Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH2:1]([O:8][C:9]([N:11]1[CH2:15][C@H:14]([CH:16]2[CH2:21][CH2:20][CH2:19][CH2:18][CH2:17]2)[CH2:13][C@H:12]1[CH2:22][OH:23])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C(=O)(O)[O-:25].[Na+].O1CCOCC1.O=O>[Pt].O>[CH2:1]([O:8][C:9]([N:11]1[CH2:15][C@H:14]([CH:16]2[CH2:17][CH2:18][CH2:19][CH2:20][CH2:21]2)[CH2:13][C@H:12]1[C:22]([OH:25])=[O:23])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: O=C(OCc1ccccc1)N1C[C@H](C2CCCCC2)C[C@H]1CO
Reactant: O=C([O-])O
Agent: [Pt]
Agent: O=O
Agent: [Na+]
Solvent: O
Solvent: C1COCCO1
Product: O=C(O)[C@@H]1C[C@@H](C2CCCCC2)CN1C(=O)OCc1ccccc1

Procedure:
To a mixture of (2S-trans)-1-[(benzyloxy)carbonyl]-4-cyclohexyl-2-pyrrolidinemethanol (0.65 g), sodium bicarbonate (0.5 g), dioxane (20 ml), and water (20 ml) was added freshly prepared platinum black (prepared by hydrogenating 0.3 g of platinum oxide). Oxygen was passed through the solution at room temperature for 16 hours with vigorous stirring. Filtration and acidification, followed by extractive work-up yielded (trans)-1-[(benzyloxy)carbonyl]-4-cyclohexyl-L-proline as a glassy solid. This compound can be deprotected using catalytic hydrogenation as described in Method I.
Reaction SMILES: [CH3:1][N:2]1[CH2:7][CH2:6][C:5]([CH3:11])([C:8]([OH:10])=O)[CH2:4][CH2:3]1.C1C=CC2N(O)N=NC=2C=1.C(Cl)CCl.C(=O)(O)[O-].[Na+].[NH:31]1[C:35]2[CH:36]=[CH:37][CH:38]=[CH:39][C:34]=2[N:33]=[C:32]1[C:40]1[C:48]2[C:43](=[CH:44][CH:45]=[C:46]([NH2:49])[CH:47]=2)[N:42]([CH:50]2[CH2:55][CH2:54][CH2:53][CH2:52][O:51]2)[N:41]=1>CN(C=O)C>[NH:33]1[C:34]2[CH:39]=[CH:38][CH:37]=[CH:36][C:35]=2[N:31]=[C:32]1[C:40]1[C:48]2[C:43](=[CH:44][CH:45]=[C:46]([NH:49][C:8]([C:5]3([CH3:11])[CH2:4][CH2:3][N:2]([CH3:1])[CH2:7][CH2:6]3)=[O:10])[CH:47]=2)[N:42]([CH:50]2[CH2:55][CH2:54][CH2:53][CH2:52][O:51]2)[N:41]=1
Reactant: Nc1ccc2c(c1)c(-c1nc3ccccc3[nH]1)nn2C1CCCCO1
Reactant: CN1CCC(C)(C(=O)O)CC1
Agent: O=C([O-])O
Agent: On1nnc2ccccc21
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: ClCCCl
Product: CN1CCC(C)(C(=O)Nc2ccc3c(c2)c(-c2nc4ccccc4[nH]2)nn3C2CCCCO2)CC1
Temperature: 25 °C
Reaction time: 24 h
Yield: 39 %

Procedure:
1,4-Dimethylpiperidine-4-carboxylic acid (3 mg, 0.019 mmol), HOBt (4 mg, 0.029 mmol), EDC (5.5 mg, 0.028 mmol) and sodium bicarbonate (1.6 mg, 0.019 mmol) were added to a solution of 3-(1H-benzo[d]imidazol-2-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-indazol-5-amine (6.4 mg, 0.019 mmol) in DMF (6 mL). The reaction mixture was stirred at room temperature for 24 h, and then the solvent was removed in vacuo. Purification by flash chromatography (6% CH3OH/CH2Cl2) afforded the title compound (3.5 mg) as a solid. 1H NMR (400 MHz, CD3OD): δ 8.54 (s, 1H), 7.77 (m, 1H), 7.71 (m, 2H), 7.38 (m, 2H), 7.29 (m, 2H), 5.94 (d, 1H, J=8.0 Hz) 4.00 (m, 1H), 3.85 (m, 1H), 3.46 (m, 2H), 2.89 (s, 3H), 2.69 (m, 2H), 2.56 (m, 1H), 2.15 (m, 3H), 1.86 (m, 3H), 1.72 (m, 3H), 1.46 (s, 3H).
Reaction SMILES: Cl.[N:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[CH2:8]Cl.[Cl:10][C:11]1[CH:12]=[C:13]([NH:18][C:19]2[C:28]3[C:23](=[CH:24][CH:25]=[CH:26][C:27]=3[O:29][CH2:30][C@H:31]([N:33]([CH3:38])[C:34](=[O:37])[CH2:35][OH:36])[CH3:32])[N:22]=[CH:21][N:20]=2)[CH:14]=[CH:15][C:16]=1[OH:17]>>[Cl:10][C:11]1[CH:12]=[C:13]([NH:18][C:19]2[C:28]3[C:23](=[CH:24][CH:25]=[CH:26][C:27]=3[O:29][CH2:30][C@H:31]([N:33]([CH3:38])[C:34](=[O:37])[CH2:35][OH:36])[CH3:32])[N:22]=[CH:21][N:20]=2)[CH:14]=[CH:15][C:16]=1[O:17][CH2:8][C:3]1[CH:4]=[CH:5][CH:6]=[CH:7][N:2]=1
Reactant: C[C@H](COc1cccc2ncnc(Nc3ccc(O)c(Cl)c3)c12)N(C)C(=O)CO
Reactant: ClCc1ccccn1
Agent: Cl
Product: C[C@H](COc1cccc2ncnc(Nc3ccc(OCc4ccccn4)c(Cl)c3)c12)N(C)C(=O)CO
Yield: 8 %

Procedure:
The procedure described in Example 3 was repeated using picolyl chloride hydrochloride and N-[(1R)-2-({4-[(3-chloro-4-hydroxyphenyl)amino]quinazolin-5-yl}oxy)-1-methylethyl]-2-hydroxy-N-methylacetamide to give the title compound in 8% yield; NMR spectrum (DMSO-d6) 1.19 (d, 3H), 2.79 (s, 3H), 3.87-4.26 (m, 3H), 4.38-4.48 (m, 2H), 5.11-5.22 (m, 1H), 5.29 (s, 2H), 7.18-7.25 (m, 2H), 7.32-7.38 (m, 2H), 7.48 (d, 1H), 7.58 (d, 1H), 7.72 (t, 1H), 7.87 (t, 1H), 7.94 (d, 1H), 8.44 (s, 1H), 8.59 (d, 1H), 9.58 (s, 1H); Mass spectrum MH+ 508.3.
Reaction SMILES: [NH2:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[C:9]3[C:10]([C:15](=[O:25])[N:16]([C:18]4[CH:23]=[CH:22][C:21]([Cl:24])=[CH:20][CH:19]=4)[N:17]=3)=[CH:11][NH:12][C:13]=2[CH3:14])=[CH:4][CH:3]=1.[N:26]1[CH:31]=[CH:30][CH:29]=[CH:28][C:27]=1[CH:32]=O.C(O)(=O)C.C([BH3-])#N.[Na+]>CO>[Cl:24][C:21]1[CH:22]=[CH:23][C:18]([N:16]2[C:15](=[O:25])[C:10]3=[CH:11][NH:12][C:13]([CH3:14])=[C:8]([C:5]4[CH:6]=[CH:7][C:2]([NH:1][CH2:32][C:27]5[CH:28]=[CH:29][CH:30]=[CH:31][N:26]=5)=[CH:3][CH:4]=4)[C:9]3=[N:17]2)=[CH:19][CH:20]=1
Reactant: Cc1[nH]cc2c(=O)n(-c3ccc(Cl)cc3)nc-2c1-c1ccc(N)cc1
Reactant: O=Cc1ccccn1
Agent: [BH3-]C#N
Agent: [Na+]
Solvent: CO
Solvent: CC(=O)O
Product: Cc1[nH]cc2c(=O)n(-c3ccc(Cl)cc3)nc-2c1-c1ccc(NCc2ccccn2)cc1
Reaction time: 24 h
Yield: 40 %

Procedure:
To a stirred mixture of 7-(4-aminophenyl)-2-(4-chlorophenyl)-2,5-dihydro-6-methylpyrazolo[4,3-c]pyridin-3-one (0.150 g, 0.43 mmol), 2-pyridinecarboxaldehyde (81 μl, 0.85 mmol) and acetic acid (18 μl, 0.31 mmol) in anhydrous MeOH (3 ml) under nitrogen was added sodium cyanoborohydride (0.02 g, 0.32 mmol) and the mixture was stirred for 24 h. The mixture was quenched with saturated aqueous K2CO3 (0.5 ml) and the solvent was removed in vacuo. The residue was purified by flash chromatography (silica gel, 5-10% MeOH/CH2Cl2) to give 0.076 g (39.7%) of the title compound as a yellow solid; 1H NMR (360 MHz, DMSO-d6) δ12.32 (1H, br s), 8.57 (1H, d, J 2.1 Hz), 8.47 (1H, s), 8.14 (2H, d, J 8.7 Hz), 7.77 (1H, t, J 7.5 Hz), 7.43 (3H, m), 7.25 (3H, m), 6.68 (2H, d, J 8.3 Hz), 6.56 (2H, t, J 2.5 Hz), 4.41 (2H, d, J 5.8 Hz), 2.26 (3H, s); MS (ES+) m/z 442/444 [MH]+, 221/222 [(M+2H)/2]+.
Reaction SMILES: [CH:1]1([NH:4][C:5](=[O:23])[C:6]2[CH:11]=[C:10]([F:12])[C:9]([CH3:13])=[C:8](B3OC(C)(C)C(C)(C)O3)[CH:7]=2)[CH2:3][CH2:2]1.Cl[C:25]1[CH:34]=[CH:33][C:28]([C:29]([O:31]C)=[O:30])=[CH:27][N:26]=1.C(=O)([O-])O.[Na+]>CC(O)C>[CH:1]1([NH:4][C:5]([C:6]2[CH:11]=[C:10]([F:12])[C:9]([CH3:13])=[C:8]([C:25]3[CH:34]=[CH:33][C:28]([C:29]([OH:31])=[O:30])=[CH:27][N:26]=3)[CH:7]=2)=[O:23])[CH2:2][CH2:3]1
Reactant: Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1
Reactant: COC(=O)c1ccc(Cl)nc1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: CC(C)O
Product: Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc(C(=O)O)cn1
Temperature: 90 °C

Procedure:
N-Cyclopropyl-5-fluoro-4-methyl-3-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-benzamide (3.2 g), methyl 6-chloronicotinate (1.73 g), tetralcis(triphenylphosphine)palladium (210 mg) and aqueous sodium hydrogen carbonate (1M, 30 ml) were mixed in propan-2-ol (100 ml) and heated at 90° C. for 18 hours. The reaction was allowed to cool and the propan-2-ol removed under vacuum. The residue was partitioned between ethyl acetate and aqueous sodiumhydrogen carbonate (1M). The aqueous phase was acidified with hydrochloric acid (2N) and extracted with ethyl acetate (x2). The organic extracts were washed with brine, dried (magnesium sulphate) and reduced to dryness under vacuum. The resulting foam was triturated with ether to give 6-{5-[(cyclopropylamino)carbonyl]-3-fluoro-2-methylphenyl}nicotinic acid as a solid.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][CH:11]([C:14]2[O:23][C:17]3=[CH:18][N:19]=[C:20](Cl)[CH:21]=[C:16]3[CH:15]=2)[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[F:24][C:25]1[CH:30]=[C:29]([S:31]([CH3:34])(=[O:33])=[O:32])[CH:28]=[CH:27][C:26]=1B(O)O.C([O-])([O-])=O.[Na+].[Na+].CO>O1CCOCC1>[C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][CH:11]([C:14]2[O:23][C:17]3=[CH:18][N:19]=[C:20]([C:26]4[CH:27]=[CH:28][C:29]([S:31]([CH3:34])(=[O:33])=[O:32])=[CH:30][C:25]=4[F:24])[CH:21]=[C:16]3[CH:15]=2)[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2]
Reactant: CS(=O)(=O)c1ccc(B(O)O)c(F)c1
Reactant: CC(C)(C)OC(=O)N1CCC(c2cc3cc(Cl)ncc3o2)CC1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: C1COCCO1
Solvent: CO
Product: CC(C)(C)OC(=O)N1CCC(c2cc3cc(-c4ccc(S(C)(=O)=O)cc4F)ncc3o2)CC1

Procedure:
A mixture of 4-(5-chloro-furo[2,3-c]pyridin-2-yl)-piperidine-1-carboxylic acid tert-butyl ester (100 mg), 2-fluoro-4-(methanesulfonyl)phenylboronic acid (97 mg), 2 M aqueous Na2CO3 solution (0.33 mL), methanol (0.5 mL), and 1,4-dioxane (1.5 mL) is sparged with Ar for 10 min. PdCl2 [1,1′-bis(diphenylphosphino)-ferrocene]*CH2Cl2 complex (22 mg) is added and the mixture is stirred at reflux temperature for 2 h. The mixture is diluted with water and methanol and purified by HPLC on reversed phase (methanol/water) to give the title compound. LC (method 5): tR=1.29 min; Mass spectrum (ESI+): m/z=475 [M+H]+.
Reaction SMILES: [Br:1][C:2]1[N:10]([CH2:11][C:12]2[CH:17]=[CH:16][C:15]([Cl:18])=[CH:14][CH:13]=2)[C:9]2[C:8](=[O:19])[NH:7][C:6](=[O:20])[N:5]([CH3:21])[C:4]=2[N:3]=1.Br[CH2:23][CH2:24][CH2:25][O:26][CH:27]1[CH2:32][CH2:31][CH2:30][CH2:29][O:28]1.C(=O)([O-])[O-].[K+].[K+]>CN(C=O)C>[Br:1][C:2]1[N:10]([CH2:11][C:12]2[CH:13]=[CH:14][C:15]([Cl:18])=[CH:16][CH:17]=2)[C:9]2[C:8](=[O:19])[N:7]([CH2:23][CH2:24][CH2:25][O:26][CH:27]3[CH2:32][CH2:31][CH2:30][CH2:29][O:28]3)[C:6](=[O:20])[N:5]([CH3:21])[C:4]=2[N:3]=1
Reactant: BrCCCOC1CCCCO1
Reactant: Cn1c(=O)[nH]c(=O)c2c1nc(Br)n2Cc1ccc(Cl)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: Cn1c(=O)n(CCCOC2CCCCO2)c(=O)c2c1nc(Br)n2Cc1ccc(Cl)cc1
Temperature: 50 °C
Reaction time: 3 h
Yield: 72.4 %

Procedure:
To a solution of 8-bromo-7-(4-chlorobenzyl)-3-methyl-1H-purine-2,6(3H,7H)-dione (0.5 g, 1.35 mmol, intermediate 8) in DMF (5 mL) was added 2-(3-bromopropoxy)tetrahydro-2H-pyran (0.45 g, 2.03 mmol, intermediate 3), potassium carbonate (0.37 g, 2.7 mmol). The mixture was stirred at 50° C. for 3 h; then it was partitioned between ethyl acetate and water. The organic phase was washed with brine, dried over sodium sulfate, filtered and concentrated to give a crude product which was washed with ethanol and dried under vacuum to give 8-bromo-7-(4-chlorobenzyl)-3-methyl-1-(3-(tetrahydro-2H-pyran-2-yloxy)propyl)-1H-purine-2,6(3H,7H)-dione (0.5 g, 72.2%) as a white solid. LCMS retention time 1.732 min, LCMS MH+-THP 429.
Reaction SMILES: [Br:1][C:2]1[CH:9]=[CH:8][C:5]([C:6]#[N:7])=[CH:4][C:3]=1[CH3:10].[Br:11]N1C(=O)CCC1=O>C(Cl)(Cl)(Cl)Cl.C(Cl)Cl>[Br:1][C:2]1[CH:9]=[CH:8][C:5]([C:6]#[N:7])=[CH:4][C:3]=1[CH2:10][Br:11]
Reactant: O=C1CCC(=O)N1Br
Reactant: Cc1cc(C#N)ccc1Br
Solvent: ClCCl
Solvent: ClC(Cl)(Cl)Cl
Product: N#Cc1ccc(Br)c(CBr)c1
Yield: 14.3 %

Procedure:
To a stirred solution of 4-bromo-3-methyl benzonitrile (5 g, 25.5 mmol) in CCl4 (200 mL), was added N-bromosuccinimide (4.99 g, 28.05 mmol) and 2,2-Azobisisobutyronitrile (335 mg, 2.04 mmol). The mixture was heated to reflux overnight then cooled, diluted with CH2Cl2 and quenched with 10% NaHSO3. The layers were separated and the CH2Cl2 layer was washed with saturated NaHCO3 and brine, dried over MgSO4, filtered and concentrated under vacuum. Column chromatography on silica gel (5-10% ethyl acetate/hexanes) afforded 4.31 g (3.65 mmol, 61%) of a mixture of mono- and di-bromo intermediates. 1H NMR (400 MHz, CHLOROFORM-D) δ ppm 4.55 (s, 2H) 7.42 (dd, J=8.31, 2.01 Hz, 1H) 7.67-7.78 (m, 2H). Mass spec.: 275.94 (MH)+.
Reaction SMILES: C[O:2][C:3](=[O:41])[C@H:4]([CH3:40])[NH:5][C:6](=[O:39])[C@@H:7]([CH2:29][C:30]1[C:38]2[C:33](=[CH:34][CH:35]=[CH:36][CH:37]=2)[NH:32][CH:31]=1)[NH:8][C:9](=[O:28])[C@H:10]([CH2:22][C:23]1[N:27]=[CH:26][NH:25][CH:24]=1)[NH:11][C:12]([O:14][CH2:15][C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1)=[O:13].CO.[OH-].[Na+]>CO.O>[CH2:15]([O:14][C:12]([NH:11][C@H:10]([C:9]([NH:8][C@@H:7]([C:6]([NH:5][C@H:4]([C:3]([OH:41])=[O:2])[CH3:40])=[O:39])[CH2:29][C:30]1[C:38]2[C:33](=[CH:34][CH:35]=[CH:36][CH:37]=2)[NH:32][CH:31]=1)=[O:28])[CH2:22][C:23]1[N:27]=[CH:26][NH:25][CH:24]=1)=[O:13])[C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1
Reactant: COC(=O)[C@H](C)NC(=O)[C@@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)OCc1ccccc1
Agent: [Na+]
Agent: [OH-]
Solvent: CO
Solvent: O
Product: C[C@H](NC(=O)[C@@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)OCc1ccccc1)C(=O)O
Reaction time: 48 h

Procedure:
Under an argon atmosphere, the viscous oil containing tripeptide 20 (ca. 0.253 mol), was hydrolyzed in a solution of MeOH (1500 mL), H20 (500 mL) and NaOH (0.08 g/mL, 11.11 g, 0.278 mol). The reaction was allowed to react at room temperature (ca. 25° C.) while being monitored by HPLC. After two days, HPLC analysis indicated that hydrolysis was complete. The solution was concentrated to a residue in vacuo. Water (500 mL) was then added to the residue. The pH of the resulting solution was ca. 10. This aqueous solution was then extracted with EtOAc (2×500 mL). After this extraction the pH of the aqueous layer was ca. 9. All insoluble material in the aqueous layer was collected by vacuum filtration. The pH of the filtrate was then adjusted to ca. 5 with 2N HCl. This resulted in the precipitation of an oil which was isolated from the aqueous layer by decantation. The oil was taken up in a methanol-water solution and concentrated to a residue in vacuo (109.42 g, 0.200 mol, ca. 79% overall yield from dipeptide 26). This isolated material was consistent with 27 by 1H NMR FDMS=547, M+1.
Reaction SMILES: [CH3:1][NH:2][C:3]1[S:4][C:5]([CH3:8])=[N:6][N:7]=1.[C:9](Cl)(=[O:16])[C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1>N1C=CC=CC=1>[CH3:1][N:2]([C:3]1[S:4][C:5]([CH3:8])=[N:6][N:7]=1)[C:9](=[O:16])[C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1
Reactant: CNc1nnc(C)s1
Reactant: O=C(Cl)c1ccccc1
Solvent: c1ccncc1
Product: Cc1nnc(N(C)C(=O)c2ccccc2)s1

Procedure:
2-(N-Methyl-amino)-5-methyl-1,3,4-thiadiazole (6 g, 0.046 mole) in pyridine (190 ml) was refluxed for 6 hours with benzoyl chloride (9.7 g, 0.069 mole) and the pyridine then evaporated off under reduced pressure. The residue was treated with water, made alkaline with sodium hydroxide solution and extracted with chloroform. The chloroform was washed with a saturated solution of sodium bicarbonate and a saturated solution of sodium chloride, dried, filtered and evaporated to yield title product which was recrystallised from ethanol.
Reaction SMILES: [Br:1][C:2]1[CH:3]=[CH:4][C:5]2[C:6]3[N:14]([CH2:15][CH:16]4[CH2:21][CH2:20][CH2:19][CH2:18][CH2:17]4)[C:13]([CH2:22][O:23][CH2:24][CH3:25])=[N:12][C:7]=3[CH:8]=[N:9][C:10]=2[CH:11]=1.ClC1C=C(C=CC=1)C(OO)=O.[OH-].[NH4+:38].C1(C)C=CC(S(Cl)(=O)=O)=CC=1>C(#N)C>[Br:1][C:2]1[CH:3]=[CH:4][C:5]2[C:6]3[N:14]([CH2:15][CH:16]4[CH2:21][CH2:20][CH2:19][CH2:18][CH2:17]4)[C:13]([CH2:22][O:23][CH2:24][CH3:25])=[N:12][C:7]=3[C:8]([NH2:38])=[N:9][C:10]=2[CH:11]=1
Reactant: CCOCc1nc2cnc3cc(Br)ccc3c2n1CC1CCCCC1
Reactant: [NH4+]
Agent: Cc1ccc(S(=O)(=O)Cl)cc1
Agent: O=C(OO)c1cccc(Cl)c1
Agent: [OH-]
Solvent: CC#N
Product: CCOCc1nc2c(N)nc3cc(Br)ccc3c2n1CC1CCCCC1

Procedure:
The method described in Part J of Example 365 was used to oxidize and aminate 7-bromo-1-cylcohexylmethyl-2-ethoxymethyl-1H-imidazo[4,5-c]quinoline (7.58 g, 22.0 mmol). 3-Chloroperoxybenzoic acid (9.1 g of 50% pure material, 26.4 mmol) was added in five portions during the oxidation step, and the amination with ammonium hydroxide (55 mL) and p-toluenesulfonyl chloride (6.3 g, 33 mmol) proceeded overnight. The crude product was obtained as an oil, which was treated with acetonitrile to form a precipitate. The precipitate was isolated by filtration and washed with a small amount of acetonitrile. A portion of the brown solid was purified by flash column chromatography on silica gel (eluting with chloroform:CMA in a gradient from 95:5 to 85:15) to provide 7-bromo-1-cylcohexylmethyl-2-ethoxymethyl-1H-imidazo[4,5-c]quinolin-4-amine as a brown solid, mp 215-216° C.
Reaction SMILES: [C:1]([C:3]1[CH:4]=[C:5]([NH:9][C:10](=[O:33])[NH:11][C:12]2[CH:17]=[CH:16][C:15]([S:18]([NH:21][CH2:22][C:23]3[CH:28]=[CH:27][C:26]([S:29](=[O:32])(=[O:31])[NH2:30])=[CH:25][CH:24]=3)(=[O:20])=[O:19])=[CH:14][CH:13]=2)[CH:6]=[CH:7][CH:8]=1)#[N:2].[CH:34]([N:37]1[CH2:42][CH2:41][NH:40][CH2:39][CH2:38]1)([CH3:36])[CH3:35]>>[NH:2]=[C:1]([N:40]1[CH2:41][CH2:42][N:37]([CH:34]([CH3:36])[CH3:35])[CH2:38][CH2:39]1)[C:3]1[CH:4]=[C:5]([NH:9][C:10](=[O:33])[NH:11][C:12]2[CH:17]=[CH:16][C:15]([S:18]([NH:21][CH2:22][C:23]3[CH:28]=[CH:27][C:26]([S:29](=[O:32])(=[O:31])[NH2:30])=[CH:25][CH:24]=3)(=[O:20])=[O:19])=[CH:14][CH:13]=2)[CH:6]=[CH:7][CH:8]=1
Reactant: N#Cc1cccc(NC(=O)Nc2ccc(S(=O)(=O)NCc3ccc(S(N)(=O)=O)cc3)cc2)c1
Reactant: CC(C)N1CCNCC1
Product: CC(C)N1CCN(C(=N)c2cccc(NC(=O)Nc3ccc(S(=O)(=O)NCc4ccc(S(N)(=O)=O)cc4)cc3)c2)CC1
Yield: 3 %

Procedure:
The title compound was prepared from 4-(3-(3-cyanophenyl)ureido)-N-(4-sulfamoylbenzyl)benzenesulfonamide following procedure C and using 1.5 equivalents of 1-isopropylpiperazine as secondary amine. The product was purified by preparative HPLC.
Reaction SMILES: [OH:1][C:2]1[CH:7]=[CH:6][C:5]([NH:8][CH2:9][C:10]([OH:12])=[O:11])=[CH:4][CH:3]=1.[CH3:13]O>>[CH3:13][O:11][C:10](=[O:12])[CH2:9][NH:8][C:5]1[CH:6]=[CH:7][C:2]([OH:1])=[CH:3][CH:4]=1
Reactant: O=C(O)CNc1ccc(O)cc1
Reactant: CO
Product: COC(=O)CNc1ccc(O)cc1
Temperature: 25 °C
Reaction time: 48 h
Yield: 99 %

Procedure:
The p-hydroxy phenyl glycine (74.0 g, 442 mmol) was suspended in methanol (500 mL), cooled in an ice bath and HCl (gas) was bubbled through the reaction mixture for 20 minutes, to give a clear solution. The reaction was stirred at rt for 48 h, concentrated in vacuo to give an oil which was triturated with ethyl ether to give the p-hydroxy phenyl glycine methyl ester (95.8 g, 99%) as a white powder. MS found: (M+H)+=182.
Reaction SMILES: C([NH:5][S:6]([C:9]1[S:10][C:11]([C:14]2[CH:19]=[C:18]([C:20]3[N:25]=[C:24]([CH3:26])[CH:23]=[C:22]([C:27]4[CH:28]=[N:29][C:30]([C:33]([F:36])([F:35])[F:34])=[CH:31][CH:32]=4)[N:21]=3)[CH:17]=[CH:16][N:15]=2)=[CH:12][CH:13]=1)(=[O:8])=[O:7])(C)(C)C.C(O)(C(F)(F)F)=O>ClCCl>[CH3:26][C:24]1[CH:23]=[C:22]([C:27]2[CH:28]=[N:29][C:30]([C:33]([F:35])([F:36])[F:34])=[CH:31][CH:32]=2)[N:21]=[C:20]([C:18]2[CH:17]=[CH:16][N:15]=[C:14]([C:11]3[S:10][C:9]([S:6]([NH2:5])(=[O:8])=[O:7])=[CH:13][CH:12]=3)[CH:19]=2)[N:25]=1
Reactant: Cc1cc(-c2ccc(C(F)(F)F)nc2)nc(-c2ccnc(-c3ccc(S(=O)(=O)NC(C)(C)C)s3)c2)n1
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: Cc1cc(-c2ccc(C(F)(F)F)nc2)nc(-c2ccnc(-c3ccc(S(N)(=O)=O)s3)c2)n1
Temperature: 25 °C
Reaction time: 15 h
Yield: 16.3 %

Procedure:
To a cooled and stirred solution of 5-{4-[4-methyl-6-(6-trifluoromethyl-pyridin-3-yl)-pyrimidin-2-yl]-pyridin-2-yl}-thiophene-2-sulfonic-acid tert-butylamide (0.11 g) in dichloromethane (3 ml) was added TFA (3 ml) and the reaction mixture was allowed to stir at room temperature for 15 h. The mixture was evaporated to dryness, poured into 2N Na2CO3 solution (20 ml) and extracted with ethyl acetate (3×50 ml). The combined organic layers were washed with brine (50 ml), dried (MgSO4) and evaporated. Further purification by column chromatography on silica gel (dichloromethane/MeOH/NH4OH 16:1:0.1) and crystallization (MeOH, diethyl ether) yielded the title compound as a white solid (0.016 g, 7%). MS (ISP) 478.1 [(M+H)+]; mp 289° C.
Reaction SMILES: Cl.[CH:2]1[C:11]2[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=2)[CH2:5][CH2:4][N:3]=1.[CH2:12]([C:14]([C:16]1[CH2:21][CH2:20][CH2:19][CH2:18][CH:17]=1)=[O:15])[CH3:13].O>C(O)C>[CH3:13][CH:12]1[CH:2]2[N:3]([CH2:4][CH2:5][C:6]3[CH:7]=[CH:8][CH:9]=[CH:10][C:11]=32)[CH:17]2[CH2:18][CH2:19][CH2:20][CH2:21][CH:16]2[C:14]1=[O:15]
Reactant: C1=NCCc2ccccc21
Reactant: CCC(=O)C1=CCCCC1
Agent: Cl
Solvent: CCO
Solvent: O
Product: CC1C(=O)C2CCCCC2N2CCc3ccccc3C12

Procedure:
A mixture of 16.75 g (0.1 mole) of 3,4-dihydroisoquinoline hydrochloride and 28.0 g of (0.2 mole) of 1-cyclohexen-1-yl ethyl ketone in 28 ml of ethanol is refluxed for 52 hours then poured into 300 ml of water and extracted with ether. The aqueous layer is separated and made basic by slowly adding ammonium hydroxide solution with stirring. Stirring is continued until a solid is formed after which the liquid is decanted. The solid is washed with water, dissolved in methylene chloride, dried over sodium sulfate and concentrated to an oil. The oil is dissolved in refluxing hexane, filtered, concentrated and cooled to give a solid which is recrystallized from hexane-benzene to give 2,3,4,4a,6,7,11b,12,13,13a-decahydro-12-methyl-1H-dibenzo[a,f]quinolizin-13-one, M.P. 144.5°-147.5°C.
Reaction SMILES: F[C:2]1[C:3]([N+:15]([O-:17])=[O:16])=[C:4]2[C:9](=[CH:10][C:11]=1[F:12])[NH:8][C:7](=[O:13])[C:6](=[O:14])[NH:5]2.[CH3:18][O-:19].[Na+].Cl>O>[F:12][C:11]1[CH:10]=[C:9]2[C:4]([NH:5][C:6](=[O:14])[C:7](=[O:13])[NH:8]2)=[C:3]([N+:15]([O-:17])=[O:16])[C:2]=1[O:19][CH3:18]
Reactant: C[O-]
Reactant: O=c1[nH]c2cc(F)c(F)c([N+](=O)[O-])c2[nH]c1=O
Agent: Cl
Agent: [Na+]
Solvent: O
Product: COc1c(F)cc2[nH]c(=O)c(=O)[nH]c2c1[N+](=O)[O-]
Reaction time: 0 h
Yield: 77.5 %

Procedure:
To a solution of 21 mg (0.086 mmol) of 6,7-difluoro-5-nitro-1,4-dihydroquinoxaline-2,3-dione in 0.5 mL of DMSO-d6 was added 16 mg (0.29 mmol) of sodium methoxide. The solution was shaken in a vortex for 10 s and kept at room temperature for 3 h. It was then added to 3 mL of water and acidified with 2N HCl to pH=4. The precipitate was filtered, washed with water, and dried to leave a yellow solid (17 mg, 77%); mp 290°-292° C.; 1H NMR (DMSO-d6), 3.899 (s, 3), 7.163 (1, d, J=11.6), 11.97 (mb, 1), 12.137 (s, 1). 19F NMR, -134.48 (mb). MS, 255 (M+, 100), 243 (15), 179 (16), 151 (40). HRMS, Calcd for C9H6FN3O5 255.0287, found 255.0308.
Reaction SMILES: [P:1]([O-:32])([O:28][CH2:29][CH2:30]Br)([O:3][C@@H:4]1[CH2:9][CH2:8][CH2:7][O:6][C@H:5]1[CH2:10][O:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH3:27])=[O:2].[N:33]1[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=1>>[P:1]([O-:32])([O:28][CH2:29][CH2:30][N+:33]1[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=1)([O:3][C@@H:4]1[CH2:9][CH2:8][CH2:7][O:6][C@H:5]1[CH2:10][O:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH3:27])=[O:2]
Reactant: c1ccncc1
Reactant: CCCCCCCCCCCCCCCCOC[C@@H]1OCCC[C@H]1OP(=O)([O-])OCCBr
Product: CCCCCCCCCCCCCCCCOC[C@@H]1OCCC[C@H]1OP(=O)([O-])OCC[n+]1ccccc1
Temperature: 80 °C
Reaction time: 20 h

Procedure:
1.512 g of dl-trans-2-hexadecyloxymethyltetrahydropyran-3-yl 2-bromoethyl phosphate (prepared as described in the first half of Example 1) was dissolved in 20 ml of pyridine, and the resulting solution was heated, with stirring, at 80° C. for 20 hours. The mixture was then cooled and the pyridine was removed by distillation under reduced pressure. The residue was subjected to column chromatography through 45 g of silica gel. The fraction eluted with a 60:35:5 by volume mixture of methylene chloride, methanol and water gave 1.422 g of the title compound as a white powder, melting at 123°-129° C.
Reaction SMILES: [N:1]([C@H:4]([CH2:14][O:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH3:31])[CH2:5][O:6][Si](C(C)(C)C)(C)C)=[N+:2]=[N-:3].CCCC[N+](CCCC)(CCCC)CCCC.[F-]>C1COCC1.CCOCC>[N:1]([C@H:4]([CH2:14][O:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH3:31])[CH2:5][OH:6])=[N+:2]=[N-:3]
Reactant: CCCCCCCCCCCCCCCCOC[C@H](CO[Si](C)(C)C(C)(C)C)N=[N+]=[N-]
Agent: CCCC[N+](CCCC)(CCCC)CCCC
Agent: [F-]
Solvent: C1CCOC1
Solvent: CCOCC
Product: CCCCCCCCCCCCCCCCOC[C@H](CO)N=[N+]=[N-]

Procedure:
A solution of (R)-(2-azido-3-(hexadecyloxy)propoxy)(tert-butyl)dimethylsilane (1 eq), and 1M TBAF in THF (1.1 eq) in THF (0.2 M) was stirred at 25° C. for 20 minutes. The reaction was diluted with Et2O and washed with saturated NH4Cl, H2O, and brine. The organic phase was dried over anhydrous sodium sulfate and concentrated en vaccuo. The resulting crude was purified by flash chromatography on a COMBIFLASH® system (ISCO) using 0-30% EtOAc/Hex to give (S)-2-azido-3-(hexadecyloxy)propan-1-ol as a colorless oil.