Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][C:2]1[CH:11]=[C:10]([CH3:12])[C:9]2[C:4](=[CH:5][CH:6]=[CH:7][CH:8]=2)[N:3]=1.C(=O)([O-])[O-].[K+].[K+].I[C:20]1[CH:25]=[CH:24][CH:23]=[CH:22][CH:21]=1>[Cu]>[CH3:12][C:10]1[C:9]2[C:4](=[CH:5][CH:6]=[CH:7][CH:8]=2)[N:3]([C:20]2[CH:25]=[CH:24][CH:23]=[CH:22][CH:21]=2)[C:2](=[O:1])[CH:11]=1
Reactant: Ic1ccccc1
Reactant: Cc1cc(O)nc2ccccc12
Agent: [Cu]
Agent: O=C([O-])[O-]
Agent: [K+]
Product: Cc1cc(=O)n(-c2ccccc2)c2ccccc12
Temperature: 25 °C
Yield: 54.7 %

Procedure:
The starting 1,2-dihydro-4-methyl- 1 -phenyl-2-quinolone (1) is prepared either by an Ullmann coupling according to a literature procedure (Wawzonek et al., supra.) or via the reaction of the corresponding diarylamine with dikctene followed by acid cyclization (Elderfield, supra). Thus 10.0 g (62.9 mmoles) of 2-hydroxy-4-methylquinoline is heated at reflux with 24.0 g (377 mmolcs) of copper powder, 8.68 g (62.9 mmoles) of potassium carbonate and 19.2 g (94 mmoles) of iodobenzene for 48 hours. The reaction is cooled to room temperature, partitioned between water and ethyl acetate, filtered, and the organic layer is dried over magnesium sulfate. The crude product is purified on a silica gel column, eluting with 1:1 ethyl acetate/hexanes to yield 8.1 g of the desired product.
Reaction SMILES: [CH:1](=[O:10])[CH:2]=[CH:3][C:4]1[CH:9]=[CH:8][CH:7]=[CH:6][CH:5]=1.[Br:11]Br.C([O-])([O-])=O.[K+].[K+].O>C(O)(=O)C>[Br:11][C:2](=[CH:3][C:4]1[CH:9]=[CH:8][CH:7]=[CH:6][CH:5]=1)[CH:1]=[O:10]
Reactant: BrBr
Reactant: O=CC=Cc1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC(=O)O
Solvent: O
Product: O=CC(Br)=Cc1ccccc1

Procedure:
1.33 g (10 mmol) cinnamaldehyde was dissolved in 5 mL glacial acetic acid and cooled on an ice-water bath. 1.62 g bromine was added, and anhydrous K2CO3 was then added, and it was stirred until no gas was evolving. After refluxing for 30 min, the reaction mixture was poured into 100 mL cold water with stirring, extracted with 50 mL ethyl ether three times. The combined ethyl ether layers were washed with water one time, saturated aqueous NaCl solution one time, dried over MgSO4 for 2 hours, filtrated, and the filtrate was dried under vacuum, and washed with anhydrous ethyl ether: petroleum ether (1:1) to give the title compound as light yellow powder.
Reaction SMILES: Cl[CH2:2][CH2:3][C:4]1[S:13][C:12]2[CH2:11][CH2:10][CH2:9][C:8](=[O:14])[NH:7][C:6]=2[CH:5]=1.Cl.[F:16][C:17]1[CH:18]=[CH:19][C:20]2[C:24]([CH:25]3[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]3)=[CH:23][S:22][C:21]=2[CH:31]=1>>[F:16][C:17]1[CH:18]=[CH:19][C:20]2[C:24]([CH:25]3[CH2:26][CH2:27][N:28]([CH2:2][CH2:3][C:4]4[S:13][C:12]5[CH2:11][CH2:10][CH2:9][C:8](=[O:14])[NH:7][C:6]=5[CH:5]=4)[CH2:29][CH2:30]3)=[CH:23][S:22][C:21]=2[CH:31]=1
Reactant: O=C1CCCc2sc(CCCl)cc2N1
Reactant: Fc1ccc2c(C3CCNCC3)csc2c1
Agent: Cl
Product: O=C1CCCc2sc(CCN3CCC(c4csc5cc(F)ccc45)CC3)cc2N1
Yield: 25.4 %

Procedure:
The reaction and procedure were conducted in a similar manner as in Example 24 using 0.5 g of 2-(2-chloroethyl)-4,6,7,8-tetrahydro-5H-thieno[3,2-b]azepin-5-one and 0.5 g of 4-(6-fluorobenzo(b)thiophen-3-yl)piperidine hydrochloride to give 0.2 g of 2-(2-(4-(6-fluoro-benzo(b)thiophen-3-yl)piperidin-1-yl)ethyl)-4,6,7,8-tetrahydro-5H-thieno[3,2-b]azepin-5-one, m.p. 191°-193° C.
Reaction SMILES: [NH2:1][C:2]1[CH:10]=[CH:9][C:8]([O:11][C:12]2[CH:17]=[CH:16][C:15]([F:18])=[CH:14][C:13]=2[F:19])=[CH:7][C:3]=1[C:4]([NH2:6])=[O:5].N[C:21](N)=[O:22].O>CN1C(=O)CCC1>[F:19][C:13]1[CH:14]=[C:15]([F:18])[CH:16]=[CH:17][C:12]=1[O:11][C:8]1[CH:7]=[C:3]2[C:2](=[CH:10][CH:9]=1)[NH:1][C:21](=[O:22])[NH:6][C:4]2=[O:5]
Reactant: NC(N)=O
Reactant: NC(=O)c1cc(Oc2ccc(F)cc2F)ccc1N
Solvent: O
Solvent: CN1CCCC1=O
Product: O=c1[nH]c(=O)c2cc(Oc3ccc(F)cc3F)ccc2[nH]1
Temperature: 25 °C
Reaction time: 1 h
Yield: 86.9 %

Procedure:
Compound (1D) (23 g, 0.09 mol) and urea (25.42 g, 0.41 mol) in NMP (150 mL) were heated to 170° C. for 18 h. After cooling to room temperature, the reaction mixture was poured into water (200 mL) and stirred for 1 h. The precipitate was filtered, washed with water, and dried to afford 22.7 g of 6-(2,4-difluoro-phenoxy)-1H-quinazoline-2,4-dione (1E).
Reaction SMILES: [CH3:1][O:2][C:3]1[C:8]2[N:9]=[C:10]([NH2:12])[S:11][C:7]=2[C:6]([N:13]2[CH2:18][CH2:17][O:16][CH2:15][CH2:14]2)=[CH:5][CH:4]=1.C(N(C(C)C)C(C)C)C.[Cl:28][CH2:29][C:30]1[CH:31]=[C:32]([CH:36]=[CH:37][N:38]=1)[C:33](Cl)=[O:34]>O1CCCC1>[Cl:28][CH2:29][C:30]1[CH:31]=[C:32]([CH:36]=[CH:37][N:38]=1)[C:33]([NH:12][C:10]1[S:11][C:7]2[C:6]([N:13]3[CH2:18][CH2:17][O:16][CH2:15][CH2:14]3)=[CH:5][CH:4]=[C:3]([O:2][CH3:1])[C:8]=2[N:9]=1)=[O:34]
Reactant: O=C(Cl)c1ccnc(CCl)c1
Reactant: COc1ccc(N2CCOCC2)c2sc(N)nc12
Solvent: C1CCOC1
Solvent: CCN(C(C)C)C(C)C
Product: COc1ccc(N2CCOCC2)c2sc(NC(=O)c3ccnc(CCl)c3)nc12
Temperature: 0 °C
Yield: 79.6 %

Procedure:
To a solution of 4-methoxy-7-morpholin-4-yl-benzothiazol-2-yl-amine (2.3 g, 8.7 mmol) in tetrahydrofurane (80 ml) is added N-ethyldiisopropylamine (6.0 ml, 35 mmol) and the solution cooled to 0° C. 2-chloromethyl-isonicotinoyl chloride (2.4 g, 10.5 mmol), dissolved in tetrahydrofurane (50 ml), is added over 15 minutes and the mixture heated to 70° C. for 1 h. After evaporation of the volatile components, the residue was disolved in ethyl acetate and water, filtered and the residue combined with the dryed and evaporated organic phase. Recrystallization from dichloromethane/ethyl acetate afforded the title compound as light brown solid (2.9 g, 81% yield). MS: m/e=420(M+H+).
Reaction SMILES: [Br:1][C:2]1[CH:33]=[CH:32][C:5]2[C:6]([C:9]3[CH:31]=[CH:30][CH:29]=[CH:28][C:10]=3/[CH:11]=[N:12]/C(C3C=CC(F)=CC=3)C3C=CC(F)=CC=3)=[N:7][O:8][C:4]=2[CH:3]=1.CC(C)([O-])C.[K+].I[CH2:41][CH:42]1[CH2:44][CH2:43]1.Cl>O1CCCC1.CC(C)=O>[Br:1][C:2]1[CH:33]=[CH:32][C:5]2[C:6]([C:9]3[CH:31]=[CH:30][CH:29]=[CH:28][C:10]=3[CH:11]([NH2:12])[CH2:41][CH:42]3[CH2:44][CH2:43]3)=[N:7][O:8][C:4]=2[CH:3]=1
Reactant: Fc1ccc(C(/N=C/c2ccccc2-c2noc3cc(Br)ccc23)c2ccc(F)cc2)cc1
Reactant: ICC1CC1
Agent: CC(C)(C)[O-]
Agent: Cl
Agent: [K+]
Solvent: C1CCOC1
Solvent: CC(C)=O
Product: NC(CC1CC1)c1ccccc1-c1noc2cc(Br)ccc12
Temperature: 25 °C
Yield: 41 %

Procedure:
A solution of (E)-N-(2-(6-bromobenzo[d]isoxazol-3-yl)benzylidene)-1,1-bis(4-fluorophenyl)methanamine (Compound 8) (1.34 g) in dry tetrahydrofuran (15 mL) under nitrogen was cooled to −78° C. with stirring and a 1M solution of potassium tert-butoxide in tetrahydrofuran (3.2 mL) added dropwise. Solution turned dark purple. After 20 min (iodomethyl)cyclopropane (1.45 g) was added in one portion and solution slowly warmed to room temperature, stirred at this temperature for 1.5 h then quenched by the addition of water (10 mL) and extracted with ethyl acetate. The organic extract was dried over anhydrous magnesium sulfate and evaporated to leave a dark red gum that was dissolved in acetone (20 mL) and an aqueous 2N HCl solution (15 mL) added and the mixture stirred overnight. The acetone was removed by evaporation and the aqueous solution extracted with dichloromethane. The aqueous solution was made basic with sodium bicarbonate and extracted with dichloromethane, dried over anhydrous magnesium sulfate and evaporated under reduced pressure. SCX purification (eluting with methanol then ammonia in methanol) followed by flash chromatography on silica eluting with 0 to 5% methanol in dichloromethane gave the title product (0.39 g).
Reaction SMILES: C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.[N:20]([CH2:23][C:24]1[CH:37]=[C:36]([Br:38])[CH:35]=[CH:34][C:25]=1[O:26][CH2:27][CH2:28][N:29]1[CH2:33][CH2:32][CH2:31][CH2:30]1)=[N+]=[N-].O>C1COCC1>[Br:38][C:36]1[CH:35]=[CH:34][C:25]([O:26][CH2:27][CH2:28][N:29]2[CH2:33][CH2:32][CH2:31][CH2:30]2)=[C:24]([CH:37]=1)[CH2:23][NH2:20]
Reactant: [N-]=[N+]=NCc1cc(Br)ccc1OCCN1CCCC1
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: C1CCOC1
Solvent: O
Product: NCc1cc(Br)ccc1OCCN1CCCC1
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
0.66 g (2.50 mmol) of triphenylphosphine was added to a solution of 0.40 g (1.23 mmol) 1-[2-(2-azidomethyl-4-bromophenoxy)ethyl]pyrrolidine in 5 mL of THF and the mixture was stirred for 30 minutes at RT. Water was added and the aqueous phase was exhaustively extracted with DCM. The combined organic extracts were dried over magnesium sulfate and evaporated down in vacuo. Yield: 0.185 g (50% of theoretical); C13H19BrN2O (M=299.207); calc.: molpeak (M+H)+: 299/301 (Br); found: molpeak (M+H)+: 299/301 (Br); HPLC-MS: 1.38 minutes (method A).
Reaction SMILES: Cl[C:2]1[CH:7]=[C:6]([CH:8]([S:17][C:18]2[CH:23]=[CH:22][C:21]([Cl:24])=[CH:20][CH:19]=2)[C:9]2[CH:14]=[C:13]([F:15])[CH:12]=[CH:11][C:10]=2[F:16])[C:5]([Cl:25])=[CH:4][N:3]=1.[C:26]([O:30][C:31](=[O:36])[NH:32][CH2:33][CH2:34][NH2:35])([CH3:29])([CH3:28])[CH3:27]>O1CCOCC1>[Cl:25][C:5]1[C:6]([CH:8]([S:17][C:18]2[CH:19]=[CH:20][C:21]([Cl:24])=[CH:22][CH:23]=2)[C:9]2[CH:14]=[C:13]([F:15])[CH:12]=[CH:11][C:10]=2[F:16])=[CH:7][C:2]([NH:35][CH2:34][CH2:33][NH:32][C:31](=[O:36])[O:30][C:26]([CH3:28])([CH3:27])[CH3:29])=[N:3][CH:4]=1
Reactant: Fc1ccc(F)c(C(Sc2ccc(Cl)cc2)c2cc(Cl)ncc2Cl)c1
Reactant: CC(C)(C)OC(=O)NCCN
Solvent: C1COCCO1
Product: CC(C)(C)OC(=O)NCCNc1cc(C(Sc2ccc(Cl)cc2)c2cc(F)ccc2F)c(Cl)cn1
Temperature: 25 °C
Yield: 22.3 %

Procedure:
A 1,4-dioxane (6.0 ml) solution of the 2,5-dichloro-4-[(4-chlorophenylthio)-(2,5-difluorophenyl)methyl]pyridine (610 mg, 1.46 mmol) obtained in Example 54 and t-butyl(2-aminoethyl)carbamate (700 mg, 4.38 mmol) was stirred at 120° C. for 4 days under an argon atmosphere. After cooling to room temperature, the reaction mixture was concentrated under reduced pressure. The residue was purified by silica gel chromatography (hexane:ethyl acetate=4:1) to give the title compound (176 mg, 22%) as an oil.
Reaction SMILES: [CH:1]([C:5]1[N:6]([CH2:13][C:14]2[CH:19]=[CH:18][C:17]([C:20]3[CH:25]=[CH:24][CH:23]=[CH:22][C:21]=3[C:26]([O:28][CH3:29])=[O:27])=[CH:16][CH:15]=2)[C:7]([CH2:11][OH:12])=[C:8]([Cl:10])[N:9]=1)=[CH:2][CH2:3][CH3:4].[Si:30](Cl)([C:33]([CH3:36])([CH3:35])[CH3:34])([CH3:32])[CH3:31].N1C=CN=C1>CN(C=O)C>[CH:1]([C:5]1[N:6]([CH2:13][C:14]2[CH:19]=[CH:18][C:17]([C:20]3[CH:25]=[CH:24][CH:23]=[CH:22][C:21]=3[C:26]([O:28][CH3:29])=[O:27])=[CH:16][CH:15]=2)[C:7]([CH2:11][O:12][Si:30]([C:33]([CH3:36])([CH3:35])[CH3:34])([CH3:32])[CH3:31])=[C:8]([Cl:10])[N:9]=1)=[CH:2][CH2:3][CH3:4]
Reactant: CC(C)(C)[Si](C)(C)Cl
Reactant: CCC=Cc1nc(Cl)c(CO)n1Cc1ccc(-c2ccccc2C(=O)OC)cc1
Agent: c1c[nH]cn1
Solvent: CN(C)C=O
Product: CCC=Cc1nc(Cl)c(CO[Si](C)(C)C(C)(C)C)n1Cc1ccc(-c2ccccc2C(=O)OC)cc1
Yield: 83.8 %

Procedure:
2-(But-1-en-1-yl)-1-[(2'-carbomethoxybiphenyl-4-yl)methyl]-4-chloro-5-(hydroxymethyl)-imidazole (1.4 g), t-butyldimethylsilyl chloride (0.55 g), and imidazole (0.5 g) were mixed and stirred in DMF (5 mL) for 18 hours at room temperature. Dilution with ethyl acetate and washing the organic phase with water followed by drying (MgSO4), evaporation of the solvent in vacuo, and flash chromatography in 3:1 hexane/ethyl acetate yielded 1.5 g of a clear oil. NMR (200 MHz, CDCl3) δ7.83 (d, 1H); 7.52 (t, 1H); 7.40 (t, 1H); 7.33-7.24 (m, 3H); 7.08 (d, 2H); 6.83 (d of t, 1H); 6.13 (d, 1H); 5.30 (s, 2H); 4.57 (s, 2H); 3.64 (s, 3H); 2.21 (quint., 2H); 1.04 (t, 3H); 0.86 (s, 9H); 0.05 (s, 6H).
Reaction SMILES: [NH2:1][C:2]1[S:6][N:5]=[C:4](/[C:7](=[N:11]/[O:12][CH2:13][F:14])/[C:8](O)=[O:9])[N:3]=1.P(Cl)(Cl)([Cl:17])=O.CN(C)C=O>O1CCCC1>[NH2:1][C:2]1[S:6][N:5]=[C:4](/[C:7](=[N:11]/[O:12][CH2:13][F:14])/[C:8]([Cl:17])=[O:9])[N:3]=1
Reactant: O=P(Cl)(Cl)Cl
Reactant: Nc1nc(/C(=N/OCF)C(=O)O)ns1
Solvent: C1CCOC1
Solvent: CN(C)C=O
Product: Nc1nc(/C(=N/OCF)C(=O)Cl)ns1
Temperature: -12 °C
Reaction time: 0.33 h

Procedure:
In 30.0 ml of tetrahydrofuran (THF), 10.0 g (45.42 mmol) of 2-(5-amino-1,2,4-thiadiazol-3-yl)-2(Z)fluoromethoxyiminoacetic acid were stirred at room temperature to completely dissolve the latter in the former, followed by cooling to -12° C. Added dropwise to the reaction mixture was a chlorinating reagent, which had been prepared beforehand by gradually adding 7.65 g (49.89 mmol) of phosphorus oxychloride at 5° C. into a mixture of 20 ml of THF and 3.7 g (49.93 mmol) of N,N-dimethylformamide (DMF) and then reacting them for 30 minutes. Subsequent to their reaction for 60 minutes with the temperature maintained at -15° C., the reaction mixture was poured into 150 ml of ice water and was then stirred for 20 minutes to precipitate crystals. The crystals were collected by filtration, washed twice with 15 ml aliquots of ice water and then, under reduced pressure, dried, whereby the title compound was obtained. Yield: 8.50 g (77.9%). Purity: 95.7%.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][N:5]2[N:8]=[C:9]([C:23]3[CH:28]=[CH:27][C:26]([F:29])=[CH:25][CH:24]=3)[C:10]([C:11]3[CH:16]=[CH:15][N:14]=[C:13]([NH:17][CH:18]4[CH2:22][CH2:21][CH2:20][CH2:19]4)[N:12]=3)=[C:4]2[CH:3]=1.C([Li])CCC.C(Cl)(Cl)(Cl)[Cl:36]>O1CCCC1>[CH:18]1([NH:17][C:13]2[N:12]=[C:11]([C:10]3[C:9]([C:23]4[CH:24]=[CH:25][C:26]([F:29])=[CH:27][CH:28]=4)=[N:8][N:5]4[C:6]([Cl:36])=[CH:7][C:2]([Cl:1])=[CH:3][C:4]=34)[CH:16]=[CH:15][N:14]=2)[CH2:19][CH2:20][CH2:21][CH2:22]1
Reactant: Fc1ccc(-c2nn3ccc(Cl)cc3c2-c2ccnc(NC3CCCC3)n2)cc1
Reactant: ClC(Cl)(Cl)Cl
Agent: [Li]CCCC
Solvent: C1CCOC1
Product: Fc1ccc(-c2nn3c(Cl)cc(Cl)cc3c2-c2ccnc(NC3CCCC3)n2)cc1
Temperature: -78 °C
Reaction time: 0.17 h
Yield: 45 %

Procedure:
To a solution of 4-[5-chloro-2-(4-fluorophenyl)pyrazolo[1,5-a]pyridin-3-yl]-N-cyclopentyl-2-pyrimidinamine (100 mg, 0.25 mmol) in anhydrous tetrahydrofuran (5 mL) at −78° C. was added n-butyllithium (0.5 mL of 1.6 M solution in hexanes, 0.8 mmol). The resulting reaction mixture was stirred at −78° C. for 10 minutes, followed by addition of carbon tetrachloride (1 mL) and stirring at −78° C. for additional 20 minutes. The reaction was then quenched by the addition of water. The mixture was extracted with ethyl acetate. The ethyl acetate phase was washed with brine, dried (magnesium sulfate), filtered and concentrated in vocuo. The resulting residue was purified by flash chromatography (1:1 ethyl acetate-hexane) to give 50 mg (45%) of N-cyclopentyl-4-[5,7-dichloro-2-(4-fluorophenyl)pyrazolo[1,5-a]pyridin-3-yl]-2-pyrimidinamine as a yellow foam. 1H NMR (CDCl3): δ 8.53 (broad s, 1H), 8.06 (d, 1H), 7.63 (m, 2H), 7.15 (t, 2H), 7.05 (d, 1H), 6.27 (d, 1H), 5.17 (d, 1H), 4.35 (m, 1H), 2.0–2.1 (m, 2H), 1.4–1.9 (m, 6H); 19F NMR (CDCl3): δ 112.2; MS m/z 442 (M+1).
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]([N:12]2[CH:16]=[CH:15][CH:14]=[N:13]2)[C:5]([N+:9]([O-:11])=[O:10])=[C:6]([NH2:8])[CH:7]=1.[N:17]1[CH:22]=[CH:21][CH:20]=[C:19](B(CC)CC)[CH:18]=1.C(=O)([O-])[O-].[Na+].[Na+]>C1COCC1.C(OCC)(=O)C>[N+:9]([C:5]1[C:4]([N:12]2[CH:16]=[CH:15][CH:14]=[N:13]2)=[CH:3][C:2]([C:19]2[CH:18]=[N:17][CH:22]=[CH:21][CH:20]=2)=[CH:7][C:6]=1[NH2:8])([O-:11])=[O:10]
Reactant: Nc1cc(Br)cc(-n2cccn2)c1[N+](=O)[O-]
Reactant: CCB(CC)c1cccnc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: Nc1cc(-c2cccnc2)cc(-n2cccn2)c1[N+](=O)[O-]
Temperature: 70 °C
Reaction time: 8 h
Yield: 60.1 %

Procedure:
To a solution of 5-bromo-2-nitro-3-pyrazol-1-yl-phenylamine (200 mg, 0.71 mmol) in THF (8 mL) was added, successively, 3-pyridyl-diethyl borane (157 mg), (tetrakistriphenylphosphine) palladium(0) (84 mg), and sodium carbonate (1.1 mL, 2.2 mmom of 2M aqueous). The resulting mixture was stirred at 70° C. overnight then cooled to room temperature. The reaction mixture was diluted with ethyl acetate (100 mL) and washed with water (50 mL), brine (50 mL), dried (MgSO4) then concentrated in vacuo. The resulting residue was purified by column chromatography over silica gel eluted with a gradient of ethyl acetate:hexanes (1:3, 1:2, 1:0, 2:1, 4:1, 8:1), to afford 120 mg (60%) of the title compound as a yellow solid. 1H NMR (DMSO-d6) δ 6.45 (br, s 2H), 6.55 (t, 1H), 7.1 (s, 1H), 7.25 (s, 1H), 7.55 (m, 1H), 7.7 (s, 1H), 8.1 (dt, 1H), 8.3 (d, 1H), 8.7 (d, 1H), 8.9 (s, 1H).
Reaction SMILES: C[Si]([NH:5][OH:6])(C)C.[Cl:7][C:8]1[CH:17]=[C:16]2[C:11]([C:12]([OH:24])=[C:13]([C:19](OCC)=[O:20])[C:14](=[O:18])[NH:15]2)=[CH:10][CH:9]=1.O>CN(C)C=O>[Cl:7][C:8]1[CH:17]=[C:16]2[C:11]([C:12]([OH:24])=[C:13]([C:19]([NH:5][OH:6])=[O:20])[C:14](=[O:18])[NH:15]2)=[CH:10][CH:9]=1
Reactant: C[Si](C)(C)NO
Reactant: CCOC(=O)c1c(O)c2ccc(Cl)cc2[nH]c1=O
Solvent: O
Solvent: CN(C)C=O
Product: O=C(NO)c1c(O)c2ccc(Cl)cc2[nH]c1=O
Temperature: 100 °C
Reaction time: 2 h
Yield: 58.1 %

Procedure:
2 ml of trimethylsilylhydroxylamine (15 mmol) were sprayed at room temperature into a suspension of 2.64 g of ethyl 7-chloro-4-hydroxy-2-oxo-1,2-dihydro-quinoline-3-carboxylate (10 mmol) in 2.0 ml of dimethylformamide. After heating to 100° C. all passed slowly into solution. The reaction mixture was left to stir at 80° C. for 2 hrs., cooled to room temperature and stirred overnight. After the addition of 6 ml of water a voluminous precipitate separated and was filtered off, washed with water and dried in a high vacuum. 1.48 g of 7-chloro-4,N-dihydroxy-2-oxo-1,2-dihydro-quinoline-3-carboxamide (58%) were obtained as pale beige crystals.
Reaction SMILES: [Cl:1][CH2:2][CH2:3][NH:4][C:5]1[CH:6]=[C:7]2[C:11](=[CH:12][CH:13]=1)[C:10](=[O:14])[O:9][CH2:8]2.C=O.[C:17]([BH3-])#N.[Na+]>CC(O)=O.C(#N)C>[Cl:1][CH2:2][CH2:3][N:4]([CH3:17])[C:5]1[CH:6]=[C:7]2[C:11](=[CH:12][CH:13]=1)[C:10](=[O:14])[O:9][CH2:8]2
Reactant: [BH3-]C#N
Reactant: O=C1OCc2cc(NCCCl)ccc21
Agent: C=O
Agent: [Na+]
Solvent: CC(=O)O
Solvent: CC#N
Product: CN(CCCl)c1ccc2c(c1)COC2=O
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 78 %

Procedure:
A mixture of 5-(2-chloro-ethylamino)-3H-isobenzofuran-1-one (3.0 g, 14.2 mmol), 37% formaldehyde aqueous solution (10 ml, 134 mmol) and sodium cyanoborohydride (3.6 g, 56.8 mmol) in a mixture of 10% AcOH aqueous solution (40 ml) and acetonitrile (40 ml) was stirred at 0° C. for 30 minutes. The mixture was allowed to warm to room temperature and was continuously stirred for 2 hours. The mixture was concentrated under reduced pressure, basified with 1M NaOH aqueous solution, and extracted with EtOAc (3×100 ml). The combined organic layers were washed with 1M NaOH aqueous solution (100 ml) and then water (2×100 ml), dried over anhydrous Na2SO4. Removal of the solvent led to a light yellow oil, which was crystallized with diethyl ether to produce 5-[(2-chloro-ethyl)-methyl-amino]-3H-isobenzofuran-1-one as a yellow solid (2.5 g, 78%).
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([N:8]2[C:12]3[CH:13]=[CH:14][C:15]([C:17]([O:19]C)=[O:18])=[CH:16][C:11]=3[N:10]=[CH:9]2)=[CH:4][CH:3]=1.[OH-].[Na+]>CCO>[F:1][C:2]1[CH:3]=[CH:4][C:5]([N:8]2[C:12]3[CH:13]=[CH:14][C:15]([C:17]([OH:19])=[O:18])=[CH:16][C:11]=3[N:10]=[CH:9]2)=[CH:6][CH:7]=1
Reactant: COC(=O)c1ccc2c(c1)ncn2-c1ccc(F)cc1
Agent: [Na+]
Agent: [OH-]
Solvent: CCO
Product: O=C(O)c1ccc2c(c1)ncn2-c1ccc(F)cc1
Temperature: 25 °C
Reaction time: 96 h

Procedure:
To a solution of 27e (0.18 g, 0.666 mmol) in EtOH (10 mL) was added 1N aqueous NaOH (2.5 mL, 2.5 mmol). The mixture was stirred at room temperature for 4 d. The solvent was evaporated and 1N aqueous HCl was added, followed by extraction with EtOAc. The organic layer was dried over MgSO4 and concentrated. The crude product 27f was purified by preparative reverse phase chromatography. MS m/z (M+H+) 257.1.
Reaction SMILES: [CH2:1]([O:8][C:9](=[O:32])[NH:10][C:11]1[CH:16]=[CH:15][CH:14]=[C:13]([CH:17]([NH:27][CH2:28][CH2:29][O:30][CH3:31])[CH2:18][O:19][Si:20]([C:23]([CH3:26])([CH3:25])[CH3:24])([CH3:22])[CH3:21])[CH:12]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C(N(CC)CC)C.[O:40](C(OC(C)(C)C)=O)[C:41]([O:43][C:44]([CH3:47])([CH3:46])[CH3:45])=O>C(Cl)Cl>[CH2:1]([O:8][C:9](=[O:32])[NH:10][C:11]1[CH:16]=[CH:15][CH:14]=[C:13]([CH:17]([N:27]([C:41]([O:43][C:44]([CH3:47])([CH3:46])[CH3:45])=[O:40])[CH2:28][CH2:29][O:30][CH3:31])[CH2:18][O:19][Si:20]([C:23]([CH3:26])([CH3:25])[CH3:24])([CH3:22])[CH3:21])[CH:12]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: COCCNC(CO[Si](C)(C)C(C)(C)C)c1cccc(NC(=O)OCc2ccccc2)c1
Reactant: CC(C)(C)OC(=O)OC(=O)OC(C)(C)C
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: COCCN(C(=O)OC(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)c1cccc(NC(=O)OCc2ccccc2)c1
Temperature: 0 °C
Yield: 32.8 %

Procedure:
{3-[2-(tert-Butyl-dimethyl-silanyloxy)-1-(2-methoxy-ethylamino)-ethyl]-phenyl}-carbamic acid benzyl ester (1 g) was dissolved in dry DCM (10 mL) and stirred under argon at 0° C. Triethylamine (0.4 g) and (BOC)2O (0.52 g) were added and the reaction mixture was stirred at room temperature for 2 days. The reaction was quenched by addition of water and the mixture extracted with DCM. The organic phase was separated, dried over Na2SO4 and concentrated to give a crude product which was purified by column chromatography to give the title compound (400 mg).
Reaction SMILES: [Cl:1][C:2]1[C:10]2[N:9]=[C:8]3[N:11]([C:15]4[CH:20]=[CH:19][C:18]([Cl:21])=[CH:17][C:16]=4[Cl:22])[CH2:12][CH2:13][CH2:14][N:7]3[C:6]=2[C:5]([CH:23]([NH2:26])[CH2:24][CH3:25])=[CH:4][CH:3]=1.C(N(CC)CC)C.[F:34][C:35]([F:42])([F:41])[C:36](OCC)=[O:37]>C(#N)C>[Cl:1][C:2]1[C:10]2[N:9]=[C:8]3[N:11]([C:15]4[CH:20]=[CH:19][C:18]([Cl:21])=[CH:17][C:16]=4[Cl:22])[CH2:12][CH2:13][CH2:14][N:7]3[C:6]=2[C:5]([CH:23]([NH:26][C:36](=[O:37])[C:35]([F:42])([F:41])[F:34])[CH2:24][CH3:25])=[CH:4][CH:3]=1
Reactant: CCOC(=O)C(F)(F)F
Reactant: CCC(N)c1ccc(Cl)c2nc3n(c12)CCCN3c1ccc(Cl)cc1Cl
Solvent: CC#N
Solvent: CCN(CC)CC
Product: CCC(NC(=O)C(F)(F)F)c1ccc(Cl)c2nc3n(c12)CCCN3c1ccc(Cl)cc1Cl
Temperature: 25 °C
Reaction time: 3 h
Yield: 83 %

Procedure:
To a solution of 1-[9-chloro-1-(2,4-dichlorophenyl)-1,2,3,4-tetrahydropyrimido[1,2-a]benzimidazol-6-yl]propan-1-amine (600 mg, <1.46 mmol) and triethylamine (0.41 mL, 2.94 mmol) in acetonitrile (10 mL) was added ethyl trifluoroacetate (0.35 mL, 2.94 mmol) at room temperature. The mixture was stirred at room temperature for 3 hr. Ethyl trifluoroacetate (0.35 mL, 2.94 mmol) and triethylamine (0.5 mL, 3.59 mmol) were added to the reaction mixture at room temperature. The mixture was stirred at room temperature for 18 hr and at 60° C. for 20 hr. The reaction mixture was concentrated in vacuo. Water was added to the residue and the mixture was extracted with ethyl acetate. The organic layer was washed with brine, dried over anhydrous magnesium sulfate, and concentrated in vacuo. The residue was purified by flash chromatography on silica gel eluting with a 30-70% ethyl acetate/n-hexane gradient mixture to give the title compound (611.7 mg, 1.21 mmol, 83%) as a pale yellow solid.
Reaction SMILES: Cl[C:2]1[CH:11]=[C:10]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][C:13]=2[CH3:18])[C:5]([C:6]([NH:8][CH3:9])=[O:7])=[CH:4][N:3]=1.[NH:19]1[CH2:24][CH2:23][O:22][CH2:21][CH2:20]1.C(N(C(C)C)C(C)C)C>CN(C1C=CN=CC=1)C.C(OCC)(=O)C>[CH3:9][NH:8][C:6](=[O:7])[C:5]1[C:10]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][C:13]=2[CH3:18])=[CH:11][C:2]([N:19]2[CH2:24][CH2:23][O:22][CH2:21][CH2:20]2)=[N:3][CH:4]=1
Reactant: C1COCCN1
Reactant: CNC(=O)c1cnc(Cl)cc1-c1ccccc1C
Agent: CN(C)c1ccncc1
Solvent: CCOC(C)=O
Solvent: CCN(C(C)C)C(C)C
Product: CNC(=O)c1cnc(N2CCOCC2)cc1-c1ccccc1C
Temperature: 25 °C
Yield: 92.8 %

Procedure:
A mixture of 1.00 g (3.84 mmol) 6-chloro-N-methyl-4-o-tolyl-nicotinamide, 0.37 ml (4.22 mmol) morpholine, 2.0 ml (12 mmol) N-ethyldiisopropylamine and a catalytic amount of 4-(N,N-dimethylamino)-pyridine was heated at 100° C. over night. After cooling to room temperature the mixture was dissolved in ethyl acetate and washed with two portions of water. The combined aqueous layers were extracted with 3 portions of dichloromethane. Drying with sodium sulfate and concentration gave 1.23 g of the crude product. Flash column chromatography afforded 1.11 g (92.9%) of the title compound as an off-white solid. M.p. 156-158° C.