Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [C:1]([C:3]([C:6]1[CH:7]=[C:8]([CH:21]=[CH:22][CH:23]=1)[C:9]([NH:11][C:12]1[CH:17]=[CH:16][CH:15]=[C:14]([NH:18][CH:19]=O)[CH:13]=1)=[O:10])([CH3:5])[CH3:4])#[N:2].C(=O)([O-])O.[Na+]>O1CCCC1>[C:1]([C:3]([C:6]1[CH:7]=[C:8]([CH:21]=[CH:22][CH:23]=1)[C:9]([NH:11][C:12]1[CH:17]=[CH:16][CH:15]=[C:14]([NH:18][CH3:19])[CH:13]=1)=[O:10])([CH3:5])[CH3:4])#[N:2]
Reactant: CC(C)(C#N)c1cccc(C(=O)Nc2cccc(NC=O)c2)c1
Agent: O=C([O-])O
Agent: [Na+]
Solvent: C1CCOC1
Product: CNc1cccc(NC(=O)c2cccc(C(C)(C)C#N)c2)c1
Temperature: 25 °C
Reaction time: 2.5 h

Procedure:
To a solution of 3-(1-cyano-1-methylethyl)-N-[3-(formylamino)phenyl]benzamide (405 mg, 1.32 mmol) produced in Example D3(ii) in tetrahydrofuran (15 mL) was added borane dimethylsulfide complex (361 μL, 3.42 mmol), and the mixture was stirred at room temperature for 2.5 hr. To the reaction mixture was added saturated aqueous sodium hydrogen carbonate solution (20 mL), and the mixture was extracted with ethyl acetate (20 mL, 10 mL). The combined organic layer was washed with saturated brine (5 mL), and dried over anhydrous sodium sulfate. The insoluble material was filtered off, and the filtrate was concentrated under reduced pressure to give 3-(1-cyano-1-methylethyl)-N-[3-(methylamino)phenyl]benzamide as a brown oil. The obtained compound was used for the next reaction without further purification.
Reaction SMILES: [C:1]([O:5][C:6](=[O:22])[NH:7][C@@H:8]1[CH2:13][CH2:12][CH2:11][CH2:10][C@H:9]1[O:14]CC1C=CC=CC=1)([CH3:4])([CH3:3])[CH3:2].C(OCC)(=O)C>[Pd].CO>[C:1]([O:5][C:6](=[O:22])[NH:7][C@@H:8]1[CH2:13][CH2:12][CH2:11][CH2:10][C@H:9]1[OH:14])([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)OC(=O)N[C@@H]1CCCC[C@H]1OCc1ccccc1
Agent: [Pd]
Solvent: CO
Solvent: CCOC(C)=O
Product: CC(C)(C)OC(=O)N[C@@H]1CCCC[C@H]1O
Reaction time: 4 h
Yield: 94.9 %

Procedure:
To a solution of (1R,2R) (2-benzyloxycyclohexyl) carbamic acid tert-butyl ester (7 g, 23 mmoles) in a 9:1 mixture of ethyl acetate and methanol (80 mL), 10% Pd—C (1.13 g) was added and hydrogenated at 35 psi for 4 h. The catalyst was removed by filtration through a celite pad. The filtrate was concentrated to give the title compound as an oil (4.7 g, 95%). MS: (M+1): 215.95
Reaction SMILES: O1CCCC1.Cl.[C:7]([C:9]1([O:16][Si](C)(C)C)[CH2:14][CH:13]2[CH2:15][CH:10]1[CH2:11][CH2:12]2)#[N:8].C(=O)([O-])O.[K+]>O>[C:7]([C:9]1([OH:16])[CH2:14][CH:13]2[CH2:15][CH:10]1[CH2:11][CH2:12]2)#[N:8]
Reactant: C[Si](C)(C)OC1(C#N)CC2CCC1C2
Agent: Cl
Agent: O=C([O-])O
Agent: [K+]
Solvent: C1CCOC1
Solvent: O
Product: N#CC1(O)CC2CCC1C2
Temperature: 25 °C

Procedure:
Into a 200 milliliter Erlenmeyer flask, 38.37 grams (183.3 millimoles) of 2-cyano-2-trimethylsiloxynorbornane obtained in A, a PTFE-coated stirrer bar, 30 milliliters of tetrahydrofuran, 10 milliliters of water, and 1 milliliter of 2N hydrochloric acid were placed. This mixture was vigorously stirred at room temperature. Three hours later, the disappearance of the starting norbornane compound was confirmed by thin-layer chromatography, and 1 milliliter of 2N aqueous potassium hydrogencarbonate solution was then added to the reaction mixture and the mixture was vigorously stirred for 5 minutes. The reaction mixture was poured into water and extracted three times with diethyl ether, and the extracts were combined, washed with brine, and dried with anhydrous sodium sulfate. The sodium sulfate was then filtered out. The solvent was subsequently removed in vacuo to thereby yield a crude product. Distillation of the crude product under reduced pressure gave 2-cyano-2-hydroxynorbornane (exo/endo mixture) as a colorless, clear liquid having a boiling point of 85.5°-86.0° C. (0.35 mmHg).
Reaction SMILES: C([O:4][CH:5]1[CH:9]([NH:10][C:11]2[CH:16]=[C:15]([Cl:17])[C:14]([Cl:18])=[CH:13][C:12]=2[N+:19]([O-])=O)[CH2:8][CH:7]([CH2:22][O:23]C(=O)C)[CH:6]1[O:27]C(=O)C)(=O)C.[CH:31](O)(C)[CH3:32]>[Ni]>[Cl:18][C:14]1[C:15]([Cl:17])=[CH:16][C:11]2[N:10]([CH:9]3[CH:5]([OH:4])[CH:6]([OH:27])[CH:7]([CH2:22][OH:23])[CH2:8]3)[C:31]([CH3:32])=[N:19][C:12]=2[CH:13]=1
Reactant: CC(=O)OCC1CC(Nc2cc(Cl)c(Cl)cc2[N+](=O)[O-])C(OC(C)=O)C1OC(C)=O
Reactant: CC(C)O
Agent: [Ni]
Product: Cc1nc2cc(Cl)c(Cl)cc2n1C1CC(CO)C(O)C1O
Temperature: 25 °C
Reaction time: 18 h
Yield: 67 %

Procedure:
(±)-(1R*, 2S*, 3S*, 5S*)-3-(Acetoxymethyl)-5-(4,5-dichloro-2-nitroanilino)-1,2-cyclopentanediyl diacetate (1.00 g, 2.16 mmol), Raney nickel (Aldrich, slurry in water, 100 mg wet), and isopropanol (200 mL) were shaken under hydrogen (50 psi) for 1.25 hours. Catalyst was filtered off with Celite and the filtrate-wash evaporated to dryness. The residual yellow oil was dissolved in triethylorthoaceate (20 mL) with 1 drop of methanesulfonic acid and the solution stirred at ambient temperature for 18 hours. Volatiles were removed in vacuo and the residue stirred in dioxane (20 mL)-1N sodium hydroxide (10 mL) for 5 hours at ambient temperature. The pH was then adjusted to 1 with concentrated hydrochloric acid and stirring continued for 15 minutes, at which point TLC (silica gel, developed with 20% methanol-chloroform) showed one UV-absorbing spot at Rf 0.25. The solution was neutralized with sodium hydroxide and volatiles evaporated in vacuo. The residue was chromatographed on a silica gel column and title compound eluted with 10-15% methanol-chloroform. Crystallization from ethanol-methanol-water gave (±)-(1R*, 2S*, 3S*, 5S*)-5-(5,6-dichloro-2-methyl-1H-benzimidazol-1-yl)-3-(hydroxymethyl)-1,2-cyclopentanediol as fine white crystals (0.482 g, 67%), m.p. 222°-226° C.; 1 H-NMR(DMSO-d6)δ: 8.30 and 7.72 (both s, 2, 2 aromatic CH), 5.0-4.8 (m, 3, 2 OH and NCH), 4.56 (t, J=5.1 Hz, 1, CH2OH), 4.2-4.1 (m, 2, 2 OCH), 3.8-3.5 (m, 2, CH2O), 2.58 (s, 3, CH3), 2.4-2.2 (m, 1, CH), 2.2-1.9 (m, 2, CH2); mass spectrum (CI): 332 (M +1).
Reaction SMILES: [C:1]([C:3]1[CH:8]=[CH:7][C:6]([N:9]2[C:16](=[O:17])[C:12]3([CH2:15][CH2:14][CH2:13]3)[N:11]([C:18]3[CH:23]=[CH:22][C:21]([CH2:24][CH2:25][CH2:26][C:27]([OH:29])=O)=[CH:20][CH:19]=3)[C:10]2=[S:30])=[CH:5][C:4]=1[C:31]([F:34])([F:33])[F:32])#[N:2].S(Cl)(Cl)=O.C[N:40](C=O)C>>[C:1]([C:3]1[CH:8]=[CH:7][C:6]([N:9]2[C:16](=[O:17])[C:12]3([CH2:15][CH2:14][CH2:13]3)[N:11]([C:18]3[CH:23]=[CH:22][C:21]([CH2:24][CH2:25][CH2:26][C:27]([NH2:40])=[O:29])=[CH:20][CH:19]=3)[C:10]2=[S:30])=[CH:5][C:4]=1[C:31]([F:34])([F:33])[F:32])#[N:2]
Reactant: CN(C)C=O
Reactant: N#Cc1ccc(N2C(=O)C3(CCC3)N(c3ccc(CCCC(=O)O)cc3)C2=S)cc1C(F)(F)F
Solvent: O=S(Cl)Cl
Product: N#Cc1ccc(N2C(=O)C3(CCC3)N(c3ccc(CCCC(N)=O)cc3)C2=S)cc1C(F)(F)F
Temperature: 0 °C
Reaction time: 1 h

Procedure:
To a solution of 4-(4-(7-(4-Cyano-3-(trifluoromethyl)phenyl)-8-oxo-6-thioxo-5,7-diazaspiro[3.4]octan-5-yl)phenyl)butanoic acid, RD141 (Formula 51) (60 mg, 0.12 mmol) in DMF (3 mL) was added thionyl chloride (0.01 mL, 0.15 mmol) at 0° C. The mixture was stirred at 0° C. for 1 hour. Then ammonia was bubbled into the mixture. The mixture was partitioned with ethyl acetate (25 mL) and water (25 mL). The organic layer was dried over MgSO4, concentrated and chromatographed (dichloromethane:acetone, 70:30) to yield 4-(4-(7-(4-Cyano-3-(trifluoromethyl)phenyl)-8-oxo-6-thioxo-5,7-diazaspiro[3.4]octan-5-yl)phenyl)butanamide, RD130 (Formula 52) (37 mg, 61%) as a white powder. 1H NMR δ 7.97 (d, 1H, J=1.8 Hz), 7.95 (d, 1H, J=8.3 Hz), 7.85 (dd, 1H, J=8.3 Hz), 7.39 (d, 2H, J=8.3 Hz), 7.22 (d, 2H, J=8.3 Hz), 5.59 (br s, 2H), 2.77 (t, 2H, J=7.5 Hz), 2.62-2.68 (m, 2H), 2.51-2.59 (m, 2H), 2.31 (t, 2H, J=7.5 Hz), 2.16-2.25 (m, 1H), 2.05 (p, 2H, J=7.5 Hz), 1.57-1.70 (m, 1H).
Reaction SMILES: [CH2:1]([CH:3]1[CH:29]=[C:28]([CH3:30])[CH2:27][CH:26]([CH3:31])[CH2:25][CH:24]([O:32][CH3:33])[CH:23]2[O:34][C:19]([OH:38])([CH:20]([CH3:37])[CH2:21][CH:22]2[O:35][CH3:36])[C:18](=[O:39])[C:17](=[O:40])[N:16]2[CH:11]([CH2:12][CH2:13][CH2:14][CH2:15]2)[C:10](=[O:41])[O:9][CH:8]([C:42]([CH3:71])=[CH:43][CH:44]2[CH2:49][CH2:48][CH:47]([O:50][C:51]3[CH:60]=[CH:59][C:58]4[C:53](=[CH:54][CH:55]=[C:56]([O:61][Si](C(C)(C)C)(C)C)[CH:57]=4)[CH:52]=3)[CH:46]([O:69][CH3:70])[CH2:45]2)[CH:7]([CH3:72])[CH:6]([OH:73])[CH2:5][C:4]1=[O:74])[CH3:2].C1(C)C=CC(S(O)(=O)=O)=CC=1>C(Cl)Cl.CO>[CH2:1]([CH:3]1[CH:29]=[C:28]([CH3:30])[CH2:27][CH:26]([CH3:31])[CH2:25][CH:24]([O:32][CH3:33])[CH:23]2[O:34][C:19]([OH:38])([CH:20]([CH3:37])[CH2:21][CH:22]2[O:35][CH3:36])[C:18](=[O:39])[C:17](=[O:40])[N:16]2[CH:11]([CH2:12][CH2:13][CH2:14][CH2:15]2)[C:10](=[O:41])[O:9][CH:8]([C:42]([CH3:71])=[CH:43][CH:44]2[CH2:49][CH2:48][CH:47]([O:50][C:51]3[CH:60]=[CH:59][C:58]4[C:53](=[CH:54][CH:55]=[C:56]([OH:61])[CH:57]=4)[CH:52]=3)[CH:46]([O:69][CH3:70])[CH2:45]2)[CH:7]([CH3:72])[CH:6]([OH:73])[CH2:5][C:4]1=[O:74])[CH3:2]
Reactant: CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C)=CC3CCC(Oc4ccc5cc(O[Si](C)(C)C(C)(C)C)ccc5c4)C(OC)C3)C(C)C(O)CC1=O)C(C)CC2OC
Agent: Cc1ccc(S(=O)(=O)O)cc1
Solvent: CO
Solvent: ClCCl
Product: CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C)=CC3CCC(Oc4ccc5cc(O)ccc5c4)C(OC)C3)C(C)C(O)CC1=O)C(C)CC2OC
Reaction time: 4 h
Yield: 67.6 %

Procedure:
To a stirred solution of 17-ethyl-1,14-dihydroxy-12-[2'-(4"-(6'"-tert-butyldimethylsilyloxynaphth-2-yloxy)-3"-methoxycyclohexyl)-1'-methylvinyl]-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-dioxa-4-azatricyclo[22.3.1.04,9 ]octacos-18-ene-2,3,10,16-tetraone (73 mg, 0.07 mmol) in CH2Cl2 (2 mL) was added a solution of p-toluenesulfonic acid in methanol (2 mL, 10% solution). The flask was capped and the mixture stirred 4 hours. The reaction was quenched with saturated aqueous NaHCO3 and extracted 4× with CH2Cl2. The organic extracts were combined and dried over anhydrous Na2SO4. The mixture was filtered and concentrated in vacuo. The product was isolated by preparative TLC on silica gel (eluted with 2:1 hexanes/acetone) to afford 44.2 mg of 17-ethyl-1,14-dihydroxy-12-[2'-(4"-(6'"-hydroxynaphth-2-yloxy)-3"-methoxycyclohexyl)-1'-methylvinyl]-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-dioxa-4-azatricyclo[22.3.1.04,9 ]octacos-18-ene-2,3,10,16-tetraone (Rf =0.23). (1H NMR and mass spectral analysis were consistent with the desired structure).
Reaction SMILES: [C:1]1(=[O:11])[C:5]2([CH2:10][CH2:9][CH2:8][CH2:7][CH2:6]2)[CH2:4][CH2:3][NH:2]1.[H-].[Na+].Br[CH2:15][C:16]1[C:21]([Cl:22])=[CH:20][C:19]([O:23][CH2:24][C:25]2[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=2)=[CH:18][C:17]=1[Cl:31].Cl>CN(C=O)C.C(OCC)C>[CH2:24]([O:23][C:19]1[CH:18]=[C:17]([Cl:31])[C:16]([CH2:15][N:2]2[CH2:3][CH2:4][C:5]3([CH2:10][CH2:9][CH2:8][CH2:7][CH2:6]3)[C:1]2=[O:11])=[C:21]([Cl:22])[CH:20]=1)[C:25]1[CH:26]=[CH:27][CH:28]=[CH:29][CH:30]=1
Reactant: O=C1NCCC12CCCCC2
Reactant: Clc1cc(OCc2ccccc2)cc(Cl)c1CBr
Agent: Cl
Agent: [H-]
Agent: [Na+]
Solvent: CCOCC
Solvent: CN(C)C=O
Product: O=C1N(Cc2c(Cl)cc(OCc3ccccc3)cc2Cl)CCC12CCCCC2
Temperature: 25 °C
Reaction time: 0.33 h
Yield: 90.2 %

Procedure:
Treat a solution of 2-aza-spiro[4.5]decan-1-one (0.50 g, 3.26 mmol) in DMF (8 mL) with 60% sodium hydride (0.20 g, 5.0 mmol) and stir at room temperature for 20 minutes under N2. Cool the reaction to 0° C., treat with 2-bromomethyl-1,3-dichloro-5-benzyloxy-benzene (1.24 g, 3.58 mmol), stir for 15 minutes at 0° C., warm to room temperature, and stir for 2 hours under N2. Acidify the reaction with 1 N HCl, dilute the reaction with diethyl ether, and then wash with water. Dry the organic layer with Na2SO4 and remove the solvent in vacuo to afford crude product. Purify with a 0 to 100% ethyl acetate in hexanes gradient on silica gel to afford 1.23 g (90%) of the titled product. Rf=0.23 (3/1 ethyl acetate/hexanes). MS (m/z): 418 (M+).
Reaction SMILES: [C:1]1([CH:8]=[CH:7][C:5]([OH:6])=[CH:4][CH:3]=1)[OH:2].[CH2:9]([CH:11]1[O:13][CH2:12]1)Cl.[OH-].[Na+]>O>[O:13]1[CH2:12][CH:11]1[CH2:9][O:2][C:1]1[CH:8]=[CH:7][C:5]([OH:6])=[CH:4][CH:3]=1
Reactant: Oc1ccc(O)cc1
Reactant: ClCC1CO1
Agent: [Na+]
Agent: [OH-]
Solvent: O
Product: Oc1ccc(OCC2CO2)cc1
Temperature: 0 °C
Reaction time: 72 h

Procedure:
To an ice-cooled solution of 55 g. (0.5 mole) of hydroquinone and 46 g. (0.5 mole) of epichlorohydrin in 900 ml. of water was added an ice-cooled solution of 20 g. (0.5 mole) of sodium hydroxide in 900 ml. of water. The mixture was allowed to stand at 0° C. for 3 days. After washing with ether, the solution was added to 72 g. of sodium hydroxide in 4 l. of water and stored at 10° C. for 3 hours. The solution was saturated with ammonium carbonate and extracted with chloroform. After drying (Na2SO4) and concentrating the chloroform, the residual oil was predominantly 4-(2,3-epoxy-1-propoxy)-phenol (23%) which was used in later step without further purification.
Reaction SMILES: Br[C:2]1[CH:21]=[CH:20][C:5]2[N:6]([C:11]3[CH:16]=[CH:15][C:14]([CH2:17][CH2:18][OH:19])=[CH:13][CH:12]=3)[C:7]([CH2:9][CH3:10])=[N:8][C:4]=2[CH:3]=1.C([O-])([O-])=O.[K+].[K+]>COCCOC.O.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>[CH2:9]([C:7]1[N:6]([C:11]2[CH:16]=[CH:15][C:14]([CH2:17][CH2:18][OH:19])=[CH:13][CH:12]=2)[C:5]2[CH:20]=[CH:21][C:2]([C:2]3[CH:21]=[CH:20][CH:5]=[CH:4][CH:3]=3)=[CH:3][C:4]=2[N:8]=1)[CH3:10]
Reactant: CCc1nc2cc(Br)ccc2n1-c1ccc(CCO)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: [K+]
Solvent: COCCOC
Solvent: O
Product: CCc1nc2cc(-c3ccccc3)ccc2n1-c1ccc(CCO)cc1
Temperature: 95 °C
Reaction time: 11 h
Yield: 53.3 %

Procedure:
To a solution of 2-[4-(5-bromo-2-ethyl-1H-benzimidazol-1-yl)phenyl]ethanol (step 4, 116 mg, 0.57 mmol) in 1,2-dimethoxyethane (DME, 6 ml) was added PhB (OH)2 (141 mg, 1.16 mmol), K2CO3 (240 mg, 1.75 mmol) and Pd(PPh3)4 (67 mg, 0.06 mmol). This mixture was stirred at 95° C. for 11 h. The reaction mixture was diluted with water and extracted with CH2Cl2 (4×10 ml). The organic layer was dried (MgSO4) and concentrated to give brown oil. This mixture was purified by SiO2 preparative TLC (hexane/ethyl acetate=1/5) to afford 52 mg (27%) of the title compound.
Reaction SMILES: [OH:1][C:2]1[C:11]2[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=2)[C@@:5]([CH3:17])([CH2:12][CH2:13][CH:14]([CH3:16])[CH3:15])[C:4](=[O:18])[C:3]=1[C:19]1[NH:24][C:23]2[CH:25]=[CH:26][C:27]([NH:29][S:30]([C:33]3[C:42]4[C:37](=[CH:38][CH:39]=[CH:40][CH:41]=4)[CH:36]=[CH:35][CH:34]=3)(=[O:32])=[O:31])=[CH:28][C:22]=2[S:21](=[O:44])(=[O:43])[N:20]=1.[OH-].[Na+:46]>O>[CH3:17][C@@:5]1([CH2:12][CH2:13][CH:14]([CH3:16])[CH3:15])[C:6]2[C:11](=[CH:10][CH:9]=[CH:8][CH:7]=2)[C:2]([O-:1])=[C:3]([C:19]2[NH:24][C:23]3[CH:25]=[CH:26][C:27]([NH:29][S:30]([C:33]4[C:42]5[C:37](=[CH:38][CH:39]=[CH:40][CH:41]=5)[CH:36]=[CH:35][CH:34]=4)(=[O:32])=[O:31])=[CH:28][C:22]=3[S:21](=[O:44])(=[O:43])[N:20]=2)[C:4]1=[O:18].[Na+:46]
Reactant: CC(C)CC[C@@]1(C)C(=O)C(C2=NS(=O)(=O)c3cc(NS(=O)(=O)c4cccc5ccccc45)ccc3N2)=C(O)c2ccccc21
Agent: [Na+]
Agent: [OH-]
Solvent: O
Product: CC(C)CC[C@@]1(C)C(=O)C(C2=NS(=O)(=O)c3cc(NS(=O)(=O)c4cccc5ccccc45)ccc3N2)=C([O-])c2ccccc21
Yield: 67.1 %

Procedure:
A mixture of Example 105A (30.0 mg, 0.048 mmol) and 0.998 M sodium hydroxide (0.048 mL, 0.048 mmol) in water (3 mL) was stirred at rt for 16 h. The reaction mixture was concentrated in vacuo to give the title compound (21 mg, 68% yield). 1H NMR (300 MHz, DMSO-d6) δ 0.40 m, 1 H) 0.65 (d, J=6.62 Hz, 3 H) 0.67 m, 3 H) 0.75 (m, 1 H) 1.26 (m, 1H) 1.34 (s, 3 H) 1.69 m, 1 H) 2.10 m, 1 H) 7.12 m, 2 H) 7.23 (s, 1 H) 7.29 (m, 1 H) 7.44 m, 2 H) 7.64 m, 2 H) 7.74 m, 1 H) 8.00 (d, J=7.72 Hz, 1 H) 8.07 (d, J=7.72 Hz, 1 H) 8.16 (d, J=7.35 Hz, 1 H) 8.20 m, 1 H) 8.76 (s, 1 H) 10.82 (s, 1 H) 15.39 (s, 1 H). MS (ESI+) m/z 652.0 (M+H)+, 630.0 (M+H—Na)+, 647 (M−Na+NH4)+, (ESI−) m/z 628.0 (M−H—Na)−.
Reaction SMILES: [NH2:1][C:2]1[C:3]([Cl:9])=[N:4][CH:5]=[N:6][C:7]=1Cl.CCN(CC)CC.[CH2:17]([NH2:25])[CH2:18][C:19]1[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=1>C(O)CCC>[Cl:9][C:3]1[N:4]=[CH:5][N:6]=[C:7]([NH:25][CH2:17][CH2:18][C:19]2[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=2)[C:2]=1[NH2:1]
Reactant: NCCc1ccccc1
Reactant: Nc1c(Cl)ncnc1Cl
Solvent: CCN(CC)CC
Solvent: CCCCO
Product: Nc1c(Cl)ncnc1NCCc1ccccc1
Reaction time: 12 h

Procedure:
A solution of 5-amino-4,6-dichloropyrimidine (1 mmol) in nBuOH was treated with Et3N (1.2 mmol) and phenethylamine (1.05 mmol) at 80° C. After 12 h, the cooled reaction mixture was evaporated under vacuum and the residue was chromatographed to give 6-chloro-5-amino-4-(phenethylamino)-pyrimidine as a yellow solid. mp 156-157° C.; TLC: Rf=0.41, 50% EtOAc-hexane.
Reaction SMILES: [NH2:1][CH2:2][C:3]1([CH2:16][NH2:17])[CH2:8][CH2:7][N:6]([CH2:9][C:10]2[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=2)[CH2:5][CH2:4]1.CO.OO.[O-]Cl.[Na+]>O>[CH2:9]([N:6]1[CH2:5][CH2:4][C:3]2([CH2:2][N:1]=[N:17][CH2:16]2)[CH2:8][CH2:7]1)[C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1
Reactant: NCC1(CN)CCN(Cc2ccccc2)CC1
Agent: OO
Agent: [Na+]
Agent: [O-]Cl
Solvent: O
Solvent: CO
Product: c1ccc(CN2CCC3(CC2)CN=NC3)cc1
Temperature: 25 °C
Reaction time: 1 h
Yield: 90.3 %

Procedure:
2.48 g of C-(4-Aminomethyl-1-benzyl-piperidin-4-yl)-methylamine was suspended in 40 mL H2O and 10 mL MeOH and cooled with an ice bath. Simultaneously, 6.7 mL 30% H2O2 (6 equiv.) and 15.2 mL 10% NaClO (2.4 equiv.) were added dropwise. The mixture was stirred at room temperature for 1 hour. The mixture was extracted 2 times with DCM, the combined organic layers were dried over Na2SO4, filtrated and concentrated to yield 2.20 g of a yellow oil which was used without further purification in the subsequent step.
Reaction SMILES: [C:1]([C:5]1[CH:9]=[C:8]([NH:10][C:11]([O:13]C2C=CC=CC=2)=O)[N:7]([CH2:20][C:21]([O:23][CH2:24][CH3:25])=[O:22])[N:6]=1)([CH3:4])([CH3:3])[CH3:2].[CH3:26][O:27][C:28]1[CH:29]=[C:30]2[C:35](=[CH:36][C:37]=1[O:38][CH3:39])[N:34]=[CH:33][N:32]=[C:31]2[S:40][C:41]1[CH:42]=[C:43]([CH:45]=[CH:46][CH:47]=1)[NH2:44].C(N(CC)C(C)C)(C)C>C1COCC1>[C:1]([C:5]1[CH:9]=[C:8]([NH:10][C:11]([NH:44][C:43]2[CH:45]=[CH:46][CH:47]=[C:41]([S:40][C:31]3[C:30]4[C:35](=[CH:36][C:37]([O:38][CH3:39])=[C:28]([O:27][CH3:26])[CH:29]=4)[N:34]=[CH:33][N:32]=3)[CH:42]=2)=[O:13])[N:7]([CH2:20][C:21]([O:23][CH2:24][CH3:25])=[O:22])[N:6]=1)([CH3:2])([CH3:3])[CH3:4]
Reactant: COc1cc2ncnc(Sc3cccc(N)c3)c2cc1OC
Reactant: CCOC(=O)Cn1nc(C(C)(C)C)cc1NC(=O)Oc1ccccc1
Solvent: CCN(C(C)C)C(C)C
Solvent: C1CCOC1
Product: CCOC(=O)Cn1nc(C(C)(C)C)cc1NC(=O)Nc1cccc(Sc2ncnc3cc(OC)c(OC)cc23)c1
Yield: 59 %

Procedure:
Using the procedure described in Example 159B, using ethyl 2-[3-tert-butyl-5-(phenoxycarbonylamino)-1H-pyrazol-1-yl]acetate described in Example 166A (0.138 g, 0.4 mmol), 3-(6,7-dimethoxyquinazolin-4-ylthio)aniline from Example 115B (0.125 g, 0.4 mmol), and N,N-diisopropylethylamine (0.5 mL) in THF (6 mL) at 50° C. for 7 hours, to afford ethyl 2-(3-tert-butyl-5-{3-[3-(6,7-dimethoxyquinazolin-4-ylthio)phenyl]ureido}-1H-pyrazol-1-yl)acetate as solid (133 mg, 59%). 1H NMR (300 MHz, DMSO-d6) δ 8.98 (s, 1H), 8.70 (s, 1H), 8.60 (m, 1H), 7.83 (s, 1H), 7.51 (d, 1H), 7.43 (t, 1H), 7.35 (s, 1H), 7.34 (s, 1H), 7.25 (d, 1H), 6.12 (s, 1H), 4.85 (s, 2H), 4.15 (q, 2H), 3.99 (s, 6H), 1.20 (s and t, 12H); LC-MS (ESI) m/z 565 (M+H)+.
Reaction SMILES: [SH:1][CH2:2][CH2:3][N:4]([CH2:19][CH2:20][C:21]1[CH:26]=[CH:25][CH:24]=[CH:23][CH:22]=1)[C:5](=[O:18])[NH:6][C@@H:7]([CH2:11][C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1)[C:8]([OH:10])=[O:9].C(N(CC)C(C)C)(C)C.[CH2:36]([O:43][C:44](Cl)=[O:45])[C:37]1[CH:42]=[CH:41][CH:40]=[CH:39][CH:38]=1>C(Cl)Cl>[CH2:36]([O:43][C:44]([S:1][CH2:2][CH2:3][N:4]([CH2:19][CH2:20][C:21]1[CH:22]=[CH:23][CH:24]=[CH:25][CH:26]=1)[C:5](=[O:18])[NH:6][C@@H:7]([CH2:11][C:12]1[CH:13]=[CH:14][CH:15]=[CH:16][CH:17]=1)[C:8]([OH:10])=[O:9])=[O:45])[C:37]1[CH:42]=[CH:41][CH:40]=[CH:39][CH:38]=1
Reactant: O=C(O)[C@H](Cc1ccccc1)NC(=O)N(CCS)CCc1ccccc1
Reactant: O=C(Cl)OCc1ccccc1
Solvent: ClCCl
Solvent: CCN(C(C)C)C(C)C
Product: O=C(OCc1ccccc1)SCCN(CCc1ccccc1)C(=O)N[C@@H](Cc1ccccc1)C(=O)O
Yield: 69 %

Procedure:
(2S)-2-[3-(2-Mercaptoethyl)-3-phenethylureido]-3-phenylpropionic acid (Compound No. 11-1, 108 mg) is dissolved in anhydrous methylene chloride (1.5 ml) under a nitrogen atmosphere, and the solution is stirred. To the solution are added N,N-diisopropylethylamine (0.07 ml) and benzyloxycarbonyl chloride (0.05 ml) successively under ice cooling, and the mixture is stirred at room temperature overnight. The reaction mixture is concentrated under reduced pressure, water is added to the residue, and the whole is extracted with ethyl acetate. The organic layer is washed with a 10% aqueous citric acid solution, water and saturated brine successively, dried over anhydrous sodium sulfate and concentrated under reduced pressure. The resulting oily matter is purified by silica gel column chromatography to give 102 mg (69%) of the titled compound (Compound No. 12-1).
Reaction SMILES: P12(SP3(SP(SP(S3)(S1)=S)(=S)S2)=S)=[S:2].[NH2:15][C:16]1[C:21](=[O:22])[N:20]([CH3:23])[C:18](=[O:19])[C:17]=1[C:24]#[N:25]>>[NH2:15][C:16]1[C:21](=[O:22])[N:20]([CH3:23])[C:18](=[O:19])[C:17]=1[C:24](=[S:2])[NH2:25]
Reactant: S=P12SP3(=S)SP(=S)(S1)SP(=S)(S2)S3
Reactant: CN1C(=O)C(N)=C(C#N)C1=O
Product: CN1C(=O)C(N)=C(C(N)=S)C1=O
Temperature: 100 °C
Reaction time: 3 h
Yield: 59 %

Procedure:
A mixture of 100 parts of phosphorus pentasulfide and 450 parts of methylglycol is heated at the boil for 0.5 hour, after which 90 parts of 3-amino-2-cyano-N-methylmaleimide are introduced into this solution at 100° C. The mixture is stirred for 3 hours at 100° C. and then overnight at room temperature. The resulting precipitate is filtered off under suction, washed with methanol and then with water, and dried to give 65.1 parts (59% of theory) of 3-amino-2-thiocarbamyl-N-methylmaleimide.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([CH:8]([NH2:19])[C:9]([C:12]2[CH:17]=[CH:16][C:15]([Cl:18])=[CH:14][CH:13]=2)([NH2:11])[CH3:10])=[CH:4][CH:3]=1.CO[C:22](=O)[C:23]1[CH:28]=[CH:27][C:26]([C:29]([CH3:32])([CH3:31])[CH3:30])=[CH:25][C:24]=1[O:33][CH2:34][CH3:35].C[Al](C)C>>[C:29]([C:26]1[CH:27]=[CH:28][C:23]([C:22]2[NH:19][C@H:8]([C:5]3[CH:6]=[CH:7][C:2]([Cl:1])=[CH:3][CH:4]=3)[C@@:9]([C:12]3[CH:13]=[CH:14][C:15]([Cl:18])=[CH:16][CH:17]=3)([CH3:10])[N:11]=2)=[C:24]([O:33][CH2:34][CH3:35])[CH:25]=1)([CH3:32])([CH3:30])[CH3:31]
Reactant: CCOc1cc(C(C)(C)C)ccc1C(=O)OC
Reactant: CC(N)(c1ccc(Cl)cc1)C(N)c1ccc(Cl)cc1
Agent: C[Al](C)C
Product: CCOc1cc(C(C)(C)C)ccc1C1=N[C@@](C)(c2ccc(Cl)cc2)[C@@H](c2ccc(Cl)cc2)N1

Procedure:
In a manner analogous to the method described in example 2, rac-(1R*,2S*)-1,2-bis-(4-chloro-phenyl)-propane-1,2-diamine was reacted with 4-tert-butyl-2-ethoxy-benzoic acid methyl ester (prepared as described in Fotouhi, N. et al. WO 2005110996) in the presence of trimethylaluminum to give the title compound as a racemic mixture.
Reaction SMILES: Cl[C:2]1[C:11]2[C:6](=[CH:7][C:8]([F:13])=[CH:9][C:10]=2[F:12])[N:5]=[C:4]([N:14]2[CH2:19][CH2:18][N:17]([CH:20]3[CH2:25][CH2:24][CH2:23][CH2:22][CH2:21]3)[CH2:16][CH2:15]2)[C:3]=1[CH3:26].[O:27]1[CH2:32][CH2:31][N:30]([C:33]2[CH:34]=[C:35]([NH2:39])[CH:36]=[N:37][CH:38]=2)[CH2:29][CH2:28]1>C1(C)C=CC=CC=1>[CH:20]1([N:17]2[CH2:18][CH2:19][N:14]([C:4]3[C:3]([CH3:26])=[C:2]([NH:39][C:35]4[CH:36]=[N:37][CH:38]=[C:33]([N:30]5[CH2:31][CH2:32][O:27][CH2:28][CH2:29]5)[CH:34]=4)[C:11]4[C:6](=[CH:7][C:8]([F:13])=[CH:9][C:10]=4[F:12])[N:5]=3)[CH2:15][CH2:16]2)[CH2:25][CH2:24][CH2:23][CH2:22][CH2:21]1
Reactant: Cc1c(N2CCN(C3CCCCC3)CC2)nc2cc(F)cc(F)c2c1Cl
Reactant: Nc1cncc(N2CCOCC2)c1
Solvent: Cc1ccccc1
Product: Cc1c(N2CCN(C3CCCCC3)CC2)nc2cc(F)cc(F)c2c1Nc1cncc(N2CCOCC2)c1

Procedure:
Essentially prepared according to Procedure H using 4-chloro-2-(4-cyclohexylpiperazin-1-yl)-5,7-difluoro-3-methylquinoline (22.0 mg, 0.058 mmol) and 5-morpholinopyridin-3-amine in toluene to give 2-(4-cyclohexylpiperazin-1-yl)-5,7-difluoro-3-methyl-N-(5-morpholinopyridin-3-yl)quinolin-4-amine. 1H NMR (CDCl3) δ ppm 7.93 (1H, d, J=2.3 Hz), 7.70 (1H, d, J=1.8 Hz), 7.27-7.33 (1H, m), 6.86 (1H, d, J=12.9 Hz), 6.78 (1H, ddd, J=13.9, 8.6, 2.5 Hz), 6.57 (1H, t, J=2.3 Hz), 3.79-3.91 (4H, m), 3.35-3.61 (4H, m), 3.07-3.23 (4H, m), 2.70-2.98 (4H, m), 2.06 (3H, s), 1.91-2.03 (2H, m), 1.77-1.91 (2H, m), 1.67 (1H, d, J=12.9 Hz), 1.05-1.41 (6H, m). Mass Spectrum (ESI) m/e=524.3 (M+1).