Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][C:2]1[CH:3]=[CH:4][C:5]([N+:10]([O-:12])=[O:11])=[C:6]([CH:9]=1)[CH:7]=[O:8].[C:13](OC(=O)C)(=[O:15])[CH3:14]>O>[C:13]([O:1][C:2]1[CH:3]=[CH:4][C:5]([N+:10]([O-:12])=[O:11])=[C:6]([CH:9]=1)[CH2:7][OH:8])(=[O:15])[CH3:14]
Reactant: O=Cc1cc(O)ccc1[N+](=O)[O-]
Reactant: CC(=O)OC(C)=O
Solvent: O
Product: CC(=O)Oc1ccc([N+](=O)[O-])c(CO)c1

Procedure:
A mixture of 5-hydroxy-2-nitrobenzaldehyde (4 g.) and acetic anhydride (10 ml.) was heated on a steam bath for 1 hour, then poured into water (100 ml.) and extracted with diethyl ether (3×50 ml.). The extracts were combined and dried, and the solvent was evaporated. The residue of 5-acetoxy-2-nitrobenzaldehyde was dissolved in absolute ethanol (100 ml.), and stirred and ice-cooled while sodium borohydride (1.5 g.) was added in portions. The reaction mixture was stirred at room temperature for 1 hour, then water (100 ml.) was added, and the mixture was extracted with ether (3×70 ml.). The extracts were combined and dried, and the solvent was evaporated to give 5-acetoxy-2-nitrobenzyl alcohol, which was hydrogenated by the general process described in the latter part of Example 13(a) to give the required starting material.
Reaction SMILES: [Br:1][C:2]1[NH:3][C:4]2[C:9]([C:10]=1[CH:11]1[CH2:16][CH2:15][CH2:14][CH2:13][CH2:12]1)=[CH:8][CH:7]=[C:6]([C:17]([O:19][CH3:20])=[O:18])[CH:5]=2.[H-].[Na+].[CH3:23][O:24][CH:25]([O:28][CH3:29])[CH2:26]Br>CN(C=O)C>[Br:1][C:2]1[N:3]([CH2:26][CH:25]([O:28][CH3:29])[O:24][CH3:23])[C:4]2[C:9]([C:10]=1[CH:11]1[CH2:16][CH2:15][CH2:14][CH2:13][CH2:12]1)=[CH:8][CH:7]=[C:6]([C:17]([O:19][CH3:20])=[O:18])[CH:5]=2
Reactant: COC(=O)c1ccc2c(C3CCCCC3)c(Br)[nH]c2c1
Reactant: COC(CBr)OC
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: COC(=O)c1ccc2c(C3CCCCC3)c(Br)n(CC(OC)OC)c2c1
Temperature: 80 °C
Reaction time: 1 h
Yield: 79 %

Procedure:
To a stirred solution of methyl 2-bromo-3-cyclohexyl-1H-indole-6-carboxylate (prepared as described in published International patent application WO2004/087714) (0.2 M, 1 eq.) in DMF at RT was added NaH (60% dispersion in mineral oil, 1.75 eq). After 1 h, KI (8 mol %) and bromoacetaldehyde dimethyl acetal (2.5 eq) were added and the reaction heated at 80° C. for 17 h. After cooling to RT, the reaction was quenched by addition of aqueous HCl (1N) and extracted into EtOAc (×3). The combined organics were washed with HCl (1N), H2O and brine before being dried (Na2SO4), filtered and concentrated in vacuo. Purification by flash column chromatography (Biotage, 5-10% EtOAc/PE gradient) gave the title compound as a white solid (79%); MS (ES+) m/z 446 (M+H)+, 448 (M+H)+.
Reaction SMILES: [C:1]([C:4]1[CH:11]=[CH:10][C:7]([C:8]#[N:9])=[CH:6][CH:5]=1)(=[O:3])[CH3:2].[CH2:12]([Mg]Cl)[C:13]([CH3:16])([CH3:15])[CH3:14].C(OCC)C>C(OCC)C.C1COCC1>[OH:3][C:1]([C:4]1[CH:11]=[CH:10][C:7]([C:8]#[N:9])=[CH:6][CH:5]=1)([CH3:2])[CH2:12][C:13]([CH3:16])([CH3:15])[CH3:14]
Reactant: CC(=O)c1ccc(C#N)cc1
Reactant: CC(C)(C)C[Mg]Cl
Solvent: CCOCC
Solvent: C1CCOC1
Product: CC(C)(C)CC(C)(O)c1ccc(C#N)cc1
Temperature: 0 °C
Reaction time: 8 h
Yield: 24 %

Procedure:
Dissolve 4-acetylbenzonitrile (1 g, 6.88 mmol) in diethyl ether/THF (1:1, 60 mL) and cool the solution to 0° C. Add 1 M neopentylmagnesium chloride in diethyl ether (8.3 mL, 8.3 mmol) under nitrogen and stir the mixture at room temperature overnight. Add saturated aqueous NH4Cl and extract the mixture twice with EtOAc. Dry the combined organic extracts over MgSO4, filter and concentrate in vacuo. Purify the crude mixture by chromatography on silica gel eluting with hexane and hexane/EtOAc (19:1, 9:1) to give the desired intermediate (364 mg, 24%).
Reaction SMILES: [CH2:1]([N:8]1[C:13](=[O:14])[C:12](=[C:15]2[S:19][CH:18]=[CH:17][S:16]2)[C:11](=[O:20])[CH:10](C(OCC)=O)[CH2:9]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[OH-].[Na+].Cl>C(O)C>[CH2:1]([N:8]1[CH2:9][CH2:10][C:11](=[O:20])[C:12](=[C:15]2[S:16][CH:17]=[CH:18][S:19]2)[C:13]1=[O:14])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: CCOC(=O)C1CN(Cc2ccccc2)C(=O)C(=C2SC=CS2)C1=O
Agent: Cl
Agent: [Na+]
Agent: [OH-]
Solvent: CCO
Product: O=C1CCN(Cc2ccccc2)C(=O)C1=C1SC=CS1
Yield: 78 %

Procedure:
Ethyl 1-benzyl-5-(1,3-dithiol-2-ylidene)-4,6-dioxopiperidine-3-carboxylate (2.0 g) is dissolved in ethanol (160 ml), and a 10% aqueous sodium hydroxide solution (8.0 ml) is added thereto. The mixture is refluxed for 2 hours. The mixture is cooled, neutralized with 10% hydrochloric acid, and then evaporated under reduced pressure to remove the solvent. The residue is dissolved in ethyl acetate, and the solution is washed with water, dried and then evaporated to remove the solvent. The residue thus obtained is recrystallized from isopropanol, whereby 1-benzyl-3-(1,3-dithiol-2-ylidene)-2,4-dioxopiperidine (1.26 g) is obtained as pale yellow needles. Yield: 78%.
Reaction SMILES: Cl.[NH2:2][C@@H:3]1[CH2:8][CH2:7][C@H:6]([NH:9][C:10]([C:12]2[C:16]3=[N:17][CH:18]=[CH:19][C:20]([C:21]4[CH:26]=[CH:25][C:24]([O:27][CH3:28])=[CH:23][C:22]=4[O:29][CH2:30][CH:31]4[CH2:33][CH2:32]4)=[C:15]3[NH:14][C:13]=2[CH3:34])=[O:11])[CH2:5][CH2:4]1.C([O:38][C@@H:39]([CH3:43])[C:40](Cl)=[O:41])(=O)C>>[CH:31]1([CH2:30][O:29][C:22]2[CH:23]=[C:24]([O:27][CH3:28])[CH:25]=[CH:26][C:21]=2[C:20]2[CH:19]=[CH:18][N:17]=[C:16]3[C:12]([C:10]([NH:9][C@H:6]4[CH2:7][CH2:8][C@@H:3]([NH:2][C:40](=[O:41])[C@@H:39]([OH:38])[CH3:43])[CH2:4][CH2:5]4)=[O:11])=[C:13]([CH3:34])[NH:14][C:15]=23)[CH2:32][CH2:33]1
Reactant: CC(=O)O[C@@H](C)C(=O)Cl
Reactant: COc1ccc(-c2ccnc3c(C(=O)N[C@H]4CC[C@@H](N)CC4)c(C)[nH]c23)c(OCC2CC2)c1
Agent: Cl
Product: COc1ccc(-c2ccnc3c(C(=O)N[C@H]4CC[C@@H](NC(=O)[C@H](C)O)CC4)c(C)[nH]c23)c(OCC2CC2)c1

Procedure:
Starting from N-(cis-4-aminocyclohexyl)-7-[2-(cyclopropylmethoxy)-4-methoxyphenyl]-2-methyl-1H-pyrrolo[3,2-b]pyridine-3-carboxamide hydrochloride (example D.f13) and commercially available (2S)-1-chloro-1-oxopropan-2-yl acetate the title compound is obtained as colorless solid.
Reaction SMILES: [CH3:1][C:2]([Si:5]([CH3:23])([CH3:22])[O:6][CH2:7][C@H:8]1[C@H:12]([CH2:13][O:14][Si:15]([C:18]([CH3:21])([CH3:20])[CH3:19])([CH3:17])[CH3:16])[C:9]21[O:11][CH2:10]2)([CH3:4])[CH3:3].[I-].[Li+]>C(Cl)Cl>[CH3:4][C:2]([Si:5]([CH3:22])([CH3:23])[O:6][CH2:7][C@H:8]1[C@H:12]([CH2:13][O:14][Si:15]([C:18]([CH3:20])([CH3:19])[CH3:21])([CH3:16])[CH3:17])[CH2:10][C:9]1=[O:11])([CH3:3])[CH3:1]
Reactant: CC(C)(C)[Si](C)(C)OC[C@H]1[C@H](CO[Si](C)(C)C(C)(C)C)C12CO2
Agent: [I-]
Agent: [Li+]
Solvent: ClCCl
Product: CC(C)(C)[Si](C)(C)OC[C@@H]1CC(=O)[C@H]1CO[Si](C)(C)C(C)(C)C
Temperature: 0 °C
Reaction time: 1 h

Procedure:
A solution of 12.752 g (35.6 mmol) of [4R,5R]-4,5-bis(((1,1-dimethylethyl)-dimethylsilyl)oxymethyl)-1-oxaspiro[2,2]pentane, from Step D, in 50 mL of methylene chloride was added to a solution of 3.814 g (28.5 mmol) of lithium iodide in 200 mL of methylene chloride which had been cooled in an ice bath. After stirring the reaction mixture for 1 h at 0° C., the ice bath was removed and the reaction mixture was stirred for 20 minutes at ambient temperature. The reaction mixture was then washed with 5% aqueous sodium bicarbonate solution, 5% sodium bisulfite solution and brine, dried over anhydrous magnesium sulfate, filtered and concentrated under reduced pressure to give 12.317 g (96.6% crude yield) of the title compound which was taken on to the next step without purifiaction; MS DCI-NH3M/Z: 376 (M+NH4)+.
Reaction SMILES: [CH3:1][C:2]1[O:6][C:5]([C:7]2[CH:12]=[CH:11][CH:10]=[CH:9][CH:8]=2)=[N:4][C:3]=1[CH2:13][CH2:14][C:15]([C:17]1[CH:22]=[CH:21][C:20]([Br:23])=[CH:19][CH:18]=1)=[O:16].[BH4-].[Na+]>C1COCC1.C(O)C>[CH3:1][C:2]1[O:6][C:5]([C:7]2[CH:8]=[CH:9][CH:10]=[CH:11][CH:12]=2)=[N:4][C:3]=1[CH2:13][CH2:14][CH:15]([C:17]1[CH:22]=[CH:21][C:20]([Br:23])=[CH:19][CH:18]=1)[OH:16]
Reactant: Cc1oc(-c2ccccc2)nc1CCC(=O)c1ccc(Br)cc1
Agent: [BH4-]
Agent: [Na+]
Solvent: C1CCOC1
Solvent: CCO
Product: Cc1oc(-c2ccccc2)nc1CCC(O)c1ccc(Br)cc1
Temperature: 0 °C
Reaction time: 3 h
Yield: 90.9 %

Procedure:
The title compound of Example 2 (5.0 g, 13 mmol) was dissolved in THF (75 mL) and added dropwise over 20 minutes to a suspension of sodium borohydride (513 mg, 13 mmol) in 75 mL of ethanol at 0° C. and the reaction mixture was stirred for 3 hours at 0° C. The reaction mixture was poured onto ice-water (500 mL) and extracted twice with diethyl ether (700 mL). The organic extracts were combined and washed with water (250 mL), brine (250 mL) and dried (MgSO4). The solvent was removed in vacuo and the residue was recrystallized from hexane to afford 4.4 g (92%) of the racemic title compound. mp 82-83° C. 1HNMR (60 MHz, CDCl3): δ2.0 (m, 2H), 2.2 (s, 3H), 2.5 (t, J=6 Hz, 2H), 4.6 (m, 1H), 4.7 (broad s, 1H, hydroxyl proton), 7.1-7.5 (m, 7H), 7.8-8.0 (m, 2H).
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[C:4]([CH:19]=[CH:20][CH:21]=1)[O:5][C:6]1[CH:7]=[CH:8][C:9]2[N:10]([CH:12]=[C:13]([C:15]([NH:17][CH3:18])=[O:16])[N:14]=2)[N:11]=1.[CH3:22][N:23]1[C:27]([C:28](Cl)=[O:29])=[CH:26][C:25]([CH3:31])=[N:24]1.O>CN(C)C(=O)C>[CH3:22][N:23]1[C:27]([C:28]([NH:1][C:2]2[CH:3]=[C:4]([CH:19]=[CH:20][CH:21]=2)[O:5][C:6]2[CH:7]=[CH:8][C:9]3[N:10]([CH:12]=[C:13]([C:15]([NH:17][CH3:18])=[O:16])[N:14]=3)[N:11]=2)=[O:29])=[CH:26][C:25]([CH3:31])=[N:24]1
Reactant: CNC(=O)c1cn2nc(Oc3cccc(N)c3)ccc2n1
Reactant: Cc1cc(C(=O)Cl)n(C)n1
Solvent: CC(=O)N(C)C
Solvent: O
Product: CNC(=O)c1cn2nc(Oc3cccc(NC(=O)c4cc(C)nn4C)c3)ccc2n1
Temperature: 25 °C
Reaction time: 1 h
Yield: 73.4 %

Procedure:
To a solution of 6-(3-aminophenoxy)-N-methylimidazo[1,2-b]pyridazine-2-carboxamide (250 mg, 0.88 mmol) in N,N-dimethylacetamide (2.5 mL) was added 1,3-dimethyl-1H-pyrazole-5-carbonyl chloride (253 mg, 1.59 mmol). After stirring at room temperature for 1 hr, water was added to the reaction mixture, and the precipitate was collected by filtration. The obtained residue was washed with water, acetonitrile and diethyl ether to give the title compound (262 mg, 73%) as a white powder.
Reaction SMILES: [OH-].[K+].[N:3]1[CH:8]=[CH:7][C:6]([CH:9]=[O:10])=[CH:5][CH:4]=1.[N+:11]([CH2:13][C:14]([N:16]1[CH2:21][CH2:20][N:19]([CH3:22])[CH2:18][CH2:17]1)=[O:15])#[C-:12]>CO>[N:3]1[CH:8]=[CH:7][C:6]([C@@H:9]2[O:10][CH:12]=[N:11][C@H:13]2[C:14]([N:16]2[CH2:17][CH2:18][N:19]([CH3:22])[CH2:20][CH2:21]2)=[O:15])=[CH:5][CH:4]=1
Reactant: O=Cc1ccncc1
Reactant: [C-]#[N+]CC(=O)N1CCN(C)CC1
Agent: [K+]
Agent: [OH-]
Solvent: CO
Product: CN1CCN(C(=O)[C@@H]2N=CO[C@H]2c2ccncc2)CC1
Yield: 78 %

Procedure:
To a stirred and cooled (0° C.) solution of KOH (0.335 g, 5.98 mmol) in 7 mL MeOH were added successively pyridine-4-carbaldehyde (0.705 g, 6.58 mmol) and 2-isocyano-1-(4-methyl-piperazin-1-yl)-ethanone VIB 01128 (1.00 g, 6.58 mmol). The mixture was stirred at 0° C. until precipitation and concentrated. The mixture was partitioned between EtOAc (20 mL) and H2O (10 mL). The aqueous layer was extracted twice with EtOAc (60 mL). The EtOAc fractions were combined, washed twice with brine (2×10 mL), dried over MgSO4 and filtered. After evaporation and drying trans-(4,5-dihydro-5-(pyridin-4-yl)oxazol-4-yl)(4-methylpiperazin-1-yl)methanone VIB 01130 was obtained (1.282 g, 78% yield) as a yellow oil.
Reaction SMILES: [NH2:1][C:2]1[C:10]([N+:11]([O-])=O)=[CH:9][CH:8]=[CH:7][C:3]=1[C:4]([OH:6])=[O:5].[H][H]>CO.[Pd]>[NH2:1][C:2]1[C:10]([NH2:11])=[CH:9][CH:8]=[CH:7][C:3]=1[C:4]([OH:6])=[O:5]
Reactant: Nc1c(C(=O)O)cccc1[N+](=O)[O-]
Reactant: [H][H]
Agent: [Pd]
Solvent: CO
Product: Nc1cccc(C(=O)O)c1N
Reaction time: 4 h

Procedure:
14 g (76.9 mmol) of 2-amino-3-nitrobenzoic acid (1b) were dissolved in 500 ml of methanol, treated with Pd/C, and hydrogenated with hydrogen. After 4 h, the catalyst was filtered off with suction and concentrated. A dark-brown solid was obtained. Yield: 11.67 g (99%).
Reaction SMILES: Br[C:2]1[CH:3]=[N:4][N:5]([CH3:18])[C:6]=1[C:7]1[CH:8]=[C:9]([C:14]([O:16][CH3:17])=[O:15])[S:10][C:11]=1[CH2:12][CH3:13].C(=O)([O-])[O-].[K+].[K+].O1CCO[CH2:27][CH2:26]1>O.CC(C)([P](C(C)(C)C)([Pd][P](C(C)(C)C)(C(C)(C)C)C(C)(C)C)C(C)(C)C)C>[CH:26]([C:2]1[CH:3]=[N:4][N:5]([CH3:18])[C:6]=1[C:7]1[CH:8]=[C:9]([C:14]([O:16][CH3:17])=[O:15])[S:10][C:11]=1[CH2:12][CH3:13])=[CH2:27]
Reactant: CCc1sc(C(=O)OC)cc1-c1c(Br)cnn1C
Reactant: C1COCCO1
Agent: CC(C)(C)[P]([Pd][P](C(C)(C)C)(C(C)(C)C)C(C)(C)C)(C(C)(C)C)C(C)(C)C
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Product: C=Cc1cnn(C)c1-c1cc(C(=O)OC)sc1CC
Yield: 73 %

Procedure:
A solution of methyl 4-(4-bromo-1-methyl-1H-pyrazol-5-yl)-5-ethyl-2-thiophenecarboxylate (300 mg, 0.91 mmol), potassium carbonate (630 mg, 4.56 mmol), bis(tri-t-butylphosphine)palladium(0) (23 mg, 0.05 mmol) and 2,4,6-trivinylcycloboroxane-pyridine complex (110 mg, 0.46 mmol) in 1,4-dioxane (5 ml) and water (1 ml) was stirred at 80° C. in a sealed tube for 2 h. The reaction contents were partitioned between H2O-DCM and the aqueous phase was washed several times with DCM. The combined organic fractions were dried over Na2SO4, concentrated and purified via column chromatography (10-50% EtOAc in hexanes) affording methyl 4-(4-ethenyl-1-methyl-1H-pyrazol-5-yl)-5-ethyl-2-thiophenecarboxylate (187 mg, 0.66 mmol, 73% yield) as a clear oil: LCMS (ES) m/z=277 (M+H)+.
Reaction SMILES: Cl[CH2:2][C:3]1[N:4]=[C:5]([NH:18][C:19](=[O:28])[C:20]2[C:25]([F:26])=[CH:24][CH:23]=[CH:22][C:21]=2[F:27])[S:6][C:7]=1[C:8]1[CH:13]=[CH:12][CH:11]=[C:10]([C:14]([F:17])([F:16])[F:15])[CH:9]=1.[NH:29]([CH3:31])[CH3:30].CCN(CC)CC>C1COCC1>[CH3:30][N:29]([CH2:2][C:3]1[N:4]=[C:5]([NH:18][C:19](=[O:28])[C:20]2[C:25]([F:26])=[CH:24][CH:23]=[CH:22][C:21]=2[F:27])[S:6][C:7]=1[C:8]1[CH:13]=[CH:12][CH:11]=[C:10]([C:14]([F:17])([F:16])[F:15])[CH:9]=1)[CH3:31]
Reactant: CNC
Reactant: O=C(Nc1nc(CCl)c(-c2cccc(C(F)(F)F)c2)s1)c1c(F)cccc1F
Solvent: CCN(CC)CC
Solvent: C1CCOC1
Product: CN(C)Cc1nc(NC(=O)c2c(F)cccc2F)sc1-c1cccc(C(F)(F)F)c1
Temperature: 25 °C
Reaction time: 1 h
Yield: 84 %

Procedure:
Into a solution of Compound 70 (50 mg, 0.12 mmol) in 5 mL of THF was added NH(Me)2 (40% solution in water, 0.1 mL) and NEt3 (0.1 ml) at room temperature. The solution was stirred at room temperature for 1 hour. The solution was washed with 5 mL of water and dried (Na2SO4), filtered and concentrated. The residue was purified on silica (eluted with 5-100% ethyl acetate in hexane) to give Compound 71 (44 mg, 84%) as a white solid.
Reaction SMILES: Cl.[CH2:2]([CH:10]1[CH2:18][C:17]2[C:12](=[CH:13][CH:14]=[C:15]([C:19](=[NH:21])[NH2:20])[CH:16]=2)[CH2:11]1)[CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH3:9].C[O-].[Na+]>CO>[CH2:2]([CH:10]1[CH2:18][C:17]2[C:12](=[CH:13][CH:14]=[C:15]([C:19]3[N:20]=[CH:13][C:12]([CH2:11][CH2:10][CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH3:9])=[CH:17][N:21]=3)[CH:16]=2)[CH2:11]1)[CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH3:9]
Reactant: CCCCCCCCC1Cc2ccc(C(=N)N)cc2C1
Agent: C[O-]
Agent: Cl
Agent: [Na+]
Solvent: CO
Product: CCCCCCCCCCc1cnc(-c2ccc3c(c2)CC(CCCCCCCC)C3)nc1
Reaction time: 48 h
Yield: 108.8 %

Procedure:
1.00 g (3.24 mM) of 2-octyl-5-amidinoindan hydrochloride, 0.40 g (7.40 mM) of sodium methylate, 0.82 g (3.43 mM) of α-octyloxy-β-dimethylaminoacrolein and 15 ml of methanol were placed in a 30 ml-round bottomed flask, followed by refluxing for 10.5 hours under stirring. After the reaction, the reaction mixture was left standing in a refrigerator for 2 days to precipitate a crystal. The crystal was recovered by filtration and dissolved in toluene, followed by drying with anhydrous sodium sulfate and filtration. The filtrate was evaporated to obtain a residue. The residue was purified by silica gel column chromatography (eluent: toluene/ethyl acetate=100/1) and recrystallized from a mixture solvent (toluene/methanol) to obtain 0.79 g of 2-octyl-5-(5-decylpyrimidine-2-yl)indan (Yield: 54.4%). ##STR151##
Reaction SMILES: [NH:1]([C:5]1[CH:10]=[CH:9][CH:8]=[CH:7][C:6]=1[CH2:11][C:12]([OH:14])=O)[C:2]([NH2:4])=[O:3].FC(F)(F)C(OC(=O)C(F)(F)F)=O>FC(F)(F)C(O)=O>[N:1]1([C:2]([NH2:4])=[O:3])[C:5]2[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=2)[CH2:11][C:12]1=[O:14]
Reactant: NC(=O)Nc1ccccc1CC(=O)O
Solvent: O=C(O)C(F)(F)F
Solvent: O=C(OC(=O)C(F)(F)F)C(F)(F)F
Product: NC(=O)N1C(=O)Cc2ccccc21
Yield: 34.6 %

Procedure:
To a solution of 194 mg (1.0 mmole) of 2-(2-ureidophenyl)acetic acid in 4 ml of trifluoroacetic acid was added 630 mg (3.0 mmole) of trifluoroacetic anhydride, and the mixture was then heated under reflux for ca. 1 hour. The reaction mixture was cooled and the solvent was removed by evaporation in vacuo. The residue was triturated under 5-8 ml of saturated sodium bicarbonate solution, and the material which remained out of solution was collected by filtration. The solid thus obtained was recrystallized from ethanol to give 61 mg of the title compound as colorless needles, m.p. 179°-180° C. (slight decomposition).
Reaction SMILES: [C:1]([NH:5][C:6]([C:8]1[C:16]2[C:11](=[N:12][CH:13]=[C:14]([C:17]3[C:25]4[C:20](=[CH:21][C:22]([F:26])=[CH:23][CH:24]=4)[N:19]([CH2:27][CH:28]4[CH2:31][N:30](C(OC(C)(C)C)=O)[CH2:29]4)[N:18]=3)[N:15]=2)[N:10](COCC[Si](C)(C)C)[CH:9]=1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[F:47][C:48]([F:53])([F:52])[C:49]([OH:51])=[O:50]>ClCCl>[F:47][C:48]([F:53])([F:52])[C:49]([OH:51])=[O:50].[C:1]([NH:5][C:6]([C:8]1[C:16]2[C:11](=[N:12][CH:13]=[C:14]([C:17]3[C:25]4[C:20](=[CH:21][C:22]([F:26])=[CH:23][CH:24]=4)[N:19]([CH2:27][CH:28]4[CH2:29][NH:30][CH2:31]4)[N:18]=3)[N:15]=2)[NH:10][CH:9]=1)=[O:7])([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)NC(=O)c1cn(COCC[Si](C)(C)C)c2ncc(-c3nn(CC4CN(C(=O)OC(C)(C)C)C4)c4cc(F)ccc34)nc12
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: CC(C)(C)NC(=O)c1c[nH]c2ncc(-c3nn(CC4CNC4)c4cc(F)ccc34)nc12
Yield: 17 %

Procedure:
To a stirred solution of tert-butyl 3-((3-(7-(tert-butylcarbamoyl)-5-((2-(trimethylsilyl)ethoxy)methyl)-5H-pyrrolo[2,3-b]pyrazin-2-yl)-6-fluoro-1H-indazol-1-yl)methyl)azetidine-1-carboxylate (70 mg, 107 μmol) in dichloromethane (5 mL) was added trifluoroacetic acid (1 mL). After 15 h the mixture was concentrated in vacuo and the residue dissolved in 25 mL of a Jan. 10, 1960 mixture of ammonium hydroxide/methanol/dichloromethane. After 1 h the mixture was concentrated in vacuo. Purification by chromatography (silica, 24 g Analogix column, 0-6% methanol containing 10% ammonium hydroxide in dichloromethane) followed by SFC chromatography (eluent contained TFA) gave 2-(1-azetidin-3-ylmethyl-6-fluoro-1H-indazol-3-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid tert-butyl amide trifluoroacetate (10 mg, 17%). MS (M+H)+=422; 1H NMR (DMSO-d6) δ: 9.09 (s, 1H), 8.49 (dd, J=8.9, 5.4 Hz, 1H), 8.40 (s, 1H), 7.92 (s, 1H), 7.77 (dd, J=9.8, 1.9 Hz, 1H), 7.20 (d, J=2.1 Hz, 1H), 4.77 (d, J=7.0 Hz, 2H), 3.87-4.18 (m, 4H), 1.52 (s, 9H), 1.24 (d, J=4.5 Hz, 1H).
Reaction SMILES: [O:1]1[C:5]2[CH:6]=[CH:7][C:8]([CH:10]([O:14][CH3:15])[C:11]([OH:13])=O)=[CH:9][C:4]=2[O:3][CH2:2]1.[NH2:16][CH2:17][C:18]1[CH:25]=[CH:24][C:21]([C:22]#[N:23])=[CH:20][CH:19]=1>>[O:1]1[C:5]2[CH:6]=[CH:7][C:8]([CH:10]([O:14][CH3:15])[C:11]([NH:23][CH2:22][C:21]3[CH:24]=[CH:25][C:18]([C:17]#[N:16])=[CH:19][CH:20]=3)=[O:13])=[CH:9][C:4]=2[O:3][CH2:2]1
Reactant: COC(C(=O)O)c1ccc2c(c1)OCO2
Reactant: N#Cc1ccc(CN)cc1
Product: COC(C(=O)NCc1ccc(C#N)cc1)c1ccc2c(c1)OCO2

Procedure:
(RS)-Benzo[1,3]dioxol-5-yl-methoxy-acetic acid was coupled with 4-aminomethyl benzonitrile according to general procedure C to give (RS)-2-benzo[1,3]dioxol-5-yl-N-(4-cyano-benzyl)-2-methoxy-acetamide. Light yellow solid.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]2[C:10](=[CH:11][C:12]=1[O:13][CH3:14])[N:9]=[CH:8][N:7]=[C:6]2[N:15]1[CH2:20][CH2:19][CH:18]([N:21]2[C:30](=[O:31])[C:29]3[C:24](=[CH:25][CH:26]=[C:27]([N+:32]([O-:34])=[O:33])[CH:28]=3)[NH:23][C:22]2=[O:35])[CH2:17][CH2:16]1.[CH:36]1([CH2:39]Br)[CH2:38][CH2:37]1>>[CH:36]1([CH2:39][N:23]2[C:24]3[C:29](=[CH:28][C:27]([N+:32]([O-:34])=[O:33])=[CH:26][CH:25]=3)[C:30](=[O:31])[N:21]([CH:18]3[CH2:19][CH2:20][N:15]([C:6]4[C:5]5[C:10](=[CH:11][C:12]([O:13][CH3:14])=[C:3]([O:2][CH3:1])[CH:4]=5)[N:9]=[CH:8][N:7]=4)[CH2:16][CH2:17]3)[C:22]2=[O:35])[CH2:38][CH2:37]1
Reactant: COc1cc2ncnc(N3CCC(n4c(=O)[nH]c5ccc([N+](=O)[O-])cc5c4=O)CC3)c2cc1OC
Reactant: BrCC1CC1
Product: COc1cc2ncnc(N3CCC(n4c(=O)c5cc([N+](=O)[O-])ccc5n(CC5CC5)c4=O)CC3)c2cc1OC
Yield: 27 %

Procedure:
The procedure similar to that described in Example 1 was repeated, except that 300 mg (0.63 mmol) of Compound 24 was used and cyclopropylmethyl bromide was used in place of methyl iodide. As a result, 89 mg (yield: 27%) of Compound 26 was obtained as pale yellow crystals.
Reaction SMILES: CC(N=NC(C#N)(C)C)([C:4]#[N:5])C.C1C(=O)N(Br)C(=O)C1.[CH3:21][C:22]1[CH:31]=[C:30]([N+:32]([O-:34])=[O:33])[CH:29]=[CH:28][C:23]=1[C:24](OC)=[O:25]>C(Cl)(Cl)(Cl)Cl>[CH3:4][N:5]1[CH2:21][C:22]2[C:23](=[CH:28][CH:29]=[C:30]([N+:32]([O-:34])=[O:33])[CH:31]=2)[C:24]1=[O:25]
Reactant: CC(C)(C#N)N=NC(C)(C)C#N
Reactant: COC(=O)c1ccc([N+](=O)[O-])cc1C
Agent: O=C1CCC(=O)N1Br
Solvent: ClC(Cl)(Cl)Cl
Product: CN1Cc2cc([N+](=O)[O-])ccc2C1=O
Temperature: 79 °C
Reaction time: 2 h

Procedure:
AIBN (84 mg, 0.51), NBS (1.1 gram, 6.4 mmol), and the methyl 2-methyl-4-nitrobenzoate (1 g, 5.1 mmol, as prepared in Step 1, Example 44) were suspended in CCl4 (12.8 ml), the vessel evacuated and backfilled with N2 (2×) and the mixture heated under N2 at 79° C. overnight. The solution was filtered, and concentrated in vacuum. One third of the crude material was dissolved in 2 N methylamine in methanol (18 ml), 2N methylamine in THF added (18 ml) and the solution stirred for 2 hours at RT. The volatiles were removed in vacuum and the product was purified by chromatography on SiO2 eluting with 10% acetone:DCM to give the titled compound.
Reaction SMILES: [NH2:1][C:2]1[CH:10]=[CH:9][CH:8]=[C:7]2[C:3]=1[CH:4]([CH2:17][C:18]([O:20]C)=O)[CH2:5][N:6]2[CH2:11][C:12]([O:14][CH2:15][CH3:16])=[O:13].O.C1(C)C=CC(S(O)(=O)=O)=CC=1>C1(C)C=CC=CC=1>[O:20]=[C:18]1[CH2:17][CH:4]2[CH2:5][N:6]([CH2:11][C:12]([O:14][CH2:15][CH3:16])=[O:13])[C:7]3[C:3]2=[C:2]([CH:10]=[CH:9][CH:8]=3)[NH:1]1
Reactant: CCOC(=O)CN1CC(CC(=O)OC)c2c(N)cccc21
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: Cc1ccccc1
Solvent: O
Product: CCOC(=O)CN1CC2CC(=O)Nc3cccc1c32
Temperature: 25 °C

Procedure:
To a solution of (±)-ethyl methyl 2,2′-(4-amino-2,3-dihydro-1H-indole-1,3-diyl)diacetate from Step D (490 mg, 1.70 mmol) in toluene (35 mL) was added p-toluenesulfonic acid monohydrate (5 mg, 0.026 mmol) and the mixture was heated at reflux for 48 h. The mixture was cooled to ambient temperature and was partitioned between saturated aqueous NaHCO3 (5 mL) and EtOAc (40 mL). The organic layer was dried over Na2SO4, filtered, and concentrated in vacuo. The crude product was purified by silica gel chromatography, eluting with a gradient of CHCl3:EtOAc—90:10 to 40:60, to give the racemic product. The enantiomers were resolved by HPLC, utilizing a Chiralpak AS column and eluting with MeOH. The first major peak to elute was ethyl (4-oxo-2a,3,4,5-tetrahydropyrrolo[4,3,2-de]quinolin-1(2H)-yl)acetate, enantiomer A, and the second major peak to elute was ethyl (4-oxo-2a,3,4,5-tetrahydropyrrolo[4,3,2-de]quinolin-1(2H)-yl)acetate, enantiomer B, the title compound. MS: m/z=261 (M+1).
Reaction SMILES: [NH2:1][C:2]1[C:7]([N+:8]([O-])=O)=[CH:6][C:5]([OH:11])=[CH:4][C:3]=1[CH3:12]>CO.[Pd]>[NH2:8][C:7]1[CH:6]=[C:5]([OH:11])[CH:4]=[C:3]([CH3:12])[C:2]=1[NH2:1]
Reactant: Cc1cc(O)cc([N+](=O)[O-])c1N
Agent: [Pd]
Solvent: CO
Product: Cc1cc(O)cc(N)c1N

Procedure:
6.00 g (35.7 mmol) 4-amino-3-methyl-5-nitro-phenol in 200 mL MeOH was combined with 0.600 g palladium on charcoal (Pd/C 10%) and hydrogenated for 4 h under a hydrogen atmosphere of 60 psi at 50° C. The catalyst was removed by suction filtering, the filtrate was evaporated down and the residue was dried under HV.