Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [Br:1][C:2]1[CH:7]=[C:6]([CH:8]=[O:9])[CH:5]=[CH:4][N:3]=1.[CH3:10][Mg]Cl>C1COCC1>[Br:1][C:2]1[CH:7]=[C:6]([CH:8]([OH:9])[CH3:10])[CH:5]=[CH:4][N:3]=1
Reactant: O=Cc1ccnc(Br)c1
Reactant: C[Mg]Cl
Solvent: C1CCOC1
Product: CC(O)c1ccnc(Br)c1
Temperature: 25 °C
Reaction time: 1 h

Procedure:
To a chilled (−78° C.) solution of 2-bromo-pyridine-4-carbaldehyde (10.0 g, 53.8 mmol) in THF (100 mL) was added a 3 M solution of methylmagnesium chloride in THF (18 mL, 54 mmol) over a 10 minute period. After 1 hour, the yellow solution was allowed to warm gradually to room temperature over a 3 hour period. The reaction was quenched by the slow addition of saturated aqueous NH4Cl (50 mL) and extracted with EtOAc (2×200 mL). The combined organic layers were washed with brine, dried over sodium sulfate, and concentrated to afford a brown oil. The crude material was purified by silica gel chromatography eluting with a gradient of 10-45% EtOAc in hexanes to afford 1-(2-bromo-pyridin-4-yl)-ethanol.
Reaction SMILES: [CH3:1][N:2]1[CH2:6][CH2:5][CH2:4][C@H:3]1[C:7]1[N:11]2[CH:12]=[C:13]([O:16][C@H:17]3[C:26]4[C:21](=[CH:22][CH:23]=[CH:24][CH:25]=4)[C@@H:20]([NH2:27])[CH2:19][CH2:18]3)[CH:14]=[CH:15][C:10]2=[N:9][N:8]=1.ClC(Cl)(Cl)C[O:31][C:32](=O)[NH:33][C:34]1[N:35]([C:43]2[CH:48]=[CH:47][CH:46]=[C:45]([O:49][CH2:50][CH2:51][O:52]C3CCCCO3)[CH:44]=2)[N:36]=[C:37]([C:39]([CH3:42])([CH3:41])[CH3:40])[CH:38]=1.CCN(C(C)C)C(C)C>O1CCOCC1>[C:39]([C:37]1[CH:38]=[C:34]([NH:33][C:32]([NH:27][C@@H:20]2[C:21]3[C:26](=[CH:25][CH:24]=[CH:23][CH:22]=3)[C@H:17]([O:16][C:13]3[CH:14]=[CH:15][C:10]4[N:11]([C:7]([C@@H:3]5[CH2:4][CH2:5][CH2:6][N:2]5[CH3:1])=[N:8][N:9]=4)[CH:12]=3)[CH2:18][CH2:19]2)=[O:31])[N:35]([C:43]2[CH:48]=[CH:47][CH:46]=[C:45]([O:49][CH2:50][CH2:51][OH:52])[CH:44]=2)[N:36]=1)([CH3:42])([CH3:40])[CH3:41]
Reactant: CN1CCC[C@H]1c1nnc2ccc(O[C@@H]3CC[C@H](N)c4ccccc43)cn12
Reactant: CC(C)(C)c1cc(NC(=O)OCC(Cl)(Cl)Cl)n(-c2cccc(OCCOC3CCCCO3)c2)n1
Solvent: CCN(C(C)C)C(C)C
Solvent: C1COCCO1
Product: CN1CCC[C@H]1c1nnc2ccc(O[C@@H]3CC[C@H](NC(=O)Nc4cc(C(C)(C)C)nn4-c4cccc(OCCO)c4)c4ccccc43)cn12
Temperature: 90 °C
Reaction time: 4.5 h
Yield: 85.9 %

Procedure:
A mixture of Intermediate 5c (150 mg, 0.410 mmol) and Intermediate 39b (230 mg, 0.430 mmol) in 1,4-dioxane (4 mL) and DIPEA (113 μL, 0.65 mmol) was stirred at 90° C. for 4.5 h. The mixture was concentrated in vacuo. The residue was purified by FCC twice, using 0-10% MeOH in DCM, to give the title compound as a pale yellow foam (234 mg, 76%). LCMS (Method 3): Rt 3.03 min, m/z 749.2 [MH+].
Reaction SMILES: Br[C:2]1[CH:7]=[C:6]([CH3:8])[CH:5]=[C:4]([F:9])[C:3]=1[NH:10][C:11]([NH:13][CH:14]1[CH2:19][CH2:18][N:17]([C:20]([O:22][C:23]([CH3:26])([CH3:25])[CH3:24])=[O:21])[CH2:16][CH2:15]1)=[O:12]>O1CCOCC1.C(OCC)(=O)C.C1(P(C2C=CC=CC=2)[C-]2C=CC=C2)C=CC=CC=1.[C-]1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=C1.[Fe+2]>[F:9][C:4]1[C:3]2[NH:10][C:11](=[O:12])[N:13]([CH:14]3[CH2:19][CH2:18][N:17]([C:20]([O:22][C:23]([CH3:26])([CH3:25])[CH3:24])=[O:21])[CH2:16][CH2:15]3)[C:2]=2[CH:7]=[C:6]([CH3:8])[CH:5]=1
Reactant: Cc1cc(F)c(NC(=O)NC2CCN(C(=O)OC(C)(C)C)CC2)c(Br)c1
Agent: [Fe+2]
Agent: c1ccc(P(c2ccccc2)[c-]2cccc2)cc1
Solvent: C1COCCO1
Solvent: CCOC(C)=O
Product: Cc1cc(F)c2[nH]c(=O)n(C3CCN(C(=O)OC(C)(C)C)CC3)c2c1
Temperature: 25 °C
Reaction time: 0.25 h

Procedure:
Under an argon atmosphere, bis(3,5,3′,5′-dimethoxy-dibenzylideneacetone) palladium (0) (6% mol, 1.1 mmol, 0.9 g), 1,1′-bis(diphenylphosphino)ferrocene (6% mol, 0.61 g), NatBuO (2 eq., 36 mmol, ˜3.5 g), were all dissolved in 1,4-dioxane (40 ml) and the system was purged through with argon. The mixture was stirred at room temperature for 15 minutes and 1,1-dimethylethyl 4-({[(2-bromo-6-fluoro-4-methylphenyl)amino]-carbonyl}amino)-1-piperidinecarboxylate (D32) (7.7 g, 17.9 mmol) was added at room temperature and the mixture was heated to 80° C. for 1.5 hours and then to 100° C. for extra 2 hours; the mixture was then cooled to room temperature, diluted with ethyl acetate and the organic phase obtained was washed with water and brine. Organics were dried over Na2SO4, filtered and the solvent was evaporated to afford the crude product that was purified by chromatography (ethyl acetate-n-hexane) to afford the title compound, 4.3 g, 70%, pale-grey solid, M+−H=348.
Reaction SMILES: [OH:1][C:2]1[C:3]([N+:11]([O-:13])=[O:12])=[C:4]([CH:8]=[CH:9][CH:10]=1)[C:5]([OH:7])=O.[CH3:14][O:15][C:16]1[CH:22]=[CH:21][C:19]([NH2:20])=[CH:18][CH:17]=1.Cl.C(N=C=NCCCN(C)C)C.ON1C2C=CC=CC=2N=N1>CN(C)C=O.C(N(CC)CC)C>[OH:1][C:2]1[C:3]([N+:11]([O-:13])=[O:12])=[C:4]([CH:8]=[CH:9][CH:10]=1)[C:5]([NH:20][C:19]1[CH:21]=[CH:22][C:16]([O:15][CH3:14])=[CH:17][CH:18]=1)=[O:7]
Reactant: O=C(O)c1cccc(O)c1[N+](=O)[O-]
Reactant: COc1ccc(N)cc1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Product: COc1ccc(NC(=O)c2cccc(O)c2[N+](=O)[O-])cc1
Temperature: 25 °C
Reaction time: 66 h
Yield: 70.9 %

Procedure:
3-Hydroxy-2-nitrobenzoic acid (1.83 g) was dissolved in 50 ml of N,N-dimethylformamide, then 1.23 g of 4-methoxyaniline, 2.50 g of 1-ethyl-3-dimethylaminopropylcarbodiimide hydrochloride, 1.35 g of 1-hydroxybenzotriazole and 1.81 ml of triethylamine were added and the mixture was stirred at room temperature for 66 hours. The reaction solution was concentrated in vacuo, water was added and the mixture was extracted with ethyl acetate. The organic layer was washed with a saturated aqueous solution of sodium chloride, dried over magnesium sulfate and concentrated in vacuo. Chloroform was added to the resulting residue and the resulting precipitate was filtered to give 2.04 g of 3-hydroxy-4′-methoxy-2-nitrobenzanilide. The filtrate was purified by silica gel column chromatography using chloroform-methanol (98:2) as an eluting solvent, chloroform was added to the resulting crude product and the resulting precipitate was filtered to give additional 0.24 g of 3-hydroxy-4′-methoxy-2-nitrobenzanilide.
Reaction SMILES: [Br:1][C:2]1[CH:3]=[C:4]([CH:7]=O)[S:5][CH:6]=1.[Cl:9][C:10]1[C:15]([Cl:16])=[CH:14][C:13]([NH2:17])=[C:12]([NH2:18])[CH:11]=1>>[Br:1][C:2]1[CH:3]=[C:4]([C:7]2[NH:18][C:12]3[CH:11]=[C:10]([Cl:9])[C:15]([Cl:16])=[CH:14][C:13]=3[N:17]=2)[S:5][CH:6]=1
Reactant: O=Cc1cc(Br)cs1
Reactant: Nc1cc(Cl)c(Cl)cc1N
Product: Clc1cc2nc(-c3cc(Br)cs3)[nH]c2cc1Cl

Procedure:
2-(4-Bromothiophen-2-yl)-5,6-dichlorobenzimidazole was prepared from 4-bromo-2-thiophenecarboxaldehyde and 4,5-dichloro-1,2-phenylenediamine by following General Procedure 2.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[F:8].[CH2:9]([OH:14])[CH2:10][CH2:11][C:12]#[CH:13]>C(#N)C.[Cu]I.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>[F:8][C:3]1[CH:4]=[CH:5][CH:6]=[CH:7][C:2]=1[C:13]#[C:12][CH2:11][CH2:10][CH2:9][OH:14]
Reactant: Fc1ccccc1Br
Reactant: C#CCCCO
Agent: [Cu]I
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Solvent: CC#N
Product: OCCCC#Cc1ccccc1F

Procedure:
1-Bromo-2-fluorobenzene [1072-85-1] (3.0 g, 17 mmol, 1.0 equiv) and pent-4-yn-1-ol [5390-04-5] (2.3 mL, 25 mmol, 1.5 equiv) were dissolved in acetonitrile (40 mL). CuI (0.13 g, 0.68 mmol, 0.04 equiv) and TEA (3.4 mL, 25 mmol, 1.5 equiv) was added to the stirred solution followed by tetrakis(triphenylphosphine)palladium(0) (0.39 g, 0.34 mmol, 0.02 equiv). The solution was heated at reflux for 16 hours. The solution was cooled, filtered through Celite, the Celite pad rinsed with EtOAc and the solvent removed by rotoevaporation. Column chromatography (9:1 hexanes:ethyl acetate) of the residue afforded pure 5-(2-fluorophenyl)pent-4-yn-1-ol Intermediate 60 (1.3 g, 43%).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH2:20][C:21]([OH:23])=O)[CH:6]=[CH:7][C:8]=1[NH:9][C:10]([NH:12][C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=1[CH3:19])=[O:11].[CH3:24][O:25][C@@H:26]1[CH2:30][NH:29][C@H:28]([CH2:31][O:32][C:33]2[CH:42]=[CH:41][C:36]([C:37]([O:39][CH3:40])=[O:38])=[CH:35][CH:34]=2)[CH2:27]1.CCN=C=NCCCN(C)C.Cl.C1C=CC2N(O)N=NC=2C=1.CCN(CC)CC>CN(C=O)C>[CH3:24][O:25][C@@H:26]1[CH2:30][N:29]([C:21](=[O:23])[CH2:20][C:5]2[CH:6]=[CH:7][C:8]([NH:9][C:10]([NH:12][C:13]3[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=3[CH3:19])=[O:11])=[C:3]([O:2][CH3:1])[CH:4]=2)[C@H:28]([CH2:31][O:32][C:33]2[CH:42]=[CH:41][C:36]([C:37]([O:39][CH3:40])=[O:38])=[CH:35][CH:34]=2)[CH2:27]1
Reactant: COc1cc(CC(=O)O)ccc1NC(=O)Nc1ccccc1C
Reactant: COC(=O)c1ccc(OC[C@@H]2C[C@H](OC)CN2)cc1
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Product: COC(=O)c1ccc(OC[C@@H]2C[C@H](OC)CN2C(=O)Cc2ccc(NC(=O)Nc3ccccc3C)c(OC)c2)cc1
Temperature: 25 °C
Reaction time: 13 h
Yield: 97.3 %

Procedure:
A mixture of 3-methoxy-4-[N′-(2-methylphenyl)ureido]phenylacetic acid (375 mg, 1.19 mmol), methyl 4-[(2S,4S)-4-methoxy-2-pyrrolidinyl]methoxybenzoate (317 mg, 1.19 mmol), EDC.HCl (342 mg, 1.79 mmol), HOBT (242 mg, 1.79 mmol) and Et3N (0.83 ml, 5.95 mmol) in DMF (5 ml) was stirred at room temperature for 13 h. The mixture was poured into ice water and extracted with EtOAc. The combined extracts were washed with ice water and brine. After dried over Na2SO4, the extracts were concentrated in vacuo. The residue was chromatographed on silica gel [50 g, CHCl3/Aectone (10/1)CHCl3/MeOH (20/1)], to give methyl 4-[(2S,4S)-4-methoxy-1-[3-methoxy-4-[N′-(2-methylphenyl)ureido]phenylacetyl]-2-pyrrolidinyl]methoxybenzoate (650 mg, 98%) as a pale brown amorphous solid 1H-NMR (CDCl3) δ2.03 (m, 1H), 2.31 (s, 3H), 2.32 (m, 1H), 3.29 (d, J=1.0 Hz, 3H), 3.57-3.68 (m, 5H), 3.88 (d, J=1.0 Hz, 3H), 3.99-4.06 (m, 2H), 4.46 (m, 1H), 6.19 (m, 1H), 6.80 (s, 1H), 6.81 (d, J=9.0 Hz, 1H), 6.96-7.19 (m, 4H), 7.29 (m, 2H), 7.50 (d, J=6.7 Hz, 1H), 7.95-8.10 (m, 3H); MS (ESI) m/z 562 (M++1).
Reaction SMILES: [C:1]([C@H:5]1[CH2:10][CH2:9][C@H:8]([O:11][C:12]2[CH:13]=[C:14]3[C:19](=[CH:20][CH:21]=2)[CH:18]=[C:17]([CH:22]([N:24]2[CH2:29][CH2:28][CH:27]([C:30]([O:32]CC)=[O:31])[CH2:26][CH2:25]2)[CH3:23])[CH:16]=[CH:15]3)[CH2:7][CH2:6]1)([CH3:4])([CH3:3])[CH3:2].[OH-].[Na+]>CCO.O>[C:1]([C@H:5]1[CH2:10][CH2:9][C@H:8]([O:11][C:12]2[CH:13]=[C:14]3[C:19](=[CH:20][CH:21]=2)[CH:18]=[C:17]([CH:22]([N:24]2[CH2:25][CH2:26][CH:27]([C:30]([OH:32])=[O:31])[CH2:28][CH2:29]2)[CH3:23])[CH:16]=[CH:15]3)[CH2:7][CH2:6]1)([CH3:2])([CH3:3])[CH3:4]
Reactant: CCOC(=O)C1CCN(C(C)c2ccc3cc(O[C@H]4CC[C@H](C(C)(C)C)CC4)ccc3c2)CC1
Agent: [Na+]
Agent: [OH-]
Solvent: O
Solvent: CCO
Product: CC(c1ccc2cc(O[C@H]3CC[C@H](C(C)(C)C)CC3)ccc2c1)N1CCC(C(=O)O)CC1
Temperature: 85 °C
Reaction time: 2 h

Procedure:
Ethyl 1-(1-(6-((trans-4-(tert-butyl)cyclohexyl)oxy)naphthalen-2-yl)ethyl)piperidine-4-carboxylate (100 mg, 0.22 mmol) was dissolved in EtOH (5 mL). Then sodium hydroxide (44 mg, 1.1 mmol, 5.0 eq) in water (0.5 mL) was added. The mixture was stirred at 85° C. for 2 h. Solvent was removed and the residue was dissolved in H2O (3 mL). 1M aqueous HCl was added to adjust pH=7. The mixture was filtrated to give 1-(1-(6-((trans-4-(tert-butyl)cyclohexyl)oxy)naphthalen-2-yl)ethyl)piperidine-4-carboxylic acid as white solid (50 mg, 50%). ESI-MS (M+H+): 438.3. HPLC: 100%. 1H NMR (400 MHz, CD3OD) δ: 7.80-7.78 (m, 2H), 7.34 (d, J=8.8 Hz, 1H), 7.42 (dd, J=8.4, 1.6 Hz, 1H), 7.22 (d, J=2.0 Hz, 1H), 7.11 (dd, J=8.8, 2.0 Hz, 1H), 4.37-4.28 (m, 2H), 3.24-3.17 (m, 2H), 2.82-2.76 (m, 2H), 2.23-2.19 (m, 3H), 1.97-1.84 (m, 5H), 1.71 (d, J=6.8 Hz, 3H), 1.41-1.32 (m, 2H), 1.26-1.16 (m, 3H), 1.10-1.04 (m, 1H), 0.86 (s, 9H).
Reaction SMILES: [CH3:1][C:2]1[N:3]=[C:4]([NH:19][C:20](=[O:22])[CH3:21])[S:5][C:6]=1[C:7]1[CH:12]=[CH:11][N:10]=[C:9](N2CCOCC2)[N:8]=1.Cl.C(N)(=N)[C:25]1[CH:30]=[CH:29][CH:28]=[N:27][CH:26]=1>>[CH3:1][C:2]1[N:3]=[C:4]([NH:19][C:20](=[O:22])[CH3:21])[S:5][C:6]=1[C:7]1[CH:12]=[CH:11][N:10]=[C:9]([C:25]2[CH:26]=[N:27][CH:28]=[CH:29][CH:30]=2)[N:8]=1
Reactant: N=C(N)c1cccnc1
Reactant: CC(=O)Nc1nc(C)c(-c2ccnc(N3CCOCC3)n2)s1
Agent: Cl
Product: CC(=O)Nc1nc(C)c(-c2ccnc(-c3cccnc3)n2)s1

Procedure:
The titled compound is prepared by an analogous procedure to N-[4-Methyl-5-(2-morpholin-4-yl-pyrimidin-4-yl)-thiazol-2-yl]-acetamide (25e) by replacing morpholinoformamidine hydrobromide (part 25c) with nicotinamidine hydrochloride.
Reaction SMILES: [CH3:1][C:2]1([C:7]2[N:12]=[N:11][C:10]([CH2:13][CH2:14][CH2:15][O:16][C:17]3[C:22]([CH3:23])=[CH:21][C:20]([N:24]4[CH2:28][N:27]=[C:26]([C:29]([F:32])([F:31])[F:30])[O:25]4)=[CH:19][C:18]=3[CH3:33])=[CH:9][CH:8]=2)OCC[O:3]1.C(O)(=O)C.C(=O)(O)[O-].[Na+]>O>[C:2]([C:7]1[N:12]=[N:11][C:10]([CH2:13][CH2:14][CH2:15][O:16][C:17]2[C:22]([CH3:23])=[CH:21][C:20]([N:24]3[CH2:28][N:27]=[C:26]([C:29]([F:32])([F:31])[F:30])[O:25]3)=[CH:19][C:18]=2[CH3:33])=[CH:9][CH:8]=1)(=[O:3])[CH3:1]
Reactant: Cc1cc(N2CN=C(C(F)(F)F)O2)cc(C)c1OCCCc1ccc(C2(C)OCCO2)nn1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: CC(=O)O
Solvent: O
Product: CC(=O)c1ccc(CCCOc2c(C)cc(N3CN=C(C(F)(F)F)O3)cc2C)nn1
Yield: 65.8 %

Procedure:
A mixture of 0.5 g (1.08 mmol) of 6-(2-methyl-1,3-dioxolan-2-yl)-3-[3-[2,6-dimethyl-4-(5-trifluoromethyl-1,2,4-oxadiazol-2-yl)-phenoxy]-propyl]-pyridazine from example 8f, 8 mL of acetic acid, and 2 mL of water was heated to reflux. After adding acid solution, the reaction mixture was refluxed for 5 h. Upon cooling, the above reaction mixture was added to a freshly prepared sodium bicarbonate solution with stirring. The product was isolated and purified by chromatography on MPLC eluting with 30-50% ethyl acetate/hexane and recrystallized from hexane to afford 0.30 g (66%) of 6-acetyl-3-[3-[2,6-dimethyl-4-(5-trifluoromethyl-1,2,4-oxadiazol-2-yl)-phenoxy]-propyl]-pyridazine (R1, R2 =3,5-dimethyl, R3 =6-acetyl, R4 =hydrogen, R5 =5-trifluoromethyl-1,2,4-oxadiazolyl, Y=1,3-propylene), as a crystalline solid, m.p. 86°-87° C.
Reaction SMILES: [CH2:1]([O:3][C:4]([CH:6]([CH2:11][C:12]1[C:21]2[C:16](=[CH:17][CH:18]=[CH:19][CH:20]=2)[CH:15]=[CH:14][CH:13]=1)[CH2:7][C:8](O)=[O:9])=[O:5])[CH3:2].C(N1C=CN=C1)(N1C=CN=C1)=O.[NH2:34][CH2:35][CH2:36][C:37]1[C:45]2[C:40](=[CH:41][CH:42]=[CH:43][CH:44]=2)[NH:39][CH:38]=1>ClCCl>[CH2:1]([O:3][C:4](=[O:5])[CH:6]([CH2:11][C:12]1[C:21]2[C:16](=[CH:17][CH:18]=[CH:19][CH:20]=2)[CH:15]=[CH:14][CH:13]=1)[CH2:7][C:8](=[O:9])[NH:34][CH2:35][CH2:36][C:37]1[C:45]2[C:40](=[CH:41][CH:42]=[CH:43][CH:44]=2)[NH:39][CH:38]=1)[CH3:2]
Reactant: NCCc1c[nH]c2ccccc12
Reactant: CCOC(=O)C(CC(=O)O)Cc1cccc2ccccc12
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: ClCCl
Product: CCOC(=O)C(CC(=O)NCCc1c[nH]c2ccccc12)Cc1cccc2ccccc12
Temperature: 25 °C
Reaction time: 1 h
Yield: 65 %

Procedure:
To a solution of 1.45 g of the butyric acid obtained in 30 ml of dichloromethane was added 0.86 g of 1,1'-carbonyldiimidazole. The mixture was stirred for 1 hour at room temperature. Then, 0.82 g of triptamine was added to the reaction mixture, and the mixture was stirred for 1.5 hours. The reaction mixture was concentrated under reduced pressure, and a 5% aqueous sodium bicarbonate solution was added to the residue. The mixture was extracted with ethyl acetate. The organic layer was washed successively with water, diluted hydrochloric acid and water, then dried over anhydrous magnesium sulfate, and concentrated under reduced pressure. The residue was purified by silica gel flash column chromatography (eluent: ethyl acetate/benzene=1/1 by volume) to obtain 1.41 g of 3-[2-(3-indolyl)ethylcarbamoyl]-2-(1-naphthylmethyl)propionic acid ethyl ester as a light brown powder.
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([NH:8][C:9]([C:11]2([C:14]([NH:16][C:17]3[CH:22]=[CH:21][C:20]([OH:23])=[C:19]([F:24])[CH:18]=3)=[O:15])[CH2:13][CH2:12]2)=[O:10])=[CH:4][CH:3]=1.[CH2:25]([O:32][C:33]1[CH:42]=[C:41]2[C:36]([C:37](OS(C(F)(F)F)(=O)=O)=[CH:38][CH:39]=[N:40]2)=[CH:35][C:34]=1[O:51][CH3:52])[C:26]1[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=1.N1C(C)=CC=CC=1C>>[F:1][C:2]1[CH:3]=[CH:4][C:5]([NH:8][C:9]([C:11]2([C:14]([NH:16][C:17]3[CH:22]=[CH:21][C:20]([O:23][C:37]4[C:36]5[C:41](=[CH:42][C:33]([O:32][CH2:25][C:26]6[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=6)=[C:34]([O:51][CH3:52])[CH:35]=5)[N:40]=[CH:39][CH:38]=4)=[C:19]([F:24])[CH:18]=3)=[O:15])[CH2:13][CH2:12]2)=[O:10])=[CH:6][CH:7]=1
Reactant: COc1cc2c(OS(=O)(=O)C(F)(F)F)ccnc2cc1OCc1ccccc1
Reactant: O=C(Nc1ccc(F)cc1)C1(C(=O)Nc2ccc(O)c(F)c2)CC1
Solvent: Cc1cccc(C)n1
Product: COc1cc2c(Oc3ccc(NC(=O)C4(C(=O)Nc5ccc(F)cc5)CC4)cc3F)ccnc2cc1OCc1ccccc1
Temperature: 143 °C
Yield: 48 %

Procedure:
To a flask containing cyclopropane-1,1-dicarboxylic acid (3-fluoro-4-hydroxy-phenyl)-amide(4-fluoro-phenyl)-amide (2.25 g, 6.7 mmol) and trifluoromethanesulfonic acid 7-benzyloxy-6-methoxy-quinolin-4-yl ester (1.87 g, 4.5 mmol) was added dry 2,6-lutidine (9 mL). The reaction mixture was heated to reflux (143° C.) with vigorous stirring. The reaction progress was monitored by LC-MS. 2,6-Lutidine was removed under reduced pressure when the reaction was complete (about 6 h). The residue was treated with charcoal (1.5 g) in refluxing EtOAc (50 mL) for 15 min, and filtered through celite. The volume of the filtrate was reduced to about 20 mL and was added 20 mL of 1N HCl. The crude product precipitated as the HCl salt, which was filtered and washed with EtOAc and H2O (88% purity by analytical HPLC). The HCl salt was free-based with saturated aqueous NaHCO3 solution. Further purification by column chromatography (hexans:EtOAc=1:4) gave cyclopropane-1,1-dicarboxylic acid [4-(7-benzyloxy-6-methoxy-quinolin-4-yloxy)-3-fluoro-phenyl]-amide(4-fluoro-phenyl)-amide as an off-white solid (1.3 g, 48% yield. 1H NMR (400 MHz, DMSO, d6): 10.41 (s, 1H), 10.02 (s, 1H), 8.48 (d, 1H), 7.92 (dd, 1H), 7.65 (m, 2H), 7.54 (m, 5H), 7.41 (m, 4H), 7.17 (m, 2H), 6.43 (d, 1H), 5.32 (s, 2H), 3.97 (s, 3H), 1.48 (m, 4H). LC/MS Calcd for [M+H]+596.2. found 596.3.
Reaction SMILES: F[C:2]1[CH:9]=[CH:8][C:7]([C:10]#[N:11])=[CH:6][C:3]=1[CH:4]=O.O.[NH2:13][NH2:14]>>[NH:13]1[C:2]2[C:3](=[CH:6][C:7]([C:10]#[N:11])=[CH:8][CH:9]=2)[CH:4]=[N:14]1
Reactant: N#Cc1ccc(F)c(C=O)c1
Reactant: NN
Solvent: O
Product: N#Cc1ccc2[nH]ncc2c1
Temperature: 25 °C
Reaction time: 18 h

Procedure:
2-fluoro-5-cyanobenzaldehyde (1.1 g) is dissolved in hydrazine hydrate (19 ml) and stirred at room temperature for 18 hours. The solution is then distilled and the residue purified by flash column chromatography on silica, eluting with DCM. This gives the title compound (300 mg).
Reaction SMILES: [CH3:1][C:2]1[C:6]([C:7]2[CH:13]=[C:12]([N+:14]([O-])=O)[C:10]([NH2:11])=[C:9]([I:17])[CH:8]=2)=[C:5]([CH3:18])[O:4][N:3]=1.Cl[Sn]Cl>CCO>[CH3:1][C:2]1[C:6]([C:7]2[CH:13]=[C:12]([NH2:14])[C:10]([NH2:11])=[C:9]([I:17])[CH:8]=2)=[C:5]([CH3:18])[O:4][N:3]=1
Reactant: Cc1noc(C)c1-c1cc(I)c(N)c([N+](=O)[O-])c1
Agent: Cl[Sn]Cl
Solvent: CCO
Product: Cc1noc(C)c1-c1cc(N)c(N)c(I)c1
Temperature: 75 °C
Reaction time: 7 h

Procedure:
4-(3,5-dimethylisoxazol-4-yl)-2-iodo-6-nitroaniline (0.9 g, 2.5 mmol) was added to EtOH (50 ml), to the mixture were added SnCl2 (2.4 g, 12.5 mmol). The reaction mixture was stirred at 75° C. for 7 h. The solvent was evaporated and then the residue was dissolved in EtOAc (100 ml) and washed with 1N NaOH (100 ml×3). The organic solvent was evaporated and the residue was dissolved in DCM and purified with combi-flash column chromatography (product came out at 60% EtOAc/Hexane) to afford 5-(3,5-dimethylisoxazol-4-yl)-3-iodobenzene-1,2-diamine. LCMS m/z [M+H]+ C11H12IN3O requires: 330.00. Found 330.03 1H NMR (400 MHz, CD3OD) δ2.21 (s, 3H), 2.39 (s, 3H), 7.16 (d, 1H), 7.62 (d, 1H).
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[C:12](=[O:13])[CH2:11][CH2:10][C@H:9]1[C:14]([O:16][CH2:17][C:18]1[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=1)=[O:15])=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH3:24][O:25][C:26]1[CH:27]=[C:28]([Mg]Br)[CH:29]=[CH:30][C:31]=1[O:32][CH3:33]>C1COCC1>[CH2:17]([O:16][C:14](=[O:15])[CH:9]([NH:8][C:6]([O:5][C:1]([CH3:4])([CH3:3])[CH3:2])=[O:7])[CH2:10][CH2:11][C:12]([C:29]1[CH:28]=[CH:27][C:26]([O:25][CH3:24])=[C:31]([O:32][CH3:33])[CH:30]=1)=[O:13])[C:18]1[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=1
Reactant: COc1ccc([Mg]Br)cc1OC
Reactant: CC(C)(C)OC(=O)N1C(=O)CC[C@H]1C(=O)OCc1ccccc1
Solvent: C1CCOC1
Product: COc1ccc(C(=O)CCC(NC(=O)OC(C)(C)C)C(=O)OCc2ccccc2)cc1OC
Reaction time: 2 h
Yield: 88 %

Procedure:
A solution of (2S)5-oxo-pyrrolidine-1,2-dicarboxylic acid 2-benzyl ester 1-tert-butyl ester (8.20 g, 0.026 mol, 1.0 equivalent) in anhydrous THF was cooled to 0° C. in an ice bath under N2. A chilled 0.5M solution of 3,4-dimethoxyphenylmagnesium bromide in THF (52.1 mL, 0.026 mol, 1.0 equivalent) was slowly added. The reaction mixture was allowed to stir for two hours. The reaction was quenched upon addition of saturated NH4Cl solution (10 ml). The mixture was partitioned between ethyl acetate and brine. The organic extract was washed with brine (3×100 ml). The ethyl acetate layer was dried over anhydrous Na2SO4 and concentrated in vacuo. The resulting crude blue oil was filtered through a layer of silica. The filtrate was concentrated in vacuo to afford 2-tert-butoxycarbonylamino-5-(3,4-dimethoxy-phenyl)-5-oxo-pentanoic acid benzyl ester (10.46 g, 0.023 mol, 88% yield). Analysis H1 NMR (400 MHz, CDCl3): 7.5-7.3 (6H, m), 7.0-6.7 (2H, m), 5.2 (2H, m), 4.0-3.8 (6H, m), 3.0 (1H, m), 2.6-1.9 (4H, m), 1.4 (9H, s). MS (LC-MS): Calculated for C25H31NO7 457.21, found 458.19 (M+H)+.
Reaction SMILES: O.[F:2][C:3]1[C:21]([N:22]2[C:27](=[O:28])[CH:26]=[C:25]([C:29]([F:32])([F:31])[F:30])[N:24]([CH3:33])[C:23]2=[O:34])=[CH:20][C:6]([O:7][C:8]2[C:9]([O:14][CH2:15][C:16]([O:18][CH3:19])=[O:17])=[N:10][CH:11]=[CH:12][CH:13]=2)=[C:5]([N+:35]([O-])=O)[CH:4]=1>C(O)(=O)C.[Fe]>[NH2:35][C:5]1[CH:4]=[C:3]([F:2])[C:21]([N:22]2[C:27](=[O:28])[CH:26]=[C:25]([C:29]([F:30])([F:32])[F:31])[N:24]([CH3:33])[C:23]2=[O:34])=[CH:20][C:6]=1[O:7][C:8]1[C:9]([O:14][CH2:15][C:16]([O:18][CH3:19])=[O:17])=[N:10][CH:11]=[CH:12][CH:13]=1
Reactant: COC(=O)COc1ncccc1Oc1cc(-n2c(=O)cc(C(F)(F)F)n(C)c2=O)c(F)cc1[N+](=O)[O-]
Agent: [Fe]
Solvent: O
Solvent: CC(=O)O
Product: COC(=O)COc1ncccc1Oc1cc(-n2c(=O)cc(C(F)(F)F)n(C)c2=O)c(F)cc1N
Reaction time: 2 h
Yield: 85 %

Procedure:
To a mixture of 0.3 g of iron powder, 3 ml of acetic acid, and 0.3 ml of water was added dropwise a solution of 0.30 g of 3-{4-fluoro-5-[3-methyl-2,6-dioxo-4-(trifluoromethyl)-1,2,3,6-tetrahydropyrim idin-1-yl]-2-nitrophenoxy}-2-(methoxycarbonyl)methoxypyridine in 2 ml of acetic acid, while the temperature of the reaction mixture was kept at 35° C. or lower. After completion of the dropwise addition, the mixture was stirred for 2 hours and then filtered through Celite. The filtrate was diluted with ethyl acetate, and the mixture was neutralized with saturated aqueous sodium bicarbonate solution. The organic layer was washed with saturated aqueous sodium chloride solution, dried over anhydrous magnesium sulfate, and then concentrated. The residue was subjected to silica gel column chromatography to give 0.24 g of 3-{2-amino-4-fluoro-5-[3-methyl-2,6-dioxo-4-(trifluoromethyl)-1,2,3,6-tetrahydropyrimidin-1-yl]phenoxy}-2-(methoxycarbonyl)methoxypyridine.
Reaction SMILES: [CH3:1][CH2:2][O:3][C:4]([CH2:6][C:7]([C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1)=[O:8])=[O:5].[CH2:15](OCC)C>>[OH:8][C@:7]([C:9]1[CH:10]=[CH:11][CH:12]=[CH:13][CH:14]=1)([CH3:15])[CH2:6][C:4]([O:3][CH2:2][CH3:1])=[O:5]
Reactant: CCOCC
Reactant: CCOC(=O)CC(=O)c1ccccc1
Product: CCOC(=O)C[C@@](C)(O)c1ccccc1
Reaction time: 24 h

Procedure:
Ethyl benzoyl acetate (192 mg, 1 mmol) was added to diethylether (10 mL) and the solution applied to a sheet of filter paper. The solvent was left to evaporate. Yeast (10 g/mmol) was mixed with water (10 ml) and the resultant paste spread onto the filter paper and left for 24 h. The product was extracted from the yeast using ethyl acetate (2×30 mL). Evaporation under reduced pressure produced an essentially pure ethyl (R)-3-hydroxy-3-phenylbutanoate as an oil.