Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [NH:1]1[CH2:6][CH2:5][NH:4][CH2:3][CH2:2]1.C(=O)([O-])[O-].[K+].[K+].Cl[C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][C:15]=1[N+:20]([O-:22])=[O:21]>C(#N)C.C(Cl)Cl>[N+:20]([C:15]1[CH:16]=[CH:17][CH:18]=[CH:19][C:14]=1[N:1]1[CH2:6][CH2:5][NH:4][CH2:3][CH2:2]1)([O-:22])=[O:21]
Reactant: C1CNCCN1
Reactant: O=[N+]([O-])c1ccccc1Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: ClCCl
Solvent: CC#N
Product: O=[N+]([O-])c1ccccc1N1CCNCC1
Reaction time: 1 h

Procedure:
Piperazine (24.46 g) is dissolved in acetonitrile (200 ml) and anhydrous potassium carbonate (10.47 g) is added. Then 2-chloronitrobenzene (10.0 g) is added dropwise. After stirring 1 hr at 20°, the reaction mixture is diluted with methylene chloride, washed with water, and saturated aqueous potassium carbonate. After drying over anhydrous sodium sulfate, the reaction mixture is concentrated under reduced pressure to give the title compound, NMR (300 MHz, CDCl3) 7.75, 7.49, 7.14, 7.04, 3.03 and 1.93δ.
Reaction SMILES: [Mg].C(Br)C.[C:5]1([C@H:11]([CH3:20])[CH2:12][C:13]2[CH:18]=[CH:17][C:16](Cl)=[CH:15][CH:14]=2)[CH:10]=[CH:9][CH:8]=[CH:7][CH:6]=1.[I:21]I.Cl>O1CCCC1>[C:5]1([C@H:11]([CH3:20])[CH2:12][C:13]2[CH:18]=[CH:17][C:16]([I:21])=[CH:15][CH:14]=2)[CH:10]=[CH:9][CH:8]=[CH:7][CH:6]=1
Reactant: C[C@H](Cc1ccc(Cl)cc1)c1ccccc1
Reactant: II
Agent: Cl
Agent: [Mg]
Solvent: CCBr
Solvent: C1CCOC1
Product: C[C@H](Cc1ccc(I)cc1)c1ccccc1
Temperature: 25 °C
Reaction time: 1 h
Yield: 100 %

Procedure:
35 ml of tetrahydrofuran (THF) was added to 11.6 g (0.48 mol) of magnesium, and a solution having 23.6 g (0.22 mol) of ethyl bromide dissolved in 70 ml of THF was dropwise added thereto over a period of 1 hour at room temperature with stirring, followed by stirring for 1 hour. A solution having 50.0 g (0.22 mol) of (R)-2-phenyl-1-(4-chlorophenyl)propane dissolved in 50 ml of THF was dropwise added thereto over a period of 30 minutes at room temperature, followed by stirring under reflux for 5 hours. After the mixture was cooled to room temperature, 250 ml of THF was added thereto, and the mixture was further cooled to −30° C. A solution having 112 g (0.44 mol) of iodine dissolved in 300 ml of THF was dropwise added thereto at −30° C. over a period of 30 minutes, followed by stirring for 1 hour. The temperature was raised to 0° C., and 120 ml of 4M hydrochloric acid was dropwise added thereto, followed by stirring for 10 minutes. After extraction with toluene from the reaction liquid, washing with water and drying were carried out to obtain 69.8 g of (R)-2-phenyl-1-(4-iodophenyl)propane (GC purity: 95.2%, 0.22 mol).
Reaction SMILES: [Cl:1][C:2]1[N:7]=[CH:6][C:5]([C:8]2[CH:17]=[CH:16][C:11]([C:12]([O:14]C)=[O:13])=[CH:10][CH:9]=2)=[CH:4][CH:3]=1.O[Li].O>C1COCC1.O>[Cl:1][C:2]1[N:7]=[CH:6][C:5]([C:8]2[CH:17]=[CH:16][C:11]([C:12]([OH:14])=[O:13])=[CH:10][CH:9]=2)=[CH:4][CH:3]=1
Reactant: COC(=O)c1ccc(-c2ccc(Cl)nc2)cc1
Agent: [Li]O
Solvent: C1CCOC1
Solvent: O
Product: O=C(O)c1ccc(-c2ccc(Cl)nc2)cc1
Temperature: 25 °C

Procedure:
A solution of Example 252F (1.56 g, 6.4 mmol) in THF (30 mL) at room temperature was treated with a solution of LiOH.H2O (0.537 g, 12.8 mmol) in water (5 mL), heated to reflux for 4 hours, cooled to room temperature and concentrated. The mixture was neutralized with 1N HCl and extracted ethyl acetate (3×50 mL). The combined extracts were washed with brine, dried (Na2SO4), filtered, and concentrated to provide the desired product. MS (APCI) m/e 234 (M+H)+.
Reaction SMILES: [NH2:1][N:2]1[CH2:6][C:5](=[O:7])[N:4]([C:8]2[CH:13]=[CH:12][C:11]([C:14]([OH:16])=[O:15])=[CH:10][CH:9]=2)[C:3]1=[S:17].[CH3:18][C:19]1[CH:20]=[C:21]([N:26]2[C:30]([OH:31])=[C:29]([CH:32]=O)[C:28]([CH3:34])=[N:27]2)[CH:22]=[CH:23][C:24]=1[CH3:25].C(O)C>CO>[C:14]([C:11]1[CH:10]=[CH:9][C:8]([N:4]2[C:5](=[O:7])[CH2:6][N:2]([N:1]=[CH:32][C:29]3[C:28]([CH3:34])=[N:27][N:26]([C:21]4[CH:22]=[CH:23][C:24]([CH3:25])=[C:19]([CH3:18])[CH:20]=4)[C:30]=3[OH:31])[C:3]2=[S:17])=[CH:13][CH:12]=1)([OH:16])=[O:15]
Reactant: Cc1ccc(-n2nc(C)c(C=O)c2O)cc1C
Reactant: NN1CC(=O)N(c2ccc(C(=O)O)cc2)C1=S
Solvent: CO
Solvent: CCO
Product: Cc1ccc(-n2nc(C)c(C=NN3CC(=O)N(c4ccc(C(=O)O)cc4)C3=S)c2O)cc1C
Yield: 93.8 %

Procedure:
50 mg (0.2 mmol) of the 1-amino-3-(4-carboxyphenyl)-2-thioxoimidazolidin-4-one synthesized above in 1) and 55 mg (0.22 mmol) of the 1-(3,4-dimethylphenyl)-5-hydroxy-3-methyl-1H-pyrazole-4-carbaldehyde synthesized in 1) of Reference Synthetic Example 1 were stirred in a liquid mixture of 10 ml of ethanol and 5 ml of methanol at room temperature for 96 hours. The resulting insoluble was collected by filtration to obtain 87 mg of the desired product as a yellow solid (yield 85%).
Reaction SMILES: [CH2:1]([O:4][C:5]1[CH:15]=[CH:14][CH:13]=[CH:12][C:6]=1[O:7][CH2:8][CH:9]1[O:11][CH2:10]1)[CH:2]=[CH2:3].[NH:16]1[CH2:21][CH2:20][CH:19]([N:22]2[CH2:27][CH2:26][CH2:25][NH:24][C:23]2=[O:28])[CH2:18][CH2:17]1>C(O)C>[CH2:1]([O:4][C:5]1[CH:15]=[CH:14][CH:13]=[CH:12][C:6]=1[O:7][CH2:8][CH:9]([OH:11])[CH2:10][N:16]1[CH2:21][CH2:20][CH:19]([N:22]2[CH2:27][CH2:26][CH2:25][NH:24][C:23]2=[O:28])[CH2:18][CH2:17]1)[CH:2]=[CH2:3]
Reactant: C=CCOc1ccccc1OCC1CO1
Reactant: O=C1NCCCN1C1CCNCC1
Solvent: CCO
Product: C=CCOc1ccccc1OCC(O)CN1CCC(N2CCCNC2=O)CC1

Procedure:
A solution of 10.3 g of 1-(o-allyloxy-phenoxy)-2,3-epoxy-propane and 9.15 g of 1-(4-piperidyl)-2-oxo-hexahydro-pyrimidine in 7 ml abs. ethanol is heated for 5 hours to 95°C and then evaporated in vacuo. The residue is recrystallised from isopropanol to yield the 1-[3-(o-allyloxy-phenoxy)-2-hydroxypropyl]-4-(2-oxo-hexahydro-1-pyrimidinyl)piperidine, which melts at 122°-125°C.
Reaction SMILES: [C:1]([C:5]1[CH:6]=[C:7]([CH:9]=[CH:10][CH:11]=1)[NH2:8])([CH3:4])([CH3:3])[CH3:2].[N:12]1([C:18]2[N:19]=[C:20]([CH2:25][C:26]([O-])=[O:27])[NH:21][C:22](=[O:24])[CH:23]=2)[CH2:17][CH2:16][O:15][CH2:14][CH2:13]1.[Na+].O.[Cl-].COC1N=C(OC)N=C([N+]2(C)CCOCC2)N=1>CO>[CH3:3][C:1]([C:5]1[CH:6]=[C:7]([NH:8][C:26](=[O:27])[CH2:25][C:20]2[NH:21][C:22](=[O:24])[CH:23]=[C:18]([N:12]3[CH2:17][CH2:16][O:15][CH2:14][CH2:13]3)[N:19]=2)[CH:9]=[CH:10][CH:11]=1)([CH3:4])[CH3:2]
Reactant: CC(C)(C)c1cccc(N)c1
Reactant: O=C([O-])Cc1nc(N2CCOCC2)cc(=O)[nH]1
Agent: COc1nc(OC)nc([N+]2(C)CCOCC2)n1
Agent: [Cl-]
Agent: [Na+]
Solvent: CO
Solvent: O
Product: CC(C)(C)c1cccc(NC(=O)Cc2nc(N3CCOCC3)cc(=O)[nH]2)c1
Temperature: 25 °C
Reaction time: 0.08 h
Yield: 63.5 %

Procedure:
224 mg of 3-(tert-butyl)aniline are added to a solution of 261 mg of sodium [4-(morpholin-4-yl)-6-oxo-1,6-dihydropyrimidin-2-yl]acetate prepared in stage 2 of Example 1 in 10 ml of methanol. The reaction mixture is stirred at ambient temperature for 5 minutes and then 442 mg of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholin-4-ium chloride hydrate are added. The resulting mixture is thus stirred for 30 minutes at ambient temperature. The reaction mixture is concentrated under reduced pressure. The evaporation residue is taken up with 10 ml of water and 10 ml of ethyl acetate. The resulting product is then stirred for 30 minutes. The precipitate formed is filtered off. 235 mg of N-[3-(2-methylpropan-2-yl)phenyl]-2-[4-(morpholin-4-yl)-6-oxo-1,6-dihydropyrimidin-2-yl]acetamide are thus obtained in the form of a white solid, the characteristics of which are the following:
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][CH2:9][CH2:10][O:11][C:12]1[CH:17]=[CH:16][C:15]([CH2:18][C:19]([NH:21][C:22]2[CH:27]=[CH:26][CH:25]=[C:24](I)[CH:23]=2)=[O:20])=[CH:14][C:13]=1[O:29][CH3:30])=[O:7])([CH3:4])([CH3:3])[CH3:2].[C:31]1(B(O)O)[CH:36]=[CH:35][CH:34]=[CH:33][CH:32]=1.C(=O)([O-])[O-].[Cs+].[Cs+].O>O1CCCC1.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>[C:1]([O:5][C:6]([NH:8][CH2:9][CH2:10][O:11][C:12]1[CH:17]=[CH:16][C:15]([CH2:18][C:19]([NH:21][C:22]2[CH:27]=[CH:26][CH:25]=[C:24]([C:31]3[CH:36]=[CH:35][CH:34]=[CH:33][CH:32]=3)[CH:23]=2)=[O:20])=[CH:14][C:13]=1[O:29][CH3:30])=[O:7])([CH3:4])([CH3:3])[CH3:2]
Reactant: COc1cc(CC(=O)Nc2cccc(I)c2)ccc1OCCNC(=O)OC(C)(C)C
Reactant: OB(O)c1ccccc1
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: [Cs+]
Solvent: O
Solvent: C1CCOC1
Product: COc1cc(CC(=O)Nc2cccc(-c3ccccc3)c2)ccc1OCCNC(=O)OC(C)(C)C
Yield: 77.3 %

Procedure:
Intermediate 4 (500 mg) is dissolved in tetrahydrofuran (10 ml), and thereto are added tetrakis(triphenylphosphine)palladium (0) (110 mg), phenylboronic acid (230 mg), cesium carbonate (1.2 g) and water (2 ml), and the mixture is heated under reflux for 18 hours under argon atmosphere. The solvent is evaporated under reduced pressure, and the residue is purified by silica gel column chromatography (eluent: gradient from 0% to 100% hexane/ethyl acetate) to give 4-[2-(tert-butoxycarbonylamino)ethoxy]-3-methoxy-N-(3-phenylphenyl)phenylacetamide (350 mg). This product is treated with 10% hydrogen chloride-methanol to give the desired compound (210 mg).
Reaction SMILES: [Br:1][CH2:2][C:3]([N:5]([CH:12]([CH3:14])[CH3:13])[C:6]1[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1)=[O:4].[F:15]C1C=CC(NC(C)C)=CC=1.BrCC(Br)=O>>[Br:1][CH2:2][C:3]([N:5]([C:6]1[CH:11]=[CH:10][C:9]([F:15])=[CH:8][CH:7]=1)[CH:12]([CH3:14])[CH3:13])=[O:4]
Reactant: CC(C)N(C(=O)CBr)c1ccccc1
Reactant: CC(C)Nc1ccc(F)cc1
Agent: O=C(Br)CBr
Product: CC(C)N(C(=O)CBr)c1ccc(F)cc1

Procedure:
Following the procedure described for Preparation 1(A), (4-fluoro-phenyl)-isopropyl-amine (13.70 g, 89.54 mmol) was alkylated with bromoacetyl bromide (7.78 mL, 89.54 mmol) to provide 15.02 g of 2-bromo-N-(4-fluoro-phenyl)-N-isopropyl-acetamide as an oil. 1H NMR (CD2Cl2) δ 7.14-7.23 (m, 4H), 4.90 (m, 1H), 3.53 (s, 2H), 1.05 (d, 6H).
Reaction SMILES: Cl/[C:2](=[N:15]\[OH:16])/[C:3]1[CH:8]=[CH:7][C:6]([P:9]([CH3:14])(=[O:13])[O:10][CH2:11][CH3:12])=[CH:5][CH:4]=1.[C:17]([C:19]1[C:20]([O:31][CH2:32][C:33]2[CH:38]=[CH:37][C:36]([O:39][CH3:40])=[CH:35][CH:34]=2)=[N:21][C:22]([C:25]2[CH:30]=[CH:29][CH:28]=[CH:27][N:26]=2)=[N:23][CH:24]=1)#[CH:18].C(N(CC)CC)C>C1COCC1>[CH3:40][O:39][C:36]1[CH:35]=[CH:34][C:33]([CH2:32][O:31][C:20]2[C:19]([C:17]3[O:16][N:15]=[C:2]([C:3]4[CH:8]=[CH:7][C:6]([P:9]([CH3:14])(=[O:13])[O:10][CH2:11][CH3:12])=[CH:5][CH:4]=4)[CH:18]=3)=[CH:24][N:23]=[C:22]([C:25]3[CH:30]=[CH:29][CH:28]=[CH:27][N:26]=3)[N:21]=2)=[CH:38][CH:37]=1
Reactant: CCOP(C)(=O)c1ccc(/C(Cl)=N/O)cc1
Reactant: C#Cc1cnc(-c2ccccn2)nc1OCc1ccc(OC)cc1
Solvent: C1CCOC1
Solvent: CCN(CC)CC
Product: CCOP(C)(=O)c1ccc(-c2cc(-c3cnc(-c4ccccn4)nc3OCc3ccc(OC)cc3)on2)cc1
Temperature: 25 °C
Reaction time: 12 h
Yield: 55.3 %

Procedure:
A mixture of compound 38-e (750 mg, 2.8 mmol), compound 37-j (820 mg, 2.6 mmol) and triethylamine (780 mg, 7.8 mmol) in THF (20 mL) was stirred at room temperature for 12 h. The resulting mixture was concentrated under reduce pressure, purified by column chromatography on silica gel (DCM:MeOH=30:1) to give compound 38-f (780 mg). LC-MS 543 [M+H]+
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.S(=O)(=O)(O)O.[C:13]([C:16]1([CH3:22])[O:21][C:19](=[O:20])[CH2:18][CH2:17]1)(O)=[O:14]>CCOCC>[F:1][C:2]1[CH:7]=[CH:6][C:5]([C:13]([C:16]2([CH3:22])[O:21][C:19](=[O:20])[CH2:18][CH2:17]2)=[O:14])=[CH:4][CH:3]=1
Reactant: CC1(C(=O)O)CCC(=O)O1
Reactant: Fc1ccccc1
Agent: O=S(=O)(O)O
Solvent: CCOCC
Product: CC1(C(=O)c2ccc(F)cc2)CCC(=O)O1
Temperature: 10 °C

Procedure:
To 0.5 moles of fluorobenzene and 0.2 moles of sulfuric acid at 80° C is added portionwise 0.2 , moles of gamma-carboxy-gamma-valerolactone (I). The mixture is kept at 80° C for an additional hour. The mixture is cooled to 10° C and 100 ml of ether is added. The mixture is poured onto ice and 100 ml of ether is added. The layers are separated and the aqueous layer is back extracted with ether and the ether extracts are combined. The combined ether extracts are washed with water, saturated sodium bicarbonate (twice), water, dried and concentrated to give the crude product (III).
Reaction SMILES: N1C=CN=C1.[Cl:6][C:7]1[CH:14]=[C:13]([OH:15])[CH:12]=[CH:11][C:8]=1[CH:9]=[O:10].[C:16]([Si:20]([C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1)([C:22]1[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=1)Cl)([CH3:19])([CH3:18])[CH3:17].O>C(Cl)Cl>[Si:20]([O:15][C:13]1[CH:12]=[CH:11][C:8]([CH:9]=[O:10])=[C:7]([Cl:6])[CH:14]=1)([C:16]([CH3:19])([CH3:18])[CH3:17])([C:28]1[CH:29]=[CH:30][CH:31]=[CH:32][CH:33]=1)[C:22]1[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=1
Reactant: CC(C)(C)[Si](Cl)(c1ccccc1)c1ccccc1
Reactant: O=Cc1ccc(O)cc1Cl
Agent: c1c[nH]cn1
Solvent: ClCCl
Solvent: O
Product: CC(C)(C)[Si](Oc1ccc(C=O)c(Cl)c1)(c1ccccc1)c1ccccc1
Temperature: 25 °C
Reaction time: 8 h
Yield: 107.2 %

Procedure:
To a solution of imidazole (4.28 g, 62.89 mmol) and 2-chloro-4-hydroxybenzaldehyde (8.95 g, 57.16 mmol) in CH2Cl2 (500 ml)was added dropwise a solution of t-butyldiphenylchlorosilane (17.27 g, 62.86 mmol) in CH2Cl2, (200 mL). The solution was stirred overnight at ambient temperature. The mixture was then poured into H2O (500 mL) and the organic layer washed with NaHCO3, H2O, brine, and dried (MgSO4). The solvent was removed in vacuo to provide 24.2 g of the title compound.
Reaction SMILES: [NH2:1][C:2]1[C:3](=[O:14])[N:4]([CH2:12][CH3:13])[C:5](=[O:11])[N:6]([CH2:9][CH3:10])[C:7]=1[NH2:8].[CH3:15][C:16](=[CH:20][C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1)[C:17](O)=O>>[CH2:12]([N:4]1[C:3](=[O:14])[C:2]2[NH:1][C:15](/[C:16](/[CH3:17])=[CH:20]/[C:21]3[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=3)=[N:8][C:7]=2[N:6]([CH2:9][CH3:10])[C:5]1=[O:11])[CH3:13]
Reactant: CCn1c(N)c(N)c(=O)n(CC)c1=O
Reactant: CC(=Cc1ccccc1)C(=O)O
Product: CCn1c(=O)c2[nH]c(/C(C)=C/c3ccccc3)nc2n(CC)c1=O
Yield: 49.8 %

Procedure:
Substantially the same procedure as in Example 7 was repeated using 2.00 g (10.1 mmol) of 5,6-diamino-1,3-diethyluracil and 1.80 g (11.1 mmol) of α-methylcinnamic acid. Then, the resultant crude crystals were recrystallized from ethanol/water to give 1.63 g (yield 50%) of Compound 134 as white needles.
Reaction SMILES: Cl.[NH2:2][OH:3].[Cl:4][C:5]1[CH:6]=[C:7]([CH:15]([CH2:25][CH:26]2[CH2:31][CH2:30][C:29](=O)[CH2:28][CH2:27]2)[C:16]([NH:18][C:19]2[CH:24]=[N:23][CH:22]=[CH:21][N:20]=2)=[O:17])[CH:8]=[CH:9][C:10]=1[S:11]([CH3:14])(=[O:13])=[O:12]>CO.N1C=CC=CC=1>[Cl:4][C:5]1[CH:6]=[C:7]([CH:15]([CH2:25][CH:26]2[CH2:31][CH2:30][C:29](=[N:2][OH:3])[CH2:28][CH2:27]2)[C:16]([NH:18][C:19]2[CH:24]=[N:23][CH:22]=[CH:21][N:20]=2)=[O:17])[CH:8]=[CH:9][C:10]=1[S:11]([CH3:14])(=[O:13])=[O:12]
Reactant: NO
Reactant: CS(=O)(=O)c1ccc(C(CC2CCC(=O)CC2)C(=O)Nc2cnccn2)cc1Cl
Agent: Cl
Solvent: CO
Solvent: c1ccncc1
Product: CS(=O)(=O)c1ccc(C(CC2CCC(=NO)CC2)C(=O)Nc2cnccn2)cc1Cl
Temperature: 25 °C
Yield: 80.1 %

Procedure:
A solution of hydroxylamine hydrochloride (19 mg, 0.27 mmol) in methanol (0.5 mL) and pyridine (0.5 mL) was treated with 2-(3-chloro-4-methanesulfonyl-phenyl)-3-(4-oxo-cyclohexyl)-N-pyrazin-2-yl-propionamide (prepared as in Example 58, 80 mg, 0.18 mmol). The reaction mixture was heated under reflux for 2 h, cooled to 25° C., and concentrated in vacuo to remove methanol. The resulting residue was suspended in ethyl acetate (10 mL), washed with water 1×5 mL), dried over magnesium sulfate, filtered, and concentrated in vacuo. Biotage chromatography (FLASH 12M, Silica, 35/65 hexanes/ethyl acetate to 1/1 hexanes/ethyl acetate) afforded 2-(3-chloro-4-methanesulfonyl-phenyl)-3-(4-hydroxyimino-cyclohexyl)-N-pyrazin-2-yl-propionamide (65 mg, 80%) was a white foam: EI-HRMS m/e calcd for C20H23ClN4O4S (M+H)+ 451.1202. found 451.1206.
Reaction SMILES: [C:1]1([CH2:7][C:8]([O:10][CH2:11][CH3:12])=[O:9])[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.[O-]CC.[Na+].[Na].[CH2:18]=[C:19]1[C:24](=[O:25])[CH:23]2[CH2:26][CH2:27][N:20]1[CH2:21][CH2:22]2>C(O)C.C(O)(=O)C>[O:25]=[C:24]1[CH:23]2[CH2:26][CH2:27][N:20]([CH2:21][CH2:22]2)[CH:19]1[CH2:18][CH:7]([C:1]1[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1)[C:8]([O:10][CH2:11][CH3:12])=[O:9]
Reactant: CCOC(=O)Cc1ccccc1
Reactant: C=C1C(=O)C2CCN1CC2
Agent: CC[O-]
Agent: [Na+]
Agent: [Na]
Solvent: CCO
Solvent: CC(=O)O
Product: CCOC(=O)C(CC1C(=O)C2CCN1CC2)c1ccccc1
Reaction time: 16 h

Procedure:
Ethyl phenylacetate, 49.2 g was added to a solution of sodium ethoxide previously prepared from metallic sodium, 2.9 g and ethanol, 100 ml. The mixture was cooled to 5°, then a solution of 2-methylenequinuclidin-3-one, 39.4 g, in ethanol, 50 ml. was added dropwise and with stirring. After 16 hours at room temperature, the solution was neutralized with acetic acid then subjected to evaporation at reduced pressure. Water, 100 ml. was added to the residue and the mixture was extracted with chloroform. Evaporation of this solvent gave ethyl (3-oxoquinuclidin-2-yl)methylphenylacetate, 54 g (60%); b.p. 195°-200° at 1 mm Hg; m.p. of methiodide salt, 194.7-195.6°.
Reaction SMILES: Cl[C:2]1[N:3]=[CH:4][C:5]2[N:11]([CH3:12])[C:10](=[O:13])[C:9]([F:15])([F:14])[CH2:8][N:7]([CH:16]3[CH2:19][CH2:18][CH2:17]3)[C:6]=2[N:20]=1.O.C1(C)C(S(O)(=O)=O)=CC=CC=1.[NH2:33][C:34]1[CH:50]=[CH:49][C:37]([C:38]([NH:40][CH:41]2[CH2:46][CH2:45][N:44]([CH2:47][CH3:48])[CH2:43][CH2:42]2)=[O:39])=[CH:36][C:35]=1[O:51][CH3:52]>C(O)(C)C>[CH:16]1([N:7]2[CH2:8][C:9]([F:15])([F:14])[C:10](=[O:13])[N:11]([CH3:12])[C:5]3[CH:4]=[N:3][C:2]([NH:33][C:34]4[CH:50]=[CH:49][C:37]([C:38]([NH:40][CH:41]5[CH2:42][CH2:43][N:44]([CH2:47][CH3:48])[CH2:45][CH2:46]5)=[O:39])=[CH:36][C:35]=4[O:51][CH3:52])=[N:20][C:6]2=3)[CH2:19][CH2:18][CH2:17]1
Reactant: CCN1CCC(NC(=O)c2ccc(N)c(OC)c2)CC1
Reactant: CN1C(=O)C(F)(F)CN(C2CCC2)c2nc(Cl)ncc21
Agent: Cc1ccccc1S(=O)(=O)O
Solvent: CC(C)O
Solvent: O
Product: CCN1CCC(NC(=O)c2ccc(Nc3ncc4c(n3)N(C3CCC3)CC(F)(F)C(=O)N4C)c(OC)c2)CC1
Yield: 41.6 %

Procedure:
A mixture of 0.0605 g (0.20 mmole) 2-chloro-9-cyclobutyl-7,7-difluoro-5-methyl-5,7,8,9-tetrahydro-pyrimido[4,5-b][1,4]diazepin-6-one (VII-1), 0.0571 g (0.30 mmole) of toluenesulfonic acid monohydrate, 0.0555 g (0.20 mmole) of 4-amino-N-(1-ethyl-piperidin-4-yl)-3-methoxy-benzamide and 1 mL of isopropanol was heated in a sealed vessel at 140 degrees for 25 hours, cooled and concentrated under reduced pressure. The residue taken up in ethyl acetate and washed successively with 50 mL of saturated aqueous sodium bicarbonate, 50 mL of water, 50 mL of brine. The organic layer was dried over anhydrous sodium sulfate, filtered and concentrated under reduced pressure. The residue was purified by silica gel chromatography, eluting with acetonitrile-methanol-triethylamine (90:10:1) and then recrystallization from acetonitrile to give 0.0452 g of 4-(9-cyclobutyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-ylamino)-N-(1-ethyl-piperidin-4-yl)-3-methoxy-benzamide (I-10) as a white solid.
Reaction SMILES: [CH3:1][O:2][C:3](=[O:28])[C:4]1[CH:9]=[CH:8][C:7]([CH2:10][N:11]([C:16]2[CH:21]=[CH:20][C:19]([CH:22]3[CH2:27][CH2:26][CH2:25][CH2:24][CH2:23]3)=[CH:18][CH:17]=2)[C:12](=[O:15])[NH:13]Cl)=[CH:6][CH:5]=1.C(N(CC)CC)C.[Cl:36][C:37]1[CH:42]=[CH:41][C:40]([C@@H:43](N)[CH3:44])=[CH:39][CH:38]=1>CN1CCCC1=O>[CH3:1][O:2][C:3](=[O:28])[C:4]1[CH:9]=[CH:8][C:7]([CH2:10][N:11]([C:16]2[CH:21]=[CH:20][C:19]([CH:22]3[CH2:27][CH2:26][CH2:25][CH2:24][CH2:23]3)=[CH:18][CH:17]=2)[C:12]([NH:13][C@H:43]([C:40]2[CH:41]=[CH:42][C:37]([Cl:36])=[CH:38][CH:39]=2)[CH3:44])=[O:15])=[CH:6][CH:5]=1
Reactant: C[C@H](N)c1ccc(Cl)cc1
Reactant: COC(=O)c1ccc(CN(C(=O)NCl)c2ccc(C3CCCCC3)cc2)cc1
Solvent: CCN(CC)CC
Solvent: CN1CCCC1=O
Product: COC(=O)c1ccc(CN(C(=O)N[C@@H](C)c2ccc(Cl)cc2)c2ccc(C3CCCCC3)cc2)cc1
Reaction time: 2 h

Procedure:
A 2 L reaction flask equipped with mechanical stirring was charged with N-chlorocarbamoyl-4-[(4-cyclohexylphenylamino)methyl]benzoic acid methyl ester (94 g, 0.244 mol), N-methyl-2-pyrrolidinone (1.0 L) and triethylamine (68 mL, 0.487 mol). To the clear solution was added drop wise (S)-1-(4-chlorophenyl)ethylamine (38.0 g, 0.244 mol), keeping the internal reaction temperature below 30° C. Stirring was continued for 2 hours, then the reaction mixture was partitioned between water (1.0 L) and ethyl acetate (1.0 L). After extensive mixing, the organic layer was separated, and washed with a 5% aqueous solution of citric acid (500 mL), and saturated ammonium chloride (500 mL), before drying with anhydrous sodium sulphate. Solvent was removed, and the residual oil was evaporated once from acetonitrile. This product was sufficiently pure for further synthesis. Yield: 103 g (84%).
Reaction SMILES: [NH2:1][C:2]1[CH:29]=[CH:28][C:5]2[NH:6][C:7]([C:12]3[C:13](=[O:27])[N:14]([CH2:22][CH2:23][CH:24]([CH3:26])[CH3:25])[N:15]=[C:16]([CH:19]([CH3:21])[CH3:20])[C:17]=3[OH:18])=[N:8][S:9](=[O:11])(=[O:10])[C:4]=2[CH:3]=1.C(N(CC)CC)C.[C:37](Cl)(=[O:44])[C:38]1[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=1.C([O-])(O)=O.[Na+]>CN(C)C1C=CN=CC=1.CN(C=O)C>[OH:18][C:17]1[C:16]([CH:19]([CH3:21])[CH3:20])=[N:15][N:14]([CH2:22][CH2:23][CH:24]([CH3:25])[CH3:26])[C:13](=[O:27])[C:12]=1[C:7]1[NH:6][C:5]2[CH:28]=[CH:29][C:2]([NH:1][C:37](=[O:44])[C:38]3[CH:43]=[CH:42][CH:41]=[CH:40][CH:39]=3)=[CH:3][C:4]=2[S:9](=[O:10])(=[O:11])[N:8]=1
Reactant: O=C(Cl)c1ccccc1
Reactant: CC(C)CCn1nc(C(C)C)c(O)c(C2=NS(=O)(=O)c3cc(N)ccc3N2)c1=O
Agent: CN(C)c1ccncc1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: CCN(CC)CC
Solvent: CN(C)C=O
Product: CC(C)CCn1nc(C(C)C)c(O)c(C2=NS(=O)(=O)c3cc(NC(=O)c4ccccc4)ccc3N2)c1=O
Temperature: 80 °C
Reaction time: 4 h
Yield: 52.1 %

Procedure:
To a solution of 5j (0.048 g, 0.11 mmol) and 4-dimethylaminopyridine (0.0014 g, 0.011 mmol) in DMF was added triethylamine (18 μL, 0.125 mmol) followed by benzoyl chloride (16 μL, 0.137 mmol). The reaction mixture was stirred 4 h at 80° C. and cooled to room temperature. The reaction mixture was treated with sat NaHCO3 (1 mL) and extracted two times with EtOAc (3 mL). The combined organic layer was washed with brine (1 mL), dried over MgSO4, and concentrated in vacuo. The crude mixture was purified by flash column chromatography using silica gel (0-40% EtOAc/hexanes) to give 5k (0.030 g, 50%) as a yellow solid. 1H NMR (400 MHz, D6-DMSO) δ 10.63 (br s), 8.45 (d, J=2.4 Hz, 1H), 8.09 (dd, J=8.8, 2 Hz, 1 H), 8.97 (d, J=7.2 Hz, 2 H), 7.67 (d, J=9.2 Hz, 1 H), 7.60 (d, J=7.2 Hz, 1 H), 7.54 (t, J=7.2 Hz, 2 H), 4.13 (d, J=6.8 Hz, 2 H), 3.25 (m, 1 H), 1.63 (m, 3 H), 1.22 (d, J=6.8 Hz, 6 H), 0.93 (d, J=6.4 Hz, 6 H). LC-MS(ESI+) m/e 524 [M+H]+.
Reaction SMILES: [ClH:1].[NH2:2][C:3]1[N:8]=[CH:7][C:6](/[CH:9]=[CH:10]/[C:11]([OH:13])=O)=[CH:5][C:4]=1[CH2:14][N:15]1[CH2:20][CH2:19][N:18]([CH3:21])[CH2:17][CH2:16]1.Cl.CN1CC2C=C(/C=C/C(O)=O)C=NC=2NC(=O)C1.[CH3:41][NH:42][CH2:43][C:44]1[S:48][C:47]2[CH:49]=[CH:50][CH:51]=[CH:52][C:46]=2[C:45]=1[CH3:53].CNCC1C=CC2C(=CC=CC=2)C=1CCC>>[ClH:1].[NH2:2][C:3]1[N:8]=[CH:7][C:6](/[CH:9]=[CH:10]/[C:11]([N:42]([CH3:41])[CH2:43][C:44]2[S:48][C:47]3[CH:49]=[CH:50][CH:51]=[CH:52][C:46]=3[C:45]=2[CH3:53])=[O:13])=[CH:5][C:4]=1[CH2:14][N:15]1[CH2:20][CH2:19][N:18]([CH3:21])[CH2:17][CH2:16]1
Reactant: CNCc1sc2ccccc2c1C
Reactant: CN1CCN(Cc2cc(/C=C/C(=O)O)cnc2N)CC1
Agent: CCCc1c(CNC)ccc2ccccc12
Agent: CN1CC(=O)Nc2ncc(/C=C/C(=O)O)cc2C1
Agent: Cl
Product: Cc1c(CN(C)C(=O)/C=C/c2cnc(N)c(CN3CCN(C)CC3)c2)sc2ccccc12
Yield: 46 %

Procedure:
According to the procedure of Example 1, except substituting (E)-3-[6-amino-5-(4-methyl-piperazin-1-ylmethyl)pyridin-3-yl]acrylic acid hydrochloride for the (E)-3-(4-methyl-2-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-e][1,4]diazepin-7-yl)acrylic acid hydrochloride, and substituting methyl-(3-methyl-benzo[b]thiophen-2-ylmethyl)amine for the methyl-(1-propyl-naphthalen-2-ylmethyl)amine, the title compound (101 mg, 46%) was prepared as a light, yellow powder and as a mixture of amide rotamers: 1H NMR (300 MHz, DMSO-d6) δ 10.6 (br s, 1H), 8.27 (s, 1H), 8.16 (s, 1H), 7.87 (d, J=7.6 Hz, 1H), 7.73 (d, J=7.1 Hz, 1H), 7.52-7.28 (m, 5H), 7.11 (d, J=15.3 Hz, 1H), 5.11-4.89 (m, 2H), 3.55 (br s, 2H), 3.37-3.23 (m, 4H), 3.14 (s, 2H), 3.10-2.92 (m, 5H), 2.72 (s, 3H), 2.42 (s, 3H); MS (ESI) m/e 450 (M+H)+.