Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([S:8]([N:11]2[CH:16]3[CH2:17][CH:18]([C:20]4[O:24][N:23]=[C:22]([CH3:25])[N:21]=4)[CH2:19][CH:12]2[CH2:13][C:14](=[O:26])[CH2:15]3)(=[O:10])=[O:9])=[CH:4][CH:3]=1.[CH:27](OCC)=[O:28].[O-]CC.[Na+]>C1COCC1.CCO>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([S:8]([N:11]2[CH:12]3[CH2:19][CH:18]([C:20]4[O:24][N:23]=[C:22]([CH3:25])[N:21]=4)[CH2:17][CH:16]2[C:15](=[CH:27][OH:28])[C:14](=[O:26])[CH2:13]3)(=[O:9])=[O:10])=[CH:6][CH:7]=1
Reactant: Cc1noc(C2CC3CC(=O)CC(C2)N3S(=O)(=O)c2ccc(Cl)cc2)n1
Reactant: CCOC=O
Agent: CC[O-]
Agent: [Na+]
Solvent: CCO
Solvent: C1CCOC1
Product: Cc1noc(C2CC3CC(=O)C(=CO)C(C2)N3S(=O)(=O)c2ccc(Cl)cc2)n1
Temperature: 50 °C
Reaction time: 1 h

Procedure:
9-[(4-Chlorophenyl)sulfonyl]-7-(3-methyl-1,2,4-oxadiazol-5-yl)-9-azabicyclo[3.3.1]nonan-3-one (52) (0.357 g, 0.902 mmol) was dissolved in THF/EtOH (2 mL, 1/1, v/v). Ethyl formate (0.725 mL, 9.02 mmol) was added followed by sodium ethoxide (1.01 mL of 21% solution in EtOH). The resulting mixture was stirred at 50° C. for 1 hour after which the solution was cooled back to room temperature and quenched by the addition of saturated aqueous NH4Cl. The resulting mixture was extracted with EtOAc and the combined organic phases were dried (Na2SO4), filtered and concentrated under vacuum to give 9-[(4-chlorophenyl)sulfonyl]-2-(hydroxymethylidene)-7-(3-methyl-1,2,4-oxadiazol-5-yl)-9-azabicyclo[3.3.1]nonan-3-one (53). MS (ESI) 424.0 (M+H).
Reaction SMILES: [C:1]([C:4]1[CH:9]=[CH:8][C:7]([N:10]2[C:14](=[O:15])[CH2:13][C:12]([CH3:16])=[N:11]2)=[CH:6][CH:5]=1)([OH:3])=[O:2].[CH3:17][N:18]([CH3:29])[C:19]1[CH:28]=[CH:27][C:22]([CH:23]=[CH:24][CH:25]=O)=[CH:21][CH:20]=1.C(O)(=O)C>CCO>[C:1]([C:4]1[CH:5]=[CH:6][C:7]([N:10]2[C:14](=[O:15])[C:13](=[CH:25][CH:24]=[CH:23][C:22]3[CH:21]=[CH:20][C:19]([N:18]([CH3:29])[CH3:17])=[CH:28][CH:27]=3)[C:12]([CH3:16])=[N:11]2)=[CH:8][CH:9]=1)([OH:3])=[O:2]
Reactant: CC1=NN(c2ccc(C(=O)O)cc2)C(=O)C1
Reactant: CN(C)c1ccc(C=CC=O)cc1
Solvent: CCO
Solvent: CC(=O)O
Product: CC1=NN(c2ccc(C(=O)O)cc2)C(=O)C1=CC=Cc1ccc(N(C)C)cc1
Temperature: 25 °C
Reaction time: 0.08 h

Procedure:
1-(4-Carboxyphenyl)-3-methyl-2-pyrazolin-5-one (2.18 gm, 0.010 mol), 4-dimethylaminocinnamaldehyde (1.75 gm, 0.010 mol) and glacial acetic acid (10 ml) were mixed together to form a slurry. It was heated to reflux with stirring, held at reflux for five minutes and then cooled to RT. EtOH (20 ml) was added to the reaction mixture which was heated again to reflux, held there for five minutes and cooled to RT. The product was isolated by filtration, washed in succession with ethanol and ligroin, and dried. The reaction was repeated twice on the same scale and the products obtained were all combined. They were treated further by first slurrying in refluxing EtOH (150 ml), isolating the solid by filtration while hot, and then slurrying in refluxing MeOH (200 ml) and isolating it again, while hot, by filtration. The mp was 282°-284° C. The NMR and IR spectra were consistent for the structure assigned. The C,H and N elemental analyses were in agreement with those calculated for the empirical formula of the dye.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([NH:9][C:10](=[O:18])[C:11]2[CH:16]=[CH:15][CH:14]=[CH:13][C:12]=2[OH:17])=[CH:5][CH:4]=1.C(N(CC)CC)C.[C:26]([C:30]1[CH:38]=[CH:37][C:33]([C:34](Cl)=[O:35])=[CH:32][CH:31]=1)([CH3:29])([CH3:28])[CH3:27]>C(Cl)Cl>[CH3:1][O:2][C:3]1[CH:4]=[CH:5][C:6]([NH:9][C:10](=[O:18])[C:11]2[CH:16]=[CH:15][CH:14]=[CH:13][C:12]=2[O:17][C:34](=[O:35])[C:33]2[CH:37]=[CH:38][C:30]([C:26]([CH3:28])([CH3:27])[CH3:29])=[CH:31][CH:32]=2)=[CH:7][CH:8]=1
Reactant: COc1ccc(NC(=O)c2ccccc2O)cc1
Reactant: CC(C)(C)c1ccc(C(=O)Cl)cc1
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: COc1ccc(NC(=O)c2ccccc2OC(=O)c2ccc(C(C)(C)C)cc2)cc1
Temperature: 25 °C
Yield: 60.5 %

Procedure:
To a solution of N-(4-methoxyphenyl)-2-hydroxybenzamide (0.484 g, 2.00 mmol) in methylene chloride (35 mL) cooled to 0° C. was added 0.28 mL triethylamine (0.28 mL, 2.0 mmol), followed by the dropwise addition of a solution of 4-tert-butylbenzoyl chloride (0.393 mL, 2.00 mmol) in methylene chloride (15 mL). The reaction mixture was allowed to warm to room temperature over 16 h and washed with cold water. The organic layer was dried (magnesium sulfate), filtered, and concentrated in vacuo. Trituration with hexane provided 0.488 g (61%) of the title compound.
Reaction SMILES: Cl.Cl[CH2:3][C:4]1[CH:9]=[CH:8][CH:7]=[CH:6][N:5]=1.[OH:10][C:11]1[CH:16]=[CH:15][C:14]([C:17]([O:19][CH2:20][CH3:21])=[O:18])=[CH:13][CH:12]=1>>[N:5]1[CH:6]=[CH:7][CH:8]=[CH:9][C:4]=1[CH2:3][O:10][C:11]1[CH:12]=[CH:13][C:14]([C:17]([O:19][CH2:20][CH3:21])=[O:18])=[CH:15][CH:16]=1
Reactant: CCOC(=O)c1ccc(O)cc1
Reactant: ClCc1ccccn1
Agent: Cl
Product: CCOC(=O)c1ccc(OCc2ccccn2)cc1
Yield: 83.7 %

Procedure:
2-Chloromethylpyridine hydrochloride (500 mg) and ethyl 4-hydroxybenzenecarboxylate (506 mg) were processed in the same manner as in Production Example 1-1 to obtain the entitled compound (656 mg).
Reaction SMILES: [C:1]([CH2:4][CH:5]1[CH2:10][CH:9]2[CH2:11][CH2:12][N:6]1[CH2:7][CH2:8]2)([OH:3])=[O:2].[ClH:13].[CH2:14](O)[CH3:15]>>[ClH:13].[CH2:14]([O:2][C:1]([CH2:4][CH:5]1[CH2:10][CH:9]2[CH2:8][CH2:7][N:6]1[CH2:12][CH2:11]2)=[O:3])[CH3:15]
Reactant: O=C(O)CC1CC2CCN1CC2
Reactant: CCO
Agent: Cl
Product: CCOC(=O)CC1CC2CCN1CC2

Procedure:
28 g of 2-carboxymethyl-quinuclidine were esterified by treatment with a solution of anhydrous hydrogen chloride in absolute ethanol for 48 hours at room temperature. 25 g of 2-ethoxycarbonylmethyl-quinuclidine hydrochloride were obtained.
Reaction SMILES: [N+:1]([C:4]1[CH:9]=[CH:8][C:7]([OH:10])=[CH:6][CH:5]=1)([O-:3])=[O:2].Cl[C:12]([F:18])([F:17])C(OC)=O.C(=O)([O-])[O-].[K+].[K+].C(OCC)(=O)C>CN(C=O)C>[F:17][CH:12]([F:18])[O:10][C:7]1[CH:8]=[CH:9][C:4]([N+:1]([O-:3])=[O:2])=[CH:5][CH:6]=1
Reactant: COC(=O)C(F)(F)Cl
Reactant: O=[N+]([O-])c1ccc(O)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Product: O=[N+]([O-])c1ccc(OC(F)F)cc1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 63.5 %

Procedure:
4-Nitrophenol (0.14 g, 1.0 mmol, Aldrich), methyl chlorodifluoroacetate (0.29 g, 2.0 mmol, Aldrich) and potassium carbonate (0.29 g, 2.1 mmol) were combined in dry DMF (0.5 mL) under an argon atmosphere. After stirring at 95°-100° C. for 0.5 h, the mixture was cooled to RT, ethyl acetate (20 mL) was added and the organic layer was washed three times with 10% NaOH. The organic extract was dried (MgSO4), filtered and evaporated. The residue was purified by flash chromatography (silica gel, 20% ether/hexanes) to provide the title compound as a white solid (0.12 g, 65%). mp 33°-35° C.
Reaction SMILES: COC1C=CC(C[N:8]2[C:12]3[N:13]=[C:14]([C:32]4[CH:37]=[CH:36][C:35]([O:38][CH3:39])=[CH:34][CH:33]=4)[C:15]4[C:16](=[O:31])[NH:17][C:18]5[CH:24]=[C:23]([N:25]6[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]6)[CH:22]=[CH:21][C:19]=5[C:20]=4[C:11]=3[C:10]([CH3:40])=[N:9]2)=CC=1.C(OC(C)C)(C)C.[F:50][C:51]([F:56])([F:55])[C:52]([OH:54])=[O:53]>>[F:50][C:51]([F:56])([F:55])[C:52]([OH:54])=[O:53].[CH3:39][O:38][C:35]1[CH:36]=[CH:37][C:32]([C:14]2[C:15]3[C:16](=[O:31])[NH:17][C:18]4[CH:24]=[C:23]([N:25]5[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]5)[CH:22]=[CH:21][C:19]=4[C:20]=3[C:11]3[C:10]([CH3:40])=[N:9][NH:8][C:12]=3[N:13]=2)=[CH:33][CH:34]=1
Reactant: COc1ccc(Cn2nc(C)c3c4c(c(-c5ccc(OC)cc5)nc32)c(=O)[nH]c2cc(N3CCNCC3)ccc24)cc1
Solvent: O=C(O)C(F)(F)F
Solvent: CC(C)OC(C)C
Product: COc1ccc(-c2nc3[nH]nc(C)c3c3c2c(=O)[nH]c2cc(N4CCNCC4)ccc23)cc1
Temperature: 25 °C
Reaction time: 4 h

Procedure:
A solution of 4.5 g (8.03 mmol) of 3-(4-methoxybenzyl)-5-(4-methoxyphenyl)-1-methyl-9-(piperazin-1-yl)-3H-benzo[f]pyrazolo[3,4-c][2,7]naphthyridin-6(7H)-one dissolved in 70 ml of trifluoroacetic acid is carried at 70° C. for 4 hours and then cooled to room temperature before the addition of isopropyl ether (150 ml). The reaction medium is stirred at room temperature for 30 minutes and then the precipitate obtained is filtered to yield 5-(4-methoxyphenyl)-1-methyl-9-(piperazin-1-yl)-3H-benzo[f]pyrazolo[3,4-c][2,7]naphthyridin-6(7H)-one trifluoroacetate. The solid is dissolved in 180 ml of anhydrous dichloroethane. The reaction medium is cooled to 0° C. before the slow addition of 43.3 ml (43.3 mmol) of a 1 M solution of boron tribromide in dichloromethane. The reaction medium is carried at reflux for 7 hours and then cooled again to 0° C. Methanol (approximately 200 ml) is added and then the reaction medium is stirred for 2 hours. The solid obtained is filtered and then triturated several times in hot methanol. A final filtration yields 2.6 g (47%) of 5-(4-hydroxyphenyl)-1-methyl-9-(piperazin-1-yl)-3H-benzo[f]pyrazolo[3,4-c][2,7]naphthyridin-6(7H)-one hydrobromide in the form of an orange solid.
Reaction SMILES: [N+:1]([C:4]1[CH:5]=[C:6]([CH:9]=[CH:10][CH:11]=1)[CH:7]=O)([O-:3])=[O:2].[CH:12]([O:15][C:16](=[O:23])[CH:17]=[C:18]([NH2:22])[O:19][CH2:20][CH3:21])([CH3:14])[CH3:13]>C(O)C>[CH:12]([O:15][C:16]([C:17]1[CH:7]([C:6]2[CH:9]=[CH:10][CH:11]=[C:4]([N+:1]([O-:3])=[O:2])[CH:5]=2)[CH:17]([C:16]([O:15][CH:12]([CH3:13])[CH3:14])=[O:23])[C:18]([O:19][CH2:20][CH3:21])=[N:22][C:18]=1[NH2:22])=[O:23])([CH3:14])[CH3:13]
Reactant: O=Cc1cccc([N+](=O)[O-])c1
Reactant: CCOC(N)=CC(=O)OC(C)C
Solvent: CCO
Product: CCOC1=NC(N)=C(C(=O)OC(C)C)C(c2cccc([N+](=O)[O-])c2)C1C(=O)OC(C)C
Yield: 45 %

Procedure:
Heating a solution of 6.1 g of 3-nitrobenzaldehyde and 13.9 g of 3-amino-3-ethoxyacrylic acid isopropyl ester in 100 ml of ethanol for 8 hours yields 2-amino-6-ethoxy-4-(3-nitrophenyl)-4,5-dihydropyridine-3,5-dicarboxylic acid diisopropyl ester of melting point 130° C (ether/petroleum ether). Yield: 45% of theory.
Reaction SMILES: [C:1]([C:3]1[CH:8]=[C:7]([N+:9]([O-:11])=[O:10])[CH:6]=[CH:5][C:4]=1[S:12]([NH:15][C:16]1[CH:25]=[C:24]2[C:19]([C:20]([CH3:32])=[C:21]([CH2:27][C:28]([O:30]C)=[O:29])[C:22](=[O:26])[O:23]2)=[CH:18][CH:17]=1)(=[O:14])=[O:13])#[N:2].Cl>C1COCC1.O>[C:1]([C:3]1[CH:8]=[C:7]([N+:9]([O-:11])=[O:10])[CH:6]=[CH:5][C:4]=1[S:12]([NH:15][C:16]1[CH:25]=[C:24]2[C:19]([C:20]([CH3:32])=[C:21]([CH2:27][C:28]([OH:30])=[O:29])[C:22](=[O:26])[O:23]2)=[CH:18][CH:17]=1)(=[O:14])=[O:13])#[N:2]
Reactant: COC(=O)Cc1c(C)c2ccc(NS(=O)(=O)c3ccc([N+](=O)[O-])cc3C#N)cc2oc1=O
Agent: Cl
Solvent: O
Solvent: C1CCOC1
Product: Cc1c(CC(=O)O)c(=O)oc2cc(NS(=O)(=O)c3ccc([N+](=O)[O-])cc3C#N)ccc12
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
Compound 2a was dissolved in THF (3.5 ml), lithium hydroxide•monohydrate (22.2 mg, 0.53 mmol, 7.6 equivalents) dissolved in H2O (3.5 ml) was added under cooling on ice, and the mixture was stirred. After 30 min, the reaction mixture was warmed to room temperature and further stirred. After 3 hr, the disappearance of the starting materials was confirmed by TLC and the reaction mixture was acidified with 5% HCl and extracted with CHCl3. The organic layer was washed with saturated brine, and dried over Na2SO4. The solvent was evaporated, and the residue was purified by silica gel column chromatography (eluate: 1% acetic acid-containing CHCl3:MeOH=20:1) (compound 3a: 29.6 mg, 0.07 mmol, 95%).
Reaction SMILES: [CH3:1][N:2]([CH3:34])[C:3]([C:5]1[CH:10]=[CH:9][C:8]([CH:11]2[CH:20]([C:21]3[CH:26]=[CH:25][C:24]([F:27])=[CH:23][CH:22]=3)[C:19](=O)[C:18]3[C:17]([C:29]([O:31]CC)=O)=[CH:16][CH:15]=[CH:14][C:13]=3[NH:12]2)=[CH:7][CH:6]=1)=[O:4].O.[NH2:36][NH2:37]>>[F:27][C:24]1[CH:25]=[CH:26][C:21]([CH:20]2[C:19]3=[N:36][NH:37][C:29](=[O:31])[C:17]4[CH:16]=[CH:15][CH:14]=[C:13]([C:18]=43)[NH:12][CH:11]2[C:8]2[CH:7]=[CH:6][C:5]([C:3]([N:2]([CH3:34])[CH3:1])=[O:4])=[CH:10][CH:9]=2)=[CH:22][CH:23]=1
Reactant: NN
Reactant: CCOC(=O)c1cccc2c1C(=O)C(c1ccc(F)cc1)C(c1ccc(C(=O)N(C)C)cc1)N2
Solvent: O
Product: CN(C)C(=O)c1ccc(C2Nc3cccc4c(=O)[nH]nc(c34)C2c2ccc(F)cc2)cc1
Temperature: 40 °C
Reaction time: 3 h
Yield: 24 %

Procedure:
A mixture of ethyl 2-(4-(dimethylcarbamoyl)phenyl)-3-(4-fluorophenyl)-4-oxo-1,2,3,4-tetrahydroquinoline-5-carboxylate (490 mg, 1 mmol) and hydrazine monohydrate (15 mL) was stirred at 40° C. for 3 h. Then the mixture was cooled to room temperature and filtered to give the title compound (110 mg, yield 24%) as a white solid. 1H-NMR (400 MHz, DMSO-d6) δ (ppm): 2.82 (s, 1H), 2.93 (s, 1H), 4.36-4.38 (d, J=9.2 Hz, 1H), 4.78-4.80 (d, J=9.2 Hz, 1H), 7.01-7.03 (m, 2H), 7.14-7.19 (m, 3H), 7.25-7.28 (m, 2H), 7.32-7.40 (m, 3H), 7.45 (s, 1H), 7.56-7.60 (t, J=8 Hz, 1H), 12.17 (s, 1H); LC-MS (ESI) m/z: 429 (M+1)+.
Reaction SMILES: [OH-].[K+].C([O:5][C:6]([C:8]1([CH2:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][C:23]2([CH:26]([F:28])[F:27])[CH2:25][CH2:24]2)[CH2:10][CH2:9]1)=[O:7])C.Cl>C(O)C.O>[F:27][CH:26]([F:28])[C:23]1([CH2:22][CH2:21][CH2:20][CH2:19][CH2:18][CH2:17][CH2:16][CH2:15][CH2:14][CH2:13][CH2:12][CH2:11][C:8]2([C:6]([OH:7])=[O:5])[CH2:9][CH2:10]2)[CH2:25][CH2:24]1
Reactant: CCOC(=O)C1(CCCCCCCCCCCCC2(C(F)F)CC2)CC1
Agent: Cl
Agent: [K+]
Agent: [OH-]
Solvent: O
Solvent: CCO
Product: O=C(O)C1(CCCCCCCCCCCCC2(C(F)F)CC2)CC1
Temperature: 40 °C
Reaction time: 16 h
Yield: 71.5 %

Procedure:
To a solution of potassium hydroxide (0.63 g, 11.2 mol) in 90% ethanol (5 mL) was added product of Example 38 (0.5 g, 1.3 mmol) at 40° C. and the reaction mass was stirred at 40° C. over a period of 16 h. The crude product obtained upon evaporation of the solvent was diluted with water (5 mL), acidified to pH=2 (1N HCl) and extracted with ethyl acetate (100 mL×3). The crude product obtained upon evaporation of the solvent was purified by silica gel column (5% ethyl acetate in petroleum ether) to give product as white solid 0.32 g (69.5%). mp: 54.0° C.-54.8° C.
Reaction SMILES: [NH:1](C(OCC1C=CC=CC=1)=O)[C@H:2]([C:11]([NH:13][C@@H:14]([C:16]([NH:18][CH2:19][C:20]([NH:22][C@H:23]([C:31]([N:33]1[CH2:40][CH2:39][CH2:38][C@H:34]1[C:35](O)=[O:36])=[O:32])[CH2:24][C:25]1[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=1)=[O:21])=[O:17])[CH3:15])=[O:12])[CH2:3][C:4]1[CH:9]=[CH:8][C:7]([OH:10])=[CH:6][CH:5]=1.Cl.[CH2:52]([NH2:54])[CH3:53].C(N(CC)CC)C.C1(N=C=NC2CCCCC2)CCCCC1>CN(C)C=O>[CH2:52]([NH:54][C:35](=[O:36])[C@@H:34]1[CH2:38][CH2:39][CH2:40][N:33]1[C:31](=[O:32])[C@H:23]([CH2:24][C:25]1[CH:26]=[CH:27][CH:28]=[CH:29][CH:30]=1)[NH:22][C:20](=[O:21])[CH2:19][NH:18][C:16](=[O:17])[C@@H:14]([CH3:15])[NH:13][C:11](=[O:12])[C@H:2]([CH2:3][C:4]1[CH:5]=[CH:6][C:7]([OH:10])=[CH:8][CH:9]=1)[NH2:1])[CH3:53]
Reactant: C[C@@H](NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)OCc1ccccc1)C(=O)NCC(=O)N[C@@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)O
Reactant: CCN
Agent: C(=NC1CCCCC1)=NC1CCCCC1
Agent: Cl
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Product: CCNC(=O)[C@@H]1CCCN1C(=O)[C@H](Cc1ccccc1)NC(=O)CNC(=O)[C@@H](C)NC(=O)[C@@H](N)Cc1ccc(O)cc1
Reaction time: 24 h

Procedure:
0.7 g. (1 mmoles) of Z-Tyr-D-Ala-Gly-Phe-Pro-OH (3rd step of Example 5) are dissolved in 2 ml. of dimethyl formamide, then 0.1 g. (1.24 mmoles) of ethylamine hydrochloride, 0.17 ml. (1.24 mmoles) of triethylamine and 0.21 g. (1 mmole) of dicyclohexyl-carbodiimide are added. The reaction mixture is allowed to stand for one day, filtered and diluted with 30 ml. of ethyl acetate. The solution is washed with 0.5N sulphuric acid, water, 5% solution of sodium hydrogen carbonate and water, then dried and evaporated. The residue on evaporation (Rf2 0.80-0.85) is dissolved in 30 ml. of methanol and hydrogenated in the presence of palladium as catalyst. At the end of the reaction the catalyst is filtered off, the solution evaporated, rubbed with ether, filtered, washed with ether and dried. Yield: 0.43 g. (75%) of the named pentapeptide; Rf4 0.34-0.44.
Reaction SMILES: [NH2:1][CH:2]1[CH2:8][CH2:7][C:6]2[CH:9]=[C:10]([S:13][CH3:14])[CH:11]=[CH:12][C:5]=2[NH:4][C:3]1=[O:15].[C:16]([O:20][C:21]([NH:23][C:24]([CH3:30])([CH3:29])[CH2:25][C:26](O)=[O:27])=[O:22])([CH3:19])([CH3:18])[CH3:17]>>[C:16]([O:20][C:21]([NH:23][C:24]([CH3:30])([CH3:29])[CH2:25][C:26]([NH:1][CH:2]1[CH2:8][CH2:7][C:6]2[CH:9]=[C:10]([S:13][CH3:14])[CH:11]=[CH:12][C:5]=2[NH:4][C:3]1=[O:15])=[O:27])=[O:22])([CH3:19])([CH3:18])[CH3:17]
Reactant: CC(C)(CC(=O)O)NC(=O)OC(C)(C)C
Reactant: CSc1ccc2c(c1)CCC(N)C(=O)N2
Product: CSc1ccc2c(c1)CCC(NC(=O)CC(C)(C)NC(=O)OC(C)(C)C)C(=O)N2

Procedure:
Prepared from the intermediate obtained in Step D and 3-t-butoxycarbonylamino-3-methyl-butanoic acid (Example 31, Step E) by the procedure described in Example 1, Step F. 1H NMR (200 MHz, CDCl3): 1.33 (s,6H), 1.40 (s,9H), 1.91 (m,1H), 2.4-3.0 (m,5H), 2.48 (s,3H), 4.50 (m,1H), 5.22 (br s,1H), 6.68 (d,7 Hz,1H), 6.90 (d,8 Hz,1H), 7.11 (m,2H), 7.66 (br s,1H).
Reaction SMILES: [Br:1][C:2]1[C:3](F)=[C:4]2[C:10]([NH:11][C:12]([CH:14]3[CH2:18][CH2:17][CH2:16][CH2:15]3)=[O:13])=[CH:9][NH:8][C:5]2=[N:6][CH:7]=1.[NH:20]1[CH2:25][CH2:24][CH2:23][C@@H:22]([NH:26][C:27](=[O:33])[O:28][C:29]([CH3:32])([CH3:31])[CH3:30])[CH2:21]1>CCCCO>[Br:1][C:2]1[C:3]([N:20]2[CH2:25][CH2:24][CH2:23][C@@H:22]([NH:26][C:27](=[O:33])[O:28][C:29]([CH3:31])([CH3:30])[CH3:32])[CH2:21]2)=[C:4]2[C:10]([NH:11][C:12]([CH:14]3[CH2:18][CH2:17][CH2:16][CH2:15]3)=[O:13])=[CH:9][NH:8][C:5]2=[N:6][CH:7]=1
Reactant: CC(C)(C)OC(=O)N[C@@H]1CCCNC1
Reactant: O=C(Nc1c[nH]c2ncc(Br)c(F)c12)C1CCCC1
Solvent: CCCCO
Product: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2c(Br)cnc3[nH]cc(NC(=O)C4CCCC4)c23)C1
Temperature: 160 °C
Reaction time: 18 h
Yield: 22 %

Procedure:
A solution of N-(5-bromo-4-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)cyclopentanecarboxamide (205 mg, 0.629 mmol) in n-BuOH (5 mL) was treated with (R)-tert-butyl piperidin-3-ylcarbamate (629 mg, 3.14 mmol) and stirred at 160° C. for 18 hours in a sealed tube. The solvent was removed in vacuo, and the residue was dissolved in EtOAc (50 mL) and washed with water (2×10 mL). The organic layer was dried (MgSO4), filtered, and concentrated in vacuo. The residue was purified by C-18 reverse phase flash chromatography (Biotage SP4 unit, C-18 25M column, 5-80% CH3CN/water gradient; 25 CV) to yield a solid, which was crystallized from CH3CN to provide (R)-tert-butyl 1-(5-bromo-3-(cyclopentane carboxamido)-1H-pyrrolo[2,3-b]pyridin-4-yl)piperidin-3-ylcarbamate (70 mg, 22% yield) as a solid. 1H NMR (400 MHz, (CD3)2SO) δ 11.56 (s, 1H), 9.36 (s, 1H), 8.14 (s, 1H), 7.64 (br s, 1H), 6.90 (br s, 1H), 3.56-3.47 (m, 1H), 3.20-3.11 (m, 2H), 3.04-2.97 (m, 1H), 2.81-2.74 (m, 1H), 1.91-1.80 (m, 4H), 1.78-1.70 (m, 3H), 1.67-1.59 (m, 3H), 1.55-1.50 (m, 2H), 1.42-1.34 (m, 1H); LCMS (APCI+) m/z 407.9 [(M-Boc)+H]+, Retention time=4.03 minutes (Method 2).
Reaction SMILES: Br[C:2]1[C:10]2[C:9]([NH2:11])=[N:8][CH:7]=[N:6][C:5]=2[N:4]([CH:12]([CH3:14])[CH3:13])[CH:3]=1.CC1(C)C(C)(C)OB([C:23]2[CH:24]=[C:25]3[C:29](=[CH:30][CH:31]=2)[N:28]([C:32](=[O:44])[CH2:33][C:34]2[CH:39]=[CH:38][CH:37]=[C:36]([C:40]([F:43])([F:42])[F:41])[CH:35]=2)[CH2:27][CH2:26]3)O1.O1CCOCC1.C([O-])(O)=O.[Na+]>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>[CH3:13][CH:12]([N:4]1[C:5]2[N:6]=[CH:7][N:8]=[C:9]([NH2:11])[C:10]=2[C:2]([C:23]2[CH:24]=[C:25]3[C:29](=[CH:30][CH:31]=2)[N:28]([C:32](=[O:44])[CH2:33][C:34]2[CH:39]=[CH:38][CH:37]=[C:36]([C:40]([F:43])([F:41])[F:42])[CH:35]=2)[CH2:27][CH2:26]3)=[CH:3]1)[CH3:14]
Reactant: CC1(C)OB(c2ccc3c(c2)CCN3C(=O)Cc2cccc(C(F)(F)F)c2)OC1(C)C
Reactant: CC(C)n1cc(Br)c2c(N)ncnc21
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: O
Solvent: C1COCCO1
Product: CC(C)n1cc(-c2ccc3c(c2)CCN3C(=O)Cc2cccc(C(F)(F)F)c2)c2c(N)ncnc21
Temperature: 100 °C
Yield: 47.2 %

Procedure:
To 5-bromo-7-(1-methylethyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (70 mg, 0.274 mmol) and 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-{[3-(trifluoromethyl)phenyl]acetyl}-2,3-dihydro-1H-indole (166 mg, 0.384 mmol) were added 1,4-Dioxane (2 mL) and saturated NaHCO3 (1 mL) in a 5 ml sealable vessel. The mixture was then bubbled with N2 gas for 5 minutes then added Pd(Ph3P)4 (317 mg, 0.274 mmol) and the vessel was capped. The reaction was then heated at 100° C. overnight. The reaction was then diluted with water (2 ml) then extracted with EtOAc (3×3 ml). The organics were then combined and washed with brine, dried over MgSO4, filtered and concentrated. The residue was dissolved in 3 mL of DMSO and then purified by HPLC: (HPLC condition: open-access Gilson using Trilution software with a Sunfire 5u C18(2) 100A. 50×30.00 mm 5 micron. 7.3-minute run (47 ml/min, 35% ACN/H2O, 0.1% TFA to 60% ACN/H2O, 0.1% TFA) with UV detection at 220 nm). Product fractions were combined and the volume was reduced to remove most of the MeCN. To the water left behind was added saturated NaHCO3 and the mixture was extracted with EtOAc (3×15 mL). The organics were combined wash with saturated NaCl solution, dried over MgSO4, filtered and concentrated. The product was transferred to a 40 mL vial with MeCN then water was added and the solution was freeze-dried to provide 7-(1-methylethyl)-5-(1-{[3-(trifluoromethyl)phenyl]acetyl}-2,3-dihydro-1H-indol-5-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (62 mg, 47.1% yield) as a white solid. LC-MS (ES) m/z=480.5 [M+H]+. 1H NMR (400 MHz, DMSO-d6) δ 8.23 (s, 1H), 8.13 (d, J=8.34 Hz, 1H), 7.69 (s, 1H), 7.57-7.67 (m, 3H), 7.54 (s, 1H), 7.36 (s, 1H), 7.26 (d, J=8.08 Hz, 1H), 6.57 (br. s., 2H), 4.99 (quin, J=6.76 Hz, 1H), 4.28 (t, J=8.46 Hz, 2H), 4.04 (s, 2H), 3.23-3.28 (m, 2H), 1.47 (d, J=6.82 Hz, 6H).
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:26][CH2:25][N:11]2[C:12](=[O:24])[C:13]3[C:18]([C@@H:10]2[CH2:9]1)=[CH:17][C:16](Br)=[CH:15][C:14]=3[C:20]([F:23])([F:22])[F:21])=[O:7])([CH3:4])([CH3:3])[CH3:2].B1(B2OC(C)(C)C(C)(C)O2)OC(C)(C)C(C)(C)[O:28]1.C([O-])(=O)C.[K+]>CN(C=O)C.C([O-])(=O)C.[Pd+2].C([O-])(=O)C>[C:1]([O:5][C:6]([N:8]1[CH2:26][CH2:25][N:11]2[C:12](=[O:24])[C:13]3[C:18]([C@@H:10]2[CH2:9]1)=[CH:17][C:16]([OH:28])=[CH:15][C:14]=3[C:20]([F:23])([F:22])[F:21])=[O:7])([CH3:4])([CH3:3])[CH3:2]
Reactant: CC(C)(C)OC(=O)N1CCN2C(=O)c3c(cc(Br)cc3C(F)(F)F)[C@@H]2C1
Reactant: CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: CC(C)(C)OC(=O)N1CCN2C(=O)c3c(cc(O)cc3C(F)(F)F)[C@@H]2C1
Temperature: 80 °C
Reaction time: 0.25 h
Yield: 93.2 %

Procedure:
To a stirring degassed solution of N-(t-butoxycarbonyl)-(R)-1,3,4,10b-tetrahydro-9-bromo-7-trifluoromethyl-pyrazino[2,1-a]isoindol-6(2H)-one (435 mg, 1.0 mmol), bis(pinacolato)diboron (279 mg, 1.1 mmol), and potassium acetate (294 mg, 3.0 mmol) in dry DMF (5.0 mL) was added palladium(II) acetate (6.7 mg, 0.03 mmol). The reaction was heated to 80° C. for 2 h and then cooled to room temp. The reaction was quenched with water and extracted with EtOAc (3×5 mL). The organic layers were combined, dried over Na2SO4, and conc. in vacuo to a brown oil. The oil was dissolved in THF (5 mL) and acetic acid (0.05 mL) and treated with hydrogen peroxide (0.25 mL). The reaction was stirred for 15 min and then quenched with st. aq. NaHSO3. The reaction was extracted with EtOAc (3×5 mL). The organic layers were combined, dried over Na2SO4, and conc. in vacuo to a brown oil. The oil was purified by flash chromatography (silica gel, 0–70% EtOAc in hexanes) to give 347 mg of the desired product as a pale yellow solid. MS (ESI) 373 (M+H).