Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [OH:1][N:2]1[C:6](=[O:7])[C:5]2=[CH:8][CH:9]=[CH:10][CH:11]=[C:4]2[C:3]1=[O:12].[C:13]1(B(O)O)[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1.N1C=CC=CC=1>[Cu]Cl.ClCCCl>[O:1]([N:2]1[C:3](=[O:12])[C:4]2=[CH:11][CH:10]=[CH:9][CH:8]=[C:5]2[C:6]1=[O:7])[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1
Reactant: OB(O)c1ccccc1
Reactant: O=C1c2ccccc2C(=O)N1O
Agent: Cl[Cu]
Solvent: c1ccncc1
Solvent: ClCCCl
Product: O=C1c2ccccc2C(=O)N1Oc1ccccc1
Temperature: 25 °C
Yield: 90.3 %

Procedure:
A 20 mL scintillation vial was charged with N-hydroxyphthalimide (163 mg, 1.0 mmol), copper (I) chloride (99 mg, 1.0 mmol), freshly activated 4 Å molecular sieves (˜250 mg), and phenylboronic acid (244 mg, 2.0 mmol). 1,2-Dichloroethane (5 mL) was added followed by pyridine (90 μL, 1.1 mmol), resulting in a light brown suspension. The cap was loosely applied such that the reaction suspension was open to air and stirred at room temperature until completion as detected by analytical RP-HPLC (mixture color turned from brown to emerald green as the reaction proceeded). Upon completion (˜48 h), the mixture was adsorbed onto silica gel and concentrated to a powder. Flash chromatographic purification over silica (25% EtOAc in hexanes) afforded N-phenoxyphthalimide 9 as a white solid (216 mg, 90%); see below for characterization data.
Reaction SMILES: [CH2:1]([C:8]([C:21]#[N:22])([CH2:14][C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=1)[C:9]([O:11]CC)=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[OH-].[K+]>O.C(O)C.O>[CH2:14]([C:8]([C:21]#[N:22])([CH2:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1)[C:9]([OH:11])=[O:10])[C:15]1[CH:16]=[CH:17][CH:18]=[CH:19][CH:20]=1
Reactant: CCOC(=O)C(C#N)(Cc1ccccc1)Cc1ccccc1
Agent: [K+]
Agent: [OH-]
Solvent: CCO
Solvent: O
Product: N#CC(Cc1ccccc1)(Cc1ccccc1)C(=O)O
Yield: 100 %

Procedure:
Ethyl 2-benzyl-2-cyano-3-phenylpropionate (3.20 g, 11 mmol) was saponified at room temperature overnight with potassium hydroxide (6.17 g, 0.11 mol) in 10% water/ethanol. The mixture was diluted with water (200 mL) and extracted with hexane (2×50 mL). The aqueous layer was acidified with 1M phosphoric acid and extracted with methylene chloride (4×100 mL). The combined organic extracts were dried over magnesium sulfate and freed of solvent to afford 2-benzyl-2-cyano-3-phenylpropionic acid (2.94 g, 11 mmol) as a colorless solid: 1H NMR (CDCl3, 300 MHz) δ 7.34 (br s, 10 H), 3.24 (dd, J=13.5, 57 Hz); mass spectrum m/e 283 (M+NH4+).
Reaction SMILES: C(OC([O:8][NH:9][C:10]([C:12]1[CH:13]=[N:14][C:15]([N:18]2[CH2:23][CH:22]3[CH:20]([CH:21]3[CH2:24][NH:25][CH2:26][C:27]3[CH:36]=[CH:35][C:34]4[C:29](=[CH:30][CH:31]=[CH:32][CH:33]=4)[CH:28]=3)[CH2:19]2)=[N:16][CH:17]=1)=[O:11])C)C(C)C.Cl.O1CCOCC1>C(Cl)Cl>[OH:8][NH:9][C:10]([C:12]1[CH:13]=[N:14][C:15]([N:18]2[CH2:23][CH:22]3[CH:20]([CH:21]3[CH2:24][NH:25][CH2:26][C:27]3[CH:36]=[CH:35][C:34]4[C:29](=[CH:30][CH:31]=[CH:32][CH:33]=4)[CH:28]=3)[CH2:19]2)=[N:16][CH:17]=1)=[O:11]
Reactant: CC(C)COC(C)ONC(=O)c1cnc(N2CC3C(CNCc4ccc5ccccc5c4)C3C2)nc1
Agent: Cl
Solvent: ClCCl
Solvent: C1COCCO1
Product: O=C(NO)c1cnc(N2CC3C(CNCc4ccc5ccccc5c4)C3C2)nc1
Reaction time: 0.17 h
Yield: 45.6 %

Procedure:
N-(1-Isobutoxyethoxy) 2-(6-{[(naphthalen-2-ylmethyl)amino]methyl}-3-azabicyclo[3.1.0]hex-3-yl)pyrimidine-5-carboxamide (43 mg, 0.09 mmol) was stirred in DCM (2 ml) at r.t. under N2 and 4M HCl in dioxane (45 μl, 0.18 mmol) was added. This immediately caused a solid to precipitate. The reaction was allowed to stir for 10 min and then the solvent was removed in vacuo to give the title compound as a white solid (16 mg, 50%). LCMS purity 98%, m/z 390 [M+H]+, 1H NMR (300 MHz, d6-DMSO) δ: 1.91 (2H, m), 2.50 (1H, m), 2.99 (2H, m), 3.55 (2H, m), 3.88 (2H, d, J=11.7 Hz), 4.34 (2H, m), 7.58 (2H, m), 7.68 (1H, m), 7.95 (2H, m), 8.03 (2H, m), 8.66 (2H, s), 9.11 (2H, br s), 11.07 (1H, br s).
Reaction SMILES: Cl[C:2]1[C:11]2[C:6](=[N:7][CH:8]=[CH:9][CH:10]=2)[N:5]=[CH:4][CH:3]=1.[NH2:12][C:13]1[CH:18]=[C:17]([O:19][CH2:20][C:21]2[CH:26]=[CH:25][C:24]([Cl:27])=[CH:23][CH:22]=2)[CH:16]=[CH:15][C:14]=1[S:28][C:29]1[CH:34]=[CH:33][C:32]([OH:35])=[CH:31][CH:30]=1>>[Cl:27][C:24]1[CH:25]=[CH:26][C:21]([CH2:20][O:19][C:17]2[CH:16]=[CH:15][C:14]([S:28][C:29]3[CH:34]=[CH:33][C:32]([OH:35])=[CH:31][CH:30]=3)=[C:13]([NH:12][C:2]3[C:11]4[C:6](=[N:7][CH:8]=[CH:9][CH:10]=4)[N:5]=[CH:4][CH:3]=3)[CH:18]=2)=[CH:22][CH:23]=1
Reactant: Nc1cc(OCc2ccc(Cl)cc2)ccc1Sc1ccc(O)cc1
Reactant: Clc1ccnc2ncccc12
Product: Oc1ccc(Sc2ccc(OCc3ccc(Cl)cc3)cc2Nc2ccnc3ncccc23)cc1

Procedure:
The product from Example 16c (50 mg, 0.30 mmol) was reacted with the product from Example 143a (107 mg, 0.30 mmol) for 24 h following the procedure from Example 1g giving the crude title compound which was purified by HPLC with TFA providing the product as a trifluoroacetic acid (50 mg, 27%). 1H NMR (300 MHz, DMSO-d6) δ ppm: 5.14 (s, 2 H) 6.31 (d, J=7.36 Hz, 1 H) 6.64 (d, J=8.82 Hz, 2 H) 7.05-7.40 (m, J=8.46 Hz, 4 H) 7.46 (m, J=5.52 Hz, 3 H) 7.93 (m, J=4.41 Hz, 1 H) 8.48 (d, J=6.98 Hz, 1 H) 9.17 (m, J=1.47 Hz, J=5.88 Hz, 3 H) 9.79 (s,1 H) 11.15 (br s, 1 H) 14.54 (br s, 1 H); MS (ESI+) m/z,486 (M+H−TFA)+; (ESI−) m/z,484 (M−H−TFA)−.
Reaction SMILES: [OH-].[Na+].C([O:5][C:6](=[O:26])[CH2:7][CH2:8][CH2:9][CH2:10][CH2:11][CH2:12][N:13]1[CH:17]=[CH:16][C:15]([C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][C:19]=2[O:24][CH3:25])=[N:14]1)C>CO>[CH3:25][O:24][C:19]1[CH:20]=[CH:21][CH:22]=[CH:23][C:18]=1[C:15]1[CH:16]=[CH:17][N:13]([CH2:12][CH2:11][CH2:10][CH2:9][CH2:8][CH2:7][C:6]([OH:26])=[O:5])[N:14]=1
Reactant: CCOC(=O)CCCCCCn1ccc(-c2ccccc2OC)n1
Agent: [Na+]
Agent: [OH-]
Solvent: CO
Product: COc1ccccc1-c1ccn(CCCCCCC(=O)O)n1
Reaction time: 8 h
Yield: 88.8 %

Procedure:
Add 2 N sodium hydroxide (20 mL) to a solution of 7-[3-(2-Methoxyphenyl)pyrazol-1-yl]heptanoic acid ethyl ester (3.75 g, 11.4 mmol) in methanol (40 mL) at room temperature under nitrogen and stir the mixture for 8 hours. Remove the solvent under reduced pressure, dilute the residue with water (100 mL), acidify to pH 3 with 1 N HCl, extract with ethyl acetate (200 mL), and dry over sodium sulfate. Remove the solvent under reduced pressure to provide 7-[3-(2-methoxyphenyl)pyrazol-1-yl]heptanoic acid (3.06 g, 89%). APCI mass spectrum m/z 303 [C17H22N2O3+H]+.
Reaction SMILES: C([N:4]1[C:12]2[C:7](=[CH:8][CH:9]=[C:10]([C:13]([O:15][CH3:16])=[O:14])[CH:11]=2)[C:6](=[C:17](OCC)[C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=2)[C:5]1=[O:27])(=O)C.[CH3:28][N:29]([CH3:44])[CH2:30][CH2:31][N:32]([C:37]1[CH:43]=[CH:42][C:40]([NH2:41])=[CH:39][CH:38]=1)[C:33](=[O:36])[CH2:34][CH3:35]>>[CH3:44][N:29]([CH3:28])[CH2:30][CH2:31][N:32]([C:37]1[CH:38]=[CH:39][C:40]([NH:41]/[C:17](=[C:6]2\[C:5](=[O:27])[NH:4][C:12]3[C:7]\2=[CH:8][CH:9]=[C:10]([C:13]([O:15][CH3:16])=[O:14])[CH:11]=3)/[C:18]2[CH:23]=[CH:22][CH:21]=[CH:20][CH:19]=2)=[CH:42][CH:43]=1)[C:33](=[O:36])[CH2:34][CH3:35]
Reactant: CCC(=O)N(CCN(C)C)c1ccc(N)cc1
Reactant: CCOC(=C1C(=O)N(C(C)=O)c2cc(C(=O)OC)ccc21)c1ccccc1
Product: CCC(=O)N(CCN(C)C)c1ccc(N/C(=C2\C(=O)Nc3cc(C(=O)OC)ccc32)c2ccccc2)cc1

Procedure:
Prepared from 1-acetyl-3-(1-ethoxy-1-phenylmethylene)-6-methoxycarbonyl-2-indolinone and 4-(N-(2-dimethylamino-ethyl)-N-propionyl-amino)-aniline Rf value: 0.5 (silica gel, methylene chloride/methanol=9:1) C30H32N4O4
Reaction SMILES: Cl.[NH2:2][CH2:3][C:4]1[C:13](=[O:14])[C:12]2[C:7](=[N:8][C:9]([C:15]([F:18])([F:17])[F:16])=[CH:10][CH:11]=2)[N:6]([C:19]2[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=2)[C:5]=1[C:25]([O:27][CH3:28])=[O:26].[Cl:29][C:30]1[CH:31]=[C:32]([CH:36]=[CH:37][C:38]=1[Cl:39])[C:33](O)=[O:34]>>[CH3:28][O:27][C:25]([C:5]1[N:6]([C:19]2[CH:20]=[CH:21][CH:22]=[CH:23][CH:24]=2)[C:7]2[C:12]([C:13](=[O:14])[C:4]=1[CH2:3][NH:2][C:33](=[O:34])[C:32]1[CH:36]=[CH:37][C:38]([Cl:39])=[C:30]([Cl:29])[CH:31]=1)=[CH:11][CH:10]=[C:9]([C:15]([F:16])([F:17])[F:18])[N:8]=2)=[O:26]
Reactant: O=C(O)c1ccc(Cl)c(Cl)c1
Reactant: COC(=O)c1c(CN)c(=O)c2ccc(C(F)(F)F)nc2n1-c1ccccc1
Agent: Cl
Product: COC(=O)c1c(CNC(=O)c2ccc(Cl)c(Cl)c2)c(=O)c2ccc(C(F)(F)F)nc2n1-c1ccccc1

Procedure:
3-[(3,4-Dichloro-benzoylamino)-methyl]-4-oxo-1-phenyl-7-trifluoromethyl-1,4-dihydro-[1,8]-naphthyridine-2-carboxylic acid methyl ester was prepared starting from intermediate J and 3,4-dichlorobenzoic acid. 1H NMR (400 MHz, DMSO-d6) δ ppm 8.90 (d, J=8.06 Hz, 1H) 8.80 (t, J=4.63 Hz, 1H) 8.04 (d, J=1.81 Hz, 1H) 7.97 (d, J=8.06 Hz, 1H) 7.67-7.83 (m, 2H) 7.51-7.60 (m, 3H) 7.35-7.47 (m, 2H) 4.44 (d, J=4.83 Hz, 2H) 3.39 (s, 3H). MS calcd. for C25H16Cl2F3N3O4 [(M+H)+] 549.0, obsd. 549.9.
Reaction SMILES: [NH2:1][C@@H:2]([C:6]([OH:8])=[O:7])[C@H:3]([CH3:5])[OH:4].C([O-])(O)=O.[Na+].[C:14]1([CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][O:26][C:27](N2C=CC=CC2=O)=[O:28])[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1>O.C1COCC1>[OH:4][C@@H:3]([CH3:5])[C@@H:2]([NH:1][C:27]([O:26][CH2:25][CH2:24][CH2:23][CH2:22][CH2:21][CH2:20][C:14]1[CH:15]=[CH:16][CH:17]=[CH:18][CH:19]=1)=[O:28])[C:6]([OH:8])=[O:7]
Reactant: C[C@H](O)[C@@H](N)C(=O)O
Reactant: O=C(OCCCCCCc1ccccc1)n1ccccc1=O
Agent: O=C([O-])O
Agent: [Na+]
Solvent: O
Solvent: C1CCOC1
Product: C[C@H](O)[C@@H](NC(=O)OCCCCCCc1ccccc1)C(=O)O
Reaction time: 15 h
Yield: 77.3 %

Procedure:
To a stirred mixture of D-threonine (0.12 g, 1.0 mmol) and NaHCO3 (0.13 g, 1.5 mmol) in H2O (3.5 mL), the crude mixture containing 6-phenylhexyl-2-pyridyl-carbonate and 6-phenylhexyl-2-oxopyridine 1-carboxylate (0.45 g, 1.5 mmol) in THF (3.5 mL) was added. After 15 h at rt, the crude mixture was rotary evaporated to remove the organics and subsequently extracted with Et2O (3×5 mL). The aqueous phase was acidified with 2M HCl solution to pH 2-3 and subsequently extracted with AcOEt (3×10 mL). The organic fraction was dried over Na2SO4, filtered and concentrated to dryness to afford the title compound (0.25 g, 78%) as transparent oil, which was used in the next step without further purification. MS (ESI) m/z: 324 [M−H]+; (ESI) m/z: 322 [M−H]−. 1H NMR (DMSO-d6): δ 1.08 (d, J=6.4 Hz, 3H), 1.24-1.40 (m, 4H), 1.46-1.63 (m, 4H), 2.56 (t, J=7.6 Hz, 2H), 3.88-3.99 (m, 3H), 4.00-4.12 (m, 1H), 6.67 (d, J=9.0 Hz, 1H), 7.13-7.21 (m, 3H), 7.22-7.31 (m, 2H), 12.40 (br s, 1H).
Reaction SMILES: [CH:1]1([NH2:7])[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.[Cl:8][C:9]1[CH:14]=[C:13]([Cl:15])[CH:12]=[CH:11][C:10]=1[C:16]1[N:17]=[C:18]([C:30](OCC)=[O:31])[N:19]([CH3:29])[C:20]=1[C:21]1[CH:26]=[CH:25][C:24]([Cl:27])=[CH:23][C:22]=1[Cl:28]>>[CH:1]1([NH:7][C:30]([C:18]2[N:19]([CH3:29])[C:20]([C:21]3[CH:26]=[CH:25][C:24]([Cl:27])=[CH:23][C:22]=3[Cl:28])=[C:16]([C:10]3[CH:11]=[CH:12][C:13]([Cl:15])=[CH:14][C:9]=3[Cl:8])[N:17]=2)=[O:31])[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1
Reactant: CCOC(=O)c1nc(-c2ccc(Cl)cc2Cl)c(-c2ccc(Cl)cc2Cl)n1C
Reactant: NC1CCCCC1
Product: Cn1c(C(=O)NC2CCCCC2)nc(-c2ccc(Cl)cc2Cl)c1-c1ccc(Cl)cc1Cl

Procedure:
Using essentially the same procedure as Example 30, Step E, but using cyclohexylamine (1 mL), ethyl 4,5-di-(2,4-dichlorophenyl)-1-methylimidazole-2-carboxylate (10 mg, 0.022 mmol) from Example 30, Step D was converted to the title compound. HPLC/MS: 496 (M+1), 498 (100%, M+3), 500 (M+5); Rt=5.04 min.
Reaction SMILES: [C:1]1([N:7]=[C:8]=[O:9])[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[F:10][C:11]1[CH:29]=[CH:28][C:14]2[C:15]([CH:18]3[CH2:23][CH2:22][N:21]([CH2:24][CH2:25][CH2:26][OH:27])[CH2:20][CH2:19]3)=[N:16][O:17][C:13]=2[CH:12]=1.[ClH:30]>C1(C)C=CC=CC=1.CCOCC>[ClH:30].[F:10][C:11]1[CH:29]=[CH:28][C:14]2[C:15]([CH:18]3[CH2:23][CH2:22][N:21]([CH2:24][CH2:25][CH2:26][O:27][C:8](=[O:9])[NH:7][C:1]4[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=4)[CH2:20][CH2:19]3)=[N:16][O:17][C:13]=2[CH:12]=1
Reactant: O=C=Nc1ccccc1
Reactant: OCCCN1CCC(c2noc3cc(F)ccc23)CC1
Agent: Cl
Solvent: Cc1ccccc1
Solvent: CCOCC
Product: O=C(Nc1ccccc1)OCCCN1CCC(c2noc3cc(F)ccc23)CC1
Temperature: 25 °C

Procedure:
Phenylisocyanate (0.36 g, 3 mmol) and 3-[4-(6-fluoro-1,2-benzisoxazol-3-yl)piperidino]propanol (0.3 g, 1.1 mmol) was refluxed in toluene (25 ml) for 6 h. The mixture was cooled to room temperature and hydrochloric acid in ether was added. The resulting precipitate was recrystallized from ethanol/ether and isopropanol/ether to give 180 mg of the title compound as white crystals. M.p. 204.5°-205.5° C. MS (70 eV): m/z 397 (39%, M+), 278 (4), 259 (26), 233 (50), 178 (28), 96 (100).
Reaction SMILES: [O:1]=[C:2]1[CH2:10][C:9]2[C:4](=[CH:5][C:6]([C:11]([C:13]3[CH:14]=[C:15]([NH:19][C:20](=[O:22])[CH3:21])[CH:16]=[CH:17][CH:18]=3)=[O:12])=[CH:7][CH:8]=2)[NH:3]1.[CH:23](OCC)=[O:24].[O-]CC.[Na+].Cl>C(O)C>[OH:24][CH:23]=[C:10]1[C:9]2[C:4](=[CH:5][C:6]([C:11]([C:13]3[CH:14]=[C:15]([NH:19][C:20](=[O:22])[CH3:21])[CH:16]=[CH:17][CH:18]=3)=[O:12])=[CH:7][CH:8]=2)[NH:3][C:2]1=[O:1]
Reactant: CC(=O)Nc1cccc(C(=O)c2ccc3c(c2)NC(=O)C3)c1
Reactant: CCOC=O
Agent: CC[O-]
Agent: Cl
Agent: [Na+]
Solvent: CCO
Product: CC(=O)Nc1cccc(C(=O)c2ccc3c(c2)NC(=O)C3=CO)c1
Temperature: 78 °C
Yield: 71.7 %

Procedure:
N-[3-(2-Oxo-2,3-dihydro-1H-indole-6-carbonyl)-phenyl]-acetamide (0.957 g, 3.25 mmol) and ethyl formate (0.781 mL, 9.75 mmol) were dissolved in anhydrous ethanol (6.50 mL). The resulting solution was treated in dropwise fashion with a 21 wt % solution of sodium ethoxide in ethanol (6.07 mL, 16.26 mmol). This reaction mixture was heated at 78° C. for 1 h, producing a black oil. Subsequently, the reaction mixture was cooled to room temperature, and then the reaction pH was adjusted to pH 1 with dropwise addition of 1M HCl(aq) causing the formation of a pale orange precipitate. The suspension was filtered yielding an orange solid as the pure N-[3-(3-Hydroxymethylene-2-oxo-2,3-dihydro-1H-indole-6-carbonyl)-phenyl]-acetamide (0.752 g, 2.33 mmol, 71%).
Reaction SMILES: C[O:2][C:3](=[O:24])[C@@H:4]1[CH2:8][CH2:7][CH2:6][N:5]1[CH:9]([C:17]([O:19][C:20]([CH3:23])([CH3:22])[CH3:21])=[O:18])[C@@H:10]1[C@@H:14]([CH2:15][CH3:16])[CH2:13][CH2:12][NH:11]1.[OH-].[Na+].Cl>CO>[C:20]([O:19][C:17]([CH:9]([C@@H:10]1[C@@H:14]([CH2:15][CH3:16])[CH2:13][CH2:12][NH:11]1)[N:5]1[CH2:6][CH2:7][CH2:8][C@H:4]1[C:3]([OH:24])=[O:2])=[O:18])([CH3:23])([CH3:22])[CH3:21]
Reactant: CC[C@H]1CCN[C@@H]1C(C(=O)OC(C)(C)C)N1CCC[C@H]1C(=O)OC
Agent: Cl
Agent: [Na+]
Agent: [OH-]
Solvent: CO
Product: CC[C@H]1CCN[C@@H]1C(C(=O)OC(C)(C)C)N1CCC[C@H]1C(=O)O
Temperature: 0 °C
Reaction time: 3 h

Procedure:
N-[(tert-Butyloxy)carbonyl-3(S)-ethylpyrrolidin-2(S)-ylmethyl]-proline methyl ester 0.081 g, 0.238 mmol) was dissolved in CH3OH (2 mL), cooled to 0° C. and treated with 1N NaOH solution (0.952 mL, 0.952 mmol). After stirring at 23° C. for 3 h, the solution was neutralized with 1N HCl (0.952 mL, 0.952 mmol), concentrated to remove the CH3OH, then lyophilized and the residue used as is.
Reaction SMILES: C(=O)([O-])[O-].[K+].[K+].[C:7]([O:11][C:12]([N:14]1[CH2:19][CH2:18][N:17]([C:20]([O:22][CH2:23][C:24]2[CH:29]=[CH:28][CH:27]=[C:26]([OH:30])[CH:25]=2)=[O:21])[CH2:16][CH2:15]1)=[O:13])([CH3:10])([CH3:9])[CH3:8].Br[CH2:32][CH2:33][C:34]1[CH:39]=[CH:38][CH:37]=[CH:36][CH:35]=1>CC(C)=O>[C:7]([O:11][C:12]([N:14]1[CH2:19][CH2:18][N:17]([C:20]([O:22][CH2:23][C:24]2[CH:29]=[CH:28][CH:27]=[C:26]([O:30][CH2:32][CH2:33][C:34]3[CH:39]=[CH:38][CH:37]=[CH:36][CH:35]=3)[CH:25]=2)=[O:21])[CH2:16][CH2:15]1)=[O:13])([CH3:10])([CH3:8])[CH3:9]
Reactant: CC(C)(C)OC(=O)N1CCN(C(=O)OCc2cccc(O)c2)CC1
Reactant: BrCCc1ccccc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CC(C)=O
Product: CC(C)(C)OC(=O)N1CCN(C(=O)OCc2cccc(OCCc3ccccc3)c2)CC1
Temperature: 25 °C
Yield: 47.3 %

Procedure:
potassium carbonate (0.072 g, 0.52 mmol) was added to a solution of piperazine-1,4-dicarboxylic acid (3-hydroxy)benzyl ester tert-butyl ester (0.16 g, 0.48 mmol) in acetone (5 mL) at 0° C. and the reaction mixture was stirred at 0° C. for 30 min. (2-Bromoethyl)-benzene (0.097 g, 0.52 mmol) was added and the reaction mixture was allowed to warm to room temperature and then heated under reflux for 24 h. After cooling, the reaction mixture was concentrated in vacuo and the residue was partitioned between water (20 mL) and ethyl acetate (20 mL). The organic phase was separated, washed with saturated brine (25 mL), dried (MgSO4) and concentrated in vacuo to give an oil which was purified by column chromatography [SiO2; heptane-ethyl acetate (3:1)] to yield the title compound (0.10 g, 48%) as a colourless oil. 1H-NMR (400 MHz, CDCl3): 1.46 (9H, s), 3.10 (2H, t, J=7.0 Hz), 3.40 (4H, m), 3.46 (4H, m), 4.18 (2H, t, J=7.0 Hz), 5.09 (2H, s), 6.84 (1H, m), 6.88 (1H, m), 6.91 (1H, m) and 7.22–7.34 (6H, m).
Reaction SMILES: [C:1]([Si:5]([CH2:8]Cl)([CH3:7])[CH3:6])([CH3:4])([CH3:3])[CH3:2].[I-:10].[Na+]>CC(C)=O>[C:1]([Si:5]([CH2:8][I:10])([CH3:7])[CH3:6])([CH3:4])([CH3:3])[CH3:2]
Reactant: [I-]
Reactant: CC(C)(C)[Si](C)(C)CCl
Agent: [Na+]
Solvent: CC(C)=O
Product: CC(C)(C)[Si](C)(C)CI
Reaction time: 24 h
Yield: 81576.9 %

Procedure:
t-Butyl(chloromethyl)dimethylsilane [Makoto Kumada, Mitsuo Ishikawa, Sajiro Meada and Katsuyata Ikura, J. Organometal. Chem. 2, 146, (1964)] (16.4 g, 0.1 mmol) and sodium iodide (60 g, 0.4 mmol) in acetone (500 ml) are refluxed with stirring during 24 hours. The reaction mixture is cooled, filtered and the solvent is evaporated under reduced pressure. The residue is dissolved in ether and washed with water. The organic layer is dried over sodium sulfate, filtered and concentrated under reduced pressure to afford t-butyl(iodomethyl)dimethylsilane (20.9 g, 80%) as a slightly yellow oil.
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([CH3:8])[N:5]=[C:4]([NH2:9])[N:3]=1.[Cl:10][C:11]1[CH:12]=[C:13](B(O)O)[C:14]([F:17])=[N:15][CH:16]=1.C([O-])(=O)C.[K+]>CCO.O>[Cl:10][C:11]1[CH:12]=[C:13]([C:2]2[N:7]=[C:6]([CH3:8])[N:5]=[C:4]([NH2:9])[N:3]=2)[C:14]([F:17])=[N:15][CH:16]=1
Reactant: OB(O)c1cc(Cl)cnc1F
Reactant: Cc1nc(N)nc(Cl)n1
Agent: CC(=O)[O-]
Agent: [K+]
Solvent: CCO
Solvent: O
Product: Cc1nc(N)nc(-c2cc(Cl)cnc2F)n1
Temperature: 100 °C
Yield: 56.3 %

Procedure:
To a 20 mL microwave reaction tube was added 4-chloro-6-methyl-1,3,5-triazin-2-amine (Example 9, 1.00 g, 6.94 mmol), 5-chloro-2-fluoropyridin-3-ylboronic acid (Combi-Blocks, 1.62 g, 9.22 mmol), potassium acetate (Aldrich, 2.07 g, 21.1 mmol) and Am-Phos (Aldrich, 0.247 g, 0.349 mmol) in EtOH (12 mL) and water (1.2 mL). The mixture was degassed by bubbling argon through for 5 min. The tube was heated in an microwave reactor (Biotage) at 100° C. for 20 min. The reaction mixture was partitioned between water (100 mL) and 25% IPA in chloroform with 1% NH4OH (60 mL). The aqueous phase was extracted with 25% IPA in chloroform with 1% NH4OH (2×50 mL). The combined organic phases were washed with saturated aqueous sodium chloride (40 mL). The organic phase was dried over sodium sulfate, filtered and concentrated in vacuo. Adding DCM to the residue resulted in precipitate formation. The solid was collected via filtration and washed with MeOH to afford 4-(5-chloro-2-fluoropyridin-3-yl)-6-methyl-1,3,5-triazin-2-amine (0.937 g) as a light yellow powder. The filtrate and the wash were combined and concentrated, then purified by column chromatography (eluent: iPrOH (w/10% NH4OH) in CHCl3 0.25% to 6.25%) followed by washing with MeOH to afford additional product (0.149 g) as a white solid. The total yield is 1.08 g (65%). 1H NMR (400 MHz, DMSO-d6) δ ppm 8.54 (dd, J=8.02, 2.74 Hz, 1H) 8.46-8.51 (m, 1H) 7.73 (s, 2H) 2.37 (s, 3H). m/z (ESI, positive ion) m/z: 240.1 (M+H)+.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([C:9]2[CH2:10][CH:11]([CH3:16])[C:12](=[O:15])[NH:13][N:14]=2)=[CH:5][CH:4]=1.CI.[C:19]([O-])([O-])=O.[Cs+].[Cs+]>>[CH3:1][O:2][C:3]1[CH:8]=[CH:7][C:6]([C:9]2[CH:10]=[C:11]([CH3:16])[C:12](=[O:15])[N:13]([CH3:19])[N:14]=2)=[CH:5][CH:4]=1
Reactant: O=C([O-])[O-]
Reactant: COc1ccc(C2=NNC(=O)C(C)C2)cc1
Agent: [Cs+]
Solvent: CI
Product: COc1ccc(-c2cc(C)c(=O)n(C)n2)cc1

Procedure:
The product of step 2 (6-(4-methoxy-phenyl)-2,4-dimethyl-2H-pyridazin-3-one) was prepared as described for example 22 step 2 using 6-(4-methoxy-phenyl)-4-methyl-4,5-dihydro-2H-pyridazin-3-one, MeI and Cs2CO3.
Reaction SMILES: [CH:1]([O:4][C:5]([N:7]1[CH2:12][CH2:11][CH:10]([CH:13]2[CH2:17][C:16]3[CH:18]=[C:19](B4OC(C)(C)C(C)(C)O4)[CH:20]=[CH:21][C:15]=3[O:14]2)[CH2:9][CH2:8]1)=[O:6])([CH3:3])[CH3:2].Br[C:32]1[CH:37]=[CH:36][C:35]([S:38]([CH3:41])(=[O:40])=[O:39])=[CH:34][N:33]=1>>[CH:1]([O:4][C:5]([N:7]1[CH2:12][CH2:11][CH:10]([CH:13]2[CH2:17][C:16]3[CH:18]=[C:19]([C:32]4[CH:37]=[CH:36][C:35]([S:38]([CH3:41])(=[O:40])=[O:39])=[CH:34][N:33]=4)[CH:20]=[CH:21][C:15]=3[O:14]2)[CH2:9][CH2:8]1)=[O:6])([CH3:3])[CH3:2]
Reactant: CC(C)OC(=O)N1CCC(C2Cc3cc(B4OC(C)(C)C(C)(C)O4)ccc3O2)CC1
Reactant: CS(=O)(=O)c1ccc(Br)nc1
Product: CC(C)OC(=O)N1CCC(C2Cc3cc(-c4ccc(S(C)(=O)=O)cn4)ccc3O2)CC1
Yield: 58 %

Procedure:
The title compound is prepared from 4-[5-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-2,3-dihydro-benzofuran-2-yl]-piperidine-1-carboxylic acid isopropyl ester and 2-bromo-5-methanesulfonyl-pyridine following a procedure analogous to that described in Example 1.
Reaction SMILES: [CH2:1]([N:3]1[C:7]2=[N:8][C:9]([CH2:48][CH3:49])=[C:10]([CH2:19][NH:20][C:21]([C:23]3[CH:28]=[CH:27][CH:26]=[C:25]([C:29]([NH:31][CH2:32][C:33]4[CH:34]=[C:35]([C:40]5[CH:45]=[CH:44][CH:43]=[C:42]([CH2:46][OH:47])[CH:41]=5)[C:36]([F:39])=[CH:37][CH:38]=4)=[O:30])[CH:24]=3)=[O:22])[C:11]([NH:12][CH:13]3[CH2:18][CH2:17][O:16][CH2:15][CH2:14]3)=[C:6]2[CH:5]=[N:4]1)[CH3:2]>C1COCC1.O=[Mn]=O>[CH2:1]([N:3]1[C:7]2=[N:8][C:9]([CH2:48][CH3:49])=[C:10]([CH2:19][NH:20][C:21]([C:23]3[CH:28]=[CH:27][CH:26]=[C:25]([C:29]([NH:31][CH2:32][C:33]4[CH:34]=[C:35]([C:40]5[CH:45]=[CH:44][CH:43]=[C:42]([CH:46]=[O:47])[CH:41]=5)[C:36]([F:39])=[CH:37][CH:38]=4)=[O:30])[CH:24]=3)=[O:22])[C:11]([NH:12][CH:13]3[CH2:18][CH2:17][O:16][CH2:15][CH2:14]3)=[C:6]2[CH:5]=[N:4]1)[CH3:2]
Reactant: CCc1nc2c(cnn2CC)c(NC2CCOCC2)c1CNC(=O)c1cccc(C(=O)NCc2ccc(F)c(-c3cccc(CO)c3)c2)c1
Agent: O=[Mn]=O
Solvent: C1CCOC1
Product: CCc1nc2c(cnn2CC)c(NC2CCOCC2)c1CNC(=O)c1cccc(C(=O)NCc2ccc(F)c(-c3cccc(C=O)c3)c2)c1
Temperature: 25 °C
Reaction time: 16 h
Yield: 97.7 %

Procedure:
To N-{[1,6-diethyl-4-(tetrahydro-2H-pyran-4-ylamino)-1H-pyrazolo[3,4-b]pyridin-5-yl]methyl}-N′-{[6-fluoro-3′-(hydroxymethyl)-3-biphenylyl]methyl}-1,3-benzenedicarboxamide (0.665 g, 1 mmol) in THF (20 mL) was added MnO2 (0.869 g, 10.00 mmol) and the mixture was stirred at room temperature for 16 h. More MnO2 (10 eq) was added and stirred at room temperature for 4 h and then again for 22 h and then more MnO2 (10 eq) was added. This mixture was stirred at room temperature for 21 h and 94 h then filtered and concentrated to afford the title compound (0.6472 g, 98%). LC-MS m/z 663 (M+H)+.
Reaction SMILES: [C:1]([NH:3][C:4](=[N:7][CH2:8][CH2:9][S:10][CH2:11][C:12]1[NH:16][CH:15]=[N:14][C:13]=1[CH3:17])SC)#[N:2].[CH2:18]([NH2:23])[CH2:19][CH2:20][C:21]#[CH:22]>C(#N)C>[C:1]([NH:3][C:4]([NH:7][CH2:8][CH2:9][S:10][CH2:11][C:12]1[NH:16][CH:15]=[N:14][C:13]=1[CH3:17])=[N:23][CH2:18][CH2:19][CH2:20][C:21]#[CH:22])#[N:2]
Reactant: CSC(=NCCSCc1[nH]cnc1C)NC#N
Reactant: C#CCCCN
Solvent: CC#N
Product: C#CCCCN=C(NC#N)NCCSCc1[nH]cnc1C
Reaction time: 96 h

Procedure:
A mixture of N-cyano-N'-{2-[(4-methyl-5-imidazolyl)methylthio]ethyl}-S-methylisothiourea (3.00 g., 0.0111 mole) and 4-pentyn-1-amine (3.69 g., 0.0445 mole) in 60 ml. of acetonitrile was stirred at reflux for 24 hours, and then allowed to stand at room temperature for 96 hours. The solvent and excess amine were removed under reduced pressure and the residual yellow gum was purified by chromatography on 50 g. of 100-200 mesh silica gel, using gradient elution with methylene chloride/methanol (99:1-96:4). The middle fractions indicated by TLC to be pure were combined and evaporated to give 1.91 g. of yellow gum which was crystallized at -15° C. from 18 ml. of ethyl acetate. The resulting white solid (1.25 g.) was recrystallized at -15° C. from 10 ml. of acetonitrile to give 1.063 g. of product; m.p. 99°-103° C.
Reaction SMILES: C(OC([N:8]1[CH2:12][CH2:11][C@H:10]([O:13][NH2:14])[CH2:9]1)=O)(C)(C)C.[ClH:15]>CCOC(C)=O>[ClH:15].[ClH:15].[NH:8]1[CH2:12][CH2:11][C@H:10]([O:13][NH2:14])[CH2:9]1
Reactant: CC(C)(C)OC(=O)N1CC[C@H](ON)C1
Agent: Cl
Solvent: CCOC(C)=O
Product: NO[C@H]1CCNC1
Yield: 73 %

Procedure:
(S)-1-tert-Butoxycarbonyl-3-pyrrolidinyloxyamine (1.67 g) was dissolved in a 5M HCl solution in EtOAc (20 ml). After 1 h the solvent was removed under reduced pressure to give (S)-3-pyrrolidinyloxyamine dihydrochloride (1.04 g, 73%) as an off-white solid.