Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [F:1][C:2]1[CH:7]=[C:6](OS(C(F)(F)F)(=O)=O)[CH:5]=[C:4]([F:16])[C:3]=1[C:17]1[N:22]=[C:21]([C:23]([O:25][CH3:26])=[O:24])[CH:20]=[CH:19][C:18]=1[F:27].[S:28]1[CH2:33][CH:32]=[C:31](B(O)O)[CH2:30][CH2:29]1.C(Cl)Cl>COCCOC.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.Cl[Pd]Cl.[Fe+2]>[S:28]1[CH2:29][CH:30]=[C:31]([C:6]2[CH:5]=[C:4]([F:16])[C:3]([C:17]3[N:22]=[C:21]([C:23]([O:25][CH3:26])=[O:24])[CH:20]=[CH:19][C:18]=3[F:27])=[C:2]([F:1])[CH:7]=2)[CH2:32][CH2:33]1
Reactant: COC(=O)c1ccc(F)c(-c2c(F)cc(OS(=O)(=O)C(F)(F)F)cc2F)n1
Reactant: OB(O)C1=CCSCC1
Agent: Cl[Pd]Cl
Agent: [Fe+2]
Agent: c1ccc(P(c2ccccc2)[c-]2cccc2)cc1
Solvent: COCCOC
Solvent: ClCCl
Product: COC(=O)c1ccc(F)c(-c2c(F)cc(C3=CCSCC3)cc2F)n1
Temperature: 90 °C
Yield: 60 %

Procedure:
To a degassed solution of methyl 6-(2,6-difluoro-4-(trifluoromethylsulfonyloxy)phenyl)-5-fluoropicolinate (1.0 equiv.) and 3,6-dihydro-2H-thiopyran-4-ylboronic acid (1.5 equiv.) in DME/2M Na2CO3 (3/1, 0.10 M) was added PdCl2(dppf).CH2Cl2 adduct (0.10 equiv.). The reaction was heated to 90° C. in an oil bath for 15 min. The reaction mixture was partitioned with water and EtOAc; the organics were dried over MgSO4, filtered, and concentrated. The crude was purified via ISCO SiO2 chromatography. Pure fractions were combined and concentrated to yield methyl 6-(4-(3,6-dihydro-2H-thiopyran-4-yl)-2,6-difluorophenyl)-5-fluoropicolinate in 60% yield. LC/MS=366.1 (M+H), Rt=1.00 min.
Reaction SMILES: Cl[N:2]1[CH2:7][CH2:6][CH:5]([N:8]2[C:13]3[CH:14]=[CH:15][CH:16]=[CH:17][C:12]=3[CH2:11][O:10][C:9]2=[O:18])[CH2:4][CH2:3]1.O=O.[K+].C1OCCOCCOCCOCCOCCOC1.C[Si]([C:44]#[N:45])(C)C>CCOCC>[C:44]([CH:3]1[CH2:4][CH:5]([N:8]2[C:13]3[CH:14]=[CH:15][CH:16]=[CH:17][C:12]=3[CH2:11][O:10][C:9]2=[O:18])[CH2:6][CH2:7][NH:2]1)#[N:45]
Reactant: O=C1OCc2ccccc2N1C1CCN(Cl)CC1
Reactant: C[Si](C)(C)C#N
Agent: C1COCCOCCOCCOCCOCCO1
Agent: O=O
Agent: [K+]
Solvent: CCOCC
Product: N#CC1CC(N2C(=O)OCc3ccccc32)CCN1
Temperature: 25 °C
Reaction time: 18 h

Procedure:
1-(N-chloro-4-piperidyl)-3,1-benzoxazin-2-one from Step 1 above (230 mg, 0.86 mmol) was dissolved in warm ether (30 mL) and the solution was added dropwise to a suspension of potassium superoxide (135 mg, 1.9 mmol) and 18-crown-6 (10 mg, 0.04 mmol) in ether (10 mL). The mixture was stirred at ambient temperature for five days, with two additional lots of 135 mg each of potassium superoxide being added on the second and third days. The reaction was filtered and the filtrate was added dropwise to an ether solution of trimethylsilylcyanide (0.172 mL, 128 mg, 1.3 mmol). The mixture was stirred at ambient temperature for 18 hours, then evaporated to dryness in vacuo. The residue was chromatographed on silica gel eluted with 4:96 MeOH:CH2Cl2. The combined product fractions were evaporated to dryness in vacuo, and the residue was evaporated twice from ether to give 1-(2-cyano-4-piperidyl)-3,1-benzoxazin-2-one: MS (FAB): M+H @ m/e=258.
Reaction SMILES: [C:1]([C:4]1[CH:5]=[CH:6][C:7]2[NH:13][CH:12]([CH2:14][C:15]([O:17][CH3:18])=[O:16])[C:11](=[O:19])[N:10]([CH3:20])[CH2:9][C:8]=2[CH:21]=1)([OH:3])=[O:2].[C:22](OC(=O)C)(=[O:24])[CH3:23]>C(O)(=O)C>[C:22]([N:13]1[C:7]2[CH:6]=[CH:5][C:4]([C:1]([OH:3])=[O:2])=[CH:21][C:8]=2[CH2:9][N:10]([CH3:20])[C:11](=[O:19])[CH:12]1[CH2:14][C:15]([O:17][CH3:18])=[O:16])(=[O:24])[CH3:23]
Reactant: COC(=O)CC1Nc2ccc(C(=O)O)cc2CN(C)C1=O
Reactant: CC(=O)OC(C)=O
Solvent: CC(=O)O
Product: COC(=O)CC1C(=O)N(C)Cc2cc(C(=O)O)ccc2N1C(C)=O
Reaction time: 48 h
Yield: 78 %

Procedure:
Methyl (±)-7-carboxy-4-methyl-3-oxo-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-2-acetate (2.0 g, 8.6 mmol), acetic anhydride (25 mL) and acetic acid (1 mL) were heated to reflux. After 48 h, the reaction was concentrated, and the residue was diluted with H2O (20 mL) and MeOH (15 mL). The resulting solution was concentrated to give the tide compound (1.8 g, 78%): 1H NMR (400 MHz, DMSO-d6) δ1.7-1.8 (s, 3H), 2.2-2.6 (m, 2H), 2.9-3.0 (s, 3H), 3.5-3.6 (s, 3H), 4.2-4.3 (d, 1H), 4.7-4.8 (d, 1H), 5.8-5.9 (t, 1H), 7.5-7.6 (d, 1H), 7.9-8.0 (dd, 1H), 8.1-8.2 (d, 1H); MS (ES) m/e 335.0 (M+H)+.
Reaction SMILES: [C:1]([O:4][CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH2:14][C:15](Cl)=[O:16])(=[O:3])[CH3:2].[Cl-].[Al+3].[Cl-].[Cl-].[CH3:22][O:23][C:24]1[CH:25]=[C:26]([CH3:34])[CH:27]=[C:28]([O:32]C)[C:29]=1[O:30][CH3:31]>ClCCCl>[C:1]([O:4][CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][CH2:13][CH2:14][C:15]([C:27]1[C:28]([OH:32])=[C:29]([O:30][CH3:31])[C:24]([O:23][CH3:22])=[CH:25][C:26]=1[CH3:34])=[O:16])(=[O:3])[CH3:2]
Reactant: CC(=O)OCCCCCCCCCCC(=O)Cl
Reactant: COc1cc(C)cc(OC)c1OC
Agent: [Al+3]
Agent: [Cl-]
Solvent: ClCCCl
Product: COc1cc(C)c(C(=O)CCCCCCCCCCOC(C)=O)c(O)c1OC
Temperature: 25 °C
Reaction time: 2 h
Yield: 79.8 %

Procedure:
To a solution (150 ml) of 11-acetoxy-n-undecanoyl chloride (27.6 g) in 1,2-dichloroethane is added aluminum chloride (28 g), and the mixture is stirred at room temperature for 2 hours. The reaction mixture is cooled to 5° C. followed by addition of a solution (50 ml) of 3,4,5-trimethoxytoluene (19.1 g) in 1,2-dichloroethane and the whole mixture is stirred at room temperature for 72 hours. The reaction mixture is then heated to 50°-60° C. and stirred for 30 minutes. After cooling, 300 ml of ice water is added to the reaction mixture and the product is extracted with dichloromethane. The dichloromethane layer is washed with water and dried over anhydrous magnesium sulfate, and the solvent is distilled off to give a light-yellow oil of 6-(11-acetoxy-1-oxoundecyl)-2,3-dimethoxy-5-methylphenol (33 g).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([NH:9][C:10]2[N:15]=[C:14](Cl)[N:13]=[C:12]([Cl:17])[N:11]=2)=[CH:5][CH:4]=1.[NH2:18][C:19]1[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=1.C(N(C(C)C)CC)(C)C>C(#N)C>[Cl:17][C:12]1[N:11]=[C:10]([NH:9][C:6]2[CH:5]=[CH:4][C:3]([O:2][CH3:1])=[CH:8][CH:7]=2)[N:15]=[C:14]([NH:18][C:19]2[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=2)[N:13]=1
Reactant: COc1ccc(Nc2nc(Cl)nc(Cl)n2)cc1
Reactant: Nc1ccccc1
Solvent: CC#N
Solvent: CCN(C(C)C)C(C)C
Product: COc1ccc(Nc2nc(Cl)nc(Nc3ccccc3)n2)cc1
Reaction time: 24 h
Yield: 57 %

Procedure:
To a solution of 2-(4-methoxyphenyl)amino-4,6-dichloro-1,3,5-triazine (57 mg, 0.21 mmoles) in acetonitrile (0.5 ml) was added a solution of aniline (0.021 ml, 0.23 mmoles) and diisopropylethylamine (0.05 ml, 0.29 mmoles) in acetonitrile (0.5 ml). After stirring for 24 hours, the mixture was concentrated under vacuum and the residue was dissolved in ethyl acetate (10 ml). The solution was washed with a solution composed of saturated aqueous sodium chloride solution and 1 M hydrochloric acid (1: 1, 2×10 ml), dried over sodium sulfate, filtered, and concentrated under vacuum. The residue was purified by flash chromatography on silica gel eluting with 10% ethyl acetate-hexane to provide CT-31942 (38 mg, 57% yield). 1H NMR (d6-DMSO) δ 10.00–10.22 (m, 2 H), 7.26–7.82 (m, 6 H), 7.01–7.10 (m, 1 H), 6.91 (d, J=9 Hz, 2 H), 3.74 (s, 3 H).
Reaction SMILES: C(OC([N:8]1[CH2:13][CH2:12][N:11]([CH2:14][CH2:15][N:16]2[CH2:21][CH2:20][O:19][C@H:18]([CH2:22][O:23][CH3:24])[CH2:17]2)[CH2:10][C@H:9]1[CH2:25][C:26]1[CH:31]=[CH:30][C:29]([CH3:32])=[C:28]([O:33][Si:34]([C:47]([CH3:50])([CH3:49])[CH3:48])([C:41]2[CH:46]=[CH:45][CH:44]=[CH:43][CH:42]=2)[C:35]2[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=2)[CH:27]=1)=O)(C)(C)C.FC(F)(F)C(O)=O>ClCCl>[Si:34]([O:33][C:28]1[CH:27]=[C:26]([CH:31]=[CH:30][C:29]=1[CH3:32])[CH2:25][C@@H:9]1[CH2:10][N:11]([CH2:14][CH2:15][N:16]2[CH2:21][CH2:20][O:19][C@H:18]([CH2:22][O:23][CH3:24])[CH2:17]2)[CH2:12][CH2:13][NH:8]1)([C:47]([CH3:48])([CH3:49])[CH3:50])([C:35]1[CH:40]=[CH:39][CH:38]=[CH:37][CH:36]=1)[C:41]1[CH:42]=[CH:43][CH:44]=[CH:45][CH:46]=1
Reactant: COC[C@@H]1CN(CCN2CCN(C(=O)OC(C)(C)C)[C@H](Cc3ccc(C)c(O[Si](c4ccccc4)(c4ccccc4)C(C)(C)C)c3)C2)CCO1
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: COC[C@@H]1CN(CCN2CCN[C@H](Cc3ccc(C)c(O[Si](c4ccccc4)(c4ccccc4)C(C)(C)C)c3)C2)CCO1
Temperature: 25 °C
Reaction time: 0.5 h
Yield: 101 %

Procedure:
To a solution of (2R)-1-tert-butoxycarbonyl-2-(3-tert-butyldiphenylsilyloxy-4-methylbenzyl)-4-[2-[(2S)-2-methoxymethylmorpholino]ethyl]piperazine (13.43 g) in dichloromethane (67.0 ml) was added trifluoroacetic acid (67.0 ml) at 0° C. After stirring at room temperature for 30 minutes, the mixture was concentrated and was added dropwise saturated aqueous sodium hydrogen carbonate solution. After stirring at room temperature for 30 minutes, the mixture was extracted with dichloromethane (100 ml×1, 50 ml×2). The combined extracts were dried over magnesium sulfate and evaporated under reduced pressure to give (2R)-2-(3-tert-butyldiphenylsilyloxy-4-methylbenzyl)-4-[2-[(2S)-2-methoxymethylmorpholino]ethyl]piperazine (11.63 g) as a brown oil.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([CH:16]=[CH:17][C:18]=1[Cl:19])[CH2:5][S:6][C:7]1[C:8](=[O:15])[O:9][C:10]([CH3:14])=[CH:11][C:12]=1[OH:13].C(OO)(=[O:22])C>C(O)(=O)C>[Cl:1][C:2]1[CH:3]=[C:4]([CH:16]=[CH:17][C:18]=1[Cl:19])[CH2:5][S:6]([C:7]1[C:8](=[O:15])[O:9][C:10]([CH3:14])=[CH:11][C:12]=1[OH:13])=[O:22]
Reactant: CC(=O)OO
Reactant: Cc1cc(O)c(SCc2ccc(Cl)c(Cl)c2)c(=O)o1
Solvent: CC(=O)O
Product: Cc1cc(O)c(S(=O)Cc2ccc(Cl)c(Cl)c2)c(=O)o1

Procedure:
3-(3,4-Dichlorobenzylthio)-4-hydroxy-6-methyl-2-pyrone (12.0 g., 0.037 mole) and 40% peroxyacetic acid (7.2 g., 0.0378 mole) were dissolved in glacial acetic acid (200 ml.). After a day there was no peroxide left and a solid had crystallized. The mixture was diluted with water and extracted with methylene chloride. The extract was dried (MgSO4) and evaporated to dryness leaving 11.9 g. (95 percent) of an off-white solid. Recrystallization from benzene gave the pure product as a white solid, m.p. 144°-146°C.
Reaction SMILES: [CH3:1][C:2]1[CH:3]=[CH:4][CH:5]=[C:6]2[C:10]=1[NH:9][C:8](=[O:11])[C:7]2=[O:12].S(OOS([O-])(=O)=O)([O-])(=O)=[O:14].[K+].[K+].S(=O)(=O)(O)O>>[CH3:1][C:2]1[C:10]2[NH:9][C:8](=[O:11])[C:7](=[O:12])[O:14][C:6]=2[CH:5]=[CH:4][CH:3]=1
Reactant: Cc1cccc2c1NC(=O)C2=O
Reactant: O=S(=O)([O-])OOS(=O)(=O)[O-]
Agent: O=S(=O)(O)O
Agent: [K+]
Product: Cc1cccc2oc(=O)c(=O)[nH]c12

Procedure:
32.2 parts of 7-methylisatin are introduced into a solution of 56 parts of potassium peroxydisulfate in 450 parts of 92% strength sulfuric acid at from 0° C. to 10° C. The mixture is then stirred for a few minutes, after which it is poured onto ice. The product is filtered off and dried, giving 31.4 parts of 5-methyl-2,3-dioxo-1,4-benzoxazine, of melting point 247°-249° C.
Reaction SMILES: Cl.Cl.[CH2:3]([NH:10][C@@H:11]1[CH2:15][CH2:14][NH:13][CH2:12]1)[C:4]1[CH:9]=[CH:8][CH:7]=[CH:6][CH:5]=1.Cl[C:17]1[N:22]([CH3:23])[C:21](=[O:24])[CH:20]=[C:19]([C:25]2[CH:30]=[CH:29][N:28]=[CH:27][CH:26]=2)[N:18]=1.C(N(CC)CC)C>O1CCCC1>[CH2:3]([NH:10][C@@H:11]1[CH2:15][CH2:14][N:13]([C:17]2[N:22]([CH3:23])[C:21](=[O:24])[CH:20]=[C:19]([C:25]3[CH:26]=[CH:27][N:28]=[CH:29][CH:30]=3)[N:18]=2)[CH2:12]1)[C:4]1[CH:5]=[CH:6][CH:7]=[CH:8][CH:9]=1
Reactant: c1ccc(CN[C@@H]2CCNC2)cc1
Reactant: Cn1c(Cl)nc(-c2ccncc2)cc1=O
Agent: Cl
Solvent: CCN(CC)CC
Solvent: C1CCOC1
Product: Cn1c(N2CC[C@@H](NCc3ccccc3)C2)nc(-c2ccncc2)cc1=O
Yield: 73.8 %

Procedure:
A solution of (R)-benzylpyrrolidin-3-yl-amine dihydrochloride (3.0 g, 12 mmol), 2-chloro-3-methyl-6-(pyridin-4-yl)-3H-pyrimidin-4-one (2.6 g, 12 mmol), and triethylamine (6 g, 60 mmol) in tetrahydrofuran (40 ml) was stirred for 12 hours at 95° C. The solvent was evaporated off under reduced pressure and the residue was partitioned between water and dichloromethane. The organic layer was dried over sodium sulfate and the solvent was evaporated under reduced pressure. The obtained residue was purified by silica gel column chromatography (eluent; ethyl acetate) to afford 2-((R)-3-benzylaminopyrrolidin-1-yl)-3-methyl-6-pyridin-4-yl-3H-pyrimidin-4-one (3.2 g, 75%) as pale yellow oil.
Reaction SMILES: Cl.[NH2:2][C@H:3]1[CH2:8][CH2:7][C@H:6]([NH:9][C:10]([C:12]2[C:16]3[N:17]=[CH:18][N:19]=[C:20]([C:21]4[CH:26]=[C:25]([CH:27]([CH3:29])[CH3:28])[CH:24]=[CH:23][C:22]=4[O:30][CH2:31][CH:32]4[CH2:34][CH2:33]4)[C:15]=3[NH:14][C:13]=2[CH3:35])=[O:11])[CH2:5][CH2:4]1.[CH3:36][O:37][CH2:38][C:39](Cl)=[O:40]>>[CH:32]1([CH2:31][O:30][C:22]2[CH:23]=[CH:24][C:25]([CH:27]([CH3:29])[CH3:28])=[CH:26][C:21]=2[C:20]2[C:15]3[NH:14][C:13]([CH3:35])=[C:12]([C:10]([NH:9][C@H:6]4[CH2:7][CH2:8][C@H:3]([NH:2][C:39](=[O:40])[CH2:38][O:37][CH3:36])[CH2:4][CH2:5]4)=[O:11])[C:16]=3[N:17]=[CH:18][N:19]=2)[CH2:33][CH2:34]1
Reactant: COCC(=O)Cl
Reactant: Cc1[nH]c2c(-c3cc(C(C)C)ccc3OCC3CC3)ncnc2c1C(=O)N[C@H]1CC[C@H](N)CC1
Agent: Cl
Product: COCC(=O)N[C@H]1CC[C@H](NC(=O)c2c(C)[nH]c3c(-c4cc(C(C)C)ccc4OCC4CC4)ncnc23)CC1

Procedure:
Starting from N-(trans-4-aminocyclohexyl)-4-[2-(cyclopropylmethoxy)-5-(propan-2-yl)phenyl]-6-methyl-5H-pyrrolo[3,2-d]pyrimidine-7-carboxamide hydrochloride (example D.f53) and commercially available methoxy-acetyl chloride the title compound is obtained as colorless solid.
Reaction SMILES: C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.BrN1C(=O)CCC1=O.[Br:28][C:29]1[CH:37]=[C:36]2[C:32]([C:33]([C:41]([OH:43])=O)=[CH:34][N:35]2[CH:38]([CH3:40])[CH3:39])=[CH:31][CH:30]=1.[NH2:44][C:45]1[S:46][CH:47]=[CH:48][N:49]=1>C(Cl)Cl>[S:46]1[CH:47]=[CH:48][N:49]=[C:45]1[NH:44][C:41]([C:33]1[C:32]2[C:36](=[CH:37][C:29]([Br:28])=[CH:30][CH:31]=2)[N:35]([CH:38]([CH3:39])[CH3:40])[CH:34]=1)=[O:43]
Reactant: Nc1nccs1
Reactant: CC(C)n1cc(C(=O)O)c2ccc(Br)cc21
Agent: O=C1CCC(=O)N1Br
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: ClCCl
Product: CC(C)n1cc(C(=O)Nc2nccs2)c2ccc(Br)cc21
Temperature: 0 °C
Reaction time: 0.25 h
Yield: 11.6 %

Procedure:
A solution of triphenylphosphine (2.42 mg, 9.22 mmol) in methylene chloride (25 mL) cooled to 0° C. was treated with N-bromosuccinimide (1.64 mg, 9.22 mmol). The reaction was stirred at 0° C. for 15 min. At this time, the reaction was treated with 6-bromo-1-isopropyl-1H-indole-3-carboxylic acid (2.0 g, 7.09 mmol). The reaction was stirred at 0° C. for 15 min and then was allowed to warm to 25° C. where it was stirred for 15 min. The reaction was then treated with 2-aminothiazole (1.63 g, 16.31 mmol) and stirred at 25° C. for 18 h. At this time, the mixture was partitioned between water (150 mL) and ethyl acetate (150 mL) and treated with a 1N aqueous hydrochloric acid solution (100 mL). The organic layer was washed with a saturated aqueous sodium bicarbonate solution (1×100 mL), water (1×100 mL), and a saturated aqueous sodium chloride solution (1×100 mL). The organic layer was then dried over magnesium sulfate, filtered, and concentrated in vacuo. Biotage chromatography (FLASH 40M, Silica, 1/1 hexanes/ethyl acetate) afforded 6-bromo-1-isopropyl-1H-indole-3-carboxylic acid thiazol-2-ylamide (300 mg, 11.6%) as white solid: mp 205-207° C.; EI-HRMS m/e calcd for C15H14BrN3OS (M+) 363.0041, found 363.0034.
Reaction SMILES: [CH2:1]([O:3][C:4]([C:6]1[O:10][C:9]([C:11]2[CH:16]=[CH:15][C:14]([O:17][CH3:18])=[CH:13][CH:12]=2)=[N:8][C:7]=1[CH2:19][OH:20])=[O:5])[CH3:2].[O:21]1[CH:26]=[CH:25][CH2:24][CH2:23][CH2:22]1.C1(C)C=CC(S([O-])(=O)=O)=CC=1.[NH+]1C=CC=CC=1>ClCCl>[CH2:1]([O:3][C:4]([C:6]1[O:10][C:9]([C:11]2[CH:16]=[CH:15][C:14]([O:17][CH3:18])=[CH:13][CH:12]=2)=[N:8][C:7]=1[CH2:19][O:20][CH:22]1[CH2:23][CH2:24][CH2:25][CH2:26][O:21]1)=[O:5])[CH3:2]
Reactant: CCOC(=O)c1oc(-c2ccc(OC)cc2)nc1CO
Reactant: C1=COCCC1
Agent: Cc1ccc(S(=O)(=O)[O-])cc1
Agent: c1cc[nH+]cc1
Solvent: ClCCl
Product: CCOC(=O)c1oc(-c2ccc(OC)cc2)nc1COC1CCCCO1
Temperature: 25 °C
Reaction time: 8 h

Procedure:
10.0 g 4-Hydroxymethyl-2-(4-methoxy-phenyl)-oxazole-5-carboxylic acid ethyl ester were dissolved in 85 ml dichloromethane. 4.0 ml 3,4-dihydro-2H-pyran and 1.85 mg pyridinium p-toluenesulfonate were added and the reaction mixture stirred at room temperature overnight. The solvent was removed in vacuo and the residue purified by flash chromatography on silica gel (eluting with n-heptane:ethyl acetate=4:1=>1:1) to obtain 12.3 g 2-(4-Methoxy-phenyl)-4-(tetrahydro-pyran-2-yloxymethyl)-oxazole-5-carboxylic acid ethyl ester as an oil.
Reaction SMILES: [CH3:1][N:2]([CH3:17])[S:3]([O:6][C:7]1[CH:12]=[CH:11][CH:10]=[CH:9][C:8]=1[S:13]([NH2:16])(=[O:15])=[O:14])(=[O:5])=[O:4].CCCCN=[C:23]=[O:24].C1N2CCN(CC2)C1.C(Cl)(Cl)=O>>[CH3:1][N:2]([CH3:17])[S:3]([O:6][C:7]1[CH:12]=[CH:11][CH:10]=[CH:9][C:8]=1[S:13]([N:16]=[C:23]=[O:24])(=[O:15])=[O:14])(=[O:4])=[O:5]
Reactant: CN(C)S(=O)(=O)Oc1ccccc1S(N)(=O)=O
Reactant: CCCCN=C=O
Agent: C1CN2CCN1CC2
Agent: O=C(Cl)Cl
Product: CN(C)S(=O)(=O)Oc1ccccc1S(=O)(=O)N=C=O
Temperature: 25 °C

Procedure:
To 6.0 g (0.021 mole) 2-(dimethylaminosulfonyloxy)benzenesulfonamide suspended in 75 ml dry xylenes was added 2.1 g (0.021 mole) N-butyl isocyanate and a catalytic amount of 1,4-diazobicyclo[2.2.2]octane (~0.05 g). This mixture was rapidly heated to reflux temperature (~135° C.) and 3.0 ml of phosgene was slowly added (at such a rate as to keep the reaction temperature greater than 128° C.). The phosgene addition required ~3 hours. The reaction was cooled to room temperature, filtered under N2, and the solvent evaporated under reduced pressure. The infrared spectrum of the resultant oil ws consistent for 2-(dimethylaminosulfonyloxy)benzenesulfonyl isocyanate (2240 cm-1).
Reaction SMILES: Br[C:2]1C(Cl)=NC(Cl)=NC=1.[Br:10][C:11]1[C:12]([NH:18][CH:19]([CH:29]([CH3:31])[CH3:30])[CH2:20][NH:21][C:22](=[O:28])[O:23][C:24]([CH3:27])([CH3:26])[CH3:25])=[N:13][C:14]([Cl:17])=[N:15][CH:16]=1>>[Br:10][C:11]1[C:12]([NH:18][C@@H:19]([C:29]([CH3:2])([CH3:31])[CH3:30])[CH2:20][NH:21][C:22](=[O:28])[O:23][C:24]([CH3:25])([CH3:26])[CH3:27])=[N:13][C:14]([Cl:17])=[N:15][CH:16]=1
Reactant: Clc1ncc(Br)c(Cl)n1
Reactant: CC(C)C(CNC(=O)OC(C)(C)C)Nc1nc(Cl)ncc1Br
Product: CC(C)(C)OC(=O)NC[C@@H](Nc1nc(Cl)ncc1Br)C(C)(C)C

Procedure:
Intermediate J was hydrogenated using 10% Pd/C under hydrogen at 50 psi in a pressure vessel to afford tert-butyl N-[(2S)-2-amino-3,3-dimethyl-butyl]carbamate which was then reacted with 5-bromo-2,4-dichloro-pyrimidine using analogous reaction conditions as described using analogous reaction conditions as described for tert-butyl N-[2-[(5-bromo-2-chloro-pyrimidin-4-yl)amino]-3-methyl-butyl]carbamate to afford tert-butyl N-[(2S)-2-[(5-bromo-2-chloro-pyrimidin-4-yl)amino]-3,3-dimethyl-butyl]carbamate. LCMS (ESI) 407 (M+H).
Reaction SMILES: [CH2:1]([O:3][CH2:4][C:5](Cl)=[O:6])[CH3:2].[F:8][C:9]1[CH:14]=[CH:13][C:12]([C:15]2[CH:19]=[C:18]([CH2:20][NH:21][C:22]3[C:27]([CH3:28])=[C:26]([CH3:29])[N:25]=[C:24]([N:30]([CH2:40][C:41]4[CH:46]=[CH:45][C:44]([O:47][CH3:48])=[CH:43][CH:42]=4)[CH2:31][C:32]4[CH:37]=[CH:36][C:35]([O:38][CH3:39])=[CH:34][CH:33]=4)[C:23]=3[NH2:49])[O:17][N:16]=2)=[CH:11][CH:10]=1.C(N(CC)CC)C>ClCCl>[CH3:48][O:47][C:44]1[CH:43]=[CH:42][C:41]([CH2:40][N:30]([CH2:31][C:32]2[CH:33]=[CH:34][C:35]([O:38][CH3:39])=[CH:36][CH:37]=2)[C:24]2[C:23]([NH:49][C:5](=[O:6])[CH2:4][O:3][CH2:1][CH3:2])=[C:22]([NH:21][CH2:20][C:18]3[O:17][N:16]=[C:15]([C:12]4[CH:13]=[CH:14][C:9]([F:8])=[CH:10][CH:11]=4)[CH:19]=3)[C:27]([CH3:28])=[C:26]([CH3:29])[N:25]=2)=[CH:46][CH:45]=1
Reactant: COc1ccc(CN(Cc2ccc(OC)cc2)c2nc(C)c(C)c(NCc3cc(-c4ccc(F)cc4)no3)c2N)cc1
Reactant: CCOCC(=O)Cl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CCOCC(=O)Nc1c(N(Cc2ccc(OC)cc2)Cc2ccc(OC)cc2)nc(C)c(C)c1NCc1cc(-c2ccc(F)cc2)no1
Reaction time: 0.7 h
Yield: 91.3 %

Procedure:
Under a nitrogen atmosphere, ethoxyacetyl chloride (1.4 g, 11 mmol) was added dropwise to a solution of N4-{[3-(4-fluorophenyl)isoxazol-5-yl]methyl}-N2,N2-bis(4-methoxybenzyl)-5,6-dimethylpyridine-2,3,4-triamine (5.898 g, 10.39 mmol) and triethylamine (2.2 mL, 15 mmol) in dichloromethane (30 mL) at 0° C. After the reaction was stirred for 0.7 hours, an analysis by HPLC indicated the presence of starting material, and additional ethoxyacetyl chloride (0.54 g) was added. The stirring was continued, and after 1.5 hours, the reaction mixture was diluted with dichloromethane and washed sequentially with saturated aqueous potassium carbonate, water, and brine; dried over sodium sulfate, filtered, and concentrated under reduced pressure to provide 6.2 g of N-[2-[bis(4-methoxybenzyl)amino]-4-({[3-(4-fluorophenyl)isoxazol-5-yl]methyl}amino)-5,6-dimethylpyridin-3-yl]-2-ethoxyacetamide as a yellow oil.
Reaction SMILES: [CH3:1][C:2]1([CH3:17])[CH2:7][O:6][P:5](=[O:16])([O:8][CH2:9][CH:10]2[CH2:15][CH2:14][CH2:13][CH:12]=[CH:11]2)[O:4][CH2:3]1.C(OO)(=[O:20])C.O>C(Cl)Cl>[CH3:1][C:2]1([CH3:17])[CH2:3][O:4][P:5](=[O:16])([O:8][CH2:9][CH:10]2[CH2:15][CH2:14][CH:13]3[CH:12]([O:20]3)[CH2:11]2)[O:6][CH2:7]1
Reactant: CC(=O)OO
Reactant: CC1(C)COP(=O)(OCC2C=CCCC2)OC1
Solvent: ClCCl
Solvent: O
Product: CC1(C)COP(=O)(OCC2CCC3OC3C2)OC1

Procedure:
A 500 mL round bottom flask equipped with a stirrer bar was charged with 15.5 g (0.058 mol) 3-(5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorinanoxymethyl)-1-cyclohexene, and 100 mL of methylene chloride. Peracetic acid (13.76 g, 35 wt. % in acetic acid; 0.058 mol) in methylene chloride (60 mL) was added dropwise to above mixture over 20 min. in an ice bath. After the above mixture was reacted at room temperature overnight, 100 mL of water was added to above reaction mixture, the water layer was extracted with methylene chloride (2×100 mL), the organic layer was combined, and washed with saturated sodium carbonate solution (2×100 mL), then with water (2×100 mL), dried with sodium sulfate. The solvent was evaporated and the residue distilled to give pure product.
Reaction SMILES: COC1C=C(OC)C=CC=1C[NH:6][C:7]1[CH:16]=[N:15][C:14]2[C:9](=[CH:10][CH:11]=[C:12]([O:17][CH3:18])[CH:13]=2)[N:8]=1.C(O)(C(F)(F)F)=O>ClCCl>[CH3:18][O:17][C:12]1[CH:13]=[C:14]2[C:9](=[CH:10][CH:11]=1)[N:8]=[C:7]([NH2:6])[CH:16]=[N:15]2
Reactant: COc1ccc(CNc2cnc3cc(OC)ccc3n2)c(OC)c1
Solvent: ClCCl
Solvent: O=C(O)C(F)(F)F
Product: COc1ccc2nc(N)cnc2c1
Yield: 99.4 %

Procedure:
N-(2,4-Dimethoxybenzyl)-6-methoxyquinoxalin-2-amine (2.8 g, 8.61 mmol) was stirred in TFA (10 mL, 130 mmol) and dichloromethane (10 mL) at ambient temperature for 30 min. The solvents were removed in vacuo. Saturated aq. sodium hydrogen carbonate (200 mL) was added to the red residue, which then precipitated a yellow solid. The mixture was extracted extensively with dichloromethane. The organic layer was dried over sodium sulfate, filtered and concentrated in vacuo to afford 6-methoxyquinoxalin-2-amine (1.50 g, 8.56 mmol, 99% yield). 1H NMR (400 MHz, CDCl3) δ ppm 8.27 (1H, s), 7.54-7.58 (1H, m), 7.25-7.29 (2H, m), 4.71 (2H, br. s.), 3.90 (3H, s). MS (LC/MS) R.T.=0.86; [M+H]+=176.23.
Reaction SMILES: [CH2:1]([O:4][C:5]1[CH:10]=[CH:9][C:8]([CH:11]2[CH2:16][CH2:15][NH:14][CH2:13][CH2:12]2)=[CH:7][CH:6]=1)[CH2:2][CH3:3].Br[C:18]1[CH:23]=[CH:22][C:21]([C@@H:24]([NH:26][C:27](=[O:29])[CH3:28])[CH3:25])=[CH:20][CH:19]=1.C(P(C(C)(C)C)C1C=CC=CC=1C1C=CC=CC=1)(C)(C)C>O1CCOCC1>[CH2:1]([O:4][C:5]1[CH:10]=[CH:9][C:8]([CH:11]2[CH2:12][CH2:13][N:14]([C:18]3[CH:23]=[CH:22][C:21]([C@@H:24]([NH:26][C:27](=[O:29])[CH3:28])[CH3:25])=[CH:20][CH:19]=3)[CH2:15][CH2:16]2)=[CH:7][CH:6]=1)[CH2:2][CH3:3]
Reactant: CC(=O)N[C@@H](C)c1ccc(Br)cc1
Reactant: CCCOc1ccc(C2CCNCC2)cc1
Agent: CC(C)(C)P(c1ccccc1-c1ccccc1)C(C)(C)C
Solvent: C1COCCO1
Product: CCCOc1ccc(C2CCN(c3ccc([C@H](C)NC(C)=O)cc3)CC2)cc1
Temperature: 70 °C
Reaction time: 12 h

Procedure:
80 mg (0.37 mmol) 4-(4-Propoxy-phenyl)-piperidine (II.3) are added to a mixture of 88 mg (0.37 mmol) (S)—N-[1-(4-bromo-phenyl)-ethyl]-acetamide (III.1), 145 mg (97%, 1.46 mmol) sodium tert-butyrat, 44 mg (0.15 mmol) 2-(di-tert-butylphosphino)biphenyl and 33 mg (0.036 mmol) tris-(dibenzylidenaceton)-dipalladium(0) in 2.0 mL 1,4-dioxane. The mixture is stirred for 12 h at 70° C. After that time, the mixture is filtered over celite, the solvent is removed in vacuo and the residue is purified by HPLC (column: Waters XBridge 5 μM; eluent A: water+0.3% NH4OH, eluent B: MeOH) to yield the desired product.