Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [C:1]([O:5][C@@H:6]([C:12]1[C:13]([CH3:34])=[N:14][C:15]([CH3:33])=[C:16]([C:26]2[CH:31]=[CH:30][C:29](O)=[CH:28][CH:27]=2)[C:17]=1[N:18]1[CH2:23][CH2:22][C:21]([CH3:25])([CH3:24])[CH2:20][CH2:19]1)[C:7]([O:9]CC)=[O:8])([CH3:4])([CH3:3])[CH3:2].[F:35][C:36]1[CH:41]=[CH:40][C:39]([F:42])=[CH:38][C:37]=1[CH2:43][CH2:44][OH:45].C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.CCOC(/N=N/C(OCC)=O)=O.[OH-].[Na+]>C1COCC1.CO>[C:1]([O:5][C@@H:6]([C:12]1[C:13]([CH3:34])=[N:14][C:15]([CH3:33])=[C:16]([C:26]2[CH:27]=[CH:28][C:29]([O:45][CH2:44][CH2:43][C:37]3[CH:38]=[C:39]([F:42])[CH:40]=[CH:41][C:36]=3[F:35])=[CH:30][CH:31]=2)[C:17]=1[N:18]1[CH2:19][CH2:20][C:21]([CH3:25])([CH3:24])[CH2:22][CH2:23]1)[C:7]([OH:9])=[O:8])([CH3:4])([CH3:2])[CH3:3]
Reactant: OCCc1cc(F)ccc1F
Reactant: CCOC(=O)[C@@H](OC(C)(C)C)c1c(C)nc(C)c(-c2ccc(O)cc2)c1N1CCC(C)(C)CC1
Agent: CCOC(=O)/N=N/C(=O)OCC
Agent: [Na+]
Agent: [OH-]
Solvent: C1CCOC1
Solvent: CO
Product: Cc1nc(C)c([C@H](OC(C)(C)C)C(=O)O)c(N2CCC(C)(C)CC2)c1-c1ccc(OCCc2cc(F)ccc2F)cc1
Reaction time: 18 h
Yield: 12.8 %

Procedure:
To a stirred solution of (S)-ethyl 2-(tert-butoxy)-2-(4-(4,4-dimethylpiperidin-1-yl)-5-(4-hydroxyphenyl)-2,6-dimethylpyridin-3-yl)acetate (20 mg, 0.043 mmol), 2-(2,5-difluorophenyl)ethanol (33.7 mg, 0.213 mmol) and Ph3P-resin (55.8 mg, 0.213 mmol) in THF (2 mL) was added DEAD (0.014 mL, 0.085 mmol) at rt. After 18 h, mixture was filtered to remove polymer, concentrated and treated with 1N NaOH (0.854 mL, 0.854 mmol) in MeOH (1 mL) at 75° C. for 16 h. Mixture was then cooled and purified by prep-HPLC to afford (S)-2-(tert-butoxy)-2-(5-(4-(2,5-difluorophenethoxy)phenyl)-4-(4,4-dimethylpiperidin-1-yl)-2,6-dimethylpyridin-3-yl)acetic acid (3.2 mg, 5.51 μmol, 12.91% yield). 1H NMR (500 MHz, DMSO-d6) δ 7.33-7.27 (m, 1H), 7.27-7.17 (m, 3H), 7.17-7.11 (m, 1H), 7.07-6.98 (m, 4H), 5.87 (s, 1H), 4.32-4.23 (m, 2H), 3.09 (t, J=6.2 Hz, 2H), 2.80 (t, J=11.9 Hz, 1H), 2.43 (s, 3H), 2.05 (s, 3H), 1.98-1.91 (m, 1H), 1.49 (br. s., 1H), 1.29 (br. s., 1H), 1.18 (d, J=11.7 Hz, 1H), 1.13 (s, 9H), 1.05-0.95 (m, 1H), 0.85 (br. s., 3H), 0.60 (br. s., 3H). LCMS (M+H)=581.2.
Reaction SMILES: [C:1]([C:5]1[CH:12]=[CH:11][C:8]([C:9]#[N:10])=[C:7]([OH:13])[CH:6]=1)([CH3:4])([CH3:3])[CH3:2].[C:14](=O)([O-])[O-].[K+].[K+].IC>CN(C)C=O>[C:1]([C:5]1[CH:12]=[CH:11][C:8]([C:9]#[N:10])=[C:7]([O:13][CH3:14])[CH:6]=1)([CH3:4])([CH3:2])[CH3:3]
Reactant: O=C([O-])[O-]
Reactant: CC(C)(C)c1ccc(C#N)c(O)c1
Agent: [K+]
Solvent: CI
Solvent: CN(C)C=O
Product: COc1cc(C(C)(C)C)ccc1C#N
Temperature: 50 °C
Reaction time: 2 h
Yield: 32.4 %

Procedure:
4-t-Butyl-2-hydroxybenzonitrile (1.16 g) and potassium carbonate (376 mg) were dissolved in dimethylformamide (4 ml) and to the solution was added dropwise iodomethane (226 μl), followed by stirring at 50° C. for 2 hours. The resulting mixture was filtered to remove the remaining potassium carbonate and concentrated under reduced pressure. The obtained residue was purified by column-chromatography (hexane/ethyl acetate=10/1) to yield the compound 13-2a (167 mg, 97%).
Reaction SMILES: [NH2:1][C:2]1[CH:23]=[CH:22][C:5]([O:6][C:7]2[CH:8]=[CH:9][C:10]3[N:11]([CH:13]=[C:14]([NH:16][C:17]([CH:19]4[CH2:21][CH2:20]4)=[O:18])[N:15]=3)[CH:12]=2)=[C:4]([F:24])[CH:3]=1.[F:25][C:26]1[CH:31]=[CH:30][C:29]([N:32]2[C:37]([CH3:38])=[C:36]([CH3:39])[CH:35]=[C:34]([C:40](O)=[O:41])[C:33]2=[O:43])=[CH:28][CH:27]=1.C(N(CC)C(C)C)(C)C.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.C(=O)([O-])O.[Na+]>CN(C)C=O.C(C(C)=O)C.O1CCCC1.C(OCC)(=O)C>[CH:19]1([C:17]([NH:16][C:14]2[N:15]=[C:10]3[CH:9]=[CH:8][C:7]([O:6][C:5]4[CH:22]=[CH:23][C:2]([NH:1][C:40]([C:34]5[C:33](=[O:43])[N:32]([C:29]6[CH:28]=[CH:27][C:26]([F:25])=[CH:31][CH:30]=6)[C:37]([CH3:38])=[C:36]([CH3:39])[CH:35]=5)=[O:41])=[CH:3][C:4]=4[F:24])=[CH:12][N:11]3[CH:13]=2)=[O:18])[CH2:21][CH2:20]1
Reactant: Nc1ccc(Oc2ccc3nc(NC(=O)C4CC4)cn3c2)c(F)c1
Reactant: Cc1cc(C(=O)O)c(=O)n(-c2ccc(F)cc2)c1C
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Agent: O=C([O-])O
Solvent: C1CCOC1
Solvent: CCN(C(C)C)C(C)C
Solvent: CCC(C)=O
Product: Cc1cc(C(=O)Nc2ccc(Oc3ccc4nc(NC(=O)C5CC5)cn4c3)c(F)c2)c(=O)n(-c2ccc(F)cc2)c1C
Temperature: 25 °C
Reaction time: 6 h
Yield: 62 %

Procedure:
To a solution of N-[6-(4-amino-2-fluorophenoxy)imidazo[1,2-a]pyridin-2-yl]cyclopropanecarboxamide (83 mg, 0.255 mmol) and 1-(4-fluorophenyl)-5,6-dimethyl-2-oxo-1,2-dihydropyridine-3-carboxylic acid (80 mg, 0.306 mmol) in N,N-dimethylformamide (1 mL) were added N,N-diisopropylethylamine (88 μL, 0.51 mmol) and HATU (116 mg, 0.306 mmol), and the mixture was stirred at room temperature for 6 hr. Ethyl acetate, tetrahydrofuran and saturated aqueous sodium hydrogen carbonate solution were added to the reaction mixture, and the mixture was extracted 3 times with ethyl acetate. The organic layer was washed with saturated brine, dried over anhydrous magnesium sulfate and filtered, and the solvent was evaporated under reduced pressure. The obtained residue was purified by silica gel column chromatography (ethyl acetate alone) to give a white solid. The obtained solid was suspended in methyl ethyl ketone, stirred at 80° C. and collected by filtration to give the title compound (90 mg, 62%) as a white solid.
Reaction SMILES: [CH2:1]([N:3]1[CH2:8][CH2:7][N:6]([C:9]2[CH:10]=[C:11]([CH:13]=[CH:14][CH:15]=2)[NH2:12])[CH2:5][CH2:4]1)[CH3:2].[CH3:16][C:17]1[CH:22]=[CH:21][CH:20]=[C:19]([CH3:23])[C:18]=1[C:24]1[C:33]2[N:32]=[CH:31][CH:30]=[N:29][C:28]=2[C:27]([C:34](O)=[O:35])=[CH:26][CH:25]=1.CC1C=CC=C(C)C=1B(O)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>[CH2:1]([N:3]1[CH2:4][CH2:5][N:6]([C:9]2[CH:10]=[C:11]([NH:12][C:34]([C:27]3[C:28]4[N:29]=[CH:30][CH:31]=[N:32][C:33]=4[C:24]([C:18]4[C:19]([CH3:23])=[CH:20][CH:21]=[CH:22][C:17]=4[CH3:16])=[CH:25][CH:26]=3)=[O:35])[CH:13]=[CH:14][CH:15]=2)[CH2:7][CH2:8]1)[CH3:2]
Reactant: CCN1CCN(c2cccc(N)c2)CC1
Reactant: Cc1cccc(C)c1-c1ccc(C(=O)O)c2nccnc12
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: Cc1cccc(C)c1B(O)O
Product: CCN1CCN(c2cccc(NC(=O)c3ccc(-c4c(C)cccc4C)c4nccnc34)c2)CC1

Procedure:
The title compound was prepared in analogy to the procedure described in Step 14.1 but using 3-(4-ethylpiperazin-1-yl)aniline (Step 2.1) and 8-(2,6-dimethyl-phenyl)-quinoxaline-5-carboxylic acid. The carboxylic acid was synthesized as described in Steps 1.2-1.7 but using 2,6-dimethylphenylboronic acid and Pd(PPh3)4 in Step 1.4. Title compound: ESI-MS: 466.2 [M+H]+; tR=3.74 min (System 3).
Reaction SMILES: [NH:1]1[CH2:6][CH2:5][CH:4]([NH:7][C:8](=[O:14])[O:9][C:10]([CH3:13])([CH3:12])[CH3:11])[CH2:3][CH2:2]1.CCN(C(C)C)C(C)C.Cl[C:25]1[N:30]=[CH:29][C:28]([CH2:31][CH3:32])=[CH:27][N:26]=1.O>CN(C=O)C>[CH2:31]([C:28]1[CH:27]=[N:26][C:25]([N:1]2[CH2:2][CH2:3][CH:4]([NH:7][C:8](=[O:14])[O:9][C:10]([CH3:11])([CH3:13])[CH3:12])[CH2:5][CH2:6]2)=[N:30][CH:29]=1)[CH3:32]
Reactant: CC(C)(C)OC(=O)NC1CCNCC1
Reactant: CCc1cnc(Cl)nc1
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Solvent: O
Product: CCc1cnc(N2CCC(NC(=O)OC(C)(C)C)CC2)nc1
Temperature: 100 °C
Reaction time: 18 h
Yield: 40 %

Procedure:
To a solution of tert-butyl piperidin-4-ylcarbamate (5.0 g, 25 mmol) and DIEA (13.0 mL, 74.9 mmol) in DMF (50 mL) was added 2-chloro-5-ethylpyrimidine (4.3 g, 30 mmol). This mixture stirred at 100° C. for 18 hours in a sealed tube. The mixture was poured into water (500 mL) and extracted into EtOAc (3×100 mL). The combined organic layers were washed with brine, dried over MgSO4, filtered and concentrated in vacuo. The residue was purified over silica gel (100% EtOAc) to yield tert-butyl 1-(5-ethylpyrimidin-2-yl)piperidin-4-ylcarbamate (3.2 g, 10 mmol, 42%).
Reaction SMILES: [F:1][C:2]([F:6])([F:5])[CH2:3][NH2:4].C(N(CC)CC)C.[CH:14]([C:16]1[CH:24]=[CH:23][C:19]([C:20](Cl)=[O:21])=[CH:18][CH:17]=1)=[O:15]>C(Cl)(Cl)Cl.O>[CH:14]([C:16]1[CH:24]=[CH:23][C:19]([C:20]([NH:4][CH2:3][C:2]([F:6])([F:5])[F:1])=[O:21])=[CH:18][CH:17]=1)=[O:15]
Reactant: NCC(F)(F)F
Reactant: O=Cc1ccc(C(=O)Cl)cc1
Solvent: ClC(Cl)Cl
Solvent: O
Solvent: CCN(CC)CC
Product: O=Cc1ccc(C(=O)NCC(F)(F)F)cc1
Yield: 85.7 %

Procedure:
In a suspension of 1.00 g of 4-formyl benzoic acid in 15 ml of benzene, 0.87 g of thionyl chloride and 2 drops of N,N-dimethylformamide were added, and stirred under reflux with heat for 2 hours. After the completion of the reaction, the reaction mixture was left and cooled to room temperature, and the solvent was distilled off under reduced pressure to obtain 1.14 g of crude 4-formyl benzoic acid chloride as white crystal. In a solution of 0.66 g of 2,2,2-trifluoroethylamine and 0.81 g of triethylamine in 6 ml of chlororform, the solution of 1.14 g of the crude 4-formyl benzoic acid chloride in 6 ml of chloroform was added dropwise under cooling with ice and with stirring, after the completion of the addition dropwise, continued to stir at room temperature for further 18 hours. After the completion of the reaction, the reaction mixture was added in 30 ml of water, extracted with chloroform (20 ml×3). The organic phase was washed with water, dried over anhydrous sodium sulfate, the solvent was distilled off under reduced pressure, the residual solid was washed with hexane to obtain 1.32 g of the aimed product as white crystal. Melting point 83.0 to 84.0° C.
Reaction SMILES: BrC1C=CC(C(O)C(O)=O)=CC=1.C(C1C=C(O)C(CCCCCCCC)=CC=1O)CCCCCCC.[Br:37][C:38]1[CH:43]=[CH:42][C:41]([CH:44]2[C:48](=[O:49])[O:47][C:46]3=[C:50]([CH2:73][CH2:74][CH2:75][CH2:76][CH2:77][CH2:78][CH2:79][CH3:80])[C:51]4[CH:55]([C:56]5[CH:61]=[CH:60][C:59]([Br:62])=[CH:58][CH:57]=5)[C:54](=[O:63])[O:53][C:52]=4[C:64]([CH2:65][CH2:66][CH2:67][CH2:68][CH2:69][CH2:70][CH2:71][CH3:72])=[C:45]23)=[CH:40][CH:39]=1.C1(Cl)C(=O)C(Cl)=C(Cl)C(=O)C=1Cl>ClC1C=CC=C(Cl)C=1Cl.C(O)(=O)C>[Br:62][C:59]1[CH:58]=[CH:57][C:56]([C:55]2[C:54](=[O:63])[O:53][C:52]3=[C:64]([CH2:65][CH2:66][CH2:67][CH2:68][CH2:69][CH2:70][CH2:71][CH3:72])[C:45]4[C:46](=[C:50]([CH2:73][CH2:74][CH2:75][CH2:76][CH2:77][CH2:78][CH2:79][CH3:80])[C:51]=23)[O:47][C:48](=[O:49])[C:44]=4[C:41]2[CH:42]=[CH:43][C:38]([Br:37])=[CH:39][CH:40]=2)=[CH:61][CH:60]=1
Reactant: CCCCCCCCc1c2c(c(CCCCCCCC)c3c1C(c1ccc(Br)cc1)C(=O)O3)C(c1ccc(Br)cc1)C(=O)O2
Agent: CCCCCCCCc1cc(O)c(CCCCCCCC)cc1O
Agent: Clc1cccc(Cl)c1Cl
Agent: O=C(O)C(O)c1ccc(Br)cc1
Solvent: CC(=O)O
Product: CCCCCCCCc1c2c(c(CCCCCCCC)c3c1=C(c1ccc(Br)cc1)C(=O)O3)=C(c1ccc(Br)cc1)C(=O)O2
Temperature: 200 °C
Reaction time: 2 h
Yield: 8.6 %

Procedure:
In a 100 cm3 flask fitted with a condenser and a reverse Dean-Stark apparatus, (4-bromo-phenyl)-hydroxy-acetic acid (6.043 g, 26.16 mmol) and 2,5-dioctyl-benzene-1,4-diol (Bao, Z.; Chan, W. K.; Yu, L. J. Am. Chem. Soc. 1995, 117, 12426-12435.) (3.500 g, 10.46 mmol) are dissolved in 1,2-dichlorochlorobenzene (35 cm3). The reaction mixture is heated to 200° C. and the generated water is distilled off the using a reverse Dean-Stark apparatus. After 2 hours stirring, the reaction mixture is cooled down and the solvent was removed in vacuo. (9.501 g, Crude yield: 125%). The crude 3,7-bis-(4-bromo-phenyl)-4,8-dioctyl-3,7-dihydro-benzo[1,2-b;4,5-b′]difuran-2,6-dione (7.500 g, 10.35 mmol) is dissolved into acetic acid (125 cm3) at 50° C. before adding chloranil (5.090 g, 20.70 mmol). After 16 hours stirring, the reaction mixture is cooled down and the resulting precipitate is filtered. The recovered solid is purified by column chromatography (95:5, petroleum ether (40-60):Ethyl acetate as eluant) to obtain a crystalline orange solid (0.642 g, Yield: 9%). NMR (1H, 300 MHz, CDCl3): δ 7.63 (d, J=8.5 Hz, 4H); 7.30 (d, J=8.5 Hz, 4H); 2.46 (m, 4H); 1.19 (m, 16H); 0.98 (m, 8H); 0.88 (t, J=7.1 Hz, 6H)
Reaction SMILES: [CH2:1]([O:8][C:9](=S)[CH2:10][C:11]([C:13]1[CH:18]=[CH:17][C:16]([O:19][CH3:20])=[CH:15][CH:14]=1)=O)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.Cl.[CH:23]([NH:26][NH2:27])([CH3:25])[CH3:24].C(N(CC)CC)C.O>C(#N)C>[CH2:1]([O:8][C:9]1[CH:10]=[C:11]([C:13]2[CH:18]=[CH:17][C:16]([O:19][CH3:20])=[CH:15][CH:14]=2)[N:26]([CH:23]([CH3:25])[CH3:24])[N:27]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: COc1ccc(C(=O)CC(=S)OCc2ccccc2)cc1
Reactant: CC(C)NN
Agent: Cl
Solvent: O
Solvent: CCN(CC)CC
Solvent: CC#N
Product: COc1ccc(-c2cc(OCc3ccccc3)nn2C(C)C)cc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 62.1 %

Procedure:
To a suspension of 3-(4-methoxyphenyl)-3-oxothiopropionic acid O-benzyl ester (0.60 g) and isopropylhydrazine hydrochloride (0.29 g) in acetonitrile (2 mL) was added triethylamine (0.81 g) and the mixture was stirred at room temperature overnight. Water was added to the reaction mixture and the mixture was extracted with dichloromethane. The solvent of the organic layer was removed under reduced pressure and the residue was purified by column chromatography on silica gel (eluent: hexane/dichloromethane=3/1-1/3) to give the title compound (0.40 g).
Reaction SMILES: CC(C1C=C(C(C)C)C=C(C(C)C)C=1S(O[CH:20]([C:22]1([OH:45])[CH2:25][N:24]([C:26]([C:28]2[CH:33]=[CH:32][C:31]([F:34])=[C:30]([F:35])[C:29]=2[NH:36][C:37]2[CH:42]=[CH:41][C:40]([I:43])=[CH:39][C:38]=2[F:44])=[O:27])[CH2:23]1)[CH3:21])(=O)=O)C.[H-].[Na+].C(OCC)(=O)C>O1CCCC1>[F:35][C:30]1[C:31]([F:34])=[CH:32][CH:33]=[C:28]([C:26]([N:24]2[CH2:25][C:22]3([O:45][CH:20]3[CH3:21])[CH2:23]2)=[O:27])[C:29]=1[NH:36][C:37]1[CH:42]=[CH:41][C:40]([I:43])=[CH:39][C:38]=1[F:44]
Reactant: CC(C)c1cc(C(C)C)c(S(=O)(=O)OC(C)C2(O)CN(C(=O)c3ccc(F)c(F)c3Nc3ccc(I)cc3F)C2)c(C(C)C)c1
Agent: [H-]
Agent: [Na+]
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: CC1OC12CN(C(=O)c1ccc(F)c(F)c1Nc1ccc(I)cc1F)C2
Temperature: 0 °C
Reaction time: 0.25 h
Yield: 98.8 %

Procedure:
1-[1-({3,4-Difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}carbonyl)-3-hydroxyazetidin-3-yl]ethyl 2,4,6-tris(1-methylethyl)benzenesulfonate (194 mg, 0.256 mmol) was dissolved in tetrahydrofuran (2 mL) and was cooled to 0° C. Sodium hydride (60 wt % dispersion in oil; 31 mg, 0.775 mmol) was added and the mixture was stirred at 0° C. for 15 minutes. The mixture was quenched with saturated sodium bicarbonate solution and partitioned with ethyl acetate. The aqueous portion was extracted with ethyl acetate. The combined organic portion was washed with brine, dried over anhydrous sodium sulfate, filtered and concentrated in vacuo. Column chromatography (silica gel, 50% ethyl acetate in hexanes) gave 2,3-difluoro-N-(2-fluoro-4-iodophenyl)-6-[(2-methyl-1-oxa-5-azaspiro[2.3]hex-5-yl)carbonyl]aniline (120 mg, 0.253 mmol, 99% yield): MS (EI) for C18H14F3IN2O2: 475 (MH+).
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([NH:8][C@@H:9]2[CH2:14][CH2:13][CH2:12][CH2:11][C@H:10]2[NH:15][C:16](=[O:21])[C:17]([F:20])([F:19])[F:18])[C:5]([Cl:22])=[CH:4][N:3]=1.[CH3:23][O:24][CH2:25][CH2:26][N:27]1[CH2:33][CH2:32][C:31]2[CH:34]=[C:35]([NH2:38])[CH:36]=[CH:37][C:30]=2[CH2:29][CH2:28]1.Cl.CCOCC>COCCO.O1CCOCC1>[Cl:22][C:5]1[C:6]([NH:8][C@@H:9]2[CH2:14][CH2:13][CH2:12][CH2:11][C@H:10]2[NH:15][C:16](=[O:21])[C:17]([F:20])([F:19])[F:18])=[N:7][C:2]([NH:38][C:35]2[CH:36]=[CH:37][C:30]3[CH2:29][CH2:28][N:27]([CH2:26][CH2:25][O:24][CH3:23])[CH2:33][CH2:32][C:31]=3[CH:34]=2)=[N:3][CH:4]=1
Reactant: COCCN1CCc2ccc(N)cc2CC1
Reactant: O=C(N[C@@H]1CCCC[C@H]1Nc1nc(Cl)ncc1Cl)C(F)(F)F
Agent: Cl
Solvent: COCCO
Solvent: CCOCC
Solvent: C1COCCO1
Product: COCCN1CCc2ccc(Nc3ncc(Cl)c(N[C@@H]4CCCC[C@H]4NC(=O)C(F)(F)F)n3)cc2CC1
Temperature: 120 °C
Reaction time: 3 h

Procedure:
N-[(1R,2R)-2-(2,5-Dichloro-pyrimidin-4-ylamino)-cyclohexyl]-2,2,2-trifluoro-acetamide (776 mg, 2.17 mmol) was added into a Vial, followed by a solution of 3-(2-Methoxy-ethyl)-2,3,4,5-tetrahydro-1H-benzo[d]azepin-7-ylamine (447 mg, 2.03 mmol) in 2-Methoxyethanol (15 mL). 4.00 M of Hydrogen chloride in 1,4-Dioxane (1.1 mL) was added and the reaction was heated at 120° C. After 3 h, the reaction was cooled to room temperature, and 85 mL ether was added. The HCl salt formed as an oil, not a solid, so it was redissolved by adding MeOH and DCM. Macroporous carbonate resin (3.16 mmol/g loading; 2.45 g, 7.7 mmol) was then added and stirred for 1 h and filtered before concentration. The residue was dissolved in DCM, then chromatographed (2×12 g SiO2, ISCO, 0-10% MeOH:DCM) to afford N-((1R,2R)-2-{5-Chloro-2-[3-(2-methoxy-ethyl)-2,3,4,5-tetrahydro-1H-benzo[d]azepin-7-ylamino]-pyrimidin-4-ylamino}-cyclohexyl)-2,2,2-trifluoro-acetamide (414 mg, 38%) as a beige solid. m.p.=180-182° C.; LCMS (m/e) 541 (M+1); 1H-NMR (CDCl3, 400 MHz) δ 7.92 (s, 1H), 7.88 (m, 1H), 7.23 (s, 1H), 7.22 (d, 1H, J=8.5 Hz), 7.04 (d, 1H, J=8.5 Hz), 6.81 (s, 1H), 5.22 (d, 1H, J=7.5 Hz), 4.0 (m, 1H), 3.68 (m, 1H), 3.54 (t, 1H, J=5.5 Hz), 3.36 (s, 3H), 2.92 (m, 4H), 2.74 (m, 4H), 2.28 (m, 1H), 2.15 (m, 1H), 1.80 (m, 4H), 1.2-1.5 (m, 4H).
Reaction SMILES: [C:1](Cl)(Cl)=[O:2].[CH3:5][S:6]([C:8]1[S:12][C:11]([NH2:13])=[N:10][N:9]=1)=[O:7]>C(OCC)(=O)C>[CH3:5][S:6]([C:8]1[S:12][C:11]([N:13]=[C:1]=[O:2])=[N:10][N:9]=1)=[O:7]
Reactant: O=C(Cl)Cl
Reactant: CS(=O)c1nnc(N)s1
Solvent: CCOC(C)=O
Product: CS(=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-methylsulfinyl-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-methylsulfinyl-1,3,4-thiadiazol-2-yl isocyanate dimer.
Reaction SMILES: [C:1]([O:5][CH:6]([C:12]1[C:21]([CH3:22])=[C:20]([CH3:23])[C:19]2[C:14](=[CH:15][CH:16]=[CH:17][CH:18]=2)[C:13]=1[C:24]1[CH:29]=[CH:28][C:27]([Cl:30])=[CH:26][CH:25]=1)[C:7]([O:9]CC)=[O:8])([CH3:4])([CH3:3])[CH3:2].O>C1COCC1.CCO>[C:1]([O:5][CH:6]([C:12]1[C:21]([CH3:22])=[C:20]([CH3:23])[C:19]2[C:14](=[CH:15][CH:16]=[CH:17][CH:18]=2)[C:13]=1[C:24]1[CH:29]=[CH:28][C:27]([Cl:30])=[CH:26][CH:25]=1)[C:7]([OH:9])=[O:8])([CH3:4])([CH3:2])[CH3:3]
Reactant: CCOC(=O)C(OC(C)(C)C)c1c(C)c(C)c2ccccc2c1-c1ccc(Cl)cc1
Solvent: O
Solvent: CCO
Solvent: C1CCOC1
Product: Cc1c(C(OC(C)(C)C)C(=O)O)c(-c2ccc(Cl)cc2)c2ccccc2c1C
Temperature: 100 °C
Yield: 40 %

Procedure:
A solution of the crude ethyl 2-tert-butoxy-2-(1-(4-chlorophenyl)-3,4-dimethylnaphthalen-2-yl)acetate in THF (500 μL), EtOH (Absolute, 250 μL), and H2O (250 μL) was treated with LiOH monohydrate (61 mg, 1.45 mmol) and heated to 100° C. in a sealed vessel for 4 h. The reaction was cooled to 23° C., filtered through a 0.45 micron filter, and directly purified by reverse phase HPLC (Gemini, 5 to 100% ACN/H2O+0.1% TFA). The product-containing fractions were combined and lyophilized, giving the title compound (parent form) (8.0 mg, 40% over 2 steps). 1H NMR (400 MHz, DMSO-d6) δ 12.73 (s, broad, 1H), 8.15 (d, J=8.2 Hz, 1H), 7.72-7.62 (m, 2H), 7.57-7.47 (m, 2H), 7.39-7.32 (m, 2H), 7.19 (d, J=8.2 Hz, 1H), 5.07 (s, 1H), 2.63 (s, 3H), 2.51 (s, 3H), 0.93 (s, 9H).
Reaction SMILES: [C:1]([O:5][C:6](=[O:20])[N:7]([C:13]1[CH:14]=[N:15][CH:16]=[CH:17][C:18]=1I)[CH2:8][C:9]([F:12])([F:11])[F:10])([CH3:4])([CH3:3])[CH3:2].[Cl:21][C:22]1[CH:27]=[CH:26][CH:25]=[CH:24][C:23]=1B(O)O>CCCCCCC.CCOC(C)=O>[C:1]([O:5][C:6](=[O:20])[N:7]([C:13]1[CH:14]=[N:15][CH:16]=[CH:17][C:18]=1[C:23]1[CH:24]=[CH:25][CH:26]=[CH:27][C:22]=1[Cl:21])[CH2:8][C:9]([F:12])([F:11])[F:10])([CH3:4])([CH3:3])[CH3:2]
Reactant: CC(C)(C)OC(=O)N(CC(F)(F)F)c1cnccc1I
Reactant: OB(O)c1ccccc1Cl
Solvent: CCCCCCC
Solvent: CCOC(C)=O
Product: CC(C)(C)OC(=O)N(CC(F)(F)F)c1cnccc1-c1ccccc1Cl

Procedure:
The title compound was prepared in analogy to example 72, from (4-iodo-pyridin-3-yl)-(2,2,2-trifluoro-ethyl)-carbamic acid tert-butyl ester and 2-chlorophenylboronic acid (CAS RN 1679-18-1) and using a gradient of n-heptane:EtOAc (100:0 to 30:70) for the chromatographic purification. Colorless oil (69%). MS (ESI): m/z=403.012 [M+H]+.
Reaction SMILES: C([N:8]([C@H:10]([C:21]#[CH:22])[C@H:11]([O:13][Si](C(C)(C)C)(C)C)[CH3:12])[CH3:9])(OC(C)(C)C)=O.[F:23][C:24]1[C:25](I)=[C:26]2[C:30](=[CH:31][CH:32]=1)[NH:29][C:28](=[O:33])/[C:27]/2=[CH:34]\[C:35]1[NH:36][CH:37]=[CH:38][C:39]=1[O:40][CH3:41]>CN(C=O)C.CCN(CC)CC.CCOC(C)=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.[Cu]I>[F:23][C:24]1[C:25]([C:22]#[C:21][C@@H:10]([NH:8][CH3:9])[C@H:11]([OH:13])[CH3:12])=[C:26]2[C:30](=[CH:31][CH:32]=1)[NH:29][C:28](=[O:33])/[C:27]/2=[CH:34]\[C:35]1[NH:36][CH:37]=[CH:38][C:39]=1[O:40][CH3:41]
Reactant: C#C[C@H]([C@@H](C)O[Si](C)(C)C(C)(C)C)N(C)C(=O)OC(C)(C)C
Reactant: COc1cc[nH]c1/C=C1\C(=O)Nc2ccc(F)c(I)c21
Agent: [Cu]I
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Solvent: CCOC(C)=O
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Product: CN[C@H](C#Cc1c(F)ccc2c1/C(=C/c1[nH]ccc1OC)C(=O)N2)[C@@H](C)O
Reaction time: 2 h

Procedure:
Using Method C above, (2R,3R)-3-(N-Boc-N-methylamino)-2-(tert-butyldimethylsilyloxy)-pent-4-yne (370 mg, 1.13 mmol) (Example 117C above) was coupled with (Z)-1,3-dihydro-5-fluoro-4-iodo-3-[(3-methoxy-1H-pyrrol-2-yl)methylene]-2H-indol-2-one (150 mg, 0.39 mmol) (Starting Material 6) using (Ph3P)4Pd (45 mg, 0.04 mmol) and a catalylic amount of CuI in a mixture of DMF (5 mL) and Et3N (5 mL) as solvent at 80° C. for 5 hrs. Upon completion, the reaction mixture was diluted with EtOAc and extracted with H2O. The organic layer was dried over Na2SO4, concentrated and the residue was chromatographed on a silica gel column with a 0-40% EtOAc in hexanes gradient. The resulting intermediate was dissolved in 5 mL of a 50% trifluoroacetic acid in CH2Cl2 solution that contained 0.5 mL of H2O at 0° C. and stirred for 2 hrs. Upon completion, the reaction mixture was diluted with EtOAc and extracted with ammonium hydroxide. The organic layer was dried over Na2SO4 and concentrated. (Z)-1,3-Dihydro-5-fluoro-4-[(3R,4R)-4-hydroxy-3-methylamino-1-pentynyl]-3-[(3-methoxy-1H-pyrrol-2-yl)methylene]-2H-indol-2-one was obtained after silica gel column chromatography with a 0-10% MeOH in CH2Cl2 gradient and precipitation out of THF with excess pentane. (Yield 53 mg, 37%).
Reaction SMILES: [NH2:1][CH2:2][C:3]1[N:7]2[C:8]3[CH:33]=[CH:32][CH:31]=[CH:30][C:9]=3[O:10][C:11]3([CH2:16][CH2:15][N:14]([C:17]([C:19]4[CH:24]=[CH:23][C:22]([O:25][CH:26]([CH3:28])[CH3:27])=[C:21]([CH3:29])[CH:20]=4)=[O:18])[CH2:13][CH2:12]3)[C:6]2=[CH:5][CH:4]=1.[C:34](OC(=O)C)(=[O:36])[CH3:35]>ClCCl.N1C=CC=CC=1>[CH:26]([O:25][C:22]1[CH:23]=[CH:24][C:19]([C:17]([N:14]2[CH2:15][CH2:16][C:11]3([O:10][C:9]4[CH:30]=[CH:31][CH:32]=[CH:33][C:8]=4[N:7]4[C:3]([CH2:2][NH:1][C:34](=[O:36])[CH3:35])=[CH:4][CH:5]=[C:6]34)[CH2:12][CH2:13]2)=[O:18])=[CH:20][C:21]=1[CH3:29])([CH3:27])[CH3:28]
Reactant: CC(=O)OC(C)=O
Reactant: Cc1cc(C(=O)N2CCC3(CC2)Oc2ccccc2-n2c(CN)ccc23)ccc1OC(C)C
Solvent: ClCCl
Solvent: c1ccncc1
Product: CC(=O)NCc1ccc2n1-c1ccccc1OC21CCN(C(=O)c2ccc(OC(C)C)c(C)c2)CC1
Temperature: 0 °C
Reaction time: 0.5 h

Procedure:
Crude (1-(aminomethyl)spiro[benzo[b]pyrrolo[1,2-d][1,4]oxazine-4,4′-piperidine]-1′-yl)(4-isopropoxy-3-methylphenyl)methanone (49 mg, 0.11 mmol) was dissolved in a solution of dry dichloromethane (0.5 mL) and pyridine (0.3 mL) and was cooled to 0° C. Acetic anhydride (52 μL, 0.55 mmol) was added and the reaction mixture was stirred for 30 minutes. The reaction mixture was quenched by the addition of methanol (0.5 mL), concentrated, and purified by reverse phase HPLC [10-99% acetonitrile in water (HCl modifier)] to give N-((1′-(4-isopropoxy-3-methylbenzoyl)spiro[benzo[b]pyrrolo[1,2-d][1,4]oxazine-4,4′-piperidine]-1-yl)methyl)acetamide. 1H NMR (400 MHz, CDCl3) δ 7.41 (d, J=7.9 Hz, 1H), 7.33-7.21 (m, 2H), 7.13 (d, J=4.2 Hz, 2H), 7.10-7.02 (m, 1H), 6.83 (d, J=8.1 Hz, 1H), 6.26 (d, J=3.4 Hz, 1H), 5.99 (d, J=3.5 Hz, 1H), 5.68 (s, 1H), 4.71 (d, J=4.7 Hz, 2H), 4.64-4.50 (m, 1H), 3.50 (s, 2H), 2.22 (s, 3H), 2.17-1.76 (m, 7H), 1.67 (s, 2H), 1.36 (d, J=6.0 Hz, 6H). ESI-MS m/z talc. 487.6, found 488.5 (M+1)+; Retention time: 1.81 minutes (3 min run).