Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [H-].[Na+].[S:3]1[CH:7]=[CH:6][CH:5]=[C:4]1[SH:8].CN(C=O)C.CS(O[CH2:19][CH2:20][CH:21]([C:29]1([CH2:43][CH:44]([CH3:46])[CH3:45])[CH2:33][CH2:32][N:31]([CH2:34][CH2:35][C:36]2[CH:41]=[CH:40][CH:39]=[CH:38][CH:37]=2)[C:30]1=[O:42])[C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])(=O)=O>C1COCC1>[CH3:45][CH:44]([CH3:46])[CH2:43][C:29]1([CH:21]([CH2:20][CH2:19][S:8][C:4]2[S:3][CH:7]=[CH:6][CH:5]=2)[C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])[CH2:33][CH2:32][N:31]([CH2:34][CH2:35][C:36]2[CH:37]=[CH:38][CH:39]=[CH:40][CH:41]=2)[C:30]1=[O:42]
Reactant: Sc1cccs1
Reactant: CC(C)CC1(C(CCOS(C)(=O)=O)C(=O)OC(C)(C)C)CCN(CCc2ccccc2)C1=O
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: C1CCOC1
Product: CC(C)CC1(C(CCSc2cccs2)C(=O)OC(C)(C)C)CCN(CCc2ccccc2)C1=O
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 70.5 %

Procedure:
Sodium hydride (60%, 41 mg, 1.0 mmol) is added to a solution of thiophenethiol (118 mg, 1.02 mmol), THF (25 mL) and DMF (25 mL) at 0° C. The mixture is stirred for 30 minutes at 0° C. and a solution of tert-butyl α-[2-(methanesulfonyloxy)ethyl]-3-(2-methylpropyl)-2-oxo-1-(2-phenylethyl)-3-pyrrolidineacetate (490 mg, 1.02 mmol) in THF (15 mL) is added. The solution is allowed to warm slowly and is stirred at room temperature overnight. Concentration, aqueous workup (EtOAc, MgSO4), and purification by flash chromatography (25% EtOAc/hexane) gives 361 mg (71%) of title compound as a colorless oil.
Reaction SMILES: [OH-].[K+].[OH:3][C:4]1[C:9]2[S:10][C:11]([C:22]3[CH:27]=[CH:26][C:25]([O:28][CH2:29][CH2:30][N:31]4[CH2:35][CH2:34][CH2:33][CH2:32]4)=[CH:24][CH:23]=3)=[C:12]([C:13]([C:15]3[CH:20]=[CH:19][C:18]([F:21])=[CH:17][CH:16]=3)=[O:14])[C:8]=2[CH:7]=[CH:6][CH:5]=1.[CH3:36]I.O>CS(C)=O>[CH3:36][O:3][C:4]1[C:9]2[S:10][C:11]([C:22]3[CH:27]=[CH:26][C:25]([O:28][CH2:29][CH2:30][N:31]4[CH2:32][CH2:33][CH2:34][CH2:35]4)=[CH:24][CH:23]=3)=[C:12]([C:13]([C:15]3[CH:20]=[CH:19][C:18]([F:21])=[CH:17][CH:16]=3)=[O:14])[C:8]=2[CH:7]=[CH:6][CH:5]=1
Reactant: O=C(c1ccc(F)cc1)c1c(-c2ccc(OCCN3CCCC3)cc2)sc2c(O)cccc12
Reactant: CI
Agent: [K+]
Agent: [OH-]
Solvent: O
Solvent: CS(C)=O
Product: COc1cccc2c(C(=O)c3ccc(F)cc3)c(-c3ccc(OCCN4CCCC4)cc3)sc12
Reaction time: 1.5 h
Yield: 28.7 %

Procedure:
To a suspension of powdered KOH (177 mg, 3.15 mmol) in 1.6 mL of dry DMSO was added 4-fluorophenyl 7-hydroxy-2-[4-[2-(1-pyrrolidinyl)ethoxy]phenyl]benzo[b]thiophen-3-yl ketone (350370) (Example 75, Part G) (364 mg, 0.788 mmol) at room temperature. The reaction mixture turned orange in color. To the alkoxide was added slowly methyl iodide (49 μL, 0.79 mmol) over a period of 15 min. The reaction mixture was then stirred for 1.5 h. Another portion of MeI (20 μL, 0.32 mmol) was added, stirred for 1.5 h., followed by another addition of 20 μL (0.32 mmol) of MeI and stirring for an additional 30 min at room temperature. The reaction mixture was then poured into 20 mL of H2O. This mixture was extracted with CH2Cl2 (3×20 mL). The combined organic layers were washed with H2O (5×10 mL), dried over MgSO4, and concentrated under reduced pressure. The residue was then purified by flash chromatography (silica gel, 4%[10% NH4OH in MeOH]/CH2Cl2) to afford 108 mg (0.226 mmol, 29%) of a white foam.
Reaction SMILES: C([N-]C(C)C)(C)C.[Li+].[F:9][C:10]1[CH:15]=[CH:14][C:13]([CH2:16][C:17]([OH:19])=[O:18])=[CH:12][C:11]=1[C:20]([F:23])([F:22])[F:21].I[CH2:25][CH:26]1[CH2:30][CH2:29][CH2:28][CH2:27]1>O1CCCC1.CN1CCCN(C)C1=O.CN1CCCN(C)C1=O>[CH:26]1([CH2:25][CH:16]([C:13]2[CH:14]=[CH:15][C:10]([F:9])=[C:11]([C:20]([F:21])([F:22])[F:23])[CH:12]=2)[C:17]([OH:19])=[O:18])[CH2:30][CH2:29][CH2:28][CH2:27]1
Reactant: ICC1CCCC1
Reactant: O=C(O)Cc1ccc(F)c(C(F)(F)F)c1
Agent: CC(C)[N-]C(C)C
Agent: [Li+]
Solvent: C1CCOC1
Solvent: CN1CCCN(C)C1=O
Product: O=C(O)C(CC1CCCC1)c1ccc(F)c(C(F)(F)F)c1
Temperature: -78 °C
Reaction time: 1 h
Yield: 84.1 %

Procedure:
A solution of freshly prepared lithium diisopropylamide (35.3 mL of a 0.31 M stock solution, 10.9 mmol) cooled to −78° C. was treated with (4-fluoro-3-trifluoromethyl-phenyl)-acetic acid (1.11 g, 5.0 mmol) in tetrahydrofuran/1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (12.4 mL, 3:1). The resulting solution was stirred at −78° C. for 1 h. At this time, the reaction was treated with a solution of iodomethylcyclopentane (1.16 g, 5.52 mmol) in 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (1.2 mL). The reaction mixture was stirred at −78° C. for 4 h. The reaction was then warmed to 25° C. and was stirred at 25° C. for 48 h. This solution was then quenched by the slow addition of the reaction mixture to an aqueous solution of 2N hydrochloric acid (50 mL). The product was extracted into ethyl acetate (3×100 mL) and diethyl ether (1×50 mL). The organic layers were dried over magnesium sulfate and sodium sulfate, filtered, and concentrated in vacuo. Flash chromatography (Merck Silica gel 60, 230-400 mesh, 50/50 hexanes/ethyl acetate with acetic acid) afforded 3-cyclopentyl-2-(4-fluoro-3-trifluoromethyl-phenyl)-propionic acid (1.28 g, 84.3%) as a white solid: mp 66-68° C.: EI-HRMS m/e calcd for C15H16F4O2 (M+) 305.1165, found 305.1174.
Reaction SMILES: CS(C)=O.C(Cl)(=O)C(Cl)=O.[CH2:11]([O:18][C:19]([NH:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][OH:28])=[O:20])[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1.C(N(C(C)C)C(C)C)C>C(Cl)Cl>[CH2:11]([O:18][C:19]([NH:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH:27]=[O:28])=[O:20])[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1
Reactant: O=C(NCCCCCCO)OCc1ccccc1
Agent: O=C(Cl)C(=O)Cl
Solvent: CS(C)=O
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: O=CCCCCCNC(=O)OCc1ccccc1
Temperature: 0 °C
Reaction time: 0.42 h

Procedure:
0.32 ml (4.40 mmol) of dimethyl sulfoxide is added dropwise under nitrogen to a solution of 0.19 ml (2.20 mmol) of oxalyl chloride in 10 ml of methylene chloride which is being stirred at -50°. The mixture is stirred for 15 minutes, and then 0.5 g (2 mmol) of 6-(N-benzyloxycarbonylamino)hexan-1-ol is added. Stirring is continued at -50° for 25 minutes, 1.78 ml (10 mmol) of N-ethyl-N,N-diisopropylamine are added dropwise and the mixture is poured into 10 ml of ice-water. The organic phase is separated off and the aqueous phase is extracted with 10 ml of methylene chloride. The organic phases are combined, washed twice with 5 ml of N-hydrochloric acid each time and once with 10 ml of saturated sodium chloride solution, dried over magnesium sulfate and concentrated to dryness by evaporation. The resulting oil is purified by chromatography on silica gel with hexane/ethyl acetate (1:1) as eluant. 6-(N-benzyloxycarbonylamino)hexanal is obtained.
Reaction SMILES: [CH:1]([C:3]1[CH:52]=[CH:51][C:6]([C:7]([O:9][CH2:10][O:11][C:12]([N:14]2[C:22]3[C:17](=[CH:18][CH:19]=[CH:20][CH:21]=3)[C:16]([CH2:23][C:24]([NH:37][C:38]([O:40][CH2:41][C:42]3[O:43][C:44]4[CH:50]=[CH:49][CH:48]=[CH:47][C:45]=4[CH:46]=3)=[O:39])([C:26](=[O:36])[NH:27][CH:28]([C:30]3[CH:35]=[CH:34][CH:33]=[CH:32][CH:31]=3)[CH3:29])[CH3:25])=[CH:15]2)=[O:13])=[O:8])=[CH:5][CH:4]=1)=O.[NH:53]1[CH2:58][CH2:57][NH:56][CH2:55][CH2:54]1.C(Cl)(Cl)[Cl:60]>>[ClH:60].[ClH:60].[N:53]1([CH2:1][C:3]2[CH:4]=[CH:5][C:6]([C:7]([O:9][CH2:10][O:11][C:12]([N:14]3[C:22]4[C:17](=[CH:18][CH:19]=[CH:20][CH:21]=4)[C:16]([CH2:23][C:24]([NH:37][C:38]([O:40][CH2:41][C:42]4[O:43][C:44]5[CH:50]=[CH:49][CH:48]=[CH:47][C:45]=5[CH:46]=4)=[O:39])([C:26](=[O:36])[NH:27][CH:28]([C:30]4[CH:31]=[CH:32][CH:33]=[CH:34][CH:35]=4)[CH3:29])[CH3:25])=[CH:15]3)=[O:13])=[O:8])=[CH:51][CH:52]=2)[CH2:58][CH2:57][NH:56][CH2:55][CH2:54]1
Reactant: CC(NC(=O)C(C)(Cc1cn(C(=O)OCOC(=O)c2ccc(C=O)cc2)c2ccccc12)NC(=O)OCc1cc2ccccc2o1)c1ccccc1
Reactant: C1CNCCN1
Reactant: ClC(Cl)Cl
Product: CC(NC(=O)C(C)(Cc1cn(C(=O)OCOC(=O)c2ccc(CN3CCNCC3)cc2)c2ccccc12)NC(=O)OCc1cc2ccccc2o1)c1ccccc1
Product: Cl
Reaction time: 0.17 h
Yield: 43 %

Procedure:
NaHB(OAc)3 (42 mg, 0.2 mmol, 1.4 eq.) was added to a solution of compound 19 (0.1 g, 0.14 mmol) and piperazine (0.074 g, 0.85 mmol, 6 eq.) in dry chloroform (5 mL) under N2 in an ice bath and stirred 10 minutes. The reaction mixture stirred at room temperature for 19 hours. The reaction was worked up and purified similar as above to give compound 20e as a white foam (47.3 mg, 43%).
Reaction SMILES: Cl.C(O)(=O)C.C([NH:10][C:11]1[N:16]=[C:15]([N:17]2[C:26]3[C:21](=[CH:22][C:23]([F:29])=[C:24]([F:28])[C:25]=3[Cl:27])[C:20](=[O:30])[C:19]([C:31]([O:33]CC)=[O:32])=[CH:18]2)[CH:14]=[CH:13][C:12]=1[F:36])(C)(C)C>O>[NH2:10][C:11]1[N:16]=[C:15]([N:17]2[C:26]3[C:21](=[CH:22][C:23]([F:29])=[C:24]([F:28])[C:25]=3[Cl:27])[C:20](=[O:30])[C:19]([C:31]([OH:33])=[O:32])=[CH:18]2)[CH:14]=[CH:13][C:12]=1[F:36]
Reactant: CCOC(=O)c1cn(-c2ccc(F)c(NC(C)(C)C)n2)c2c(Cl)c(F)c(F)cc2c1=O
Agent: Cl
Solvent: O
Solvent: CC(=O)O
Product: Nc1nc(-n2cc(C(=O)O)c(=O)c3cc(F)c(F)c(Cl)c32)ccc1F
Reaction time: 3 h
Yield: 93.3 %

Procedure:
To 2,ml of mixed solution (1:1) of 4N hydrochloric acid and acetic acid was added 450 mg of ethyl 1-[6-(t-butylamino)-5-fluoropyridin-2-yl]-8-chloro-6,7-difluoro-4-oxo-1,4-dihydroquinoline-3-carboxylate, and the mixture was heated under reflux with stirring for 3 hours. After adding 1 ml of distilled water, the mixture was allowed to cool, and the precipitate was collected by filtration and washed with ethanol and diisopropylether successively to obtain 342 mg of the title compound as a colorless powder.
Reaction SMILES: [CH2:1](/[C:3](/[CH:11]([N+:13]([O-:15])=[O:14])[CH3:12])=[CH:4]\[C:5](=[N:9][OH:10])[C:6]([NH2:8])=[O:7])[CH3:2].[N+](=[CH2:18])=[N-].C(O)(=O)C>CO>[CH2:1](/[C:3](/[CH:11]([N+:13]([O-:15])=[O:14])[CH3:12])=[CH:4]\[C:5](=[N:9][O:10][CH3:18])[C:6]([NH2:8])=[O:7])[CH3:2]
Reactant: C=[N+]=[N-]
Reactant: CC/C(=C\C(=NO)C(N)=O)C(C)[N+](=O)[O-]
Solvent: CC(=O)O
Solvent: CO
Product: CC/C(=C\C(=NOC)C(N)=O)C(C)[N+](=O)[O-]

Procedure:
To (E)-4-ethyl-2-hydroxyimino-5-nitro-3-hexenamide (37 mg) in methanol (5 ml) was added excess etheral diazomethane at -20° C. The resulting mixture was allowed to stand at 0° C. for an hour and then acetic acid was added thereto until the yellow color of the solution was discharged. The resulting reaction mixture was evaporated under reduced pressure to give an oil which was purified by preparative thin layer chromatography, developing with chloroform containing 5% methanol to give (E)-4-ethyl-2-methoxyimino-5-nitro-3-hexenamide (21.5 mg).
Reaction SMILES: [NH2:1][C@@H:2]([C:24]1[CH:29]=[CH:28][C:27]([F:30])=[CH:26][CH:25]=1)[C:3]([NH:5][C@@H:6]1[C:12](=[O:13])[NH:11][C:10]2[CH:14]=[CH:15][CH:16]=[CH:17][C:9]=2[O:8][C@@H:7]1[C:18]1[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=1)=[O:4].[CH:31]1([CH2:37][C:38](O)=[O:39])[CH2:36][CH2:35][CH2:34][CH2:33][CH2:32]1.C1C=CC2N(O)N=NC=2C=1.CN1CCOCC1.CCN=C=NCCCN(C)C.Cl>ClCCl>[CH:31]1([CH2:37][C:38]([NH:1][C@@H:2]([C:24]2[CH:25]=[CH:26][C:27]([F:30])=[CH:28][CH:29]=2)[C:3]([NH:5][C@@H:6]2[C:12](=[O:13])[NH:11][C:10]3[CH:14]=[CH:15][CH:16]=[CH:17][C:9]=3[O:8][C@@H:7]2[C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=2)=[O:4])=[O:39])[CH2:36][CH2:35][CH2:34][CH2:33][CH2:32]1
Reactant: O=C(O)CC1CCCCC1
Reactant: N[C@H](C(=O)N[C@@H]1C(=O)Nc2ccccc2O[C@@H]1c1ccccc1)c1ccc(F)cc1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CN1CCOCC1
Solvent: ClCCl
Product: O=C(CC1CCCCC1)N[C@H](C(=O)N[C@@H]1C(=O)Nc2ccccc2O[C@@H]1c1ccccc1)c1ccc(F)cc1
Temperature: 25 °C
Reaction time: 5 h
Yield: 84.4 %

Procedure:
To a stirred solution of (2S)-2-amino-2-(4-fluorophenyl)-N-[(2R,3S)-4-oxo-2-phenyl-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]acetamide (65b) (81 mg, 0.199 mmol) in dichloromethane (2 mL) under nitrogen was added cyclohexylacetic acid (35 mg, 0.246 mmol), HOBt (35 mg, 0.259 mmol), NMM (30 mg, 0.297 mmol) and EDAC-HCl (50 mg, 0.261 mmol). The mixture was stirred 5 h at ambient temperature then evaporated. The residue was dissolved in ethyl acetate and extracted in succession with saturated sodium bicarbonate, 1N aqueous HCl, and brine. The organic solution was dried, filtered and evaporated. The residue was purified by flash chromatography on silica gel eluting with 6:1 (v/v) dichloromethane:ethyl acetate to afford the title compound (89 mg, 84%) as a white solid. TLC Rf=0.42 (6:1 dichloromethane:ethyl acetate). 1H NMR (300 MHz, CDCl3) δ0.81-1.37 (m, 5H), 1.59-1.87 (m, 6H), 2.09 (d, 2H, J=6.5 Hz), 5.09 (t, 1H, J=7.0 Hz), 5.26 (d, 1H, J=7.0 Hz), 5.83 (d, 1H, J=7.0 Hz), 6.24 (br d, 1H, J=6.5 Hz), 6.48 (br d, 1H, J=6.5 Hz), 6.88-7.05 (m, 3H), 7.12-7.30 (m, 5H), 7.36 (s, 5H), 7.56 (br s, 1H). MS APCI, m/z=530 (M+1). LC/MS: 2.69 min.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:11]=[C:10]2[C:6]([C:7]([C:13]([OH:15])=O)=[CH:8][N:9]2[CH3:12])=[CH:5][CH:4]=1.C(Cl)(=O)C(Cl)=O.[CH3:22][NH2:23]>>[CH3:22][NH:23][C:13]([C:7]1[C:6]2[C:10](=[CH:11][C:3]([O:2][CH3:1])=[CH:4][CH:5]=2)[N:9]([CH3:12])[CH:8]=1)=[O:15]
Reactant: COc1ccc2c(C(=O)O)cn(C)c2c1
Reactant: CN
Agent: O=C(Cl)C(=O)Cl
Product: CNC(=O)c1cn(C)c2cc(OC)ccc12
Yield: 45 %

Procedure:
This material was prepared from 6-methoxy-1-methyl-1H-indole-3-carboxylic acid 16b (2.39 g, 10.9 mmole), oxalyl chloride and methylamine in a manner as previously described for example 16d to give a brown solid (1.08 g, 45%). 1H NMR (300 MHz, DMSO-d6) δ7.97 (1H, d, J=8.7 Hz), 7.76 (2H, m), 6.99 (1H, d, J=2.3 Hz), 6.77 (1H, dd, J=2.3, 8.7 Hz), 3.80 (3H, s), 3.76 (3H, s), 2.74 (3H, s); ESIMS (MH+): 219.05.
Reaction SMILES: [CH3:1]I.[OH:3][CH:4]([C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][C:11]=1[CH2:16][O:17][CH:18]1[CH2:23][CH2:22][CH2:21][CH2:20][O:19]1)[C:5]([O:7][CH2:8][CH3:9])=[O:6].[H-].[Na+].O>CN(C)C=O>[CH3:1][O:3][CH:4]([C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][C:11]=1[CH2:16][O:17][CH:18]1[CH2:23][CH2:22][CH2:21][CH2:20][O:19]1)[C:5]([O:7][CH2:8][CH3:9])=[O:6]
Reactant: CCOC(=O)C(O)c1ccccc1COC1CCCCO1
Reactant: CI
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: CCOC(=O)C(OC)c1ccccc1COC1CCCCO1
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 95.4 %

Procedure:
Methyl iodide (20.25 g, 143 mmol) was added to a solution of ethyl α-hydroxy-2-(tetrahydropyran-2-yloxymethyl)phenylacetate (14.00 g, 47.6 mmol) in N,N-dimethylformamide (40 ml), and the mixture was stirred at 0° C. 60% oily sodium hydride (1.90 g, 47.5 mmol) was added thereto. After 30 minutes, water (100 ml) was added, and the mixture was extracted with ether and dried over anhydrous magnesium sulfate. The solvent was evaporated, and the residue was purified by column chromatography on silica gel (n-hexane/ ethyl acetate=4/1) to give the desired compound ethyl α-methoxy-2-(tetrahydropyran-2-yloxymethyl)phenylacetate (14.00 g, 95.5%) as an oil.
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[S:12][CH:11]([C:13]3[CH:23]=[CH:22][CH:21]=[CH:20][C:14]=3[O:15][CH2:16][C:17](O)=[O:18])[N:10]([C:24](=[O:34])[C:25]3[C:30]([F:31])=[CH:29][C:28]([F:32])=[CH:27][C:26]=3[F:33])[N:9]=2)=[CH:4][CH:3]=1.CCN(C(C)C)C(C)C.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.[CH3:68][C:69]1[O:73][N:72]=[C:71]([NH2:74])[CH:70]=1>CN(C=O)C>[F:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[S:12][CH:11]([C:13]3[CH:23]=[CH:22][CH:21]=[CH:20][C:14]=3[O:15][CH2:16][C:17]([NH:74][C:71]3[CH:70]=[C:69]([CH3:68])[O:73][N:72]=3)=[O:18])[N:10]([C:24](=[O:34])[C:25]3[C:30]([F:31])=[CH:29][C:28]([F:32])=[CH:27][C:26]=3[F:33])[N:9]=2)=[CH:4][CH:3]=1
Reactant: Cc1cc(N)no1
Reactant: O=C(O)COc1ccccc1C1SC(c2ccc(F)cc2)=NN1C(=O)c1c(F)cc(F)cc1F
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: Cc1cc(NC(=O)COc2ccccc2C2SC(c3ccc(F)cc3)=NN2C(=O)c2c(F)cc(F)cc2F)no1
Reaction time: 12 h

Procedure:
To a solution of {2-[5-(4-fluoro-phenyl)-3-(2,4,6-trifluoro-benzoyl)-2,3-dihydro-[1,3,4]thiadiazol-2-yl]-phenoxy}-acetic acid (0.031 mmol) in DMF (1 mL) is added DIEA (0.058 mmol), HATU (0.058 mmol) and 5-methyl-isoxazol-3-ylamine (0.058 mmol). The reaction mixture is stirred for 12 hours. The mixture is purified by preparative LC/MS (20-100% MeCN/H2O) to give 2-{2-[5-(4-fluoro-phenyl)-3-(2,4,6-trifluoro-benzoyl)-2,3-dihydro-[1,3,4]thiadiazol-2-yl]-phenoxy}-N-(5-methyl-isoxazol-3-yl)-acetamide: 1H NMR (400 MHz, CDCl3) δ 7.55-7.51 (m, 3H), 7.35-7.26 (m, 2H), 7.05-6.96 (m, 3H), 6.85 (d, J=8 Hz, 1H), 6.69 (t, J=7.6 Hz, 2H), 6.56 (s, 1H), 4.72 (s, 2H), 2.33 (s, 3H); LC/MS (ES+): 571.1 (M+1)+.
Reaction SMILES: [H-].[Na+].CCCCCC.[Br:9][C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][C:11]=1[OH:16].[CH3:17][O:18][CH2:19]Br>CN(C)C=O>[Br:9][C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][C:11]=1[O:16][CH2:17][O:18][CH3:19]
Reactant: COCBr
Reactant: Oc1ccccc1Br
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: CCCCCC
Product: COCOc1ccccc1Br
Reaction time: 0.5 h
Yield: 97.1 %

Procedure:
The oil was removed from 4.5 g (60% in oil, 112 mmol, Aldrich) of sodium hydride dispersion by three-20 mL washes with hexane then the residue was covered with 75 mL of dimethylformamide (Burdick and Jackson). The resulting mixture was heated to about 50° and 18.1 g (105 mmol, Aldrich) of 2-bromophenol was added dropwise over 15 minutes. Vigorous gas evolution was observed. The reaction was stirred for an additional 30 minutes then the resulting gray-brown solution was cooled to 0° and 9.6 mL (117 mmol, Aldrich) of bromomethyl methyl ether was added dropwise over 15 minutes. The reaction mixture was stirred for 1 hour at 0° then at room temperature for 16 hours. The resulting slurry was partitioned between 200 mL of 1M aqueous sodium hydroxide solution and 150 mL of 4:1 hexane/diethyl ether. The aqueous layer was separated and extracted with an additional 100 mL of 4:1 hexane/diethyl ether. The organic extracts were combined, washed with two-200 mL portions of water, dried (magnesium sulfate) and concentrated in vacuo to give 22.2 g (102 mmol, 97%) of title compound as a pale yellow liquid.
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[CH:9][C:8]([C:11]2[N:12]=[C:13]([CH3:16])[S:14][CH:15]=2)=[CH:7][C:3]=1[C:4]([OH:6])=O.[NH2:17][CH2:18][C:19]1([OH:26])[CH2:25][CH2:24][CH2:23][CH2:22][CH2:21][CH2:20]1.ON1C2C=CC=CC=2N=N1.Cl.CN(C)CCCN=C=NCC.C(N(CC)CC)C>CN(C)C=O.C(OCC)(=O)C>[Cl:1][C:2]1[CH:10]=[CH:9][C:8]([C:11]2[N:12]=[C:13]([CH3:16])[S:14][CH:15]=2)=[CH:7][C:3]=1[C:4]([NH:17][CH2:18][C:19]1([OH:26])[CH2:25][CH2:24][CH2:23][CH2:22][CH2:21][CH2:20]1)=[O:6]
Reactant: NCC1(O)CCCCCC1
Reactant: Cc1nc(-c2ccc(Cl)c(C(=O)O)c2)cs1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: Cc1nc(-c2ccc(Cl)c(C(=O)NCC3(O)CCCCCC3)c2)cs1
Temperature: 25 °C
Reaction time: 16 h
Yield: 33.2 %

Procedure:
A mixture of 2-chloro-5-(2-methyl-thiazol-4-yl)-benzoic acid (7 mg, 0.027 mmol), 1-aminomethyl-cycloheptanol (6 mg, 0.03 mmol), 1-hydroxybenzotriazole (5 mg, 0.03 mmol), 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (6 mg, 0.03 mmol) and triethylamine (5 μL, 0.03 mmol) in N,N-dimethylformamide (0.5 mL) was stirred at room temperature for 16 h. The mixture was diluted with ethyl acetate and washed with 5% citric acid, water, then brine. The organic layer was dried over sodium sulfate, filtered, and concentrated in vacuo. The residue was purified by column chromatography (1:1 ethyl acetate-hexanes) to afford the title compound (3.4 mg).
Reaction SMILES: [N+:1]([C:4]1[CH:17]=[C:16]([N+:18]([O-:20])=[O:19])[CH:15]=[CH:14][C:5]=1[NH:6][C:7]1[CH:12]=[CH:11][C:10]([OH:13])=[CH:9][CH:8]=1)([O-:3])=[O:2].[C:21](=O)([O-])[O-].[K+].[K+].CI>CN(C)C=O>[N+:1]([C:4]1[CH:17]=[C:16]([N+:18]([O-:20])=[O:19])[CH:15]=[CH:14][C:5]=1[NH:6][C:7]1[CH:12]=[CH:11][C:10]([O:13][CH3:21])=[CH:9][CH:8]=1)([O-:3])=[O:2]
Reactant: O=C([O-])[O-]
Reactant: O=[N+]([O-])c1ccc(Nc2ccc(O)cc2)c([N+](=O)[O-])c1
Agent: [K+]
Solvent: CN(C)C=O
Solvent: CI
Product: COc1ccc(Nc2ccc([N+](=O)[O-])cc2[N+](=O)[O-])cc1

Procedure:
1.43 g of 4-(2,4-dinitroanilino)phenol, 500 mg of potassium carbonate and 0.32 ml of methyl iodide were stirred in 5 ml of N,N-dimethylformamide for 2 days at 20° C. The mixture was poured onto water, extracted three times with ethyl acetate, the extracts were dried on sodium sulfate, concentrated by evaporation in a vacuum, and the residue was chromatographed on silica gel.
Reaction SMILES: [CH3:1][O:2][C:3](=[O:12])[C:4]1[CH:9]=[C:8]([Cl:10])[CH:7]=[CH:6][C:5]=1[NH2:11].[Br:13][C:14]1[CH:15]=[C:16]([CH:19]=[CH:20][CH:21]=1)[CH:17]=O.[CH2:22]=[C:23]([CH3:25])[CH3:24].FC(F)(F)S([O-])(=O)=O.[Yb+3].FC(F)(F)S([O-])(=O)=O.FC(F)(F)S([O-])(=O)=O>C(#N)C.C(OCC)(=O)C>[CH3:1][O:2][C:3]([C:4]1[CH:9]=[C:8]([Cl:10])[CH:7]=[C:6]2[C:5]=1[NH:11][CH:17]([C:16]1[CH:19]=[CH:20][CH:21]=[C:14]([Br:13])[CH:15]=1)[CH2:22][C:23]2([CH3:25])[CH3:24])=[O:12]
Reactant: C=C(C)C
Reactant: COC(=O)c1cc(Cl)ccc1N
Reactant: O=Cc1cccc(Br)c1
Agent: O=S(=O)([O-])C(F)(F)F
Agent: [Yb+3]
Solvent: CC#N
Solvent: CCOC(C)=O
Product: COC(=O)c1cc(Cl)cc2c1NC(c1cccc(Br)c1)CC2(C)C
Temperature: 85 °C
Reaction time: 18 h
Yield: 20.9 %

Procedure:
To a stirred solution of 2-amino-5-chloro-benzoic acid methyl ester (14.5 g, 78.4 mmol) and 3-bromobenzaldehyde (9.2 mL, 78.4 mmol) in acetonitrile (150 mL) were added isobutene (21.0 mL, 313.5 mmol) and ytterbium(III) trifluoromethanesulfonate (Yb(OTf)3) (5.8 g, 9.5 mmol). The resulting mixture was stirred at 85° C. for 18 h in sealed tube. The mixture was diluted with ethyl acetate (300 mL) and washed with water (100 mL×2) and brine (100 mL×2) and then dried over anhydrous sodium sulfate. The solvent was removed in vacuo and the residue was purified by ISCO combi-flash chromatography (gradient elution, 10-30% ethyl acetate in petroleum ether) to afford 2-(3-bromo-phenyl)-6-chloro-4,4-dimethyl-1,2,3,4-tetrahydro-quinoline-8-carboxylic acid methyl ester (6.7 g, 21.2%) as a light yellow oil: LC/MS m/e obsd. (ESI+) [(M+H)+] 408.0 & 410.0.
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([F:8])[C:3]=1[C:9]1[NH:10][C:11]2[C:17]([N+:18]([O-:20])=[O:19])=[CH:16][CH:15]=[CH:14][C:12]=2[N:13]=1.[F:21][C:22]1[CH:29]=[CH:28][CH:27]=[C:26]([F:30])[C:23]=1[CH2:24]Br>>[F:21][C:22]1[CH:29]=[CH:28][CH:27]=[C:26]([F:30])[C:23]=1[CH2:24][N:13]1[C:12]2[CH:14]=[CH:15][CH:16]=[C:17]([N+:18]([O-:20])=[O:19])[C:11]=2[N:10]=[C:9]1[C:3]1[C:2]([F:1])=[CH:7][CH:6]=[CH:5][C:4]=1[F:8]
Reactant: O=[N+]([O-])c1cccc2nc(-c3c(F)cccc3F)[nH]c12
Reactant: Fc1cccc(F)c1CBr
Product: O=[N+]([O-])c1cccc2c1nc(-c1c(F)cccc1F)n2Cc1c(F)cccc1F

Procedure:
2-(2,6-difluorophenyl)-4-nitrobenzimidazole (7.7 g, 28 mmol) was reacted with 2,6-difluorobenzylbromide (6.95 g, 33.6 mmol). The crude product was purified by recrystallization from diethylether:hexane (3:1), 9.8 g (24.4 mmol, 87%), yielding white crystals 1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)-4-nitrobenzimidazole. M.p. 168-170° C. 1H-NMR (300 MHz, CD2Cl2): δ8.13 (dd, J=8.1, 0.9 Hz, 1H, H5), 7.86 (dd, J=8.1, 0.9 Hz, 1H, H7), 7.59 (m, 1H, H4′), 7.43 (dd, J=8.1 Hz, H6), 7.28 (m, 1H, H4″), 7.12 (m, 2H, H3′,5′), 6.84 (m, 2H, H3″,5″), 5.44 (s, 2H, CH2).
Reaction SMILES: Br[CH2:2][C:3]1[CH:8]=[CH:7][C:6]([C:9](=[O:27])[CH2:10][N:11]2[CH:16]=[CH:15][C:14]([O:17][CH2:18][C:19]3[CH:24]=[CH:23][C:22]([Br:25])=[CH:21][N:20]=3)=[CH:13][C:12]2=[O:26])=[C:5]([CH3:28])[CH:4]=1.Cl.[OH:30][CH2:31][C@H:32]1[CH2:37][CH2:36][CH2:35][CH2:34][NH:33]1.C([O-])([O-])=O.[K+].[K+]>CN(C=O)C>[Br:25][C:22]1[CH:23]=[CH:24][C:19]([CH2:18][O:17][C:14]2[CH:15]=[CH:16][N:11]([CH2:10][C:9]([C:6]3[CH:7]=[CH:8][C:3]([CH2:2][N:33]4[CH2:34][CH2:35][CH2:36][CH2:37][C@@H:32]4[CH2:31][OH:30])=[CH:4][C:5]=3[CH3:28])=[O:27])[C:12](=[O:26])[CH:13]=2)=[N:20][CH:21]=1
Reactant: Cc1cc(CBr)ccc1C(=O)Cn1ccc(OCc2ccc(Br)cn2)cc1=O
Reactant: OC[C@H]1CCCCN1
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: Cc1cc(CN2CCCC[C@@H]2CO)ccc1C(=O)Cn1ccc(OCc2ccc(Br)cn2)cc1=O
Temperature: 80 °C
Reaction time: 2 h

Procedure:
To a solution of 1-[2-(4-bromomethyl-2-methyl-phenyl)-2-oxo-ethyl]-4-(5-bromo-pyridin-2-ylmethoxy)-1H-pyridin-2-one (preparation 4b, 100 mg, 0.20 mmol) in DMF (2 mL) is added (R)-2-hydroxymethylpiperidine hydrochloride (75 mg, 0.50 mmol) and K2CO3 (55 mg, 0.40 mmol). The reaction mixture is stirred 2 h at 80° C. The mixture is purified via reverse phase HPLC chromatography (Phenomenex Gemini-C18 10 μm, gradient 5%→90% acetonitrile in water+0.3% NH4OH, 120 mL/min).