Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([C:19]2[N:23]=[C:22]([C:24]([NH:26][CH2:27][C:28]3[CH:33]=[CH:32][C:31]([OH:34])=[CH:30][CH:29]=3)=[O:25])[O:21][N:20]=2)[CH:5]=[C:6]([Cl:18])[C:7]=1[O:8]CC1C=CC(OC)=CC=1.[F:35][C:36]1[CH:41]=[CH:40][C:39](B(O)O)=[CH:38][C:37]=1[C:45]([F:48])([F:47])[F:46].N1C=CC=CC=1>ClCCl.CC([O-])=O.CC([O-])=O.[Cu+2]>[Cl:1][C:2]1[CH:3]=[C:4]([C:19]2[N:23]=[C:22]([C:24]([NH:26][CH2:27][C:28]3[CH:29]=[CH:30][C:31]([O:34][C:39]4[CH:40]=[CH:41][C:36]([F:35])=[C:37]([C:45]([F:48])([F:47])[F:46])[CH:38]=4)=[CH:32][CH:33]=3)=[O:25])[O:21][N:20]=2)[CH:5]=[C:6]([Cl:18])[C:7]=1[OH:8]
Reactant: COc1ccc(COc2c(Cl)cc(-c3noc(C(=O)NCc4ccc(O)cc4)n3)cc2Cl)cc1
Reactant: OB(O)c1ccc(F)c(C(F)(F)F)c1
Agent: [Cu+2]
Agent: CC(=O)[O-]
Solvent: ClCCl
Solvent: c1ccncc1
Product: O=C(NCc1ccc(Oc2ccc(F)c(C(F)(F)F)c2)cc1)c1nc(-c2cc(Cl)c(O)c(Cl)c2)no1
Temperature: 25 °C
Reaction time: 24 h
Yield: 70.8 %

Procedure:
3-(3,5-Dichloro-4-(4-methoxybenzyloxy)phenyl)-N-(4-hydroxybenzyl)-1,2,4-oxadiazole-5-carboxamide (compound G, 60 mg, 0.12 mmol), 4-fluoro-3-(trifluoromethyl)phenylboronic acid (50 mg, 0.24 mmol), Cu(OAc)2 (44 mg, 0.24 mmol) and 3A powdered molecular sieves (70 mg) were stirred in an open tube in dichloromethane (3 mL). Pyridine (57 mg, 0.72 mmol) was added and the dark green suspension stirred vigorously at room temperature in an open tube for 1 d. The molecular sieves were filtered, washed with dichloromethane and the filtrate concentrated in vacuo. The residue was dissolved in dichloromethane (3 mL) and trifluoroacetic acid (0.3 mL) was added. The dark solution was stirred at room temperature for 5 h, then methanol (1 mL) was added and the solution concentrated in vacuo. The residue was purified by preparative HPLC providing the title compound (46 mg, 0.085 mmol, 71%). 1H NMR δ (ppm) (DMSO-d6): 4.53 (2 H, d, J=6.20 Hz), 7.06-7.13 (2 H, m), 7.36-7.48 (4 H, m), 7.53-7.60 (1 H, m), 8.01 (2 H, s), 10.03 (1 H, t, J=6.20 Hz), 11.20 (1 H, s). LCMS (10 cm_esci_Bicarb_MeCN) tR 3.48 min; m/z 540/542/544 [M−H]−.
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:25])[CH2:5][CH:6]1[O:10][B:9]([OH:11])[C:8]2[CH:12]=[C:13]([OH:24])[CH:14]=[C:15]([O:16][CH2:17][C:18]3[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=3)[C:7]1=2)[CH3:2].C([O-])([O-])=O.[Cs+].[Cs+].Cl[C:33]1[CH:38]=[N:37][CH:36]=[CH:35][N:34]=1>CN(C=O)C>[CH2:1]([O:3][C:4](=[O:25])[CH2:5][CH:6]1[O:10][B:9]([OH:11])[C:8]2[CH:12]=[C:13]([O:24][C:33]3[CH:38]=[N:37][CH:36]=[CH:35][N:34]=3)[CH:14]=[C:15]([O:16][CH2:17][C:18]3[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=3)[C:7]1=2)[CH3:2]
Reactant: Clc1cnccn1
Reactant: CCOC(=O)CC1OB(O)c2cc(O)cc(OCc3ccccc3)c21
Agent: O=C([O-])[O-]
Agent: [Cs+]
Solvent: CN(C)C=O
Product: CCOC(=O)CC1OB(O)c2cc(Oc3cnccn3)cc(OCc3ccccc3)c21
Temperature: 80 °C
Yield: 46.9 %

Procedure:
A suspension of (4-benzyloxy-1,6-dihydroxy-1,3-dihydro-benzo[c][1,2]oxaborol-3-yl)-acetic acid ethyl ester (710 mg, 2.08 mmol) and Cs2CO3 (1.36 g, 4.16 mmol) in DMF (10 mL) was treated with 2-chloropyrazine (357 mg, 3.11 mmol) at room temperature and the reaction was heated to 80° C. for 3 h. The reaction mixture was concentrated to dryness. The residue was diluted with water and adjusted pH to 3 by 1N HCl. The aqueous phase was extracted with ethyl acetate. The organic phase was separated, dried (Na2SO4), and concentrated. The residue was purified by preparative HPLC to afford the title compound (410 mg, 50%). MS calcd for (C22H21BN2O6+H)+: 421.2. MS found: (M+H)+=421.2.
Reaction SMILES: [CH3:1][CH:2]1[C:6]2[CH:7]=[CH:8][C:9]([C:11]([O:13]C)=[O:12])=[CH:10][C:5]=2[O:4][CH2:3]1.C(N(CC)CC)C.C1(P(C2C=CC=CC=2)CCCP(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1>CO.C([O-])(=O)C.[Pd+2].C([O-])(=O)C>[CH3:1][CH:2]1[C:6]2[CH:7]=[CH:8][C:9]([C:11]([OH:13])=[O:12])=[CH:10][C:5]=2[O:4][CH2:3]1
Reactant: COC(=O)c1ccc2c(c1)OCC2C
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: c1ccc(P(CCCP(c2ccccc2)c2ccccc2)c2ccccc2)cc1
Solvent: CCN(CC)CC
Solvent: CO
Product: CC1COc2cc(C(=O)O)ccc21
Yield: 78.6 %

Procedure:
To a reversible vial was added methyl 3-methyl-2,3-dihydrobenzofuran-6-carboxylate (384 mg, 2 mmol) in methanol (16 mL) was added triethylamine (900 mg, 9 mmol), palladium acetate (116 mg, 0.5 mmol) and 1,3-bis(diphenylphosphino) propane (480 mg, 1 mmol). Then the reaction mixture was charged with carbonate monoxide under 15 atm at 110° C. for 12 hours. The suspension was concentrated in vacuum and quenched with aqueous 1N hydrochloric acid (5 mL). The residue was taken up with water (50 mL) and extracted with dichloromethane (50 mL). The combined extract was dried over sodium sulphate, evaporated and purified by column chromatography (silica gel, dichloromethane/methanol=20:1) to give the product 3-methyl-2,3-dihydrobenzofuran-6-carboxylic acid (0.28 g, 78%) as colorless oil.
Reaction SMILES: [OH:1][C:2]1[CH:7]=[CH:6][C:5]([OH:8])=[CH:4][C:3]=1[C:9](=[O:11])[CH3:10].Br[CH2:13][CH:14]1[CH2:16][CH2:15]1.C(=O)([O-])[O-].[K+].[K+]>C(#N)C>[CH:14]1([CH2:13][O:8][C:5]2[CH:6]=[CH:7][C:2]([OH:1])=[C:3]([C:9](=[O:11])[CH3:10])[CH:4]=2)[CH2:16][CH2:15]1
Reactant: CC(=O)c1cc(O)ccc1O
Reactant: BrCC1CC1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC#N
Product: CC(=O)c1cc(OCC2CC2)ccc1O
Temperature: 25 °C
Yield: 104.8 %

Procedure:
A solution of 2′,5′-dihydroxyacetophenone (25.0 g), bromomethylcyclopropane (24.43 g), potassium carbonate (27.2 g) in acetonitrile (400 mL) was stirred with heating under reflux for 2.5 hr. Bromomethylcyclopropane (4.4 g) was added to the mixture, and the mixture was further stirred with heating under reflux for 14 hr. The reaction mixture was cooled to room temperature, the insoluble material was filtered off, and the filtrate was concentrated under reduced pressure. The residue was purified by silica gel column chromatography (hexane-ethyl acetate 100:0-10:90, v/v) to give 1-[5-(cyclopropylmethoxy)-2-hydroxyphenyl]ethanone (35.5 g) as a yellow oil at purity 70%. A solution of the obtained 1-[5-(cyclopropylmethoxy)-2-hydroxyphenyl]ethanone (35.5 g), 1-bromo-3-methylbutan-2-one (35.5 g) synthesized above and potassium carbonate (66.3 g) in N,N-dimethylformamide (350 mL) was stirred at room temperature for 1 hr. Water was added to the reaction mixture, and the mixture was extracted with ethyl acetate. The extract was washed with saturated brine, dried over magnesium sulfate, and concentrated under reduced pressure. 1,8-Diazabicyclo[5.4.0]undec-7-ene (22.5 mL) and N,N-dimethylformamide (300 mL) were added to the obtained residue, and the mixture was stirred at 100° C. for 30 min. The reaction mixture was cooled to room temperature, 1N hydrochloric acid (300 mL) was added, and the mixture was extracted with ethyl acetate. The extract was washed with saturated brine, dried over magnesium sulfate, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (hexane-ethyl acetate 100:0-90:10, v/v) to give the title compound (19.91 g, 45%) as a colorless solid.
Reaction SMILES: [CH2:1](O)[CH2:2][CH3:3].CC1C=CC=C(C)N=1.FC(F)(F)S(OS(C(F)(F)F)(=O)=O)(=O)=O.[CH2:28]([O:35][NH2:36])[C:29]1[CH:34]=[CH:33][CH:32]=[CH:31][CH:30]=1>C(Cl)Cl>[CH2:28]([O:35][NH:36][CH2:1][CH2:2][CH3:3])[C:29]1[CH:34]=[CH:33][CH:32]=[CH:31][CH:30]=1
Reactant: NOCc1ccccc1
Reactant: CCCO
Agent: O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F
Solvent: Cc1cccc(C)n1
Solvent: ClCCl
Product: CCCNOCc1ccccc1
Temperature: -78 °C
Reaction time: 0.5 h
Yield: 81.5 %

Procedure:
To a solution of propan-1-ol (6.25 mL, 83.2 mmol) and 2,6-dimethylpyridine (11.6 mL, 99.8 mmol) in CH2Cl2 (500 mL) under a nitrogen atmosphere at −78° C. was added dropwise trifluoromethanesulfonic anhydride (14.0 mL, 83.2 mmol). After stirring for 30 min at −78° C., a solution of O-benzylhydroxylamine (10.7 ml, 91.5 mmol) in CH2Cl2 (10 mL) was added dropwise. The resulting mixture was stirred at −78° C. for 1 h, then warmed to room temperature, and stirred for additional 2 h. The reaction mixture was diluted with ice water (250 mL) and the organic layer was separated, washed with saturated aq. NaHCO3 (100 mL) and brine (100 mL) The aqueous layers were extracted again with EtOAc (1×200 mL). The combined organic layers were dried over MgSO4, filtered, and concentrated under reduced pressure to give the crude material that was purified by silica gel flash column chromatography (CH2Cl2). To the fraction containing product and 2,6-dimethylpyridine was added 2 M aq KOH (100 mL), that was then washed with MTBE. The aqueous layer was then brought to a pH of ˜5 with 1 M aq HCl and then extracted with MTBE (3×50 mL). The combined organic layers were dried over MgSO4, filtered, and concentrated under reduced pressure to afford 11.2 g (75%) of O-benzyl-N-propylhydroxylamine.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[C:4]([CH:15]=[CH:16][C:17]=1[O:18][CH3:19])[C:5]([NH:7][C:8]1[CH:13]=[CH:12][CH:11]=[C:10]([Cl:14])[CH:9]=1)=[O:6].[F:20][C:21]1[CH:26]=[CH:25][C:24]([N:27]=[C:28]=[S:29])=[CH:23][CH:22]=1>CO>[Cl:14][C:10]1[CH:9]=[C:8]([NH:7][C:5](=[O:6])[C:4]2[CH:15]=[CH:16][C:17]([O:18][CH3:19])=[C:2]([NH:1][C:28]([NH:27][C:24]3[CH:25]=[CH:26][C:21]([F:20])=[CH:22][CH:23]=3)=[S:29])[CH:3]=2)[CH:13]=[CH:12][CH:11]=1
Reactant: COc1ccc(C(=O)Nc2cccc(Cl)c2)cc1N
Reactant: Fc1ccc(N=C=S)cc1
Solvent: CO
Product: COc1ccc(C(=O)Nc2cccc(Cl)c2)cc1NC(=S)Nc1ccc(F)cc1
Yield: 89.7 %

Procedure:
Prepared according to the procedure described for Example 100 using 3-amino-N-(3-chlorophenyl)-4-methoxy-benzamide from Example 16 (0.5545 g, 2.01 mmol) and 4-fluorophenyl isothiocyanate (0.3073 g, 2.01 mmol), and omitting the trituration in methanol to afford the product (0.775 g); m.p. 184-185° C.
Reaction SMILES: [NH2:1][C:2]1[S:3][C:4]2[C:9]([N:10]=1)=[CH:8][CH:7]=[C:6]([O:11][C:12]1[CH:13]=[CH:14][C:15]([CH3:32])=[C:16]([NH:18][C:19](=[O:31])[C:20]3[CH:25]=[CH:24][CH:23]=[C:22]([C:26]4([C:29]#[N:30])[CH2:28][CH2:27]4)[CH:21]=3)[CH:17]=1)[N:5]=2.[CH:33]1([C:36](Cl)=[O:37])[CH2:35][CH2:34]1>N1C=CC=CC=1>[C:29]([C:26]1([C:22]2[CH:21]=[C:20]([CH:25]=[CH:24][CH:23]=2)[C:19]([NH:18][C:16]2[CH:17]=[C:12]([O:11][C:6]3[N:5]=[C:4]4[S:3][C:2]([NH:1][C:36]([CH:33]5[CH2:35][CH2:34]5)=[O:37])=[N:10][C:9]4=[CH:8][CH:7]=3)[CH:13]=[CH:14][C:15]=2[CH3:32])=[O:31])[CH2:27][CH2:28]1)#[N:30]
Reactant: Cc1ccc(Oc2ccc3nc(N)sc3n2)cc1NC(=O)c1cccc(C2(C#N)CC2)c1
Reactant: O=C(Cl)C1CC1
Solvent: c1ccncc1
Product: Cc1ccc(Oc2ccc3nc(NC(=O)C4CC4)sc3n2)cc1NC(=O)c1cccc(C2(C#N)CC2)c1
Temperature: 25 °C
Reaction time: 2 h
Yield: 63.3 %

Procedure:
To a solution of N-{5-[(2-amino[1,3]thiazolo[5,4-b]pyridin-5-yl)oxy]-2-methylphenyl}-3-(1-cyanocyclopropyl)benzamide (47 mg, 0.124 mmol) in pyridine (2.0 mL) was added cyclopropanecarbonyl chloride (25 μL, 0.273 mmol), and the mixture was stirred at room temperature for 2 hr. The reaction mixture was concentrated under reduced pressure, and the residue was dissolved in methanol (1.0 mL)/water (1.0 mL). 1N Aqueous sodium hydroxide solution (1.0 mL) was added, and the mixture was stirred at room temperature for 30 min. The reaction mixture was concentrated under reduced pressure, and the residue was diluted with ethyl acetate (100 mL), washed with water (50 mL) and saturated brine (50 mL), and dried over anhydrous sodium sulfate. The insoluble material was filtered off, and the filtrate was concentrated under reduced pressure. The obtained residue was purified by silica gel column chromatography (hexane/ethyl acetate=70/30→0/100), and the obtained solution was concentrated under reduced pressure. The residue was triturated with ethyl acetate/hexane to give the title compound (40 mg, 64%) as a colorless powder.
Reaction SMILES: C(OO)(=[O:3])C.[NH2:6][C:7]1[N:12]=[C:11]([NH:13][C:14]([O:16][CH3:17])=[O:15])[CH:10]=[C:9]([O:18][S:19]([C:22]2[CH:27]=[CH:26][C:25]([CH3:28])=[CH:24][CH:23]=2)(=[O:21])=[O:20])[N:8]=1.S([O-])([O-])=O.[Na+].[Na+].C(OCC)(=O)C>C(O)C>[NH2:6][C:7]1[N+:12]([O-:3])=[C:11]([NH:13][C:14]([O:16][CH3:17])=[O:15])[CH:10]=[C:9]([O:18][S:19]([C:22]2[CH:27]=[CH:26][C:25]([CH3:28])=[CH:24][CH:23]=2)(=[O:21])=[O:20])[N:8]=1
Reactant: COC(=O)Nc1cc(OS(=O)(=O)c2ccc(C)cc2)nc(N)n1
Reactant: CC(=O)OO
Agent: O=S([O-])[O-]
Agent: [Na+]
Solvent: CCO
Solvent: CCOC(C)=O
Product: COC(=O)Nc1cc(OS(=O)(=O)c2ccc(C)cc2)nc(N)[n+]1[O-]
Temperature: 25 °C
Reaction time: 48 h

Procedure:
6.75 ml of 40% peracetic acid are added dropwise at 0° to a suspension of 3.4 g (10 mmol) of methyl 2-amino-6-([p-toluenesulfonyl)oxy]-4-pyrimidinecarbamate in 120 ml of absolute ethanol. The mixture is stirred at room temperature for 48 hours and thereafter poured into an aqueous solution of sodium sulfite. Ethyl acetate is added thereto, the organic phase is separated, dried over sodium sulphate and evaporated under reduced pressure. The residue is recrystallized from methylene chloride/methanol, there being obtained methyl 2-amino-6-[(p-toluenesulfonyl)oxy]-4-pyrimidinecarbamate-3-oxide of melting point 144°-145°.
Reaction SMILES: [CH2:1]([O:3][Si:4]([O:24][CH2:25][CH3:26])([O:21][CH2:22][CH3:23])[C:5]1[CH:10]=[CH:9][CH:8]=[C:7]([Si:11]([O:18][CH2:19][CH3:20])([O:15][CH2:16][CH3:17])[O:12][CH2:13][CH3:14])[CH:6]=1)[CH3:2].Br[C:28]1[CH:33]=C(Br)C=C(Br)C=1.[I-].[Cs+]>>[CH2:16]([O:15][Si:11]([O:12][CH2:13][CH3:14])([O:18][CH2:19][CH3:20])[C:7]1[CH:8]=[C:9]([Si:4]([O:24][CH2:33][CH3:28])([O:21][CH2:22][CH3:23])[O:3][CH2:1][CH3:2])[CH:10]=[C:5]([Si:4]([O:24][CH2:25][CH3:26])([O:21][CH2:22][CH3:23])[O:3][CH2:1][CH3:2])[CH:6]=1)[CH3:17]
Reactant: Brc1cc(Br)cc(Br)c1
Reactant: CCO[Si](OCC)(OCC)c1cccc([Si](OCC)(OCC)OCC)c1
Agent: [Cs+]
Agent: [I-]
Product: CCO[Si](OCC)(OCC)c1cc([Si](OCC)(OCC)OCC)cc([Si](OCC)(OCC)OCC)c1

Procedure:
The procedure used for the preparation of 1,3-di(triethoxysilyl)benzene was followed using 1,3,5-tribromobenzene (100.0 g, 0.318 mol) in place of 1,3-dibromobenzene. Two distillations gave a clear, colorless oil (0.1 mmHg, 196-198° C., 23.4 g, 13%). Anal. Calcd for C24H48O9Si3 : C, 51.0: H, 8.56. Found: C, 51.2; H, 8.53. IR (Neat, CsI, cm-1) : 2964 s, 2920 s, 2880 s, 2730 w, 1560 m, 1480 w, 1440 m, 1386 s, 1290 m, 1160 s, 1090 vs, 955 s, 825 s, 775 s, 710 m, 670 m, 487 s. 1H NMR (benzene -d6, 22° C., 300 MHz : δ 1.16 (t, J=7.1 Hz, 18 H, OCH2CH 3), 3.87 (q, J=7.1 Hz, 12 H, OCH2CH3, 8.55 (s, 1H, C6H4). 13C{1H} NMR (benzene-d6, 22° C., 75.5 MHz ): δ 18.43 (OCH2CH3), 58.92 (OCH2CH3), 130.83, 143.60 (C6H4).
Reaction SMILES: [Br:1][C:2]1[CH:7]=[C:6]([S:8][CH3:9])[CH:5]=[C:4]([Br:10])[N:3]=1.ClC1C=CC=C(C(OO)=[O:19])C=1>ClCCl>[Br:1][C:2]1[CH:7]=[C:6]([S:8]([CH3:9])=[O:19])[CH:5]=[C:4]([Br:10])[N:3]=1
Reactant: O=C(OO)c1cccc(Cl)c1
Reactant: CSc1cc(Br)nc(Br)c1
Solvent: ClCCl
Product: CS(=O)c1cc(Br)nc(Br)c1
Temperature: 25 °C
Reaction time: 3 h
Yield: 87.3 %

Procedure:
To a solution of 0.282 g 2,6-dibromo-4-methylsulfanyl-pyridine (Example 45a) in 5.0 ml dichlormethane was added 0.246 g m-chloroperbenzoic acid at 0° C. and the mixture was then stirred at room temperature for 3 h. The reaction mixture was partitioned between 10% potassium carbonate and ethyl acetate. The phases were separated and the organic phase was washed with brine, dried over sodium sulphate and purified by chromatography on silica gel with ethyl acetate to yield 0.260 g of the title compound as white crystals melting at 98-100° C.
Reaction SMILES: [H-].[Na+].[CH:3]1([C@@H:6]2[O:16][CH2:15][C:9]3=[N:10][O:11][C@@H:12]([CH2:13][OH:14])[C@@H:8]3[CH2:7]2)[CH2:5][CH2:4]1.I[CH3:18].O>CN(C)C=O>[CH:3]1([C@@H:6]2[O:16][CH2:15][C:9]3=[N:10][O:11][C@@H:12]([CH2:13][O:14][CH3:18])[C@@H:8]3[CH2:7]2)[CH2:4][CH2:5]1
Reactant: CI
Reactant: OC[C@@H]1ON=C2CO[C@@H](C3CC3)C[C@H]21
Agent: [H-]
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: COC[C@@H]1ON=C2CO[C@@H](C3CC3)C[C@H]21
Temperature: 0 °C
Reaction time: 0.5 h

Procedure:
Sodium hydride (60% in oil, 395 mg, 9.88 mmol) was slurried in N,N-dimethylformamide (30 mL) and cooled in an ice bath. A solution of rel-[(3R,3aR,5R)-5-cyclopropyl-3,3a,4,5-tetrahydro-7H-pyrano[3,4-c][1,2]oxazol-3-yl]methanol (C37) (1.30 g, 6.59 mmol) in minimal N,N-dimethylformamide was added drop-wise, and the reaction mixture was stirred at 0° C. for 30 minutes. Iodomethane (0.45 mL, 7.2 mmol) was then added in a drop-wise manner, and the reaction was allowed to proceed for an additional 30 minutes at 0° C. Water was added, and the mixture was warmed to room temperature and extracted twice with ethyl acetate. The combined organic layers were washed with saturated aqueous sodium chloride solution, dried over sodium sulfate, filtered, and concentrated in vacuo. Chromatography on silica gel (Gradient: 0% to 60% ethyl acetate in heptane) provided the product as an oil. Yield: 1.0 g, 4.7 mmol, 71%. LCMS m/z 212.1 [M+H+].
Reaction SMILES: [CH:1]1([N:6]2[C:10]3[N:11]=[C:12]([NH:15][C:16]4[CH:24]=[CH:23][C:19]([C:20](O)=[O:21])=[CH:18][N:17]=4)[N:13]=[CH:14][C:9]=3[CH:8]=[C:7]2[C:25](=[O:29])[N:26]([CH3:28])[CH3:27])[CH2:5][CH2:4][CH2:3][CH2:2]1.[CH3:30][N:31]([CH3:38])[CH:32]1[CH2:37][CH2:36][NH:35][CH2:34][CH2:33]1.CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>CN(C=O)C>[CH3:27][N:26]([CH3:28])[C:25]([C:7]1[N:6]([CH:1]2[CH2:2][CH2:3][CH2:4][CH2:5]2)[C:10]2[N:11]=[C:12]([NH:15][C:16]3[CH:24]=[CH:23][C:19]([C:20]([N:35]4[CH2:36][CH2:37][CH:32]([N:31]([CH3:38])[CH3:30])[CH2:33][CH2:34]4)=[O:21])=[CH:18][N:17]=3)[N:13]=[CH:14][C:9]=2[CH:8]=1)=[O:29]
Reactant: CN(C)C1CCNCC1
Reactant: CN(C)C(=O)c1cc2cnc(Nc3ccc(C(=O)O)cn3)nc2n1C1CCCC1
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Product: CN(C)C(=O)c1cc2cnc(Nc3ccc(C(=O)N4CCC(N(C)C)CC4)cn3)nc2n1C1CCCC1
Temperature: 25 °C
Reaction time: 48 h
Yield: 47.6 %

Procedure:
To a solution of 6-(7-cyclopentyl-6-dimethylcarbamoyl-7H-pyrrolo[2,3-d]pyrimidin-2-ylamino)-nicotinic acid (100 mg, 0.25 mmol) (Example D) in 3 mL of DMF is added dimethyl-piperidin-4-yl-amine (33 mg, 0.25 mmol), HBTU (140 mg, 0.38 mmol), and DIPEA (0.088 mL, 0.51 mmol). Alter 48 h stirring at room temperature, the resulting mixture is concentrated and diluted with saturated NaHCO3 and extracted with ethyl acetate (3×100 mL). The combine organics are dried over Na2CO3 and concentrated to give a reddish residue. Preparative HPLC to give 7-cyclopentyl-2-[5-(4-dimethylamino-piperidine-1-carbonyl)-pyridin-2-ylamino]-7H-pyrrolo[2,3-d]pyrimidine-6-carboxylic acid dimethylamide (60 mg, 46%). MS(ESI) m/z 505.5 (M+H)+
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[N:9]([OH:15])[CH:10]=[CH:11][C:12]=2[C:13]#[N:14])=[CH:4][CH:3]=1.O1CCC[CH2:17]1.CC(C)([O-])C.[K+].CI>O>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[N:9]([O:15][CH3:17])[CH:10]=[CH:11][C:12]=2[C:13]#[N:14])=[CH:4][CH:3]=1
Reactant: C1CCOC1
Reactant: N#Cc1ccn(O)c1-c1ccc(Cl)cc1
Agent: CC(C)(C)[O-]
Agent: [K+]
Solvent: O
Solvent: CI
Product: COn1ccc(C#N)c1-c1ccc(Cl)cc1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 77 %

Procedure:
To a stirred solution of 2-(p-chlorophenyl)-1-hydroxypyrrole-3-carbonitrile (2.88 g, 0.0132 mol) and anhydrous tetrahydrofuran is added potassium tert-butoxide (1.55 g, 0.0138 mol). After 30 minutes, methyl iodide (2.06 g, 0.9 mL, 0.0145 mol) is added and the resulting slurry is stirred at room temperature for hours, diluted with water and extracted with ether. The combined ether extracts are washed sequentially with water and brine, dried over anhydrous magnesium sulfate and concentrated in vacuo to yield a solid. Crystallization of the solid from ether/hexanes gives the title compound as a brown solid (2.35 g, 77%), mp 105°-106° C.
Reaction SMILES: [ClH:1].O1CCOCC1.C(OC([N:15]1[CH2:19][CH2:18][C:17]([NH2:39])([C:20](=[O:38])[NH:21][C:22]2[CH:23]=[C:24]3[C:28](=[CH:29][CH:30]=2)[NH:27][N:26]=[C:25]3[C:31]2[CH:36]=[CH:35][C:34]([F:37])=[CH:33][CH:32]=2)[CH2:16]1)=O)(C)(C)C>C(Cl)Cl>[ClH:1].[F:37][C:34]1[CH:35]=[CH:36][C:31]([C:25]2[C:24]3[C:28](=[CH:29][CH:30]=[C:22]([NH:21][C:20]([C:17]4([NH2:39])[CH2:18][CH2:19][NH:15][CH2:16]4)=[O:38])[CH:23]=3)[NH:27][N:26]=2)=[CH:32][CH:33]=1
Reactant: CC(C)(C)OC(=O)N1CCC(N)(C(=O)Nc2ccc3[nH]nc(-c4ccc(F)cc4)c3c2)C1
Agent: Cl
Solvent: C1COCCO1
Solvent: ClCCl
Product: NC1(C(=O)Nc2ccc3[nH]nc(-c4ccc(F)cc4)c3c2)CCNC1
Temperature: 25 °C
Reaction time: 1 h
Yield: 69 %

Procedure:
4M HCl/dioxane (2 ml) was added to a solution of 3-Amino-3-[3-(4-fluoro-phenyl)-1H-indazol-5-ylcarbamoyl]-pyrrolidine-1-carboxylic acid tert-butyl ester (1P) (60 mg, 0.088 mmol) in MeCl2 (1 ml) at room temperature then stirred for 1 hour at room temperature. The solvent was evaporated. Hexanes (20 ml) was added and supernatant decanted. The residue was dried yielding title compound 2P as a white solid (20 mg, 69%). ESMS (MH 340).
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][C@H:9]([CH2:29][C:30]1[CH:35]=[C:34]([F:36])[C:33]([F:37])=[CH:32][C:31]=1[F:38])[CH2:10][C:11]([N:13]1[CH2:18][CH2:17][N:16]2[C:19]([C:25]([F:28])([F:27])[F:26])=[N:20][C:21]([C:22](O)=[O:23])=[C:15]2[CH2:14]1)=[O:12])=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH3:39][S:40]([CH2:43][CH2:44][NH2:45])(=[O:42])=[O:41].O=C1N([ClH]P([ClH]N2CCOC2=O)=O)CCO1.C(N(CC)CC)C>ClCCl>[C:1]([O:5][C:6](=[O:7])[NH:8][C@H:9]([CH2:29][C:30]1[CH:35]=[C:34]([F:36])[C:33]([F:37])=[CH:32][C:31]=1[F:38])[CH2:10][C:11]([N:13]1[CH2:18][CH2:17][N:16]2[C:19]([C:25]([F:28])([F:26])[F:27])=[N:20][C:21]([C:22](=[O:23])[NH:45][CH2:44][CH2:43][S:40]([CH3:39])(=[O:42])=[O:41])=[C:15]2[CH2:14]1)=[O:12])([CH3:2])([CH3:4])[CH3:3]
Reactant: CS(=O)(=O)CCN
Reactant: CC(C)(C)OC(=O)N[C@@H](CC(=O)N1CCn2c(C(F)(F)F)nc(C(=O)O)c2C1)Cc1cc(F)c(F)cc1F
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(C)(C)OC(=O)N[C@@H](CC(=O)N1CCn2c(C(F)(F)F)nc(C(=O)NCCS(C)(=O)=O)c2C1)Cc1cc(F)c(F)cc1F
Yield: 33.9 %

Procedure:
(R)-7-[3-tert-Butoxycarbonylamino-4-(2,4,5-trifluoro-phenyl)-butyryl]-3-trifluoromethyl-5,6,7,8-tetrahydro-imidazo[1,5-a]pyrazine-1-carboxylic acid 2a (0.15 g, 0.27 mmol), 2-methanesulfonyl-ethylamine (65.5 mg, 0.41 mmol) and bis (2-oxo-3-oxazolidinyl)phosphonic chloride (0.104 g, 0.41 mmol) were dissolved in 5 mL of dichloromethane under stirring, and triethylamine (0.25 mL, 1.62 mmol) was then added to the solution. The reaction mixture was reacted at room temperature overnight and monitored by thin layer chromatography until the disappearance of the starting materials. The reaction mixture was concentrated under reduced pressure. The resulting residue was purified by silica gel column chromatography to obtain the title compound (R)-[3-[1-(2-methanesulfonyl-ethylcarbamoyl)-3-trifluoromethyl-5,6-dihydro-8H-imidazo[1,5-a]pyrazin-7-yl]-3-oxo-1-(2,4,5-trifluoro-benzyl)-propyl]-carbamic acid tert-butyl ester 2b (60 mg, yield 34%) as a white solid.
Reaction SMILES: [C:1]([OH:5])(=[O:4])[C:2]#[CH:3].[CH3:6][O:7][CH2:8][CH2:9][O:10][CH2:11][CH2:12]O.C1(C)C=CC=CC=1>O>[C:1]([O:5][CH2:12][CH2:11][O:10][CH2:9][CH2:8][O:7][CH3:6])(=[O:4])[C:2]#[CH:3]
Reactant: COCCOCCO
Reactant: C#CC(=O)O
Solvent: Cc1ccccc1
Solvent: O
Product: C#CC(=O)OCCOCCOC

Procedure:
12.3 ml (0.2 mol) of propiolic acid were boiled at reflux for 20 hours together with 23.6 ml (0.2 mol) of diethylene glycol monomethyl ether, 1.5 g (8 mmol) of P-toluenesulphonic acid monohydrate and 80 ml of toluene, with the resulting reaction water being distilled off azeotropically and being collected in a water separator. After completion of the water separation the reaction mixture was washed in succession with saturated sodium bicarbonate solution and with water. The toluene phase was dried over sodium sulphate and concentrated. The crude product was purified by flash chromatography on 500 g of silica gel (elution agent methylene chloride/ethyl acetate 9:1). There was obtained 2-(2-methoxyethoxy)ethyl propiolate as a colorless oil.