Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [F:1][C:2]1[CH:7]=[C:6]([CH:8]([CH3:12])[C:9]([OH:11])=[O:10])[CH:5]=[CH:4][C:3]=1[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1.[CH2:19](O)[CH3:20]>>[CH2:19]([O:10][C:9](=[O:11])[CH:8]([C:6]1[CH:5]=[CH:4][C:3]([C:13]2[CH:14]=[CH:15][CH:16]=[CH:17][CH:18]=2)=[C:2]([F:1])[CH:7]=1)[CH3:12])[CH3:20]
Reactant: CC(C(=O)O)c1ccc(-c2ccccc2)c(F)c1
Reactant: CCO
Product: CCOC(=O)C(C)c1ccc(-c2ccccc2)c(F)c1
Temperature: 50 °C
Reaction time: 5 h

Procedure:
To 2-(2-fluoro-4-biphenylyl)-propionic acid (30.0 g, 0.123 mol) in ethanol (300 ml) was added conc. sulfonic acid (3.0 g). After the addition, the mixture was stirring at 50° C. for 5 h, then concentrated and extracted with benzene. The benzene extracts were washed with aqueous sodium hydrogen carbonate solution then with water, and dried over. The extracts were evaporated under reduced pressure to afford ethyl-2-(2-fluoro-4-biphenylyl)propionate (33.6 g, 0.123 mol) as oily residue.
Reaction SMILES: [CH3:1][C@H:2]1[CH2:7][CH2:6][CH2:5][CH2:4][N:3]1[C:8]1[C:9](OS(C(F)(F)F)(=O)=O)=[N:10][C:11]2[C:16]([N:17]=1)=[CH:15][C:14]([C:18]([O:20][CH3:21])=[O:19])=[CH:13][CH:12]=2.[F:30][C:31]1[CH:32]=[CH:33][C:34]2[O:38][C:37](B(O)O)=[CH:36][C:35]=2[CH:42]=1.[O-]P([O-])([O-])=O.[K+].[K+].[K+]>O1CCOCC1.O.C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1>[F:30][C:31]1[CH:32]=[CH:33][C:34]2[O:38][C:37]([C:9]3[C:8]([N:3]4[CH2:4][CH2:5][CH2:6][CH2:7][C@@H:2]4[CH3:1])=[N:17][C:16]4[C:11](=[CH:12][CH:13]=[C:14]([C:18]([O:20][CH3:21])=[O:19])[CH:15]=4)[N:10]=3)=[CH:36][C:35]=2[CH:42]=1
Reactant: OB(O)c1cc2cc(F)ccc2o1
Reactant: COC(=O)c1ccc2nc(OS(=O)(=O)C(F)(F)F)c(N3CCCC[C@@H]3C)nc2c1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=P([O-])([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: C1COCCO1
Product: COC(=O)c1ccc2nc(-c3cc4cc(F)ccc4o3)c(N3CCCC[C@@H]3C)nc2c1
Temperature: 90 °C
Reaction time: 1 h

Procedure:
To a solution of (S)-methyl 3-(2-methylpiperidin-1-yl)-2-(trifluoromethylsulfonyloxy)quinoxaline-6-carboxylate (240 mg, crude) in dioxane (5 mL) was added 5-fluorobenzofuran-2-ylboronic acid (337 mg, 1.87 mmol), K3PO4 (397 mg, 1.87 mmol), Pd(PPh3)4 (36 mg, 0.03 mmol) and water (5 drops). The resulting solution was stirred for 1 hour at 90° C. and then concentrated under vacuum to give a residue, which was purified via silica gel column chromatography (2% ethyl acetate in petroleum ether) to afford (S)-methyl 2-(5-fluorobenzofuran-2-yl)-3-(2-methylpiperidin-1-yl)quinoxaline-6-carboxylate as a yellow solid (135.0 mg, 59% 2 steps).
Reaction SMILES: [F:1][C:2]([F:43])([F:42])[C:3]1[CH:4]=[C:5]([CH:39]=[CH:40][CH:41]=1)[CH2:6][NH:7][C:8](=[O:38])[C:9]1[CH:14]=[CH:13][N:12]=[C:11]([C:15]2[CH:20]=[C:19]([N:21]3[CH2:26][CH2:25][CH2:24][CH2:23][CH2:22]3)[CH:18]=[CH:17][C:16]=2[NH:27][C:28](=[O:37])[C:29]2[CH:34]=[CH:33][CH:32]=[C:31]([CH2:35]Br)[CH:30]=2)[CH:10]=1.[CH3:44][N:45]1[CH2:51][CH2:50][CH2:49][NH:48][CH2:47][CH2:46]1.C(=O)([O-])[O-].[K+].[K+]>CN(C)C=O.O>[CH3:44][N:45]1[CH2:51][CH2:50][CH2:49][N:48]([CH2:35][C:31]2[CH:30]=[C:29]([CH:34]=[CH:33][CH:32]=2)[C:28]([NH:27][C:16]2[CH:17]=[CH:18][C:19]([N:21]3[CH2:26][CH2:25][CH2:24][CH2:23][CH2:22]3)=[CH:20][C:15]=2[C:11]2[CH:10]=[C:9]([CH:14]=[CH:13][N:12]=2)[C:8]([NH:7][CH2:6][C:5]2[CH:39]=[CH:40][CH:41]=[C:3]([C:2]([F:43])([F:42])[F:1])[CH:4]=2)=[O:38])=[O:37])[CH2:47][CH2:46]1
Reactant: CN1CCCNCC1
Reactant: O=C(NCc1cccc(C(F)(F)F)c1)c1ccnc(-c2cc(N3CCCCC3)ccc2NC(=O)c2cccc(CBr)c2)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CN(C)C=O
Product: CN1CCCN(Cc2cccc(C(=O)Nc3ccc(N4CCCCC4)cc3-c3cc(C(=O)NCc4cccc(C(F)(F)F)c4)ccn3)c2)CC1
Temperature: 70 °C
Reaction time: 3 h
Yield: 38.9 %

Procedure:
Into a 50-mL round-bottom flask, was placed a solution of N-(3-(trifluoromethyl)benzyl)-2-(2-(3-(bromomethyl)benzamido)-5-(piperidin-1-yl)phenyl)isonicotinamide (100 mg, 0.15 mmol, 1.00 equiv) in N,N-dimethylformamide (2 mL), 1-methyl-1,4-diazepane (65.4 mg, 0.57 mmol, 3.74 equiv), KI (12.7 mg, 0.08 mmol, 0.50 equiv), and potassium carbonate (42.4 mg, 0.31 mmol, 2.00 equiv). The resulting solution was stirred for 3 h at 70° C. in an oil bath. The reaction progress was monitored by LCMS. The resulting solution was diluted with 20 mL of water. The resulting solution was extracted with 3×20 mL of ethyl acetate and the organic layers combined. The resulting mixture was washed with 3×20 mL of brine, dried over anhydrous sodium sulfate, and concentrated under vacuum. The crude product was purified by reverse phase HPLC eluting with a water/CH3CN gradient containing 0.05% TFA. The product was obtained as 40 mg (23%) of a yellow solid. 1H-NMR (400 MHz, CD3OD, ppm): δ 8.95-8.93 (d, J=4.2 Hz, 1H), 8.75-8.73 (d, J=6.6 Hz, 1H), 8.46 (s, 1H), 8.18-8.17 (d, J=4.2 Hz, 1H), 8.09 (s, 1H), 8.02-8.00 (d, J=8 Hz, 1H), 7.90-7.88 (m, 1H), 7.75-7.55 (m, 1H), 4.72 (s, 2H), 4.19 (s, 2H), 3.70-3.67 (t, J=5.6 Hz, 4H), 3.55-3.49 (m, 4H), 3.18-3.16 (t, J=5.6 Hz, 2H), 2.95 (s, 3H), 2.22-2.18 (m, 2H), 2.07-2.05 (t, J=5.2 Hz, 4H), 1.84-1.83 (d, J=5.2 Hz, 1H). MS (ES, m/z): 685 [M+H]+.
Reaction SMILES: [F:1][C:2]1[C:10]([OH:11])=[C:9]([F:12])[C:8]([F:13])=[C:4]([C:5]([OH:7])=O)[C:3]=1[C:14]([OH:16])=O.FC1C(F)=C(F)C(F)=C2C(=O)OC(=O)C=12.[F:32][C:33]1[C:38]([CH2:39]C(O)=O)=[C:37]([F:43])[C:36]([F:44])=[C:35]([F:45])[C:34]=1[F:46].C(N(CC)CC)C>C(N(CC)CC)C.C(OC(=O)C)(=O)C>[OH:11][C:10]1[C:2]([F:1])=[C:3]2[C:4](=[C:8]([F:13])[C:9]=1[F:12])[C:5](=[O:7])[O:16][C:14]2=[CH:39][C:38]1[C:37]([F:43])=[C:36]([F:44])[C:35]([F:45])=[C:34]([F:46])[C:33]=1[F:32]
Reactant: O=C(O)c1c(F)c(O)c(F)c(F)c1C(=O)O
Reactant: O=C(O)Cc1c(F)c(F)c(F)c(F)c1F
Agent: O=C1OC(=O)c2c(F)c(F)c(F)c(F)c21
Solvent: CCN(CC)CC
Solvent: CC(=O)OC(C)=O
Product: O=C1OC(=Cc2c(F)c(F)c(F)c(F)c2F)c2c(F)c(O)c(F)c(F)c21

Procedure:
A process for preparing 3,5,6-trifluoro-4-hydroxyphthalic acid used here as the starting material is described in Osadchii, S. A., Bakahash, V. A.; Zh. Org. Khim., Vol. 6 (8), p. 1636 (1970) (Chemical Abstract, 73, 109544p). According to this litrature, when tetrafluorophthalic anhydride and pentafluorophenylacetic acid are reacted in triethylamine-acetic anhydride, a triethylamine salt of 5-hydroxy-4,6,7-trifluoro-3-(pentafluorobenzylidene)phthalide is obtained. And, by treatment of the by-products of this reaction, 3,5,6-trifluoro-4-hydroxyphthalic acid is obtained.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([C:9]2[N:10]=[C:11]([CH:14]3[O:19][CH2:18][CH2:17][NH:16][CH2:15]3)[NH:12][CH:13]=2)=[CH:5][CH:4]=1.[Cl:20][C:21]1[CH:26]=[C:25](Cl)[N:24]=[C:23]([NH2:28])[N:22]=1.CCN(C(C)C)C(C)C>C(O)C>[Cl:20][C:21]1[CH:26]=[C:25]([N:16]2[CH2:17][CH2:18][O:19][CH:14]([C:11]3[NH:12][CH:13]=[C:9]([C:6]4[CH:7]=[CH:8][C:3]([O:2][CH3:1])=[CH:4][CH:5]=4)[N:10]=3)[CH2:15]2)[N:24]=[C:23]([NH2:28])[N:22]=1
Reactant: COc1ccc(-c2c[nH]c(C3CNCCO3)n2)cc1
Reactant: Nc1nc(Cl)cc(Cl)n1
Solvent: CCN(C(C)C)C(C)C
Solvent: CCO
Product: COc1ccc(-c2c[nH]c(C3CN(c4cc(Cl)nc(N)n4)CCO3)n2)cc1
Yield: 72.5 %

Procedure:
A solution of 2-{4-[4-(methyloxy)phenyl]-1H-imidazol-2-yl}morpholine (1.9 g, 6.42 mmol), 4,6-dichloro-2-pyrimidinamine (1.053 g, 6.42 mmol) and Hunig's base (2.8 mL, 16.1 mmol) in ethanol (80 mL) was heated overnight at 85° C. The reaction mixture was concentrated, and the resulting residue was purified by silica gel chromatography using as eluent 40% EtOAc in CH2Cl2 to afford the title compound (1.8 g) as a white solid. LC-MS (ES) m/z=387 [M+H]+.
Reaction SMILES: [F:1][C:2]1[CH:9]=[C:8]([OH:10])[CH:7]=[C:6]([F:11])[C:3]=1[CH2:4][OH:5].Cl[CH2:13][C:14]1[N:18]=[C:17]([C:19]2[S:20][CH:21]=[CH:22][CH:23]=2)[O:16][N:15]=1.Cl[C:25]([N:27]1[C@H:32]([CH3:33])[CH2:31][N:30](C(OC(C)(C)C)=O)[CH2:29][C@@H:28]1[CH3:41])=[O:26]>>[F:1][C:2]1[CH:9]=[C:8]([O:10][CH2:13][C:14]2[N:18]=[C:17]([C:19]3[S:20][CH:21]=[CH:22][CH:23]=3)[O:16][N:15]=2)[CH:7]=[C:6]([F:11])[C:3]=1[CH2:4][O:5][C:25]([N:27]1[C@H:32]([CH3:33])[CH2:31][NH:30][CH2:29][C@@H:28]1[CH3:41])=[O:26]
Reactant: ClCc1noc(-c2cccs2)n1
Reactant: OCc1c(F)cc(O)cc1F
Reactant: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)Cl
Product: C[C@@H]1CNC[C@H](C)N1C(=O)OCc1c(F)cc(OCc2noc(-c3cccs3)n2)cc1F

Procedure:
cis-2,6-Dimethyl-piperazine-1-carboxylic acid 2,6-difluoro-4-(5-thiophen-2-yl-[1,2,4]oxadiazol-3-ylmethoxy)-benzyl ester was prepared from 2,6-difluoro-4-hydroxybenzyl alcohol, 3-chloromethyl-5-thiophen-2-yl-[1,2,4]oxadiazole and cis-1-chlorocarbonyl-2,6-dimethyl-4-tert-butoxycarbonylpiperazine according to the methods described for Example 54 and 121 to give the product as a yellow oil: δH(400 MHz; d6-DMSO) 1.14 (6H, d, J 6.5 Hz), 2.60 (2H, dd, J 12, 5 Hz), 2.66 (2H, d, J 12 Hz), 3.77–3.87 (2H, m), 5.05 (2H, s), 5.42 (2H, s), 6.93–7.01 (2H, m), 7.36 (1H, dd, J 5.0, 4 Hz), 8.06 (1H, dd, J 4, 1.0 Hz) and 8.12 (1H, dd, J 5.0, 1.0 Hz); HPLC (XTERRA, 50–80%, 235 nm) 99.4% (5.04 min).
Reaction SMILES: [F:1][C:2]1[CH:18]=[CH:17][C:5]([CH2:6][O:7][C:8]2[CH:13]=[CH:12][N:11]=[CH:10][C:9]=2[N+:14]([O-])=O)=[CH:4][CH:3]=1.[CH3:19][C:20]([Mg]Br)=[CH:21][CH3:22].[Cl-].[NH4+]>O1CCCC1>[F:1][C:2]1[CH:18]=[CH:17][C:5]([CH2:6][O:7][C:8]2[CH:13]=[CH:12][N:11]=[C:10]3[C:20]([CH3:19])=[C:21]([CH3:22])[NH:14][C:9]=23)=[CH:4][CH:3]=1
Reactant: CC=C(C)[Mg]Br
Reactant: O=[N+]([O-])c1cnccc1OCc1ccc(F)cc1
Agent: [Cl-]
Agent: [NH4+]
Solvent: C1CCOC1
Product: Cc1[nH]c2c(OCc3ccc(F)cc3)ccnc2c1C
Temperature: -20 °C
Reaction time: 5 h
Yield: 46.9 %

Procedure:
4-(4-Fluorobenzyloxy)-3-nitropyridine (4.8 g, 19.34 mmol) prepared in Preparation 2 was dissolved in anhydrous tetrahydrofuran (200 ml) under a nitrogen atmosphere. 1-Methyl-1-propenyl magnesium bromide (0.5M in tetrahydrofuran solution, 116 ml, 58.02 mmol) was added at −78° C. to the solution, which was then stirred for 5 hours at −20° C. 20% Ammonium chloride solution (20 ml) was added to the reaction mixture, which was then extracted with ethyl acetate (200 ml) twice. The separated organic layer was dried on anhydrous magnesium sulfate and then concentrated under reduced pressure. The resulting residue was purified with silica gel column chromatography (ethyl acetate/methylene chloride/methanol=10/10/1, (v/v/v)) to give the titled compound as a pale yellow solid (2.45 g, 28.3%).
Reaction SMILES: Cl[CH2:2][CH2:3][CH2:4][S:5][C:6]1[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1.[NH:12]1[CH2:17][CH2:16][CH:15]([C:18]2[CH:19]=[C:20]([NH:24][C:25](=[O:28])[CH2:26][CH3:27])[CH:21]=[CH:22][CH:23]=2)[CH2:14][CH2:13]1>>[C:6]1([S:5][CH2:4][CH2:3][CH2:2][N:12]2[CH2:17][CH2:16][CH:15]([C:18]3[CH:19]=[C:20]([NH:24][C:25](=[O:28])[CH2:26][CH3:27])[CH:21]=[CH:22][CH:23]=3)[CH2:14][CH2:13]2)[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1
Reactant: ClCCCSc1ccccc1
Reactant: CCC(=O)Nc1cccc(C2CCNCC2)c1
Product: CCC(=O)Nc1cccc(C2CCN(CCCSc3ccccc3)CC2)c1

Procedure:
Prepared by Procedure G and Scheme B1 using [(3-chloropropyl)sulfanyl]benzene and N-[3-(4-piperidinyl)phenyl]propanamide: ESMS m/e: 382.9 (M+H)+.
Reaction SMILES: [CH2:1]([S:3]([CH2:6][CH2:7][CH2:8][C:9]12[CH2:16][CH2:15][C:12]([C:17]([OH:19])=O)([CH2:13][CH2:14]1)[CH2:11][CH2:10]2)(=[O:5])=[O:4])[CH3:2].C(Cl)(=O)C(Cl)=O.CN(C=O)C.[CH:31]12[CH2:40][CH:35]3[CH2:36][CH:37]([CH2:39][CH:33]([CH2:34]3)[CH:32]1[NH2:41])[CH2:38]2>C(Cl)Cl.C(N(CC)CC)C>[CH:31]12[CH2:40][CH:35]3[CH2:36][CH:37]([CH2:39][CH:33]([CH2:34]3)[CH:32]1[NH:41][C:17]([C:12]13[CH2:11][CH2:10][C:9]([CH2:8][CH2:7][CH2:6][S:3]([CH2:1][CH3:2])(=[O:4])=[O:5])([CH2:14][CH2:13]1)[CH2:16][CH2:15]3)=[O:19])[CH2:38]2
Reactant: CCS(=O)(=O)CCCC12CCC(C(=O)O)(CC1)CC2
Reactant: NC1C2CC3CC(C2)CC1C3
Agent: O=C(Cl)C(=O)Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Solvent: CN(C)C=O
Product: CCS(=O)(=O)CCCC12CCC(C(=O)NC3C4CC5CC(C4)CC3C5)(CC1)CC2
Temperature: 25 °C
Reaction time: 1.5 h

Procedure:
Carboxylic acid 2-8 (0.100 g, 0.348 mmol) was dissolved in 2 mL of anhydrous methylene chloride under nitrogen atmosphere, treated with oxalyl chloride (2 M in methylene chloride, 2 eq., 0.348 mL, 0.696 mmol) and subsequently with 0.050 ml of DMF. The reaction was stirred at room temperature under nitrogen atmosphere for 90 min, then evaporated and placed under vacuum for 20 min. The acid chloride was dissolved in anhydrous methylene chloride (2 mL), and then treated with triethylamine (0.100 ml) and 2-adamantylamine (2 eq., 105 mg). The reaction stirred at ambient temperature for 1 hr. The mixture was diluted with 20 mL of methylene chloride and washed with 1N aqueous HCl, saturated aqueous sodium bicarbonate, and brine. The organic layer was dried over anhydrous sodium sulfate and evaporated. The product was purified using a Gilson HPLC with UV detection equipped with a C18 reverse phase column running a gradient of water/acetonitrile (0.1% TFA). The fractions containing product were concentrated to remove some of the acetonitrile and the lyophilized to provide pure product N-2-adamantyl-4-[3-(ethylsulfonyl)propyl]bicyclo[2.2.2]octane-1-carboxamide (2-9) as a white fluffy amorphous solid.
Reaction SMILES: C1C(C(O)=[O:8])=CC(C2C3C=CC(O)=CC=3OC3C=2C=CC(C=3)=O)=C(C(O)=O)C=1.ON1C(=O)CCC1=O.[CH:37]1([N:43]=[C:44]=[N:45][CH:46]2[CH2:51][CH2:50][CH2:49][CH2:48][CH2:47]2)[CH2:42][CH2:41][CH2:40][CH2:39][CH2:38]1>CN(C=O)C>[C:44]([NH:43][CH:37]1[CH2:38][CH2:39][CH2:40][CH2:41][CH2:42]1)([NH:45][CH:46]1[CH2:51][CH2:50][CH2:49][CH2:48][CH2:47]1)=[O:8]
Reactant: O=C(O)c1ccc(C(=O)O)c(-c2c3ccc(=O)cc-3oc3cc(O)ccc23)c1
Reactant: C(=NC1CCCCC1)=NC1CCCCC1
Agent: O=C1CCC(=O)N1O
Solvent: CN(C)C=O
Product: O=C(NC1CCCCC1)NC1CCCCC1
Reaction time: 0.17 h

Procedure:
To a stirred solution of 5- or 6-carboxyfluorescein (0.5 mmol) in dry DMF (5 mL) were added N-hydroxysuccinimide (1.1 equiv.) and 1,3-dicylcohexylcarbodiimide (1.1 equiv.). After about 10 minutes, a white solid (dicyclohexylurea) started forming. The reaction mixture was stirred under nitrogen at room temperature overnight. TLC (9:1 CH2Cl2—MeOH) indicated complete disappearance of the starting material.
Reaction SMILES: [CH2:1]([N:3]1[C:9](=[O:10])[C:8]([CH3:12])([CH3:11])[C:7](=[O:13])[N:6]([CH3:14])[C:5]2[CH:15]=[C:16]([CH:19]=[O:20])[CH:17]=[CH:18][C:4]1=2)[CH3:2].CC(=CC)C.P([O-])(O)(O)=[O:27].[Na+].Cl([O-])=O.[Na+]>O.C(O)(C)(C)C>[CH2:1]([N:3]1[C:9](=[O:10])[C:8]([CH3:12])([CH3:11])[C:7](=[O:13])[N:6]([CH3:14])[C:5]2[CH:15]=[C:16]([C:19]([OH:27])=[O:20])[CH:17]=[CH:18][C:4]1=2)[CH3:2]
Reactant: CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(C=O)ccc21
Reactant: O=P([O-])(O)O
Agent: CC=C(C)C
Agent: [Na+]
Agent: [O-][Cl+][O-]
Solvent: O
Solvent: CC(C)(C)O
Product: CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(C(=O)O)ccc21
Temperature: 25 °C
Reaction time: 8 h
Yield: 44 %

Procedure:
To a t-butanol (20 ml) and H2O (5 ml) solution of 1-ethyl-3,3,5-trimethyl-2,4-dioxo-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepine-7-carbaldehyde (2.25 g) and 2-methyl-2-butene(3.25 ml) were added sodium dihydrogenphosphate (0.92 g) and sodium chlorite (2.081 g), and the mixture was stirred at room temperature overnight. Water was added to the reaction mixture, followed by extraction using ethyl acetate. The organic layer was dried with sodium sulfate, and was condensed under reduced pressure to give the title compound (0.98 g) as a white powder.
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][C@@H:9]([CH2:14][C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=1)[C@@H:10]([OH:13])[CH:11]=[CH2:12])=[O:7])([CH3:4])([CH3:3])[CH3:2].N1C=CN=C1.Cl[Si:27]([CH:34]([CH3:36])[CH3:35])([CH:31]([CH3:33])[CH3:32])[CH:28]([CH3:30])[CH3:29].O>CN(C=O)C>[C:1]([O:5][C:6]([NH:8][C@@H:9]([CH2:14][C:15]1[CH:16]=[CH:17][CH:18]=[CH:19][CH:20]=1)[C@@H:10]([O:13][Si:27]([CH:34]([CH3:36])[CH3:35])([CH:31]([CH3:33])[CH3:32])[CH:28]([CH3:30])[CH3:29])[CH:11]=[CH2:12])=[O:7])([CH3:2])([CH3:3])[CH3:4]
Reactant: C=C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C
Reactant: CC(C)[Si](Cl)(C(C)C)C(C)C
Agent: c1c[nH]cn1
Solvent: CN(C)C=O
Solvent: O
Product: C=C[C@H](O[Si](C(C)C)(C(C)C)C(C)C)[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C
Yield: 82 %

Procedure:
A solution of (3S,4S)-N-[(tertbutyloxy)carbonyl]-4-amino-3-hydroxy-5-phenyl pentene [prepared by the method of Hanson et al, J. Org. Chem., 50, 5399 (1985)] (10.0 g, 64.5 mmol), imidazole (9.14g, 13 mmol), and chlorotriisopropylsilane (12.44 g, 43.3 mmol) in anhydrous DMF (40 mL) was stirred for 5 days at room temperature under an N2 atmosphere. The solution was poured into H2O (500 mL) and extracted with Et2O (2×25 mL). The combined organic layers were washed with H2O (250 mL), a 0.5M citric acid solution (2×120 mL), a 5% KHCO3 solution (2×100 mL), and brine (2×100 mL). After the organic layer was dried over MgSO4, the filtrate was concentrated and purified by medium pressure column chromatography (silica gel, 10% ethyl acetate in hexane, Rf 0.23) to give 12.9 g (82 % yield) of the title compound as a clear, colorless oil. 1H and 13C NMR spectral data were consistent with the proposed structure.
Reaction SMILES: [NH2:1][C:2]1[S:3][C:4]([C:13]2[CH:18]=[CH:17][N:16]=[C:15]([NH:19][C:20]3[CH:25]=[CH:24][CH:23]=[C:22](I)[CH:21]=3)[N:14]=2)=[C:5]([C:7]2[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=2)[N:6]=1.[CH3:27][O:28][C:29]1[CH:30]=[C:31](B(O)O)[CH:32]=[CH:33][C:34]=1[O:35][CH3:36]>C(COC)OC.C(=O)([O-])[O-].[K+].[K+]>[NH2:1][C:2]1[S:3][C:4]([C:13]2[CH:18]=[CH:17][N:16]=[C:15]([NH:19][C:20]3[CH:21]=[C:22]([C:32]4[CH:31]=[CH:30][C:29]([O:28][CH3:27])=[C:34]([O:35][CH3:36])[CH:33]=4)[CH:23]=[CH:24][CH:25]=3)[N:14]=2)=[C:5]([C:7]2[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=2)[N:6]=1
Reactant: COc1ccc(B(O)O)cc1OC
Reactant: Nc1nc(-c2ccccc2)c(-c2ccnc(Nc3cccc(I)c3)n2)s1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: COCCOC
Product: COc1ccc(-c2cccc(Nc3nccc(-c4sc(N)nc4-c4ccccc4)n3)c2)cc1OC

Procedure:
A solution of N-[4-(2-amino-4-phenyl-thiazol-5-yl)-pyrimidin-2-yl]-N-(3-iodo-phenyl)-amine (300 mg, 0.64 mmol) and 3,4-dimethoxyphenylboronic acid (122 mg, 0.66 mmol) in dimethoxyethane (8 ml) and aqueous potassium carbonate (13 ml) are stirred in the presence of tetrakis triphenylphosphine palladium (15 mg) under a nitrogen atmosphere at reflux for 1 hour. After an aqueous work-up the residue is purified by chromatography (eluent: 2:1 mixture of ethyl acetate/hexane) to give the N-[4-(2-amino-4-phenyl-thiazol-5-yl)-pyrimidin-2-yl]-N-(3′,4′-dimethoxy-biphenyl-3-yl)-amine, m.p. 236–237° C.
Reaction SMILES: [NH2:1][C@H:2]1[CH2:7][CH2:6][C@H:5]([NH2:8])[CH2:4][CH2:3]1.[Cl:9][C:10]1[N:18]=[C:17]2[C:13]([N:14]=[CH:15][N:16]2[CH:19]2[CH2:23][CH2:22][CH2:21][CH2:20]2)=[C:12]([NH:24][C:25]2[CH:30]=[CH:29][C:28]([S:31]([NH2:34])(=[O:33])=[O:32])=[CH:27][CH:26]=2)[N:11]=1>>[ClH:9].[ClH:9].[NH2:1][C@H:2]1[CH2:7][CH2:6][C@H:5]([NH:8][C:10]2[N:18]=[C:17]3[C:13]([N:14]=[CH:15][N:16]3[CH:19]3[CH2:20][CH2:21][CH2:22][CH2:23]3)=[C:12]([NH:24][C:25]3[CH:30]=[CH:29][C:28]([S:31]([NH2:34])(=[O:33])=[O:32])=[CH:27][CH:26]=3)[N:11]=2)[CH2:4][CH2:3]1
Reactant: NS(=O)(=O)c1ccc(Nc2nc(Cl)nc3c2ncn3C2CCCC2)cc1
Reactant: N[C@H]1CC[C@H](N)CC1
Product: Cl
Product: NS(=O)(=O)c1ccc(Nc2nc(N[C@H]3CC[C@H](N)CC3)nc3c2ncn3C2CCCC2)cc1
Reaction time: 3 h

Procedure:
400 mg of trans-1,4-diaminocyclohexane is taken to approximately 150° C. then 275 mg of the product obtained in Stage 1 above is added, the reaction medium is left under agitation for 3 hours then left to return to ambient temperature, followed by evaporating the solvents, and chromatography on silica (eluent: MeOH/NH4OH 98/2). The residue is taken up in an ethanolic solution of hydrochloric acid, followed by evaporating the solvents, impasting in ether, separating, drying under reduced pressure at ambient temperature and 205 mg of expected product is recovered.
Reaction SMILES: [NH2:1][CH2:2][CH2:3][NH:4][C:5]([C:7]1[CH:12]=[C:11]([O:13][C:14]2[CH:33]=[CH:32][C:17]3[N:18]([CH3:31])[C:19]([NH:21][C:22]4[CH:27]=[CH:26][CH:25]=[C:24]([CH:28]([CH3:30])[CH3:29])[CH:23]=4)=[N:20][C:16]=3[CH:15]=2)[CH:10]=[CH:9][N:8]=1)=[O:6].C([O-])([O-])=O.[K+].[K+].C(#N)C.[C:43]1([CH2:49][S:50](Cl)(=[O:52])=[O:51])[CH:48]=[CH:47][CH:46]=[CH:45][CH:44]=1>O>[C:43]1([CH2:49][S:50]([NH:1][CH2:2][CH2:3][NH:4][C:5]([C:7]2[CH:12]=[C:11]([O:13][C:14]3[CH:33]=[CH:32][C:17]4[N:18]([CH3:31])[C:19]([NH:21][C:22]5[CH:27]=[CH:26][CH:25]=[C:24]([CH:28]([CH3:30])[CH3:29])[CH:23]=5)=[N:20][C:16]=4[CH:15]=3)[CH:10]=[CH:9][N:8]=2)=[O:6])(=[O:52])=[O:51])[CH:48]=[CH:47][CH:46]=[CH:45][CH:44]=1
Reactant: O=S(=O)(Cl)Cc1ccccc1
Reactant: CC(C)c1cccc(Nc2nc3cc(Oc4ccnc(C(=O)NCCN)c4)ccc3n2C)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CC#N
Product: CC(C)c1cccc(Nc2nc3cc(Oc4ccnc(C(=O)NCCNS(=O)(=O)Cc5ccccc5)c4)ccc3n2C)c1
Temperature: 25 °C
Reaction time: 1 h

Procedure:
To a mixture containing 4-[2-(3-Isopropyl-phenylamino)-1-methyl-1H-benzo-imidazol-5-yloxy]-pyridine-2-carboxylic acid (2-amino-ethyl)-amide (1 eq) (prepared using previously described example 3), K2CO3 (5 eq), (0.2 M in a 5:1 mixture of acetonitrile and water) were added α-toluenesulfonyl chloride (1 eq) via syringe. The resulting heterogeneous mixture was allowed to stir for 1 hour at room temperature. The mixture was then diluted with water and extracted with dichloromethane. The organics were washed with water and a saturated solution of sodium chloride, dried with sodium sulfate and concentrated in vacuo to viscous oil. Purification by chromatography yielded 4-[2-(3-Isopropyl-phenylamino)-1-methyl-1H-benzoimidazol-5-yloxy]-pyridine-2-carboxylic acid (2-phenylmethanesulfonylamino-ethyl)-amide. MS: MH+599
Reaction SMILES: [Cl:1][C:2]1[CH:6]=[C:5]([C:7]2[N:8]([CH3:12])[N:9]=[CH:10][N:11]=2)[S:4][C:3]=1[C:13]1[N:17]2[N:18]=[C:19]([CH3:27])[CH:20]=[C:21]([CH:22]([CH2:25][CH3:26])[CH2:23][CH3:24])[C:16]2=[N:15][C:14]=1[CH3:28].C1COCC1.[Li]C(C)(C)C.[F:39]NS(C1C=CC=CC=1)(=O)=O>CCOC(C)=O>[Cl:1][C:2]1[CH:6]=[C:5]([C:7]2[N:8]([CH3:12])[N:9]=[C:10]([F:39])[N:11]=2)[S:4][C:3]=1[C:13]1[N:17]2[N:18]=[C:19]([CH3:27])[CH:20]=[C:21]([CH:22]([CH2:23][CH3:24])[CH2:25][CH3:26])[C:16]2=[N:15][C:14]=1[CH3:28]
Reactant: CCC(CC)c1cc(C)nn2c(-c3sc(-c4ncnn4C)cc3Cl)c(C)nc12
Reactant: O=S(=O)(NF)c1ccccc1
Agent: [Li]C(C)(C)C
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: CCC(CC)c1cc(C)nn2c(-c3sc(-c4nc(F)nn4C)cc3Cl)c(C)nc12
Temperature: 25 °C
Yield: 22.2 %

Procedure:
To a −78° C. solution of 3-[3-chloro-5-(2-methyl-2H-[1,2,4]triazol-3-yl)-thiophen-2-yl]-8-(1-ethyl-propyl)-2,6-dimethyl-imidazo[1,2-b]pyridazine (0.40 g, 0.72 mmol) and THF (8 mL) is added 1.7 M tert-BuLi (0.47 mL, 0.80 mmol). After 30 minutes the solution is transferred via a cannula into a solution of N-fluorobenzenesulfonamide (0.40 g, 1.25 mmol) and THF. After 30 minutes the solution warmed to ambient temperature. The solution is diluted with EtOAc (40 mL), washed with water (30 mL), brine (30 mL), dried over MgSO4, filtered and concentrated. The solution is purified by ISCO (20%-30% EtOAc gradient) furnish the title compound (0.068 g, 0.16 mmol, 16%). 1H NMR (CDCl3) δ 0.87 (t, J=7.5 Hz, 6H), 1.71-1.93 (m, 4H), 2.53 (s, 3H), 2.54 (s, 3H), 3.26-3.36 (m, 1H), 4.08 (d J=2.7 Hz, 3H), 6.75 (s, 1H), 7.97 (s, 1H). LC/MS (m/z): calcd. for C20H22ClFN6S (M+H)+: 433.2; found: 433.2.
Reaction SMILES: Br[C:2]1[CH:3]=[CH:4][C:5]([C:8]#[N:9])=[N:6][CH:7]=1.[N:10]1([C:16]([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17])[CH2:15][CH2:14][NH:13][CH2:12][CH2:11]1.C(=O)([O-])[O-].[K+].[K+].C(OCC)(=O)C>CN(C)C=O>[C:8]([C:5]1[N:6]=[CH:7][C:2]([N:13]2[CH2:12][CH2:11][N:10]([C:16]([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17])[CH2:15][CH2:14]2)=[CH:3][CH:4]=1)#[N:9]
Reactant: CC(C)(C)OC(=O)N1CCNCC1
Reactant: N#Cc1ccc(Br)cn1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Product: CC(C)(C)OC(=O)N1CCN(c2ccc(C#N)nc2)CC1
Temperature: 120 °C
Reaction time: 63 h
Yield: 74 %

Procedure:
To a solution of 5-bromopyridine-2-carbonitrile (551.3 mg, 3.012 mmol) in anhydrous dimethylformamide (6.0 ml) were added tert-butyl piperazine-1-carboxylate (670.6 mg, 3.601 mmol) and potassium carbonate (829.0 mg, 5.998 mmol). The mixture was stirred at 120° C. for 63 hrs and cooled to room temperature. Ethyl acetate (30 ml) was added, and the precipitate was collected by filtration. Water (30 ml) was added to the filtrate, and the precipitated solid was collected by filtration and dried under reduced pressure to give tert-butyl 4-(6-cyanopyridin-3-yl)piperazine-1-carboxylate (642.9 mg, yield 74.0%) as a slightly yellow solid.