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CAS No. : | 23669-79-6 | MDL No. : | MFCD00063410 |
Formula : | C30H30N2O7 | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | BYGKUWPLEGHFKX-ZRRKCSAHSA-N |
M.W : | 530.57 | Pubchem ID : | 90230 |
Synonyms : |
5'-O-DMT-dU
|
Num. heavy atoms : | 39 |
Num. arom. heavy atoms : | 24 |
Fraction Csp3 : | 0.27 |
Num. rotatable bonds : | 9 |
Num. H-bond acceptors : | 7.0 |
Num. H-bond donors : | 2.0 |
Molar Refractivity : | 144.17 |
TPSA : | 112.01 Ų |
GI absorption : | High |
BBB permeant : | No |
P-gp substrate : | Yes |
CYP1A2 inhibitor : | No |
CYP2C19 inhibitor : | No |
CYP2C9 inhibitor : | Yes |
CYP2D6 inhibitor : | Yes |
CYP3A4 inhibitor : | Yes |
Log Kp (skin permeation) : | -7.42 cm/s |
Log Po/w (iLOGP) : | 3.54 |
Log Po/w (XLOGP3) : | 2.98 |
Log Po/w (WLOGP) : | 2.78 |
Log Po/w (MLOGP) : | 1.37 |
Log Po/w (SILICOS-IT) : | 4.04 |
Consensus Log Po/w : | 2.94 |
Lipinski : | 1.0 |
Ghose : | None |
Veber : | 0.0 |
Egan : | 0.0 |
Muegge : | 0.0 |
Bioavailability Score : | 0.55 |
Log S (ESOL) : | -4.87 |
Solubility : | 0.00719 mg/ml ; 0.0000135 mol/l |
Class : | Moderately soluble |
Log S (Ali) : | -5.0 |
Solubility : | 0.00536 mg/ml ; 0.0000101 mol/l |
Class : | Moderately soluble |
Log S (SILICOS-IT) : | -8.01 |
Solubility : | 0.00000517 mg/ml ; 0.0000000098 mol/l |
Class : | Poorly soluble |
PAINS : | 0.0 alert |
Brenk : | 0.0 alert |
Leadlikeness : | 2.0 |
Synthetic accessibility : | 4.93 |
Signal Word: | Warning | Class: | N/A |
Precautionary Statements: | P261-P280-P305+P351+P338 | UN#: | N/A |
Hazard Statements: | H302-H315-H319-H332-H335 | Packing Group: | N/A |
GHS Pictogram: |
* 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.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
89% | With lithium carbonate; N-ethyl-N,N-diisopropylamine In tetrahydrofuran at 20℃; Heating | The unprotected nucleoside (1 eq.) and Li2CO3 (5 eq.) were dried together overnight under vacuum (<0.1 mm Hg). A solution of N,N-diisopropylethylamine (3 eq.) in THF was then added and heated to dissolve the starting materials. The solution was cooled to room temperature and dimethoxytrityl tetrafluoroborate 10 was added in portions of 0.2-0.3 eq., in 30 min intervals. When TLC analysis indicated complete consumption of starting material, or competing formation of di-DMT-protected nucleosides was observed, the additions were stopped and the reaction was allowed to proceed for another 2 h. The mixture was then diluted with CH2Cl2, washed with sat. NaHCO3, H2O and brine, dried over MgSO4, and filtered. Solvents were removed in vacuo and the residue was purified by automated column chromatography on silica gel. Drying under vacuum (<0.1 mm Hg) afforded the DMT-protected products. A detailed representative procedure is given for the preparation of compound 4. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
43 g | at 25℃; for 12 h; | To a solution of 308-1 (22.80 g, 99.91 mmol) in anhydrous pyridine (200 mE) was added DMTC1 (37.24 g, 109.90 mmol), and the mixture stirred at 25° C. for 12 h. The reaction was quenched with a sat. NH4C1 solution (200 mE), and extracted with EA (3x200 mE). The combined organic layers were washed with brine (2x 100 mE), dried over anhydrous Na2SO4 and concentrated under reduced pressure. The residue was purified by column chromatography (PE:EA2: 1 to 0:1) to give the desired product (43.00 g, 72.94 mmol) as a yellow foam. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86% | With pyridine; at 20℃; for 12h; | 2-Deoxyuridine (1.0 g; 4.4 mmol; 1.0 equiv.) was dissolved in pyridine (10 mL) followed by portion-wise addition of DMT-Cl (1.9 g; 5.6 mmol; 1.3 equiv.). The reaction mixture was stirred at ambient temperature and the reaction was monitored by TLC. After complete consumption of the starting material (12 hours), MeOH (2 mL) was added and the resulting mixture was concentrated under vacuum. The residue was dissolved in CH2Cl2 and the organic phase was washed consecutively with saturated aqueous NaHCO3 solution and dried over Na2SO4. After filtration, the solvent was evaporated and the residue was purified via column chromatography (50-70% EtOAc in hexanes containing 1% trimethylamine v/v). The product was obtained as a yellow foam (2.1 g; 3.8 mmol; 86 %). TLC: Rf 0.11 (CH2Cl2/EtOAc; UV). 1H NMR (600 MHz, Acetonitrile-d3) delta 9.13 (bs, 1H), 7.61 (d, J = 8.1 Hz, 1H), 7.50-7.38 (m, 2H), 7.36-7.26 (m, 6H), 7.27-7.19 (m, 1H), 6.88 (d, J = 9.0 Hz, 4H), 6.16 (t, J = 6.4 Hz, 1H), 5.35 (d, J = 8.1 Hz, 1H), 4.43 (dt, J = 6.4, 4.4 Hz, 1H), 3.97-3.89 (m, 1H), 3.77 (s, 6H), 3.40 (bs, 1H), 3.31 (dd, J = 10.7, 4.4 Hz, 1H), 3.27 (dd, J = 10.7, 3.2 Hz, 1H), 2.27 (ddd, J = 13.7, 6.5, 4.6 Hz, 1H), 2.21 (dt, J = 13.7, 6.4 Hz, 1H). 13C NMR (151 MHz, Acetonitrile-d3) delta 164.04, 159.71, 151.34, 145.90, 141.38, 136.75, 136.58, 131.05, 129.02, 128.89, 127.91, 114.10, 114.09, 102.43, 87.39, 86.78, 85.71, 71.49, 64.16, 55.92, 41.01.. |
With pyridine; at 0 - 20℃; for 25h;Inert atmosphere; | 2,3'-Anhydro-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)uridine 51; 4,4'-Dimethoxytrityl chloride (5.39 g, 15.9 mmol) is added to a solution, maintained under argon at 0 C., of 2'-deoxyuridine (3.3 g, 14.5 mmol) in anhydrous pyridine (50 ml). The mixture is left stirring for 1 hour at 0 C. and then for 24 h at ambient temperature. Mesyl chloride (1.35 ml, 17.4 mmol) is added and the mixture is left reacting for 4 hours. Water (5 ml) is subsequently added and, after 30 minutes, the solvents are evaporated and coevaporated with toluene. The residue obtained is taken up in dichloromethane (100 ml) and the solution is washed with water (50 ml) and dried over sodium sulfate before being evaporated to dryness. The yellow foam obtained is dissolved in the minimum amount of dichloromethane in order to be chromatographed on silica gel in a dichloromethane-methanol (95:5) mixture comprising 1% of triethylamine. | |
43 g | With pyridine; at 25℃; for 12h; | To a solution of 308-1 (22.80 g, 99.91 mmol) in anhydrous pyridine (200 mE) was added DMTC1 (37.24 g, 109.90 mmol), and the mixture stirred at 25 C. for 12 h. The reaction was quenched with a sat. NH4C1 solution (200 mE), and extracted with EA (3x200 mE). The combined organic layers were washed with brine (2x 100 mE), dried over anhydrous Na2SO4 and concentrated under reduced pressure. The residue was purified by column chromatography (PE:EA2: 1 to 0:1) to give the desired product (43.00 g, 72.94 mmol) as a yellow foam. |
With pyridine; at 25℃; for 12h; | To a solution of 354-1 (22.80 g, 99.91 mmol) in anhydrous pyridine (200 mL) was added DMTCl (37.24 g, 109.90 mmol), and the mixture stirred at 25 C. for 12 h. The reaction was quenched with a sat. NH4Cl solution (200 mL), and extracted with EA (3×200 mL). The combined organic layers were washed with brine (2×100 mL), dried over anhydrous Na2SO4 and concentrated under reduced pressure. The residue was purified by column chromatography (PE:EA=2:1 to 0:1) to give the desired product (43.00 g, 72.94 mmol) as a yellow foam. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
79% | With pyridine; dmap; for 12h; | Secondary alcohol SI4 296 mg; 0.558 mmol; 1 equiv.) was dissolved in pyridine (3 mL). DMAP (14 mg; 0.11 mmol; 0.2 equiv.) and benzoyl chloride (168 mL; 1.45 mmol; 2.6 equiv.) was added. After 2.5 hours, TLC (hexanes/EtOAc 1:2; UV) showed full consumption of the starting material, and the reaction was quenched by addtion of aqueous NaHCO3 (30 mL) and EtOAc (20 mL). The phases were separated and the organic phase was washed with dilute aqueous NH4Cl (2 × 10 mL) and brine (10 mL), dried over Na2SO4, filtered and concentrated. The crude product was purified by column chromatography (12 g silica; 0-70% EtOAc in hexanes) to give the pure product B as as white foam (281 mg; 0.443 mol; 79%). TLC: Rf 0.32 (Hexanes/EtOAc 1:2; UV). 1H NMR (600 MHz, Acetonitrile-d3) delta 8.94 (s, 1H), 8.04-7.96 (m, 2H), 7.60 (ddt, J = 8.8, 7.3, 1.3 Hz, 1H), 7.57 (d, J = 8.2 Hz, 1H), 7.50-7.43 (m, 2H), 7.42-7.35 (m, 2H), 7.31-7.22 (m, 6H), 7.23-7.15 (m, 1H), 6.85-6.78 (m, 4H), 6.24 (dd, J = 7.7, 6.2 Hz, 1H), 5.54 (dt, J = 6.5, 3.0 Hz, 1H), 5.37 (d, J = 8.1 Hz, 1H), 4.25-4.20 (m, 1H), 3.70 (s, 6H), 3.44 (dd, J = 10.6, 4.3 Hz, 1H), 3.34 (dd, J = 10.6, 3.3 Hz, 1H), 2.53 (ddd, J = 14.4, 6.2, 2.9 Hz, 1H), 2.47-2.38 (m, 1H). 13C NMR (151 MHz, Acetonitrile-d3) delta 166.26, 163.37, 159.34, 150.85, 145.39, 140.76, 136.19, 136.07, 134.01, 130.63, 130.35, 130.04, 129.20, 128.57, 128.51, 127.55, 113.72, 113.71, 102.43, 87.22, 85.46, 84.11, 75.47, 64.01, 55.49, 37.97. MS (ESI) m/z calculated for C37H34N2O8Na (M+Na)+ 657.2207 found 657.2205. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
43 g | With 1H-imidazole; silver nitrate; In N,N-dimethyl-formamide; at 0 - 25℃; for 12h; | To a solution of this product (20.00 g, 37.70 mmol), AgNO3 (6.40 g, 37.70 mmol) and imidazole (5.13 g, 75.39 mmol) in DMF (200.00 mE) was added, followed by TI3SC1 (8.52 g, 56.54 mmol) at 0 C. The mixture was stirred at 25 C. for 12 h, and then the mixture was concentrated under reduced pressure to remove the DMF. The residue was diluted with ice-water (300 mE) and extracted with EA (3x1 00 mE). The combined organic layers were washed with brine (3x50 mE), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure. The residue was purified by column chromatography (PE:EA3:1 to 1:1) to give 1-[(2R,4S,5R)- 5-[[bis(4-methoxyphenyl)-phenyl-methoxy]methyl] -4-[tert- butyl(dimethyl)silyl]oxy-tetrahydrofuran-2-yl]pyrimidine- 2,4-dione (15.70 g, 24.35 mmol) as a white solid. |
15.7 g | With 1H-imidazole; silver nitrate; In N,N-dimethyl-formamide; at 0 - 25℃; for 12h; | To a solution of this product (20.00 g, 37.70 mmol), AgNO3 (6.40 g, 37.70 mmol) and imidazole (5.13 g, 75.39 mmol) in DMF (200.00 mL) was added, followed by TBSCl (8.52 g, 56.54 mmol) at 0 C. The mixture was stirred at 25 C. for 12 h, and then the mixture was concentrated under reduced pressure to remove the DMF. The residue was diluted with ice-water (300 mL) and extracted with EA (3×100 mL). The combined organic layers were washed with brine (3×50 mL), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure. The residue was purified by column chromatography (PE:EA=3:1 to 1:1) to give 1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenyl-methoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxy-tetrahydrofuran-2-yl]pyrimidine-2,4-dione (15.70 g, 24.35 mmol) as a white solid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With di-isopropyl azodicarboxylate; triphenylphosphine; In tetrahydrofuran; at 20℃; | Example 12; The synthesis of 2'-deoxy-3-(3-azidopropyl)-5'-O-(4,4'-dimethoxy- trityl)uracil, 4; 2'-Deoxy-5'-O-(4,4'-dimethoxytrityl)uracil (0.53 g, 1.0 mmol), 3-azido- 5 propan-1-ol (0.11 g, 1.1 mmol) and triphenylphosphine (0.29, g, 1.1 mmol) were dissolved in dry THF (20 ml_). Diisopropylazodicarboxylate {0.22 mul_, 1.1 mmol) was added in four portions, and the reaction was allowed to proceed overnight at RT. All volatiles were removed in vacuo. Purification on silica gel using diethyl ether as the eluent yielded the title compound. ESI TOF MS for 10 C33H35N5 NaO7 (M+Na)+: calcd, 636.24; found, 636.26. vmax 2098 crtauT1 (-N3). 1H NMR (CDCI3): 7.76 (1 H, d, J 8.3); 7.39-7.26 (9H); 6.83 (4H1 d, J 8.7); 6.31 (1 h, t, J 6.2); 5.55 (1 H, d, J 8.3); 4.54 81 H, m); 4.00 (2H, t J 6.1 ); 3.79 (6H1 s); 3.50 (1 H1 m); 3.45 (2H, m); 3.35 (2H, t, J 6.8); 2.44 (1H1 m); 2.26 (1 H1 m); 2.19 (1H, br s9; 1.91 (2H, p). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86% | Example 7 Synthesis of 2'-deoxy-5'-O-(4,4'-dimethoxytrityl)-N3(hex-5-yn-1-yl) uridine (9) 5-Hexynol was allowed to react with <strong>[23669-79-6]2'-deoxy-5'-O-(4,4'-dimethoxytrityl)uridine</strong> under Mitsunobu conditions described in example 1. Purification on silica gel (eluent diethyl ether) yielded the title compound as a solid (86 %) Compound 9:1H NMR (DMSO-d6, 400 MHz): delta 7.70 (1H, d, J8.1, H-6); 7.39 (2H, DMT); 7.31 (2H, DMT); 7.25 (5H, DMT); 6.90 (4H, d, J8.0); 6.18 (1H, t, J6.3, H-1'); 5.49 (1H, J 8.1, H-5); 5.38 (1H, d, J4.6, 3'-OH); 4.31 (1H, m, H-3'); 3.90 (1H, m,H-4'); 3.78 (2H, m, NCH2); 3.74 (6H, s, 2 · OCH3); 3.26 (1H, dd, J5.4 and 10.7, H-5'); 3.19 (1H, dd, J2.9 and 10.7, H-5'); 2.23 (3H, H-2', H-2' and CH2C?); 1.63 (2H, p, CH2); 1.47 (1H, t, ?CH); 1.43 (2H, p, CH2). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
89% | With lithium carbonate; N-ethyl-N,N-diisopropylamine; In tetrahydrofuran; at 20℃;Heating; | The unprotected nucleoside (1 eq.) and Li2CO3 (5 eq.) were dried together overnight under vacuum (<0.1 mm Hg). A solution of N,N-diisopropylethylamine (3 eq.) in THF was then added and heated to dissolve the starting materials. The solution was cooled to room temperature and dimethoxytrityl tetrafluoroborate 10 was added in portions of 0.2-0.3 eq., in 30 min intervals. When TLC analysis indicated complete consumption of starting material, or competing formation of di-DMT-protected nucleosides was observed, the additions were stopped and the reaction was allowed to proceed for another 2 h. The mixture was then diluted with CH2Cl2, washed with sat. NaHCO3, H2O and brine, dried over MgSO4, and filtered. Solvents were removed in vacuo and the residue was purified by automated column chromatography on silica gel. Drying under vacuum (<0.1 mm Hg) afforded the DMT-protected products. A detailed representative procedure is given for the preparation of compound 4. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With sodium hydride; In N,N-dimethyl-formamide; at 0 - 20℃; | General procedure: Sodium hydride (0.6g, 15.2mmol) was added at 0C to a stirred solution of 5?-O-dimethoxytrityl thymidine (15a) (2.0g, 3.8mmol) and methyl tosyloxymethanephosphonate [48] (2.1g, 7.6mmol) in DMF (30mL). The resulting mixture was left to warm gradually to rt, stirred overnight (TLC in H-3), then quenched by the addition of glacial acetic acid (0.4mL; 7.6mmol) at 0C, and concentrated under reduced pressure. The product was purified by silica gel chromatography using a linear gradient of H-1 (0-100%) in ethyl acetate. This product (2.1g, 3.2mmol) was treated with 80% aq. acetic acid (30mL) at rt for 30min (TLC in C-1). The reaction mixture was concentrated at reduced pressure, the residue was diluted with chloroform (100mL), and the solution was washed with water (3×50mL). Water layers were combined, evaporated, and the pure product 19a was co-distilled subsequently with ethanol and acetonitrile, diluted in dry acetonitrile (10mL), and treated with bromotrimethylsilane (1.7mL, 12.8mmol) and 2,6-lutidine (2.9mL, 25.6mmol). The resulting mixture was stirred at rt overnight and concentrated under reduced pressure. The crude product 23a was purified by RP HPLC |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With N-chloro-succinimide; In pyridine; at 90℃; for 0.75h; | N-chlorosuccinimide (1.8g, 13.5mmol) was added under stirring to a solution of 2?-deoxy-5?-O-dimethoxytrityluridine 17a (4.8g, 9.0mmol) in pyridine (90mL). The resulting mixture was heated at 90C for 45min and then concentrated under reduced pressure. The separation on silica gel column using a linear gradient of ethanol (0?10%) in chloroform afforded the product 18a (4.5g, 8.0mmol) which was transformed into the title compound 26a by the procedure described for compound 23a |
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P410 + P403 | Protect from sunlight. Store in a well-ventilated place. |
P410 + P412 | Protect from sunlight. Do not expose to temperatures exceeding 50 oC/122oF. |
P411 + P235 | Keep cool. |
Disposal | |
Code | Phrase |
P501 | Dispose of contents/container to ... |
P502 | Refer to manufacturer/supplier for information on recovery/recycling |
Physical hazards | |
Code | Phrase |
H200 | Unstable explosive |
H201 | Explosive; mass explosion hazard |
H202 | Explosive; severe projection hazard |
H203 | Explosive; fire, blast or projection hazard |
H204 | Fire or projection hazard |
H205 | May mass explode in fire |
H220 | Extremely flammable gas |
H221 | Flammable gas |
H222 | Extremely flammable aerosol |
H223 | Flammable aerosol |
H224 | Extremely flammable liquid and vapour |
H225 | Highly flammable liquid and vapour |
H226 | Flammable liquid and vapour |
H227 | Combustible liquid |
H228 | Flammable solid |
H229 | Pressurized container: may burst if heated |
H230 | May react explosively even in the absence of air |
H231 | May react explosively even in the absence of air at elevated pressure and/or temperature |
H240 | Heating may cause an explosion |
H241 | Heating may cause a fire or explosion |
H242 | Heating may cause a fire |
H250 | Catches fire spontaneously if exposed to air |
H251 | Self-heating; may catch fire |
H252 | Self-heating in large quantities; may catch fire |
H260 | In contact with water releases flammable gases which may ignite spontaneously |
H261 | In contact with water releases flammable gas |
H270 | May cause or intensify fire; oxidizer |
H271 | May cause fire or explosion; strong oxidizer |
H272 | May intensify fire; oxidizer |
H280 | Contains gas under pressure; may explode if heated |
H281 | Contains refrigerated gas; may cause cryogenic burns or injury |
H290 | May be corrosive to metals |
Health hazards | |
Code | Phrase |
H300 | Fatal if swallowed |
H301 | Toxic if swallowed |
H302 | Harmful if swallowed |
H303 | May be harmful if swallowed |
H304 | May be fatal if swallowed and enters airways |
H305 | May be harmful if swallowed and enters airways |
H310 | Fatal in contact with skin |
H311 | Toxic in contact with skin |
H312 | Harmful in contact with skin |
H313 | May be harmful in contact with skin |
H314 | Causes severe skin burns and eye damage |
H315 | Causes skin irritation |
H316 | Causes mild skin irritation |
H317 | May cause an allergic skin reaction |
H318 | Causes serious eye damage |
H319 | Causes serious eye irritation |
H320 | Causes eye irritation |
H330 | Fatal if inhaled |
H331 | Toxic if inhaled |
H332 | Harmful if inhaled |
H333 | May be harmful if inhaled |
H334 | May cause allergy or asthma symptoms or breathing difficulties if inhaled |
H335 | May cause respiratory irritation |
H336 | May cause drowsiness or dizziness |
H340 | May cause genetic defects |
H341 | Suspected of causing genetic defects |
H350 | May cause cancer |
H351 | Suspected of causing cancer |
H360 | May damage fertility or the unborn child |
H361 | Suspected of damaging fertility or the unborn child |
H361d | Suspected of damaging the unborn child |
H362 | May cause harm to breast-fed children |
H370 | Causes damage to organs |
H371 | May cause damage to organs |
H372 | Causes damage to organs through prolonged or repeated exposure |
H373 | May cause damage to organs through prolonged or repeated exposure |
Environmental hazards | |
Code | Phrase |
H400 | Very toxic to aquatic life |
H401 | Toxic to aquatic life |
H402 | Harmful to aquatic life |
H410 | Very toxic to aquatic life with long-lasting effects |
H411 | Toxic to aquatic life with long-lasting effects |
H412 | Harmful to aquatic life with long-lasting effects |
H413 | May cause long-lasting harmful effects to aquatic life |
H420 | Harms public health and the environment by destroying ozone in the upper atmosphere |
Sorry,this product has been discontinued.
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