Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][CH2:2][CH2:3][CH2:4][C:5]([O:7][CH2:8][C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][CH:10]=1)=[O:6].N1C=CC=CC=1.Cl[C:22]([O:24][CH2:25][Cl:26])=[O:23]>C(OCC)C>[C:22](=[O:23])([O:1][CH2:2][CH2:3][CH2:4][C:5]([O:7][CH2:8][C:9]1[CH:10]=[CH:11][CH:12]=[CH:13][CH:14]=1)=[O:6])[O:24][CH2:25][Cl:26]
Reactant: O=C(CCCO)OCc1ccccc1
Reactant: O=C(Cl)OCCl
Solvent: c1ccncc1
Solvent: CCOCC
Product: O=C(CCCOC(=O)OCCl)OCc1ccccc1
Temperature: 25 °C
Reaction time: 20 h

Procedure:
To a solution of benzyl 4-hydroxybutanoate (synthesized by the procedure described in Weber et al., J. Med. Chem, 1991, 34, 2692-2701, 5.0 g) in diethyl ether (100 ml), pyridine (2.3 ml) was added under a nitrogen atmosphere, and chloromethyl chloroformate (3.7 g) was added dropwise at −10° C. The reaction mixture was stirred at room temperature for 20 hours. The reaction mixture was filtered with glass filter and then the filtrate was washed with water and a saturated sodium chloride aqueous solution successively. The organic layer was dried over magnesium sulfate, and then the solvent was distilled off under reduced pressure, and thus the residue was subjected to silica gel column chromatography and eluted with acetone/hexane (1:1 v/v) to obtain chloromethyl (3-benzyloxycarbonylpropyl) carbonate (7.25 g) as a colorless oily product.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([CH2:8][C:9]([OH:11])=O)=[CH:4][C:3]=1[C:12]([F:15])([F:14])[F:13].[NH2:16][C:17]1[CH:26]=[CH:25][CH:24]=[C:23]2[C:18]=1[CH:19]=[CH:20][N:21]([CH2:28][C:29]1[CH:30]=[N:31][C:32]([C:35]([F:38])([F:37])[F:36])=[CH:33][CH:34]=1)[C:22]2=[O:27].C(N(CC)C(C)C)(C)C.CO>S(Cl)(Cl)=O>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([CH2:8][C:9]([NH:16][C:17]2[CH:26]=[CH:25][CH:24]=[C:23]3[C:18]=2[CH:19]=[CH:20][N:21]([CH2:28][C:29]2[CH:30]=[N:31][C:32]([C:35]([F:38])([F:37])[F:36])=[CH:33][CH:34]=2)[C:22]3=[O:27])=[O:11])=[CH:4][C:3]=1[C:12]([F:15])([F:14])[F:13]
Reactant: Nc1cccc2c(=O)n(Cc3ccc(C(F)(F)F)nc3)ccc12
Reactant: O=C(O)Cc1ccc(Cl)c(C(F)(F)F)c1
Solvent: CO
Solvent: CCN(C(C)C)C(C)C
Solvent: O=S(Cl)Cl
Product: O=C(Cc1ccc(Cl)c(C(F)(F)F)c1)Nc1cccc2c(=O)n(Cc3ccc(C(F)(F)F)nc3)ccc12
Temperature: 60 °C
Reaction time: 3 h
Yield: 74.7 %

Procedure:
2-(4-Chloro-3-(trifluoromethyl)phenyl)acetic acid (142 mg, 0.000595 mol) was dissolved in thionyl chloride (10 mL) and the mixture was stirred at 60° C. for 3 hours. The volatiles were removed and the residue was dissolved in tetrahydrofuran. 5-Amino-2-((6-(trifluoromethyl)pyridin-3-yl)methyl)isoquinolin-1(2H)-one (100.0 mg, 0.0002975 mol) and N,N-diisopropylethylamine (0.104 mL, 0.000595 mol) were added and the mixture was stirred for 1 hour at room temperature. Methanol was added to quench the reaction and the volatiles were removed. The residue was dissolved in ethylacetate, washed with water, sodium carbonate solution and brine and purified by column to obtain the product as a beige solid (120 mg). MS m/z=540.4(M+H).
Reaction SMILES: [F:1][C:2]1([F:44])[CH2:7][C@H:6]([O:8][C:9]2[C:14]([F:15])=[CH:13][C:12]([S:16]([N:19](CC3C=CC(OC)=CC=3OC)[C:20]3[CH:25]=[CH:24][N:23]=[CH:22][N:21]=3)(=[O:18])=[O:17])=[C:11]([F:37])[CH:10]=2)[C@@H:5]([C:38]2[N:42]([CH3:43])[N:41]=[CH:40][CH:39]=2)[CH2:4][CH2:3]1.C([SiH](CC)CC)C.FC(F)(F)C(O)=O>ClCCl>[F:44][C:2]1([F:1])[CH2:7][C@H:6]([O:8][C:9]2[C:14]([F:15])=[CH:13][C:12]([S:16]([NH:19][C:20]3[CH:25]=[CH:24][N:23]=[CH:22][N:21]=3)(=[O:17])=[O:18])=[C:11]([F:37])[CH:10]=2)[C@@H:5]([C:38]2[N:42]([CH3:43])[N:41]=[CH:40][CH:39]=2)[CH2:4][CH2:3]1
Reactant: COc1ccc(CN(c2ccncn2)S(=O)(=O)c2cc(F)c(O[C@H]3CC(F)(F)CC[C@@H]3c3ccnn3C)cc2F)c(OC)c1
Agent: CC[SiH](CC)CC
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: Cn1nccc1[C@H]1CCC(F)(F)C[C@@H]1Oc1cc(F)c(S(=O)(=O)Nc2ccncn2)cc1F
Yield: 94.4 %

Procedure:
The reaction and aftertreatment were conducted in the same manner as in Example 1b by using the 4-{[(1S*,2R*)-5,5-difluoro-2-(1-methyl-1H-pyrazol-5-yl)cyclohexyl]oxy}-N-(2,4-dimethoxybenzyl)-2,5-difluoro-N-(pyrimidin-4-yl)benzenesulfonamide (212 mg, 0.334 mmol) prepared in Example 47c, triethylsilane (0.30 mL), trifluoroacetic acid (3.0 mL) and dichloromethane (3.0 mL), to yield the title compound (153 mg, 95%) as a colorless solid.
Reaction SMILES: C([O:5][C:6]([CH2:8][CH2:9][CH2:10][O:11][C:12]1[CH:20]=[C:19]([Cl:21])[C:18]([C:22]2[CH:23]=[N:24][C:25]([C:30]([F:33])([F:32])[F:31])=[CH:26][C:27]=2[C:28]#[N:29])=[CH:17][C:13]=1[C:14]([OH:16])=O)=[O:7])(C)(C)C.[CH3:34][O:35][C:36]1[CH:43]=[CH:42][CH:41]=[CH:40][C:37]=1[NH:38][CH3:39].C(N(CC)CC)C.F[P-](F)(F)(F)(F)F.N1(OC(N(C)C)=[N+](C)C)C2N=CC=CC=2N=N1>ClCCl.CN(C=O)C>[Cl:21][C:19]1[C:18]([C:22]2[CH:23]=[N:24][C:25]([C:30]([F:32])([F:31])[F:33])=[CH:26][C:27]=2[C:28]#[N:29])=[CH:17][C:13]([C:14](=[O:16])[N:38]([C:37]2[CH:40]=[CH:41][CH:42]=[CH:43][C:36]=2[O:35][CH3:34])[CH3:39])=[C:12]([CH:20]=1)[O:11][CH2:10][CH2:9][CH2:8][C:6]([OH:5])=[O:7]
Reactant: CNc1ccccc1OC
Reactant: CC(C)(C)OC(=O)CCCOc1cc(Cl)c(-c2cnc(C(F)(F)F)cc2C#N)cc1C(=O)O
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: ClCCl
Solvent: CN(C)C=O
Solvent: CCN(CC)CC
Product: COc1ccccc1N(C)C(=O)c1cc(-c2cnc(C(F)(F)F)cc2C#N)c(Cl)cc1OCCCC(=O)O
Temperature: 25 °C
Reaction time: 16 h

Procedure:
A mixture of 2-(3-tert-butoxycarbonyl-propoxy)-4-chloro-5-(4-cyano-6-trifluoromethyl-pyridin-3-yl)-benzoic acid (30 mg, 0.06 mmol), 2-methoxy-N-methylaniline (9.4 mg, 0.07 mmol), triethylamine (12.5 mg, 0.12 mmol) and 2-(7-aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HATU, 35 mg, 0.09 mL) in dichloromethane (1 mL) containing DMF (0.1 mL) was stirred at rt for 16 hrs. The mixture was then partitioned in water and dichloromethane. The organic layer was washed with water, dried and concentrated to yield a crude 4-{5-chloro-4-(4-cyano-6-trifluoromethyl-pyridin-3-yl)-2-[(2-methoxy-phenyl)-methyl-carbamoyl]-phenoxy}-butyric acid t-butyl ester.
Reaction SMILES: [N:1]([O-])=O.[Na+].[NH:5]([C:7]1[C:16]2[N:17]=[CH:18][N:19]([CH2:20][CH:21]([CH3:23])[CH3:22])[C:15]=2[C:14]2[CH:13]=[CH:12][CH:11]=[CH:10][C:9]=2[N:8]=1)[NH2:6]>O.C(O)(=O)C>[CH3:22][CH:21]([CH3:23])[CH2:20][N:19]1[C:15]2[C:14]3[C:9](=[CH:10][CH:11]=[CH:12][CH:13]=3)[N:8]3[N:1]=[N:6][N:5]=[C:7]3[C:16]=2[N:17]=[CH:18]1
Reactant: O=N[O-]
Reactant: CC(C)Cn1cnc2c(NN)nc3ccccc3c21
Agent: [Na+]
Solvent: CC(=O)O
Solvent: O
Product: CC(C)Cn1cnc2c1c1ccccc1n1nnnc21
Temperature: 25 °C
Reaction time: 0.25 h
Yield: 375.5 %

Procedure:
A solution of sodium nitrite (2.0 g, 3 mmole) in water (5 mL) was added to a solution of 4-hydrazino-1-(2-methylpropyl)-1H-imidazo[4,5-c]quinoline (4.0 g, 15.7 mmole, Example 7) in a mixture of acetic acid (5 mL) and water (50 mL). The reaction mixture was stirred at ambient temperature for 15 minutes. A precipitate was isolated by filtration, washed with water then air dried to provide 4.1 g of crude product. This material was recrystallized from dichloromethane/ethanol to provide 3.0 g of 6-(2-methylpropyl)-6H-imidazo[4,5-c]tetrazolo[1,5-a]quinoline as a cream colored crystalline solid, m.p. 208-212° C. Analysis: Calculated for C14H14N6 : % C, 63.14; % H, 5.30; % N, 31.56; Found: % C, 62.60; % H, 5.2; % N, 31.5.
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:13]=[C:12]([O:14][C:15]3[CH:20]=[CH:19][CH:18]=[CH:17][N:16]=3)[CH:11]=[C:10]([C:21](O)=[O:22])[CH:9]=2)=[CH:4][CH:3]=1.Cl.Cl.[CH3:26][C:27]1[N:32]=[CH:31][C:30]([C@H:33]([NH2:35])[CH3:34])=[CH:29][CH:28]=1.F[P-](F)(F)(F)(F)F.C[N+](C)=C(N(C)C)ON1C2N=CC=CC=2N=N1.C(N(CC)C(C)C)(C)C>CN(C)C=O>[CH3:1][C:2]1[CH:3]=[CH:4][C:5]([C:8]2[CH:13]=[C:12]([O:14][C:15]3[CH:20]=[CH:19][CH:18]=[CH:17][N:16]=3)[CH:11]=[C:10]([C:21]([NH:35][C@@H:33]([C:30]3[CH:31]=[N:32][C:27]([CH3:26])=[CH:28][CH:29]=3)[CH3:34])=[O:22])[CH:9]=2)=[CH:6][CH:7]=1
Reactant: Cc1ccc([C@@H](C)N)cn1
Reactant: Cc1ccc(-c2cc(Oc3ccccn3)cc(C(=O)O)c2)cc1
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: Cl
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: Cc1ccc(-c2cc(Oc3ccccn3)cc(C(=O)N[C@H](C)c3ccc(C)nc3)c2)cc1
Temperature: 25 °C
Reaction time: 16 h

Procedure:
To a solution of 4′-methyl-5-(pyridin-2-yloxy)biphenyl-3-carboxylic acid (50 mg, 0.16 mmol) in N,N-dimethylformamide (1 mL) were added (R)-1-(6-methylpyridin-3-yl)ethanamine dihydrochloride (70 mg, 0.34 mmol), N,N,N′,N′-tetramethyl-O-(7-azabenzotriazol-1-yl)uronium hexafluorophosphate (150 mg, 0.39 mmol), and N,N-diisopropylethylamine (400 μL, 2.30 mmol). The reaction mixture was stirred for 16 hours at 25° C., and then purified by preparative HPLC to afford the final product as a light color solid.
Reaction SMILES: [P:1]([O-:37])([O-:36])([O:3][C:4](C(C)(C)C)(C(C)(C)C)[N:5]1[CH:13]=[C:12]2[C:7]([CH:8]=[CH:9][C:10]([C:14]3[C:15]([C:20]4[CH:25]=[CH:24][C:23]([F:26])=[C:22]([CH3:27])[CH:21]=4)=[N:16][CH:17]=[CH:18][CH:19]=3)=[CH:11]2)=[N:6]1)=[O:2].O>CC(O)=O.CC(C)=O>[P:1]([OH:37])([OH:36])([O:3][CH2:4][N:5]1[CH:13]=[C:12]2[C:7]([CH:8]=[CH:9][C:10]([C:14]3[C:15]([C:20]4[CH:25]=[CH:24][C:23]([F:26])=[C:22]([CH3:27])[CH:21]=4)=[N:16][CH:17]=[CH:18][CH:19]=3)=[CH:11]2)=[N:6]1)=[O:2]
Reactant: Cc1cc(-c2ncccc2-c2ccc3nn(C(OP(=O)([O-])[O-])(C(C)(C)C)C(C)(C)C)cc3c2)ccc1F
Solvent: CC(=O)O
Solvent: O
Solvent: CC(C)=O
Product: Cc1cc(-c2ncccc2-c2ccc3nn(COP(=O)(O)O)cc3c2)ccc1F
Reaction time: 1 h
Yield: 72.6 %

Procedure:
Di-tert-butyl[5-(2-(4-fluoro-3-methylphenyl)pyridin-3-yl)-2H-indazol-2-yl]methyl phosphate (N2, 100 mg, 0.21 mmol) was dissolved in AcOH:H2O (0.5 mL, 4:1) and the clear homogenous solution heated at 60° C. After 1 h, analysis of the reaction mixture LC/MS indicated the 97% consumption of di-tert-butyl[5-(2-(4-fluoro-3-methylphenyl)pyridin-3-yl)-2H-indazol-2-yl]methyl phosphate leading to the desired product of [5-(2-(4-fluoro-3-methylphenyl)pyridin-3-yl)-2H-indazol-2-yl]methyl dihydrogen phosphate (AUC 85%). At this stage heating was discontinued and the reaction mixture was polish filtered by suction. Concentration of the filtrate by rotary evaporator under vacuum (water bath temp 26-28° C.) resulted in a thick viscous liquid which was diluted with acetone (7 mL). The white heterogenous suspension was stirred for 30 min and filtered. The filter cake was washed with acetone (25 mL) and suction dried for a period of 1 h. The collected filter cake was further processed by drying under high vacuum over P2O5 for 24 h to provide [5-(2-(4-fluoro-3-methylphenyl)pyridin-3-yl)-2H-indazol-2-yl]methyl dihydrogen phosphate (63 mg, 71%). 1H NMR (DMSO-d6): δ 8.64 (dd, 1H, J=0.5 and 4.7 Hz), 8.51 (s, 1H), 7.86 (d, 1H, J=7.6 Hz), 7.70 (s, 1H), 7.50-7.41 (app m, 3H), 7.00-6.88 (m, 3H), 6.05 (d, 2H, 3JPH=10 Hz), 2.13 (s, 3H). 19F NMR (DMSO-d6): δ −118.60. 31P NMR (DMSO-d6): δ −2.63. LCMS: 97%, MS (m/e) 414 (MH+).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[CH:10]=[C:9]([C:11]([OH:13])=O)[NH:8][C:5]2=[CH:6][N:7]=1.[S:14]1[CH:18]=[CH:17][CH:16]=[C:15]1[CH2:19][CH2:20][NH2:21]>>[S:14]1[CH:18]=[CH:17][CH:16]=[C:15]1[CH2:19][CH2:20][NH:21][C:11]([C:9]1[NH:8][C:5]2=[CH:6][N:7]=[C:2]([Cl:1])[CH:3]=[C:4]2[CH:10]=1)=[O:13]
Reactant: O=C(O)c1cc2cc(Cl)ncc2[nH]1
Reactant: NCCc1cccs1
Product: O=C(NCCc1cccs1)c1cc2cc(Cl)ncc2[nH]1

Procedure:
The title compound was prepared as outlined in EXAMPLE 1 from 5-chloro-1H-pyrrolo[2,3-c]pyridine-2-carboxylic acid (Preparation 18) and 2-thiophen-2-ylethylamine. The product was purified by chromatography on silica gel eluting with methanol/dichloromethane (3:97) to give the title compound as a yellow solid. δH (CD3OD): 3.16 (2H, t), 3.65 (2H, t), 6.89–6.94 (2H, m), 7.03 (1H, s), 7.20 (1H, d), 7.66 (1H, s), 8.57 (1H, s); m/z (ES+)=306 [M+H]+.
Reaction SMILES: [NH2:1][C:2]1[C:3]([C:8]([F:17])([F:16])[C:9]([F:15])([F:14])[C:10]([F:13])([F:12])[F:11])=[N:4][NH:5][C:6]=1[CH3:7].C([O-])([O-])=O.[K+].[K+].Cl[CH2:25][C:26]([N:28]1[CH2:33][CH2:32][N:31]([C:34]2[CH:39]=[CH:38][C:37]([Cl:40])=[CH:36][CH:35]=2)[CH2:30][CH2:29]1)=[O:27].CN(C=O)C>CCCCCC.C(OCC)(=O)C>[NH2:1][C:2]1[C:3]([C:8]([F:17])([F:16])[C:9]([F:14])([F:15])[C:10]([F:11])([F:12])[F:13])=[N:4][N:5]([CH2:25][C:26]([N:28]2[CH2:29][CH2:30][N:31]([C:34]3[CH:39]=[CH:38][C:37]([Cl:40])=[CH:36][CH:35]=3)[CH2:32][CH2:33]2)=[O:27])[C:6]=1[CH3:7]
Reactant: Cc1[nH]nc(C(F)(F)C(F)(F)C(F)(F)F)c1N
Reactant: O=C(CCl)N1CCN(c2ccc(Cl)cc2)CC1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CCCCCC
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: Cc1c(N)c(C(F)(F)C(F)(F)C(F)(F)F)nn1CC(=O)N1CCN(c2ccc(Cl)cc2)CC1

Procedure:
Protocol T was followed using 4-Amino-3-heptafluoropropyl-5-methyl-1H-pyrazole, K2CO3, 2-Chloro-1-[4-(4-chloro-phenyl)-piperazin-1-yl]-ethanone and DMF. Column chromatography using a solvent mixture (hexane/ethyl acetate=1/4, Rf=0.42) afforded the title compound as colorless oil. 1H NMR (400 MHz, CDCl3); 6.88-6.94 (d, 2H), 7.22-7.26 (d, 2H), 4.98 (s, 2H), 3.64-3.82 (m, 4H), 3.1-3.22 (m, 4H), 2.98 (s, 2H), 2.18 (s, 3H). MS (ES) M+H) expected=501.82, found 502.1.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:23]=[CH:22][C:6]([CH2:7][NH:8][S:9]([C:12]2[CH:21]=[CH:20][C:15]([C:16]([O:18]C)=[O:17])=[CH:14][CH:13]=2)(=[O:11])=[O:10])=[CH:5][CH:4]=1.Br[CH2:25][C:26]1[CH:31]=[CH:30][CH:29]=[C:28]([F:32])[C:27]=1[F:33]>>[F:33][C:27]1[C:28]([F:32])=[CH:29][CH:30]=[CH:31][C:26]=1[CH2:25][N:8]([CH2:7][C:6]1[CH:22]=[CH:23][C:3]([O:2][CH3:1])=[CH:4][CH:5]=1)[S:9]([C:12]1[CH:13]=[CH:14][C:15]([C:16]([OH:18])=[O:17])=[CH:20][CH:21]=1)(=[O:10])=[O:11]
Reactant: COC(=O)c1ccc(S(=O)(=O)NCc2ccc(OC)cc2)cc1
Reactant: Fc1cccc(CBr)c1F
Product: COc1ccc(CN(Cc2cccc(F)c2F)S(=O)(=O)c2ccc(C(=O)O)cc2)cc1

Procedure:
Prepared as in example 5-10 from Methyl 4-(N-(4-methoxybenzyl)sulfamoyl)-benzoate (Example 5-10b) and 1-(bromomethyl)-2,3-difluorobenzene. 1H NMR (400 MHz, DMSO-d6): δ, ppm: 3.30 (s, 3H), 4.29 (s, 2H), 4.32(s, 2H), 6.87 (d, 2H, J=8 Hz), 7.02-7.20 (m, 5H), 7.95 (d, 2H, J=8 Hz). 8.05 (d, 2H, J=8 Hz).
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[CH:9][C:8]([C:11]2[N:12]([C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])[C:13]3[C:18]([CH:19]=2)=[CH:17][C:16]([CH:20]=O)=[CH:15][CH:14]=3)=[C:7]2[C:3]=1[CH2:4][NH:5][C:6]2=[O:29].[NH:30]1[CH2:34][CH2:33][CH2:32][CH2:31]1.C(O)(=O)C.C(O[BH-](OC(=O)C)OC(=O)C)(=O)C.[Na+].Cl>C(#N)C.C(OCC)(=O)C>[Cl:1][C:2]1[CH:10]=[CH:9][C:8]([C:11]2[N:12]([C:22]([O:24][C:25]([CH3:27])([CH3:28])[CH3:26])=[O:23])[C:13]3[C:18]([CH:19]=2)=[CH:17][C:16]([CH2:20][N:30]2[CH2:34][CH2:33][CH2:32][CH2:31]2)=[CH:15][CH:14]=3)=[C:7]2[C:3]=1[CH2:4][NH:5][C:6]2=[O:29]
Reactant: C1CCNC1
Reactant: CC(C)(C)OC(=O)n1c(-c2ccc(Cl)c3c2C(=O)NC3)cc2cc(C=O)ccc21
Agent: CC(=O)O[BH-](OC(C)=O)OC(C)=O
Agent: Cl
Agent: [Na+]
Solvent: CCOC(C)=O
Solvent: CC(=O)O
Solvent: CC#N
Product: CC(C)(C)OC(=O)n1c(-c2ccc(Cl)c3c2C(=O)NC3)cc2cc(CN3CCCC3)ccc21
Yield: 103.8 %

Procedure:
In a similar manner to Step 2 of Example 6, 4-chloro-7-[1-(tert-butoxycarbonyl)-5-formylindol-2-yl]isoindolinone (30.0 mg, 0.0730 mmol) was dissolved in acetonitrile (2 mL), and the solution was treated with pyrrolidine (0.096 mL, 1.2 mmol), acetic acid (0.084 mL, 1.5 mmol) and sodium triacetoxyborohydride (77 mg, 0.36 mmol). The reaction mixture was added with 1 mol/L hydrochloric acid and ethyl acetate, followed by extracting with 1 mol/L hydrochloric acid. The aqueous layer was added with sodium carbonate to adjust the pH to 9, then extracted with ethyl acetate. The organic layer was washed with saturated brine and dried over anhydrous sodium sulfate. The solvent was evaporated under reduced pressure to obtain 4-chloro-7-[1-(tert-butoxycarbonyl)-5-(pyrrolidin-1-ylmethyl)indol-2-yl]isoindolinone (35.3 mg).
Reaction SMILES: [CH2:1]([O:8][CH2:9][CH2:10][N:11]1[C:17](=[O:18])[C@@H:16]([NH:19][C:20](=[O:28])[CH:21]([O:25][CH2:26][CH3:27])[C:22]([OH:24])=O)[C:15]2[CH:29]=[CH:30][CH:31]=[CH:32][C:14]=2[C:13]2[CH:33]=[CH:34][CH:35]=[CH:36][C:12]1=2)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[F:37][C:38]([F:45])([C:41]([F:44])([F:43])[F:42])[CH2:39][NH2:40]>>[CH2:1]([O:8][CH2:9][CH2:10][N:11]1[C:17](=[O:18])[C@@H:16]([NH:19][C:20](=[O:28])[CH:21]([O:25][CH2:26][CH3:27])[C:22]([NH:40][CH2:39][C:38]([F:45])([F:37])[C:41]([F:44])([F:43])[F:42])=[O:24])[C:15]2[CH:29]=[CH:30][CH:31]=[CH:32][C:14]=2[C:13]2[CH:33]=[CH:34][CH:35]=[CH:36][C:12]1=2)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: NCC(F)(F)C(F)(F)F
Reactant: CCOC(C(=O)O)C(=O)N[C@@H]1C(=O)N(CCOCc2ccccc2)c2ccccc2-c2ccccc21
Product: CCOC(C(=O)NCC(F)(F)C(F)(F)F)C(=O)N[C@@H]1C(=O)N(CCOCc2ccccc2)c2ccccc2-c2ccccc21

Procedure:
Using N—[(S)-5-(2-benzyloxy-ethyl)-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl]-2-ethoxy-malonamic acid and 2,2,3,3,3-pentafluoropropylamine, the title compound was prepared in the same manner as described for example 1c. White solid. (82%). MS: m/e=620(M+H+).
Reaction SMILES: [C:1]([O:4][CH:5]=[CH2:6])(=[O:3])[CH3:2].OC([C:10]1[NH:15][C:14](=[O:16])[CH:13]=[CH:12][N:11]=1)C>O1CCOCC1>[C:1]([O:4][C@@H:5]([C:10]1[NH:15][C:14](=[O:16])[CH:13]=[CH:12][N:11]=1)[CH3:6])(=[O:3])[CH3:2]
Reactant: CC(O)c1nccc(=O)[nH]1
Reactant: C=COC(C)=O
Solvent: C1COCCO1
Product: CC(=O)O[C@H](C)c1nccc(=O)[nH]1
Temperature: 50 °C
Reaction time: 24 h

Procedure:
To a solution of vinyl acetate (4.3 g, 50 mmol) in dioxane (63 mL) was added 2-(1-hydroxy-ethyl)-3H-pyrimidin-4-one (prepared according to the method of Preparation Twelve, 2.1 g, 15.1 mmol), and the mixture was heated to 50° C. To the resulting solution was added lipase P30 (0.21 g, 10 wt %) and the heating was continued for 24 h. The reaction mixture was filtered and the filtrate was evaporated to obtain a thick syrupy liquid residue. The residue was purified by flash column chromatography (95:5 dichloromethane:methanol) to give the title compound as a colorless liquid, 0.97 g (92% of theory). 1H NMR (CDCl3, 300 MHz) δ1.61 (d, 3H), 2.20 (s, 3H), 5.65 (q, 1H), 6.35 (d, 1H), 7.97 (d, 1H), 11.94 (s, 1H); [α]D +39.9 (c 1.0, MeOH).
Reaction SMILES: [NH2:1][C@H:2]1[CH2:7][CH2:6][C@H:5]([NH:8][C:9]2[CH:14]=[C:13]([C:15]3[CH:20]=[CH:19][C:18]([F:21])=[C:17]([NH:22][CH2:23][CH:24]4[CH2:29][CH2:28][O:27][CH2:26][CH2:25]4)[N:16]=3)[C:12]([Cl:30])=[CH:11][N:10]=2)[CH2:4][CH2:3]1.[C:31](=O)([O-])[O-].[K+].[K+].CC1C=CC(S(OC[CH:49]2[CH2:52][CH2:51][O:50]2)(=O)=O)=CC=1>CS(C)=O.O>[Cl:30][C:12]1[C:13]([C:15]2[CH:20]=[CH:19][C:18]([F:21])=[C:17]([NH:22][CH2:23][CH:24]3[CH2:29][CH2:28][O:27][CH2:26][CH2:25]3)[N:16]=2)=[CH:14][C:9]([NH:8][C@H:5]2[CH2:6][CH2:7][C@H:2]([N:1]([CH:49]3[CH2:52][CH2:51][O:50]3)[CH3:31])[CH2:3][CH2:4]2)=[N:10][CH:11]=1
Reactant: O=C([O-])[O-]
Reactant: N[C@H]1CC[C@H](Nc2cc(-c3ccc(F)c(NCC4CCOCC4)n3)c(Cl)cn2)CC1
Reactant: Cc1ccc(S(=O)(=O)OCC2CCO2)cc1
Agent: [K+]
Solvent: CS(C)=O
Solvent: O
Product: CN(C1CCO1)[C@H]1CC[C@H](Nc2cc(-c3ccc(F)c(NCC4CCOCC4)n3)c(Cl)cn2)CC1
Temperature: 83 °C

Procedure:
To a stirred solution of N2′-(trans-4-aminocyclohexyl)-5′-chloro-5-fluoro-N6-((tetrahydro-2H-pyran-4-yl)methyl)-2,4′-bipyridine-2′,6-diamine (90 mg, 0.207 mmol)) in DMSO (1.0 ml) was add potassium carbonate (71.7 mg, 0.518 mmol), followed by follow oxetan-2-yl-methyl 4-methylbenzenesulfonate (151 mg, 0.622 mmol). The mixture was heated at 83° C. for 2 h. The mixture was allowed to cool to ambient temperature, then diluted with water and then extracted with EtOAc (×3). The organics were combined then washed with water (×2), saturated brine (×2), then dried (Na2SO4), filtered and evaporated under reduced pressure. The resulting residue was purified by reverse phase prep HPLC and lyophilized to yield titled compound. LCMS (m/z): 504.4/506.5 (MH+) retention time=0.60 min as a TFA salt.
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]2[C:8](=[C:9]([C:11]([NH2:13])=[O:12])[CH:10]=1)[NH:7][CH:6]=[C:5]2[CH:14]1[CH2:19][CH2:18][N:17]([S:20]([CH2:23][CH3:24])(=[O:22])=[O:21])[CH2:16][CH2:15]1.[CH:25]([C:27]1[CH:28]=[C:29](B(O)O)[CH:30]=[CH:31][CH:32]=1)=[O:26].C([O-])([O-])=O.[Cs+].[Cs+]>O1CCOCC1.O>[CH2:23]([S:20]([N:17]1[CH2:18][CH2:19][CH:14]([C:5]2[C:4]3[C:8](=[C:9]([C:11]([NH2:13])=[O:12])[CH:10]=[C:2]([C:31]4[CH:30]=[CH:29][CH:28]=[C:27]([CH:25]=[O:26])[CH:32]=4)[CH:3]=3)[NH:7][CH:6]=2)[CH2:15][CH2:16]1)(=[O:22])=[O:21])[CH3:24]
Reactant: O=Cc1cccc(B(O)O)c1
Reactant: CCS(=O)(=O)N1CCC(c2c[nH]c3c(C(N)=O)cc(Br)cc23)CC1
Agent: O=C([O-])[O-]
Agent: [Cs+]
Solvent: C1COCCO1
Solvent: O
Product: CCS(=O)(=O)N1CCC(c2c[nH]c3c(C(N)=O)cc(-c4cccc(C=O)c4)cc23)CC1
Temperature: 160 °C

Procedure:
To a solution of 5-bromo-3-[1-(ethylsulfonyl)-4-piperidinyl]-1H-indole-7-carboxamide (200 mg, 0.483 mmol) in dioxane (3.0 mL) and H2O (1.0 mL) was added (3-formylphenyl)boronic acid (317 mg, 1.93 mmol), and Cs2CO3 (315 mg, 0.97 mmol) in a microwave tube. The reaction mixture was degassed for 5 min before addition of tetrakis(triphenylphosphosphine) palladium (0) (48 mg, 0.043 mmol). The reaction was heated in a microwave for 30 min at 160° C. The organic layer was separated and concentrated. The residue was dissolved in MeOH until solid precipitated to yield 3-[1-(ethylsulfonyl)-4-piperidinyl]-5-(3-formylphenyl)-1H-indole-7-carboxamide.
Reaction SMILES: ClC1C=CC=C(C(OO)=[O:9])C=1.[CH3:12][O:13][C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][C:15]=1[S:20][CH3:21].[OH2:22]>C(Cl)Cl>[CH3:21][S:20]([C:15]1[CH:16]=[CH:17][CH:18]=[CH:19][C:14]=1[O:13][CH3:12])(=[O:9])=[O:22]
Reactant: COc1ccccc1SC
Reactant: O
Reactant: O=C(OO)c1cccc(Cl)c1
Solvent: ClCCl
Product: COc1ccccc1S(C)(=O)=O
Reaction time: 1 h
Yield: 91.6 %

Procedure:
m-Chloroperbenzoic acid (280 mg, 1.62 mmol) was added to a cold (0-4° C.) solution of 1-methoxy-2-methylsulfanyl-benzene (100 mg, 0.64 mmol) in DCM (3 mL) and stirring was continued for 1 hr. The reaction mixture was diluted with water and extracted with dichloromethane. The organic layer was washed with saturated brine solution, dried over sodium sulfate and concentrated under reduced pressure to afford 110 mg (91.6% Yield) of 1-methanesulfonyl-2-methoxy-benzene. Boron tribromide (370 mg, 1.47 mmol) was added to a cold solution (−70° C.) solution of 1-methanesulfonyl-2-methoxy-benzene (10 mg, 0.591 mmol) in DCM (2 mL) and stirring was continued for 10 minutes. After which the reaction mixture was stirred at ambient temperature overnight. The reaction mixture was diluted with water and extracted with dichloromethane. The organic layer was washed with saturated brine solution, dried over sodium sulfate and concentrated under reduced pressure to afford 65 mg (64.35% Yield) of 2-methanesulfonyl-phenol. 2-Methylsulfonyl-phenol was converted to 4-(2-methanesulfonyl-phenoxy)-piperidine hydrochloride according to Step 1 of the General Scheme).
Reaction SMILES: [Zn:1].[Br:2]CCBr.Cl[Si](C)(C)C.Br[CH2:12][C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=1[C:19]([F:22])([F:21])[F:20]>O1CCCC1>[Br-:2].[F:20][C:19]([F:22])([F:21])[C:14]1[CH:15]=[CH:16][CH:17]=[CH:18][C:13]=1[CH2:12][Zn+:1]
Reactant: [Zn]
Reactant: BrCCBr
Reactant: FC(F)(F)c1ccccc1CBr
Agent: C[Si](C)(C)Cl
Solvent: C1CCOC1
Product: FC(F)(F)c1ccccc1C[Zn+]
Product: [Br-]
Temperature: 60 °C
Reaction time: 0.25 h

Procedure:
In a dried flask zinc powder (2.489 g, 38.07 mmol) was suspended in anhydrous tetrahydrofuran (50 mL) under nitrogen. The resulting suspension was warmed to 60° C., then 1,2-dibromoethane (0.126 mL, 1.46 mmol) was added and stirred at that temperature for 15 min. It was cooled to room temperature, then chlorotrimethylsilane (0.149 mL, 1.17 mmol) was added and stirred for 20 min. 1-(Bromomethyl)-2-(trifluoromethyl)benzene (4.46 mL, 29.28 mmol) in THF (2 mL) was added dropwise and stirring was continued at room temperature for 4 h. Stirring was switched off to let the precipitates settle. The supernatant was used in the next transformation.