Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [NH2:1][C:2]1[C:7]([F:8])=[C:6](Br)[N:5]=[C:4]([C:10]([O:12][CH3:13])=[O:11])[C:3]=1[Cl:14].[Cl:15][C:16]1[CH:21]=[CH:20][C:19](B2OCCCO2)=[C:18]([F:28])[C:17]=1[O:29][CH3:30].[F-].[K+]>C(#N)C.O>[NH2:1][C:2]1[C:7]([F:8])=[C:6]([C:19]2[CH:20]=[CH:21][C:16]([Cl:15])=[C:17]([O:29][CH3:30])[C:18]=2[F:28])[N:5]=[C:4]([C:10]([O:12][CH3:13])=[O:11])[C:3]=1[Cl:14]
Reactant: COc1c(Cl)ccc(B2OCCCO2)c1F
Reactant: COC(=O)c1nc(Br)c(F)c(N)c1Cl
Agent: [F-]
Agent: [K+]
Solvent: CC#N
Solvent: O
Product: COC(=O)c1nc(-c2ccc(Cl)c(OC)c2F)c(F)c(N)c1Cl
Temperature: 50 °C
Reaction time: 5 h
Yield: 71.6 %

Procedure:
A stream of nitrogen was passed through a colorless mixture of methyl 4-amino-6-bromo-3-chloro-5-fluoropicolinate (2.8 g, 10 mmol) and 2-(4-chloro-2-fluoro-3-methoxyphenyl)-1,3,2-dioxaborinane (3.2 g, 13 mmol) in acetonitrile (CH3CN; 40 mL) and KF (1.7 g, 30 mmol) in H2O (20 mL) while heating to 50° C. (20-30 min). Dichloro-bis(triphenylphosphine)palladium(II) (PdCl2(PPh3)2; 140 mg, 0.2 mmol) was added, and the mixture was heated to 65° C. The reaction was monitored by HPLC and was complete after 5 h. The reaction mixture was filtered hot through a short pad of Celite then was diluted with H2O (20 mL) and allowed to cool. The product was collected by filtration. The light tan solid was dried under vacuum to give methyl 4-amino-3-chloro-6-(4-chloro-2-fluoro-3-methoxyphenyl)-5-fluoropicolinate (2.6 g, 72%): mp 169-170.5° C.; 1H NMR (400 MHz, DMSO-d6) δ 7.48 (d, J=8.4 Hz, 1H), 7.32 (t, J=7.7 Hz, 1H), 7.15 (s, 2H), 3.96 (s, 3H), 3.90 (s, 3H); 13C{1H} NMR (101 MHz, DMSO-d6) δ 164.85 (s), 153.11 (d, J=252.5 Hz), 146.29 (s), 144.52 (d, J=4.3 Hz), 143.74 (s), 142.75 (dd, J=227.1, 14.0 Hz), 136.38 (d, J=13.4 Hz), 128.58 (d, J=3.2 Hz), 125.87 (s), 125.54 (d, J=3.5 Hz), 122.89 (dd, J=13.8, 4.0 Hz), 113.01 (d, J=3.0 Hz), 61.61 (d, J=4.2 Hz), 52.70 (s); ESIMS m/z 364 ([M+H]+). Anal. Calcd for C14H10Cl2F2N2O3: C, 46.30; H, 2.78; N, 7.71. Found: C, 46.60; H, 2.68; N, 7.51.
Reaction SMILES: [C:1](Cl)(Cl)=[O:2].[CH3:5][S:6]([C:9]1[S:13][C:12]([NH2:14])=[N:11][N:10]=1)(=[O:8])=[O:7]>C(OCC)(=O)C>[CH3:5][S:6]([C:9]1[S:13][C:12]([N:14]=[C:1]=[O:2])=[N:11][N:10]=1)(=[O:8])=[O:7]
Reactant: CS(=O)(=O)c1nnc(N)s1
Reactant: O=C(Cl)Cl
Solvent: CCOC(C)=O
Product: CS(=O)(=O)c1nnc(N=C=O)s1
Reaction time: 16 h

Procedure:
A saturated solution of phosgene in ethyl acetate (100 ml) is charged into a glass reaction vessel equipped with a mechanical stirrer. A slurry of 5-methylsulfonyl-2-amino-1,3,4-thiadiazole (50 grams) in ethyl acetate (300 ml) is added to the reaction vessel, and the resulting mixture is stirred for a period of about 16 hours, resulting in the formation of a precipitate. The reaction mixture is then purged with nitrogen gas to remove unreacted phosgene. The purged mixture is then filtered to recover the precipitate. The precipitate is then recrystallized to yield the desired product 5-methylsulfonyl-1,3,4-thiadiazol-2-yl isocyanate dimer.
Reaction SMILES: [NH2:1][C:2]1[N:3]([CH3:22])[C:4](=[O:21])[C:5]2[C:10]([C:11]3[C:16]([CH3:17])=[CH:15][C:14]([CH3:18])=[CH:13][C:12]=3[CH3:19])=[CH:9][N:8]([CH3:20])[C:6]=2[N:7]=1.Br[CH2:24][CH2:25][CH2:26][CH2:27][CH2:28]Br.[H-].[Na+]>CN(C)C=O>[C:12]1([CH3:19])[CH:13]=[C:14]([CH3:18])[CH:15]=[C:16]([CH3:17])[C:11]=1[C:10]1[C:5]2[C:4](=[O:21])[N:3]([CH3:22])[C:2]([N:1]3[CH2:28][CH2:27][CH2:26][CH2:25][CH2:24]3)=[N:7][C:6]=2[N:8]([CH3:20])[CH:9]=1
Reactant: BrCCCCCBr
Reactant: Cc1cc(C)c(-c2cn(C)c3nc(N)n(C)c(=O)c23)c(C)c1
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: Cc1cc(C)c(-c2cn(C)c3nc(N4CCCCC4)n(C)c(=O)c23)c(C)c1
Temperature: 25 °C
Reaction time: 1 h
Yield: 67.3 %

Procedure:
To a solution of 2-amino-5-mesityl-3,7-dimethyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (0.063 g, 0.212 mmol) in N,N-dimethylformamide (1 mL) was added 1,5-dibromopentane (0.029 mL, 0.212 mmol) and sodium hydride (66% in oil, 0.015 g, 0.426 mmol) at 0° C., and the mixture was allowed to stir at room temperature for 1 hour. The reaction mixture was diluted with ice-cold water and extracted with ethyl acetate. The organic layer was washed with water and brine, dried over sodium sulfate and concentrated in vacuo. The residue was purified by silica gel column chromatography eluting with hexane/ethyl acetate (10:1-3:1). The oil obtained was crystallized from diisopropyl ether-hexane to give 0.052 g (67%) of the title compound.
Reaction SMILES: [C:1]1([N:7]([C:11]2[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=2)[C:8](=[O:10])[CH3:9])[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.C([N-]C(C)C)(C)C.[Li+].[C:25]([CH2:27][C@@H:28]([OH:35])[CH2:29][C:30](OCC)=[O:31])#[N:26].Cl>O1CCCC1.O1CCCC1.CCCCCCC>[C:25]([CH2:27][C@@H:28]([OH:35])[CH2:29][C:30](=[O:31])[CH2:9][C:8]([N:7]([C:11]1[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=1)[C:1]1[CH:2]=[CH:3][CH:4]=[CH:5][CH:6]=1)=[O:10])#[N:26]
Reactant: CCOC(=O)C[C@H](O)CC#N
Reactant: CC(=O)N(c1ccccc1)c1ccccc1
Agent: CC(C)[N-]C(C)C
Agent: Cl
Agent: [Li+]
Solvent: C1CCOC1
Solvent: CCCCCCC
Product: N#CC[C@@H](O)CC(=O)CC(=O)N(c1ccccc1)c1ccccc1
Reaction time: 0.5 h

Procedure:
To a stirred -10° C. solution of N,N-diphenylacetamide (211 g, 1.0 mol) in tetrahydrofuran (1.0 L) is slowly added a solution of lithium diisopropylamide in tetrahydrofuran-heptane (0.5 L of 2M) while maintaining the temperature between -10° C. to -5° C. The mixture is stirred at -0° C. to 20° C. for 30 minutes. (R)-4-cyano-3-hydroxybutyric acid, ethyl ester (Brower, supra) (40 g, 0.25 mol) as a solution in 200 mL of tetrahydrofuran is added to the previously prepared anion. The reaction mixture is stirred for 30 minutes at -5° C. to -20° C., and transferred to a 2.2N aqueous hydrochloric acid solution (1L). The aqueous layer is extracted with 500 mL of ethyl acetate, the aqueous layer is separated and reextracted with 100 mL of ethyl acetate, the extracts are combined and concentrated in vacuo to afford crude (R)-6-cyano- 5-hydroxy-3-oxo-N,N-diphenylhexanamide which is not isolated. A small sample is purified by column chromatography on flash silica gel (60:40 hexane:ethyl acetate) as an oil.
Reaction SMILES: CS(O[CH2:6][CH2:7][O:8][C:9]1[CH:14]=[CH:13][CH:12]=[C:11]([Br:15])[CH:10]=1)(=O)=O.[C:16]1(=[O:26])[NH:20][C:19](=[O:21])[C:18]2=[CH:22][CH:23]=[CH:24][CH:25]=[C:17]12.[K]>CN(C=O)C>[Br:15][C:11]1[CH:10]=[C:9]([CH:14]=[CH:13][CH:12]=1)[O:8][CH2:7][CH2:6][N:20]1[C:19](=[O:21])[C:18]2=[CH:22][CH:23]=[CH:24][CH:25]=[C:17]2[C:16]1=[O:26]
Reactant: O=C1NC(=O)c2ccccc21
Reactant: CS(=O)(=O)OCCOc1cccc(Br)c1
Agent: [K]
Solvent: CN(C)C=O
Product: O=C1c2ccccc2C(=O)N1CCOc1cccc(Br)c1
Temperature: 60 °C
Reaction time: 14 h
Yield: 78.2 %

Procedure:
To a solution of mesylate 16 (24.05 g, 81.5 mmol) in anhydrous DMF (160 ml) was added potassium phthalimide (15.53 g, 83.8 mmol) and the reaction mixture stirred at 60° C. for 14 h. After cooling to room temperature, the mixture was concentrated under reduced pressure. The residue was diluted with hexanes-EtOAc (7:1, 150 ml) and water (150 ml) and the mixture shaken in separating funnel. A precipitate formed which was removed by filtration, washed excessively with water and hexane, then dried under vacuum to give N-(2-(3-bromophenoxy)ethyl)phthalimide (17) as white fluffy crystals (22.05 g, 78%). The organic layer of the filtrate was concentrated under reduced pressure and the residue was suspended in 10% EtOAc-hexanes. The solution was washed with water and the precipitate collected by filtration, washed with water then hexanes and dried under vacuum to give additional phthalimide 17 (5.65 g). Combined yield (21.18 g, 98%): 1H NMR (400 MHz, CDCl3) δ 7.86 (m, 2H), 7.73 (m, 2H), 7.03-7.12 (m, 3H), 6.80 (ddd, J=8.0, 2.5 and 1.4 Hz, 1H), 4.21 (t, J=6.9 Hz, 2H), 4.10 (t, J=6.0 Hz, 2H).
Reaction SMILES: [CH:1]1[C:6]2[C:7](=O)[NH:8][C:9]3[CH:15]=[CH:14][CH:13]=[CH:12][C:10]=3[O:11][C:5]=2[CH:4]=[CH:3][CH:2]=1.P(Cl)(Cl)([Cl:19])=O>>[Cl:19][C:7]1=[N:8][C:9]2[CH:15]=[CH:14][CH:13]=[CH:12][C:10]=2[O:11][C:5]2[CH:4]=[CH:3][CH:2]=[CH:1][C:6]1=2
Reactant: O=C1Nc2ccccc2Oc2ccccc21
Reactant: O=P(Cl)(Cl)Cl
Product: ClC1=Nc2ccccc2Oc2ccccc21
Temperature: 25 °C
Yield: 86 %

Procedure:
A solution of 10,11-dihydrodibenz[b,f][1,4]oxazepin-11-one (1.00 g, 4.74 mmol) and phosphorus oxychloride (40 mL) was stirred for 5 h at reflux. The reaction mixture was then cooled to room temperature and concentrated under reduced pressure. The residue was dissolved into AcOEt and washed with water and brine. The organic layer was dried (Na2SO4), filtered and concentrated to give an orange oil. The residue was purified by silica gel column chromatography with EtOAc (10%) in Hexanes to afford 1 (939 mg, 86%) as a yellow solid. LRMS (ESI): (calc) 229.0 (found) 230.1 (MH)+.
Reaction SMILES: [CH3:1][Si:2]([CH3:23])([CH3:22])[CH2:3][CH2:4][O:5][CH2:6][N:7]1[CH:11]=[C:10]([C:12]2[NH:17][C:16](=O)[N:15]3[CH:19]=[CH:20][N:21]=[C:14]3[CH:13]=2)[CH:9]=[N:8]1.CCN(C(C)C)C(C)C.O=P(Cl)(Cl)[Cl:35]>C(Cl)Cl>[Cl:35][C:16]1[N:15]2[CH:19]=[CH:20][N:21]=[C:14]2[CH:13]=[C:12]([C:10]2[CH:9]=[N:8][N:7]([CH2:6][O:5][CH2:4][CH2:3][Si:2]([CH3:23])([CH3:22])[CH3:1])[CH:11]=2)[N:17]=1
Reactant: O=P(Cl)(Cl)Cl
Reactant: C[Si](C)(C)CCOCn1cc(-c2cc3nccn3c(=O)[nH]2)cn1
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: C[Si](C)(C)CCOCn1cc(-c2cc3nccn3c(Cl)n2)cn1
Temperature: 25 °C
Reaction time: 0.08 h
Yield: 51 %

Procedure:
To a solution of 7-(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazol-4-yl)imidazo[1,2-c]pyrimidin-5(6H)-one (Step B, 772 mg, 2.33 mmol) in dry DCM (15 mL) was added DIEA (1.22 mL, 6.99 mmol) and the mixture was stirred at ambient temperature for 5 minutes. The mixture was cooled to 0° C. and POCl3 (855 μL, 9.32 mmol) was added. The mixture was stirred for 1 hour at 0° C. then at ambient temperature for 18 hours. The reaction mixture was concentrated and the residual syrup was dissolved in EtOAc (15 mL). The solution was added dropwise to stirred 1M K2CO3 (20 mL) cooled to 0° C. and stirred for 30 minutes. The mixture was allowed to reach ambient temperature and the EtOAc layer was removed. The remaining aqueous layer was extracted with EtOAc (2×) and the combined EtOAc fractions were washed with saturated NaCl. The EtOAc solution was dried over MgSO4/activated carbon, filtered through a packed Celite plug (EtOAc elution) and concentrated. The residual dark syrup was dissolved in Et2O, treated with activated carbon and filtered through a packed Celite pug (Et2O elution). The Et2O solution was concentrated to give a brittle tan foam that was pulverized to a flowing solid and dried in vacuum. This afforded the title compound (416 mg, 51.0% yield) as a light tan solid. MS (apci) m/z=350.1 (M+H).
Reaction SMILES: [C@@H:1]1([N:10]2[C:19]3[N:18]=[CH:17][N:16]=[C:14]([NH2:15])[C:13]=3[N:12]=[CH:11]2)[O:9][C@H:6]([CH2:7][OH:8])[C@@H:4]([OH:5])[C@H:2]1[OH:3].C1N=C(N)C2N=CN([C@@H]3[O:34][C@H](CO)[C@@H](O)[C@@H]3O)C=2N=1.O.OO>C(O)(=O)C.[C].[Pd]>[C@@H:1]1([N:10]2[C:19]3[C:13](=[C:14]([N+:16]([O-:34])=[CH:17][N:18]=3)[NH2:15])[N:12]=[CH:11]2)[O:9][C@H:6]([CH2:7][OH:8])[C@@H:4]([OH:5])[C@H:2]1[OH:3]
Reactant: Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O
Reactant: Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
Agent: [Pd]
Agent: OO
Solvent: O
Solvent: CC(=O)O
Product: Nc1c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c2nc[n+]1[O-]
Temperature: 25 °C
Reaction time: 120 h

Procedure:
Twenty grams of adenosine with a product code of A9251-25G, commercialized by Sigma-Aldrich Japan K.K., Tokyo, Japan, was dispersed in one liter of acetic acid and admixed with 100 mL of 30% hydrogen peroxide solution, followed by stirring the resulting mixture at ambient temperature for five days. An excessive amount of the remaining hydrogen peroxide was decomposed by the addition of five grams of 5% palladium carbon, commercialized by Kawaken Fine Chemicals Co., Ltd., Tokyo, Japan, followed by filtering the mixture to remove the palladium carbon, drying the resulting solution in vacuo, adding ethanol to the dried product to disperse the formed crystals, and filtering the resulting mixture to obtain crude crystals of adenosine N1-oxide. Eight grams of adenosine N1-oxide with a purity of 99.5% was obtained by dissolving the crude crystals in ethanol by heating, filtering the resulting solution, ice-chilling the filtrate to effect recrystallization, and repeating these steps twice.
Reaction SMILES: [CH2:1]([O:3][C:4]([C:6]1[C:10]([Br:11])=[C:9]([Br:12])[N:8]([CH3:13])[C:7]=1[CH2:14]Br)=[O:5])[CH3:2].[CH2:16]([O:18][C:19](=[O:29])[CH2:20][NH:21][C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])[CH3:17]>>[CH2:1]([O:3][C:4]([C:6]1[C:10]([Br:11])=[C:9]([Br:12])[N:8]([CH3:13])[C:7]=1[CH2:14][N:21]([C:22]([O:24][C:25]([CH3:26])([CH3:28])[CH3:27])=[O:23])[CH2:20][C:19]([O:18][CH2:16][CH3:17])=[O:29])=[O:5])[CH3:2]
Reactant: CCOC(=O)c1c(Br)c(Br)n(C)c1CBr
Reactant: CCOC(=O)CNC(=O)OC(C)(C)C
Product: CCOC(=O)CN(Cc1c(C(=O)OCC)c(Br)c(Br)n1C)C(=O)OC(C)(C)C

Procedure:
Prepared in analogy to that of Example 1(c) from 4,5-dibromo-2-bromomethyl-1-methyl-1H-pyrrole-3-carboxylic acid ethyl ester and tert-butoxycarbonylamino-acetic acid ethyl ester. The title compound, ESI MS (m/z): 549 (M+Na+).
Reaction SMILES: Cl[C:2]1[C:7]([C:8]#[N:9])=[C:6]([C:10]2[CH:15]=[CH:14][CH:13]=[C:12]([Cl:16])[CH:11]=2)[N:5]=[C:4]([N:17]2[CH2:22][CH2:21][O:20][CH2:19][CH2:18]2)[N:3]=1.[F:23][C:24]([F:38])([F:37])[C:25]1[C:26]([N:31]2[CH2:36][CH2:35][NH:34][CH2:33][CH2:32]2)=[N:27][CH:28]=[CH:29][CH:30]=1.C([O-])([O-])=O.[K+].[K+]>CC#N.O>[Cl:16][C:12]1[CH:11]=[C:10]([C:6]2[C:7]([C:8]#[N:9])=[C:2]([N:34]3[CH2:35][CH2:36][N:31]([C:26]4[C:25]([C:24]([F:38])([F:23])[F:37])=[CH:30][CH:29]=[CH:28][N:27]=4)[CH2:32][CH2:33]3)[N:3]=[C:4]([N:17]3[CH2:22][CH2:21][O:20][CH2:19][CH2:18]3)[N:5]=2)[CH:15]=[CH:14][CH:13]=1
Reactant: FC(F)(F)c1cccnc1N1CCNCC1
Reactant: N#Cc1c(Cl)nc(N2CCOCC2)nc1-c1cccc(Cl)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CC#N
Product: N#Cc1c(-c2cccc(Cl)c2)nc(N2CCOCC2)nc1N1CCN(c2ncccc2C(F)(F)F)CC1

Procedure:
Dissolve 4-chloro-6-(3-chlorophenyl)-2-morpholinopyrimidine-5-carbonitrile (33.5 mg, 0.1 mmoles) and 1-(3-(trifluoromethyl)-pyridin-2-yl)piperazine (23 mg, 0.1 mmoles) in CH3CN (1.0 mL) under nitrogen atmosphere. Add anhydrous powdered K2CO3 (28 mg, 0.2 mmoles) to this mixture and heat at 80° C. for 24 hours. Cool, dilute with water (5 mL), extract with EtOAc (3×2 mL) and dry over MgSO4. Filter, and concentrate under vacuum to afford crude product Purify by flash column chromatography using 30% EtOAc/hexane to afford the title product as white solid. NMR (DMSO-D6) δ 3.30 (4H, s), 3.62 (4H, m), 3.80 (4H, s), 3.93 (4H, s), 7.19 (1H, m), 7.51 (1H, m), 7.59 (1H, m), 7.76 (1H, m), 7.83 (1H, s), 8.07 (1H, d, J=2.0), 8.52 (1H, d, J=1.2). Mass spec m/z=530.12.
Reaction SMILES: O[CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][C:18]([O:20][CH2:21][CH3:22])=[O:19].C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.N1C=CN=C1.[I:47]C1C=CC(CCCCCCCCCCCCCCCCCCO)=CC=1>C(Cl)Cl.C1C=CC=CC=1>[I:47][CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][C:18]([O:20][CH2:21][CH3:22])=[O:19]
Reactant: OCCCCCCCCCCCCCCCCCCc1ccc(I)cc1
Reactant: CCOC(=O)CCCCCCCCCCCCCCCCO
Agent: c1c[nH]cn1
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: ClCCl
Solvent: c1ccccc1
Product: CCOC(=O)CCCCCCCCCCCCCCCCI
Temperature: 0 °C
Reaction time: 0.67 h
Yield: 90 %

Procedure:
Ethyl 17-hydroxy-heptadecanoate 79 (264 mg, 0.84 mmol), Ph3P (262 mg, 1 mmol) and imidazole (94 mg, 1.39 mmol) were dissolved in the mixture of CH2Cl2 (3 ml) and benzene (3 ml) and cooled to 0° C. Solid 12 (254 mg, 1 mmol) was added and the reaction mixture was stirred at 0° C. for 40 min. The reaction mixture was quenched by addition of MeOH (0.5 ml), diluted with EtOAc and washed with the aqueous NaHCO3—Na2S2O3 solution, dried over Na2SO4 and evaporated. Chromatography in hexane-EtOAc (97:3) afforded the product 80 (321 mg, 90%).
Reaction SMILES: [N:1]1[CH:6]=[CH:5][CH:4]=[CH:3][C:2]=1[CH2:7][CH2:8][C:9]([OH:11])=O.C1N=CN(C(N2C=NC=C2)=O)C=1.CCN(C(C)C)C(C)C.Cl.[F:34][C:35]([F:55])([F:54])[C:36]1[CH:41]=[CH:40][C:39]([C@@H:42]([C:44]2[C:49]([C:50]([F:53])([F:52])[F:51])=[CH:48][CH:47]=[CH:46][N:45]=2)[NH2:43])=[CH:38][CH:37]=1>C(Cl)Cl>[N:1]1[CH:6]=[CH:5][CH:4]=[CH:3][C:2]=1[CH2:7][CH2:8][C:9]([NH:43][C@@H:42]([C:39]1[CH:40]=[CH:41][C:36]([C:35]([F:55])([F:34])[F:54])=[CH:37][CH:38]=1)[C:44]1[C:49]([C:50]([F:51])([F:52])[F:53])=[CH:48][CH:47]=[CH:46][N:45]=1)=[O:11]
Reactant: N[C@@H](c1ccc(C(F)(F)F)cc1)c1ncccc1C(F)(F)F
Reactant: O=C(O)CCc1ccccn1
Agent: Cl
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: O=C(CCc1ccccn1)N[C@@H](c1ccc(C(F)(F)F)cc1)c1ncccc1C(F)(F)F
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
To a solution of 3-(pyridin-2-yl)propanoic acid (89 mg, 0.586 mmol, Oakwood) and DCM (4 mL) were added CDI (95 mg, 0.586 mmol) and DIPEA (0.20 mL, 1.148 mmol). After 0.5 hours, the reaction was treated with a solution of (S)-(4-(trifluoromethyl)phenyl)(3-(trifluoromethyl)pyridin-2-yl)methanamine hydrochloride (Intermediate 1) (125 mg, 0.390 mmol) in DCM (1.5 mL). The solution was stirred at rt. After 4 days, the resulting product was adsorbed onto a plug of silica gel and chromatographed through a Redi-Sep® pre-packed silica gel column (4 g), eluting with 0% to 60% EtOAc in hexane, to provide the title compound as a colorless oil. 1H NMR (CDCl3, 300 MHz) δ ppm 8.79 (d, J=3.8 Hz, 1H), 8.45 (d, J=4.8 Hz, 1H), 7.96 (d, J=7.9 Hz, 1H), 7.78 (d, J=7.9 Hz, 1H), 7.44-7.52 (m, 3H), 7.34-7.43 (m, 3H), 7.03-7.12 (m, 2H), 6.63 (d, J=8.0 Hz, 1H), 3.11 (td, J=6.7 & 2.5 Hz, 2H), 2.74 (td, J=7.2 & 2.5 Hz, 2H). MS (ESI pos. ion) m/z: 454.0 (M+H).
Reaction SMILES: Cl.Cl.[N:3]1([CH2:9][CH2:10][CH2:11][O:12][C:13]2[CH:14]=[CH:15][CH:16]=[C:17]3[C:22]=2[CH2:21][NH:20][CH2:19][CH2:18]3)[CH2:8][CH2:7][CH2:6][CH2:5][CH2:4]1.CCN(CC)CC.[S:30]1[CH:34]=[CH:33][CH:32]=[C:31]1[C:35](Cl)=[O:36]>C(Cl)Cl>[N:3]1([CH2:9][CH2:10][CH2:11][O:12][C:13]2[CH:14]=[CH:15][CH:16]=[C:17]3[C:22]=2[CH2:21][N:20]([C:35]([C:31]2[S:30][CH:34]=[CH:33][CH:32]=2)=[O:36])[CH2:19][CH2:18]3)[CH2:8][CH2:7][CH2:6][CH2:5][CH2:4]1
Reactant: O=C(Cl)c1cccs1
Reactant: c1cc2c(c(OCCCN3CCCCC3)c1)CNCC2
Agent: Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: O=C(c1cccs1)N1CCc2cccc(OCCCN3CCCCC3)c2C1
Temperature: 25 °C
Reaction time: 8 h
Yield: 54.7 %

Procedure:
To a mixture of 8-(3-piperidin-1-yl-propoxy)-1,2,3,4-tetrahydro-isoquinoline dihydrochloride salt (300 mg, 0.86 mmol) and NEt3 (0.36 mL, 2.6 mmol) in CH2Cl2 (10 mL) is added 2-thiophene carbonyl chloride (0.10 mL, 0.95 mmol). After stirring at room temperature overnight, the mixture is partitioned between EtOAc and water. The organic phase is washed with brine, dried (MgSO4), and concentrated. The residue is purified by flash chromatography [Biotage 40S SiO2, elute 20% (90/10/1 CH2Cl2/MeOH/NH4OH)/80% CH2Cl2 to 100% (90/10/1 CH2Cl2/MeOH/NH4OH)] to yield the title compound as a yellow oil (0.181 g, 55%). MS (ES+) 385.3.
Reaction SMILES: [CH3:1][C:2]1[CH:10]=[C:9]2[C:5]([CH2:6][CH2:7][NH:8]2)=[CH:4][CH:3]=1.[CH3:11][N:12]1[CH:16]=[C:15]([C:17]2[N:22]=[N:21][C:20]([N:23]3[CH2:28][CH2:27][C:26](=O)[CH2:25][CH2:24]3)=[CH:19][CH:18]=2)[CH:14]=[N:13]1>>[CH3:1][C:2]1[CH:10]=[C:9]2[C:5]([CH2:6][CH2:7][N:8]2[CH:26]2[CH2:27][CH2:28][N:23]([C:20]3[N:21]=[N:22][C:17]([C:15]4[CH:14]=[N:13][N:12]([CH3:11])[CH:16]=4)=[CH:18][CH:19]=3)[CH2:24][CH2:25]2)=[CH:4][CH:3]=1
Reactant: Cc1ccc2c(c1)NCC2
Reactant: Cn1cc(-c2ccc(N3CCC(=O)CC3)nn2)cn1
Product: Cc1ccc2c(c1)N(C1CCN(c3ccc(-c4cnn(C)c4)nn3)CC1)CC2

Procedure:
The title compound was prepared following the procedure as described in Example 5, STEP 4, reacting 6-methylindoline and 1-(6-(1-methyl-1H-pyrazol-4-yl)pyridazin-3-yl)piperidin-4-one.
Reaction SMILES: Cl.[NH2:2][C:3]1[CH:4]=[C:5]2[C:10](=[CH:11][CH:12]=1)[N:9]=[CH:8][N:7]=[C:6]2[NH:13][C:14]1[CH:19]=[CH:18][C:17]([F:20])=[C:16]([Cl:21])[CH:15]=1.[CH3:22][O:23][CH:24](OC)[CH2:25]OC>>[Cl:21][C:16]1[CH:15]=[C:14]([CH:19]=[CH:18][C:17]=1[F:20])[NH:13][C:6]1[C:5]2[C:10](=[CH:11][CH:12]=[C:3]([NH:2][CH2:25][CH2:24][O:23][CH3:22])[CH:4]=2)[N:9]=[CH:8][N:7]=1
Reactant: COCC(OC)OC
Reactant: Nc1ccc2ncnc(Nc3ccc(F)c(Cl)c3)c2c1
Agent: Cl
Product: COCCNc1ccc2ncnc(Nc3ccc(F)c(Cl)c3)c2c1
Yield: 8 %

Procedure:
Using an analogous reductive amination procedure to that described in Example 1, 6-amino-4-(3'-chloro-4'-fluoroanilino)quinazoline hydrochloride was reacted with 2-methoxyacetaldehyde dimethyl acetal to give 4-(3'-chloro-4'-fluoroanilino)-6-(2-methoxyethylamino)quinazoline in 8% yield, m.p. 152-154° C.; NMR Spectrum: 3.32 (s, 3H), 3.4 (t, 2H), 3.62 (t, 2H), 6.25 (t, -1H), 7.2 (d, 1H), 7.3 (m, 1H), 7.43 (t, 1H), 7.55 (d, 1H), 7.82 (m, 1H), 8.13 (m, 1H), 8.41 (s, 1H), 9.5 (s, 1H); Elemental Analysis: Found C, 57.9; H, 4.8; N, 15.3; C17H16ClFN4O 0.33H2O 0.1EtOAc requires C, 57.7; H, 4.8; N, 15.5%.
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([N:20]([CH2:27][C:28]([OH:30])=O)[C:21]3[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=3)([CH2:12][C:13]3[CH:18]=[CH:17][CH:16]=[C:15]([Cl:19])[CH:14]=3)[C:7](=[O:11])[NH:8]2)=[CH:4][CH:3]=1.[CH:31]1([NH2:37])[CH2:36][CH2:35][CH2:34][CH2:33][CH2:32]1.C1C=CC2N(O)N=NC=2C=1.CCN(C(C)C)C(C)C>C(#N)C>[Cl:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([N:20]([C:21]3[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=3)[CH2:27][C:28]([NH:37][CH:31]3[CH2:36][CH2:35][CH2:34][CH2:33][CH2:32]3)=[O:30])([CH2:12][C:13]3[CH:18]=[CH:17][CH:16]=[C:15]([Cl:19])[CH:14]=3)[C:7](=[O:11])[NH:8]2)=[CH:4][CH:3]=1
Reactant: NC1CCCCC1
Reactant: O=C(O)CN(c1ccccc1)C1(Cc2cccc(Cl)c2)C(=O)Nc2cc(Cl)ccc21
Agent: On1nnc2ccccc21
Solvent: CCN(C(C)C)C(C)C
Solvent: CC#N
Product: O=C(CN(c1ccccc1)C1(Cc2cccc(Cl)c2)C(=O)Nc2cc(Cl)ccc21)NC1CCCCC1
Temperature: 25 °C
Reaction time: 8 h
Yield: 54.2 %

Procedure:
The mixture of rac-{[6-chloro-3-(3-chloro-benzyl)-2-oxo-2,3-dihydro-1H-indol-3-yl]-phenyl-amino}-acetic acid (70 mg, 0.159 mmol), cyclohexylamine (19 mg, 0.191 mmol) EDC.HCl (36 mg, 0.191 mmol), HOBt (26 mmg, 0.191 mmol) and DIPEA (25 mg, 0.191 mmol) in acetonitrile (3 mL) was stirred at room temperature for overnight. The reaction mixture was concentrated and the residue was purified with chromatography to give 45 mg of rac-2-{[6-chloro-3-(3-chloro-benzyl)-2-oxo-2,3-dihydro-1H-indol-3-yl]-phenyl-amino}-N-cyclohexy-acetamide as a yellow solid. MS m/z 522 (M+H)+.
Reaction SMILES: [CH3:1][N:2]([CH3:15])[S:3]([N:6]1[C:10]2[CH2:11][CH2:12][CH2:13][CH2:14][C:9]=2[N:8]=[CH:7]1)(=[O:5])=[O:4].C([Li])CCC.CN([CH:24]=[O:25])C.[NH4+].[Cl-]>C1COCC1>[CH3:1][N:2]([CH3:15])[S:3]([N:6]1[C:10]2[CH2:11][CH2:12][CH2:13][CH2:14][C:9]=2[N:8]=[C:7]1[CH:24]=[O:25])(=[O:4])=[O:5]
Reactant: CN(C)C=O
Reactant: CN(C)S(=O)(=O)n1cnc2c1CCCC2
Agent: [Cl-]
Agent: [Li]CCCC
Agent: [NH4+]
Solvent: C1CCOC1
Product: CN(C)S(=O)(=O)n1c(C=O)nc2c1CCCC2
Temperature: -78 °C
Reaction time: 1 h
Yield: 51.3 %

Procedure:
2-Formyl-4,5,6,7-tetrahydro-benzoimidazole-1-sulfonic acid dimethylamide was prepared following a modification of the procedure found in the Journal of Medicinal Chemistry, 40; 14, 1997, 2205. To a solution of 4,5,6,7-tetrahydro-benzoimidazole-1-sulfonic acid dimethylamide (2.67 g, 11.6 mmol) in dry THF (100 mL) under argon at −78° C. was added dropwise 2.5 M n-butyllithium in hexanes (7.0 mL, 17.5 mmol). The reaction was stirred at −78° C. for 1 hour, then DMF (1.1 mL, 13.9 mmol) was added dropwise, and the reaction was warmed to room temperature and stirred for 2 hours. Saturated NH4Cl (25 mL) was added, and the reaction mixture was concentrated, and then diluted with CH2Cl2 (500 mL) and distilled water (25 mL). The layers were separated and the aqueous phase was extracted with CH2Cl2 (2×100 mL). The combined organic extracts were washed with brine (1×100 mL), dried (Na2SO4), and concentrated. Purification of the crude material by column chromatography on silica gel (1:1 hexanes-EtOAc) provided 1.53 g (51%) of 2-formyl-4,5,6,7-tetrahydro-benzoimidazole-1-sulfonic acid dimethylamide as a yellow solid. 1H NMR (CDCl3) δ 1.82-1.86 (m, 4H), 2.66-2.68 (m, 2H), 2.86-2.88 (m, 2H), 2.96 (s, 6H), 9.99 (s, 1H).