Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [N:1]1([CH2:6][CH2:7][C:8]([NH:10][C:11]2[CH:24]=[CH:23][C:22]3[NH:21][C:20]4[C:15](=[CH:16][CH:17]=[C:18]([NH:25][C:26](=[O:34])[CH2:27][CH2:28][N:29]5[CH2:33][CH2:32][CH2:31][CH2:30]5)[CH:19]=4)[C:14](=O)[C:13]=3[CH:12]=2)=[O:9])[CH2:5][CH2:4][CH2:3][CH2:2]1.P(Cl)(Cl)(Cl)(Cl)[Cl:37].P(Cl)(Cl)(Cl)=O.N>C(Cl)(Cl)Cl>[Cl:37][C:14]1[C:15]2[C:20]([N:21]=[C:22]3[C:13]=1[CH:12]=[C:11]([NH:10][C:8](=[O:9])[CH2:7][CH2:6][N:1]1[CH2:5][CH2:4][CH2:3][CH2:2]1)[CH:24]=[CH:23]3)=[CH:19][C:18]([NH:25][C:26](=[O:34])[CH2:27][CH2:28][N:29]1[CH2:33][CH2:32][CH2:31][CH2:30]1)=[CH:17][CH:16]=2
Reactant: ClP(Cl)(Cl)(Cl)Cl
Reactant: O=C(CCN1CCCC1)Nc1ccc2c(=O)c3cc(NC(=O)CCN4CCCC4)ccc3[nH]c2c1
Agent: N
Solvent: O=P(Cl)(Cl)Cl
Solvent: ClC(Cl)Cl
Product: O=C(CCN1CCCC1)Nc1ccc2c(Cl)c3cc(NC(=O)CCN4CCCC4)ccc3nc2c1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 62 %

Procedure:
A suspension of 2,6-bis(3-pyrrolidinopropionamido)acridone AR-ACO-10 (2.0 g, 4.2 mmol) in CHCl3 (40 mL) was treated with phosphorus pentachloride (0.9 g, 4.2 mmol), followed by cautious addition of phosphorus oxychloride (50 mL). This suspension was stirred at room temp. for 30 min and brought to a gentle reflux over 1 hr. Gentle reflux was maintained for 26 hr. The reaction mixture was cooled to rt then slowly dropped onto ice (˜600 mL) over 10 min. The aqueous mixture was made basic to pH 7/8 with ammonia whilst maintaining a temp. <25° C. The aqueous layer was extracted with CHCl3 (5×200 mL). The organic extracts were combined, washed with brine (200 mL), dried (Na2SO4) and concentrated. The resulting solid was tritrated with diethyl ether (30 mL) to give the desired product (1.3 g, 62%) as a light brown solid.
Reaction SMILES: [CH2:1]([O:8][CH2:9][CH2:10][O:11][C:12]1[CH:18]=[CH:17][C:15]([NH2:16])=[CH:14][C:13]=1[C:19]([F:22])([F:21])[F:20])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.CCN(CC)CC.[Br:30][C:31]1[CH:36]=[C:35]([F:37])[C:34]([CH2:38][C:39](Cl)=[O:40])=[C:33]([F:42])[CH:32]=1>C(Cl)Cl>[CH2:1]([O:8][CH2:9][CH2:10][O:11][C:12]1[CH:18]=[CH:17][C:15]([NH:16][C:39](=[O:40])[CH2:38][C:34]2[C:33]([F:42])=[CH:32][C:31]([Br:30])=[CH:36][C:35]=2[F:37])=[CH:14][C:13]=1[C:19]([F:20])([F:21])[F:22])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: Nc1ccc(OCCOCc2ccccc2)c(C(F)(F)F)c1
Reactant: O=C(Cl)Cc1c(F)cc(Br)cc1F
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: O=C(Cc1c(F)cc(Br)cc1F)Nc1ccc(OCCOCc2ccccc2)c(C(F)(F)F)c1
Temperature: 25 °C
Yield: 17.6 %

Procedure:
To a solution of 2-(4-bromo-2,6-difluorophenyl)acetic acid (0.3 g, 1.195 mmol) in sulfurous dichloride (5 mL, 1.195 mmol) was added DMF (9.25 μL, 0.120 mmol). The resulting mixture was stirred at 60° C. After 2 h, LCMS analysis showed the starting material had disappeared and the solvent was removed in vacuo to give 2-(4-bromo-2,6-difluorophenyl)acetyl chloride (0.35 g, 0.832 mmol, 69.6% yield). To a solution of 4-(2-(benzyloxy)ethoxy)-3-(trifluoromethyl)aniline (0.347 g, 1.113 mmol) and Et3N (0.225 g, 2.227 mmol) in DCM (30 mL) was added 2-(4-bromo-2,6-difluorophenyl)acetyl chloride (0.3 g, 1.113 mmol). The resulting mixture was stirred at 25° C. After LCMS analysis showed the starting material had disappeared, the mixture was washed with H2O (20 mL) and brine (20 mL). The organic layer was dried over Na2SO4, filtered and concentrated to give the crude product, which was purified by preparative TLC (PE/EA=3/1) to give N-(4-(2-(benzyloxy)ethoxy)-3-(trifluoromethyl)phenyl)-2-(4-bromo-2,6-difluoro phenyl)acetamide (110 mg, 0.196 mmol, 17.6% yield): 1H NMR (400 MHz, CD3OD) δ 7.81 (d, J=2.8 Hz, 1H), 7.68 (d, J=2.4 Hz, 1H), 7.32-7.25 (m, 7H), 7.15 (d, J=8.8 Hz, 1H), 4.61 (s, 2H), 4.23 (t, J=4.6 Hz, 2H), 3.84 (t, J=4.6 Hz, 2H), 3.77 (s, 2H); ES-LCMS m/z 546.0 (M+H).
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([NH:8][CH2:9][CH2:10][NH:11][C:12]2[N:17]=[C:16]([NH2:18])[C:15]([N+:19]([O-:21])=[O:20])=[CH:14][CH:13]=2)[N:5]2[CH:22]=[C:23]([CH3:25])[N:24]=[C:4]2[CH:3]=1.[CH3:26][C:27]1[CH:28]=[C:29](B(O)O)[CH:30]=[C:31]([CH3:33])[CH:32]=1>>[CH3:26][C:27]1[CH:28]=[C:29]([C:2]2[N:7]=[C:6]([NH:8][CH2:9][CH2:10][NH:11][C:12]3[N:17]=[C:16]([NH2:18])[C:15]([N+:19]([O-:21])=[O:20])=[CH:14][CH:13]=3)[N:5]3[CH:22]=[C:23]([CH3:25])[N:24]=[C:4]3[CH:3]=2)[CH:30]=[C:31]([CH3:33])[CH:32]=1
Reactant: Cc1cn2c(NCCNc3ccc([N+](=O)[O-])c(N)n3)nc(Cl)cc2n1
Reactant: Cc1cc(C)cc(B(O)O)c1
Product: Cc1cc(C)cc(-c2cc3nc(C)cn3c(NCCNc3ccc([N+](=O)[O-])c(N)n3)n2)c1

Procedure:
In analogy to the procedure described for Example 7, 4 mg (3% of theory) of the product are obtained starting from 120 mg (0.32 mmol) of N6-{2-[(7-chloro-2-methylimidazo[1,2-c]pyrimidin-5-yl)amino]ethyl}-3-nitropyridine-2,6-diamine (Example 31A) by coupling with 57 mg (0.38 mmol) of (3,5-dimethylphenyl)boronic acid and subsequent purification by preparative HPLC.
Reaction SMILES: [CH3:1][N:2]([CH:4]=O)[CH3:3].[CH2:6]([O:10][CH2:11][CH2:12][O:13][C:14]1[CH:19]=[CH:18][C:17]([C:20]2[CH:21]=[CH:22][C:23]3[N:29]([CH2:30][C:31]4[CH:36]=[CH:35][C:34]([O:37][CH3:38])=[CH:33][CH:32]=4)[CH2:28][CH2:27][C:26]([C:39](O)=[O:40])=[CH:25][C:24]=3[CH:42]=2)=[CH:16][CH:15]=1)[CH2:7][CH2:8][CH3:9].S(Cl)(Cl)=O>O1CCCC1>[CH2:6]([O:10][CH2:11][CH2:12][O:13][C:14]1[CH:15]=[CH:16][C:17]([C:20]2[CH:21]=[CH:22][C:23]3[N:29]([CH2:30][C:31]4[CH:32]=[CH:33][C:34]([O:37][CH3:38])=[CH:35][CH:36]=4)[CH2:28][CH2:27][C:26]([C:39]([NH:29][C:23]4[CH:24]=[CH:42][C:20]([CH2:4][N:2]([CH3:1])[CH:3]5[CH2:12][CH2:11][O:10][CH2:6][CH2:7]5)=[CH:21][CH:22]=4)=[O:40])=[CH:25][C:24]=3[CH:42]=2)=[CH:18][CH:19]=1)[CH2:7][CH2:8][CH3:9]
Reactant: CN(C)C=O
Reactant: CCCCOCCOc1ccc(-c2ccc3c(c2)C=C(C(=O)O)CCN3Cc2ccc(OC)cc2)cc1
Solvent: C1CCOC1
Solvent: O=S(Cl)Cl
Product: CCCCOCCOc1ccc(-c2ccc3c(c2)C=C(C(=O)Nc2ccc(CN(C)C4CCOCC4)cc2)CCN3Cc2ccc(OC)cc2)cc1
Reaction time: 1 h

Procedure:
One droplet of DMF was added to a solution of 7-(4-butoxyethoxyphenyl)-1-(4-methoxybenzyl)-2,3-dihydro-1-benzazepine-4-carboxylic acid (140 mg) in tetrahydrofuran (10 ml). Then, thionyl chloride (100 mg) was added at 0° C., the temperature was returned to room temperature, and the mixture was stirred under nitrogen atmosphere for 1 hour. The solvent and excess thionyl chloride were evaporated under reduced pressure, the resulting residue was suspended in tetrahydrofuran (25 ml), and the suspension was added to a solution of 4-[[N-methyl-N-(tetrahydropyran-4-yl)amino]methyl]aniline (74 mg) and triethylamine (344 mg) in tetrahydrofuran (10 ml) at 0° C. The suspension was stirred under nitrogen atmosphere at room temperature for 3.5 hours, to the mixture was added water, and the mixture was extracted with ethyl acetate. The organic layer was washed with saturated brine and dried with magnesium sulfate. The solvent was evaporated under reduced pressure, the resulting residue was separated and purified with silica gel column chromatography (methanol:ethyl acetate=1:8), which was recrystallized from hexane-ethyl acetate to give 7-(4-butoxyethoxyphenyl)-1-(4-methoxybenzyl)-N-[4-[[N-methyl-N-(tetrahydropyran-4-yl)amino]methyl]phenyl]-2,3-dihydro-1-benzazepine-4-carboxamide (Compound 56) (89 mg) as yellow crystals.
Reaction SMILES: [N+]([O-])([O-])=O.[Ce+4].[NH4+].[N+]([O-])([O-])=O.[N+]([O-])([O-])=O.[N+]([O-])([O-])=O.[N+]([O-])([O-])=[O:20].[CH2:23]([N:30]1[C:38]2[C:33](=[N:34][CH:35]=[CH:36][C:37]=2[N:39]2[CH2:48][CH2:47][C:46]3[C:41](=[CH:42][CH:43]=[CH:44][CH:45]=3)[CH2:40]2)[C:32]([CH3:49])=[C:31]1[CH3:50])[C:24]1[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=1>C(O)(=O)C.O>[CH2:23]([N:30]1[C:38]2[C:33](=[N:34][CH:35]=[CH:36][C:37]=2[N:39]2[CH2:48][CH2:47][C:46]3[C:41](=[CH:42][CH:43]=[CH:44][CH:45]=3)[CH2:40]2)[C:32]([CH2:49][OH:20])=[C:31]1[CH3:50])[C:24]1[CH:25]=[CH:26][CH:27]=[CH:28][CH:29]=1
Reactant: O=[N+]([O-])[O-]
Reactant: Cc1c(C)n(Cc2ccccc2)c2c(N3CCc4ccccc4C3)ccnc12
Agent: [Ce+4]
Agent: [NH4+]
Solvent: O
Solvent: CC(=O)O
Product: Cc1c(CO)c2nccc(N3CCc4ccccc4C3)c2n1Cc1ccccc1
Temperature: 55 °C
Reaction time: 4 h

Procedure:
The compound prepared in Example 6 (501.1 mg, 1.23 mmol) was treated with a saturated sodium bicarbonate solution to obtain 1-benzyl-7-(1,2,3,4-tetrahydroisoquinolin-2-yl)-2,3-dimethyl-1H-pyrrolo[3,2-b]pyridine (433.6 mg, 1.18 mmol). Ammonium cerium (IV) nitrate (1.94 g, 3.54 mmol) was added at room temperature to a solution of 1-benzyl-7-(1,2,3,4-tetrahydroisoquinolin-2-yl)-2,3-dimethyl-1H-pyrrolo[3,2-b]pyridine (433.6 mg, 1.18 mmol) in acetic acid (10 ml). The reaction mixture was stirred for 4 hours at 55° C., cooled to room temperature, poured in water, and then extracted with ethyl acetate. The resulting organic layer was washed with a saturated sodium chloride solution, dried on anhydrous magnesium sulfate, and then concentrated under reduced pressure. The resulting residue was dissolved in methanol (20 ml). 2N Lithium hydroxide (5.0 ml) was added to the solution, which was then stirred for 1 hour at room temperature. The reaction mixture was neutralized with 1N hydrochloric acid, concentrated under reduced pressure to discard methanol, and then extracted with ethyl acetate. The resulting organic layer was dried on anhydrous magnesium sulfate and then concentrated under reduced pressure. The resulting residue was purified with silica gel column chromatography to give 1-benzyl-7-(1,2,3,4-tetrahydroisoquinolin-2-yl)-3-hydroxymethyl-2-methyl-1H-pyrrolo[3,2-b]pyridine, which was then dissolved in ethyl acetate. The solution was saturated with hydrochloric acid gas and then filtered to give the titled compound as a white solid (69 mg, 13.9%).
Reaction SMILES: C([Li])CCC.Br[C:7]1[CH:15]=[CH:14][C:13]([C:16]([F:19])([F:18])[F:17])=[CH:12][C:8]=1[C:9]([OH:11])=[O:10].CN(C)[CH:22]=[O:23].[OH-].[Na+]>O1CCCC1>[CH:22]([C:7]1[CH:15]=[CH:14][C:13]([C:16]([F:19])([F:18])[F:17])=[CH:12][C:8]=1[C:9]([OH:11])=[O:10])=[O:23]
Reactant: CN(C)C=O
Reactant: O=C(O)c1cc(C(F)(F)F)ccc1Br
Agent: [Li]CCCC
Agent: [Na+]
Agent: [OH-]
Solvent: C1CCOC1
Product: O=Cc1ccc(C(F)(F)F)cc1C(=O)O
Temperature: 25 °C
Reaction time: 1 h
Yield: 30.9 %

Procedure:
To a solution of n-butyl lithium (56.0 ml, 140 mmol) in tetrahydrofuran (100 mL) at −78° C. was added a solution of 2-bromo-5-(trifluoromethyl)benzoic acid (17.9 g, 66.7 mmol) in tetrahydrofuran (100 mL) over 0.5 hour, at which time the solution turned dark red. After stirring for 1 hour, N,N-dimethylformamide (50 mL, 646 mmol) was added dropwise and the reaction mixture was allowed to warm to room temperature over 6 hours. The mixture was cooled to 0° C. and then a solution of sodium hydroxide (2 N, 120 mL) was added. The mixture was extracted with ether (2×50 mL). The aqueous layer was separated and concentrated hydrochloric acid was added to it until the pH was acidic. The mixture was extracted with ethyl acetate (3×80 mL). The organic extracts were combined, dried with sodium sulfate, filtered, and concentrated. The residue was purified on Analogix® Intelliflash280™ (SiO2, 7-100% solvent A in hexanes; solvent A=3:1:0.1 hexane:ethyl aceate:acetic acid) over 1 hour to obtain the title compound (4.5 g, 20.6 mmol, 31% yield). 1H NMR (300 MHz, DMSO-d6) δ ppm 6.78 (br, 1H) 7.93 (d, J=8.48 Hz, 1H) 8.13-8.20 (m, 2H) 8.38 (br, 1H); MS (DCI/NH3) m/z 236 (M+NH4)+.
Reaction SMILES: [CH3:1][O:2][C:3]([C@@H:5]1[CH2:9][C@@H:8]([OH:10])[CH2:7][N:6]1[C:11]([O:13][C:14]([CH3:17])([CH3:16])[CH3:15])=[O:12])=[O:4].CCN(C(C)C)C(C)C.[CH3:27][S:28](Cl)(=[O:30])=[O:29]>C(Cl)Cl>[CH3:1][O:2][C:3]([C@@H:5]1[CH2:9][C@@H:8]([O:10][S:28]([CH3:27])(=[O:30])=[O:29])[CH2:7][N:6]1[C:11]([O:13][C:14]([CH3:17])([CH3:16])[CH3:15])=[O:12])=[O:4]
Reactant: COC(=O)[C@@H]1C[C@@H](O)CN1C(=O)OC(C)(C)C
Reactant: CS(=O)(=O)Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: COC(=O)[C@@H]1C[C@@H](OS(C)(=O)=O)CN1C(=O)OC(C)(C)C
Temperature: 25 °C
Reaction time: 48 h

Procedure:
(2S,4R)-4-Hydroxypyrrolidine-1,2-dicarboxylic acid 1-t-butyl ester 2-methyl ester (10.0 g, 41 mmol) was dissolved in DCM (100 mL) and cooled in an ice bath. DIPEA (1.2 equiv) was added, followed by methanesulfonyl chloride (1.2 equiv). The mixture was stirred at room temperature for 48 hours, then diluted with DCM (100 mL). The solution was washed with 1M HCl (100 mL), saturated aqueous NaHCO3 (100 mL) and saturated aqueous NaCl (100 mL), then dried over Na2SO4. The solvent was evaporated to afford the title compound (11.9 g, 37 mmol), which was used without further purification. MS m/z: [M+H]+ calcd for C12H21NO7S, 323.4. found 324.3.
Reaction SMILES: [N+:1]([C:4]1[CH:5]=[CH:6][C:7]([O:10][C:11]2[CH:19]=[CH:18][CH:17]=[C:16]3[C:12]=2[CH2:13][CH2:14][C:15]3=[O:20])=[N:8][CH:9]=1)([O-:3])=[O:2].C1(C)C=CC(S(O)(=O)=O)=CC=1.[C:32](OC(C)=C)(=[O:34])[CH3:33]>>[C:32]([O:20][C:15]1[C:16]2[C:12](=[C:11]([O:10][C:7]3[CH:6]=[CH:5][C:4]([N+:1]([O-:3])=[O:2])=[CH:9][N:8]=3)[CH:19]=[CH:18][CH:17]=2)[CH2:13][CH:14]=1)(=[O:34])[CH3:33]
Reactant: C=C(C)OC(C)=O
Reactant: O=C1CCc2c(Oc3ccc([N+](=O)[O-])cn3)cccc21
Agent: Cc1ccc(S(=O)(=O)O)cc1
Product: CC(=O)OC1=CCc2c(Oc3ccc([N+](=O)[O-])cn3)cccc21
Temperature: 80 °C
Reaction time: 7.5 h

Procedure:
To 5.00 g of 4-[(5-nitro-2-piridinyl)oxy]-1-indanone, 10 ml of isopropenyl acetate and 70 mg of p-toluenesulfonic acid were added and the mixture was stirred at 80° C. After 7.5 hours, the reaction solution was concentrated under reduced pressure. To the resulting residue, ethyl acetate was added and the solution was washed in turn with a saturated sodium hydrogencarbonate solution and a saturated sodium chloride solution. The solution extracted with ethyl acetate was dried over anhydrous magnesium sulfate and the solvent was distilled off. The resulting residue was washed with isopropyl ether in a hot state to obtain 4.70 g of the titled compound.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[CH:8]([C:19]1[CH:28]=[CH:27][C:22]([C:23]([O:25][CH3:26])=[O:24])=[C:21]([F:29])[CH:20]=1)[CH2:9][C:10](=[O:18])[C:11]1[CH:16]=[CH:15][C:14](=[O:17])[NH:13][CH:12]=1.IC.[C:32](=O)([O-])[O-].[K+].[K+]>>[Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[CH:8]([C:19]1[CH:28]=[CH:27][C:22]([C:23]([O:25][CH3:26])=[O:24])=[C:21]([F:29])[CH:20]=1)[CH2:9][C:10]([C:11]1[CH:16]=[CH:15][C:14](=[O:17])[N:13]([CH3:32])[CH:12]=1)=[O:18]
Reactant: COC(=O)c1ccc(C(CC(=O)c2ccc(=O)[nH]c2)c2ccccc2Cl)cc1F
Reactant: O=C([O-])[O-]
Agent: [K+]
Solvent: CI
Product: COC(=O)c1ccc(C(CC(=O)c2ccc(=O)n(C)c2)c2ccccc2Cl)cc1F

Procedure:
In analogy to example 161, step 1, methyl 4-(1-(2-chlorophenyl)-3-oxo-3-(6-oxo-1,6-dihydropyridin-3-yl)propyl)-2-fluorobenzoate was reacted with iodomethane in the presence of potassium carbonate to give the title compound as an off-white foam, MS (ESI+): m/z=428.2 [M+H]+.
Reaction SMILES: C(C1[CH:4]=[CH:5][C:6]2[CH:12]=[CH:11][C:10]3[CH:13]=[C:14]([OH:17])[CH:15]=[CH:16][C:9]=3[S:8](=[O:18])[C:7]=2[CH:19]=1)#N.[OH-].[Na+].[C:22]([OH:25])(=[O:24])[CH3:23]>>[OH:17][C:14]1[CH:15]=[CH:16][C:9]2[S:8](=[O:18])[C:7]3[CH:19]=[C:23]([C:22]([OH:25])=[O:24])[CH:4]=[CH:5][C:6]=3[CH:12]=[CH:11][C:10]=2[CH:13]=1
Reactant: CC(=O)O
Reactant: N#Cc1ccc2c(c1)S(=O)c1ccc(O)cc1C=C2
Agent: [Na+]
Agent: [OH-]
Product: O=C(O)c1ccc2c(c1)S(=O)c1ccc(O)cc1C=C2

Procedure:
Suspend 100 mg. of the cyano compound of Step 2 in 5 ml. of acetic acid and 5 ml. of 20% aqueous sodium hydroxide. Reflux under nitrogen for 1 hour. Evaporate the alcohol and dilute the residue with water. Extract with ether and acidify the aqueous phase with 6N hydrochloric acid. Separate the solids by filtration. Dissolve the solids in ethanol and strip to dryness to obtain the title product (m.p., 288°-291° C. dec.).
Reaction SMILES: [F:1][C:2](I)([F:19])[C:3]([F:18])([F:17])[C:4]([F:16])([F:15])[C:5]([F:14])([F:13])[C:6]([F:12])([F:11])[C:7]([F:10])([F:9])[F:8].OCS([O-])=O.[Na+].[C:27]1([S:33]SC2C=CC=CC=2)[CH:32]=[CH:31][CH:30]=[CH:29][CH:28]=1>CN(C)C=O.O>[F:1][C:2]([S:33][C:27]1[CH:32]=[CH:31][CH:30]=[CH:29][CH:28]=1)([F:19])[C:3]([F:18])([F:17])[C:4]([F:16])([F:15])[C:5]([F:14])([F:13])[C:6]([F:12])([F:11])[C:7]([F:10])([F:9])[F:8]
Reactant: FC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)I
Reactant: c1ccc(SSc2ccccc2)cc1
Agent: O=S([O-])CO
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: FC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)Sc1ccccc1
Yield: 40 %

Procedure:
Perfluorohexyl iodide (4.5 g), sodium hydroxymethanesulphinate (4 g) and phenyl disulphide (2.2 g) in dimethylformamide (10 cc) and water (0.5 cc) are stirred for 12 hours. After the usual treatment, phenyl perfluorohexyl sulphide is obtained in 40% yield.
Reaction SMILES: [CH3:1][C:2]1[CH:14]=[CH:13][C:5]([NH:6][C:7]2[CH:12]=[CH:11][CH:10]=[CH:9][N:8]=2)=[C:4]([NH2:15])[CH:3]=1.[O:16]1[CH:20]=[CH:19][C:18](/[CH:21]=[CH:22]/[C:23](Cl)=O)=[CH:17]1.N1C=CC=CC=1N1C2C=CC=CC=2N=C1/C=C/C1C=CC=CC=1.[C:49]([OH:54])(=[O:53])[C:50]([OH:52])=[O:51]>C(OCC)(=O)C>[C:49]([OH:54])(=[O:53])[C:50]([OH:52])=[O:51].[O:16]1[CH:20]=[CH:19][C:18](/[CH:21]=[CH:22]/[C:23]2[N:6]([C:7]3[CH:12]=[CH:11][CH:10]=[CH:9][N:8]=3)[C:5]3[CH:13]=[CH:14][C:2]([CH3:1])=[CH:3][C:4]=3[N:15]=2)=[CH:17]1
Reactant: O=C(Cl)/C=C/c1ccoc1
Reactant: Cc1ccc(Nc2ccccn2)c(N)c1
Agent: C(=C/c1nc2ccccc2n1-c1ccccn1)\c1ccccc1
Agent: O=C(O)C(=O)O
Solvent: CCOC(C)=O
Product: Cc1ccc2c(c1)nc(/C=C/c1ccoc1)n2-c1ccccn1

Procedure:
Free base of the titled compound was prepared from 4-methyl-2-amino-N-(2-pyridyl)aniline and (E)-3-(3-furyl)acryloyl chloride according to the preparation of (E)-1-(2-pyridyl)-2-styryl-1H-benzimidazole (Example 1, method A). The free base and oxalic acid were dissolved into ethyl acetate. Concentration and recrystallization from ethyl acetate-hexane yielded the titled compound. MW: 391.38; mp: 197.0-198.0° C.; 1H-NMR (DMSO) δ: 8.78-8.74 (1H, m), 8.16 (1H, td, J=7.7, 2.2 Hz), 8.05 (1H, br.s), 7.77 (1H, d, J=15.8 Hz), 7.70-7.67 (2H, m), 7.65-7.59 (1H, m), 7.51 (1H, br.s), 7.32 (1H, d, J=8.4 Hz), 7.10-7.06 (1H, m), 6.89 (1H, d, J=15.8 Hz), 6.81 (1H, br.s), 2.44 (3H, s).
Reaction SMILES: [CH2:1]([C:5]1([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=2)[C:9]2[CH2:10][NH:11][CH2:12][CH2:13][C:8]=2[C:7](=[O:14])[O:6]1)[CH:2]([CH3:4])[CH3:3].CCN(C(C)C)C(C)C.[CH:30]1[C:39]2[C:34](=[CH:35][CH:36]=[CH:37][CH:38]=2)[CH:33]=[CH:32][C:31]=1[C:40](Cl)=[O:41]>C1COCC1>[CH:30]1[C:39]2[C:34](=[CH:35][CH:36]=[CH:37][CH:38]=2)[CH:33]=[CH:32][C:31]=1[C:40]([N:11]1[CH2:12][CH2:13][C:8]2[C:7](=[O:14])[O:6][C:5]([CH2:1][CH:2]([CH3:4])[CH3:3])([C:15]3[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=3)[C:9]=2[CH2:10]1)=[O:41]
Reactant: CC(C)CC1(c2ccccc2)OC(=O)C2=C1CNCC2
Reactant: O=C(Cl)c1ccc2ccccc2c1
Solvent: C1CCOC1
Solvent: CCN(C(C)C)C(C)C
Product: CC(C)CC1(c2ccccc2)OC(=O)C2=C1CN(C(=O)c1ccc3ccccc3c1)CC2
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 86.9 %

Procedure:
To a solution of 3-isobutyl-3-phenyl-4,5,6,7-tetrahydrofuro[3,4-c]pyridin-1(3H)-one (50 mg, 0.184 mmol) and N,N′-diisopropylethylamine (71 mg, 0.552 mmol) in THF (5 mL) at 0° C. was added 2-naphthoylchloride (35 mg, 0.184 mmol) and the reaction mixture was stirred at 0° C. for 30 min, then room temperature overnight. The crude mixture was concentrated to dryness and purified by column chromatography (4 g, SiO2, 0 to 30% ethyl acetate in hexanes) to provide 5-(2-naphthoyl)-3-isobutyl-3-phenyl-4,5,6,7-tetrahydrofuro[3,4-c]pyridin-1(3H)-one (68 mg, 87%) as a white solid: 1H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.77-1.08 (m, 6H), 1.63-1.78 (m, 1H), 1.79-1.95 (m, 1H), 2.28-2.59 (m, 3H), 3.28-3.60 (m, 1H), 3.73 (br. s., 1H), 4.09-4.27 (m, 1H), 4.85 (br. s., 1H), 7.29-7.51 (m, 6H), 7.52-7.62 (m, 2H), 7.77-7.98 (m, 4H); MS m/z 426 (M+H)+, 449 (M+23)+, 424 (M−H)−.
Reaction SMILES: [OH:1][C:2]1[CH:33]=[CH:32][C:5]([C:6]([N:8]([CH3:31])[C:9]2[CH:14]=[CH:13][C:12]([CH3:15])=[CH:11][C:10]=2[O:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][C:22]([N:24]2[CH2:29][CH2:28][N:27]([CH3:30])[CH2:26][CH2:25]2)=[O:23])=[O:7])=[CH:4][C:3]=1[O:34][CH3:35].[H-].[Na+].[N+:38]([C:41]1[CH:48]=[CH:47][CH:46]=[CH:45][C:42]=1[CH2:43]Br)([O-:40])=[O:39]>CN(C)C=O>[CH3:35][O:34][C:3]1[CH:4]=[C:5]([CH:32]=[CH:33][C:2]=1[O:1][CH2:43][C:42]1[CH:45]=[CH:46][CH:47]=[CH:48][C:41]=1[N+:38]([O-:40])=[O:39])[C:6]([N:8]([CH3:31])[C:9]1[CH:14]=[CH:13][C:12]([CH3:15])=[CH:11][C:10]=1[O:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][C:22]([N:24]1[CH2:29][CH2:28][N:27]([CH3:30])[CH2:26][CH2:25]1)=[O:23])=[O:7]
Reactant: O=[N+]([O-])c1ccccc1CBr
Reactant: COc1cc(C(=O)N(C)c2ccc(C)cc2OCCCCCC(=O)N2CCN(C)CC2)ccc1O
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: COc1cc(C(=O)N(C)c2ccc(C)cc2OCCCCCC(=O)N2CCN(C)CC2)ccc1OCc1ccccc1[N+](=O)[O-]
Temperature: 0 °C
Reaction time: 0.25 h
Yield: 51.3 %

Procedure:
A solution of 4-hydroxy-3-methoxy-N-methyl-N-[4-methyl-2-[5-(4-methylpiperazin-1-yl)carbonylpent-1-yloxy]phenyl]-benzamide (320 mg) in N,N-dimethylformamide (8 ml) was treated with sodium hydride (29.1 mg, 60% w/w in mineral oil) at 0° C. The reaction mixture was stirred at 0° C. for 15 minutes and then at ambient temperature for 10 minutes. o-Nitrobenzyl bromide (143 mg) was added, and the reaction mixture was stirred for 2.5 hours. The reaction was quenched with water and the mixture was diluted with ethyl acetate. The organic phase was washed with saturated aqueous sodium hydrogen carbonate, and brine. The organic solution was dried over magnesium sulfate, concentrated, and purified by silica gel column chromatography (SiO2 15 g, 3% methanol in dichloromethane) to give 3-methoxy-4-(2-nitrobenzyloxy)-N-methyl-N-[4-methyl-2-[5-(4-methylpiperazin-1-yl)carbonylpent-1-yloxy]phenyl]benzamide (210 mg).
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([N:8]2[CH:13]=[CH:12][N:11]=[C:10]([C:14]([OH:16])=O)[C:9]2=[O:17])=[CH:4][CH:3]=1.[CH3:18][O:19][C:20]1[CH:59]=[CH:58][C:23]([CH2:24][N:25]2[C:29]3=[N:30][CH:31]=[CH:32][C:33]([O:34][C:35]4[CH:40]=[CH:39][C:38]([NH2:41])=[CH:37][C:36]=4[F:42])=[C:28]3[C:27]([NH:43][C@H:44]3[CH2:49][CH2:48][N:47]([C:50]([O:52][C:53]([CH3:56])([CH3:55])[CH3:54])=[O:51])[CH2:46][C@@H:45]3[F:57])=[N:26]2)=[CH:22][CH:21]=1>>[CH3:18][O:19][C:20]1[CH:21]=[CH:22][C:23]([CH2:24][N:25]2[C:29]3=[N:30][CH:31]=[CH:32][C:33]([O:34][C:35]4[CH:40]=[CH:39][C:38]([NH:41][C:14]([C:10]5[C:9](=[O:17])[N:8]([C:5]6[CH:4]=[CH:3][C:2]([F:1])=[CH:7][CH:6]=6)[CH:13]=[CH:12][N:11]=5)=[O:16])=[CH:37][C:36]=4[F:42])=[C:28]3[C:27]([NH:43][C@H:44]3[CH2:49][CH2:48][N:47]([C:50]([O:52][C:53]([CH3:56])([CH3:54])[CH3:55])=[O:51])[CH2:46][C@@H:45]3[F:57])=[N:26]2)=[CH:58][CH:59]=1
Reactant: O=C(O)c1nccn(-c2ccc(F)cc2)c1=O
Reactant: COc1ccc(Cn2nc(N[C@H]3CCN(C(=O)OC(C)(C)C)C[C@@H]3F)c3c(Oc4ccc(N)cc4F)ccnc32)cc1
Product: COc1ccc(Cn2nc(N[C@H]3CCN(C(=O)OC(C)(C)C)C[C@@H]3F)c3c(Oc4ccc(NC(=O)c5nccn(-c6ccc(F)cc6)c5=O)cc4F)ccnc32)cc1

Procedure:
Prepared from 4-(4-fluorophenyl)-3-oxo-3,4-dihydropyrazine-2-carboxylic acid (60 mg, 0.26 mmol, prepared according to the procedure for Example 125, Step E) and ±(3S*,4S*)-tert-butyl 4-(1-(4-methoxybenzyl)-4-(4-amino-2-fluorophenoxy)-1H-pyrazolo[3,4-b]pyridin-3-ylamino)-3-fluoropiperidine-1-carboxylate (50 mg, 0.086 mmol, obtained from Example 146, Step A) according to the procedure described for Example 145, Step B. Yield: 42 mg (58%).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([CH:17]=[CH:18][CH:19]=1)[CH2:5][NH:6][C:7]1[CH:12]=[C:11](F)[CH:10]=[CH:9][C:8]=1[N+:14]([O-:16])=[O:15].[N:20]1([C:26]([O:28][C:29]([CH3:32])([CH3:31])[CH3:30])=[O:27])[CH2:25][CH2:24][NH:23][CH2:22][CH2:21]1.C(N(CC)C(C)C)(C)C>C(#N)C>[Cl:1][C:2]1[CH:3]=[C:4]([CH:17]=[CH:18][CH:19]=1)[CH2:5][NH:6][C:7]1[CH:12]=[C:11]([N:23]2[CH2:22][CH2:21][N:20]([C:26]([O:28][C:29]([CH3:32])([CH3:31])[CH3:30])=[O:27])[CH2:25][CH2:24]2)[CH:10]=[CH:9][C:8]=1[N+:14]([O-:16])=[O:15]
Reactant: O=[N+]([O-])c1ccc(F)cc1NCc1cccc(Cl)c1
Reactant: CC(C)(C)OC(=O)N1CCNCC1
Solvent: CCN(C(C)C)C(C)C
Solvent: CC#N
Product: CC(C)(C)OC(=O)N1CCN(c2ccc([N+](=O)[O-])c(NCc3cccc(Cl)c3)c2)CC1
Yield: 32.1 %

Procedure:
N-(3-Chlorobenzyl)-5-fluoro-2-nitrobenzenamine (624 mg, 2.2 mmol), t-butyl piperazine-1-carboxylate (414 mg, 2.2 mmol), N,N-diisopropylethylamine (287 mg, 2.2 mmol) were stirred at 80° C. in dry acetonitrile (10 mL) for 16 h. The solvent was evaporated and the residue was dissolved in dichloromethane and washed with water. The dichloromethane was evaporated and the crude compound was purified by silica chromatography using 25% ethyl acetate in hexanes to afford the title compound (316 mg, 32% yield). 1H NMR (400 MHz, CDCl3): δ 8.77 (s, 1H), 8.05 (d, 1H), 7.32-7.21 (m, 4H), 6.18 (d, 1H), 5.72 (s, 1H), 4.46 (d, 2H), 3.49 (m, 4H), 3.27 (m, 4H), 1.45 (s, 9H); MS (ESI) m/z: Calculated for C22H27ClN4O4: 446.17; Observed: 469.4 (M++Na).