Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [C:1]([CH2:9][C:10]([CH3:12])=[O:11])(=[O:8])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.C([Li])CCC.Br[CH2:19][C:20]1[CH:21]=[C:22]([CH:31]=[CH:32][CH:33]=1)[O:23][Si:24]([CH3:30])([CH3:29])[C:25]([CH3:28])([CH3:27])[CH3:26].[Cl-].[NH4+]>CCCCCC.C1COCC1>[CH3:30][Si:24]([CH3:29])([C:25]([CH3:27])([CH3:26])[CH3:28])[O:23][C:22]1[CH:21]=[C:20]([CH2:19][CH2:12][C:10](=[O:11])[CH2:9][C:1]([C:2]2[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=2)=[O:8])[CH:33]=[CH:32][CH:31]=1
Reactant: CC(=O)CC(=O)c1ccccc1
Reactant: CC(C)(C)[Si](C)(C)Oc1cccc(CBr)c1
Agent: [Cl-]
Agent: [Li]CCCC
Agent: [NH4+]
Solvent: C1CCOC1
Solvent: CCCCCC
Product: CC(C)(C)[Si](C)(C)Oc1cccc(CCC(=O)CC(=O)c2ccccc2)c1
Temperature: 25 °C
Reaction time: 0.17 h
Yield: 63.6 %

Procedure:
Sodium hydride (2.13 g of a 50% dispersion in mineral oil, 44 mmol) was washed twice with hexanes, covered with dry THF (150 mL) and 1-benzoylacetone (6.00 g, 37 mmol) added portionwise. The mixture was stirred at room temperature under an atmosphere of nitrogen for 10 minutes to give a slurry which was cooled to -20° C. n-Butyllithium (2.60 g, 40 mmol) in hexane (16.3 mL) was added dropwise to provide a solution which was stirred for 20 minutes prior to the dropwise addition of [3-(bromomethyl)phenoxy]dimethyl(1,1-dimethylethyl)silane (11.17 g, 37 mmol). After 15 minutes, the mixture was poured onto saturated ammonium chloride solution and extracted with CH2Cl2. The combined extracts were dried over sodium sulfate, concentrated in vacuo and the residual oil chromatographed on a column of silica gel. Elution with a mixture of hexanes and diethyl ether (9:1) gave 5-[3-[dimethyl(1,1-dimethylethyl)siloxy]phenyl]-1-phenyl- 1,3-pentanedione (9.00 g, 63%).
Reaction SMILES: [ClH:1].[N:2]12[CH2:11][CH:6]3[CH2:7][CH:8]([CH2:10][CH:4]([C@H:5]3[NH2:12])[CH2:3]1)[CH2:9]2.[CH3:13][C:14]1[S:15][CH:16]=[C:17]([C:19]2[S:23][C:22]([C:24](O)=[O:25])=[CH:21][CH:20]=2)[N:18]=1.N>>[ClH:1].[N:2]12[CH2:11][CH:6]3[CH2:7][CH:8]([CH2:10][CH:4]([C@H:5]3[NH:12][C:24]([C:22]3[S:23][C:19]([C:17]4[N:18]=[C:14]([CH3:13])[S:15][CH:16]=4)=[CH:20][CH:21]=3)=[O:25])[CH2:3]1)[CH2:9]2
Reactant: NC1C2CC3CC1CN(C3)C2
Reactant: Cc1nc(-c2ccc(C(=O)O)s2)cs1
Agent: Cl
Agent: N
Product: Cc1nc(-c2ccc(C(=O)NC3C4CC5CC3CN(C5)C4)s2)cs1

Procedure:
Prepared from (4r)-1-azatricyclo[3.3.1.13,7]dec-4-ylamine hydrochloride and 5-(2-methylthiazol-4-yl)thiophene-2-carboxylic acid according to methods A and C. 1H NMR (300 MHz, methanol-d4) δ ppm 2.08-2.34 (m, 5H), 2.51 (s, 2H), 2.74 (s, 3H), 3.42-3.64 (m, 4H), 3.88 (d, J=12.5 Hz, 2H), 4.33 (s, 1H), 7.49 (d, J=4.1 Hz, 1H), 7.68 (s, 1H), 7.79 (d, J=4.1 Hz, 1H). MS (DCI/NH3) m/z 360.
Reaction SMILES: Cl[C:2]1[N:21]=[C:5]2[C:6]([NH:10][C:11]3[CH:16]=[CH:15][CH:14]=[C:13]([S:17]([CH3:20])(=[O:19])=[O:18])[CH:12]=3)=[CH:7][CH:8]=[CH:9][N:4]2[N:3]=1.[CH3:22][N:23]1[CH2:28][CH2:27][N:26]([C:29]2[CH:30]=[C:31]([CH:33]=[CH:34][CH:35]=2)[NH2:32])[CH2:25][CH2:24]1.C1(P(C2CCCCC2)C2C=CC=CC=2C2C=CC=CC=2P(C2CCCCC2)C2CCCCC2)CCCCC1>>[CH3:20][S:17]([C:13]1[CH:12]=[C:11]([NH:10][C:6]2[C:5]3[N:4]([N:3]=[C:2]([NH:32][C:31]4[CH:33]=[CH:34][CH:35]=[C:29]([N:26]5[CH2:25][CH2:24][N:23]([CH3:22])[CH2:28][CH2:27]5)[CH:30]=4)[N:21]=3)[CH:9]=[CH:8][CH:7]=2)[CH:16]=[CH:15][CH:14]=1)(=[O:19])=[O:18]
Reactant: CN1CCN(c2cccc(N)c2)CC1
Reactant: CS(=O)(=O)c1cccc(Nc2cccn3nc(Cl)nc23)c1
Agent: c1ccc(P(C2CCCCC2)C2CCCCC2)c(-c2ccccc2P(C2CCCCC2)C2CCCCC2)c1
Product: CN1CCN(c2cccc(Nc3nc4c(Nc5cccc(S(C)(=O)=O)c5)cccn4n3)c2)CC1

Procedure:
N(8)-(3-Methanesulfonyl-phenyl)-N(2)-[3-(4-methyl-piperazin-1-yl)-phenyl]-[1,2,4]triazolo[1,5-a]pyridine-2,8-diamine was prepared from (2-chloro-[1,2,4]triazolo[1,5-a]pyridin-8-yl)-(3-methanesulfonyl-phenyl)-amine (75.0 mg, 0.232 mmol) and 3-(4-methylpiperazin-1-yl)aniline (50.0 mg, 0.261 mmol) with 2,2′-bis-dicyclohexylphosphanyl-biphenyl (25.0 mg, 0.0457 mmol) as the ligand in a manner analogous to Example 2d. Product isolated as a tan foam (0.013 g, 12%). 1H NMR (400 MHz, CDCl3, δ, ppm): 8.05 (d, J=6.1 Hz, 1H), 7.81 (s, 1H), 7.60-7.50 (m, 2H), 7.45 (d, J=7.3 Hz, 1H), 7.27-7.18 (m, 3H), 7.09 (d, J=7.3 Hz, 1H), 6.85 (s, 1H), 6.81 (t, J=7.1 Hz, 1H), 6.75 (s, 1H), 6.60 (d, J=8.3 Hz, 1H), 3.30-3.25 (m, 4H), 3.08 (s, 3H), 2.62-2.57 (m, 4H), 2.37 (s, 3H). MS=478 (MH)+.
Reaction SMILES: Cl.[O:2]=[C:3]1[NH:12][C:11]2[N:10]=[CH:9][C:8](/[CH:13]=[CH:14]/[C:15]([OH:17])=O)=[CH:7][C:6]=2[CH2:5][CH2:4]1.Cl.[CH3:19][C:20](=[CH2:27])[CH2:21][O:22][CH:23]1[CH2:26][NH:25][CH2:24]1.CCN(C(C)C)C(C)C.CCN=C=NCCCN(C)C>CN(C1C=CN=CC=1)C.CN(C=O)C>[CH3:27][C:20](=[CH2:19])[CH2:21][O:22][CH:23]1[CH2:26][N:25]([C:15](=[O:17])/[CH:14]=[CH:13]/[C:8]2[CH:7]=[C:6]3[C:11](=[N:10][CH:9]=2)[NH:12][C:3](=[O:2])[CH2:4][CH2:5]3)[CH2:24]1
Reactant: O=C(O)/C=C/c1cnc2c(c1)CCC(=O)N2
Reactant: C=C(C)COC1CNC1
Agent: CCN=C=NCCCN(C)C
Agent: CN(C)c1ccncc1
Agent: Cl
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: C=C(C)COC1CN(C(=O)/C=C/c2cnc3c(c2)CCC(=O)N3)C1
Temperature: 25 °C
Reaction time: 8 h
Yield: 16.5 %

Procedure:
A 16 mL vial flask was successively charged with (2E)-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)acrylic acid hydrochloride (60 mg, 0.24 mmol), DMF (5.8 mL), 3-[(2-methylprop-2-en-1-yl)oxy]azetidine hydrochloride (78 mg, 0.48 mmol; which may be prepared as described in Step 2), DIPEA (119 μL, 0.72 mmol), DMAP (2.4 mg, 0.02 mmol) and EDAC (56 mg, 0.29 mmol). The reaction mixture was stirred at room temperature overnight and concentrated to dryness. The residue was precipitated in methanol/water and then filtered. The resulting solid was dissolved in chloroform and washed with water to give a beige solid. This solid was triturated in diethyl ether to give the title compound (13 mg, 16%) as a white solid.
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([N:8]2[CH2:13][CH2:12][O:11][CH2:10][CH2:9]2)[C:5]([O:14][CH3:15])=[CH:4][N:3]=1.[N+:16]([C:19]1[CH:24]=[C:23](B2OC(C)(C)C(C)(C)O2)[CH:22]=[CH:21][C:20]=1[NH2:34])([O-:18])=[O:17].C(=O)([O-])[O-].[Na+].[Na+]>C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.O1CCOCC1>[CH3:15][O:14][C:5]1[C:6]([N:8]2[CH2:13][CH2:12][O:11][CH2:10][CH2:9]2)=[N:7][C:2]([C:23]2[CH:22]=[CH:21][C:20]([NH2:34])=[C:19]([N+:16]([O-:18])=[O:17])[CH:24]=2)=[N:3][CH:4]=1
Reactant: CC1(C)OB(c2ccc(N)c([N+](=O)[O-])c2)OC1(C)C
Reactant: COc1cnc(Cl)nc1N1CCOCC1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: C1COCCO1
Product: COc1cnc(-c2ccc(N)c([N+](=O)[O-])c2)nc1N1CCOCC1
Yield: 144.2 %

Procedure:
A mixture of 4-(2-chloro-5-methoxy-pyrimidin-4-yl)-morpholine (1.0 g, 1 eq.), 2-nitro-4-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-phenylamine (1.26 g, 1.1 eq.), dioxane (20 ml), Pd(PPh3)4 (0.05 g, 0.1 eq.) and 2M sodium carbonate (6.53 ml, 3.0 eq.) was heated to reflux overnight. The solvent was removed in vacuo, the residue extracted with EA, and the organic layer washed with brine and dried. The crude was purified by chromatography to give a brown solid (2.08 g, 47.83%).
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][C:10]=1[NH:15][C:16](=[O:24])[C:17]1[CH:22]=[CH:21][C:20](Br)=[CH:19][CH:18]=1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[N:25]1[C:34]2[C:29](=[CH:30][CH:31]=[CH:32][C:33]=2B(O)O)[CH:28]=[CH:27][CH:26]=1.C(=O)([O-])O.[Na+]>C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.COCCOC>[C:1]([O:5][C:6]([NH:8][C:9]1[CH:14]=[CH:13][CH:12]=[CH:11][C:10]=1[NH:15][C:16](=[O:24])[C:17]1[CH:22]=[CH:21][C:20]([C:33]2[CH:32]=[CH:31][CH:30]=[C:29]3[C:34]=2[N:25]=[CH:26][CH:27]=[CH:28]3)=[CH:19][CH:18]=1)=[O:7])([CH3:4])([CH3:3])[CH3:2]
Reactant: OB(O)c1cccc2cccnc12
Reactant: CC(C)(C)OC(=O)Nc1ccccc1NC(=O)c1ccc(Br)cc1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: COCCOC
Product: CC(C)(C)OC(=O)Nc1ccccc1NC(=O)c1ccc(-c2cccc3cccnc23)cc1
Yield: 91.5 %

Procedure:
N-(2-t-Butoxycarbonylaminophenyl)-4-bromobenzamide (Method 14; 200 mg, 0.5 mmol), 8-quinoline boronic acid (104 mg, 0.6 mmol), tetrakis(triphenylphosphine)palladium (8 mg, 0.007 mmol), 1,2-dimethoxyethane (3 ml) and a saturated aqueous solution of sodium hydrogen carbonate (3 ml) were stirred at 80° C. under an atmosphere of argon for 20 hours. The mixture was allowed to cool before being partitioned between ethyl acetate and water. The organics were washed with brine, dried over magnesium sulfate, filtered and evaporated. The resultant residue was purified by flash column chromatography, eluting with methanol/dichloromethane (0-10%), to give the title compound (201 mg, 84%); NMR Spectrum: (DMSO-d6): 1.47 (s, 9H), 7.20 (m, 2H), 7.60 (m, 4H), 7.73 (t, 1H), 7.84 (t, 3H), 8.06 (d, 2H), 8.47 (d, 1H), 8.68 (s, 1H), 8.93 (m, 1H), 9.91 (s, 1H), Mass Spectrum: M+H+: 440.
Reaction SMILES: [CH3:1][O:2]/[N:3]=[C:4](/[C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1)\[CH2:5][O:6][C:7]1[CH:27]=[CH:26][C:10]([CH2:11][O:12][C:13]2[N:18]=[CH:17][C:16]([CH2:19][CH2:20][C:21]([O:23]CC)=[O:22])=[CH:15][CH:14]=2)=[CH:9][CH:8]=1.C1COCC1.[OH-].[Na+]>C(O)C>[CH3:1][O:2]/[N:3]=[C:4](/[C:28]1[CH:29]=[CH:30][CH:31]=[CH:32][CH:33]=1)\[CH2:5][O:6][C:7]1[CH:27]=[CH:26][C:10]([CH2:11][O:12][C:13]2[N:18]=[CH:17][C:16]([CH2:19][CH2:20][C:21]([OH:23])=[O:22])=[CH:15][CH:14]=2)=[CH:9][CH:8]=1
Reactant: CCOC(=O)CCc1ccc(OCc2ccc(OC/C(=N\OC)c3ccccc3)cc2)nc1
Agent: [Na+]
Agent: [OH-]
Solvent: CCO
Solvent: C1CCOC1
Product: CO/N=C(\COc1ccc(COc2ccc(CCC(=O)O)cn2)cc1)c1ccccc1
Temperature: 25 °C
Reaction time: 2 h
Yield: 35 %

Procedure:
To a stirring solution of ethyl 3-{6-[(4-{[(2Z)-2-(methoxyimino)-2-phenylethyl]oxy}benzyl)oxy]pyridin-3-yl}propanoate (0.03 g, 0.067 mmol) in the mixture of THF and Ethanol was added aqueous NaOH (0.03 g, 0.067 mmol) at 0° C., then stirred at RT for 2 h. After the completion of the SM reaction mass was concentrated under vacuum at 25° C. to remove solvents and diluted with water. Aqueous portion was neutralized with citric acid up to neutral pH, then extracted with ethyl acetate organic layer was washed with water and brine, dried over Na2SO4 and concentrated. Crude product was purified by preparative TLC to afford colourless oil as product (0.01 g, Yield: 35%); purity: 85%.
Reaction SMILES: [NH2:1][CH:2]1[C:15](=[O:16])[N:4]2[CH:5]([C:10]3[NH:14][N:13]=[N:12][N:11]=3)[C:6]([CH3:9])([CH3:8])[S:7][C@H:3]12.C(N(CC)CC)C.Cl[Si](C)(C)C.CO[CH:31](OC)[N:32]1[CH2:38][CH2:37][CH2:36][CH2:35][CH2:34][CH2:33]1>ClCCl>[N:32]1([CH:31]=[N:1][CH:2]2[C:15](=[O:16])[N:4]3[CH:5]([C:10]4[NH:11][N:12]=[N:13][N:14]=4)[C:6]([CH3:8])([CH3:9])[S:7][C@H:3]23)[CH2:38][CH2:37][CH2:36][CH2:35][CH2:34][CH2:33]1
Reactant: COC(OC)N1CCCCCC1
Reactant: CC1(C)S[C@@H]2C(N)C(=O)N2C1c1nnn[nH]1
Agent: C[Si](C)(C)Cl
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: CC1(C)S[C@@H]2C(N=CN3CCCCCC3)C(=O)N2C1c1nnn[nH]1
Reaction time: 0.25 h
Yield: 82 %

Procedure:
To a stirred solution of 1.2 g (5 mmoles) of 6-amino-2,2-dimethyl-3-(5-tetrazolyl)penam, 1.0 g (10 mmole) of triethylamine and 30 ml of dichloromethane, cooled to 0° C., is added 0.54 g (5 mmole) of chlorotrimethylsilane. After 15 minutes, 0.86 (5 mmole) of 1-(dimethoxymethyl)hexahydroazepine (British Patent No. 1,293,590) is added, and stirring is continued for a further 1 hour. The volatile components are removed by evaporation in vacuo, and then the residue is extracted with 25 ml of acetone. The insoluble material is filtered off, and the acetone is evaporated in vacuo to a yellow foam, which changes to a white powder on trituration with ether. This affords 1.44 g (82% yield) of 6-([hexahydro-1-azepinyl]methyleneamino)-2,2-dimethyl-3-(5-tetrazolyl)penam. The infrared spectrum of the product (KBr disc) shows absorption bands at 1795 cm-1 (β-lactam), 1706 cm-1 and 1645 cm-1. The NMR spectrum (CDCl3) shows absorption bands at 8.00 ppm (singlet, 1H, N--CH=N), 5.90 and 5.60 ppm (two doublets, 2H, J = 4 Hz, C-5 and C-6 hydrogens), 5.40 ppm (singlet, 1H, C-3 hydrogen), 3.90-3.50 (multiplet, 4H, CH2 --N--CH2), 2.00-1.50 ppm (multiplet, 11H, C-2 methyl hydrogens and [CH2 ]4) and 1.20 ppm (singlet, 3H, C-2 methyl hydrogens). Examination of the product by thin-layer chromatography (0.2M NaOAc: acetone; 1:6) showed a single spot (Rf 0.23).
Reaction SMILES: [S:1]1[CH:9]2[C:4]([CH2:5][NH:6][CH2:7][CH2:8]2)=[CH:3][C:2]1=[O:10].[CH3:11][C:12]1[CH:13]=[CH:14][C:15]([S:18]([OH:21])(=[O:20])=[O:19])=[CH:16][CH:17]=1.[C:22]([Si:26]([CH3:29])([CH3:28])Cl)([CH3:25])([CH3:24])[CH3:23].C(N(CC)CC)C>C(Cl)Cl>[Si:26]([O:10][C:2]1[S:1][C:9]2[CH2:8][CH2:7][NH:6][CH2:5][C:4]=2[CH:3]=1)([C:22]([CH3:25])([CH3:24])[CH3:23])([CH3:29])[CH3:28].[CH3:11][C:12]1[CH:17]=[CH:16][C:15]([S:18]([OH:21])(=[O:20])=[O:19])=[CH:14][CH:13]=1
Reactant: O=C1C=C2CNCCC2S1
Reactant: CC(C)(C)[Si](C)(C)Cl
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(C)(C)[Si](C)(C)Oc1cc2c(s1)CCNC2

Procedure:
A mixture of 5.00 g of 5,6,7,7a-tetrahydro-4H-thieno[3,2-c]pyridin-2-one.p-toluenesulfonate, 2.47 g of tert-butyldimethylchlorosilane, 1.66 g of triethylamine and 15 ml of methylene chloride was stirred at room temperature (20° C.) for 3 hours. The produced 2-(tert-butyldimethylsilyloxy)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine-p-toluenesulfonate was not isolated, 5.90 g of 2-chloro-α-methoxycarbonylbenzyl bromide and 3.02 g of triethylamine were added thereto, and the mixture was allowed to react.
Reaction SMILES: [CH2:1]([S:8][C:9]1[N:14]=[C:13]2[N:15]([CH:27]([CH2:32][O:33][CH2:34][CH3:35])[CH2:28][O:29][CH2:30][CH3:31])[C:16](=[O:26])[N:17]([C:19]3[CH:24]=[CH:23][CH:22]=[CH:21][C:20]=3[Cl:25])[CH2:18][C:12]2=[CH:11][N:10]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.ClC1C=CC=C(C(OO)=[O:44])C=1>ClCCl>[CH2:1]([S:8]([C:9]1[N:14]=[C:13]2[N:15]([CH:27]([CH2:32][O:33][CH2:34][CH3:35])[CH2:28][O:29][CH2:30][CH3:31])[C:16](=[O:26])[N:17]([C:19]3[CH:24]=[CH:23][CH:22]=[CH:21][C:20]=3[Cl:25])[CH2:18][C:12]2=[CH:11][N:10]=1)=[O:44])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: O=C(OO)c1cccc(Cl)c1
Reactant: CCOCC(COCC)N1C(=O)N(c2ccccc2Cl)Cc2cnc(SCc3ccccc3)nc21
Solvent: ClCCl
Product: CCOCC(COCC)N1C(=O)N(c2ccccc2Cl)Cc2cnc(S(=O)Cc3ccccc3)nc21
Reaction time: 1 h

Procedure:
A suspension of 7-benzylthio-3-(2-chlorophenyl)-1-(2-ethoxy-1-ethoxymethylethyl)-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one (566 mg, 1.1 mmol) in dichloromethane (5 mL) was cooled in an ice bath and 3-chloroperbenzoic acid was added. The reaction mixture was stirred for 1 hour, concentrated in vacuo, and the residue was purified by column chromatography on silica gel using 98:2 dichloromethane/methanol. The column fractions containing product were combined and concentrated in vacuo to yield 425 mg of 7-benzylsulfinyl-3-(2-chlorophenyl)-1-(2-ethoxy-1-ethoxymethylethyl)-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one.
Reaction SMILES: [NH2:1][C:2]1[N:7]=[C:6]([N:8]2[C@H:13]([CH3:14])[CH2:12][CH2:11][C@H:10]([NH:15][C:16](=[O:23])[C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)[CH2:9]2)[CH:5]=[C:4]([C:24]2[CH:29]=[CH:28][C:27]([C:30]#[N:31])=[C:26](F)[CH:25]=2)[N:3]=1.O.[NH2:34][NH2:35]>C(O)C>[NH2:1][C:2]1[N:7]=[C:6]([N:8]2[C@H:13]([CH3:14])[CH2:12][CH2:11][C@H:10]([NH:15][C:16](=[O:23])[C:17]3[CH:22]=[CH:21][CH:20]=[CH:19][CH:18]=3)[CH2:9]2)[CH:5]=[C:4]([C:24]2[CH:25]=[C:26]3[C:27]([C:30]([NH2:31])=[N:34][NH:35]3)=[CH:28][CH:29]=2)[N:3]=1
Reactant: NN
Reactant: C[C@@H]1CC[C@H](NC(=O)c2ccccc2)CN1c1cc(-c2ccc(C#N)c(F)c2)nc(N)n1
Solvent: CCO
Solvent: O
Product: C[C@@H]1CC[C@H](NC(=O)c2ccccc2)CN1c1cc(-c2ccc3c(N)n[nH]c3c2)nc(N)n1
Temperature: 100 °C
Yield: 19.3 %

Procedure:
To N-{(3S,6R)-1-[2-amino-6-(4-cyano-3-fluorophenyl)-4-pyrimidinyl]-6-methyl-3-piperidinyl}benzamide (101 mg, 0.234 mmol) in ethanol (2 mL) into a 5 mL sealable vial was added hydrazine monohydrate (0.22 mL, 7.02 mmol), and the reaction was capped and heat overnight at 100° C. The reaction was concentrated, re dissolved in 1 mL of DMSO, and purified on HPLC (HPLC condition: open-access Gilson using Unipoint software with a Varian Polaris 5u C18(2) 100A, 50×30.00 mm 5 micron. 10-minute run (30 ml/min, 15% CH3CN/H2O, 0.1% TFA to 40% CH3CN/H2O, 0.1% TFA) with UV detection at 254 nm). Product fractions were combined and the volume was reduced to remove most of the CH3CN. To the resulting aqueous mixture was added sat. aqueous NaHCO3, and then it was extracted with EtOAc (3×15 mL). The organic was washed with brine, dried over MgSO4, filtered and concentrated to afford the title compound (20 mg) as a light yellow solid. LC-MS (ES) m/z=443 [M+H]+. 1H NMR (400 MHz, DMSO-d6): δ 1.19 (d, J=6.8 Hz, 3H), 1.24 (s, 1H), 1.66-1.93 (m, 5H), 2.54 (s, 1H), 3.89 (d, J=4.0 Hz, 1H), 5.39 (s, 2H), 6.13 (bs, 1H), 6.62 (s, 1H), 7.47-7.59 (m, 5H), 7.71 (d, J=8.6 Hz, 1H), 7.90 (d, J=7.1 Hz, 2H), 7.94 (s, 1H), 8.43 (d, J=8.1 Hz, 1H), 11.51 (bs, 1H).
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]2[NH:10][C:9](=[O:11])[C:8]3([CH2:16][CH2:15][O:14][CH2:13][CH2:12]3)[C:5]2=[N:6][CH:7]=1.[B:17]1(B2OC(C)(C)C(C)(C)O2)[O:21]C(C)(C)C(C)(C)[O:18]1.C([O-])(=O)C.[K+].CS(C)=O>C(OCC)(=O)C>[O:11]=[C:9]1[NH:10][C:4]2[C:5](=[N:6][CH:7]=[C:2]([B:17]([OH:21])[OH:18])[CH:3]=2)[C:8]21[CH2:16][CH2:15][O:14][CH2:13][CH2:12]2
Reactant: CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C
Reactant: O=C1Nc2cc(Br)cnc2C12CCOCC2
Agent: CC(=O)[O-]
Agent: [K+]
Solvent: CS(C)=O
Solvent: CCOC(C)=O
Product: O=C1Nc2cc(B(O)O)cnc2C12CCOCC2
Reaction time: 16 h

Procedure:
An oven dried resealable Schlenk tube was charged with 6′-bromo-2,3,5,6-tetrahydrospiro[pyran-4,3′-pyrrolo[3,2-b]pyridin]-2′(1′H)-one (preparation 16, 0.350 g, 1.24 mmol), bis(pinacolato)diboron (0.470 g, 1.85 mmol), potassium acetate (0.240 g, 2.48 mmol) and dimethylsulphoxide (4 mL). The Schlenk tube was subjected to three cycles of evacuation-backfilling with argon, and 1,1′-bis(diphenylphosphino)ferrocene-palladium(II) dichloride dichloromethane complex (0.06 g, 0.07 mmol) was added. After three further cycles of evacuation-backfilling with argon, the Schlenk tube was capped and placed in an oil bath at 110° C. After 16 hours, the mixture was cooled and ethyl acetate was added and the organic layer was extracted with 2M aqueous hydrochloric acid solution. The aqueous phase was washed with ethyl acetate and then the pH of the solution was adjusted to 6 with 6M aqueous sodium hydroxide solution and extracted with ethyl acetate. The organic layer was dried (MgSO4) and evaporated to give the title compound in quantitative yield as a brown oily residue, which was used without further purification.
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([C:11]([N:13]3[CH2:18][CH2:17][C:16]4([C:22]5[CH:23]=[CH:24][C:25]([F:27])=[CH:26][C:21]=5[C:20](=[O:28])[O:19]4)[CH2:15][CH2:14]3)=[O:12])=[CH:7][NH:8]2)=[CH:4][CH:3]=1.[F:29][C:30]1[CH:31]=[C:32]([S:37](Cl)(=[O:39])=[O:38])[CH:33]=[C:34]([F:36])[CH:35]=1>>[Cl:1][C:2]1[CH:10]=[C:9]2[C:5]([C:6]([C:11]([N:13]3[CH2:18][CH2:17][C:16]4([C:22]5[CH:23]=[CH:24][C:25]([F:27])=[CH:26][C:21]=5[C:20](=[O:28])[O:19]4)[CH2:15][CH2:14]3)=[O:12])=[CH:7][N:8]2[S:37]([C:32]2[CH:31]=[C:30]([F:29])[CH:35]=[C:34]([F:36])[CH:33]=2)(=[O:39])=[O:38])=[CH:4][CH:3]=1
Reactant: O=S(=O)(Cl)c1cc(F)cc(F)c1
Reactant: O=C1OC2(CCN(C(=O)c3c[nH]c4cc(Cl)ccc34)CC2)c2ccc(F)cc21
Product: O=C1OC2(CCN(C(=O)c3cn(S(=O)(=O)c4cc(F)cc(F)c4)c4cc(Cl)ccc34)CC2)c2ccc(F)cc21

Procedure:
Following the general procedure VII as described above, the sulphonylation of 1′-[(6-chloro-1H-indol-3-yl)carbonyl]-5-fluoro-3H-spiro[2-benzofuran-1,4′-piperidin]-3-one (prepared according to example 19) with commercially available 3,5-difluorobenzenesulfonyl chloride gave the title compound. ES-MS m/e (%): 575.3(M+H+).
Reaction SMILES: [CH3:1][C:2]1[NH:20][C:5]2=[N:6][C:7]([N:14]3[CH2:19][CH2:18][O:17][CH2:16][CH2:15]3)=[CH:8][C:9]([C:10]([O:12][CH3:13])=[O:11])=[C:4]2[N:3]=1.Br[CH2:22][C:23]1[CH:28]=[CH:27][CH:26]=[C:25]([C:29]([F:32])([F:31])[F:30])[C:24]=1[CH3:33].C([O-])([O-])=O.[Na+].[Na+].O>CN(C=O)C>[CH3:1][C:2]1[N:20]([CH2:22][C:23]2[CH:28]=[CH:27][CH:26]=[C:25]([C:29]([F:30])([F:31])[F:32])[C:24]=2[CH3:33])[C:5]2=[N:6][C:7]([N:14]3[CH2:15][CH2:16][O:17][CH2:18][CH2:19]3)=[CH:8][C:9]([C:10]([O:12][CH3:13])=[O:11])=[C:4]2[N:3]=1
Reactant: Cc1c(CBr)cccc1C(F)(F)F
Reactant: COC(=O)c1cc(N2CCOCC2)nc2[nH]c(C)nc12
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: COC(=O)c1cc(N2CCOCC2)nc2c1nc(C)n2Cc1cccc(C(F)(F)F)c1C
Temperature: 80 °C
Reaction time: 3 h
Yield: 95.1 %

Procedure:
A mixture of methyl 2-methyl-5-morpholino-3H-imidazo[4,5-b]pyridine-7-carboxylate (207 mg, 0.75 mmol), 1-(bromomethyl)-2-methyl-3-(trifluoromethyl)benzene (285 mg, 1.125 mmol) and Na2CO3 (239 mg, 2.25 mmol) in DMF (10 mL) was stirred at 80° C. for 3 h. TLC showed no methyl 2-methyl-5-morpholino-3H-imidazo[4,5-b]pyridine-7-carboxylate left. It was cooled to room temperature and poured into water (50 mL) and filtered. The solid was dissolved with DCM (150 mL) and it was washed with brine (100 mL×3) and the organic layer was dried over anhydrous Na2SO4, filtered and concentrated in vacuo to afford the desired product as a brown solid (320 mg, 95%); LC/MS: MS (ES+) m/e 449 (MH+); 1H NMR (300 MHz, DMSO-d6) δ ppm 2.40 (s, 3H), 2.51 (s, 3H), 3.41 (t, J=4.8 Hz, 4H), 3.68 (t, J=4.8 Hz, 4H), 3.92 (s, 3H), 5.50 (s, 2H), 6.90 (d, J=7.8 Hz, 1H), 7.07 (s, 1H), 7.28 (t, J=7.5 Hz, 1H), 7.62 (d, J=7.8 Hz, 1H).
Reaction SMILES: [NH2:1][C:2]1[N:3]=[C:4]([CH3:21])[C:5]2[CH:11]=[C:10](Br)[C:9](=[O:13])[N:8]([C@H:14]3[CH2:19][CH2:18][C@H:17]([OH:20])[CH2:16][CH2:15]3)[C:6]=2[N:7]=1.[B-](F)(F)(F)[C:23]1[NH:27][N:26]=[CH:25][CH:24]=1.[K+].C(N(CC)CC)C>C(O)C>[NH2:1][C:2]1[N:3]=[C:4]([CH3:21])[C:5]2[CH:11]=[C:10]([C:25]3[CH:24]=[CH:23][NH:27][N:26]=3)[C:9](=[O:13])[N:8]([C@H:14]3[CH2:19][CH2:18][C@H:17]([OH:20])[CH2:16][CH2:15]3)[C:6]=2[N:7]=1
Reactant: F[B-](F)(F)c1ccn[nH]1
Reactant: Cc1nc(N)nc2c1cc(Br)c(=O)n2[C@H]1CC[C@H](O)CC1
Agent: [K+]
Solvent: CCO
Solvent: CCN(CC)CC
Product: Cc1nc(N)nc2c1cc(-c1cc[nH]n1)c(=O)n2[C@H]1CC[C@H](O)CC1
Temperature: 100 °C

Procedure:
A mixture of 2-amino-6-bromo-8-((trans)-4-hydroxycyclohexyl)-4-methylpyrido[2,3-d]pyrimidin-7(8H)-one (100 mg, 0.283 mmol), potassium 1H-pyrazole-5-trifluoroborate (98.5 mg, 0.566 mmol), and triethylamine (197 uL, 1.42 mmol) in ethanol (3.0 mL) was bubbled with argon. PdCl2(dppf)1:1 w/CH2Cl2 was added, the vial was sealed and the mixture was bubbled with argon again, then heated in the microwave for 30 minutes at 100° C., then 60 minutes at 150° C. The reaction mixture was concentrated and purified by flash chromatography eluting with 1:1 ethyl acetate:chloroform/7 N ammonia in methanol (0.5-7%). The fractions containing the desired product were combined and concentrated and the solids were recrystallized from methanol/chloroform to afford 2-amino-8-((trans)-4-hydroxycyclohexyl)-4-methyl-6-(1H-pyrazol-3-yl)pyrido[2,3-d]pyrimidin-7(8H)-one (32 mg, 33%).
Reaction SMILES: [F:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][C:10]=1[NH:11][C:12]([CH2:14][O:15]C(=O)C)=[O:13])[NH:7][C:6](=[O:19])[CH2:5]2.O.[OH-].[Na+]>CO>[F:1][C:2]1[CH:3]=[C:4]2[C:8](=[CH:9][C:10]=1[NH:11][C:12](=[O:13])[CH2:14][OH:15])[NH:7][C:6](=[O:19])[CH2:5]2
Reactant: CC(=O)OCC(=O)Nc1cc2c(cc1F)CC(=O)N2
Agent: [Na+]
Agent: [OH-]
Solvent: O
Solvent: CO
Product: O=C(CO)Nc1cc2c(cc1F)CC(=O)N2
Yield: 93.3 %

Procedure:
Acetic acid (5-fluoro-2-oxo-2,3-dihydro-1H-indol-6-ylcarbamoyl)-methyl ester 27a (58 mg, 0.22 mmol) was dissolved in 1 ml of methanol under stirring, and added with 1 ml of water and sodium hydroxide (15 mg, 0.375 mmol) to the solution at room temperature. Upon completion of the addition, the reaction mixture was stirred for another 1 hour. After thin lay chromatography showed the disappearance of starting materials, the reaction mixture was filtered. The resulting solid was washed with water for three times and dried to obtain the title compound N-(5-fluoro-2-oxo-2,3-dihydro-1H-indol-6-yl)-2-hydroxy-acetamide 27b (46 mg, yield 93.8%) as a gray solid.