Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH:1]([CH2:3][P:4](=[O:11])([O:8][CH2:9][CH3:10])[O:5][CH2:6][CH3:7])=O.[C:12]1([C@H:22]([NH2:24])[CH3:23])[C:21]2[C:16](=[CH:17][CH:18]=[CH:19][CH:20]=2)[CH:15]=[CH:14][CH:13]=1>C(O)C>[C:12]1([C@H:22]([NH:24][CH:1]=[CH:3][P:4](=[O:11])([O:8][CH2:9][CH3:10])[O:5][CH2:6][CH3:7])[CH3:23])[C:21]2[C:16](=[CH:17][CH:18]=[CH:19][CH:20]=2)[CH:15]=[CH:14][CH:13]=1
Reactant: C[C@@H](N)c1cccc2ccccc12
Reactant: CCOP(=O)(CC=O)OCC
Solvent: CCO
Product: CCOP(=O)(C=CN[C@H](C)c1cccc2ccccc12)OCC
Temperature: 10 °C

Procedure:
A 1-litre, four-necked flask equipped with a mechanical stirrer, an addition funnel and a nitrogen inlet was charged with diethyl formylmethylphosphonate (100 g) and ethanol (500 mL). Under a nitrogen atmosphere, the resulting mixture was cooled to 10° C. and (R)-1-(1-naphthyl)ethylamine (85.6 g) was added under stirring. The mixture was left under stirring for an additional hour. The solvent was distilled from this mixture under reduced pressure. The resulting residue (180 g) was used in the next step without additional purification.
Reaction SMILES: Br[CH2:2][CH:3]([OH:19])[CH2:4][N:5]1[C:9]2[CH:10]=[CH:11][CH:12]=[C:13]3[CH:14]=[CH:15][CH:16]=[C:7]([C:8]=23)[S:6]1(=[O:18])=[O:17].C(N(CC)CC)C.[F:27][C:28]1[CH:33]=[CH:32][C:31]([N:34]2[CH2:39][CH2:38][NH:37][CH2:36][CH2:35]2)=[CH:30][CH:29]=1>C1(C)C=CC=CC=1>[F:27][C:28]1[CH:29]=[CH:30][C:31]([N:34]2[CH2:39][CH2:38][N:37]([CH2:2][CH:3]([OH:19])[CH2:4][N:5]3[C:9]4[CH:10]=[CH:11][CH:12]=[C:13]5[CH:14]=[CH:15][CH:16]=[C:7]([C:8]=45)[S:6]3(=[O:18])=[O:17])[CH2:36][CH2:35]2)=[CH:32][CH:33]=1
Reactant: O=S1(=O)c2cccc3cccc(c23)N1CC(O)CBr
Reactant: Fc1ccc(N2CCNCC2)cc1
Solvent: Cc1ccccc1
Solvent: CCN(CC)CC
Product: O=S1(=O)c2cccc3cccc(c23)N1CC(O)CN1CCN(c2ccc(F)cc2)CC1
Temperature: 20 °C
Yield: 46.9 %

Procedure:
2-(3-Bromo-2-hydroxypropyl)naphtho[1,8-cd]isothiazole 1,1-dioxide (26.8 g), triethylamine (11 cc) and 4(4-fluorophenyl)piperazine (14.1 g) in toluene (280 cc) are heated at boiling point for 8 hours. The mixture is then cooled to a temperature of about 20° C. and stirring is maintained for 15 hours at this temperature. The precipitate formed is separated by filtration and washed with toluene (2 x 50 cc). The filtrate is evaporated to dryness at 40° C. under reduced pressure (20 mm Hg; 2.7 kPa). The residue obtained is purified by chromatography on a silica column, with ethyl acetate as eluant, and recrystallized from boiling acetonitrile (120 cc). 2-(3[4-(4-Fluorophenyl)-1-piperaz-invl]-2-hydroxypropyl}naphtho[1,8-cd]isothiazole 1,1-dioxide (16.2 g) is obtained, m.p. 130° C.
Reaction SMILES: [Si:1]([O:18][CH2:19][C:20]1[C:25]([N:26]2[CH2:31][C@H:30]([CH3:32])[O:29][C@H:28]([CH3:33])[CH2:27]2)=[C:24]([Cl:34])[C:23]([F:35])=[CH:22][CH:21]=1)([C:14]([CH3:17])([CH3:16])[CH3:15])([C:8]1[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[CH3:36][N:37]1[CH:41]=[CH:40][N:39]=[C:38]1[CH:42]=[O:43].[Li]CCCC>>[Si:1]([O:18][CH2:19][C:20]1[C:25]([N:26]2[CH2:31][C@H:30]([CH3:32])[O:29][C@H:28]([CH3:33])[CH2:27]2)=[C:24]([Cl:34])[C:23]([F:35])=[C:22]([C:41]2[N:37]([CH3:36])[C:38]([CH2:42][OH:43])=[N:39][CH:40]=2)[CH:21]=1)([C:14]([CH3:16])([CH3:17])[CH3:15])([C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1)[C:8]1[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=1
Reactant: C[C@@H]1CN(c2c(CO[Si](c3ccccc3)(c3ccccc3)C(C)(C)C)ccc(F)c2Cl)C[C@H](C)O1
Reactant: Cn1ccnc1C=O
Agent: [Li]CCCC
Product: C[C@@H]1CN(c2c(CO[Si](c3ccccc3)(c3ccccc3)C(C)(C)C)cc(-c3cnc(CO)n3C)c(F)c2Cl)C[C@H](C)O1

Procedure:
Starting material: (2R,6S)-4-[6-({[tert-butyl(diphenyl)silyl]oxy}methyl)-2-chloro-3-fluorophenyl]-2,6-dimethylmorpholine (Intermediate 42), 1-methyl-imidazole-2-carbaldehyde and n-BuLi
Reaction SMILES: [NH2:1][C:2]1[S:3][CH:4]=[C:5]([C:12]2[CH:17]=[CH:16][C:15]([Cl:18])=[CH:14][CH:13]=2)[C:6]=1[C:7]([O:9][CH2:10][CH3:11])=[O:8].[F:19][C:20]1[CH:28]=[CH:27][C:23]([C:24](Cl)=[O:25])=[CH:22][CH:21]=1>C1COCC1.[OH-].[Na+].C(OCC)(=O)C>[F:19][C:20]1[CH:28]=[CH:27][C:23]([C:24]([NH:1][C:2]2[S:3][CH:4]=[C:5]([C:12]3[CH:13]=[CH:14][C:15]([Cl:18])=[CH:16][CH:17]=3)[C:6]=2[C:7]([O:9][CH2:10][CH3:11])=[O:8])=[O:25])=[CH:22][CH:21]=1
Reactant: CCOC(=O)c1c(-c2ccc(Cl)cc2)csc1N
Reactant: O=C(Cl)c1ccc(F)cc1
Agent: [Na+]
Agent: [OH-]
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: CCOC(=O)c1c(-c2ccc(Cl)cc2)csc1NC(=O)c1ccc(F)cc1
Temperature: 25 °C
Reaction time: 10 h

Procedure:
Ethyl cyanoacetate (5 mmol), and p-chloro-acetophenone (5 mmol) are dissolved in toluene (5 mL). Morpholine (5 mmol) is added followed by activated molecular sieves (4A). The reaction is stirred at 80° C. for 12 hours. The reaction is cooled to room temperature, filtered and concentrated. The residue is taken up in toluene (5 mL), ethanol (5 mL) and sulfur is added (0.16 g; 5 mmol). The reaction mixture is heated with mixing at 70° C. for 12 hours. The reaction is cooled to room temperature and the solvents are evaporated. The residue is purified by HPLC to provide ethyl 2-amino-4-(4-chlorophenyl)-thiophene-3-carboxylate. Ethyl 2-amino-4-(4-chlorophenyl)-thiophene-3-carboxylate (5 mmol) is treated with 4-fluorobenzoyl chloride (5 mmol) in THF (10 mL). The reaction is stirred at room temperature for 10 hours. The reaction is diluted with 1N NaOH (10 mL) and ethyl acetate (15 mL). The layers are separated, the organic layer is dried with anhydrous sodium sulfate, filtered and concentrated. The residue is purified by flash chromatography to provide ethyl 2-(4-fluorobenzamido)-4-(4-chlorophenyl)thiophene-3-carboxylate. Ethyl 2-(fluorobenzamido)-4-(4-chlorophenyl)thiophene-3-carboxylate is hydrolyzed under a variety of conditions (e.g. LiOH, water; LiOH, H2O2, water; or NaOH, water) to provide 2-(4-fluorobenzamido)-4-(4-chlorophenyl)thiophene-3-carboxylic acid.
Reaction SMILES: [CH3:1][C:2]([NH:4][C:5]1[CH:10]=[C:9](F)[CH:8]=[CH:7][C:6]=1[N+:12]([O-:14])=[O:13])=[O:3].[F:15][C:16]([F:25])([F:24])[C:17]1[CH:22]=[CH:21][C:20]([OH:23])=[CH:19][CH:18]=1.C(=O)([O-])[O-].[K+].[K+]>>[CH3:1][C:2]([NH:4][C:5]1[CH:10]=[C:9]([O:23][C:20]2[CH:21]=[CH:22][C:17]([C:16]([F:15])([F:24])[F:25])=[CH:18][CH:19]=2)[CH:8]=[CH:7][C:6]=1[N+:12]([O-:14])=[O:13])=[O:3]
Reactant: Oc1ccc(C(F)(F)F)cc1
Reactant: CC(=O)Nc1cc(F)ccc1[N+](=O)[O-]
Agent: O=C([O-])[O-]
Agent: [K+]
Product: CC(=O)Nc1cc(Oc2ccc(C(F)(F)F)cc2)ccc1[N+](=O)[O-]

Procedure:
Following the procedure of Example 4, N-methylcarbonyl 2-nitro-5-fluoroaniline (3.1 g, 15.4 mmol), 4-trifluoromethylphenol (2.5 g, 15.4 mmol) and potassium carbonate (4.3 g, 31.0 mmol) are reacted together to give N-methylcarbonyl 2-nitro-5-(4-trifluoromethylphenoxy)aniline, 4.0 g of which is then reacted with 20% hydrochloric acid (~50 ml) to give 2-nitro-5-(4-trifluoromethylphenoxy)aniline. 2-Nitro-5-(4-trifluoromethylphenoxy)aniline (2.0 g, 6.7 mmol) is reacted with potassium hydroxide (0.4 g, 7.0 mmol) and sodium hypochlorite (19 ml of 5.2% solution, 1.0 g, 13.4 mmol) to yield 5-(4-trifluormethylphenoxy)benzo-2,1,3-oxadiazole N-oxide, m.p. 40°-42°.
Reaction SMILES: [CH2:1]([NH:6][C@H:7]1[CH2:12][CH2:11][C@H:10]([C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=2)[CH2:9][CH2:8]1)[C:2]([CH3:5])([CH3:4])[CH3:3].[Cl:19][C:20]1[CH:28]=[CH:27][C:23]([C:24](Cl)=[O:25])=[CH:22][CH:21]=1>>[Cl:19][C:20]1[CH:28]=[CH:27][C:23]([C:24]([N:6]([C@H:7]2[CH2:8][CH2:9][C@H:10]([C:13]3[CH:14]=[CH:15][CH:16]=[CH:17][CH:18]=3)[CH2:11][CH2:12]2)[CH2:1][C:2]([CH3:5])([CH3:4])[CH3:3])=[O:25])=[CH:22][CH:21]=1
Reactant: CC(C)(C)CN[C@H]1CC[C@H](c2ccccc2)CC1
Reactant: O=C(Cl)c1ccc(Cl)cc1
Product: CC(C)(C)CN(C(=O)c1ccc(Cl)cc1)[C@H]1CC[C@H](c2ccccc2)CC1

Procedure:
from trans-N-neopentyl-4-phenylcyclohexylamine and 4-chlorobenzoylchloride Colourless crystals.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([CH:7]=[CH:8][C:9]=1[O:10][C:11]1[C:20]2[C:15](=[CH:16][CH:17]=[CH:18][CH:19]=2)[C:14]([CH:21]=O)=[CH:13][CH:12]=1)[C:5]#[N:6].C(O)(=O)C.[CH3:27][CH:28]([CH3:32])[CH2:29][CH2:30][NH2:31].[BH-](OC(C)=O)(OC(C)=O)OC(C)=O.[Na+]>C(Cl)Cl>[Cl:1][C:2]1[CH:3]=[C:4]([CH:7]=[CH:8][C:9]=1[O:10][C:11]1[C:20]2[C:15](=[CH:16][CH:17]=[CH:18][CH:19]=2)[C:14]([CH2:21][NH:31][CH2:30][CH2:29][CH:28]([CH3:32])[CH3:27])=[CH:13][CH:12]=1)[C:5]#[N:6]
Reactant: N#Cc1ccc(Oc2ccc(C=O)c3ccccc23)c(Cl)c1
Reactant: CC(C)CCN
Agent: CC(=O)O[BH-](OC(C)=O)OC(C)=O
Agent: [Na+]
Solvent: CC(=O)O
Solvent: ClCCl
Product: CC(C)CCNCc1ccc(Oc2ccc(C#N)cc2Cl)c2ccccc12
Temperature: 25 °C
Reaction time: 16 h

Procedure:
To a solution of 3-chloro-4-(4-formylnaphthalen-1-yloxy)benzonitrile (Preparation 82) (800 mg, 2.60 mmol) in DCM (35 mL) was added acetic acid (0.7 mL, 7.80 mmol), 3-methylbutylamine (0.91 mL, 7.80 mmol) and NaBH(OAc)3 (1.65 g, 7.80 mmol). The reaction was stirred at rt for 16 h. The mixture was partitioned between DCM (150 mL) and saturated NaHCO3 (200 mL) and the organic phase dried (MgSO4). Solvent was removed in vacuo and the residue purified by column chromatography (EtOAc:isohexane 1:1) to give the title compound: RT=3.01 min; m/z (ES+)=379.3, 381.2 [M+H]+.
Reaction SMILES: [C:1]12([C:11]3[CH:30]=[CH:29][C:14]([O:15][CH2:16][C:17]([NH:19][C:20]4[CH:21]=[C:22]([CH:26]=[CH:27][N:28]=4)[C:23]([OH:25])=O)=[O:18])=[CH:13][CH:12]=3)[CH2:10][CH:5]3[CH2:6][CH:7]([CH2:9][CH:3]([CH2:4]3)[CH2:2]1)[CH2:8]2.[NH2:31][CH2:32][CH2:33][C:34]1[CH:39]=[CH:38][N:37]=[CH:36][CH:35]=1.C1CN([P+](ON2N=NC3C=CC=CC2=3)(N2CCCC2)N2CCCC2)CC1.F[P-](F)(F)(F)(F)F.CO>CN(C1C=CN=CC=1)C.CN(C=O)C>[C:1]12([C:11]3[CH:30]=[CH:29][C:14]([O:15][CH2:16][C:17]([NH:19][C:20]4[CH:21]=[C:22]([CH:26]=[CH:27][N:28]=4)[C:23]([NH:31][CH2:32][CH2:33][C:34]4[CH:39]=[CH:38][N:37]=[CH:36][CH:35]=4)=[O:25])=[O:18])=[CH:13][CH:12]=3)[CH2:8][CH:7]3[CH2:9][CH:3]([CH2:4][CH:5]([CH2:6]3)[CH2:10]1)[CH2:2]2
Reactant: O=C(COc1ccc(C23CC4CC(CC(C4)C2)C3)cc1)Nc1cc(C(=O)O)ccn1
Reactant: NCCc1ccncc1
Agent: CN(C)c1ccncc1
Agent: F[P-](F)(F)(F)(F)F
Agent: c1ccc2c(c1)nnn2O[P+](N1CCCC1)(N1CCCC1)N1CCCC1
Solvent: CN(C)C=O
Solvent: CO
Product: O=C(COc1ccc(C23CC4CC(CC(C4)C2)C3)cc1)Nc1cc(C(=O)NCCc2ccncc2)ccn1
Yield: 85.3 %

Procedure:
To solution of 2-[2-(4-adamantan-1-yl-phenoxy)-acetylamino]-isonicotinic acid (40 mg, 0.098 mmol), 4-(2-aminoethyl)pyridine (24.06 mg, 0.196 mmol) and DMAP (24.06 mg, 0.196 mmol) in DMF was added PyBOP (102.4 mg, 0.196 mmol) at room temperature, and stirred. Reaction mixture was poured onto ice cold water, diluted by methanol/MC mixture (10%). The organic phase was separated, sequentially washed with aqueous sodium bicarbonate, brine and water, dried over anhydrous MgSO4, and concentrated. The resultant crude product was purified by PLC (MeOH:MC=1:9) to afford 2-[2-(4-adamantan-1-yl-phenoxy)acetylamino]-N-(2-pyridine-4-yl-ethyl)-isonicotinamide as a colorless solid (42.7 mg, 84% yield).
Reaction SMILES: [F:1][C:2]([F:12])([F:11])[O:3][C:4]1[CH:10]=[CH:9][C:7]([NH2:8])=[CH:6][CH:5]=1.[CH:13]([C:15]1[N:16]=[CH:17][NH:18][CH:19]=1)=O.[BH4-].[Na+].O>CO>[N:18]1[CH:19]=[C:15]([CH2:13][NH:8][C:7]2[CH:9]=[CH:10][C:4]([O:3][C:2]([F:11])([F:12])[F:1])=[CH:5][CH:6]=2)[NH:16][CH:17]=1
Reactant: O=Cc1c[nH]cn1
Reactant: Nc1ccc(OC(F)(F)F)cc1
Agent: [BH4-]
Agent: [Na+]
Solvent: CO
Solvent: O
Product: FC(F)(F)Oc1ccc(NCc2cnc[nH]2)cc1
Temperature: 60 °C
Reaction time: 8 h
Yield: 77.8 %

Procedure:
To a solution of 4-trifluoromethoxyaniline (0.89 g, 5 mmol) in methanol (5 ml) was added 4-formylimidazole (0.48 g, 5 mmol). After stirring the mixture overnight at 60° C. the solution was cooled and sodium borohydride (0.28 g, 7.5 mmol) were added. The reaction mixture was stirred at room temperature for 4 hours. Then water was added and the mixture was extracted with ethyl acetate. The organic layer was separated, washed with water, dried over magnesium sulfate and evaporated. The residue was purified by column filtration (heptane/ethyl acetate=1:1) to yield a light yellow liquid (1.0 g, 78%); MS (ISP): 258.1 ((M+H)+.).
Reaction SMILES: [CH2:1]([N:8](C(OC(C)(C)C)=O)[CH:9]1[CH2:15][CH2:14][CH2:13][C:12]2[CH:16]=[CH:17][C:18]([O:20][C:21]3[C:26]([C:27]#[N:28])=[CH:25][CH:24]=[CH:23][N:22]=3)=[CH:19][C:11]=2[CH2:10]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.Cl>C(OCC)(=O)C>[CH2:1]([NH:8][CH:9]1[CH2:10][C:11]2[CH:19]=[C:18]([O:20][C:21]3[C:26]([C:27]#[N:28])=[CH:25][CH:24]=[CH:23][N:22]=3)[CH:17]=[CH:16][C:12]=2[CH2:13][CH2:14][CH2:15]1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: CC(C)(C)OC(=O)N(Cc1ccccc1)C1CCCc2ccc(Oc3ncccc3C#N)cc2C1
Agent: Cl
Solvent: CCOC(C)=O
Product: N#Cc1cccnc1Oc1ccc2c(c1)CC(NCc1ccccc1)CCC2
Reaction time: 1 h
Yield: 89.8 %

Procedure:
To N-benzyl-N-[3-(3-cyanopyridin-2-yloxy)-6,7,8,9-tetrahydro-5H-benzocyclohepten-6-yl]-tert-butoxycarbonylamine (480 mg) was added 4N hydrogen chloride in ethyl acetate (5 ml) at room temperature, and the mixture was stirred at the same temperature for 1 hour. After evaporation in vacuo, the residue was dissolved into a mixture of saturated aqueous sodium hydrogencarbonate and ethyl acetate, followed by being made basic with saturated aqueous sodium hydrogencarbonate. After separation, the organic layer was washed with brine, dried over anhydrous magnesium sulfate and evaporated in vacuo to give 2-(8-benzylamino-6,7,8,9-tetrahydro-5H-benzocyclohepten-2-yl)oxy-3-cyanopyridine (339 mg).
Reaction SMILES: CO[C:3]1[CH:4]=[CH:5][CH:6]=[C:7]2[C:12]=1[O:11][CH:10]([C:13]([O:15]CC)=O)[CH2:9][CH2:8]2.[NH2:18][CH2:19][C:20]1[C:29]2[C:24](=[CH:25][CH:26]=[CH:27][CH:28]=2)[CH:23]=[CH:22][CH:21]=1.[C-]#N.[K+]>C1(C)C=CC=CC=1>[C:20]1([CH2:19][NH:18][C:13]([CH:10]2[CH2:9][CH2:8][C:7]3[C:12](=[CH:3][CH:4]=[CH:5][CH:6]=3)[O:11]2)=[O:15])[C:29]2[C:24](=[CH:25][CH:26]=[CH:27][CH:28]=2)[CH:23]=[CH:22][CH:21]=1
Reactant: CCOC(=O)C1CCc2cccc(OC)c2O1
Reactant: NCc1cccc2ccccc12
Agent: [C-]#N
Agent: [K+]
Solvent: Cc1ccccc1
Product: O=C(NCc1cccc2ccccc12)C1CCc2ccccc2O1
Reaction time: 2 h

Procedure:
33.0 g (0.14 mol) of ethyl 8-methoxy-chroman-2-carboxylate (content 87%) are heated together with 25.8 g (0.16 mol) of 1-aminomethylnaphthalene and 0.05 g of potassium cyanide at 120° C. for 8 hours and then at 130° C. for 2 hours. After cooling, the mixture is diluted with 100 ml of toluene and this solution is introduced onto silica gel K60. Elution with cyclohexane/ethyl acetate mixtures (100:0 to 75:25) gives the amide in the form of a viscous syrup (32.9 g, 68%), which can be further reacted directly.
Reaction SMILES: Cl[C:2]1[C:7]([CH3:8])=[N:6][C:5]([CH3:9])=[CH:4][N:3]=1.CC1(C)C(C)(C)OB([C:18]2[CH:23]=[CH:22][C:21]([N:24]([C:31]3[CH:36]=[CH:35][CH:34]=[CH:33][CH:32]=3)[C:25]3[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=3)=[CH:20][CH:19]=2)O1.C(=O)([O-])[O-].[Na+].[Na+]>Cl[Pd](Cl)([P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1)[P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1.O.C(#N)C>[CH3:8][C:7]1[C:2]([C:34]2[CH:33]=[CH:32][C:31]([N:24]([C:25]3[CH:30]=[CH:29][CH:28]=[CH:27][CH:26]=3)[C:21]3[CH:22]=[CH:23][CH:18]=[CH:19][CH:20]=3)=[CH:36][CH:35]=2)=[N:3][CH:4]=[C:5]([CH3:9])[N:6]=1
Reactant: CC1(C)OB(c2ccc(N(c3ccccc3)c3ccccc3)cc2)OC1(C)C
Reactant: Cc1cnc(Cl)c(C)n1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: O
Solvent: CC#N
Product: Cc1cnc(-c2ccc(N(c3ccccc3)c3ccccc3)cc2)c(C)n1
Temperature: 50 °C
Yield: 30 %

Procedure:
Next, there were put 0.36 g of 2-chloro-3,5-dimethylpyrazine, 0.92 g of 4,4,5,5-tetramethyl-2-(4-diphenylaminophenyl)-1,3,2-dioxaborolane obtained in Step 1, 0.26 g of sodium carbonate, 0.011 g of bis(triphenylphosphine)palladium(II) dichloride (abbreviation: Pd(PPh3)2Cl2), 10 mL of water, and 10 mL of acetonitrile in a recovery flask equipped with a reflux pipe. The air in the flask was replaced by argon. This reaction container was heated by microwave irradiation (2.45 GHz, 100 W) for 20 minutes. After that, the reaction container was cooled to 50° C. or lower, water was added to the reaction solution, and the organic layer was subjected to extraction with dichloromethane. The obtained organic layer was washed with water and dried with magnesium sulfate. After the drying, the solution was filtered. The solvent of this solution was distilled, and the obtained residue was purified by silica gel column chromatography using a mixed solvent of dichloromethane and ethyl acetate as a developing solvent, thereby obtaining the objective pyrazine derivative Hdmdpappr (white powder, 30% yield). Note that the microwave irradiation was performed using a microwave synthesis system (Discover, produced by CEM Corporation). The synthesis scheme of Step 2 is shown by (b-2).
Reaction SMILES: [Br:1]Br.[N:3]1[C:8]2[NH:9][CH:10]=[CH:11][C:7]=2[CH:6]=[N:5][CH:4]=1.[O-]S([O-])(=S)=O.[Na+].[Na+].C([O-])(O)=O.[Na+]>CN(C=O)C.O>[Br:1][C:11]1[C:7]2[CH:6]=[N:5][CH:4]=[N:3][C:8]=2[NH:9][CH:10]=1
Reactant: BrBr
Reactant: c1ncc2cc[nH]c2n1
Agent: O=C([O-])O
Agent: O=S([O-])([O-])=S
Agent: [Na+]
Solvent: O
Solvent: CN(C)C=O
Product: Brc1c[nH]c2ncncc12
Temperature: 25 °C
Reaction time: 4 h

Procedure:
A solution of bromine (0.086 mL, 1.68 mmol) in DMF (5.5 mL) was added to a solution of 7H-pyrrolo[2,3-d]pyrimidine (200 mg, 1.68 mmol) in DMF (5.5 mL). The reaction mixture was stirred at RT for 4 h and poured into a mixture of ice and water containing Na2S2O3. A saturated aqueous solution of NaHCO3 was added (until basic pH), the layers were separated and the aqueous layer was extracted twice with EtOAc. The combined organic extracts were washed with brine, dried (Na2SO4), filtered and concentrated. The material thus obtained was used without further purification in the next step. TLC, Rf (CH2Cl2/MeOH 9:1)=0.45; MS (UPLC/MS): 198.1/200.1 [M+H]+, 196.1/198.1 [M−H]−.
Reaction SMILES: [CH:1]([CH:4]1[C:9]2=[CH:10][C:11]3[CH:12]=[CH:13][C:14]([S:17][CH3:18])=[CH:15][C:16]=3[N:8]2[CH2:7][CH2:6][NH:5]1)([CH3:3])[CH3:2].CCN(C(C)C)C(C)C.Cl[C:29]1[N:34]=[C:33]([C:35]([F:38])([F:37])[F:36])[C:32]([C:39](=[O:41])[CH3:40])=[CH:31][N:30]=1>CC(O)C>[CH:1]([CH:4]1[C:9]2=[CH:10][C:11]3[CH:12]=[CH:13][C:14]([S:17][CH3:18])=[CH:15][C:16]=3[N:8]2[CH2:7][CH2:6][N:5]1[C:29]1[N:34]=[C:33]([C:35]([F:36])([F:37])[F:38])[C:32]([C:39](=[O:41])[CH3:40])=[CH:31][N:30]=1)([CH3:3])[CH3:2]
Reactant: CC(=O)c1cnc(Cl)nc1C(F)(F)F
Reactant: CSc1ccc2cc3n(c2c1)CCNC3C(C)C
Solvent: CCN(C(C)C)C(C)C
Solvent: CC(C)O
Product: CSc1ccc2cc3n(c2c1)CCN(c1ncc(C(C)=O)c(C(F)(F)F)n1)C3C(C)C
Temperature: 25 °C
Reaction time: 8 h
Yield: 70.4 %

Procedure:
To a solution of 1-isopropyl-7-(methylthio)-1,2,3,4-tetrahydropyrazino[1,2-a]indole (100 mg, 0.38 mmol) and DIPEA (246.72 mg, 1.91 mmol) in i-PrOH (2 mL) was added 1-(2-chloro-4-(trifluoromethyl)pyrimidin-5-yl)ethanone (172.50 mg, 0.76 mmol). The reaction mixture was stirred at rt overnight. The mixture was concentrated and purified by preparative TLC on silica gel eluting with PE/EtOAc 1:1 to afford 1-(2-(1-isopropyl-7-(methylthio)-3,4-dihydropyrazino[1,2-a]indol-2(1H)-yl)-4-(trifluoromethyl)pyrimidin-5-yl)ethanone (120 mg, 69.67% yield) as a colorless oil. LC-MS MS (ESI) m/z 449.2 [M+H]+. 1H NMR (CDCl3 400 MHz): δ 8.66 (s, 1H), 7.44-7.40 (m, 1H), 7.06 (d, J=8.4 Hz, 1H), 6.27-6.25 (m, 1H), 5.79-577 (m, 1H), 5.13-5.02 (m, 1H), 4.21-4.16 (m, 1H), 3.97-3.91 (m, 1H), 3.82-3.71 (m, 1H), 2.48 (s, 3H), 2.46 (s, 3H), 2.21-2.15 (m, 1H), 1.12-1.08 (m, 3H), 0.96-0.93 (m, 3H).
Reaction SMILES: [Cl:1][C:2]1[C:7]([CH3:8])=[CH:6][C:5]([C:9](=[O:11])[CH3:10])=[C:4]([OH:12])[CH:3]=1.Cl[C:14]1[C:23]2[C:18](=[CH:19][C:20]([O:26][CH3:27])=[C:21]([O:24][CH3:25])[CH:22]=2)[N:17]=[CH:16][CH:15]=1.O>CN(C)C1C=CN=CC=1.ClC1C=CC=CC=1Cl>[Cl:1][C:2]1[C:7]([CH3:8])=[CH:6][C:5]([C:9](=[O:11])[CH3:10])=[C:4]([O:12][C:14]2[C:23]3[C:18](=[CH:19][C:20]([O:26][CH3:27])=[C:21]([O:24][CH3:25])[CH:22]=3)[N:17]=[CH:16][CH:15]=2)[CH:3]=1
Reactant: CC(=O)c1cc(C)c(Cl)cc1O
Reactant: COc1cc2nccc(Cl)c2cc1OC
Agent: CN(C)c1ccncc1
Solvent: O
Solvent: Clc1ccccc1Cl
Product: COc1cc2nccc(Oc3cc(Cl)c(C)cc3C(C)=O)c2cc1OC
Temperature: 140 °C
Reaction time: 24 h
Yield: 10 %

Procedure:
1-(4-Chloro-2-hydroxy-5-methyl-phenyl)-ethanone (193 mg), 4-chloro-6,7-dimethoxyquinoline (468 mg), and 4-dimethylaminopyridine (385 mg) were suspended in o-dichlorobenzene (5 ml) to prepare a suspension which was then stirred at 140° C. for 24 hr. The reaction solution was cooled to room temperature, water was then added to the reaction solution, and the mixture was extracted with ethyl acetate. The ethyl acetate layer was then washed with water and saturated brine and was dried over anhydrous magnesium sulfate. The solvent was removed by distillation under the reduced pressure, and the residue was purified by thin layer chromatography using acetone-hexane to give the title compound (39 mg, yield 10%).
Reaction SMILES: Cl[C:2]1[C:3](=[O:15])[N:4]([C@H:9]([CH:12]2[CH2:14][CH2:13]2)[CH2:10][CH3:11])[CH:5]=[C:6]([Cl:8])[N:7]=1.[Cl:16][C:17]1[CH:18]=[C:19]2[C:23](=[C:24]([Cl:26])[CH:25]=1)[NH:22][CH2:21][CH2:20]2>>[Cl:8][C:6]1[N:7]=[C:2]([N:22]2[C:23]3[C:19](=[CH:18][C:17]([Cl:16])=[CH:25][C:24]=3[Cl:26])[CH2:20][CH2:21]2)[C:3](=[O:15])[N:4]([C@H:9]([CH:12]2[CH2:14][CH2:13]2)[CH2:10][CH3:11])[CH:5]=1
Reactant: CC[C@@H](C1CC1)n1cc(Cl)nc(Cl)c1=O
Reactant: Clc1cc(Cl)c2c(c1)CCN2
Product: CC[C@@H](C1CC1)n1cc(Cl)nc(N2CCc3cc(Cl)cc(Cl)c32)c1=O

Procedure:
Prepared in a similar fashion as described for Example 413 using 3,5-dichloro-1-[(1S)-1-cyclopropylpropyl]-2(1H)-pyrazinone and 5,7-dichloroindoline as the starting materials. mp 157-159° C.; 1H NMR (300 MHz, CDCl3): δ 7.15 (s, 1 H), 7.09 (s, 1 H), 6.99 (s, 1 H), 4.34-4.24 (m, 2 H), 4.08-3.99 (m, 0.5 H), 3.11 (t, J=7.9 Hz, 2 H), 2.42-2.36 (m, 0.5 H), 2.16-2.00 (m, 1 H), 1.94-1.74 (m, 1 H), 1.07-0.99 (m, 1 H), 0.94-0.86 (m, 3 H), 0.80-0.71 (m, 1 H), 0.53-0.42 (m, 2 H), 0.36-0.20 (m, 1 H); HRMS (ESI) calcd for C18H19N3OCl3 (M+H)+: 398.0594; found m/z 398.0602.
Reaction SMILES: [OH-].[Na+].[C:3]([S:6][CH2:7][P:8](=[O:15])([O:12][CH2:13][CH3:14])[O:9][CH2:10][CH3:11])(=O)[CH3:4].[CH3:16]/[C:17](/[CH2:22][CH2:23]/[CH:24]=[C:25](\[CH3:32])/[CH2:26][CH2:27][CH:28]=[C:29]([CH3:31])[CH3:30])=[CH:18]\CCI.O>C(O)C>[CH3:18]/[C:17](/[CH2:22][CH2:23]/[CH:24]=[C:25](\[CH3:32])/[CH2:26][CH2:27][CH:28]=[C:29]([CH3:31])[CH3:30])=[CH:16]\[CH2:4][CH2:3][S:6][CH2:7][P:8](=[O:15])([O:12][CH2:13][CH3:14])[O:9][CH2:10][CH3:11]
Reactant: CCOP(=O)(CSC(C)=O)OCC
Reactant: CC(C)=CCC/C(C)=C/CC/C(C)=C/CCI
Agent: [Na+]
Agent: [OH-]
Solvent: CCO
Solvent: O
Product: CCOP(=O)(CSCC/C=C(\C)CC/C=C(\C)CCC=C(C)C)OCC
Temperature: 25 °C
Reaction time: 8 h
Yield: 94.2 %

Procedure:
Solid sodium hydroxide (0.14 g, 3.5 mmol) was added to a stirred solution of diethyl acetylthiomethylphosphonate (0.59 g, 2.5 mmol) in ethanol (10 mL). The resulting mixture was stirred at room temperature under nitrogen until all the sodium hydroxide dissolved, then added a solution of (E,E)-4,8,12-trimethyl-3,7,11-tridecatrienyl iodide (0.84 g, 2.4 mmol) in ethanol (2 mL). The resulting mixture was stirred at room temperature under nitrogen overnight. The reaction mixture was poured into cold water and extracted with ether. The ethereal extract was washed with water, dried, filtered and evaporated to give a residue, which was purified by flash chromatography on a silica gel column. Elution of the column with methylene:acetate (10:1, v:v) afforded the title compound (0.91 g, 2.26 mmol, 94%) as a colorless oil.
Reaction SMILES: [F:1][C:2]1[CH:9]=[CH:8][C:5]([CH2:6][NH2:7])=[CH:4][CH:3]=1.C(=O)([O-])[O-].[Na+].[Na+].[Cl:16][C:17]1[CH:22]=[C:21](Cl)[N:20]=[C:19]([S:24][CH2:25][C:26]([O:28][CH2:29][CH3:30])=[O:27])[N:18]=1>C(O)C>[Cl:16][C:17]1[CH:22]=[C:21]([NH:7][CH2:6][C:5]2[CH:8]=[CH:9][C:2]([F:1])=[CH:3][CH:4]=2)[N:20]=[C:19]([S:24][CH2:25][C:26]([O:28][CH2:29][CH3:30])=[O:27])[N:18]=1
Reactant: CCOC(=O)CSc1nc(Cl)cc(Cl)n1
Reactant: NCc1ccc(F)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: CCO
Product: CCOC(=O)CSc1nc(Cl)cc(NCc2ccc(F)cc2)n1

Procedure:
A stirred mixture of 3.75 g of p-fluorobenzylamine, 3.18 g of anhydrous sodium carbonate and 8.01 g of (4,6-dichloro-2-pyrimidinylthio)acetic acid, ethyl ester in 150 ml of ethanol was heated under reflux for 5 hr. The reaction mixture was filtered and water was added to the filtrate until a precipitate was formed. The solid was collected and recrystallized from benzene-petroleum ether giving 3.6 g of product, mp. 70°-75°C.