Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: CN(C)C=O.[H-].[Na+].[Cl:8][C:9]1[CH:14]=[C:13]([O:15][C:16]2[C:25]3[C:20](=[CH:21][C:22]([O:28][CH3:29])=[C:23]([O:26][CH3:27])[CH:24]=3)[N:19]=[CH:18][N:17]=2)[CH:12]=[CH:11][C:10]=1[NH:30][C:31](=[O:41])[O:32][CH2:33][C:34]1[CH:39]=[CH:38][CH:37]=[CH:36][C:35]=1[Cl:40].[CH2:42](I)[CH3:43]>O>[Cl:8][C:9]1[CH:14]=[C:13]([O:15][C:16]2[C:25]3[C:20](=[CH:21][C:22]([O:28][CH3:29])=[C:23]([O:26][CH3:27])[CH:24]=3)[N:19]=[CH:18][N:17]=2)[CH:12]=[CH:11][C:10]=1[N:30]([CH2:42][CH3:43])[C:31](=[O:41])[O:32][CH2:33][C:34]1[CH:39]=[CH:38][CH:37]=[CH:36][C:35]=1[Cl:40]
Reactant: COc1cc2ncnc(Oc3ccc(NC(=O)OCc4ccccc4Cl)c(Cl)c3)c2cc1OC
Reactant: CCI
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: CCN(C(=O)OCc1ccccc1Cl)c1ccc(Oc2ncnc3cc(OC)c(OC)cc23)cc1Cl
Temperature: 25 °C
Reaction time: 0.17 h
Yield: 99.1 %

Procedure:
Dimethylformamide (5 ml) was added to sodium hydride (11 mg), and 2-chlorobenzyl N-{2-chloro-4-[(6,7-dimethoxy-4-quinazolinyl)oxy]phenyl}carbamate (65 mg) was added to the mixture. Subsequently, a dimethylformamide solution (2 ml) of ethyl iodide (84 mg) was added thereto, and the mixture was stirred at room temperature for 10 min. Water was added to stop the reaction, and the reaction solution was then extracted with ethyl acetate, followed by washing with water and saturated brine in that order. The extract was dried over sodium sulfate and was then concentrated. The residue was purified on a column using chloroform/methanol to give the title compound (68 mg, yield 100%).
Reaction SMILES: [NH2:1][C:2]1[CH:17]=[C:16]([Cl:18])[CH:15]=[CH:14][C:3]=1[O:4][C:5]1[CH:10]=[CH:9][C:8]([C:11](=O)[CH3:12])=[CH:7][CH:6]=1.Cl.[NH2:20][OH:21].O>C(O)C>[NH2:1][C:2]1[CH:17]=[C:16]([Cl:18])[CH:15]=[CH:14][C:3]=1[O:4][C:5]1[CH:10]=[CH:9][C:8]([C:11](=[N:20][OH:21])[CH3:12])=[CH:7][CH:6]=1
Reactant: CC(=O)c1ccc(Oc2ccc(Cl)cc2N)cc1
Reactant: NO
Agent: Cl
Solvent: O
Solvent: CCO
Product: CC(=NO)c1ccc(Oc2ccc(Cl)cc2N)cc1
Temperature: 60 °C
Yield: 41.2 %

Procedure:
To the product from Example 163a (150 mg, 0.57 mmol) in ethanol (15 mL) was added hydroxylamine hydrochloride (41.8 mg, 0.60 mmol), and disopropylethylamine (82 mg, 0.63 mmol). The reaction was heated at 60° C. for 3 h. The reaction was cooled and poured into water. The solution was extracted with ethyl ether. The organic layer washed with water, brine, and dried over sodium sulfate, filtered and concentrated under vacuum giving the title compound (65 mg, 42%).
Reaction SMILES: [OH:1][CH:2]1[CH2:19][N:18]([C:20]([O:22][C:23]([CH3:26])([CH3:25])[CH3:24])=[O:21])[CH2:17][CH2:16][C:3]21[C:7](=[O:8])[N:6]([C:9]1[CH2:10][O:11][C:12](=[O:15])[C:13]=1[CH3:14])[CH2:5][CH2:4]2.[CH3:27]I>C(#N)C.[Ag]=O>[CH3:27][O:1][CH:2]1[CH2:19][N:18]([C:20]([O:22][C:23]([CH3:26])([CH3:25])[CH3:24])=[O:21])[CH2:17][CH2:16][C:3]21[C:7](=[O:8])[N:6]([C:9]1[CH2:10][O:11][C:12](=[O:15])[C:13]=1[CH3:14])[CH2:5][CH2:4]2
Reactant: CI
Reactant: CC1=C(N2CCC3(CCN(C(=O)OC(C)(C)C)CC3O)C2=O)COC1=O
Agent: O=[Ag]
Solvent: CC#N
Product: COC1CN(C(=O)OC(C)(C)C)CCC12CCN(C1=C(C)C(=O)OC1)C2=O
Temperature: 60 °C

Procedure:
To the mixture of tert-butyl 6-hydroxy-2-(4-methyl-5-oxo-2,5-dihydrofuran-3-yl)-1-oxo-2,8-diazaspiro[4.5]decane-8-carboxylate (CIS) (2 g, 5.46 mmol) and silver oxide (1.391 g, 6.00 mmol) in acetonitrile (50 mL) was added methyl iodide (3.41 ml, 54.6 mmol). The mixture was heated at 60° C. in a sealed tube overnight. After it cooled to rt, the mixture was filtered and the filtrate was concentrated and the residue was purified by silica gel chromatography using ethyl acetate/hexane to give tert-butyl 6-methoxy-2-(4-methyl-5-oxo-2,5-dihydrofuran-3-yl)-1-oxo-2,8-diazaspiro[4.5]decane-8-carboxylate (CIS, racemate). LC/MS: (M+1)+: 380.99. The racetmate was further separated on an AD chiral column give tert-butyl 6-methoxy-2-(4-methyl-5-oxo-2,5-dihydrofuran-3-yl)-1-oxo-2,8-diazaspiro[4.5]decane-8-carboxylate (faster eluting, CIS), LC/MS: (M+1)+: 381.05, and tert-butyl 6-methoxy-2-(4-methyl-5-oxo-2,5-dihydrofuran-3-yl)-1-oxo-2,8-diazaspiro[4.5]decane-8-carboxylate (slower eluting, CIS). LC/MS: (M+1)+: 381.01.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[SH:8].ClC1C=CC=CC=1C=O.F[C:19]1[CH:24]=[CH:23][C:22]([C:25](=[O:27])[CH3:26])=[CH:21][C:20]=1[Cl:28]>>[Cl:28][C:20]1[CH:21]=[C:22]([C:25](=[O:27])[CH3:26])[CH:23]=[CH:24][C:19]=1[S:8][C:3]1[CH:4]=[CH:5][CH:6]=[CH:7][C:2]=1[Cl:1]
Reactant: CC(=O)c1ccc(F)c(Cl)c1
Reactant: Sc1ccccc1Cl
Agent: O=Cc1ccccc1Cl
Product: CC(=O)c1ccc(Sc2ccccc2Cl)c(Cl)c1

Procedure:
The title compound was prepared by the procedures described in Example 1A substituting 2,4-dichlorothiophenol with 2-chlorothiophenol, and 2-chlorobenzaldehyde with 4′-fluoro-3′-chloroacetophenone.
Reaction SMILES: [CH:1]([C:3]1[CH:8]=[CH:7][C:6]([P:9]([CH3:14])(=[O:13])[O:10][CH2:11][CH3:12])=[CH:5][CH:4]=1)=O.Cl.[NH2:16][OH:17].C([O-])(O)=O.[Na+]>C(O)C>[OH:17]/[N:16]=[CH:1]/[C:3]1[CH:8]=[CH:7][C:6]([P:9]([CH3:14])(=[O:13])[O:10][CH2:11][CH3:12])=[CH:5][CH:4]=1
Reactant: CCOP(C)(=O)c1ccc(C=O)cc1
Reactant: NO
Agent: Cl
Agent: O=C([O-])O
Agent: [Na+]
Solvent: CCO
Product: CCOP(C)(=O)c1ccc(/C=N/O)cc1
Temperature: 25 °C
Reaction time: 10 h

Procedure:
To a solution of compound 38-c (530 mg, 2.5 mmol) in ethanol (10 mL) was added hydroxylamine hydrochloride (230 mg, 3.2 mmol) and NaHCO3 (360 g, 3.60 mmol). The reaction mixture was then stirred for 10 h at room temperature. The resulting mixture was concentrated under reduce pressure to afford crude compound 38-d (570 mg). LC-MS 228 [M+H]+
Reaction SMILES: [CH3:1][C:2]1[NH:6][N:5]=[C:4]([C:7]([O:9][CH2:10][CH3:11])=[O:8])[N:3]=1.[Cl:12][C:13]1[CH:18]=[C:17]([CH2:19]Cl)[CH:16]=[CH:15][N:14]=1.C([O-])([O-])=O.[K+].[K+]>CN(C=O)C.O>[Cl:12][C:13]1[CH:18]=[C:17]([CH2:19][N:6]2[C:2]([CH3:1])=[N:3][C:4]([C:7]([O:9][CH2:10][CH3:11])=[O:8])=[N:5]2)[CH:16]=[CH:15][N:14]=1
Reactant: CCOC(=O)c1n[nH]c(C)n1
Reactant: ClCc1ccnc(Cl)c1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CN(C)C=O
Product: CCOC(=O)c1nc(C)n(Cc2ccnc(Cl)c2)n1
Temperature: 25 °C
Reaction time: 8 h
Yield: 36.9 %

Procedure:
To a solution of ethyl 5-methyl-1H-1,2,4-triazole-3-carboxylate (50 mg, 0.28 mmol) and 2-chloro-4-(chloromethyl)pyridine (50 mg, 0.31 mmol) in DMF (2 mL), K2CO3 (116 mg, 0.84 mmol) was added. The mixture was stirred at RT overnight, and was then diluted with H2O (20 mL), extracted with EtOAc (3×20 mL), 4:1 CHCl3:iPrOH (3×20 mL), dried with MgSO4 and concentrated under reduced pressure. The crude product was purified on a Biotage pre-packed silica gel column (EtOAc:Hexane 12% to 100% EtOAc) to afford ethyl 1-((2-chloropyridin-4-yl)methyl)-5-methyl-1H-1,2,4-triazole-3-carboxylate (29 mg, 40%) as a white solid. MS (ES+) C12H13ClN4O2 requires: 280 found: 281[M+H]+.
Reaction SMILES: [C:1]([O:5][C:6]1[CH:15]=[C:14](/[CH:16]=[CH:17]/[C:18]2[CH:23]=[CH:22][CH:21]=[C:20]([F:24])[CH:19]=2)[C:13]2[C:8](=[CH:9][CH:10]=[C:11]([C:25]([C:27]3[CH:32]=[CH:31][C:30]([Cl:33])=[CH:29][CH:28]=3)=[O:26])[CH:12]=2)[N:7]=1)([CH3:4])([CH3:3])[CH3:2].[S:34]1[CH:38]=[CH:37][C:36]([Mg]Br)=[CH:35]1>C1COCC1>[C:1]([O:5][C:6]1[CH:15]=[C:14](/[CH:16]=[CH:17]/[C:18]2[CH:23]=[CH:22][CH:21]=[C:20]([F:24])[CH:19]=2)[C:13]2[C:8](=[CH:9][CH:10]=[C:11]([C:25]([C:27]3[CH:32]=[CH:31][C:30]([Cl:33])=[CH:29][CH:28]=3)([C:36]3[CH:37]=[CH:38][S:34][CH:35]=3)[OH:26])[CH:12]=2)[N:7]=1)([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)Oc1cc(/C=C/c2cccc(F)c2)c2cc(C(=O)c3ccc(Cl)cc3)ccc2n1
Reactant: Br[Mg]c1ccsc1
Solvent: C1CCOC1
Product: CC(C)(C)Oc1cc(/C=C/c2cccc(F)c2)c2cc(C(O)(c3ccc(Cl)cc3)c3ccsc3)ccc2n1
Reaction time: 3 h

Procedure:
To a solution of (E)-(2-(tert-butoxy)-4-(3-fluorostyryl)quinolin-6-yl)(4-chlorophenyl)methanone (90 mg, 0.196 mmol) in THF (2 mL) was slowly added thiophen-3-ylmagnesium bromide (1.04 mL, 0.313 mmol, 0.3M in toluene) and the resulting solution was kept at 0° C. for 3 hr. The reaction was quenched with saturated NH4Cl at 0° C. and the aqueous layer was extracted with EtOAc. The combined organics were purified by silica column chromatography (20-30% EtOAc/hexanes) to yield (E)-(2-(tert-butoxy)-4-(3-fluorostyryl)quinolin-6-yl)(4-chlorophenyl)(thiophen-3-yl)methanol.
Reaction SMILES: [CH2:1]([N:3]1[CH:7]=[C:6]([CH2:8][N:9]2[C:14]3[CH:15]=[C:16]([C:18]4[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=4)[S:17][C:13]=3[C:12](=[O:24])[N:11]([CH:25]3[CH2:30][CH2:29][N:28](C(OC(C)(C)C)=O)[CH2:27][CH2:26]3)[C:10]2=[O:38])[N:5]=[N:4]1)[CH3:2].[F:39][C:40]([F:45])([F:44])[C:41]([OH:43])=[O:42]>C(Cl)Cl>[F:39][C:40]([F:45])([F:44])[C:41]([OH:43])=[O:42].[CH2:1]([N:3]1[CH:7]=[C:6]([CH2:8][N:9]2[C:14]3[CH:15]=[C:16]([C:18]4[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=4)[S:17][C:13]=3[C:12](=[O:24])[N:11]([CH:25]3[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]3)[C:10]2=[O:38])[N:5]=[N:4]1)[CH3:2]
Reactant: CCn1cc(Cn2c(=O)n(C3CCN(C(=O)OC(C)(C)C)CC3)c(=O)c3sc(-c4ccccc4)cc32)nn1
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: CCn1cc(Cn2c(=O)n(C3CCNCC3)c(=O)c3sc(-c4ccccc4)cc32)nn1

Procedure:
A solution of tert-butyl 4-{1-[(1-ethyl-1H-1,2,3-triazol-4-yl)methyl]-2,4-dioxo-6-phenyl-1,4-dihydrothieno[3,2-d]pyrimidin-3(2H)-yl}piperidine-1-carboxylate (1.27 g; compound B23) in DCM (20 ml) is reacted with trifluoroacetic acid (5 ml) according to the procedure described in example B43 to afford the title compound as a solid.
Reaction SMILES: [Cl:1][CH2:2][CH2:3][N:4]1[C:13]2[N:14]([C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)[N:15]=[CH:16][C:12]=2[C:11]2[CH:10]=[CH:9][CH:8]=[CH:7][C:6]=2[C:5]1=[O:23].[CH2:24]([NH:26][CH2:27][CH3:28])[CH3:25]>CN(C)C=O>[ClH:1].[CH2:24]([N:26]([CH2:27][CH3:28])[CH2:2][CH2:3][N:4]1[C:13]2[N:14]([C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)[N:15]=[CH:16][C:12]=2[C:11]2[CH:10]=[CH:9][CH:8]=[CH:7][C:6]=2[C:5]1=[O:23])[CH3:25]
Reactant: O=c1c2ccccc2c2cnn(-c3ccccc3)c2n1CCCl
Reactant: CCNCC
Solvent: CN(C)C=O
Product: CCN(CC)CCn1c(=O)c2ccccc2c2cnn(-c3ccccc3)c21
Product: Cl

Procedure:
Four grams (0.0123 mole) of the compound of Example 27, 3.81 ml (0.0369 mole) of diethylamine and 80 ml of dimethylformamide were heated at 80° C. for 6 hours. After evaporating the solvent, the reaction mass was taken up with chloroform, and the obtained organic solution was first washed with a saturated aqueous solution of sodium carbonate and then with water (twice). After drying over sodium sulfate, the chloroform was evaporated off and the obtained residue was passed through a silica-gel column by eluting with chloroform:methanol=99:1 (by volume). The obtained product was finally dissolved in diethyl ether and treated with a saturated solution of hydrogen chloride in diethyl ether whereby the title compound crystallized out. Yield 3.7 g. (76%). M.p. 252°-56° C.
Reaction SMILES: F[C:2]1[CH:7]=[CH:6][C:5]([N+:8]([O-:10])=[O:9])=[CH:4][C:3]=1[N+:11]([O-:13])=[O:12].C(N(CC)CC)C.[F:21][C:22]([F:48])([C:26]([F:47])([F:46])[C:27]([F:45])([F:44])[C:28]([F:43])([F:42])[C:29]([F:41])([F:40])[C:30]([F:39])([F:38])[C:31]([F:37])([F:36])[C:32]([F:35])([F:34])[F:33])[CH2:23][CH2:24][OH:25].CN(C)C(=O)C>O>[F:21][C:22]([F:48])([C:26]([F:46])([F:47])[C:27]([F:44])([F:45])[C:28]([F:42])([F:43])[C:29]([F:40])([F:41])[C:30]([F:38])([F:39])[C:31]([F:37])([F:36])[C:32]([F:35])([F:34])[F:33])[CH2:23][CH2:24][O:25][C:2]1[CH:7]=[CH:6][C:5]([N+:8]([O-:10])=[O:9])=[CH:4][C:3]=1[N+:11]([O-:13])=[O:12]
Reactant: OCCC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F
Reactant: O=[N+]([O-])c1ccc(F)c([N+](=O)[O-])c1
Solvent: CCN(CC)CC
Solvent: O
Solvent: CC(=O)N(C)C
Product: O=[N+]([O-])c1ccc(OCCC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F)c([N+](=O)[O-])c1
Temperature: 25 °C
Reaction time: 22 h
Yield: 70.1 %

Procedure:
In a flask were charged 1-fluoro-2,4-dinitrobenzene (40.94 g, 0.22 mol), triethylamine (24.29 g, 0.24 mol), 3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-heptadecafluorodecyl alcohol (102.1 g, 0.22 mol), 220 g of N,N-dimethylacetamide and stirred at room temperature for 22 hours under a nitrogen atmosphere. The resultant etherified product was introduced into water with stirring. The solids precipitated were collected and dried at 40° C. under reduced pressure to obtain 97.22 g (yield: 72%) of 4-(3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-heptadecafluorodecyloxy)-1,3-dinitrobenzene as yellow crystals.
Reaction SMILES: [CH2:1]([O:3][CH:4]([O:6][CH:7]1[CH2:23][O:22][C:10]2=[CH:11][CH:12]=[C:13]3[C:17]([N:16]([CH2:18][C@@H:19](O)[CH3:20])[N:15]=[CH:14]3)=[C:9]2[CH2:8]1)[CH3:5])[CH3:2].C(N(CC)CC)C.CS(OS(C)(=O)=O)(=O)=O.[N-:40]=[N+:41]=[N-:42].[Na+]>C1COCC1>[N:40]([C@H:19]([CH3:20])[CH2:18][N:16]1[C:17]2[C:13](=[CH:12][CH:11]=[C:10]3[O:22][CH2:23][CH:7]([O:6][CH:4]([O:3][CH2:1][CH3:2])[CH3:5])[CH2:8][C:9]3=2)[CH:14]=[N:15]1)=[N+:41]=[N-:42]
Reactant: CCOC(C)OC1COc2ccc3cnn(C[C@H](C)O)c3c2C1
Reactant: [N-]=[N+]=[N-]
Agent: CS(=O)(=O)OS(C)(=O)=O
Agent: [Na+]
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CCOC(C)OC1COc2ccc3cnn(C[C@@H](C)N=[N+]=[N-])c3c2C1
Temperature: 95 °C
Reaction time: 1 h
Yield: 79.7 %

Procedure:
To a solution of the product from Step G (0.35 g, 1.09 mmol) and triethylamine (0.55 g, 5.47 mmol) in anhydrous THF (50 ml) at 0° C. was added methanesulfonic anhydride (0.47 g, 2.73 mmol). The mixture was stirred for 1 h and sodium azide (0.71 g, 10.9 mmol) was added. The reaction mixture was evaporated to a residue that was dissolved in anhydrous DMF (80 mL) and heated at 95° C. for 3 h. The mixture was cooled, poured into a saturated solution of sodium bicarbonate (80 mL), and extracted with EtOAc (3×80 mL). The combined extracts were dried (MgSO4) and evaporated to a residue that was purified by chromatography (silica, 10% EtOAc/hexane) to give an oil (0.30 g, 80%): LC/MS (+APCI) m/z 346 (M+H).
Reaction SMILES: Cl.CN(C)CCCN=C=NCC.[C:13]([O:17][C:18]([NH:20][CH:21]([CH2:25][NH:26][C:27]1[CH:32]=[CH:31][CH:30]=[CH:29][C:28]=1[NH2:33])[C:22](O)=[O:23])=[O:19])([CH3:16])([CH3:15])[CH3:14].C(OCC)(=O)C>CN(C)C=O>[C:13]([O:17][C:18]([NH:20][C@@H:21]1[C:22](=[O:23])[NH:33][C:28]2[CH:29]=[CH:30][CH:31]=[CH:32][C:27]=2[NH:26][CH2:25]1)=[O:19])([CH3:16])([CH3:15])[CH3:14]
Reactant: CC(C)(C)OC(=O)NC(CNc1ccccc1N)C(=O)O
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: CC(C)(C)OC(=O)N[C@H]1CNc2ccccc2NC1=O
Reaction time: 18 h
Yield: 71.2 %

Procedure:
1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (8.54 g, 44.5 mmol) was added to a cooled (0° C.) solution of 2-tert-butoxycarbonylamino-3-(2-aminophenylamino)propionic acid (11.95 g, 40.5 mmol) in 100 ml of dimethylformamide and stirred for 18 hours. The reaction was poured into 700 ml of ethyl acetate and washed four times with 100 ml of water. The organic layer was dried over anhydrous sodium sulfate, filtered, and evaporated to give a brown solid that was purified by flash chromatography eluting with 3:7 ethyl acetate/hexane to give 8 g (71%) of the title compound: 1H NMR (CDCl3) δ7.78 (1H, s), 7.02-6.95 (1H, m), 6.88-6.82 (1H, m), 6.82-6.78 (1H, m), 6.75-6.70 (1H, m), 5.8-5.7 (1H, d), 4.55-4.45 (1H, m), 3.95 (1H, s), 3.9-3.82 (1H, m), 3.48-3.40 (1H,m), 1.45 (9H,s).
Reaction SMILES: [F:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([C:12]3[N:13]=[C:14]4[C:20]([C:21]([OH:23])=O)=[CH:19][N:18]([CH2:24][O:25][CH2:26][CH2:27][Si:28]([CH3:31])([CH3:30])[CH3:29])[C:15]4=[N:16][CH:17]=3)=[N:7][N:8]2[CH3:11])=[CH:4][CH:3]=1.Cl.[NH2:33][C@@H:34]([C:36]1([C:41]#[N:42])[CH2:40][CH2:39][CH2:38][CH2:37]1)[CH3:35].C(Cl)CCl.C1C=CC2N(O)N=NC=2C=1.CCN(C(C)C)C(C)C>CN(C=O)C>[C:41]([C:36]1([C@H:34]([NH:33][C:21]([C:20]2[C:14]3[C:15](=[N:16][CH:17]=[C:12]([C:6]4[C:5]5[C:9](=[CH:10][C:2]([F:1])=[CH:3][CH:4]=5)[N:8]([CH3:11])[N:7]=4)[N:13]=3)[N:18]([CH2:24][O:25][CH2:26][CH2:27][Si:28]([CH3:30])([CH3:29])[CH3:31])[CH:19]=2)=[O:23])[CH3:35])[CH2:40][CH2:39][CH2:38][CH2:37]1)#[N:42]
Reactant: C[C@@H](N)C1(C#N)CCCC1
Reactant: Cn1nc(-c2cnc3c(n2)c(C(=O)O)cn3COCC[Si](C)(C)C)c2ccc(F)cc21
Agent: Cl
Agent: On1nnc2ccccc21
Solvent: CN(C)C=O
Solvent: ClCCCl
Solvent: CCN(C(C)C)C(C)C
Product: C[C@@H](NC(=O)c1cn(COCC[Si](C)(C)C)c2ncc(-c3nn(C)c4cc(F)ccc34)nc12)C1(C#N)CCCC1
Temperature: 25 °C
Reaction time: 3 h
Yield: 92.3 %

Procedure:
In a flask were combined 2-(6-fluoro-1-methyl-1H-indazol-3-yl)-5-(2-trimethylsilanylethoxymethyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid (120 mg, 0.27 mmol), 1-((R)-1-amino-ethyl)-cyclopentanecarbonitrile hydrochloride (48 mg, 0.27 mmol), EDC (120 mg, 0.63 mmol) and HOBt (106 g, 0.63 mmol). DMF (3 mL) was added followed by i-Pr2NEt (0.28 mL, 1.63 mmol). The reaction mixture was stirred at room temperature for 3 h then quenched with water and extracted with EtOAc. The organics were washed with 10% citric acid, sat'd NaHCO3, sat'd LiCl, and sat'd NaCl then dried over MgSO4 and concentrated. The residue was purified by SiO2 chromatography (20-100% EtOAc/heptane) to give 140 mg (92%) of 2-(6-fluoro-1-methyl-1H-indazol-3-yl)-5-(2-trimethylsilanyl-ethoxymethyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid [(R)-1-(1-cyano-cyclopentyl)-ethyl]-amide as a white solid.
Reaction SMILES: [Cl:1][C:2]1[CH:13]=[CH:12][C:11]([CH2:14]O)=[CH:10][C:3]=1[CH2:4][NH:5][C:6](=[O:9])[O:7][CH3:8].P(Br)(Br)[Br:17].O.C(OCC)(=O)C>COCCOC>[Br:17][CH2:14][C:11]1[CH:12]=[CH:13][C:2]([Cl:1])=[C:3]([CH:10]=1)[CH2:4][NH:5][C:6](=[O:9])[O:7][CH3:8]
Reactant: COC(=O)NCc1cc(CO)ccc1Cl
Reactant: BrP(Br)Br
Solvent: O
Solvent: COCCOC
Solvent: CCOC(C)=O
Product: COC(=O)NCc1cc(CBr)ccc1Cl
Temperature: 25 °C
Reaction time: 1 h
Yield: 209 %

Procedure:
6.2 g of methyl N-(2-chloro-5-hydroxymethylbenzyl)carbamate was dissolved in 50 ml of ethylene glycol dimethyl ether, and 2.7 g of phosphorus tribromide was dropwise added to this solution at −20° C., followed by stirring at room temperature for 1 hour. After completion of the reaction, water was added to the reaction solution, extraction with ethyl acetate was carried out, followed by washing with an aqueous sodium hydrogencarbonate solution, and the organic layer was dried over anhydrous magnesium sulfate. The solvent was distilled off under reduced pressure to obtain 6.1 g of methyl N-(5-bromomethyl-2-chlorobenzyl)carbamate as white crystals.
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([Cl:8])[N:5]=[C:4]([N:9]2[CH2:14][CH2:13][O:12][CH2:11][CH2:10]2)[N:3]=1.Cl.[CH:16]12[NH:23][CH:20]([CH2:21][CH2:22]1)[CH2:19][O:18][CH2:17]2.CCN(CC)CC>C(Cl)Cl>[Cl:8][C:6]1[N:5]=[C:4]([N:9]2[CH2:14][CH2:13][O:12][CH2:11][CH2:10]2)[N:3]=[C:2]([N:23]2[CH:16]3[CH2:22][CH2:21][CH:20]2[CH2:19][O:18][CH2:17]3)[N:7]=1
Reactant: Clc1nc(Cl)nc(N2CCOCC2)n1
Reactant: C1CC2COCC1N2
Agent: Cl
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: Clc1nc(N2CCOCC2)nc(N2C3CCC2COC3)n1
Temperature: 25 °C
Yield: 96.2 %

Procedure:
To a solution of 4-(4,6-dichloro-1,3,5-triazin-2-yl)morpholine (2.34 g, 10 mmol) in CH2Cl2 (100 mL) were added 3-oxa-8-azabicyclo[3,2,1]octane hydrochloride (1.645 g, 11 mmol) and Et3N (4.2 mL, 30 mmol). The mixture was stirred at room temperature over night. The reaction mixture was washed with water and brine, and dried over MgSO4. The solvent was removed in vacuum to give the title compound as white solid (3.0 g, 96% yield). MS (ESI) m/z 312.1.
Reaction SMILES: [NH2:1][C:2]1[CH:11]=[CH:10][C:9]([N:12]([C:17]2[C:36]([CH:37]3[CH2:39][CH2:38]3)=[CH:35][C:20]3[C:21]([C:31](=[O:34])[NH:32][CH3:33])=[C:22]([C:24]4[CH:29]=[CH:28][C:27]([F:30])=[CH:26][CH:25]=4)[O:23][C:19]=3[CH:18]=2)[S:13]([CH3:16])(=[O:15])=[O:14])=[CH:8][C:3]=1[C:4]([O:6][CH3:7])=[O:5].C1C(=O)N([Cl:47])C(=O)C1>CN(C=O)C.CCOC(C)=O>[NH2:1][C:2]1[C:11]([Cl:47])=[CH:10][C:9]([N:12]([C:17]2[C:36]([CH:37]3[CH2:39][CH2:38]3)=[CH:35][C:20]3[C:21]([C:31](=[O:34])[NH:32][CH3:33])=[C:22]([C:24]4[CH:25]=[CH:26][C:27]([F:30])=[CH:28][CH:29]=4)[O:23][C:19]=3[CH:18]=2)[S:13]([CH3:16])(=[O:15])=[O:14])=[CH:8][C:3]=1[C:4]([O:6][CH3:7])=[O:5]
Reactant: CNC(=O)c1c(-c2ccc(F)cc2)oc2cc(N(c3ccc(N)c(C(=O)OC)c3)S(C)(=O)=O)c(C3CC3)cc12
Reactant: O=C1CCC(=O)N1Cl
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: CNC(=O)c1c(-c2ccc(F)cc2)oc2cc(N(c3cc(Cl)c(N)c(C(=O)OC)c3)S(C)(=O)=O)c(C3CC3)cc12
Temperature: 60 °C
Yield: 99 %

Procedure:
A suspension of 55.0 g (100 mmol) of methyl 2-amino-5-(N-(5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)benzofuran-6-yl)methylsulfonamido)benzoate in 320 mL of DMF was heated to 60° C. The resulting yellow solution was treated with 14.0 g (105 mmol) of NCS in one portion. The solution quickly darkened. After 5 minutes LCMS indicated complete conversion to the desired chloro compound. The solution was cooled to RT and diluted with 1 L of EtOAc. The resulting solution was washed with 5% aqueous NaCl (1×1 L), 5% aqueous sodium bisulfite (2×200 mL), saturated aqueous sodium bicarbonate (3×200 mL), and saturated aqueous brine (1×200 mL). The solution was dried over sodium sulfate and concentrated to dryness at reduced pressure to give 58.0 g (99%) of methyl 2-amino-3-chloro-5-(N-(5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)benzofuran-6-yl)methylsulfonamido)benzoate as a brown solid. This material was taken forward to the next step without purification. 1H NMR (400 MHz, DMSO-d6) δ ppm 8.46 (q, J=4.42 Hz, 1H) 8.25 (s, 1H) 7.94-8.04 (m, 3H) 7.90 (d, J=2.63 Hz, 1H) 7.34-7.46 (m, 2H) 7.18 (s, 1H) 6.93 (br. s., 2H) 3.83 (s, 3H) 3.33 (s, 3H) 2.84 (d, J=4.59 Hz, 3H) 2.26-2.36 (m, 1H) 0.84-1.11 (m, 3H) 0.40 (br. s., 1H). LCMS(ESI): 586 (M+H+).
Reaction SMILES: [C:1]([NH:8][CH2:9][CH2:10][N:11]([C:16](=[O:27])[CH2:17][N:18]1[CH:26]=[C:24]([CH3:25])[C:22](=[O:23])[NH:21][C:19]1=[O:20])[CH2:12][C:13]([OH:15])=[O:14])([O:3][C:4]([CH3:7])([CH3:6])[CH3:5])=[O:2].C(Cl)Cl.[F:31][C:32]1[C:37](O)=[C:36]([F:39])[C:35]([F:40])=[C:34]([F:41])[C:33]=1[F:42]>CN(C=O)C>[F:31][C:32]1[C:37]([O:14][C:13](=[O:15])[CH2:12][N:11]([CH2:10][CH2:9][NH:8][C:1]([O:3][C:4]([CH3:7])([CH3:6])[CH3:5])=[O:2])[C:16](=[O:27])[CH2:17][N:18]2[CH:26]=[C:24]([CH3:25])[C:22](=[O:23])[NH:21][C:19]2=[O:20])=[C:36]([F:39])[C:35]([F:40])=[C:34]([F:41])[C:33]=1[F:42]
Reactant: Cc1cn(CC(=O)N(CCNC(=O)OC(C)(C)C)CC(=O)O)c(=O)[nH]c1=O
Reactant: Oc1c(F)c(F)c(F)c(F)c1F
Solvent: CN(C)C=O
Solvent: ClCCl
Product: Cc1cn(CC(=O)N(CCNC(=O)OC(C)(C)C)CC(=O)Oc2c(F)c(F)c(F)c(F)c2F)c(=O)[nH]c1=O
Temperature: 0 °C
Reaction time: 3 h

Procedure:
N-(N-Boc-2-aminoethyl)-N-[(1-thyminyl)acetyl]glycine (5) (2.00 g; 5.20 mmol) was dissolved in DMF (5 ml) and methylene chloride (15 ml) was added. Pentafluorophenol (1.05 g; 5.72 mmol) was added and the solution was cooled to 0° C. in an ice bath. DDC then was added (1.29 g; 6.24 mmol) and the ice bath was removed after 2 min. After 3 h with stirring at ambient temperature, the precipitated DCU was removed by filtration and washed with methylene chloride. The combined filtrate was washed twice with aqueous sodium hydrogen carbonate and once with saturated sodium chloride, dried over magnesium sulfate, and evaporated to dryness, in vacuo. The solid residue was dissolved in dioxane (150 ml) and poured into water (200 ml) at 0° C. The title compound was isolated by filtration, washed with water, and dried over an appropriate drying agent, in vacuo. Yield: 2.20 g (77%). An analytical sample was obtained by recrystallisation from 2-propanol. M.p. 174–175.5° C. Analysis for C22H23N4O7F5, found(calc.): C, 48.22(48.01); H: 4.64(4.21); N: 9.67(10.18). 1H-NMR (250 MHz, CDCl3):Due to the limited rotation around the secondary amide bond several of the signals were doubled in the ratio 6:1 (indicated in the list by mj. for major and mi. for minor). 7.01 ppm (s, mi., ArH); 6.99 ppm (s, mj., ArH); 5.27 ppm (unres. t, BocNH); 4.67 ppm (s, mj., T-CH2—CO—); 4.60 ppm (s, mi., T-CH2—CO—); 4.45 ppm (s, mj., CONRCH2CO2Pfp); 4.42 ppm (s, mi., CONRCH2CO2Pfp); 3.64 ppm (t,2H,BocNHCH2CH2-); 3.87 ppm (“q”,2H,BocNHCH2CH2—); 1.44(s,9H,t-Bu). FAB-MS: 551 (10; M+1); 495 (10; M+1-tBu); 451 (80; -Boc).