Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: Cl[CH2:2][C:3]1[S:4][C:5]([C:8]2[CH:13]=[CH:12][C:11]([CH2:14][CH2:15][CH2:16][CH3:17])=[CH:10][CH:9]=2)=[CH:6][CH:7]=1.[CH2:18]([C@H:25]1[CH2:29][O:28][C:27](=[O:30])[N:26]1[C:31](=[O:46])[CH2:32][C@@H:33]([C:39]1[CH:44]=[CH:43][C:42]([OH:45])=[CH:41][CH:40]=1)[C:34]1[CH:38]=[CH:37][O:36][N:35]=1)[C:19]1[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=1.C([O-])([O-])=O.[Cs+].[Cs+]>CN(C=O)C.CCOC(C)=O>[CH2:14]([C:11]1[CH:12]=[CH:13][C:8]([C:5]2[S:4][C:3]([CH2:2][O:45][C:42]3[CH:43]=[CH:44][C:39]([C@@H:33]([C:34]4[CH:38]=[CH:37][O:36][N:35]=4)[CH2:32][C:31]([N:26]4[C@@H:25]([CH2:18][C:19]5[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=5)[CH2:29][O:28][C:27]4=[O:30])=[O:46])=[CH:40][CH:41]=3)=[CH:7][CH:6]=2)=[CH:9][CH:10]=1)[CH2:15][CH2:16][CH3:17]
Reactant: CCCCc1ccc(-c2ccc(CCl)s2)cc1
Reactant: O=C(C[C@@H](c1ccc(O)cc1)c1ccon1)N1C(=O)OC[C@@H]1Cc1ccccc1
Agent: O=C([O-])[O-]
Agent: [Cs+]
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: CCCCc1ccc(-c2ccc(COc3ccc([C@H](CC(=O)N4C(=O)OC[C@@H]4Cc4ccccc4)c4ccon4)cc3)s2)cc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 32.2 %

Procedure:
A mixture of 60.5 (0.16 mmol), 7.5 (52 mg, 0.13 mmol), and Cs2CO3 (135 mg, 0.41 mmol) in DMF (1.6 mL) was stirred overnight at room temperature. The mixture was diluted with EtOAc, washed with water and brine, dried (Na2SO4), and concentrated. The crude product was chromatographed on silica gel (0-30% EtOAc/hexane) to afford 60.6 (26 mg, 32%) as a colorless oil. 1H NMR (400 MHz, CDCl3) δ 8.29 (d, 1H), 7.48 (d, 2H), 7.28 (m, 5H), 7.19 (m, 4H), 7.14 (d, 1H), 7.04 (d, 1H), 6.96 (d, 2H), 6.13 (d, 1H), 5.17 (s, 2H), 4.75 (t, 1H), 4.61 (m, 1H), 4.13 (m, 2H), 4.02 (dd, 1H), 3.54 (dd, 1H), 3.20 (dd, 1H), 2.76 (dd, 1H), 2.62 (t, 2H), 1.61 (m, 2H), 1.37 (m, 2H), 0.94 (t, 3H).
Reaction SMILES: [C:1]([C:3]1[CH:4]=[C:5]([CH:40]=[CH:41][CH:42]=1)[CH2:6][NH:7][C:8](=[O:39])[C:9]1[CH:14]=[CH:13][C:12]([NH:15][CH:16]2[C:20]3[CH:21]=[C:22]4[C:27](=[CH:28][C:19]=3[CH2:18][CH2:17]2)[N:26]=[C:25]([CH3:29])[N:24]([CH2:30][O:31][C:32](=[O:37])[C:33]([CH3:36])([CH3:35])[CH3:34])[C:23]4=[O:38])=[CH:11][CH:10]=1)#[N:2].[CH2:43](Br)[C:44]#[CH:45]>>[C:1]([C:3]1[CH:4]=[C:5]([CH:40]=[CH:41][CH:42]=1)[CH2:6][NH:7][C:8](=[O:39])[C:9]1[CH:10]=[CH:11][C:12]([N:15]([CH:16]2[C:20]3[CH:21]=[C:22]4[C:27](=[CH:28][C:19]=3[CH2:18][CH2:17]2)[N:26]=[C:25]([CH3:29])[N:24]([CH2:30][O:31][C:32](=[O:37])[C:33]([CH3:36])([CH3:35])[CH3:34])[C:23]4=[O:38])[CH2:45][C:44]#[CH:43])=[CH:13][CH:14]=1)#[N:2]
Reactant: Cc1nc2cc3c(cc2c(=O)n1COC(=O)C(C)(C)C)C(Nc1ccc(C(=O)NCc2cccc(C#N)c2)cc1)CC3
Reactant: C#CCBr
Product: C#CCN(c1ccc(C(=O)NCc2cccc(C#N)c2)cc1)C1CCc2cc3nc(C)n(COC(=O)C(C)(C)C)c(=O)c3cc21

Procedure:
Using an analogous procedure to that described in the first paragraph of Example 1, N-(3-cyanobenzyl)-p-[N-((6RS)-2-methyl-4-oxo-3-pivaloyloxymethyl-3,4,7,8-tetrahydro-6H-cyclopenta[g]quinazolin-6-yl)amino]benzamide (0.36 g) was reacted with propargyl bromide to give N-(3-cyanobenzyl)-p-[N-(2-methyl-4-oxo-3-pivaloyloxymethyl-3,4,7,8-tetrahydro-6H-cyclopenta[g]quinazolin-6-yl)-N-(prop-2-ynyl)amino]benzamide (0.154 g).
Reaction SMILES: [CH2:1]([O:8][CH2:9][CH2:10][CH2:11][O:12][C:13]1[CH:18]=[CH:17][C:16]([CH:19]2[CH:24]([CH2:25][O:26][CH2:27][CH2:28][N:29]3[CH2:34][CH2:33][O:32][CH2:31][CH2:30]3)[CH2:23][N:22](C(OC(C)(C)C)=O)[CH2:21][CH:20]2[C:42](=[O:54])[CH2:43][C:44]2[CH:53]=[CH:52][C:51]3[C:46](=[CH:47][CH:48]=[CH:49][CH:50]=3)[CH:45]=2)=[CH:15][CH:14]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1>C(Cl)Cl.[Br-].[Zn+2].[Br-]>[CH2:1]([O:8][CH2:9][CH2:10][CH2:11][O:12][C:13]1[CH:18]=[CH:17][C:16]([CH:19]2[CH:24]([CH2:25][O:26][CH2:27][CH2:28][N:29]3[CH2:30][CH2:31][O:32][CH2:33][CH2:34]3)[CH2:23][NH:22][CH2:21][CH:20]2[C:42](=[O:54])[CH2:43][C:44]2[CH:53]=[CH:52][C:51]3[C:46](=[CH:47][CH:48]=[CH:49][CH:50]=3)[CH:45]=2)=[CH:15][CH:14]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: CC(C)(C)OC(=O)N1CC(COCCN2CCOCC2)C(c2ccc(OCCCOCc3ccccc3)cc2)C(C(=O)Cc2ccc3ccccc3c2)C1
Agent: [Br-]
Agent: [Zn+2]
Solvent: ClCCl
Product: O=C(Cc1ccc2ccccc2c1)C1CNCC(COCCN2CCOCC2)C1c1ccc(OCCCOCc2ccccc2)cc1

Procedure:
In an analogous manner to that described in Example 73 (d), from tert-butyl (3RS,4SR,5SR)-4-[4-(3-benzyloxy-propoxy)-phenyl]-5-(2-morpholin-4-yl-ethoxymethyl)-3-(naphthalen-2-yl-acetyl)-piperidine-1-carboxylate by cleavage of BOC protecting group by means of anhydrous zinc bromide in methylene chloride there was obtained 1-[(3RS,4SR,5SR)-4-[4-(3-benzyloxy-propoxy)-phenyl]-5-(2-morpholin-4-yl-ethoxymethyl)-piperidin-3-yl]-2-naphthalen-2-yl-ethanone as a yellow oil MS: 637 (M+H)+.
Reaction SMILES: [CH3:1][C:2]1([CH3:33])[CH2:7][C:6]([C:8]2[CH:21]=[CH:20][C:19]3[O:18][C:17]4[C:12](=[CH:13][C:14]([C:22]5[CH:23]=[N:24][CH:25]=[N:26][CH:27]=5)=[CH:15][CH:16]=4)[C@@:11]4([CH2:31][O:30][C:29]([NH2:32])=[N:28]4)[C:10]=3[CH:9]=2)=[CH:5][CH2:4][O:3]1.CO.[H][H]>[Pd]>[CH3:1][C:2]1([CH3:33])[CH2:7][CH:6]([C:8]2[CH:21]=[CH:20][C:19]3[O:18][C:17]4[C:12](=[CH:13][C:14]([C:22]5[CH:27]=[N:26][CH:25]=[N:24][CH:23]=5)=[CH:15][CH:16]=4)[C@@:11]4([CH2:31][O:30][C:29]([NH2:32])=[N:28]4)[C:10]=3[CH:9]=2)[CH2:5][CH2:4][O:3]1
Reactant: [H][H]
Reactant: CC1(C)CC(c2ccc3c(c2)[C@]2(COC(N)=N2)c2cc(-c4cncnc4)ccc2O3)=CCO1
Agent: [Pd]
Solvent: CO
Product: CC1(C)CC(c2ccc3c(c2)[C@]2(COC(N)=N2)c2cc(-c4cncnc4)ccc2O3)CCO1
Reaction time: 1.5 h

Procedure:
To a solution of (R)-2′-(2,2-dimethyl-3,6-dihydro-2H-pyran-4-yl)-7′-(pyrimidin-5-yl)-5H-spiro[oxazole-4,9′-xanthen]-2-amine (55 mg, 0.125 mmol) in MeOH (2 mL) palladium on carbon (66.4 mg, 0.062 mmol) was added and the mixture was hydrogenated at 50° C. (1 atm of hydrogen gas) for 30 min. Another 20 mg of Pd/C was added and hydrogenation was continued for 1.5 hr at 50° C. The mixture was filtered through a plug of celite and purified by silica gel chromatography (10-80% DCM/MeOH/NH4OH in DCM) to afford (R)-2′-(2,2-dimethyltetrahydro-2H-pyran-4-yl)-7′-(pyrimidin-5-yl)-5H-spiro[oxazole-4,9′-xanthen]-2-amine.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[C:6]([CH3:8])[CH:5]=[C:4]([CH3:9])[CH:3]=1.[Br:10]N1C(C)(C)C(=O)N(Br)C1=O>C(Cl)(Cl)(Cl)Cl.C(OOC(=O)C1C=CC=CC=1)(=O)C1C=CC=CC=1>[Br:1][C:2]1[CH:7]=[C:6]([CH3:8])[CH:5]=[C:4]([CH2:9][Br:10])[CH:3]=1
Reactant: CC1(C)C(=O)N(Br)C(=O)N1Br
Reactant: Cc1cc(C)cc(Br)c1
Agent: O=C(OOC(=O)c1ccccc1)c1ccccc1
Solvent: ClC(Cl)(Cl)Cl
Product: Cc1cc(Br)cc(CBr)c1
Temperature: 25 °C
Yield: 249.8 %

Procedure:
To a solution of 1-bromo-3,5-dimethylbenzene (25.0 g, 135.0 mmol) in CCl4 (150 mL), was added 1,3-dibromo-5,5-dimethylimidazolidine-2,4-dione (14.5 g, 54.0 mmol) and dibenzoyl peroxide (BPO) (0.2 g) and the mixture was refluxed for 7 h. After the reaction mixture was cooled to room temperature, the precipitate was filtered out using Celite, and then the solid was rinsed two times with pentane (50 mL). The combined filtrates were washed with water (50 mL), followed by saturated sodium bicarbonate (50 mL) and sodium thiosulfate (50 mL×2). The organic layer was dried over anhydrous sodium sulfate. Evaporation of the solvent afforded the compound 1-bromo-3-(bromomethyl)-5-methylbenzene (35.6 g, 99%).
Reaction SMILES: [N:1]1([S:11]([C:14]2[CH:22]=[CH:21][C:17]([C:18]([OH:20])=O)=[CH:16][CH:15]=2)(=[O:13])=[O:12])[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][CH:9]=2)[CH2:4][CH2:3][CH2:2]1.[C:23]1([C:29]2[N:30]=[C:31]([NH2:34])[S:32][CH:33]=2)[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=1>>[N:1]1([S:11]([C:14]2[CH:22]=[CH:21][C:17]([C:18]([NH:34][C:31]3[S:32][CH:33]=[C:29]([C:23]4[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=4)[N:30]=3)=[O:20])=[CH:16][CH:15]=2)(=[O:13])=[O:12])[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][CH:9]=2)[CH2:4][CH2:3][CH2:2]1
Reactant: O=C(O)c1ccc(S(=O)(=O)N2CCCc3ccccc32)cc1
Reactant: Nc1nc(-c2ccccc2)cs1
Product: O=C(Nc1nc(-c2ccccc2)cs1)c1ccc(S(=O)(=O)N2CCCc3ccccc32)cc1

Procedure:
4-(3,4-dihydroquinolin-1(2H)-ylsulfonyl)benzoic acid (1) (100 mg, 0.32 mmol) was treated with 4-phenylthiazol-2-amine (43 mg, 0.24 mmol) using method B. The residue was purified using flash chromatography eluting with 0-40% EtOAc in hexanes to give 4-(3,4-dihydroquinolin-1(2H)-ylsulfonyl)-N-(4-phenylthiazol-2-yl)benzamide as a white solid. Yield: 43 mg, (37%). 1H-NMR: 8.21 (d, J=8.5 Hz, 2H), 7.95 (d, J=8.0 Hz, 2H), 7.78-7.73 (m, 3H), 7.62 (d, J=8.5 Hz, 1H), 7.47-7.42 (t, J=7.5 Hz, 2H), 7.36-7.32 (m, 1H), 7.24-7.08 (m, 3H), 3.84-3.80 (m, 2H), 2.45 (t, J=7.0 Hz, 2H), 1.66-1.59 (m, 2H).
Reaction SMILES: [C:1]1([CH3:11])[CH:6]=[CH:5][C:4]([S:7](Cl)(=[O:9])=[O:8])=[CH:3][CH:2]=1.C(N(CC)CC)C.C(Cl)Cl.C(Cl)Cl.C[OH:26]>>[C:1]1([CH3:11])[CH:6]=[CH:5][C:4]([S:7]([OH:26])(=[O:9])=[O:8])=[CH:3][CH:2]=1
Reactant: CO
Reactant: Cc1ccc(S(=O)(=O)Cl)cc1
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: Cc1ccc(S(=O)(=O)O)cc1
Reaction time: 72 h

Procedure:
(2-tert-Butoxycarbonylamino-ethyl-2-{[tert-butoxycarbonyl-(2-tert-butoxycarbonylaminoethylamino]-methyl}-8-hydroxyoctyl)-carbonic acid tert-butyl ester (2.52 g, 3.82 mmol), p-toluenesulfonyl chloride (1.0 g, 5.2 mmol), triethylamine (1.3 g, 12.8 mmol) and CH2Cl2 (30 ml) were stirred at room temperature with the slow evaporation of solvent. The reaction was monitored by carbon NMR and after 3 days little starting material remained. The reaction volume was made up to 30 ml with CH2Cl2, extracted with water (50 ml×3), dried (MgSO4), filtered and the solvent evaporated to leave a brown residue. This residue was subjected to chromatography on silica gel using CH2Cl2/MeOH (100:5) as eluent. The first compound to elute was unreacted tosyl chloride with an rf=0.95. The title compound eluted with an rf=0.2 and was isolated as a pale yellow viscous oil. Yield (1.20 g, 39%).
Reaction SMILES: [Cl:1][C:2]1[CH:13]=[C:12]([Cl:14])[C:11]([Cl:15])=[CH:10][C:3]=1[O:4][CH2:5][C:6]([NH:8][NH2:9])=[O:7].[C:16]([C:19]1[CH:24]=[CH:23][N:22]=[CH:21][CH:20]=1)(=O)[CH3:17].O1CCOCC1>C(O)(=O)C>[N:22]1[CH:23]=[CH:24][C:19]([C:16](=[N:9][NH:8][C:6](=[O:7])[CH2:5][O:4][C:3]2[CH:10]=[C:11]([Cl:15])[C:12]([Cl:14])=[CH:13][C:2]=2[Cl:1])[CH3:17])=[CH:20][CH:21]=1
Reactant: CC(=O)c1ccncc1
Reactant: NNC(=O)COc1cc(Cl)c(Cl)cc1Cl
Solvent: C1COCCO1
Solvent: CC(=O)O
Product: CC(=NNC(=O)COc1cc(Cl)c(Cl)cc1Cl)c1ccncc1
Temperature: 25 °C
Yield: 83.7 %

Procedure:
A solution of 5.39 gm (0.02 mole) of 2,4,5-trichlorophenoxyacetic acid hydrazide, 2.42 gm (0.02 mole) of 4-acetylpyridine, 125 ml of dioxane and 2 ml of acetic acid is refluxed 4 hr. The hot solution is filtered. The filtrate is diluted with water until cloud point. The mixture is cooled to room temperature and then chilled in the refrigerator. The product is collected to yield 6.24 gm (83%) of the title compound having a melting point of 227.4° C. (decomp).
Reaction SMILES: [C:1](PCC1C(CPC(C)(C)C)=CC=CC=1)(C)(C)C.CS(O)(=O)=O.[C:24]([O-:44])(=[O:43])[CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH2:31]/[CH:32]=[CH:33]\[CH2:34][C@@H:35]([CH2:37][CH2:38][CH2:39][CH2:40][CH2:41][CH3:42])[OH:36]>CO.CC([O-])=O.CC([O-])=O.[Pd+2]>[C:24]([O:44][CH3:1])(=[O:43])[CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH2:30][CH2:31]/[CH:32]=[CH:33]\[CH2:34][C@@H:35]([CH2:37][CH2:38][CH2:39][CH2:40][CH2:41][CH3:42])[OH:36]
Reactant: CCCCCC[C@@H](O)C/C=C\CCCCCCCC(=O)[O-]
Reactant: CC(C)(C)PCc1ccccc1CPC(C)(C)C
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: CS(=O)(=O)O
Solvent: CO
Product: CCCCCC[C@@H](O)C/C=C\CCCCCCCC(=O)OC
Temperature: 65 °C

Procedure:
In a second experiment, Pd(OAc)2 (6.5 mg, 0.029 mmol) and α,α′-di-tert-butylphosphino-o-xylene (59 mg, 0.15 mmol) were dissolved in 30 mL of dry methanol. Subsequently, methanesulfonic acid (20 μL, 0.3 mmol) and ricinoleate (290 mmol). The reaction was allowed to proceed at reflux (i.e. at a temperature of around 65° C.) for 24 h (conv. 80%), and then an identical amount of freshly prepared catalyst was added to the reaction mixture. After another 24 h of reflux, the reaction had reached completion and the mixture was allowed to cool down to room temperature and the crystals were filtered off and washed with methanol. The reaction mixture was analyzed with GC and showed only methyl-12-oxo-stearate.
Reaction SMILES: O.[C:2]1([OH:10])[CH:9]=[C:7]([CH3:8])[CH:6]=[C:4]([OH:5])[CH:3]=1.[CH3:11][O:12][C:13]1[CH:18]=[CH:17][C:16]([O:19][CH3:20])=[CH:15][C:14]=1[S:21](Cl)(=[O:23])=[O:22].C([O-])(O)=O.[Na+]>CCOCC>[CH3:11][O:12][C:13]1[CH:18]=[CH:17][C:16]([O:19][CH3:20])=[CH:15][C:14]=1[S:21]([O:5][C:4]1[CH:3]=[C:2]([OH:10])[CH:9]=[C:7]([CH3:8])[CH:6]=1)(=[O:22])=[O:23]
Reactant: COc1ccc(OC)c(S(=O)(=O)Cl)c1
Reactant: Cc1cc(O)cc(O)c1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: O
Solvent: CCOCC
Product: COc1ccc(OC)c(S(=O)(=O)Oc2cc(C)cc(O)c2)c1
Temperature: 25 °C
Reaction time: 72 h
Yield: 53.9 %

Procedure:
To a solution of 1.00 g (8.05 mmol) of orcinol monohydrate and 1.75 g (7.38 mmol) of 2,5-dimethoxybenzenesulfonyl chloride in 20 mL of diethyf ether was added 20 mL of saturated aqueous NaHCO3 and the biphasic mixture stirred vigorously at ambient temperature for 3 days. The layers were separated and the aqueous layer extracted with 2×30 mL of ethyl acetate. The combined organic layers were washed with 50 mL of brine, dried (Na2SO4) and concentrated to give an amber-colored solid. Recrystallization from ethyl acetate-hexane afforded 1.29 g (54%) of the title compound as a cream-colored powder: 1H-NMR (300 MHz; CDCl3) δ 7.34 (d, 1 H, J=3.1 Hz), 7.15 (dd, 1 H, J=9.1, 3.1 Hz), 7.02 (d, 1 H, J=9.1 Hz), 6.53 (m, 2 H), 6.42 (t, 1H, J=2.2 Hz), 5.08 (br s, 1 H),3.95 (s,3 H), 3.76 (s, 3 H), and 2.23 (s, 3 H).
Reaction SMILES: Br[C:2]1[N:7]=[C:6]([C:8]2[O:9][C:10]([C:13]([O:19][Si:20]([CH:27]([CH3:29])[CH3:28])([CH:24]([CH3:26])[CH3:25])[CH:21]([CH3:23])[CH3:22])([CH3:18])[C:14]([F:17])([F:16])[F:15])=[N:11][N:12]=2)[C:5]([NH2:30])=[CH:4][C:3]=1[C:31]([F:34])([F:33])[F:32].C([O-])([O-])=O.[K+].[K+].[CH:41]1(B(O)O)[CH2:43][CH2:42]1>O1CCOCC1.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>[CH:41]1([C:2]2[N:7]=[C:6]([C:8]3[O:9][C:10]([C:13]([O:19][Si:20]([CH:21]([CH3:23])[CH3:22])([CH:27]([CH3:28])[CH3:29])[CH:24]([CH3:25])[CH3:26])([CH3:18])[C:14]([F:15])([F:16])[F:17])=[N:11][N:12]=3)[C:5]([NH2:30])=[CH:4][C:3]=2[C:31]([F:32])([F:33])[F:34])[CH2:43][CH2:42]1
Reactant: OB(O)C1CC1
Reactant: CC(C)[Si](OC(C)(c1nnc(-c2nc(Br)c(C(F)(F)F)cc2N)o1)C(F)(F)F)(C(C)C)C(C)C
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: [K+]
Solvent: C1COCCO1
Product: CC(C)[Si](OC(C)(c1nnc(-c2nc(C3CC3)c(C(F)(F)F)cc2N)o1)C(F)(F)F)(C(C)C)C(C)C
Temperature: 120 °C

Procedure:
To a stirring solution of 6-bromo-2-(5-(1,1,1-trifluoro-2-(triisopropylsilyloxy)propan-2-yl)-1,3,4-oxadiazol-2-yl)-5-(trifluoromethyl)pyridin-3-amine (step 3) (200 mg, 0.346 mmol) in dry 1,4-dioxane (10 ml) under N2 at RT was added K2CO3 (144 mg, 1.039 mmol) followed by cyclopropylboronic acid (89 mg, 1.039 mmol) and palladiumtetrakis (40.0 mg, 0.035 mmol). The resulting suspension was stirred and heated at reflux (120° C.) overnight for 4 days. The mixture was filtered through Celite® (filter material) and washed through with water (30 ml) and EtOAc (50 ml). The filtrate was separated and the organic portion was dried (MgSO4) and concentrated in vacuo to afford the title compound which was used in the next step without further purification; LC-MS Rt=7.75 min [M+H]+ 539.6 Method 10minLC_v003.
Reaction SMILES: [NH2:1][C:2]1[C:3]2[N:4]([C:8]([C@H:20]3[CH2:25][CH2:24][C@H:23]([C:26](OC)=[O:27])[CH2:22][CH2:21]3)=[N:9][C:10]=2[C:11]2[NH:12][C:13]3[C:18]([CH:19]=2)=[CH:17][CH:16]=[CH:15][CH:14]=3)[CH:5]=[CH:6][N:7]=1.[OH-].[Na+].C(O[CH2:36][CH3:37])(=O)C>>[NH2:1][C:2]1[C:3]2[N:4]([C:8]([C@H:20]3[CH2:21][CH2:22][C@H:23]([C:26]([NH:1][C:2]4[CH:3]=[N:4][CH:5]=[CH:36][CH:37]=4)=[O:27])[CH2:24][CH2:25]3)=[N:9][C:10]=2[C:11]2[NH:12][C:13]3[C:18]([CH:19]=2)=[CH:17][CH:16]=[CH:15][CH:14]=3)[CH:5]=[CH:6][N:7]=1
Reactant: CCOC(C)=O
Reactant: COC(=O)[C@H]1CC[C@H](c2nc(-c3cc4ccccc4[nH]3)c3c(N)nccn32)CC1
Agent: [Na+]
Agent: [OH-]
Product: Nc1nccn2c1c(-c1cc3ccccc3[nH]1)nc2[C@H]1CC[C@H](C(=O)Nc2cccnc2)CC1
Temperature: 25 °C
Reaction time: 0.42 h

Procedure:
After 25 min, the resulting solution was treated with methyl trans-4-(8-amino-1-(1H-indol-2-yl)imidazo[1,5-a]pyrazin-3-yl)cyclohexanecarboxylate (30 mg, 0.08 mol) and the mixture stirred at rt overnight. The mixture was then stirred with 2M NaOH (20 mL) and ethyl acetate (20 mL) for 10 min., then the organic phase was separated and the aqueous extracted EtOAc (3×15 mL). The combined organic extracts were washed with water (20 mL) and brine (20 mL), then dried over Na2SO4 and concentrated in vacuo to give crude product which was subjected to mass-directed preparative HPLC to afford pure desired product. 1H NMR (d6-DMSO, 400 MHz): δ 11.45 (br s, 1H), 10.12 (s, 1H), 8.77 (d, J=2.4 Hz, 1H), 8.25 (d, J=4.8 Hz, 1H), 8.14 (s, 1H), 8.08 (dd, J=8.0, 1.6 Hz, 1H), 7.71 (d, J=5.2 Hz, 1H), 7.59 (d, J=7.6 Hz, 1H), 7.46 (d, J=8.4 Hz, 1H), 7.34 (m, 1H), 7.15-7.00 (m, 3H), 6.65 (s, 1H), 6.42 (br s, 2H), 3.22 (m, 1H), 2.47 (m, 1H), 2.15-1.95 (m, 4H), and 1.85-1.65 (m, 4H). MS (ES+): m/z 452.17 [MH+].
Reaction SMILES: [F:1][C:2]1[CH:7]=[C:6]([Cl:8])[C:5]([OH:9])=[CH:4][C:3]=1[NH:10][C:11](=[O:15])[O:12][CH2:13][CH3:14].C(=O)([O-])[O-].[K+].[K+].[CH:22]1(Br)[CH2:26][CH2:25][CH2:24][CH2:23]1>C(#N)C>[F:1][C:2]1[CH:7]=[C:6]([Cl:8])[C:5]([O:9][CH:22]2[CH2:26][CH2:25][CH2:24][CH2:23]2)=[CH:4][C:3]=1[NH:10][C:11](=[O:15])[O:12][CH2:13][CH3:14]
Reactant: CCOC(=O)Nc1cc(O)c(Cl)cc1F
Reactant: BrC1CCCC1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: CCOC(=O)Nc1cc(OC2CCCC2)c(Cl)cc1F
Reaction time: 7 h
Yield: 98.3 %

Procedure:
Then, a solution of the resulting ethyl N-(2-fluoro-4-chloro-5-hydroxyphenyl)carbamate (10.0 g, 42.8 mmol) and potassium carbonate (8.87 g, 64.2 mmol) in acetonitrile (150 ml) was stirred for 1 hour at 80° C. Then, cyclopentyl bromide (9.57 g, 84.2 mmol) was added dropwise thereto, followed by reacting for further 7 hours. After completion of the reaction, tile solvent was distilled off under reduced pressure, and the residue was made acidic by adding 1N hydrochloric acid (100 ml) and extracted with ethyl acetate (100 ml×3 times). The organic layer was washed with water, dried, and the solvent was distilled off under reduced pressure to obtain ethyl N-(2-fluoro-4-chloro-5-cyclopentyloxyphenyl)carbamate (12.7 g, 98% yield).
Reaction SMILES: [OH:1][C:2]1[C:18]([OH:19])=[C:17]([OH:20])[CH:16]=[CH:15][C:3]=1[CH2:4][N:5]1[CH2:10][CH2:9][N:8]([C:11]([S:13][CH3:14])=[S:12])[CH2:7][CH2:6]1.C(O[C:25](=[O:27])[CH3:26])(=O)C>C(Cl)(Cl)Cl>[C:2]([O:1][C:2]1[C:18]([O:19][C:18](=[O:19])[CH3:17])=[C:17]([O:20][C:25](=[O:27])[CH3:26])[CH:16]=[CH:15][C:3]=1[CH2:4][N:5]1[CH2:6][CH2:7][N:8]([C:11]([S:13][CH3:14])=[S:12])[CH2:9][CH2:10]1)(=[O:1])[CH3:3]
Reactant: CC(=O)OC(C)=O
Reactant: CSC(=S)N1CCN(Cc2ccc(O)c(O)c2O)CC1
Solvent: ClC(Cl)Cl
Product: CSC(=S)N1CCN(Cc2ccc(OC(C)=O)c(OC(C)=O)c2OC(C)=O)CC1
Temperature: 0 °C
Reaction time: 1 h
Yield: 69.7 %

Procedure:
In 520 ml of chloroform was suspended 50 g of methyl 4-(2,3,4-trihydroxybenzyl)-1-piperazinecarbodithioate, and to the suspension was dropwise added under chilling with ice 97.3 g of acetic anhydride over a period of 15 min. The mixture was then stirred for one hour. The reaction mixture was washed successively with water and a saturated aqueous sodium chloride solution, and dried over anhydrous sodium sulfate. The sodium sulfate was removed by filtration, and the filtrate was concentrated under reduced pressure. The residual oil was crystallized by addition of 250 ml of ethyl acetate. After stirring for one hour, the crystals were collected by filtration. The crystals were washed with ethyl acetate to give 48.8 g of the desired compound as white crystals, m.p. 148°-150° C. (decomp.), yield 69.7%.
Reaction SMILES: [C:1]([C:5]([NH:7][C:8]1[CH:13]=[CH:12][CH:11]=[C:10]([C:14]2[C:23]3[C:18](=[CH:19][CH:20]=[CH:21][CH:22]=3)[C:17]([CH3:24])=[CH:16][CH:15]=2)[N:9]=1)=[O:6])([CH3:4])([CH3:3])[CH3:2].Br[N:26]1C(=O)CC[C:27]1=O>C(Cl)(Cl)(Cl)Cl>[C:1]([C:5]([NH:7][C:8]1[CH:13]=[CH:12][CH:11]=[C:10]([C:14]2[C:23]3[C:18](=[CH:19][CH:20]=[CH:21][CH:22]=3)[C:17]([CH2:24][C:27]#[N:26])=[CH:16][CH:15]=2)[N:9]=1)=[O:6])([CH3:4])([CH3:3])[CH3:2]
Reactant: Cc1ccc(-c2cccc(NC(=O)C(C)(C)C)n2)c2ccccc12
Reactant: O=C1CCC(=O)N1Br
Solvent: ClC(Cl)(Cl)Cl
Product: CC(C)(C)C(=O)Nc1cccc(-c2ccc(CC#N)c3ccccc23)n1

Procedure:
To a 100 mL round-bottomed flask equipped with condenser and N2 inlet were added 1.21 g (3.795 mmol) N-t-butylcarbonyl-6-(4-methylnaphthalen-1-yl)-pyridin-2-ylamine, 810 mg (4.554 mmol) N-bromosuccinimide, 35 mL carbon tetrachloride, and 10 mg bis-(1-cyano-1-azo)-cyclohexane. The reaction was heated at reflux for a total of 8 hours as additional portions of initiator were added at 1, 2, and 4 hours. The reaction was cooled, filtered with carbon tetrachloride, and evaporated. The red oil, 2.5 g, was used directly.
Reaction SMILES: [NH:1]1[CH2:5][CH2:4][CH2:3][CH2:2]1.C(O[BH-](OC(=O)C)OC(=O)C)(=O)C.[Na+].[Br:20][C:21]1[CH:28]=[C:27]([F:29])[C:24]([CH:25]=O)=[C:23]([F:30])[CH:22]=1.OS([O-])(=O)=O.[Na+]>ClCCl.O>[Br:20][C:21]1[CH:28]=[C:27]([F:29])[C:24]([CH2:25][N:1]2[CH2:5][CH2:4][CH2:3][CH2:2]2)=[C:23]([F:30])[CH:22]=1
Reactant: O=Cc1c(F)cc(Br)cc1F
Reactant: C1CCNC1
Agent: CC(=O)O[BH-](OC(C)=O)OC(C)=O
Agent: O=S(=O)([O-])O
Agent: [Na+]
Solvent: O
Solvent: ClCCl
Product: Fc1cc(Br)cc(F)c1CN1CCCC1
Temperature: 25 °C
Reaction time: 12 h
Yield: 79.2 %

Procedure:
Pyrrolidine (25 mL, 0.30 mol) and sodium triacetoxyborohydride (64 g, 0.30 mol) were added in portions to a stirred solution of Intermediate 18a, 4-Bromo-2,6-difluorobenzaldehyde (53.5 g, 0.24 mol) in dichloromethane (500 mL) on ice bath. The reaction mixture was intensively stirred for 12 h at RT. Water (400 mL) was added followed by addition of 5M aq. NaHSO4 to attain pH˜2. The organic layer was separated. The aqueous one was extracted with CH2Cl2 (2×200 mL). The organic layers were discarded. The aqueous fraction was alkalized with K2CO3 to pH˜10, and extracted with CHCl3 (2×300 mL). The organic extract was washed with brine, dried over anhydrous Na2SO4 (100 g) and evaporated in vacuo to give the title compound (52.5 g, 79%, 0.19 mol). LC/MS data: 275.9 and 277.9 (M+H)+ (calculated for C11H12BrF2N, 276.13). 1H NMR data (DMSO-d6): 7.40-7.48 (m, 2H Ar—H), 3.66 (s, 2H, Ar—CH2), 2.38-2.46 (m, 4H pyrrolidine (CH2)2N), 1.61-1.71 (m, 4H, CH2CH2CH2CH2).
Reaction SMILES: [CH3:1][C:2]1([C:8]([C:10]2[C:18]3[C:13](=[N:14][CH:15]=[C:16]([C:19]4[CH:24]=[CH:23][CH:22]=[C:21]([N:25]5[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]5)[CH:20]=4)[N:17]=3)[NH:12][CH:11]=2)=[O:9])[CH2:7][CH2:6][CH2:5][CH2:4][CH2:3]1.N1(O)C2C=CC=CC=2N=N1.[C:41]([CH2:43][C:44](O)=[O:45])#[N:42].Cl.CN(C)CCCN=C=NCC>C(Cl)Cl>[CH3:1][C:2]1([C:8]([C:10]2[C:18]3[C:13](=[N:14][CH:15]=[C:16]([C:19]4[CH:20]=[C:21]([N:25]5[CH2:30][CH2:29][N:28]([C:44](=[O:45])[CH2:43][C:41]#[N:42])[CH2:27][CH2:26]5)[CH:22]=[CH:23][CH:24]=4)[N:17]=3)[NH:12][CH:11]=2)=[O:9])[CH2:7][CH2:6][CH2:5][CH2:4][CH2:3]1
Reactant: CC1(C(=O)c2c[nH]c3ncc(-c4cccc(N5CCNCC5)c4)nc23)CCCCC1
Reactant: N#CCC(=O)O
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: ClCCl
Product: CC1(C(=O)c2c[nH]c3ncc(-c4cccc(N5CCN(C(=O)CC#N)CC5)c4)nc23)CCCCC1
Temperature: 25 °C
Reaction time: 16 h
Yield: 56.4 %

Procedure:
A solution of (1-methyl-cyclohexyl)-[2-(3-piperazin-1-yl-phenyl)-5H-pyrrolo[2,3-b]pyrazin-7-yl]-methanone (130 mg, 0.32 mmol), benzotriazol-1-ol (52 mg, 0.38 mmol), cyano-acetic acid (74 mg, 0.39 mmol), and 3-(3-dimethylaminopropyl)-1-ethylcarbodiimide hydrochloride (74 mg, 0.39 mmol), in DCM (35 ml), was treated with TEA (0.13 ml, 0.97 mmol). After stirring at room temperature for 16 hours, the reaction mixture was partitioned between DCM and water. The organic layers were collected, dried over MgSO4, filtered, and concentrated. Trituration of the resulting solid with 1:1 Et2O/Hex provided 85 mg (56%) of 3-(4-{3-[7-(1-methyl-cyclohexanecarbonyl)-5H-pyrrolo[2,3-b]pyrazin-2-yl]-phenyl}-piperazin-1-yl)-3-oxo-propionitrile as an off white solid. MP 214-216° C., M+H=471.