completion and then cooled down to 0oC in ice bath for 30 min.At the same time, a 500 mL round bottom flask was charged with imidazole (127 g, 1.87 mol ) and anhydrous THF (232 mL) and placed in the ice bath for 30 min. The HF-Py (24.3 mL, 70.0% purity) was slowly added and then stirred for another 15 min (A homogeneous solution was obtained from this step). The solution from the last step was slowly added to the reaction mixture from the last reaction mixture by the peristaltic pump (1 mL/5min dropping rate) and stirred for 1-2 hours at 0oC. The completion of reaction can be monitored by HPLC. HPLC showed the starting material was consumed completely. The mixture was diluted with EA (4500 mL) and slowly neutralized by NaHCO3/H2O (2500 mL) at 0oC. The organic layer was separated and washed with NaHCO3/H2O (2500 mL), brine (2000 mL). The organic layer was dried and concentrated to dryness. The crude was re- dissolved in DCM (600 mL). The crude solvent was slowly dropped to a solvent of tBuOMe (6000 mL). Desired product was precipitated out. The product was collected as a light- yellow solid after filtration, and the solid cake was washed with tBuOMe (600 mL x2). 4-9 (5' DMT-MOE CCGU-OH) (190 g, 90.5% yield, 94.8% purity) was obtained as a light yellow solid. HPLC-MS for MOE-CCGU 4mer (4-9) is shown in FIG. 4.HPLC-MS method for compound 4-9: • Column: ACQUITY UPLC BEH Shield RP18 Column, 130Å, 1.7 µm, 2.1 mm X 150 mm; • Column temperature: 60°C; • MS analysis was done on the Thermo Orbitrap Fusion with 60k resolution and mass range from 400 to 2000; • MS polarity: positive • Mobile phase A: 20 mM Ammonium Acetate in ACN:Water=25:75; Mobile phase B: acetonitrile; • Gradient:
  • 88
  • [ 51747-24-1 ]
  • [ 68892-41-1 ]
  • [ 115131-08-3 ]
YieldReaction ConditionsOperation in experiment
92% Stage #1: N,N-diisopropylamino methylphosphonamidic chloride With N-ethyl-N,N-diisopropylamine In dichloromethane; toluene for 0.0833333h; Stage #2: N2-Isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyguanosine With 9-azajulolidine In dichloromethane; toluene for 0.166667h; 4 General procedure: i) An activated resin obtained in Example 8 (AM-PS-Het5, 250 mg) was loaded into an HPLC column of stainless steel (75 mm x 4.6 mm). The resulting column packed with the activated resin was flushed with toluene at a flow rate of 1.00 mL/min for 15 minutes. The column was weighed (mToiuene + resin + column = 43.118 g), flushed with dichloromethane (DCM) with a flow rate of (0151) 1.00 mL/min for 15 minutes, and then weighted again (rriDCM + res n + column = 43.588 g). The void volume, Vvoid, of the system was determined to establish a connection between flow rate and estimated residence time of the liquid passing through the column. The void volume of the column was calculated using the formula: (0152) Am solvent switch 43.5588 g - 43.118 g (0153) ^void = 1.00 raL (0154) 1 3 0 867 wherein, Arrisoivent switch is the difference in mass and Apsoivent the difference in density when switching solvents, ii) a loaded resin was prepared by loading the activated resin 4 times with PCI (0.10 M) and L/,/V-diisopropylethylamine (DIPEA, 0.10 M) in DCM (2 mL) with flow rate of 1.00 mL/min for 5 minutes including DCM wash, iii) the substrate alcohol (0.10 M, 0.114 mmol) and DMAP (0.15 M, 0.171 mmol) or another base, such as PPY or 9AJ, were dissolved in DCM (1 mL) and eluted through the loaded resin with a flow rate of between 0.125 mL/min and 1.00 mL/min (residence time between 8 minutes and 1 minute), iV) fractions comprising the synthesized phosphoramidites were collected for 2.5 times the residence time.
92% Stage #1: N,N-diisopropylamino methylphosphonamidic chloride With N-ethyl-N,N-diisopropylamine In dichloromethane; toluene for 0.0833333h; Stage #2: N2-Isobutyryl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyguanosine With 9-azajulolidine In dichloromethane; toluene for 0.166667h; 4 General procedure: i) An activated resin obtained in Example 8 (AM-PS-Het5, 250 mg) was loaded into an HPLC column of stainless steel (75 mm x 4.6 mm). The resulting column packed with the activated resin was flushed with toluene at a flow rate of 1.00 mL/min for 15 minutes. The column was weighed (mToiuene + resin + column = 43.118 g), flushed with dichloromethane (DCM) with a flow rate of (0151) 1.00 mL/min for 15 minutes, and then weighted again (rriDCM + res n + column = 43.588 g). The void volume, Vvoid, of the system was determined to establish a connection between flow rate and estimated residence time of the liquid passing through the column. The void volume of the column was calculated using the formula: (0152) Am solvent switch 43.5588 g - 43.118 g (0153) ^void = 1.00 raL (0154) 1 3 0 867 wherein, Arrisoivent switch is the difference in mass and Apsoivent the difference in density when switching solvents, ii) a loaded resin was prepared by loading the activated resin 4 times with PCI (0.10 M) and L/,/V-diisopropylethylamine (DIPEA, 0.10 M) in DCM (2 mL) with flow rate of 1.00 mL/min for 5 minutes including DCM wash, iii) the substrate alcohol (0.10 M, 0.114 mmol) and DMAP (0.15 M, 0.171 mmol) or another base, such as PPY or 9AJ, were dissolved in DCM (1 mL) and eluted through the loaded resin with a flow rate of between 0.125 mL/min and 1.00 mL/min (residence time between 8 minutes and 1 minute), iV) fractions comprising the synthesized phosphoramidites were collected for 2.5 times the residence time.
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