Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: N[C@H]([C:8]([OH:10])=[O:9])CCCCN.NN.[CH:13]1[C:18](N=C=S)=[CH:17][C:16]2[C:22]([O:24][C:25]3([C:35]4[CH:36]=[CH:37][C:38]([OH:40])=[CH:39][C:34]=4[O:33][C:27]4[CH:28]=[C:29]([OH:32])[CH:30]=[CH:31][C:26]3=4)[C:15]=2[CH:14]=1)=[O:23].C(N(C(C)C)CC)(C)C.C1C=CC(C(O)=O)=C(C2C3C=CC(O)=CC=3OC3C=2C=CC(C=3)=O)C=1>CN(C=O)C>[CH:13]1[C:18]([C:8]([OH:10])=[O:9])=[CH:17][C:16]2[C:22]([O:24][C:25]3([C:35]4[CH:36]=[CH:37][C:38]([OH:40])=[CH:39][C:34]=4[O:33][C:27]4[CH:28]=[C:29]([OH:32])[CH:30]=[CH:31][C:26]3=4)[C:15]=2[CH:14]=1)=[O:23]
Reactant: NCCCC[C@H](N)C(=O)O
Reactant: O=C1OC2(c3ccc(O)cc3Oc3cc(O)ccc32)c2ccc(N=C=S)cc21
Agent: NN
Agent: O=C(O)c1ccccc1-c1c2ccc(=O)cc-2oc2cc(O)ccc12
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Product: O=C(O)c1ccc2c(c1)C(=O)OC21c2ccc(O)cc2Oc2cc(O)ccc21
Reaction time: 12 h

Procedure:
Peptide-resin obtained via Method 5, containing an ivDde protecting group on the epsilon nitrogen of lysine, was mixed with a solution of hydrazine in DMF (10% hydrazine/DMF, 2×10 mL, 10 min) to remove the ivDde group. The epsilon nitrogen of the lysine was labeled with fluorescein-5-isothiocyanate (0.12 mmol) and diisopropylethylamine (0.12 mmol) in DMF. The mixture was agitated for 12 h (fluorescein-containing compounds were protected from light). The resin was then washed with DMF (3×10 mL) and twice with CH2Cl2 (10 mL) and dried under nitrogen for 1 h. The peptide was cleaved from the resin using reagent B for 4 h and the solution collected by filtration. The volatiles were removed under reduced pressure, and the residue was dried under vacuum. The peptide was precipitated with ether, collected and the precipitate was dried under a stream of nitrogen. The precipitate was added to water (1 mg/mL) and the pH of the mixture was adjusted to 8 with 10% aqueous meglumine. Cyclization of the peptide was carried out for 48 h and the solution was freeze-dried. The crude cyclic peptide was dissolved in water and purified by RP-HPLC on a C18 column with a linear gradient of acetonitrile into water (both phases contained 0.1% TFA). Fractions containing the pure product were collected and freeze-dried. The peptides were characterized by ES-MS and the purity was determined by RP-HPLC (linear gradient of acetonitrile into water/0.1% TFA).
Reaction SMILES: [CH3:1][C:2]1([CH3:16])[C@@H:4]([CH:5]=[C:6](Br)Br)[C@H:3]1[C:9]([O:11][C:12]([CH3:15])([CH3:14])[CH3:13])=[O:10].C([Li])CCC.Cl[C:23]([O:25][CH3:26])=[O:24].P(O)(O)([O-])=O.[Na+]>C1CCCCC1.O1CCCC1>[CH3:1][C:2]1([CH3:16])[C@@H:4]([C:5]#[C:6][C:23]([O:25][CH3:26])=[O:24])[C@H:3]1[C:9]([O:11][C:12]([CH3:15])([CH3:14])[CH3:13])=[O:10]
Reactant: COC(=O)Cl
Reactant: CC(C)(C)OC(=O)[C@@H]1[C@H](C=C(Br)Br)C1(C)C
Agent: O=P([O-])(O)O
Agent: [Li]CCCC
Agent: [Na+]
Solvent: C1CCOC1
Solvent: C1CCCCC1
Product: COC(=O)C#C[C@H]1[C@@H](C(=O)OC(C)(C)C)C1(C)C
Temperature: -70 °C
Reaction time: 0.5 h

Procedure:
55 g of tert-butyl (1R,cis) 2,2-dimethyl-3-(2,2-dibromovinyl)-cyclopropane-carboxylate were introduced into 550 cm3 of tetrahydrofuran and the mixture was cooled to -70° C. 132 cm3 of a 20% solution of butyllithium in cyclohexane were added over 40 minutes to the mixture which was stirred for 30 minutes at -65° C. 12.5 cm3 of methyl chloroformate were then added thereto and after 2 hours reaction at -70° C., the temperature was allowed to rise again to -20° C. The mixture was poured into an aqueous solution of monosodium phosphate and the mixture was extracted with ether. The organic phase was washed, dried and evaporated to dryness under reduced pressure. 38.3 g of the residue were chromatographed over silica gel and was eluted with an 8-2 cyclohexane-ethyl acetate mixture to obtain 17.2 g of tert.-butyl (1R,cis) 2,2-dimethyl-3-[2-(methoxy carbonyl)-ethynyl]-cyclopropane-carboxylate.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][C:5]([CH2:8][CH2:9][C:10]2[NH:11][CH:12]=[C:13]([CH2:15][C:16]([CH3:20])([CH3:19])[CH2:17][CH3:18])[N:14]=2)=[CH:4][CH:3]=1.[C:21](Cl)([C:34]1[CH:39]=[CH:38][CH:37]=[CH:36][CH:35]=1)([C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1)[C:22]1[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=1.C(N(CC)CC)C>C(Cl)Cl>[Br:1][C:2]1[CH:7]=[CH:6][C:5]([CH2:8][CH2:9][C:10]2[N:11]([C:21]([C:22]3[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=3)([C:34]3[CH:35]=[CH:36][CH:37]=[CH:38][CH:39]=3)[C:28]3[CH:29]=[CH:30][CH:31]=[CH:32][CH:33]=3)[CH:12]=[C:13]([CH2:15][C:16]([CH3:19])([CH3:20])[CH2:17][CH3:18])[N:14]=2)=[CH:4][CH:3]=1
Reactant: CCC(C)(C)Cc1c[nH]c(CCc2ccc(Br)cc2)n1
Reactant: ClC(c1ccccc1)(c1ccccc1)c1ccccc1
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: CCC(C)(C)Cc1cn(C(c2ccccc2)(c2ccccc2)c2ccccc2)c(CCc2ccc(Br)cc2)n1
Reaction time: 2 h

Procedure:
To a solution of 2-[2-(4-bromophenyl)ethyl]-4-(2,2-dimethylbutyl)-1H-imidazole (33.4 g, 100 mmol) in methlyene chloride (500 mL) was added trityl chloride (41.8 g, 150 mmol) and triethylamine (42 mL, 300 mmol). The reaction was stirred for 2 h, then washed with water, dried over sodium sulfate and concentrated to give a residue. The residue was purified by silica gel column chromatography eluting with ethyl acetate/hexanes (2:8). The chromatography was repeated eluting with methylene chloride/2-propanol 99.8:0.02) and then methlyene chloride/methanol (95:5) to provide 2-[2-(4-bromophenyl)ethyl]-4-(2,2-dimethylbutyl)-1-trityl-1H-imidazole.
Reaction SMILES: Br.[NH2:2][C:3]1[N:4]=[C:5]([Br:9])[S:6][C:7]=1[CH3:8].N1C=CC=CC=1.[C:16]([O-])(=[O:18])[CH3:17].[Na+]>C(OC(=O)C)(=O)C>[C:16]([NH:2][C:3]1[N:4]=[C:5]([Br:9])[S:6][C:7]=1[CH3:8])(=[O:18])[CH3:17]
Reactant: CC(=O)[O-]
Reactant: Cc1sc(Br)nc1N
Agent: Br
Agent: [Na+]
Solvent: c1ccncc1
Solvent: CC(=O)OC(C)=O
Product: CC(=O)Nc1nc(Br)sc1C
Reaction time: 1 h
Yield: 50 %

Procedure:
A suspension of 4-amino-2-bromo-5-methylthiazole hydrobromide (50 mM, 13.7 g) in acetic anhydride (100 ml) was treated dropwise with pyridine (10 ml) while cooling in an ice bath. After stirring for 1 hour the reaction mixture was poured onto 20% aqueous sodium acetate (1 l) and the aqueous solution extracted with dichloromethane (3×500 ml.). The combined organic layers were dried and evaporated under reduced pressure to give an oil which crystallised on trituration with ether. The crude product was recrystallised from ethanol to give the 4-acetamido-2-bromo-5-methylthiazole (11.7 g, 50%). mp 129°.
Reaction SMILES: [O:1]([C:8]1[CH:9]=[C:10]([CH:16]=[CH:17][CH:18]=1)[C@H:11]([OH:15])[C:12]([OH:14])=[O:13])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.Cl.[CH3:20]O>>[O:1]([C:8]1[CH:9]=[C:10]([CH:16]=[CH:17][CH:18]=1)[C@H:11]([OH:15])[C:12]([O:14][CH3:20])=[O:13])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: O=C(O)[C@@H](O)c1cccc(Oc2ccccc2)c1
Reactant: CO
Agent: Cl
Product: COC(=O)[C@@H](O)c1cccc(Oc2ccccc2)c1
Reaction time: 24 h

Procedure:
(S)-3-Phenoxymandelic acid (13.0 g) was added to a solution of dry hydrogen chloride (15.0 g) in methanol (100 ml) and the solution thus obtained kept at the ambient temperature for 24 hours after which period the volatile portion was evaporated yielding methyl (S)-3-phenoxymandelate as a residual oil. This was then added to liquid ammonia (20 ml) in a pressure vessel which was then sealed and temperature of the mixture allowed to rise to the ambient temperature over a period of 24 hours. The vessel was then opened and the excess of ammonia allowed to evaporate. The residual material was stirred with water and the solid collected by filtration, and recrystallised from benzene (70 ml) to yield impure (S)-3-phenoxymandelamide, m.p. 93° C. [α]D25 + 25.4° (C, 2.0, methanol), (approximately 80% optically pure).
Reaction SMILES: [H-].[Na+].[CH2:3]([O:5][C:6]([C:8]1[NH:9][C:10]2[C:15]([CH:16]=1)=[CH:14][CH:13]=[C:12]([Cl:17])[CH:11]=2)=[O:7])[CH3:4].Br[CH:19]([CH3:22])[C:20]#[N:21]>CN(C)C=O>[CH2:3]([O:5][C:6]([C:8]1[N:9]([CH:19]([C:20]#[N:21])[CH3:22])[C:10]2[C:15]([CH:16]=1)=[CH:14][CH:13]=[C:12]([Cl:17])[CH:11]=2)=[O:7])[CH3:4]
Reactant: CCOC(=O)c1cc2ccc(Cl)cc2[nH]1
Reactant: CC(Br)C#N
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: CCOC(=O)c1cc2ccc(Cl)cc2n1C(C)C#N
Temperature: 0 °C
Reaction time: 1 h
Yield: 83.6 %

Procedure:
Sodiumhydride (0.89 g, 20.1 mmol) was suspended in dimethylformamide (15 mL) and a solution of 6-chloro-1H-indole-2-carboxylic acid ethyl ester (2.00 g, 8.9 mmol) in dimethylformamide (8 mL) was added at 0° C. The mixture was stirred for 1 h at 0° C. then 2-bromo-propionitrile (3.6 g, 23.95 mmol) was added. After 1 h at room temperature the mixture was heated at 75° C. for 18 hours. The reaction mixture was then added to an ice/water mixture (100 mL) and extracted with ethylacetate. The organic phases were pooled washed with brine, dried with Na2SO4 and the solvent was removed in vacuo. Chromatography on silica gel (ether/n-hexane 1:4) yielded 6-chloro-1-(cyano-methyl-methyl)-1H-indole-2-carboxylic acid ethyl ester (2.06 g, 67%) as a colorless solid, MS: m/e=277.2 (M+H+).
Reaction SMILES: [Br:1][C:2]1[CH:27]=[CH:26][C:5]([CH2:6][C:7]23[C:15](=[O:16])[N:14]([C:17]4[CH:22]=[C:21]([Cl:23])[CH:20]=[C:19]([Cl:24])[CH:18]=4)[C:13](=[O:25])[N:12]2[CH2:11][CH2:10][NH:9][CH2:8]3)=[CH:4][CH:3]=1.CCN(C(C)C)C(C)C.[CH3:37][S:38](Cl)(=[O:40])=[O:39]>C(Cl)Cl>[CH3:37][S:38]([N:9]1[CH2:8][C:7]2([CH2:6][C:5]3[CH:26]=[CH:27][C:2]([Br:1])=[CH:3][CH:4]=3)[N:12]([C:13](=[O:25])[N:14]([C:17]3[CH:22]=[C:21]([Cl:23])[CH:20]=[C:19]([Cl:24])[CH:18]=3)[C:15]2=[O:16])[CH2:11][CH2:10]1)(=[O:40])=[O:39]
Reactant: CS(=O)(=O)Cl
Reactant: O=C1N(c2cc(Cl)cc(Cl)c2)C(=O)C2(Cc3ccc(Br)cc3)CNCCN12
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: CS(=O)(=O)N1CCN2C(=O)N(c3cc(Cl)cc(Cl)c3)C(=O)C2(Cc2ccc(Br)cc2)C1
Reaction time: 1 h

Procedure:
To a solution of 6-(4-bromobenzyl)-8-(3,5-dichlorophenyl)-1,4,8-triazabicyclo[4.3.0]nonane-7,9-dione (0.063 g) in CH2Cl2 (6 mL) was added DIEA (0.05 mL) and methanesulfonyl chloride (0.015 mL). After 1 hour, the mixture was concentrated and purified by chromatography (Silica gel: 4% MeOH/CH2Cl2, Chromatotron) afforded the titled compound. (0.069 g). MS (m/z) 546 (MH+). mp 229° C.
Reaction SMILES: [C:1](OC(=O)C)(=[O:3])C.C(O)=O.[O:11]=[C:12]1[N:18]([CH:19]2[CH2:24][CH2:23][N:22]([C:25]([O:27][C@H:28]([CH2:43][C:44]3[CH:49]=[C:48]([CH3:50])[C:47]([OH:51])=[C:46]([CH3:52])[CH:45]=3)[C:29](=[O:42])[N:30]3[CH2:35][CH2:34][N:33]([CH:36]4[CH2:41][CH2:40][O:39][CH2:38][CH2:37]4)[CH2:32][CH2:31]3)=[O:26])[CH2:21][CH2:20]2)[CH2:17][CH2:16][C:15]2[CH:53]=[CH:54][CH:55]=[CH:56][C:14]=2[NH:13]1>C(Cl)Cl>[O:11]=[C:12]1[N:18]([CH:19]2[CH2:24][CH2:23][N:22]([C:25]([O:27][C@H:28]([CH2:43][C:44]3[CH:49]=[C:48]([CH3:50])[C:47]([O:51][CH:1]=[O:3])=[C:46]([CH3:52])[CH:45]=3)[C:29](=[O:42])[N:30]3[CH2:31][CH2:32][N:33]([CH:36]4[CH2:41][CH2:40][O:39][CH2:38][CH2:37]4)[CH2:34][CH2:35]3)=[O:26])[CH2:21][CH2:20]2)[CH2:17][CH2:16][C:15]2[CH:53]=[CH:54][CH:55]=[CH:56][C:14]=2[NH:13]1
Reactant: CC(=O)OC(C)=O
Reactant: Cc1cc(C[C@@H](OC(=O)N2CCC(N3CCc4ccccc4NC3=O)CC2)C(=O)N2CCN(C3CCOCC3)CC2)cc(C)c1O
Solvent: O=CO
Solvent: ClCCl
Product: Cc1cc(C[C@@H](OC(=O)N2CCC(N3CCc4ccccc4NC3=O)CC2)C(=O)N2CCN(C3CCOCC3)CC2)cc(C)c1OC=O
Temperature: 25 °C
Reaction time: 8 h

Procedure:
A solution of 25 μL acetic anhydride and 0.5 mL formic acid in 1 mL DCM was stirred for 2 h at RT (formation of the mixed anhydride). Then 38 mg (0.06 mmol) (R)-1-(4-hydroxy-3,5-dimethyl-benzyl)-2-oxo-2-[4-(tetrahydropyran-4-yl)-piperazin-1-yl]-ethyl 4-(2-oxo-1,2,4,5-tetrahydro-1,3-benzodiazepin-3-yl)-piperidine-1-carboxylate was added (Example 7i) and the reaction mixture was stirred overnight at RT. The reaction solution was evaporated down and the residue was again added to a solution of the mixed anhydride and stirred overnight at RT. The mixture was evaporated down i.vac. and the residue was purified by HPLC. The fractions containing the product were combined and lyophilised.
Reaction SMILES: [C:1]([NH:4][CH2:5][C:6]([C:9]1[CH:14]=[CH:13][C:12]([NH2:15])=[C:11]([NH2:16])[CH:10]=1)([CH3:8])[CH3:7])(=[O:3])[CH3:2].ClCCl.[CH3:20][C:21]1[CH:29]=[CH:28][C:24]([C:25](Cl)=O)=[CH:23][CH:22]=1>C(N(CC)CC)C>[C:1]([NH:4][CH2:5][C:6]([C:9]1[CH:14]=[CH:13][C:12]2[N:15]=[C:20]([C:21]3[CH:29]=[CH:28][C:24]([CH3:25])=[CH:23][CH:22]=3)[NH:16][C:11]=2[CH:10]=1)([CH3:8])[CH3:7])(=[O:3])[CH3:2]
Reactant: Cc1ccc(C(=O)Cl)cc1
Reactant: CC(=O)NCC(C)(C)c1ccc(N)c(N)c1
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(=O)NCC(C)(C)c1ccc2nc(-c3ccc(C)cc3)[nH]c2c1
Temperature: 25 °C
Reaction time: 3 h

Procedure:
To 4.4 g. of the 4-(2-acetamidomethylpropan-2-yl)-1,2-diaminobenzene (prepared in Example 1f) in 120 ml. dry dichloromethane are added 3.3 ml. triethylamine and then, with ice cooling, 3.06 g. 4-methylbenzoic acid chloride. After stirring the reaction mixture for 3 hours at ambient temperature, the solvent is removed in a vacuum. The residue is dissolved in water and extracted three times with dichloromethane, the organic phase is dried over anhydrous sodium sulphate, filtered and the solvent is removed in a vacuum. The residue (6.7 g.) is dissolved in glacial acetic acid and stirred for 3 hours at 70° C. The solvent is removed in a vacuum and the residue is purified by column chromatography (silica gel; dichloromethane containing 5% methanol). There is obtained 1.55 g. of the title compound; m.p. 230°-232° C.
Reaction SMILES: Br[C:2]1[S:6][C:5]([C:7]([O:9][CH3:10])=[O:8])=[CH:4][C:3]=1[CH3:11].C(=O)([O-])[O-].[Na+].[Na+].[CH2:18]([C:20]([C:39]1[CH:44]=[CH:43][C:42]([OH:45])=[C:41]([CH3:46])[CH:40]=1)([C:23]1[CH:28]=[CH:27][C:26](B2OC(C)(C)C(C)(C)O2)=[C:25]([CH3:38])[CH:24]=1)[CH2:21][CH3:22])[CH3:19].C(OCC)(=O)C>C1(C)C=CC=CC=1>[CH3:10][O:9][C:7]([C:5]1[S:6][C:2]([C:26]2[CH:27]=[CH:28][C:23]([C:20]([CH2:21][CH3:22])([C:39]3[CH:44]=[CH:43][C:42]([OH:45])=[C:41]([CH3:46])[CH:40]=3)[CH2:18][CH3:19])=[CH:24][C:25]=2[CH3:38])=[C:3]([CH3:11])[CH:4]=1)=[O:8]
Reactant: COC(=O)c1cc(C)c(Br)s1
Reactant: CCC(CC)(c1ccc(O)c(C)c1)c1ccc(B2OC(C)(C)C(C)(C)O2)c(C)c1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CCOC(C)=O
Solvent: Cc1ccccc1
Product: CCC(CC)(c1ccc(O)c(C)c1)c1ccc(-c2sc(C(=O)OC)cc2C)c(C)c1
Temperature: 85 °C
Reaction time: 17 h
Yield: 46.9 %

Procedure:
Methyl 5-bromo-4-methyl-2-thiophenecarboxylate (178.85 mg, 0.761 mmol), tetrakistriphenylphosphine palladium (14.7 mg, 0.013 mmol) and a 2 M sodium carbonate aqueous solution (0.3 mL, 0.6 mmol) were added to a solution of 4-{1-ethyl-1-[3-methyl-4-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-phenyl]-propyl}-2-methyl-phenol (Example 15-(2); 100 mg, 0.254 mmol) in toluene (0.5 mL) at room temperature, and the mixture was stirred at 85° C. for 17 hours. Ethyl acetate was added to the reaction solution. The organic layer was filtered through celite, and the solvent was distilled off under reduced pressure. The residue was purified by silica gel chromatography (n-hexane/ethyl acetate=3/1) to give the title compound (50.3 mg, 46.9%).
Reaction SMILES: [Br:1][C:2]1[CH:11]=[CH:10][C:5]2[C:6](=[O:9])[O:7][CH2:8][C:4]=2[C:3]=1[CH2:12][CH:13]=C.[O:15]=[O+][O-].[BH4-].[Na+]>CO.C(Cl)Cl>[Br:1][C:2]1[CH:11]=[CH:10][C:5]2[C:6](=[O:9])[O:7][CH2:8][C:4]=2[C:3]=1[CH2:12][CH2:13][OH:15]
Reactant: O=[O+][O-]
Reactant: C=CCc1c(Br)ccc2c1COC2=O
Agent: [BH4-]
Agent: [Na+]
Solvent: CO
Solvent: ClCCl
Product: O=C1OCc2c1ccc(Br)c2CCO
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
To a solution of 5-bromo-4-prop-2-en-1-yl-2-benzofuran-1(3H)-one (1.27 g, 5.02 mmol) in MeOH (50 mL) and DCM (50 mL) was bubbled O3 at −78° C. until the solution turned blue; excess ozone was removed on high vacuum. After the solution's color changed into colorless, NaBH4 (0.8 g, 20 mmol) was added to the reaction mixture and subsequently stirred at room temperature for 30 min; LC and TLC indicated that reaction had gone to completion; solvent was removed on high vacuum, the residue was then re-dissolved in EtOAc and washed with water, dried over Na2SO4, filtered and concentrated to dryness. The organic residue was absorbed into silica gel and was separated on silica gel column to give 5-bromo-4-(2-hydroxyethyl)-2-benzofuran-1(3H)-one. 1H-NMR (400 MHz, CDCl3) δ ppm 7.7 (d, J=7.8 Hz, 1H), 7.5 (d, J=7.8 Hz, 1H), 5.37 (s, 2H), 3.94 (t, J=6.3 Hz, 2H), 2.98 (t, J=6.3 Hz, 2H)
Reaction SMILES: [N:1]1[CH:6]=[CH:5][CH:4]=[CH:3][C:2]=1[NH:7][C:8]1[CH:13]=[CH:12][CH:11]=[CH:10][C:9]=1[NH2:14].[F:15][C:16]([F:29])([F:28])[C:17]1[CH:18]=[C:19]([CH:25]=[CH:26][CH:27]=1)/[CH:20]=[CH:21]/[C:22]([Cl:24])=O.N1C=CC=CC=1N1C2C=CC=CC=2N=C1/C=C/C1C=CC=CC=1.Cl>CO>[ClH:24].[F:15][C:16]([F:28])([F:29])[C:17]1[CH:18]=[C:19]([CH:25]=[CH:26][CH:27]=1)/[CH:20]=[CH:21]/[C:22]1[N:7]([C:2]2[CH:3]=[CH:4][CH:5]=[CH:6][N:1]=2)[C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][C:9]=2[N:14]=1
Reactant: O=C(Cl)/C=C/c1cccc(C(F)(F)F)c1
Reactant: Nc1ccccc1Nc1ccccn1
Agent: C(=C/c1nc2ccccc2n1-c1ccccn1)\c1ccccc1
Agent: Cl
Solvent: CO
Product: FC(F)(F)c1cccc(/C=C/c2nc3ccccc3n2-c2ccccn2)c1

Procedure:
Free base of the titled compound was prepared from N-(2-pyridyl)-o-phenylenediamine and (E)-3-trifluoromethylcinnamoyl chloride (Amino, Y.; Kawada, K.; Toi, K.; Kumashiro, I.; Fukushima, K. Chem. Pharm. Bull., 1988, 36, 4426) according to the preparation of (E)-1-(2-pyridyl)-2-styryl-1H-benzimidazole (Example 1, method A). The free base was dissolved with a 10% methanol solution of hydrogen chloride (5 ml). Concentration and recrystallization from ethanol yielded the titled compound. MW: 401.82; mp:>230° C.; 1H-NMR (DMSO) δ: 8.83-8.77 (1H, m), 8.14-8.06 (1H, m), 7.81(1H, d, J=7.7 Hz), 7.67 (1H, dd, J=7.3,4.8 Hz), 7.56-7.22 (10H, m).
Reaction SMILES: [CH:1](OC)([O:4][CH3:5])[O:2][CH3:3].O.[O-2].[O-2].[O-2].O=[Si]=O.O=[Si]=O.O=[Si]=O.O=[Si]=O.[Al+3].[Al+3].C([C:28]1[S:32][C:31]([C:33]2[S:34][CH:35]=[CH:36][CH:37]=2)=[CH:30][CH:29]=1)=O>CCCCCC>[CH3:3][O:2][CH:1]([O:4][CH3:5])[C:28]1[S:32][C:31]([C:33]2[S:34][CH:35]=[CH:36][CH:37]=2)=[CH:30][CH:29]=1
Reactant: COC(OC)OC
Reactant: O=Cc1ccc(-c2cccs2)s1
Agent: O=[Si]=O
Agent: [Al+3]
Agent: [O-2]
Solvent: CCCCCC
Solvent: O
Product: COC(OC)c1ccc(-c2cccs2)s1
Temperature: 25 °C
Reaction time: 0.17 h

Procedure:
Trimethyl orthoformate (7.5 ml) and montmorillonite K-10 (5.0 g) (Aldrich Chem. Co., Milwaukee, Wis.) were mixed and stirred at room temperature for 10 minutes. A solution of 5-formyl-2,2'-bithiophene (5.0 g) (Aldrich Chem. Co., Milwaukee, Wis.) in n-hexane (10 ml) was added and was stirred at room temperature. The reaction was monitored with thin layer chromatography until the reaction was completed. Montmorillonite K-10 was filtered. The filtrate was added to a saturated sodium bicarbonate aqueous solution and extracted with ethyl acetate (15 ml×3). The extract was washed with brine, dried over anhydrous magnesium sulfate and concentrated to give light yellowish oily product (6.4 g).
Reaction SMILES: [O:1]1[CH2:6][CH2:5][CH2:4][CH2:3][CH:2]1[O:7][C:8]1[CH:26]=[CH:25][C:11]([O:12][CH:13]([C:17]2[CH:24]=[CH:23][C:20]([C:21]#[N:22])=[CH:19][CH:18]=2)[CH2:14][CH:15]=[CH2:16])=[CH:10][CH:9]=1.B.CSC.C1C[O:34]CC1>CCOCC>[OH:34][CH2:16][CH2:15][CH2:14][CH:13]([C:17]1[CH:18]=[CH:19][C:20]([C:21]#[N:22])=[CH:23][CH:24]=1)[O:12][C:11]1[CH:25]=[CH:26][C:8]([O:7][CH:2]2[CH2:3][CH2:4][CH2:5][CH2:6][O:1]2)=[CH:9][CH:10]=1
Reactant: C1CCOC1
Reactant: C=CCC(Oc1ccc(OC2CCCCO2)cc1)c1ccc(C#N)cc1
Agent: B
Solvent: CSC
Solvent: CCOCC
Product: N#Cc1ccc(C(CCCO)Oc2ccc(OC3CCCCO3)cc2)cc1
Temperature: -5 °C
Reaction time: 1.5 h

Procedure:
4-{1-[4-(Tetrahydro-2H-pyran-2-yloxy)phenoxy]-3-butenyl}benzonitrile (4.6 g, 13 mmol; from step (d) above) was dissolved in dry THF (50 mL) under argon and cooled to −5° C. Borane-methylsulfide complex (BH3×SMe2) (3.5 mL of a 2 M solution in ether) was added dropwise at 0 to 5° C. The mixture was stirred at that temperature for 1.5 h. After 4 h at rt, tlc showed that the reaction was complete. The reaction mixture was quenched with 14 mL of H2O and 5 g of NaBO3. The mixture was stirred overnight, the solvent decanted off, and the residue treated with ether and decanted. The combined organic fractions were washed with brine, dried (Na2SO4), and evaporated. The crude product was purified by chromatography on silica (iso-propanol:ethyl acetate:heptane; 5:20:70). Yield: 2.44 g (58%).
Reaction SMILES: [Cl:1][C:2]1[C:3]2[N:4]([C:8](I)=[C:9]([C:11]3[CH:16]=[CH:15][C:14]([F:17])=[CH:13][CH:12]=3)[N:10]=2)[CH:5]=[CH:6][CH:7]=1.[F:19][C:20]1[CH:25]=[C:24](B(O)O)[CH:23]=[CH:22][N:21]=1.C(=O)([O-])[O-].[Na+].[Na+].O>CN(C)C=O.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>[Cl:1][C:2]1[C:3]2[N:4]([C:8]([C:24]3[CH:23]=[CH:22][N:21]=[C:20]([F:19])[CH:25]=3)=[C:9]([C:11]3[CH:16]=[CH:15][C:14]([F:17])=[CH:13][CH:12]=3)[N:10]=2)[CH:5]=[CH:6][CH:7]=1
Reactant: Fc1ccc(-c2nc3c(Cl)cccn3c2I)cc1
Reactant: OB(O)c1ccnc(F)c1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: Fc1ccc(-c2nc3c(Cl)cccn3c2-c2ccnc(F)c2)cc1
Temperature: 100 °C
Yield: 80.5 %

Procedure:
8-Chloro-2-(4-fluorophenyl)-3-iodoimidazo[1,2-α]pyridine (0.15 g, 0.4 mmol) was dissolved in N,N-dimethylformamide (5 mL). To this solution was added 2-fluoro-4-pyridinylboronic acid (120 mg, 0.8 mmol), dichlorobis(triphenylphosphine)palladium (II) (60 mg, 0.08 mmol) and aqueous sodium carbonate (170 mg, 1.6 mmol). The resulting solution was heated at 100° C. overnight. Water was added to the reaction mixture and the mixture was extracted with ethyl acetate. The organic phase was dried (magnesium sulfate), filtered and concentrated to a solid. Purification by silca gel chromatography (1:1 ethyl acetate:hexane) gave 8-chloro-2-(4-fluorophenyl)-3-(2-fluoropyridin-4-yl)imidazo[1,2-α]pyridine (110 mg, 81%) as a white solid. 1H NMR (CDCl3): δ 8.41 (d, 1H), 8.09 (d, 1H), 7.62 (q, 2H), 7.42 (d, 1H), 7.29 (d, 1H), 7.07 (m, 3H), 6.87 (t, 1H); 19F NMR (CDCl3) δ −65.46 and −112.94; MS m/z 342 (M+1).
Reaction SMILES: [C:1]([O-:6])(=[O:5])[CH:2]([CH3:4])[OH:3].[Li+].[H-].[Na+].Cl[C:11]1[CH:16]=[C:15]([C:17]([F:20])([F:19])[F:18])[CH:14]=[CH:13][N:12]=1.O>CN(C)C=O>[F:18][C:17]([F:20])([F:19])[C:15]1[CH:14]=[CH:13][N:12]=[C:11]([O:3][CH:2]([CH3:4])[C:1]([OH:6])=[O:5])[CH:16]=1
Reactant: CC(O)C(=O)[O-]
Reactant: FC(F)(F)c1ccnc(Cl)c1
Agent: [H-]
Agent: [Li+]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: CC(Oc1cc(C(F)(F)F)ccn1)C(=O)O
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
To a suspension of lithium lactate (7.8 g, 81 mmol) in 100 mL of anhydrous dimethylformamide was added sodium hydride (60% dispersion in mineral oil, 3.2 g, 80 mmol). After stirring at room temperature for 30 min, 2-chloro-4-trifluromethylpyridine (10 g, 55 mmol) was added, and the mixture was heated at 100° C. overnight. The reaction was cooled to room temperature, poured into 500 mL of water, and was washed with hexane (200 mL). The aqueous solution was acidified with concentrated hydrochloric acid (pH>2), and was extracted with ether (2×500 mL). The combined extracts were washed with water and brine, dried over anhydrous sodium sulfate, filtered and concentrated to dryness to give the title compound.