Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [H-].[Na+].[CH:3]([C:5]1[C:13]2[C:8](=[CH:9][CH:10]=[CH:11][CH:12]=2)[NH:7][C:6]=1[C:14]([O:16][CH2:17][CH3:18])=[O:15])=[O:4].[CH3:19][O:20][C:21]1[CH:22]=[C:23]([CH:26]=[CH:27][CH:28]=1)[CH2:24]Br.O>CS(C)=O>[CH:3]([C:5]1[C:13]2[C:8](=[CH:9][CH:10]=[CH:11][CH:12]=2)[N:7]([CH2:24][C:23]2[CH:26]=[CH:27][CH:28]=[C:21]([O:20][CH3:19])[CH:22]=2)[C:6]=1[C:14]([O:16][CH2:17][CH3:18])=[O:15])=[O:4]
Reactant: CCOC(=O)c1[nH]c2ccccc2c1C=O
Reactant: COc1cccc(CBr)c1
Agent: [H-]
Agent: [Na+]
Solvent: CS(C)=O
Solvent: O
Product: CCOC(=O)c1c(C=O)c2ccccc2n1Cc1cccc(OC)c1
Temperature: 25 °C
Reaction time: 1 h
Yield: 81.5 %

Procedure:
Sodium hydride (60% dispersion in mineral oil, 2.40 g, 60.0 mmol) was cooled to 0° C., and anhydrous methyl sulfoxide (75.0 mL, 1.06 mol) was added. The mixture was stirred at 0° C. for 15 minutes before a solution of ethyl 3-formyl-1H-indole-2-carboxylate (10.9 g, 50.2 mmol, Lit. J. Heterocyclic Chem. 1997, 34, 1431.) in 75 mL of methyl sulfoxide was added over a 20 minute period. The resulting solution was warmed to room temperature and stirred for 1 hour. 3-Methoxybenzylbromide (9.8 mL, 70.0 mmol) was added, and the solution was heated at 60° C. for 16 hours. The solution was cooled and poured into water (500 mL). The aqueous solution was extracted with ethyl acetate (3×), and the combined organic extracts were washed with 1 N hydrochloric acid (2×), water, and brine. The solution was dried over anhydrous magnesium sulfate and concentrated in vacuo. Trituration of the residue with 33% hexane/Et2O provided the title compound as a solid (13.8 g, 81%). The product had: 1H NMR (300 MHz, acetone-d6) δ 10.61 (s, 1 H), 8.43 (d, 1 H), 7.61 (d, 1 H), 7.30-7.45 (m, 2 H), 7.19 (dd, 1 H), 6.80 (dd, 1 H), 6.63-6.74 (m, 2 H), 5.88 (s, 2 H), 4.48 (dq, 2 H), 3.70 (s, 3 H), 1.37 (t, 3 H); mass spectroscopy gave MH+=338.1 (calc'd exact mass for C20H19NO4=337.13).
Reaction SMILES: [NH2:1][C:2]1[CH:24]=[C:23]([Cl:25])[C:5]([C:6]([C:8]2[C:16]3[C:11](=[C:12]([NH:17][C:18]([CH:20]4[CH2:22][CH2:21]4)=[O:19])[N:13]=[CH:14][CH:15]=3)[NH:10][CH:9]=2)=[O:7])=[C:4]([Cl:26])[CH:3]=1.N1C=CC=CC=1.[C:33](Cl)(=[O:35])[CH3:34]>ClCCl>[C:33]([NH:1][C:2]1[CH:3]=[C:4]([Cl:26])[C:5]([C:6]([C:8]2[C:16]3[C:11](=[C:12]([NH:17][C:18]([CH:20]4[CH2:21][CH2:22]4)=[O:19])[N:13]=[CH:14][CH:15]=3)[NH:10][CH:9]=2)=[O:7])=[C:23]([Cl:25])[CH:24]=1)(=[O:35])[CH3:34]
Reactant: CC(=O)Cl
Reactant: Nc1cc(Cl)c(C(=O)c2c[nH]c3c(NC(=O)C4CC4)nccc23)c(Cl)c1
Solvent: ClCCl
Solvent: c1ccncc1
Product: CC(=O)Nc1cc(Cl)c(C(=O)c2c[nH]c3c(NC(=O)C4CC4)nccc23)c(Cl)c1
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 27.8 %

Procedure:
To a solution of N-[3-(4-amino-2,6-dichlorobenzoyl)-1H-pyrrolo[2,3-c]pyridin-7-yl]cyclopropanecarboxamide (0.2 g, 0.5 mmol) in dichloromethane (10 mL), pyridine (0.081 g, 1 mmol) was added followed by addition of acetyl chloride (0.044 g, 0.56 mmol) at 0° C. After stirring at 0° C. for about 0.5 hour, the reaction was kept at room temperature for about 2 hours. Dichloromethane was evaporated; water (50 mL) was added to the reaction mixture, extracted with ethyl acetate (2×100 mL). The organic layer was dried over anhydrous sodium sulfate and concentrated under vacuum. The crude product was purified by silica gel (100-200 mesh) column chromatography. Elution with 2.5% methanol in dichloromethane afforded N-{3-[4-(acetylamino)-2,6-dichlorobenzoyl]-1H-pyrrolo[2,3-c]pyridin-7-yl}cyclopropanecarboxamide (0.06 g, 27%).
Reaction SMILES: [Cl:1][C:2]1[CH:11]=[CH:10][C:5]([C:6]([O:8][CH3:9])=[O:7])=[CH:4][C:3]=1I.[C:13]([C:15]1[CH:20]=[CH:19][C:18]([F:21])=[CH:17][CH:16]=1)#[CH:14].O1CCCC1>Cl[Pd](Cl)([P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1)[P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.[Cu]I.C(N(CC)CC)C>[Cl:1][C:2]1[CH:11]=[CH:10][C:5]([C:6]([O:8][CH3:9])=[O:7])=[CH:4][C:3]=1[C:14]#[C:13][C:15]1[CH:20]=[CH:19][C:18]([F:21])=[CH:17][CH:16]=1
Reactant: COC(=O)c1ccc(Cl)c(I)c1
Reactant: C#Cc1ccc(F)cc1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Solvent: CCN(CC)CC
Solvent: C1CCOC1
Product: COC(=O)c1ccc(Cl)c(C#Cc2ccc(F)cc2)c1
Temperature: 70 °C
Reaction time: 8 h

Procedure:
Under an inert atmosphere of nitrogen, a mixture of methyl 4-chloro-3-iodobenzoate (200 mg, 0.68 mmol, 1.00 equiv), 1-ethynyl-4-fluorobenzene (243 mg, 2.02 mmol, 3.00 equiv), Pd(PPh3)2Cl2 (94.6 mg, 0.14 mmol, 0.20 equiv), CuI (13 mg, 0.07 mmol, 0.10 equiv), tetrahydrofuran (12 mL), and triethylamine (4 mL) was stirred overnight at 70° C. in an oil bath. The solids were filtered out, and the filtrate was concentrated in vacuo. The residue was purified via silica gel column chromatography (ethyl acetate/petroleum ether (1:100)) resulting in 130 mg (67%) of methyl 4-chloro-3-(2-(4-fluorophenyl)ethynyl)benzoate as a white solid.
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:29])[CH2:5][C:6]1[N:11]=[C:10]2[S:12][CH:13]=[C:14]([C:15]3[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=3)[C:9]2=[C:8]([NH:21][CH2:22][C:23]2[CH:28]=[CH:27][CH:26]=[CH:25][N:24]=2)[CH:7]=1)[CH3:2].[C:30](=O)([O:34]CC)[O:31][CH2:32][CH3:33].[H-].[Na+]>C1COCC1.O>[CH2:1]([O:3][C:4](=[O:29])[CH:5]([C:6]1[N:11]=[C:10]2[S:12][CH:13]=[C:14]([C:15]3[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=3)[C:9]2=[C:8]([NH:21][CH2:22][C:23]2[CH:28]=[CH:27][CH:26]=[CH:25][N:24]=2)[CH:7]=1)[C:30]([O:31][CH2:32][CH3:33])=[O:34])[CH3:2]
Reactant: CCOC(=O)OCC
Reactant: CCOC(=O)Cc1cc(NCc2ccccn2)c2c(-c3ccccc3)csc2n1
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Solvent: O
Product: CCOC(=O)C(C(=O)OCC)c1cc(NCc2ccccn2)c2c(-c3ccccc3)csc2n1
Temperature: 0 °C
Reaction time: 0.17 h

Procedure:
{3-Phenyl-4-[(pyridin-2-ylmethyl)-amino]-thieno[2,3-b]pyridin-6-yl}-acetic acid ethyl ester (180 mg, 0.45 mmol) was dissolved in dry THF (10 ml) under nitrogen. Diethyl Carbonate (0.27 ml, 2.23 mmol) was added and the mixture cooled to 0° C. Sodium Hydride (36 mg, 0.89 mmol) was added and the mixture stirred at 0° C. for a further 10 min, then at room temperature for 20 min, then brought to reflux for 45 min. On cooling, the reaction was diluted with water (100 ml) and extracted with DCM (3×50 ml), the extracts combined, dried over magnesium sulphate and concentrated. The residue was purified on silica, eluting (Ethyl Acetate/DCM), 0-20%) to give 2-{3-Phenyl-4-[(pyridin-2-ylmethyl)-amino]-thieno[2,3-b]pyridin-6-yl}-malonic acid diethyl ester as a yellow solid. Yield=96 mg (45%).
Reaction SMILES: C(OC([N:8]1[CH2:13][CH2:12][C:11]2[C:14]3[CH:20]=[CH:19][C:18]([S:21]([C:24]4[CH:29]=[CH:28][CH:27]=[C:26]([O:30]CC5C=CC=CC=5)[CH:25]=4)(=[O:23])=[O:22])=[CH:17][C:15]=3[O:16][C:10]=2[CH2:9]1)=O)(C)(C)C>CO.CCOC(C)=O.[Pd]>[CH2:9]1[C:10]2[O:16][C:15]3[CH:17]=[C:18]([S:21]([C:24]4[CH:25]=[C:26]([OH:30])[CH:27]=[CH:28][CH:29]=4)(=[O:22])=[O:23])[CH:19]=[CH:20][C:14]=3[C:11]=2[CH2:12][CH2:13][NH:8]1
Reactant: CC(C)(C)OC(=O)N1CCc2c(oc3cc(S(=O)(=O)c4cccc(OCc5ccccc5)c4)ccc23)C1
Agent: [Pd]
Solvent: CO
Solvent: CCOC(C)=O
Product: O=S(=O)(c1cccc(O)c1)c1ccc2c3c(oc2c1)CNCC3

Procedure:
To a solution of 7-(3-benzyloxy-benzenesulfonyl)-3,4-dihydro-1H-benzofuro[2,3-c]pyridine-2-carboxylic acid tert-butyl ester (50 mg, 0.1 mmol) in 5 mL methanol and 1 mL EtOAc was added Pd black (10% on carbon, 45 mg, 3.4 mmol). The mixture was kept under hydrogenation at 40 psi overnight and the solvent was evaporated. After filtration, the debenzylated product was taken to the next step without further purification. Removal of N-Boc protecting group with 4N HCl using a general procedure afforded the title product. mp 279-281° C., MS m/z 330 [M+H]+. 1H-NMR (400 MHz, DMSOd6): δ 10.26 (s, 1H), 9.76 (br s, 2H), 8.24 (s, 1H), 7.84 (m, 2H), 7.39 (m, 2H), 7.30 (s, 1H), 7.02 (m, 1H), 4.47 (s, 2H), 3.44 (m, 2H), 2.94 (m, 2H).
Reaction SMILES: CC1C=CC(S(O[CH2:12][C@H:13]2[CH2:26][O:25][C:16]3[CH:17]=[CH:18][C:19]4[N:20]=[C:21]([CH3:24])[O:22][C:23]=4[C:15]=3[O:14]2)(=O)=O)=CC=1.[F:27][C:28]1[CH:29]=[CH:30][CH:31]=[C:32]2[C:36]=1[NH:35][CH:34]=[C:33]2[C:37]1[CH2:38][CH2:39][NH:40][CH2:41][CH:42]=1>CS(C)=O.C(OCC)(=O)C>[F:27][C:28]1[CH:29]=[CH:30][CH:31]=[C:32]2[C:36]=1[NH:35][CH:34]=[C:33]2[C:37]1[CH2:38][CH2:39][N:40]([CH2:12][CH:13]2[O:14][C:15]3[C:16](=[CH:17][CH:18]=[C:19]4[N:20]=[C:21]([CH3:24])[O:22][C:23]4=3)[O:25][CH2:26]2)[CH2:41][CH:42]=1
Reactant: Fc1cccc2c(C3=CCNCC3)c[nH]c12
Reactant: Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccc4nc(C)oc4c3O2)cc1
Solvent: CS(C)=O
Solvent: CCOC(C)=O
Product: Cc1nc2ccc3c(c2o1)OC(CN1CC=C(c2c[nH]c4c(F)cccc24)CC1)CO3
Temperature: 80 °C

Procedure:
[(8R)-2-Methyl-7,8-dihydro[1,4]dioxino[2,3-g][1,3]benzoxazol-8-yl]methyl 4-methylbenzenesulfonate (0.50 g, 1.31 mmole) and 7-fluoro-3-(1,2,3,6-tetrahydro4-pyridinyl)-1H-indole (1.0 g, 4.6 mmole) were combined in 10 mL of DMSO under nitrogen. This solution was heated at 80° C. under nitrogen for six hours. After completion, the reaction was cooled to room temperature and diluted to 400 mL with ethyl acetate. The organic phase was washed with 400 mL portions of saturated aqueous sodium bicarbonate, water and saturated brine and concentrated in vacuum. The crude residue was column chromatographed on silica gel using 1% methanol/chloroform to give 0.50 g of the (S)-enantiomer of the title compound, which was a yellow solid (m.p. 208-210° C.) after evaporation of the solvent.
Reaction SMILES: C(OC([N:11]1[CH2:15][C:14](=[O:16])[N:13]=[C:12]1[NH:17][CH2:18][C:19]1[CH:24]=[CH:23][C:22]([C:25]([F:28])([F:27])[F:26])=[CH:21][C:20]=1[C:29]([F:32])([F:31])[F:30])=O)C1C=CC=CC=1.[CH:33]([C:35]1[N:36]=[C:37]2[C:42](=[CH:43][CH:44]=1)[N:41]=[CH:40][C:39]([C:45]#[N:46])=[C:38]2[O:47][CH:48]([CH3:50])[CH3:49])=O.N1CCCCC1>CC(O)C>[F:32][C:29]([F:30])([F:31])[C:20]1[CH:21]=[C:22]([C:25]([F:26])([F:28])[F:27])[CH:23]=[CH:24][C:19]=1[CH2:18][NH:17][C:12]1[NH:11][C:15](=[CH:33][C:35]2[N:36]=[C:37]3[C:42](=[CH:43][CH:44]=2)[N:41]=[CH:40][C:39]([C:45]#[N:46])=[C:38]3[O:47][CH:48]([CH3:50])[CH3:49])[C:14](=[O:16])[N:13]=1
Reactant: O=C1CN(C(=O)OCc2ccccc2)C(NCc2ccc(C(F)(F)F)cc2C(F)(F)F)=N1
Reactant: CC(C)Oc1c(C#N)cnc2ccc(C=O)nc12
Solvent: C1CCNCC1
Solvent: CC(C)O
Product: CC(C)Oc1c(C#N)cnc2ccc(C=C3NC(NCc4ccc(C(F)(F)F)cc4C(F)(F)F)=NC3=O)nc12
Temperature: 25 °C

Procedure:
To a mixture of 2-(2,4-bis-trifluoromethyl-benzylamino)-4-oxo-4,5-dihydro-imidazole-1-carboxylic acid benzyl ester (82.7 mg, 0.18 mmol) (prepared as described in C-H Kwon et al. J. Med. Chem. 1991, 34, 1845-1849), 6-formyl-4-isopropoxy-[1,5]naphthyridine-3-carbonitrile (45.6 mg, 0.19 mmol) (see Example 1) and iPrOH (5 mL) in a 25-mL round bottom flask was added piperidine (0.05 mL) and the suspension was then heated under refluxing for 5 h to give a brown solution. The reaction mixture was cooled to r.t. and concentrated to give a light yellow solid, 66.3 mg, which was purified by flash column purification to give 6-[2-(2,4-bis-trifluoromethyl-benzylamino)-5-oxo-3,5-dihydro-imidazol-4-ylidenemethyl]-4-isopropoxy-[1,5]naphthyridine-3-carbonitrile, as a light yellow solid, 20.6 mg (20.9%). HR-ES (+) m/e calcd for C25H18F6N6O2 (M+H)+ 549.1468. found 549.1472.
Reaction SMILES: C(O[C:6]([N:8]1[CH2:13][CH2:12][N:11]([C:14]2[C:15]3[NH:22][CH:21]=[CH:20][C:16]=3[N:17]=[CH:18][N:19]=2)[CH2:10][CH2:9]1)=[O:7])(C)(C)C.Cl.[NH:24]([C:37]([O:39][C:40]([CH3:43])([CH3:42])[CH3:41])=[O:38])[C@@H:25](C(O)=O)[CH2:26][C:27]1[CH:32]=[CH:31][C:30]([Cl:33])=[CH:29][CH:28]=1.C1C=CC2N(O)N=NC=2C=1.CCN=C=NCCCN(C)C>C(Cl)Cl.O1CCOCC1>[C:40]([O:39][C:37](=[O:38])[NH:24][CH:25]([CH2:26][C:27]1[CH:32]=[CH:31][C:30]([Cl:33])=[CH:29][CH:28]=1)[C:6](=[O:7])[N:8]1[CH2:9][CH2:10][N:11]([C:14]2[C:15]3[NH:22][CH:21]=[CH:20][C:16]=3[N:17]=[CH:18][N:19]=2)[CH2:12][CH2:13]1)([CH3:43])([CH3:41])[CH3:42]
Reactant: CC(C)(C)OC(=O)N[C@H](Cc1ccc(Cl)cc1)C(=O)O
Reactant: CC(C)(C)OC(=O)N1CCN(c2ncnc3cc[nH]c23)CC1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: ClCCl
Solvent: C1COCCO1
Product: CC(C)(C)OC(=O)NC(Cc1ccc(Cl)cc1)C(=O)N1CCN(c2ncnc3cc[nH]c23)CC1
Temperature: 25 °C
Reaction time: 4 h
Yield: 44.2 %

Procedure:
To a solution of 4-(5H-Pyrrolo[3,2-d]pyrimidin-4-yl)-piperazine-1-carboxylic acid tert-butyl ester (43 mg, 0.14 mmol) in DCM (4 mL) was added HCl in Dioxane (4M, 1 mL). The mixture was stirred at room temperature for 4 hours. The solvent was removed and the residue was treated with TEA (2 mL), Boc-D-Phe(4-Cl)—OH (43 mg, 0.14 mmol), HOBT (30 mg, 0.222 mmol) and EDCI (41 mg, 0.214 mmol) in DCM (5 mL). The mixture was stirred at room temperature for 12 hours. The solvent was removed and the residue was subject to chromatography on silica gel to give product {1-(4-chlorobenzyl)-2-oxo-2-[4-(5H-pyrrolo[3,2-d]pyrimidin-4-yl)-piperazin-1-yl]-ethyl}-carbamic acid tert-butyl ester (30 mg, 44%). 1H NMR (CDCl3, 400 Hz) δ 9.85 (s, 1H), 8.48 (s, 1H), 7.37 (s, 1H), 7.25-7.23 (d, J=8.4 Hz, 2H), 7.13-7.11 (d, J=8.4 Hz, 2H), 6.60 (s, 1H), 5.39-5.37 (d, J=8.8 Hz, 1H), 4.83-4.78 (m, 1H), 3.81-3.43 (m, 7H), 3.31-3.27 (m, 1H), 3.00-2.91 (m, 2H), 1.41 (s, 9H). MS (ESI+) [M+H]+ 485.
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]([C:10]2[CH:15]=[CH:14][C:13]([F:16])=[CH:12][CH:11]=2)=[O:9])=[CH:4][CH:3]=1.[Cl:17][CH2:18][CH:19]([OH:22])[CH2:20]O.O.CC1C=CC(S(O)(=O)=O)=CC=1.CC1C=CC=CC=1>O>[F:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2([C:10]3[CH:15]=[CH:14][C:13]([F:16])=[CH:12][CH:11]=3)[O:22][CH:19]([CH2:18][Cl:17])[CH2:20][O:9]2)=[CH:4][CH:3]=1
Reactant: O=C(c1ccc(F)cc1)c1ccc(F)cc1
Reactant: OCC(O)CCl
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: O
Solvent: Cc1ccccc1
Product: Fc1ccc(C2(c3ccc(F)cc3)OCC(CCl)O2)cc1
Yield: 100 %

Procedure:
A mixture of 10 parts of bis(4-fluorophenyl)methanone, 22.1 parts of 3-chloro-1,2-propanediol, 0.2 parts of 4-methylbenzenesulfonic acid hydrate and 90 parts of methylbenzene was stirred and refluxed for 23 hours using a water-separator. The reaction mixture was poured onto alkaline water. Upon stirring, the layers were separated. The organic phase was washed with alkaline water, dried, filtered and evaporated, yielding 14 parts (100%) of 2,2-bis(4-fluorophenyl)-4-(chloromethyl)-1,3-dioxolane as a residue (intermediate 99).
Reaction SMILES: [C:1](Cl)(=[O:5])[CH:2]([CH3:4])[CH3:3].[Sn](Cl)(Cl)(Cl)Cl.[N:12]1([N:17]2[C:25](=[O:26])[C:24]3[C:19](=[CH:20][CH:21]=[CH:22][CH:23]=3)[C:18]2=[O:27])[CH:16]=[CH:15][CH:14]=[CH:13]1.O>C(Cl)Cl>[CH3:3][CH:2]([CH3:4])[C:1]([C:13]1[N:12]([N:17]2[C:25](=[O:26])[C:24]3[C:19](=[CH:20][CH:21]=[CH:22][CH:23]=3)[C:18]2=[O:27])[CH:16]=[CH:15][CH:14]=1)=[O:5]
Reactant: O=C1c2ccccc2C(=O)N1n1cccc1
Reactant: CC(C)C(=O)Cl
Agent: Cl[Sn](Cl)(Cl)Cl
Solvent: O
Solvent: ClCCl
Product: CC(C)C(=O)c1cccn1N1C(=O)c2ccccc2C1=O
Temperature: 25 °C
Reaction time: 72 h

Procedure:
To a stirred solution of isobutyryl chloride (5.4 ml) in DCM (250 ml) was added tin (IV) chloride (5.8 ml) at -10° C. under nitrogen. After stirring for 15 minutes in the cooling bath, 2-(1H-pyrrol-1-yl)-1H-isoindole-1,3(2H)dione (10.0 g) was added portion-wise. The reaction mixture was allowed to warm to room temperature, and stir for three days, at which time it was poured into cold water. The layers were separated and the organic phase was washed twice with water, once with 5% HCl (aq.), and subsequently dried (MgSO4). Filtration and concentration gave the crude product. Purification via preparative HPLC (silica gel, DCM) afforded 2.5 g of the product as a solid, m.p. 147°-149° C.
Reaction SMILES: [CH2:1](Cl)[CH:2]=[C:3]([CH2:5][CH2:6][CH:7]=[C:8]([CH2:10][CH2:11][CH:12]=[C:13]([CH3:15])[CH3:14])[CH3:9])[CH3:4].[O:17]1C[CH2:20][CH2:19][CH2:18]1>CN(C)P(N(C)C)(N(C)C)=O.C(OCC)C>[CH3:4]/[C:3](/[CH2:5][CH2:6]/[CH:7]=[C:8](\[CH3:9])/[CH2:10][CH2:11][CH:12]=[C:13]([CH3:15])[CH3:14])=[CH:2]\[CH2:1][CH2:20][CH2:19][CH2:18][OH:17]
Reactant: C1CCOC1
Reactant: CC(C)=CCCC(C)=CCCC(C)=CCCl
Solvent: CN(C)P(=O)(N(C)C)N(C)C
Solvent: CCOCC
Product: CC(C)=CCC/C(C)=C/CC/C(C)=C/CCCCO
Reaction time: 1 h

Procedure:
A solution of 37.5 mL (20.3 mmol, 5.1 eq.) of a 0.54M solution of Grignard reagent (Part B) in tetrahydrofuran and 9 mL of hexamethylphosphoramide at room temperature under argon was treated over 10 minutes with a solution of 955.5 mg (3.97 mmol) of farnesyl chloride (Part A) in 5 mL of tetrahydrofuran. After one hour, the reaction mixture was diluted with a mixture of 1:1 diethyl ether : hexane and quenched with 1M HCl. The organic phase was washed with three 25 mL portions of saturated NaHCO3, three 25 mL portions of H2O, and 25 mL of brine, dried over MgSO4 and evaporated to obtain 995.0 mg of crude product. Purification required two chromatographies. The first was run on 70 g of silica gel, eluting with 1:99 ethyl acetate:CH2Cl2 to provide 484.3 mg of impure material and 307.7 mg of pure title compound. The second chromatography, of the impure fractions, on 50 g of silica gel eluted with 0.75:99.25 ethyl acetate:CH2Cl2 gave 117.2 mg of slightly impure material and 302.8 mg of pure title compound. Combination of pure material from both columns gave a yield a yield of 610.5 mg (58%) of pure desired title isomer.
Reaction SMILES: [NH2:1][C:2]1[CH:18]=[CH:17][C:16]2[C:7]3[NH:8][C:9](=[O:15])[C:10]4[N:11]([CH:12]=[CH:13][N:14]=4)[C:6]=3[CH2:5][C:4]=2[CH:3]=1.[N:19]([CH2:22][C:23]([O:25][CH2:26][CH3:27])=[O:24])=[C:20]=[O:21]>CN(C)C=O>[CH2:26]([O:25][C:23]([CH2:22][NH:19][C:20](=[O:21])[NH:1][C:2]1[CH:18]=[CH:17][C:16]2[C:7]3[NH:8][C:9](=[O:15])[C:10]4[N:11]([CH:12]=[CH:13][N:14]=4)[C:6]=3[CH2:5][C:4]=2[CH:3]=1)=[O:24])[CH3:27]
Reactant: Nc1ccc2c(c1)Cc1c-2[nH]c(=O)c2nccn12
Reactant: CCOC(=O)CN=C=O
Solvent: CN(C)C=O
Product: CCOC(=O)CNC(=O)Nc1ccc2c(c1)Cc1c-2[nH]c(=O)c2nccn12

Procedure:
The preparation is carried out as in Example 7, from 3 g of 8-amino-5H,10H-imidazo[1,2-a]indeno[1,2-e]pyrazine-4-one and 2 times 2.8 ml of ethyl 2-isocyanatoacetate in 170 ml of dimethylformamide. The insoluble material thus obtained is filtered and recrystallized from dimethylformamide. After filtration, washing with water and drying under reduced pressure (1 mm Hg, 0.13 kPa) at 60° C., there are obtained 2.6 g of 8-(3-ethoxycarbonylmethylureido)-5H,10H-imidazo[1,2-a]indeno[1,2-e]pyrazine-4-one in the form of a pink solid, the melting point of which is greater than 260° C. (Analysis C18H17N5 O4.0.75H2O.0.20DMF, % calculated C: 58.85, H: 4.66, N: 19.06, % found C: 58.9, H: 5.0, N: 18.9).
Reaction SMILES: F[C:2]1[C:3]([CH3:22])=[N:4][C:5]2[C:10]([N:11]=1)=[C:9]([C:12]1[NH:20][C:19]3[CH2:18][CH2:17][NH:16][C:15](=[O:21])[C:14]=3[CH:13]=1)[CH:8]=[CH:7][CH:6]=2.[N:23]1[CH:28]=[CH:27][N:26]=[CH:25][C:24]=1[CH:29]([NH2:31])[CH3:30].CCN(C(C)C)C(C)C>CS(C)=O>[CH3:22][C:3]1[C:2]([NH:31][CH:29]([C:24]2[CH:25]=[N:26][CH:27]=[CH:28][N:23]=2)[CH3:30])=[N:11][C:10]2[C:5](=[CH:6][CH:7]=[CH:8][C:9]=2[C:12]2[NH:20][C:19]3[CH2:18][CH2:17][NH:16][C:15](=[O:21])[C:14]=3[CH:13]=2)[N:4]=1
Reactant: Cc1nc2cccc(-c3cc4c([nH]3)CCNC4=O)c2nc1F
Reactant: CC(N)c1cnccn1
Solvent: CS(C)=O
Solvent: CCN(C(C)C)C(C)C
Product: Cc1nc2cccc(-c3cc4c([nH]3)CCNC4=O)c2nc1NC(C)c1cnccn1
Temperature: 165 °C
Yield: 55.6 %

Procedure:
This compound (40 mg, 55% yield) as a yellow crystalline solid was prepared according the procedures described for Example 318, using 2-(3-fluoro-2-methylquinoxalin-5-yl)-6,7-dihydro-1H-pyrrolo[3,2-c]pyridin-4(5H)-one (126) (54 mg, 0.18 mmol), 1-(pyrazin-2-yl)ethanamine (45 mg, 0.36 mmol) (Essen Scientific LLC, cat # ES10-0543) and DIEA (64 μL, 0.36 mmol) in 2 mL of DMSO (heated in a microwave at 165° C. for 45 min). 1H NMR (400 MHz, DMSO-d6) δ ppm 11.81 (1H, br.), 8.87 (1H, m), 8.59 (1H, m), 8.50 (1H, d, J=2.5 Hz), 7.87 (1H, d, J=7.2 Hz), 7.67 (1H, d, J=7.0 Hz), 7.57 (1H, d, J=7.4 Hz), 7.32 (1H, t, J=7.8 Hz), 6.99 (1H, br.), 6.90 (1H, d, J=2.2 Hz), 5.41 (1H, m), 3.48 (2H, m), 3.03 (2H, m), 2.68 (3H, s), 1.74 (3H, d, J=7.0 Hz). m/z (ESI, +ve) 400.1 (M+H)+.
Reaction SMILES: [NH2:1][C:2]1[O:6][N:5]=[C:4]([CH3:7])[C:3]=1[Br:8].[Cl:9][C:10]1[CH:28]=[CH:27][C:13]([C:14]([NH:16][CH2:17][C:18]2[S:22][C:21]([S:23](Cl)(=[O:25])=[O:24])=[CH:20][CH:19]=2)=[O:15])=[CH:12][CH:11]=1>>[Br:8][C:3]1[C:4]([CH3:7])=[N:5][O:6][C:2]=1[NH:1][S:23]([C:21]1[S:22][C:18]([CH2:17][NH:16][C:14](=[O:15])[C:13]2[CH:27]=[CH:28][C:10]([Cl:9])=[CH:11][CH:12]=2)=[CH:19][CH:20]=1)(=[O:25])=[O:24]
Reactant: O=C(NCc1ccc(S(=O)(=O)Cl)s1)c1ccc(Cl)cc1
Reactant: Cc1noc(N)c1Br
Product: Cc1noc(NS(=O)(=O)c2ccc(CNC(=O)c3ccc(Cl)cc3)s2)c1Br
Yield: 27 %

Procedure:
N-(4-Bromo-3-methyl-5-isoxazolyl)-5-(4-chlorobenzamidomethyl)-thiophene-2-sulfonamide was prepared in the same manner as described in Example 2 from 5-amino-4-bromo-3-methylisoxazole and 5-(4-chlorobenzamidomethyl)thiophene-2-sulphonyl chloride in 27% yield. The crude product was passed through a silica gel column using hexanes/ethyl acetate as eluent. Purification was effected by recrystallization from ethyl acetate/hexanes to give a crystalline solid, m.p. 210° C. (dec).
Reaction SMILES: Cl[C:2]1[C:11]([CH3:12])=[C:10]([Cl:13])[C:9]2[C:4](=[CH:5][C:6]([F:15])=[CH:7][C:8]=2[F:14])[N:3]=1.[CH3:16][O:17][C:18]1[N:23]=[CH:22][C:21](B(O)O)=[CH:20][CH:19]=1.C(=O)([O-])[O-].[K+].[K+]>C1(C)C=CC=CC=1>[Cl:13][C:10]1[C:9]2[C:4](=[CH:5][C:6]([F:15])=[CH:7][C:8]=2[F:14])[N:3]=[C:2]([C:21]2[CH:22]=[N:23][C:18]([O:17][CH3:16])=[CH:19][CH:20]=2)[C:11]=1[CH3:12]
Reactant: Cc1c(Cl)nc2cc(F)cc(F)c2c1Cl
Reactant: COc1ccc(B(O)O)cn1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: Cc1ccccc1
Product: COc1ccc(-c2nc3cc(F)cc(F)c3c(Cl)c2C)cn1

Procedure:
The Suzuki coupled product was prepared according to Procedure F using 2,4-dichloro-5,7-difluoro-3-methylquinoline (0.50 g, 2.02 mmol), 6-methoxypyridin-3-ylboronic acid (0.308 g, 2.0 mmol), palladium tetrakistriphenylphosphine (0.23 g, 0.20 mmol), potassium carbonate (0.56 g, 4.03 mmol) in toluene (4 mL) at 100° C. for 19.5 h to give 4-chloro-5,7-difluoro-2-(6-methoxypyridin-3-yl)-3-methylquinoline as a white solid. Mass Spectrum (ESI) m/e=321.0 (M+1).
Reaction SMILES: C([O:3][C:4](=[O:30])[C:5]([CH2:23][C:24]1[CH:29]=[CH:28][CH:27]=[CH:26][CH:25]=1)([NH:11][C:12](=[O:22])[NH:13][C@@H:14]([C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1)[CH3:15])[C:6]([O:8]CC)=O)C.[OH-].[Li+:32]>O1CCCC1.CO>[CH2:23]([C:5]1([C:4]([O-:3])=[O:30])[C:6](=[O:8])[N:13]([C@@H:14]([C:16]2[CH:17]=[CH:18][CH:19]=[CH:20][CH:21]=2)[CH3:15])[C:12](=[O:22])[NH:11]1)[C:24]1[CH:25]=[CH:26][CH:27]=[CH:28][CH:29]=1.[Li+:32]
Reactant: CCOC(=O)C(Cc1ccccc1)(NC(=O)N[C@H](C)c1ccccc1)C(=O)OCC
Agent: [Li+]
Agent: [OH-]
Solvent: C1CCOC1
Solvent: CO
Product: C[C@H](c1ccccc1)N1C(=O)NC(Cc2ccccc2)(C(=O)[O-])C1=O
Reaction time: 0.5 h

Procedure:
To a solution of the product from Step C (7.8 g, 18.91 mmol) in tetrahydrofuran (60 mL) and methanol (20.00 mL) was added a 1 M lithium hydroxide solution (19.86 mL, 19.86 mmol) and the mixture stirred for 30 min. The solvent was removed in vacuo and the residue azeotroped with toluene (3×25 mL) to afford the title compound as a colorless amorphous solid. LC/MS 339.1 (M+1).
Reaction SMILES: [BH4-].[Na+].[CH3:3][C:4]1([CH3:15])[CH2:9][C:8](=[O:10])[CH2:7][CH2:6][CH:5]1[C:11]([O:13][CH3:14])=[O:12]>CO.O>[OH:10][CH:8]1[CH2:7][CH2:6][CH:5]([C:11]([O:13][CH3:14])=[O:12])[C:4]([CH3:15])([CH3:3])[CH2:9]1
Reactant: COC(=O)C1CCC(=O)CC1(C)C
Agent: [BH4-]
Agent: [Na+]
Solvent: O
Solvent: CO
Product: COC(=O)C1CCC(O)CC1(C)C
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
Sodium borohydride (6.19 g, 163 mmol) was added in portions at 0° C. to a solution of methyl 2,2-dimethyl-4-oxocyclohexanecarboxylate (10.0 g, 54.3 mmol) in methanol (200 mL). The mixture was stirred at room temperature for 30 minutes. Then the mixture was diluted with water and extracted with ethyl acetate. The organic layer was dried over sodium sulfate, filtered, and concentrated under reduced pressure to give methyl 4-hydroxy-2,2-dimethylcyclohexanecarboxylate. 1H NMR (400 MHz, CDCl3): δ 3.89-3.84 (m, 1H), 3.65 (s, 3H), 2.21 (s, 1H), 1.79-1.73 (m, 1H), 1.70-1.68 (m, 3H), 1.49-1.35 (m, 2H), 1.06 (s, 6H).