Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1]/[N:2]=[C:3](/[C:8]1[CH:13]=[CH:12][C:11]([C:14]2[N:18]([CH3:19])[C:17]([C:20]#[N:21])=[CH:16][CH:15]=2)=[CH:10][CH:9]=1)\[C:4]([CH3:7])([CH3:6])[CH3:5].[H-].[Na+].[CH3:24]I>C1COCC1>[CH3:24][O:1]/[N:2]=[C:3](/[C:8]1[CH:13]=[CH:12][C:11]([C:14]2[N:18]([CH3:19])[C:17]([C:20]#[N:21])=[CH:16][CH:15]=2)=[CH:10][CH:9]=1)\[C:4]([CH3:7])([CH3:6])[CH3:5]
Reactant: CI
Reactant: Cn1c(C#N)ccc1-c1ccc(/C(=N/O)C(C)(C)C)cc1
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: CO/N=C(/c1ccc(-c2ccc(C#N)n2C)cc1)C(C)(C)C
Reaction time: 0.17 h
Yield: 10.4 %

Procedure:
To a stirred solution of 5-{4-[(1E)-N-hydroxy-2,2-dimethylpropanimidoyl]-phenyl}-1-methyl-1H-pyrrole-2-carbonitrile (0.212 g, 0.75 mmol) in THF (7 mL) was added sodium hydride (0.03 g, 60% in mineral oil, 0.75 mmol) at 0° C. After the mixture was stirred for 10 minutes, methyl iodide (0.8 mL, 1.28 mmol) was added and the resulting mixture was stirred overnight at room temperature. The reaction mixture was then quenched with a saturated ammonium chloride solution (20 mL), and extracted several times with ethyl acetate (3×20 mL). The combined organic layers were dried over magnesium sulfate and concentrated. The residue was purified by a silica gel column (5% ethyl acetate in hexane) to afford 5-{4-[(1E)-N-methoxy-2,2-dimethylpropanimidoyl]phenyl}-1-methyl-1H-pyrrole-2-carbonitrile as a white solid (0.023 g, 10%). MS (ES) m/z 296.0; HRMS: calcd for C18H21N3O+H+, 296.17574; found (ESI, [M+H]+), 296.1753.
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:12])[C:5]1[CH:10]=[CH:9][C:8](Br)=[CH:7][CH:6]=1)[CH3:2].[C:13](=[O:16])([O-])[O-].[Na+].[Na+]>C1(C)C=CC=CC=1.C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1>[CH2:1]([O:3][C:4]([C:5]1[CH:10]=[CH:9][C:8]([C:5]2[CH:10]=[CH:9][CH:8]=[CH:7][C:6]=2[O:16][CH3:13])=[CH:7][CH:6]=1)=[O:12])[CH3:2]
Reactant: O=C([O-])[O-]
Reactant: CCOC(=O)c1ccc(Br)cc1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: [Na+]
Solvent: Cc1ccccc1
Product: CCOC(=O)c1ccc(-c2ccccc2OC)cc1
Temperature: 100 °C
Yield: 179.7 %

Procedure:
A mixture of 4-bromo benzoic acid ethyl ester (2.7 mL, 16.5 mmol), 2-methoxy boronic acid (2.5 g, 16.5 mmol) and sodium carbonate (7.7 g, 72.6 mmol) in toluene: ethanol:water (75 mL:37 mL:37 mL), was flushed with nitrogen for 1 hour. After addition of the tetrakis(triphenylphosphine)palladium(0) catalyst (0.96 g, 0.83 mmol), the reaction mixture was heated at 100° C. overnight. After cooling, the mixture was filtered through Celite which was then rinsed with ethyl acetate. The organic layer was washed with water, dried over anhydrous sodium sulfate, filtered and concentrated in vacuo to give a brown oil. Purification of the residue by flash chromatography with a solvent gradient from 25% to 50% dichloromethane in hexane provided the title compound (3.8 g, 89.9%) as a pale yellow oil.
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([C:8]2[CH:13]=[CH:12][C:11]([F:14])=[CH:10][C:9]=2[O:15][CH3:16])[C:5]([F:17])=[CH:4][N:3]=1.[Cl:18][C:19]1[CH:20]=[C:21]([CH:23]=[C:24]([CH2:26][S:27][CH3:28])[CH:25]=1)[NH2:22]>>[Cl:18][C:19]1[CH:20]=[C:21]([NH:22][C:2]2[N:7]=[C:6]([C:8]3[CH:13]=[CH:12][C:11]([F:14])=[CH:10][C:9]=3[O:15][CH3:16])[C:5]([F:17])=[CH:4][N:3]=2)[CH:23]=[C:24]([CH2:26][S:27][CH3:28])[CH:25]=1
Reactant: COc1cc(F)ccc1-c1nc(Cl)ncc1F
Reactant: CSCc1cc(N)cc(Cl)c1
Product: COc1cc(F)ccc1-c1nc(Nc2cc(Cl)cc(CSC)c2)ncc1F

Procedure:
Intermediate 56.5 was prepared under similar conditions as described in the preparation of Intermediate 28.3 using 2-chloro-5-fluoro-4-(4-fluoro-2-methoxyphenyl)pyrimidine and 3-chloro-5-[(methylsulfanyl)-methyl]aniline. The batch was purified by chromatography (hexane to hexane/ethyl acetate 30%) to give the desired product.
Reaction SMILES: I[C:2]1[CH:3]=[C:4]([CH:24]=[CH:25][CH:26]=1)[CH2:5][O:6][NH:7][C:8](=[O:23])[C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][C:10]=1[NH:15][CH2:16][C:17]1[CH:22]=[CH:21][N:20]=[CH:19][CH:18]=1.[CH2:27]([OH:30])[C:28]#[CH:29].C(N(CC)CC)C>[I-].C([N+](CCCC)(CCCC)CCCC)CCC.CN(C=O)C.[Cu]I.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>[OH:30][CH2:27][C:28]#[C:29][C:2]1[CH:3]=[C:4]([CH:24]=[CH:25][CH:26]=1)[CH2:5][O:6][NH:7][C:8](=[O:23])[C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][C:10]=1[NH:15][CH2:16][C:17]1[CH:22]=[CH:21][N:20]=[CH:19][CH:18]=1
Reactant: C#CCO
Reactant: O=C(NOCc1cccc(I)c1)c1ccccc1NCc1ccncc1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Agent: CCCC[N+](CCCC)(CCCC)CCCC
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: O=C(NOCc1cccc(C#CCO)c1)c1ccccc1NCc1ccncc1
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
N-(3-Iodo-benzyloxy)-2-[(pyridin-4-ylmethyl)-amino]-benzamide (example 361, 300 mg), propargyl alcohol (69 mg), CuI (19 mg), PdCl2(PPh3)2 (22 mg) and tetrabutylammonium iodide (241 mg) was dissolved in DMF (4 ml) and triethylamine (0.5 ml) was added drop-wise (exothermic reaction). The reaction mixture was stirred at room temperature for 30 minutes and partitioned between EtOAc and water. The aqueous phase was extracted with EtOAc and the combined organic layers were washed with brine, dried (MgSO4) and evaporated under reduced pressure. The residue was purified by chromatography on silica gel (EtOAc as eluent) and gave the title compound. 13C-NMR (DMSO-d6) δ 167.2, 149.5, 148.9, 148.3, 136.6, 132.5, 131.5, 130.9, 128.7, 128.6, 128.0, 122.3, 114.8, 113.3, 111.5, 90.0, 83.3, 76.3, 49.3, 44.8.
Reaction SMILES: [CH2:1]([CH:4]1[CH2:12][C:11]2[C:6](=[CH:7][CH:8]=[CH:9][C:10]=2[Cl:13])[C:5]1=O)[CH:2]=[CH2:3].C1(C)C=CC=CC=1.Cl.O>[Zn].C(O)(=O)C>[CH2:1]([CH:4]1[CH2:12][C:11]2[C:6](=[CH:7][CH:8]=[CH:9][C:10]=2[Cl:13])[CH2:5]1)[CH:2]=[CH2:3]
Reactant: C=CCC1Cc2c(Cl)cccc2C1=O
Agent: Cl
Agent: [Zn]
Solvent: O
Solvent: CC(=O)O
Solvent: Cc1ccccc1
Product: C=CCC1Cc2cccc(Cl)c2C1
Yield: 64.4 %

Procedure:
Amalgamated zinc (prepared from zinc powder (6 g), mercuric chloride (0.6 g)) was heated under reflux for 7 hours with 2-allyl-4-chloro-indan-1-one (3 g), toluene (20 ml), conc. hydrochloric acid (20 ml), water (8 ml) and acetic acid (2 ml). Upon cooling conventional work-up gave a crude product which was purified by chromatography (silica/hexane) to give a 2-allyl-4-chloroindane (1.8 g). 2-Allyl-4-chloroindane (0.8 g) in dry methanol (10 ml) and dry dichloromethane (2 ml) was reacted at -35° with ozone until the blue colour persisted. After purging with nitrogen the solution was stirred 16 hours with dimethyl sulphide (2.58 g). The volatiles were removed and the residue taken up in tetrahydrofuran (10 ml) and heated under reflux with 4-toluenesulphonic acid (30 mg) and water (circa 0.5 ml) for 2 hours. After conventional work up the product, 2-(4-chloro-2-indanyl) ethanol, was obtained as a yellow oil (0.8 g).
Reaction SMILES: [C:1]1([C:7]2[CH:16]=[C:15]([CH2:17][CH2:18][C:19]([OH:21])=O)[C:14]3[C:9](=[CH:10][CH:11]=[CH:12][CH:13]=3)[N:8]=2)[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.S(Cl)(Cl)=O.[NH:26]1[CH2:30][CH2:29][CH2:28][CH2:27]1>C(Cl)(Cl)Cl.C(OCC)(=O)C>[C:1]1([C:7]2[CH:16]=[C:15]([CH2:17][CH2:18][C:19]([N:26]3[CH2:30][CH2:29][CH2:28][CH2:27]3)=[O:21])[C:14]3[C:9](=[CH:10][CH:11]=[CH:12][CH:13]=3)[N:8]=2)[CH:2]=[CH:3][CH:4]=[CH:5][CH:6]=1
Reactant: C1CCNC1
Reactant: O=C(O)CCc1cc(-c2ccccc2)nc2ccccc12
Solvent: O=S(Cl)Cl
Solvent: CCOC(C)=O
Solvent: ClC(Cl)Cl
Product: O=C(CCc1cc(-c2ccccc2)nc2ccccc12)N1CCCC1

Procedure:
The procedure is as in Example 16, starting with 2-phenyl-4-quinolinepropanoic acid (3 g), thionyl chloride (2.3 cc) in chloroform (150 cc) and pyrrolidine (2.7 cc). The residue is stirred for two hours with silica gel (36 g) in ethyl acetate (80 cc). The silica is removed by filtration and washed with ethyl acetate (7×10 cc). The organic phases are combined and concentrated under reduced pressure. After recrystallization of the residue in ethyl acetate, 1-[3-(2-phenyl-4-quinolyl)propionyl]pyrrolidine (2 g), m.p. 116° C., is obtained.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([C@@H:8]([N:10]2[CH2:15][CH2:14][C@:13]([CH2:22][CH2:23][CH2:24][N:25]3[CH2:29][CH2:28][CH2:27][C:26]3=[O:30])([C:16]3[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=3)[O:12][C:11]2=[O:31])[CH3:9])=[CH:4][CH:3]=1.[CH3:32][C:33]1[CH:38]=[C:37](B(O)O)[CH:36]=[CH:35][N:34]=1>>[CH3:32][C:33]1[CH:38]=[C:37]([C:2]2[CH:7]=[CH:6][C:5]([C@@H:8]([N:10]3[CH2:15][CH2:14][C@:13]([CH2:22][CH2:23][CH2:24][N:25]4[CH2:29][CH2:28][CH2:27][C:26]4=[O:30])([C:16]4[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=4)[O:12][C:11]3=[O:31])[CH3:9])=[CH:4][CH:3]=2)[CH:36]=[CH:35][N:34]=1
Reactant: Cc1cc(B(O)O)ccn1
Reactant: C[C@@H](c1ccc(Br)cc1)N1CC[C@](CCCN2CCCC2=O)(c2ccccc2)OC1=O
Product: Cc1cc(-c2ccc([C@H](C)N3CC[C@](CCCN4CCCC4=O)(c4ccccc4)OC3=O)cc2)ccn1

Procedure:
The title compound was prepared from (R)-3-((S)-1-(4-bromophenyl)ethyl)-6-(3-(2-oxopyrrolidin-1-yl)propyl)-6-phenyl-1,3-oxazinan-2-one and 2-methylpyridine-4-boronic acid following a procedure analogous to that described in Example 1 Step 2. LC-MS Method 2 tR=0.992, m/z=498.1; 1H NMR (CDCl3) 1.21 (m, 3H), 1.48 (d, 3H), 1.61-1.95 (m, 5H), 2.12 (m, 1H), 2.26 (m, 4H), 2.52 (s, 3H), 2.83 (m, 1H), 3.11 (m, 3H), 3.22 (m, 1H), 5.67 (m, 1H), 6.95 (d, 2H), 7.18 (m, 1H), 7.21 (m, 1H), 7.23 (m, 2H), 7.29 (m, 3H), 7.30 (m, 2H), 8.41 (d, 1H).
Reaction SMILES: [O:1]([CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH:14]([C:16]1[O:17][C:18]([CH3:21])=[N:19][N:20]=1)[OH:15])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.CC(OI1(OC(C)=O)(OC(C)=O)OC(=O)C2C=CC=CC1=2)=O>C(Cl)Cl.[O-]S([O-])(=S)=O.[Na+].[Na+].C([O-])(O)=O.[Na+]>[O:1]([CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][C:14]([C:16]1[O:17][C:18]([CH3:21])=[N:19][N:20]=1)=[O:15])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: Cc1nnc(C(O)CCCCCCOc2ccccc2)o1
Agent: CC(=O)OI1(OC(C)=O)(OC(C)=O)OC(=O)c2ccccc21
Agent: O=C([O-])O
Agent: O=S([O-])([O-])=S
Solvent: ClCCl
Product: Cc1nnc(C(=O)CCCCCCOc2ccccc2)o1
Reaction time: 2 h
Yield: 82 %

Procedure:
To a solution of 64.1 (64 mg, 0.22 mmol) in wet methylene chloride (5 mL) at room temperature, under nitrogen was added Dess-Martin periodinane (140 mg, 0.33 mmol) and the resulting suspension stirred for 2 hours. The reaction mixture was diluted with Na2S2O3 (10% in H2O) and saturated aqueous NaHCO3 solution and the organic phase was separated. The aqueous layer was extracted with AcOEt and the combined organic layer was washed with brine, dried (MgSO4) and evaporated under reduced pressure. The residue obtained was purified by flash column chromatography on silica gel (50% ethyl acetate-hexane) to give 65.1 (52 mg, 82% yield) as a white solid (m p 75-77° C.).
Reaction SMILES: [C:1]([C:3]1[CH:8]=[CH:7][C:6]([C:9]2[CH:10]=[N:11][N:12]([C:15]3[CH:23]=[CH:22][C:18]([C:19]([OH:21])=O)=[CH:17][N:16]=3)[C:13]=2[OH:14])=[C:5]([F:24])[CH:4]=1)#[N:2].[CH3:25][O:26][CH2:27][CH2:28][C:29]1([NH2:32])[CH2:31][CH2:30]1>>[C:1]([C:3]1[CH:8]=[CH:7][C:6]([C:9]2[CH:10]=[N:11][N:12]([C:15]3[CH:23]=[CH:22][C:18]([C:19]([NH:32][C:29]4([CH2:28][CH2:27][O:26][CH3:25])[CH2:31][CH2:30]4)=[O:21])=[CH:17][N:16]=3)[C:13]=2[OH:14])=[C:5]([F:24])[CH:4]=1)#[N:2]
Reactant: COCCC1(N)CC1
Reactant: N#Cc1ccc(-c2cnn(-c3ccc(C(=O)O)cn3)c2O)c(F)c1
Product: COCCC1(NC(=O)c2ccc(-n3ncc(-c4ccc(C#N)cc4F)c3O)nc2)CC1

Procedure:
The title compound was prepared in a manner similar to Example 198 using 6-(4-(4-cyano-2-fluorophenyl)-5-hydroxy-1H-pyrazol-1-yl)nicotinic acid and 1-(2-methoxyethyl)cyclopropanamine 1H NMR (400 MHz, DMSO-d6) δ ppm 0.58-0.66 (m, 2 H) 0.66-0.73 (m, 2 H) 1.80 (t, J=6.9 Hz, 2 H) 3.14 (s, 3 H) 3.39 (t, J=7.1 Hz, 2 H) 7.61 (dd, J=8.2, 1.6 Hz, 1 H) 7.75 (dd, J=11.9, 1.5 Hz, 1 H) 8.14 (d, J=3.0 Hz, 1 H) 8.30 (dd, J=8.7, 2.1 Hz, 1 H) 8.40 (d, J=8.6 Hz, 1 H) 8.56 (t, J=8.0 Hz, 1 H) 8.76 (s, 1 H) 8.80 (d, J=1.5 Hz, 1H) 13.69 (br. s., 1 H). MS m/z 422 [M+H]+.
Reaction SMILES: [CH3:1][O:2][C:3]([NH:5][C@H:6]([C:10]([N:12]1[C@@H:16]([CH3:17])[CH2:15][CH2:14][C@H:13]1[C:18]1[NH:22][C:21]2[C:23]3[C:28]([CH:29]=[CH:30][C:20]=2[N:19]=1)=[CH:27][C:26]1[C:31]2[C:36]([CH2:37][O:38][C:25]=1[CH:24]=3)=[CH:35][C:34]([C:39]1[NH:43][C:42]([C@@H:44]3[CH2:48][C@H:47]([CH2:49][O:50][CH3:51])[CH2:46][N:45]3C(OC(C)(C)C)=O)=[N:41][CH:40]=1)=[CH:33][CH:32]=2)=[O:11])[CH:7]([CH3:9])[CH3:8])=[O:4].[CH3:59][O:60][C:61]([NH:63][C@H:64]([C:68]1[CH:73]=[CH:72][CH:71]=[CH:70][CH:69]=1)[C:65]([OH:67])=O)=[O:62].CCOC(C(C#N)=NOC(N1CCOCC1)=[N+](C)C)=O.F[P-](F)(F)(F)(F)F.C(N(C(C)C)CC)(C)C>Cl.CCO>[CH3:1][O:2][C:3](=[O:4])[NH:5][C@@H:6]([CH:7]([CH3:9])[CH3:8])[C:10]([N:12]1[C@@H:16]([CH3:17])[CH2:15][CH2:14][C@H:13]1[C:18]1[NH:22][C:21]2[C:23]3[C:28]([CH:29]=[CH:30][C:20]=2[N:19]=1)=[CH:27][C:26]1[C:31]2[C:36]([CH2:37][O:38][C:25]=1[CH:24]=3)=[CH:35][C:34]([C:39]1[NH:43][C:42]([C@@H:44]3[CH2:48][C@H:47]([CH2:49][O:50][CH3:51])[CH2:46][N:45]3[C:65](=[O:67])[C@H:64]([NH:63][C:61]([O:60][CH3:59])=[O:62])[C:68]3[CH:73]=[CH:72][CH:71]=[CH:70][CH:69]=3)=[N:41][CH:40]=1)=[CH:33][CH:32]=2)=[O:11]
Reactant: COC(=O)N[C@@H](C(=O)O)c1ccccc1
Reactant: COC[C@H]1C[C@@H](c2ncc(-c3ccc4c(c3)COc3cc5c(ccc6nc([C@@H]7CC[C@H](C)N7C(=O)[C@@H](NC(=O)OC)C(C)C)[nH]c65)cc3-4)[nH]2)N(C(=O)OC(C)(C)C)C1
Agent: CCOC(=O)C(C#N)=NOC(N1CCOCC1)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CCO
Product: COC[C@H]1C[C@@H](c2ncc(-c3ccc4c(c3)COc3cc5c(ccc6nc([C@@H]7CC[C@H](C)N7C(=O)[C@@H](NC(=O)OC)C(C)C)[nH]c65)cc3-4)[nH]2)N(C(=O)[C@H](NC(=O)OC)c2ccccc2)C1
Temperature: 50 °C
Reaction time: 2 h
Yield: 38.7 %

Procedure:
A solution of tert-butyl(2S,4S)-2-[5-(2-{(2S,5S)-1-[N-(methoxycarbonyl)-L-valyl]-5-methylpyrrolidin-2-yl}-1,11-dihydroisochromeno[4′,3′:6,7]naphtho[1,2-d]imidazol-9-yl)-1H-imidazol-2-yl]-4-(methoxymethyl)pyrrolidine-1-carboxylate (150 mg, 0.19 mmol) in 1.25 N HCl in EtOH (3 mL) was stirred overnight then heated to 50° C. for 3 h. The reaction was concentrated and the crude material dissolved in DMF (2 mL). To this solution was added a solution of (R)-2-(methoxycarbonylamino)-2-phenylacetic acid (52 mg, 0.25 mmol) and COMU (90 mg, 0.21 mmol). To the resulting solution was added diisopropylethylamine (0.099 mL, 0.57 mmol). After stirring for 2 h at room temperature, the reaction was quenched with 1N HCl (0.200 mL) and purified by HPLC. After lyophilization, the TFA salt was dissolved in EtOAc and washed with saturated NaHCO3. The organic phase was dried over Na2SO4 and concentrated. The free base was then dissolved in MeCN/H2O and lyophilized to afford methyl{(2S)-1-[(2S,5S)-2-(9-{2-[(2S,4S)-1-{(2R)-2-[(methoxycarbonyl)amino]-2-phenylacetyl}-4-(methoxymethyl)pyrrolidin-2-yl]-1H-imidazol-5-yl}-1,11-dihydroisochromeno[4′,3′:6,7]naphtho[1,2-d]imidazol-2-yl)-5-methylpyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl}carbamate (65 mg, 39%). LCMS-ESI+: calculated for C49H54N8O8: 882.4; observed [M+1]+: 884.1. Diagnostic peaks in NMR ′H NMR (CD3OD): 8.28 (s, 1H), 8.21 (s, 1H), 8.04 (s, 1H), 7.91-7.01 (m, 10H), 3.62 (s, 3H), 3.34 (s, 3H), 3.23 (s, 3H), 1.56 (d, 3H), 1.03 (d, 3H), 0.94 (d, 3H).
Reaction SMILES: [NH2:1][C:2]1[N:10]=[C:9]([Cl:11])[CH:8]=[CH:7][C:3]=1[C:4]([OH:6])=[O:5].[C:12](=O)([O-])[O-].[K+].[K+].IC>CN(C=O)C>[CH3:12][O:5][C:4](=[O:6])[C:3]1[CH:7]=[CH:8][C:9]([Cl:11])=[N:10][C:2]=1[NH2:1]
Reactant: Nc1nc(Cl)ccc1C(=O)O
Reactant: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Solvent: CI
Product: COC(=O)c1ccc(Cl)nc1N
Temperature: 25 °C
Reaction time: 18 h
Yield: 54 %

Procedure:
A suspension of 2-amino-6-chloronicotinic acid (500 mg, 2.90 mmol) and is potassium carbonate (441 mg, 3.19 mmol) in DMF (5 ml) was heated to reflux. The reaction mixture was cooled to room temperature and 273 μl of iodomethane (4.35 mmol) were added. The mixture was then refluxed under stirring for 18 h. After subsequent cooling, the mixture was finally filtered and the filtrate was concentrated under reduced pressure. The crude product was purified by flash chromatography on silica gel (ethyl acetate/petroleum ether=95/5). The isolated 2-amino-6-chloronicotinic acid methyl ester was obtained in 54% yield.
Reaction SMILES: COP([CH2:7][C:8](=[O:16])[C:9]([F:15])([F:14])[CH2:10][CH2:11][CH2:12][CH3:13])(=O)OC.[OH-].[K+].[C:19]([O:22][C@@H:23]1[C@H:27]([CH2:28][CH2:29][CH2:30][CH2:31][CH2:32][CH2:33][C:34]([O:36][CH3:37])=[O:35])[C@@H:26]([CH:38]=O)[C@H:25]([O:40][CH:41]2[CH2:46][CH2:45][CH2:44][CH2:43][O:42]2)[CH2:24]1)(=[O:21])[CH3:20].O>COC(C)(C)C>[C:19]([O:22][C@@H:23]1[C@H:27]([CH2:28][CH2:29][CH2:30][CH2:31][CH2:32][CH2:33][C:34]([O:36][CH3:37])=[O:35])[C@@H:26](/[CH:38]=[CH:7]/[C:8](=[O:16])[C:9]([F:14])([F:15])[CH2:10][CH2:11][CH2:12][CH3:13])[C@H:25]([O:40][CH:41]2[CH2:46][CH2:45][CH2:44][CH2:43][O:42]2)[CH2:24]1)(=[O:21])[CH3:20]
Reactant: CCCCC(F)(F)C(=O)CP(=O)(OC)OC
Reactant: COC(=O)CCCCCC[C@@H]1[C@@H](C=O)[C@H](OC2CCCCO2)C[C@@H]1OC(C)=O
Agent: [K+]
Agent: [OH-]
Solvent: O
Solvent: COC(C)(C)C
Product: CCCCC(F)(F)C(=O)/C=C/[C@@H]1[C@@H](CCCCCCC(=O)OC)[C@@H](OC(C)=O)C[C@H]1OC1CCCCO1
Temperature: 25 °C
Reaction time: 1.2 h
Yield: 80.6 %

Procedure:
To a solution of dimethyl (3,3-difluoro-2-oxoheptyl)phosphonate (1) (1.113 g, 4.31 mmol) in t-butyl methyl ether (17 ml), potassium hydroxide (0.225 g, 4.00 mmol) was added and the mixture was stirred for approximately 1.2 hours at room temperature. A solution of methyl 7-[(1R,2R,3R,5S)-5-acetoxy-2-formyl-3-(2-tetrahydro pyranyloxy)cyclopentyl]heptanate (2) (0.965 g, 2.42 mmol) in t-butyl methyl ether (3 ml) solution, and water (0.32 ml) were added thereto. The mixed solution was heat refluxed for approximately 48 hours. After cooling to room temperature, water (5.6 ml) was added to the solution and the mixture was stirred, let to stand and then separated into two layers. The aqueous layer was extracted twice with ethyl acetate (4 ml). The organic layers were combined, sequentially washed with 3% aqueous sodium chloride (6 ml) and saturated aqueous sodium chloride (6 ml), and dried with anhydrous magnesium sulfate. After concentration under reduced pressure, the residue was purified by silica gel column chromatography (Fuji Silysia BW-300SP: 33 g; ethyl acetate:hexane=1:4) to give methyl 7-[(1R,2R,3R,5S)-5-acetoxy-2-((E)-4,4-difluoro-3-oxo-1-octenyl)-3-(2-tetrahydropyranyloxy)cyclopentyl]heptanate (3) (1.035 g; 1.950 mmol; yield: 80.6%).
Reaction SMILES: [H-].[Na+].[NH:3]1[C:11]2[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=2)[CH2:5][CH2:4]1.F[C:13]1[CH:20]=[CH:19][CH:18]=[CH:17][C:14]=1[C:15]#[N:16]>CS(C)=O>[N:3]1([C:19]2[CH:18]=[CH:17][C:14]([C:15]#[N:16])=[CH:13][CH:20]=2)[C:11]2[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=2)[CH2:5][CH2:4]1
Reactant: N#Cc1ccccc1F
Reactant: c1ccc2c(c1)CCN2
Agent: [H-]
Agent: [Na+]
Solvent: CS(C)=O
Product: N#Cc1ccc(N2CCc3ccccc32)cc1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
4.94 g (0.206 mole) 99% NaH was added in one portion to a solution of 21.6 ml (0.188 mole) indoline in 85 ml sieve dried dimethylsulfoxide (DMSO) at room temperature. The resulting slurry was permitted to stir at room temperature for 2 hours and then cooled in an ice bath. A solution of 25 g (0.206 moles) 2-fluorobenzonitrile in 35 ml DMSO was added dropwise. At the end of the addition, the ice bath was removed and the mixture was permitted to stir at room temperature overnight (about 16 hours). The product was poured onto 300 ml of ice and extracted with CHCl3 (300 ml). The organic phase was thrice washed with water (500 ml portions), brine (500 ml), dried (Na2SO4) and concentrated to give 39.9 g (96.4%) of crude material. Two recrystallizations from isopropyl ether afforded 4-(1-indolinyl)benzonitrile, m.p. 88.5°-89.5° C.
Reaction SMILES: C(O[C:4]([C:6]1[N:7]=[C:8]([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][C:16]=2[O:21][CH3:22])[N:9]([CH3:14])[C:10](=[O:13])[C:11]=1[OH:12])=[O:5])C.[CH3:23][C:24]1[CH:25]=[C:26]([CH:29]=[CH:30][C:31]=1[CH3:32])[CH2:27][NH2:28]>>[CH3:23][C:24]1[CH:25]=[C:26]([CH:29]=[CH:30][C:31]=1[CH3:32])[CH2:27][NH:28][C:4]([C:6]1[N:7]=[C:8]([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][C:16]=2[O:21][CH3:22])[N:9]([CH3:14])[C:10](=[O:13])[C:11]=1[OH:12])=[O:5]
Reactant: Cc1ccc(CN)cc1C
Reactant: CCOC(=O)c1nc(-c2ccccc2OC)n(C)c(=O)c1O
Product: COc1ccccc1-c1nc(C(=O)NCc2ccc(C)c(C)c2)c(O)c(=O)n1C

Procedure:
Prepared according to the procedure described for example 2 from 5-hydroxy-2-(2-methoxy-phenyl)-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid ethyl ester (45.6 mg, 0.15 mmol) and 3,4-dimethylbenzylamine (102 mg, 0.75 mmol). The title product was obtained as a brown solid (53.5 mg, 91% yield). 1HNMR (500 MHz, CDCl3) δ: 12.50–11.95 (1H, br s), 7.85 (1H, t, J=4.58 Hz), 7.47 (1H, td, J=8.24, 1.83 Hz), 7.27 (1H, dd, J=17.63, 0.83 Hz), 7.09–7.02 (4H, m), 6.97 (1H, d, J=8.24 Hz), 4.49 (2H, d, J=5.79 Hz), 3.81 (3H, s), 3.34 (3H, s) 2.23 (3H, s), 2.22 (3H, s). HRMS (ESI) calcd for C22H24N3O4 (M+H): 394.1767; found: 394.1781.
Reaction SMILES: [Cl:1][C:2]1[C:7]([Cl:8])=[CH:6][C:5]([NH:9][CH2:10][C:11]([N:13]2[CH2:18][CH2:17][N:16](C(OC(C)(C)C)=O)[CH2:15][CH2:14]2)=[O:12])=[C:4]([CH2:26][CH3:27])[CH:3]=1>Cl.CO>[ClH:1].[Cl:1][C:2]1[C:7]([Cl:8])=[CH:6][C:5]([NH:9][CH2:10][C:11]([N:13]2[CH2:18][CH2:17][NH:16][CH2:15][CH2:14]2)=[O:12])=[C:4]([CH2:26][CH3:27])[CH:3]=1
Reactant: CCc1cc(Cl)c(Cl)cc1NCC(=O)N1CCN(C(=O)OC(C)(C)C)CC1
Agent: Cl
Solvent: CO
Product: CCc1cc(Cl)c(Cl)cc1NCC(=O)N1CCNCC1
Temperature: 25 °C
Reaction time: 1 h
Yield: 161.5 %

Procedure:
A mixture of tert-butyl 4-(2-(4,5-dichloro-2-ethylphenylamino)acetyl)piperazine-1-carboxylate (120 mg, 0.288 mmol) in HCl/MeOH (2.86 M, 10 mL) was stirred at room temperature for 1 h. The mixture was concentrated in vacuo to afford the crude product (82 mg) as a yellow solid which was used directly in the next step without further purification.
Reaction SMILES: Cl.Cl.[Cl:3][C:4]1[CH:12]=[CH:11][CH:10]=[C:9]2[C:5]=1[CH2:6][N:7]([C:13]([O:15][C@@H:16]1[CH2:20][C@@H:19]([C:21](=[O:37])[NH:22][C@:23]3([C:28](=[O:36])[NH:29][S:30]([CH:33]4[CH2:35][CH2:34]4)(=[O:32])=[O:31])[CH2:25][C@H:24]3[CH2:26][CH3:27])[NH:18][CH2:17]1)=[O:14])[CH2:8]2.[F:38][C:39]1[CH:40]=[C:41]([NH:49][C@@H:50]([C:54]([CH3:57])([CH3:56])[CH3:55])[C:51](O)=[O:52])[CH:42]=[C:43]([C:45]([F:48])([F:47])[F:46])[CH:44]=1.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C.OS([O-])(=O)=O.[K+]>C(Cl)Cl.O>[Cl:3][C:4]1[CH:12]=[CH:11][CH:10]=[C:9]2[C:5]=1[CH2:6][N:7]([C:13]([O:15][C@@H:16]1[CH2:20][C@@H:19]([C:21](=[O:37])[NH:22][C@:23]3([C:28](=[O:36])[NH:29][S:30]([CH:33]4[CH2:34][CH2:35]4)(=[O:32])=[O:31])[CH2:25][C@H:24]3[CH2:26][CH3:27])[N:18]([C:51](=[O:52])[C@@H:50]([NH:49][C:41]3[CH:42]=[C:43]([C:45]([F:48])([F:47])[F:46])[CH:44]=[C:39]([F:38])[CH:40]=3)[C:54]([CH3:57])([CH3:56])[CH3:55])[CH2:17]1)=[O:14])[CH2:8]2
Reactant: CC(C)(C)[C@H](Nc1cc(F)cc(C(F)(F)F)c1)C(=O)O
Reactant: CC[C@@H]1C[C@]1(NC(=O)[C@@H]1C[C@@H](OC(=O)N2Cc3cccc(Cl)c3C2)CN1)C(=O)NS(=O)(=O)C1CC1
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: O
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: CC[C@@H]1C[C@]1(NC(=O)[C@@H]1C[C@@H](OC(=O)N2Cc3cccc(Cl)c3C2)CN1C(=O)[C@@H](Nc1cc(F)cc(C(F)(F)F)c1)C(C)(C)C)C(=O)NS(=O)(=O)C1CC1
Temperature: 25 °C
Reaction time: 5 h
Yield: 65.1 %

Procedure:
(3R,5S)-5-((1R,2R)-1-(cyclopropylsulfonylcarbamoyl)-2-ethylcyclopropylcarbamoyl)pyrrolidin-3-yl 4-chloroisoindoline-2-carboxylate dihydrochloride (0.040 g, 0.071 mmol), (S)-2-(3-fluoro-5-(trifluoromethyl)phenylamino)-3,3-dimethylbutanoic acid (0.023 g, 0.079 mmol) and HATU (0.042 g, 0.11 mmol) in DCM (3 mL) was added DIEA (0.048 mL, 0.28 mmol) and the reaction was stirred at rt for 5 hr. H2O (5 mL) and saturated KHSO4 solution (3 mL) was added. The mixture was extracted with ether (15 mL), washed with brine (10 mL) and dried over sodium sulfate. After removal of solvent, the residue was purified by chromatography (hexane:Ethyl acetate=1:2) to give the (3R,5S)-5-((1R,2R)-1-(cyclopropylsulfonylcarbamoyl)-2-ethylcyclopropylcarbamoyl)-1-((S)-2-(3-fluoro-5-(trifluoromethyl)phenylamino)-3,3-dimethylbutanoyl)pyrrolidin-3-yl 4-chloroisoindoline-2-carboxylate (0.037 g, 65%) as white solid. MS: Calcd.: 799.2; Found: [M+H]+ 800.1. 1H NMR (400 MHz, d6-DMSO). 10.44 (s, 1H), 8.80 & 8.74 (s, 1H), 7.34 (m, 3H), 7.14 & 7.02 (m, 1H), 6.73 (m, 1H), 6.35 & 6.26 (d, J=8.4 Hz, 1H), 6.15 (m, 1H), 5.35 (m, 1H), 4.50-4.72 (m, 3H), 4.20-4.46 (m, 4H), 3.82 (m, 1H), 2.94 (m, 1H), 2.31 (m, 1H), 2.04 (m, 1H), 0.84-1.49 (m, 21H).