Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: Cl.[CH2:2]([O:9][C:10]1[CH:19]=[CH:18][CH:17]=[C:16]2[C:11]=1[CH2:12][CH2:13][CH2:14][CH:15]2[C:20]([N:22]([C:29]1[CH:30]=[N:31][C:32]([CH:35]([CH3:37])[CH3:36])=[CH:33][CH:34]=1)[CH2:23][C:24]1[CH:25]=[N:26][NH:27][CH:28]=1)=[O:21])[C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][CH:4]=1.[Cl:38][C:39]1[CH:46]=[CH:45][C:42]([CH2:43]Cl)=[CH:41][CH:40]=1>>[CH2:2]([O:9][C:10]1[CH:19]=[CH:18][CH:17]=[C:16]2[C:11]=1[CH2:12][CH2:13][CH2:14][CH:15]2[C:20]([N:22]([CH2:23][C:24]1[CH:25]=[N:26][N:27]([CH2:43][C:42]2[CH:45]=[CH:46][C:39]([Cl:38])=[CH:40][CH:41]=2)[CH:28]=1)[C:29]1[CH:30]=[N:31][C:32]([CH:35]([CH3:37])[CH3:36])=[CH:33][CH:34]=1)=[O:21])[C:3]1[CH:8]=[CH:7][CH:6]=[CH:5][CH:4]=1
Reactant: ClCc1ccc(Cl)cc1
Reactant: CC(C)c1ccc(N(Cc2cn[nH]c2)C(=O)C2CCCc3c(OCc4ccccc4)cccc32)cn1
Agent: Cl
Product: CC(C)c1ccc(N(Cc2cnn(Cc3ccc(Cl)cc3)c2)C(=O)C2CCCc3c(OCc4ccccc4)cccc32)cn1
Yield: 83.3 %

Procedure:
By the reaction and treatment in the same manner as in Example 271 using 5-benzyloxy-N-(6-isopropylpyridin-3-yl)-N-[(pyrazol-4-yl)methyl]-1,2,3,4-tetrahydronaphthalene-1-carboxamide hydrochloride (0.78 g) and 4-chlorobenzyl chloride (0.48 g) as starting materials, 5-benzyloxy-N-({1-[(4-chlorophenyl)methyl]pyrazol-4-yl}methyl)-N-(6-isopropylpyridin-3-yl)-1,2,3,4-tetrahydronaphthalene-1-carboxamide (0.76 g) was obtained.
Reaction SMILES: [Br:1][C:2]1[CH:7]=[C:6]([NH:8][CH3:9])[C:5]([NH2:10])=[CH:4][CH:3]=1.[C:11]1(C)C=CC(S(O)(=O)=O)=CC=1>C(OC)(OC)OC>[Br:1][C:2]1[CH:3]=[CH:4][C:5]2[N:10]=[CH:9][N:8]([CH3:11])[C:6]=2[CH:7]=1
Reactant: Cc1ccc(S(=O)(=O)O)cc1
Reactant: CNc1cc(Br)ccc1N
Solvent: COC(OC)OC
Product: Cn1cnc2ccc(Br)cc21
Temperature: 100 °C
Yield: 93 %

Procedure:
To a solution of 5-bromo-N1-methylbenzene-1,2-diamine (7.4 g, 37 mmol) in trimethyl orthoformate (100 mL) was added p-toluenesulfonic acid (0.36 g, 1.9 mmol). The reaction mixture was heated at 100° C. for 4 h, cooled, concentrated, dissolved in ethyl acetate, washed with brine, dried over sodium sulfate and concentrated. The crude product was used in next step without further purification. (7.3 g, yield 93%) MS (ESI+) e/z: 212.1.
Reaction SMILES: [H-].[Na+].[CH:3]1([C:9]2[NH:10][C:11](=[O:19])[C:12]([C:17]#[N:18])=[C:13]([S:15][CH3:16])[N:14]=2)[CH2:8][CH2:7][CH2:6][CH2:5][CH2:4]1.Br[CH2:21][C:22]([O:24][CH3:25])=[O:23].O>COCCOC>[C:17]([C:12]1[C:11](=[O:19])[N:10]([CH2:21][C:22]([O:24][CH3:25])=[O:23])[C:9]([CH:3]2[CH2:4][CH2:5][CH2:6][CH2:7][CH2:8]2)=[N:14][C:13]=1[S:15][CH3:16])#[N:18]
Reactant: COC(=O)CBr
Reactant: CSc1nc(C2CCCCC2)[nH]c(=O)c1C#N
Agent: [H-]
Agent: [Na+]
Solvent: O
Solvent: COCCOC
Product: COC(=O)Cn1c(C2CCCCC2)nc(SC)c(C#N)c1=O
Temperature: 0 °C
Reaction time: 1 h
Yield: 99 %

Procedure:
To a cooled (0° C.), stirred suspension of NaH (50% dispersion in mineral oil, washed with hexane, 2.2 g, 0.047 mol) in DME (350 mL) was added 2-cyclohexyl-1,6-dihydro-4-(methylthio)-6-oxo-5-pyrimidinecarbonitrile (9.5 g, 0.038 mol) in several portions. After 1 hour, methyl bromoacetate was added and the resulting solution was heated at 95°-100° C. for 2 days. The solution was cooled and water (300 mL) was added. The mixture was extracted with ethyl acetate and the combined extracts were washed with water, dried (MgSO4), and concentrated to give a beige powder (12.2 g, 99%) which was used without further purification.
Reaction SMILES: [OH:1][CH2:2][CH2:3][N:4]1[CH2:8][CH2:7][CH2:6][C:5]1=[O:9].C(N(CC)CC)C.[CH3:17][S:18](Cl)(=[O:20])=[O:19]>C1COCC1>[CH3:17][S:18]([O:1][CH2:2][CH2:3][N:4]1[CH2:8][CH2:7][CH2:6][C:5]1=[O:9])(=[O:20])=[O:19]
Reactant: CS(=O)(=O)Cl
Reactant: O=C1CCCN1CCO
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CS(=O)(=O)OCCN1CCCC1=O

Procedure:
The 1-(2-hydroxyethyl)-2-pyrrolidinone (Aldrich, 0.16 g, 1.2 mmol), triethylamine (0.56 mL, 4.1 mmol), and methanesulfonyl chloride (0.15 mL, 1.9 mmol) in 10 mL THF were processed as described in Example 1C to give the title compound that was used directly in the next reaction.
Reaction SMILES: [Cl:1][C:2]1[N:3]=[N:4][C:5]([Cl:9])=[CH:6][C:7]=1Cl.[NH3:10].CO>>[Cl:1][C:2]1[N:3]=[N:4][C:5]([Cl:9])=[CH:6][C:7]=1[NH2:10]
Reactant: N
Reactant: Clc1cc(Cl)c(Cl)nn1
Solvent: CO
Product: Nc1cc(Cl)nnc1Cl
Temperature: 25 °C
Yield: 32 %

Procedure:
A MW vial was charged with 3,4,6-trichloropyridazine (5 g, 27.3 mmol) and 7N NH3 in MeOH (19.47 mL, 136 mmol). The MW vial was sealed and the resulting mixture was submitted to MW irradiation at 100° C. for 30 min. The reaction was cooled down to RT and concentrated under reduced pressure. The crude product was purified by silica gel column chromatography (hexane/EtOAc 35-60%) to afford the title product (1.49 g, 8.63 mmol, 32% yield) as yellow solid. tR: 1.61 min (HPLC 1); tR: 0.45 min (LC-MS 2); ESI-MS: 163 [M+H]+ (LC-MS 2); Rf=0.40 (hexane/EtOAc 1:1).
Reaction SMILES: [CH2:1]([O:4][C:5]1[CH:6]=[C:7]([OH:11])[CH:8]=[CH:9][CH:10]=1)[CH:2]=[CH2:3].C([O-])([O-])=O.[K+].[K+].F[C:19]1[CH:26]=[CH:25][C:22]([CH:23]=[O:24])=[CH:21][CH:20]=1>CN(C=O)C.C(OCC)(=O)C>[CH2:1]([O:4][C:5]1[CH:6]=[C:7]([CH:8]=[CH:9][CH:10]=1)[O:11][C:19]1[CH:26]=[CH:25][C:22]([CH:23]=[O:24])=[CH:21][CH:20]=1)[CH:2]=[CH2:3]
Reactant: O=Cc1ccc(F)cc1
Reactant: C=CCOc1cccc(O)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Product: C=CCOc1cccc(Oc2ccc(C=O)cc2)c1
Temperature: 100 °C
Reaction time: 8 h
Yield: 60 %

Procedure:
The crude product from Example 61B in anhydrous DMF (40 mL) was treated with K2CO3 (15.5 g, 112 mmoles) and 4-fluorobenzaldehyde (4.82 mL, 44.9 mmoles). The reaction mixture was stirred overnight at 100° C. After cooling to room temperature, the reaction mixture was diluted with ethyl acetate. The mixture was washed with H2O (2×), brine, dried (Na2SO4), filtered, and the filtrate concentrated under reduced pressure. The residue was purified by flash chromatography (silica gel, 8% ethyl acetate:hexanes) to provide the title compound (5.75 g, 60%).
Reaction SMILES: [C:1]([CH2:4][CH2:5][CH2:6][C:7]1[C:8](=[O:19])[C:9]2[C:14]([C:15](=[O:18])[C:16]=1[CH3:17])=[CH:13][CH:12]=[CH:11][CH:10]=2)([OH:3])=O.ON1C(=O)CCC1=O.CCN=C=NCCCN(C)C.[CH2:39]([NH2:42])[CH2:40][NH2:41]>ClC(Cl)C.ClCCl>[NH2:41][CH2:40][CH2:39][NH:42][C:1]([CH2:4][CH2:5][CH2:6][C:7]1[C:8](=[O:19])[C:9]2[C:14]([C:15](=[O:18])[C:16]=1[CH3:17])=[CH:13][CH:12]=[CH:11][CH:10]=2)=[O:3]
Reactant: CC1=C(CCCC(=O)O)C(=O)c2ccccc2C1=O
Reactant: NCCN
Agent: CCN=C=NCCCN(C)C
Agent: O=C1CCC(=O)N1O
Solvent: CC(Cl)Cl
Solvent: ClCCl
Product: CC1=C(CCCC(=O)NCCN)C(=O)c2ccccc2C1=O
Reaction time: 4 h
Yield: 58.7 %

Procedure:
2-(3-carboxypropyl)-3-methyl-1,4-naphthoquinone (1.00 g, 3.9 mmol) and N-hydroxysuccinimide (534 mg, 4.64 mmol) were dissolved in dichloroethane (80 ml). WSC (EDC) (890 mg, 4.64 mmol) was added to the mixture, and the mixture was stirred for 4 hours. 2.59 ml of ethylenediamine (2.33 g, 38.7 mmol) was dissolved in dichloromethane (10 ml), and the above reaction mixture was added thereto dropwise in 15 minutes. The mixture was stirred as it was at room temperature for 2 nights. Dichloromethane (300 ml) was added to the reaction mixture, and the reaction mixture was washed with water (500 ml×1). An organic layer was dried using sodium sulfate. A solvent was removed under reduced pressure, and the mixture was purified using a silica gel chromatography (silica gel: Fuji Silysia NH-DM1020; dichloromethane:methanol=96:4) and recrystallized (dichloromethane:hexane), to thereby obtain a yellow brown powder of 2-{3-[N-(2-aminoethyl)aminocarbonyl]propyl}-3-methyl-1,4-naphthoquinone (yield: 686 mg, 2.29 mmol, 58.9%).
Reaction SMILES: [N:1]1[CH:6]=[CH:5][CH:4]=[CH:3][C:2]=1[C:7]1[C:11]([C:12]([F:15])([F:14])[F:13])=[C:10]([C:16]2[O:20][N:19]=[C:18]3[C:21]4[C:26]([CH2:27][CH2:28][C:17]=23)=[CH:25][C:24]([CH:29]=C)=[CH:23][CH:22]=4)[O:9][N:8]=1.C[N+]1([O-])CC[O:35]CC1.I([O-])(=O)(=O)=O.[Na+].O>C(OCC)(=O)C.[Os](=O)(=O)(=O)=O>[N:1]1[CH:6]=[CH:5][CH:4]=[CH:3][C:2]=1[C:7]1[C:11]([C:12]([F:15])([F:14])[F:13])=[C:10]([C:16]2[O:20][N:19]=[C:18]3[C:21]4[C:26]([CH2:27][CH2:28][C:17]=23)=[CH:25][C:24]([CH:29]=[O:35])=[CH:23][CH:22]=4)[O:9][N:8]=1
Reactant: C=Cc1ccc2c(c1)CCc1c-2noc1-c1onc(-c2ccccn2)c1C(F)(F)F
Reactant: C[N+]1([O-])CCOCC1
Agent: O=[Os](=O)(=O)=O
Agent: [Na+]
Agent: [O-][I+3]([O-])([O-])[O-]
Solvent: CCOC(C)=O
Solvent: O
Product: O=Cc1ccc2c(c1)CCc1c-2noc1-c1onc(-c2ccccn2)c1C(F)(F)F
Temperature: 25 °C
Yield: 97.5 %

Procedure:
To a mixture of 3-(3-(pyridin-2-yl)-4-(trifluoromethyl)isoxazol-5-yl)-7-vinyl-4,5-dihydronaphtho[1,2-c]isoxazole (Preparation 63F, 0.098 g, 0.239 mmol) and a 50% aqueous solution of NMO (0.050 mL, 0.239 mmol) at room temperature was added a 4% aqueous solution of osmium tetroxide (0.075 mL, 9.58 μmol). The reaction mixture was stirred at room temperature over the weekend. The intermediate diol had an HPLC ret. time=2.66 min and an LCMS M+1=443.8. Sodium periodate (0.077 g, 0.359 mmol) was added to the homogeneous mixture followed by water (0.15 mL), and the reaction was stirred for 60 min. at room temperature. Concentration under reduced pressure afforded a tan solid residue that was then diluted with ethyl acetate (40 mL), washed with the water (10 mL), and washed with brine (10 mL). The organic layer was collected, and the aqueous layer was washed with ethyl acetate (40 mL). The combined organic layers were dried over anhydrous sodium sulfate. Concentration under reduced pressure afforded 3-(3-(pyridin-2-yl)-4-(trifluoromethyl)isoxazol-5-yl)-4,5-dihydronaphtho[1,2-c]isoxazole-7-carbaldehyde (0.096 g, 0.233 mmol, 97% yield) as a pale yellow solid. The product had an HPLC ret. time=3.00 min.−Column: Chromolith SpeedROD 4.6×50 mm (4 min.); Solvent A=10% MeOH, 90% H2O, 0.1% TFA; Solvent B=90% MeOH, 10% H2O, 0.1% TFA. LC/MS M+1=411.9.
Reaction SMILES: [OH:1][CH2:2][CH2:3][CH2:4][N:5]1[CH:9]=[C:8]([C:10]2[CH:11]=[CH:12][C:13]([NH:21][C:22]3[C:27]([C:28]([F:31])([F:30])[F:29])=[CH:26][N:25]=[C:24]([NH:32][C:33]4[CH:47]=[CH:46][C:36]([CH2:37][P:38](=[O:45])([O:42][CH2:43][CH3:44])[O:39][CH2:40][CH3:41])=[CH:35][C:34]=4[O:48][CH3:49])[N:23]=3)=[C:14]3[C:18]=2[CH2:17][N:16]([CH3:19])[C:15]3=[O:20])[CH:7]=[N:6]1.NC1C=C([F:71])C(C2C=NN(CCCO)C=2)=C2C=1C(=O)N(C)C2>>[F:71][C:11]1[C:10]([C:8]2[CH:7]=[N:6][N:5]([CH2:4][CH2:3][CH2:2][OH:1])[CH:9]=2)=[C:18]2[C:14]([C:15](=[O:20])[N:16]([CH3:19])[CH2:17]2)=[C:13]([NH:21][C:22]2[C:27]([C:28]([F:31])([F:30])[F:29])=[CH:26][N:25]=[C:24]([NH:32][C:33]3[CH:47]=[CH:46][C:36]([CH2:37][P:38](=[O:45])([O:42][CH2:43][CH3:44])[O:39][CH2:40][CH3:41])=[CH:35][C:34]=3[O:48][CH3:49])[N:23]=2)[CH:12]=1
Reactant: CCOP(=O)(Cc1ccc(Nc2ncc(C(F)(F)F)c(Nc3ccc(-c4cnn(CCCO)c4)c4c3C(=O)N(C)C4)n2)c(OC)c1)OCC
Reactant: CN1Cc2c(c(N)cc(F)c2-c2cnn(CCCO)c2)C1=O
Product: CCOP(=O)(Cc1ccc(Nc2ncc(C(F)(F)F)c(Nc3cc(F)c(-c4cnn(CCCO)c4)c4c3C(=O)N(C)C4)n2)c(OC)c1)OCC

Procedure:
This compound was prepared analogously to Compound 1B replacing Compound 1C with 7-amino-5-fluoro-4-[1-(3-hydroxypropyl)-1H-pyrazol-4-yl]-2-methyl-2,3-dihydro-1H-isoindol-1-one (Compound 31C). 1H NMR (CD3OD, 400 MHz): δ 8.39 (d, J=13.9 Hz, 1H), 8.30 (s, 1H), 8.00 (s, 1H), 7.85 (d, J=7.3 Hz, 1H), 7.82 (d, J=1.3 Hz, 1H), 7.05 (s, 1H), 6.95 (d, J=8.3 Hz, 1H), 4.51 (s, 2H), 4.33 (t, J=6.9 Hz, 2H), 4.08 (quin, J=7.3 Hz, 4H), 3.91 (s, 3H), 3.58 (t, J=6.1 Hz, 2H), 3.28 (d, J=21 Hz, 2H, obscured), 3.12 (s, 3H), 2.10 (quin, J=6.5 Hz, 2H), 1.28 (t, J=7.1 Hz, 6H). MS (ESI): m/z=722.23 [M+H]+. UPLC: tR=1.43 min (UPLC-TOF: polar—3 min).
Reaction SMILES: [NH2:1][C:2]1[N:3]([CH2:27][CH3:28])[C:4]2[C:9]([C:10](=[O:25])[C:11]=1[C:12]1[N:13]([CH2:17][O:18][CH2:19][CH2:20][Si:21]([CH3:24])([CH3:23])[CH3:22])[CH:14]=[CH:15][N:16]=1)=[CH:8][CH:7]=[C:6](Cl)[N:5]=2.[F:29][C:30]([F:42])([F:41])[C:31]([C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=1)([OH:34])[C:32]#[CH:33].CN(C=O)C>Cl[Pd](Cl)([P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1)[P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.[Cu]I.C(N(CC)CC)C>[NH2:1][C:2]1[N:3]([CH2:27][CH3:28])[C:4]2[C:9]([C:10](=[O:25])[C:11]=1[C:12]1[N:13]([CH2:17][O:18][CH2:19][CH2:20][Si:21]([CH3:24])([CH3:23])[CH3:22])[CH:14]=[CH:15][N:16]=1)=[CH:8][CH:7]=[C:6]([C:33]#[C:32][C:31]([OH:34])([C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=1)[C:30]([F:29])([F:41])[F:42])[N:5]=2
Reactant: CCn1c(N)c(-c2nccn2COCC[Si](C)(C)C)c(=O)c2ccc(Cl)nc21
Reactant: C#CC(O)(c1ccccc1)C(F)(F)F
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: CCn1c(N)c(-c2nccn2COCC[Si](C)(C)C)c(=O)c2ccc(C#CC(O)(c3ccccc3)C(F)(F)F)nc21
Yield: 27.1 %

Procedure:
Same procedure as that described in example 5, stage 5.4, starting from 0.4 g (0.95 mmol) of 2-amino-7-chloro-1-ethyl-3-[1-(2-trimethylsilanyl-ethoxymethyl)-1H-imidazol-2-yl]-1H-[1,8]naphthyridin-4-one, 0.4 g (1.9 mmol) 1,1,1-trifluoro-2-phenyl-but-3-yn-2-ol, 33 mg (0.05 mmol), bis(triphenylphosphine)palladium(II) dichloride, 18 mg (0.1 mmol) copper (I) iodide, 3 ml DMF (degassed), 3 ml triethylamine (degassed). 0.15 g of the title compound is obtained.
Reaction SMILES: [F:1][C:2]([F:31])([F:30])[O:3][C:4]1[CH:29]=[CH:28][C:7]([CH2:8][O:9][C:10]2[CH:15]=[CH:14][C:13]([N:16]3[C:20]4=[N:21][CH:22]=[C:23]([C:25]([OH:27])=O)[CH:24]=[C:19]4[N:18]=[CH:17]3)=[CH:12][CH:11]=2)=[CH:6][CH:5]=1.C1N=CN(C(N2C=NC=C2)=O)C=1.CCN(C(C)C)C(C)C.[N:53]1([CH2:59][CH2:60][NH2:61])[CH2:58][CH2:57][O:56][CH2:55][CH2:54]1>C1COCC1>[F:1][C:2]([F:31])([F:30])[O:3][C:4]1[CH:29]=[CH:28][C:7]([CH2:8][O:9][C:10]2[CH:15]=[CH:14][C:13]([N:16]3[C:20]4=[N:21][CH:22]=[C:23]([C:25]([NH:61][CH2:60][CH2:59][N:53]5[CH2:58][CH2:57][O:56][CH2:55][CH2:54]5)=[O:27])[CH:24]=[C:19]4[N:18]=[CH:17]3)=[CH:12][CH:11]=2)=[CH:6][CH:5]=1
Reactant: O=C(O)c1cnc2c(c1)ncn2-c1ccc(OCc2ccc(OC(F)(F)F)cc2)cc1
Reactant: NCCN1CCOCC1
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: C1CCOC1
Solvent: CCN(C(C)C)C(C)C
Product: O=C(NCCN1CCOCC1)c1cnc2c(c1)ncn2-c1ccc(OCc2ccc(OC(F)(F)F)cc2)cc1
Temperature: 60 °C
Reaction time: 2 h

Procedure:
A mixture of 3-{4-[(4-(trifluoromethoxy)benzyl)oxy]phenyl}-3H-imidazo[4,5-b]pyridine-6-carboxylic acid (42 mg, 0.1 mmol), CDI (32.4 mg, 0.2 mmol) and DIPEA (87 μL, 0.5 mmol) in dry THF (2 mL) was stirred at 60° C. for 2 h and then treated with 2-(morpholin-4-yl)ethylamine (26 μL, 0.2 mmol). After a further 2 h at 60° C. the mixture was concentrated in vacuo and the residue chromatographed over silica gel eluting with 5% MeOH/CHCl3 to give 3-{4-[(4-(trifluoromethoxy)benzyl)oxy]phenyl}-N-(2-morpholin-4-ylethyl)-3H-imidazo[4,5-b]pyridine-6-carboxamide. 1H NMR (400 MHz, D4-MeOH) δ 2.57 (br.s, 4H), 2.65 (t, J=8 Hz, 2H), 3.60 (t, J=8 Hz, 2H), 3.71 (t, J=8 Hz, 4H), 5.21 (s, 2H), 7.22 (dd, J=6.8 and 2 Hz, 2H), 7.30 (d, J=8.4 Hz, 2H), 7.59 (d, J=8.8 Hz, 2H), 7.71 (dd, J=6.8 and 2 Hz, 2H), 8.57 (d, J=1.6 Hz, 1H), 8.71 (s, 1H) and 8.90 (d, J=1.6 Hz, 1H); MS (ES+): m/z 542 [MH+].
Reaction SMILES: [Cl:1][C:2]1[CH:8]=[CH:7][C:5]([NH2:6])=[CH:4][CH:3]=1.C([O:11][CH:12]=[C:13]([C:19]([O-])=O)[C:14]([O:16][CH2:17][CH3:18])=[O:15])C.Cl.[OH-].[Na+]>C(OCC)(=O)C.O>[CH2:17]([O:16][C:14]([C:13]1[C:12](=[O:11])[C:7]2[C:5](=[CH:4][CH:3]=[C:2]([Cl:1])[CH:8]=2)[NH:6][CH:19]=1)=[O:15])[CH3:18]
Reactant: CCOC=C(C(=O)[O-])C(=O)OCC
Reactant: Nc1ccc(Cl)cc1
Agent: Cl
Agent: [Na+]
Agent: [OH-]
Solvent: CCOC(C)=O
Solvent: O
Product: CCOC(=O)c1c[nH]c2ccc(Cl)cc2c1=O
Temperature: 25 °C
Yield: 71 %

Procedure:
A mixture of 4-chloroaniline (156.7 mmol) and ethyl ethoxymethylenemalonate (156.7 mmol) was stirred at room temperature until homogeneous. The homogeneous solution was heated in an oil bath at 165° C. for 6 hours. The reaction mixture was cooled to room temperature and 1 N HCl (3 mL) was added. The reaction mixture was stirred and heated to 115° C. for 3 hours. The mixture was cooled to room temperature and then treated with 20 mL of water. The resulting suspension treated with 10 N NaOH solutions to reach the pH about 8. It was partitioned between ethyl acetate and water. The organic layer was separated and the aqueous layer was extracted with ethyl acetate. The combined organic extracts were washed with brine, dried over MgSO4, filtered and concentrated. The crude product was purified by flash column chromatography using a 9:1 v/v hexane: ethyl acetate as solvent to afford title compound (28 g, 71% yield) as a yellow solid.
Reaction SMILES: Cl.[NH2:2][C:3]1[CH:4]=[C:5]([C:9]2[CH:17]=[CH:16][CH:15]=[C:14]3[C:10]=2/[C:11](=[CH:19]/[C:20]2[NH:21][CH:22]=[CH:23][CH:24]=2)/[C:12](=[O:18])[NH:13]3)[CH:6]=[CH:7][CH:8]=1.CCN(CC)CC.[Br:32][C:33]1[CH:34]=[C:35]([CH:39]=[CH:40][CH:41]=1)[C:36](Cl)=[O:37]>C(Cl)(Cl)Cl>[O:18]=[C:12]1[NH:13][C:14]2[C:10](/[C:11]/1=[CH:19]/[C:20]1[NH:21][CH:22]=[CH:23][CH:24]=1)=[C:9]([C:5]1[CH:4]=[C:3]([NH:2][C:36](=[O:37])[C:35]3[CH:39]=[CH:40][CH:41]=[C:33]([Br:32])[CH:34]=3)[CH:8]=[CH:7][CH:6]=1)[CH:17]=[CH:16][CH:15]=2
Reactant: O=C(Cl)c1cccc(Br)c1
Reactant: Nc1cccc(-c2cccc3c2/C(=C/c2ccc[nH]2)C(=O)N3)c1
Agent: Cl
Solvent: ClC(Cl)Cl
Solvent: CCN(CC)CC
Product: O=C1Nc2cccc(-c3cccc(NC(=O)c4cccc(Br)c4)c3)c2/C1=C/c1ccc[nH]1
Temperature: -70 °C
Reaction time: 1 h
Yield: 97.7 %

Procedure:
A solution of (Z)-4-(3-aminophenyl)-1,3-dihydro-3-[(1H-pyrrol-2-yl)methylene]-2H-indol-2-one hydrochloride (50 mg, 0.148 mmol) (from Example 5 supra) and Et3N (41 μL , 0.296 mmol) in 3 mL of chloroform was cooled to −70° C. and then treated with 3-bromobenzoyl chloride (21 μL , 0.155 mmol) (Aldrich). The reaction mixture was stirred at −70° C. for 1 hr and then stirred at room temperature for 15 h. The reaction mixture was then concentrated in vacuo. The resulting yellow solid was suspended in water and collected by suction filtration to provide pure (Z)-N-[3-[2,3-dihydro-2-oxo-3-[(1H-pyrrol-2-yl)methylene]-1H-indol-4-yl]-phenyl]-3-bromobenzamide (yield: 70 mg, 98%) as a yellow solid (mp 251-253° C.).
Reaction SMILES: [NH:1]1[CH:5]=[C:4]([C:6]([NH2:8])=[O:7])[N:3]=[CH:2]1.[H-].[Na+].[CH2:11]([O:18][C@@H:19]([CH3:36])[C@@H:20](OS(C)(=O)=O)[CH2:21][CH2:22][C:23]1[CH:28]=[CH:27][CH:26]=[CH:25][C:24]=1[S:29][CH3:30])[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1.O>CN(C=O)C>[CH2:11]([O:18][C@H:19]([C@H:20]([N:1]1[CH:5]=[C:4]([C:6]([NH2:8])=[O:7])[N:3]=[CH:2]1)[CH2:21][CH2:22][C:23]1[CH:28]=[CH:27][CH:26]=[CH:25][C:24]=1[S:29][CH3:30])[CH3:36])[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1
Reactant: NC(=O)c1c[nH]cn1
Reactant: CSc1ccccc1CC[C@H](OS(C)(=O)=O)[C@H](C)OCc1ccccc1
Agent: [H-]
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: CSc1ccccc1CC[C@H]([C@H](C)OCc1ccccc1)n1cnc(C(N)=O)c1
Temperature: 25 °C
Reaction time: 0.33 h
Yield: 10.1 %

Procedure:
A suspension of imidazole-4-carboxamide (313 mg) in DMF (3.8 ml) was treated with sodium hydride (60% in mineral oil, 129 mg) at ice-bath temperature and the mixture was stirred at room temperature for 20 min. A solution of 2-[(3S,4S)-4-benzyloxy-3-methanesulfonyloxypentyl]thioanisole (0.92 g) in DMF (7.5 ml) was added and the mixture was stirred at 85° C. for 3 days. The mixture was poured into water and extracted with ethyl acetate. The extract was washed with water, dried and concentrated in vacuo. Column chromatography (dichloromethane:methanol=30:1) gave 1-[(2S,3R)-2-benzyloxy-5-(2-(methylthio)phenyl)-3-pentyl]imidazole-4-carboxamide (1) (96.4 mg, 11.6%) as a pale yellow oil.
Reaction SMILES: [F:1][C:2]1[CH:10]=[CH:9][C:5]([C:6]([OH:8])=O)=[CH:4][CH:3]=1.O.ON1C2C=CC=CC=2N=N1.[F:22][C:23]([F:40])([F:39])[C:24]1[N:29]=[C:28]([N:30]2[CH2:34][C@@H:33]3[C@@H:35]([NH2:38])[CH2:36][CH2:37][C@@H:32]3[CH2:31]2)[CH:27]=[CH:26][CH:25]=1.C(N=C=NCCCN(C)C)C>ClCCl>[F:1][C:2]1[CH:3]=[CH:4][C:5]([C:6]([NH:38][C@@H:35]2[C@@H:33]3[C@@H:32]([CH2:31][N:30]([C:28]4[CH:27]=[CH:26][CH:25]=[C:24]([C:23]([F:40])([F:39])[F:22])[N:29]=4)[CH2:34]3)[CH2:37][CH2:36]2)=[O:8])=[CH:9][CH:10]=1
Reactant: O=C(O)c1ccc(F)cc1
Reactant: N[C@H]1CC[C@@H]2CN(c3cccc(C(F)(F)F)n3)C[C@@H]21
Agent: CCN=C=NCCCN(C)C
Agent: On1nnc2ccccc21
Solvent: O
Solvent: ClCCl
Product: O=C(N[C@H]1CC[C@@H]2CN(c3cccc(C(F)(F)F)n3)C[C@@H]21)c1ccc(F)cc1
Temperature: 25 °C
Reaction time: 0.33 h

Procedure:
p-Fluorobenzoic acid (56.8 mg, 0.405 mmol), 1-hydroxybenzotriazole hydrate (62.1 mg, 0.405 mmol 1), and (3aR,4S,6aS)-2-(6-(trifluoromethyl)pyridin-2-yl)octahydrocyclopenta[c]pyrrol-4-amine from Example 264 Step A (100 mg, 0.369 mmol) were combined in dichloromethane (1.2 mL) to give a colorless solution. After 20 minutes, N1-((ethylimino)methylene)-N3,N3-dimethylpropane-1,3-diamine (0.072 mL, 0.405 mmol) was added and the reaction mixture was stirred at room temperature overnight. The reaction mixture was quenched with water and extracted with 2×2 mL of dichloromethane. The combined extracts were applied directly to a 12 g silica gel cartridge and purified with a gradient of 1-10% methanol in (2 N ammonia)/dichloromethane over 20 minutes to give the title compound: 1H NMR (500 MHz, pyridine-d5) δ ppm 8.90 (d, J=6.9, 1H), 8.29-8.19 (m, 2H), 7.56-7.47 (m, 1H), 7.17 (ddd, J=9.7, 5.9, 2.5, 2H), 6.99 (d, J=7.2, 1H), 6.53 (d, J=8.6, 1H), 4.64-4.52 (m, 1H), 3.80 (dd, J=11.0, 3.7, 1H), 3.63 (dd, J=10.9, 8.2, 1H), 3.51 (dd, J=10.8, 8.4, 1H), 3.30 (dd, J=10.9, 4.6, 1H), 2.90-2.77 (m, 1H), 2.77-2.64 (m, 1H), 2.23 (ddd, J=19.5, 7.1, 4.7, 1H), 1.93 (dtd, J=12.7, 8.0, 4.6, 1H), 1.81 (ddd, J=16.4, 12.7, 8.1, 1H), 1.40 (dt, J=13.2, 7.6, 1H); MS (ESI+) m/z 394 (M+H)+.
Reaction SMILES: [Cl:1][C:2]1[N:6]([C:7]2[CH:14]=[CH:13][CH:12]=[CH:11][C:8]=2[CH:9]=O)[C:5](=[O:15])[N:4]([CH3:16])[N:3]=1.[F:17][C:18]([F:29])([F:28])[C:19]1[C:20]([N:25]([CH3:27])[NH2:26])=[N:21][CH:22]=[CH:23][CH:24]=1>C(O)C.C(O)(=O)C.C(=O)(O)[O-].[Na+]>[Cl:1][C:2]1[N:6]([C:7]2[CH:14]=[CH:13][CH:12]=[CH:11][C:8]=2[CH:9]=[N:26][N:25]([CH3:27])[C:20]2[C:19]([C:18]([F:29])([F:28])[F:17])=[CH:24][CH:23]=[CH:22][N:21]=2)[C:5](=[O:15])[N:4]([CH3:16])[N:3]=1
Reactant: Cn1nc(Cl)n(-c2ccccc2C=O)c1=O
Reactant: CN(N)c1ncccc1C(F)(F)F
Agent: O=C([O-])O
Agent: [Na+]
Solvent: CC(=O)O
Solvent: CCO
Product: CN(N=Cc1ccccc1-n1c(Cl)nn(C)c1=O)c1ncccc1C(F)(F)F
Temperature: 50 °C

Procedure:
The title compound of Step A (0.20 g, 0.80 mmol) was dissolved in absolute ethanol (7 mL) and a solution of 1-[3-(trifluoromethyl)pyridin-2-yl]-1-methylhydrazine in ethanol (3 mL) was added followed by 3 drops of glacial acetic acid. The mixture was warmed to 50° C. for 1 h, cooled to room temperature and then diluted with aqueous sodium bicarbonate and extracted three times with ethyl acetate. The combined organic phases were dried (MgSO4), filtered and concentrated to give 0.38 g of the title compound of Step B as a yellow solid. 1H NMR (300 MHz. CDCl3): δ 8.42 (d.1H. J=5 Hz), 8.16 (d,1H, J=8 Hz), 8.01 (d,1H, J=8 Hz), 7.51 (t,1H, J=8 Hz), 7.42 (t,1H), J=8 Hz), 7.35 (s,1H), 7.21 (d,1H, J=8 Hz), 7.03 (dd,1H, J=8, 5 Hz), 3.56 (s,6H).
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][C:5]([Br:8])=[CH:4][C:3]=1[CH3:9].C1C(=O)N([Br:17])C(=O)C1>C(Cl)(Cl)(Cl)Cl.C(OOCC1C=CC=CC=1)C1C=CC=CC=1>[Br:1][C:2]1[CH:7]=[CH:6][C:5]([Br:8])=[CH:4][C:3]=1[CH2:9][Br:17]
Reactant: Cc1cc(Br)ccc1Br
Reactant: O=C1CCC(=O)N1Br
Agent: c1ccc(COOCc2ccccc2)cc1
Solvent: ClC(Cl)(Cl)Cl
Product: BrCc1cc(Br)ccc1Br
Reaction time: 24 h
Yield: 55.2 %

Procedure:
To a solution of 75 g (0.3 mol) of 2,5-dibromotoluene in 1 L of carbon tetrachloride was added 58.73 g (0.33 mol) of NBS and 50 mg of benzyl peroxide, and the resulting mixture was refluxed with stirring for 24 h. The mixture was cooled, and concentrated in vacuo. The residue was crystallized from hot methanol and washed with hexane to afford 54.5 g (55.7%) of 2,5-dibromobenzyl bromide as a solid.