Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: O=[C:2]1[CH2:7][CH2:6][N:5]([C:8]([O:10][C:11]([CH3:14])([CH3:13])[CH3:12])=[O:9])[CH2:4][CH2:3]1.[C:15]([CH2:17][C:18]([O:20][CH2:21][CH3:22])=[O:19])#[N:16].C([O-])(=O)C.[NH4+].C(O)(=O)C>C1C=CC=CC=1>[C:15]([C:17](=[C:2]1[CH2:7][CH2:6][N:5]([C:8]([O:10][C:11]([CH3:14])([CH3:13])[CH3:12])=[O:9])[CH2:4][CH2:3]1)[C:18]([O:20][CH2:21][CH3:22])=[O:19])#[N:16]
Reactant: CC(C)(C)OC(=O)N1CCC(=O)CC1
Reactant: CCOC(=O)CC#N
Agent: CC(=O)[O-]
Agent: [NH4+]
Solvent: c1ccccc1
Solvent: CC(=O)O
Product: CCOC(=O)C(C#N)=C1CCN(C(=O)OC(C)(C)C)CC1
Temperature: 25 °C

Procedure:
A mixture of tert-butyl 4-oxo-1-piperidinecarboxylate (25.25 g, 127 mmol), ethyl cyanoacetate (13.8 ml, 130 mmol), ammonium acetate (2.73 g, 35.4 mmol), glacial acetic acid (6.3 ml) and benzene (250 ml) was heated for 4 hours at reflux under Dean Stark conditions. The reaction mixture was cooled to room temperature and washed successively with water, sodium bicarbonate solution and brine. Drying, filtration and evaporation of the organic phase provided tert-butyl 4-(1-cyano-2-ethoxy-2-oxoethylidene)piperidine-1-carboxylate as an oil that crystallized on standing (37 g, 99%). 1H NMR (400 MHz, CDCl3): δ 4.28 (q, 2H, J=7 Hz), 3.60 (br t, 2H, J=6 Hz), 3.54 (br t, 2H, J=6 Hz), 3.12 (t, 2H, J=6 Hz), 2.76 (t, 2H, J=6 Hz), 1.47 (s, 9H), and 1.35 (t, 3H, J=7 Hz). ES-LCMS m/z 293 (M−1).
Reaction SMILES: [CH3:1][C:2]([CH3:8])([C:4](=[O:7])[CH:5]=[CH2:6])[CH3:3].[Cl:9][C:10]1[CH:11]=[CH:12][C:13]([NH:16][C:17](=[S:19])[S-:18])=[N:14][CH:15]=1.C([NH+](CC)CC)C>C(#N)C.C(Cl)(Cl)Cl>[Cl:9][C:10]1[CH:11]=[CH:12][C:13]([NH:16][C:17](=[S:18])[S:19][CH2:6][CH2:5][C:4](=[O:7])[C:2]([CH3:8])([CH3:3])[CH3:1])=[N:14][CH:15]=1
Reactant: C=CC(=O)C(C)(C)C
Reactant: S=C([S-])Nc1ccc(Cl)cn1
Agent: CC[NH+](CC)CC
Solvent: ClC(Cl)Cl
Solvent: CC#N
Product: CC(C)(C)C(=O)CCSC(=S)Nc1ccc(Cl)cn1
Reaction time: 3 h
Yield: 82.6 %

Procedure:
A solution of 2,2-dimethylpent-4-en-3-one (30.0 g) in anhydrous acetonitrile (60 cc) is added, at a maximum temperature of 5° C., to a suspension of triethylammonium 5-chloropyrid-2-yldithiocarbamate (82.0 g) in anhydrous acetonitrile (400 cc). The reaction is allowed to proceed for 3 hours at between 5° and 20° C. The crystals which appear are filtered off; the filtrate is evaporated under reduced pressure (20 mmHg) at 45° C. The residue obtained and the crystals separated off beforehand are dissolved in methylene chloride (750 cc). The organic solution is washed four times with distilled water (total 600 cc), dried over sodium sulphate and evaporated. The product obtained (98.0 g) is dissolved in chloroform (400 cc). The solution is chromatographed on a column of diameter 6.8 cm, containing silica (0.063-0.2 mm; 800 g). Elution is carried out with chloroform (2.6 liters), this eluate being discarded, and then with chloroform (7.2 liters), this eluate being collected and evaporated to dryness. The product obtained (85.0 g) is purified by recrystallisation from acetonitrile (350 cc). 4,4-Dimethyl-3-oxopentyl 5-chloropyrid-2-yldithiocarbamate (70.0 g) (structure determined by IR spectroscopy in petroleum jelly), which melts at 111° C., is obtained.
Reaction SMILES: [F:1][C:2]1[CH:8]=[CH:7][C:5]([NH2:6])=[C:4]([N+:9]([O-:11])=[O:10])[CH:3]=1.[Br:12]Br>O.Br>[Br:12][C:7]1[CH:8]=[C:2]([F:1])[CH:3]=[C:4]([N+:9]([O-:11])=[O:10])[C:5]=1[NH2:6]
Reactant: Nc1ccc(F)cc1[N+](=O)[O-]
Reactant: BrBr
Agent: Br
Solvent: O
Product: Nc1c(Br)cc(F)cc1[N+](=O)[O-]
Temperature: 25 °C
Reaction time: 0.75 h
Yield: 93.6 %

Procedure:
A solution of 4-fluoro-2-nitroaniline (39.03 g, 250 mmol) in water (900 mL) and 48% hydrobromic acid (1500 mL) was treated with bromine (15.26 mL, 46 g, 288 mmol) added dropwise over 20 min. The resulting precipitate was stirred at ambient temperature for a further 45 min then diluted with ice-water (2000 mL). The solid product was collected by filtration, washed with cold water and dried to afford 2-bromo-4-fluoro-6-nitrophenylamine as an orange powder (55 g, 94%): δH (360 MHz, CDCl3) 6.49 (2H, br), 7.56 (1H, dd, J 7 and 3), 7.90 (1H, dd, J 9 and 3).
Reaction SMILES: N(OCCC(C)C)=O.[CH2:9]([O:16][C:17]1[CH:44]=[CH:43][CH:42]=[CH:41][C:18]=1[O:19][C:20]1[CH:26]=[C:25]([N:27]2[C:32](=[O:33])[CH:31]=[C:30]([C:34]([F:37])([F:36])[F:35])[N:29]([CH3:38])[C:28]2=[O:39])[C:24]([F:40])=[CH:23][C:21]=1N)[C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1.[ClH:45]>[Cu]Cl.[Cu](Cl)Cl.C(#N)C>[Cl:45][C:21]1[CH:23]=[C:24]([F:40])[C:25]([N:27]2[C:32](=[O:33])[CH:31]=[C:30]([C:34]([F:37])([F:36])[F:35])[N:29]([CH3:38])[C:28]2=[O:39])=[CH:26][C:20]=1[O:19][C:18]1[CH:41]=[CH:42][CH:43]=[CH:44][C:17]=1[O:16][CH2:9][C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1
Reactant: Cl
Reactant: Cn1c(C(F)(F)F)cc(=O)n(-c2cc(Oc3ccccc3OCc3ccccc3)c(N)cc2F)c1=O
Agent: Cl[Cu]
Agent: Cl[Cu]Cl
Agent: CC(C)CCON=O
Solvent: CC#N
Product: Cn1c(C(F)(F)F)cc(=O)n(-c2cc(Oc3ccccc3OCc3ccccc3)c(Cl)cc2F)c1=O
Reaction time: 1 h

Procedure:
First, 4.46 g of isoamyl nitrite was added dropwise to a mixture of 6.46 g of 2-(2-benzyloxyphenoxy)-5-fluoro-4-[3-methyl-2,6,-dioxo-4-(trifluoromethyl)-1,2,3,6-tetrahydropyrimidin-1-yl]aniline, 2.45 g of copper (I) chloride, 5.04 g of copper (II) chloride, and 90 ml of acetonitrile at room temperature, and the mixture was stirred for 1 hour. The reaction mixture was poured into 2% hydrochloric acid, and the mixture was extracted with ethyl acetate. The organic layer was washed with saturated aqueous sodium chloride solution, dried over anhydrous magnesium sulfate, and then concentrated. The residue was subjected to silica gel column chromatography to give 4.6 g of ([2-{2-chloro-4-fluoro-5-[3-methyl-2,6-dioxo-4-(trifluoromethyl)-1,2,3,6-tetrahydropyrimidin-1-yl]phenoxy}phenoxy]methyl)benzene.
Reaction SMILES: [NH2:1][C@H:2]([C:8]([OH:10])=[O:9])[CH2:3][CH2:4][C:5]([OH:7])=[O:6].[CH2:11](O)[C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1.CS(O)(=O)=O.O>C1(C)C=CC=CC=1>[NH2:1][C@@H:2]([CH2:3][CH2:4][C:5]([O:7][CH2:11][C:12]1[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1)=[O:6])[C:8]([OH:10])=[O:9]
Reactant: N[C@@H](CCC(=O)O)C(=O)O
Reactant: OCc1ccccc1
Agent: CS(=O)(=O)O
Solvent: Cc1ccccc1
Solvent: O
Product: N[C@@H](CCC(=O)OCc1ccccc1)C(=O)O
Temperature: 45 °C
Reaction time: 2 h

Procedure:
Glutamic acid (20 g, 0.14 mol, 1 equiv), BnOH (21.1 mls, 0.20 moles, 1.5 equiv) were dissolved in of toluene (30 ml) with stirring in a three necked RB flask. To the resultant mixture methanesulphonic acid (10.6 ml, 0.16 mol, 1.2 equiv) was added slowly whilst maintaining the temperature of the mixture at 45° C. Stirring was continued at this temperature for 2 hrs following which the mixture was cooled to 30° C. and stirred for an additional 4 hrs. Water (50 ml) was then added to the mixture and the organic phase was separated. To the aqueous phase ethanol (30 ml) was added followed by cold aq. ammonia to obtain a pH of 6.5-7. At this point a thick white precipitate was formed which could either be heated to 60° C. and stirred for 2 hrs to improve the crystallinity and then cooled to 5-10° C. or filtered at this point and washed with ethanol (2×20 ml) and water (3×20 ml). The product is then allowed to dry and used without further purification (3.45 g, 21%).
Reaction SMILES: CC1(C)C(C)(C)OB([C:9]2[CH:14]=[CH:13][C:12]([NH:15][C:16](=[O:25])[O:17][CH2:18][C:19]3[CH:24]=[CH:23][CH:22]=[CH:21][CH:20]=3)=[CH:11][CH:10]=2)O1.[NH2:27][C:28]1[N:33]=[CH:32][N:31]=[C:30]2[N:34]([CH:38]3[CH2:43][CH2:42][N:41]([C:44]([O:46][C:47]([CH3:50])([CH3:49])[CH3:48])=[O:45])[CH2:40][CH2:39]3)[N:35]=[C:36](I)[C:29]=12.C(=O)([O-])[O-].[Na+].[Na+]>COCCOC.O>[NH2:27][C:28]1[N:33]=[CH:32][N:31]=[C:30]2[N:34]([CH:38]3[CH2:43][CH2:42][N:41]([C:44]([O:46][C:47]([CH3:50])([CH3:49])[CH3:48])=[O:45])[CH2:40][CH2:39]3)[N:35]=[C:36]([C:9]3[CH:10]=[CH:11][C:12]([NH:15][C:16]([O:17][CH2:18][C:19]4[CH:20]=[CH:21][CH:22]=[CH:23][CH:24]=4)=[O:25])=[CH:13][CH:14]=3)[C:29]=12
Reactant: CC1(C)OB(c2ccc(NC(=O)OCc3ccccc3)cc2)OC1(C)C
Reactant: CC(C)(C)OC(=O)N1CCC(n2nc(I)c3c(N)ncnc32)CC1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: O
Solvent: COCCOC
Product: CC(C)(C)OC(=O)N1CCC(n2nc(-c3ccc(NC(=O)OCc4ccccc4)cc3)c3c(N)ncnc32)CC1
Temperature: 25 °C
Yield: 82.7 %

Procedure:
A mixture of benzyl N-[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]carbamate (9.54 g, 0.027 mol), tert-butyl 4-(4-amino-3-iodo-1H-pyrazolo[3,4-d]pyrimidin-1-yl)-1-piperidinecarboxylate (10.0 g, 0.0225 mol), tetrakis-(triphenylphosphine)palladium (1.56 g, 0.00135 mol) and sodium carbonate (5.97 g, 0.0563 mol) was heated in a mixture of ethylene glycol dimethyl ether (120 mL) and water (60 mL) at 80° C. for 16 hours under an atmosphere of nitrogen. The mixture was allowed to cool to ambient temperature and solvents were removed under the reduced pressure. The residue was partitioned between water (150 mL) and dichloromethane (150 mL); the organic phase was washed with brine, dried with magnesium sulfate and concentrated under reduced pressure. The residue was triturated in diethyl ether and the precipitate was collected by filtration and dried to yield tert-butyl 4-[4-amino-3-(4-[(benzyloxy)carbonyl]aminophenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-1-piperidinecarboxylate (10.1 g, 0.0186 mol) as a white solid.
Reaction SMILES: [Br:1][CH2:2][CH2:3][CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][C:9]([OH:11])=[O:10].[CH2:12](O)[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1.C1(N=C=NC2CCCCC2)CCCCC1>C(Cl)(Cl)(Cl)Cl.N1(C2C=CN=CC=2)CCCC1>[CH2:12]([O:10][C:9](=[O:11])[CH2:8][CH2:7][CH2:6][CH2:5][CH2:4][CH2:3][CH2:2][Br:1])[C:13]1[CH:18]=[CH:17][CH:16]=[CH:15][CH:14]=1
Reactant: OCc1ccccc1
Reactant: O=C(O)CCCCCCCBr
Agent: C(=NC1CCCCC1)=NC1CCCCC1
Agent: c1cc(N2CCCC2)ccn1
Solvent: ClC(Cl)(Cl)Cl
Product: O=C(CCCCCCCBr)OCc1ccccc1
Reaction time: 0.5 h

Procedure:
There were dissolved 11.6 g (52 mmol) of 8-bromooctanoic acid in 100 ml of CCl4 and around 5° C. (ice bath), there were added to the solution 5.41 g (50 mmol) of benzyl alcohol and 2.5 mmol of 4-pyrrolidino-pyridine catalyst. Thereafter, a solution of 10.73 g (52 mmol) of dicyclohexylcarbodiimide (DCC) in 10 ml of carbon tetrachloride was added portion-wise under stirring. The precipitation of the expected dicyclohexylurea (DCU) was effective after a few min and the temperature was allowed to come back to room temperature. After ½ hr, the reaction was complete as checked by TLC (hexane/ether 1:1). Then after about 1 hr, 0.5 ml of AcOH were added to quench remaining DCC and the DCU was filtered out after about one hour (yield 11.2 g=100%).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:11]=[CH:12][C:13]([OH:15])=[O:14])[CH:6]=[CH:7][C:8]=1[O:9][CH3:10].S(Cl)(Cl)=O.[CH3:20]O>>[CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:11]=[CH:12][C:13]([O:15][CH3:20])=[O:14])[CH:6]=[CH:7][C:8]=1[O:9][CH3:10]
Reactant: CO
Reactant: COc1ccc(C=CC(=O)O)cc1OC
Solvent: O=S(Cl)Cl
Product: COC(=O)C=Cc1ccc(OC)c(OC)c1
Temperature: 60 °C
Reaction time: 12 h
Yield: 80 %

Procedure:
To a suspension of 3-(3,4-dimethoxyphenyl)-2-propenoic acid (21.8 g, 105 mmol) in methanol (220 ml) was added thionyl chloride (23.0 mL, 315 mmol) under ice cooling and the mixture was stirred at 60° C. for 12 hours. The resulting mixture was concentrated under reduced pressure, and the residue was added to water and extracted with ethyl acetate. The organic layer was washed with saturated aqueous sodium bicarbonate, water and saturated aqueous sodium chloride, and dried over anhydrous sodium sulfate, and concentrated under reduced pressure. The residue was crystallized from ethyl acetate-hexane to obtain 18.7 g (yield 80%) of the title compound. mp. 72–74° C.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([O:12][CH3:13])[C:5]([O:10][CH3:11])=[C:6]([CH:9]=1)[CH:7]=[O:8].[CH3:14][Mg]Br.CCOCC.[Cl-].[NH4+]>CC(OC)(C)C>[Cl:1][C:2]1[CH:3]=[C:4]([O:12][CH3:13])[C:5]([O:10][CH3:11])=[C:6]([CH:7]([OH:8])[CH3:14])[CH:9]=1
Reactant: C[Mg]Br
Reactant: COc1cc(Cl)cc(C=O)c1OC
Agent: [Cl-]
Agent: [NH4+]
Solvent: COC(C)(C)C
Solvent: CCOCC
Product: COc1cc(Cl)cc(C(C)O)c1OC
Temperature: 33 °C
Yield: 96 %

Procedure:
To a mixture of 5-chloro-2,3-dimethoxybenzaldehyde (339, 1.69 mol) in TBME (5.6 L) was added 3M methylmagnesium bromide in ether (660 mL, 1.98 mol) over 1 hour at 9 to 12° C. The mixture was warmed at 33° C. for 1 hour 20 minutes. There was significant starting material present so more methylmagnesium bromide was added (590 mL, 1.77 mol) over 1 hour 20 minutes with the reaction temperature at 33° C. The reaction was cooled to room temperature overnight and poured into ammonium chloride (20 wt %, 3 kg) over 5 minutes. The temperature rose from 11 to 28° C. The reaction flask was rinsed with ammonium chloride solution (500 mL) and TBME (250 mL). The layers were separated and the organic layer was concentrated to an orange yellow thick oil. Yield: 348 g (96% yield, 94% purity).
Reaction SMILES: [N:1]1[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][CH:9]=2)[CH:4]=[CH:3][C:2]=1[C:11]([NH:13][C@H:14]([C:19]([OH:21])=O)[CH2:15][C:16](=[O:18])[NH2:17])=[O:12].[NH2:22][C@@H:23]([CH2:44][C:45]1[CH:50]=[CH:49][CH:48]=[CH:47][CH:46]=1)[C@H:24]([OH:43])[CH2:25][N:26]1[C@H:35]([C:36]([NH:38][C:39]([CH3:42])([CH3:41])[CH3:40])=[O:37])[CH2:34][C@H:33]2[C@H:28]([CH2:29][CH2:30][CH2:31][CH2:32]2)[CH2:27]1.ON1C(=O)C2C=CC=CC=2N=N1.C1(N=C=NC2CCCCC2)CCCCC1.CC1CCC(O)C/C/1=C/C=C1\CCCC2(C)C(C(/C=C/C(C(C)C)C)C)CCC\12>O1CCCC1.C(OCC)(=O)C>[C:39]([NH:38][C:36]([C@@H:35]1[CH2:34][C@H:33]2[C@H:28]([CH2:29][CH2:30][CH2:31][CH2:32]2)[CH2:27][N:26]1[CH2:25][C@@H:24]([OH:43])[C@@H:23]([NH:22][C:19](=[O:21])[C@H:14]([CH2:15][C:16](=[O:18])[NH2:17])[NH:13][C:11]([C:2]1[CH:3]=[CH:4][C:5]2[C:10](=[CH:9][CH:8]=[CH:7][CH:6]=2)[N:1]=1)=[O:12])[CH2:44][C:45]1[CH:46]=[CH:47][CH:48]=[CH:49][CH:50]=1)=[O:37])([CH3:42])([CH3:40])[CH3:41]
Reactant: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@@H](N)Cc1ccccc1
Reactant: NC(=O)C[C@H](NC(=O)c1ccc2ccccc2n1)C(=O)O
Agent: C(=NC1CCCCC1)=NC1CCCCC1
Agent: CC1CCC(O)C/C1=C/C=C1\CCCC2(C)C1CCC2C(C)/C=C/C(C)C(C)C
Agent: O=c1c2ccccc2nnn1O
Solvent: C1CCOC1
Solvent: CCOC(C)=O
Product: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)c1ccc2ccccc2n1
Reaction time: 2 h
Yield: 80.2 %

Procedure:
A solution of 287 mg of N-(2-quinolylcarbonyl)-L-asparagine and 401 mg of 2-[3(S)-amino-2(R)-hydroxy-4 -phenylbutyl]-N-tert.butyl-decahydro-(4aS,8aS)-isoquinoline-3(S)-carboxamide in 3 ml of tetrahydrofuran was cooled to-10° C. and 163 mg of 3-hydroxy-1,2,3-benzotriazin-4(3H)-one and 220 mg of dicyclohexylcarbodiimide were added. The mixture was stirred at-10° C. for 2 hours and at 20° C. for 16 hours, then diluted with ethyl acetate and filtered. The filtrate was washed with saturated sodium bicarbonate solution and saturated sodium chloride solution and then evaporated. The residue was chromatographed on silica gel using 4% (by volume) methanol in dichloromethane for the elution to give 537 mg of N-tert.butyl-decahydro-2-[2(R)-hydroxy-4-phenyl-3(S)-[[N-(2-quinolylcarbonyl)-L-asparaginyl]amino]butyl]-(4aS,8aS)-isoquinoline-3(S)-carboxamide as a white solid: MS: m/e 671 [M+H]+.
Reaction SMILES: [C:1](=[C:3]1N=C2C=CC=CC2=N1)=O.[CH:12]([S:15]([N:18]1[C:22]2[CH:23]=[C:24]([C:27](=[O:34])[C:28]3[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=3)[CH:25]=[CH:26][C:21]=2[N:20]=[C:19]1[NH2:35])(=[O:17])=[O:16])([CH3:14])[CH3:13].C([Mg]Br)C.CO>C(OCC)C>[CH:12]([S:15]([N:18]1[C:22]2[CH:23]=[C:24]([C:27]([C:28]3[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=3)([OH:34])[CH2:1][CH3:3])[CH:25]=[CH:26][C:21]=2[N:20]=[C:19]1[NH2:35])(=[O:16])=[O:17])([CH3:14])[CH3:13]
Reactant: CC(C)S(=O)(=O)n1c(N)nc2ccc(C(=O)c3ccccc3)cc21
Reactant: O=C=C1N=c2ccccc2=N1
Agent: CC[Mg]Br
Solvent: CO
Solvent: CCOCC
Product: CCC(O)(c1ccccc1)c1ccc2nc(N)n(S(=O)(=O)C(C)C)c2c1

Procedure:
The 1-hydroxy-1-(C1 -C7 alkyl)benzyl derivatives, the carbinols, can also be prepared by reacting the corresponding carbonyl derivative with the appropriate Grignard reagent followed by hydrolysis. The carbonyl benzimidazole, 1-isopropylsulfonyl-2-amino-6-benzoylbenzimidazole, is reacted with ethylmagnesium bromide in anhydrous ethyl ether and then hydrolyzed to form the carbinol, 1-isopropylsulfonyl-2-amino-6-(1-phenyl-1-hydroxy-1-propyl)benzimidazole. The Grignard reagent, ethylmagnesium bromide, is made from ethylbromide and metallic magnesium in anhydrous ethyl ether.
Reaction SMILES: Cl[C:2]1[CH:15]=[CH:14][C:5]([C:6]([C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=2)=[O:7])=[CH:4][CH:3]=1.[SH:16][CH2:17][C:18]([OH:20])=[O:19].CC(N(C)C)=O.[OH-].[Na+]>O>[C:18]([CH2:17][S:16][C:2]1[CH:15]=[CH:14][C:5]([C:6]([C:8]2[CH:13]=[CH:12][CH:11]=[CH:10][CH:9]=2)=[O:7])=[CH:4][CH:3]=1)([OH:20])=[O:19]
Reactant: O=C(c1ccccc1)c1ccc(Cl)cc1
Reactant: O=C(O)CS
Agent: [Na+]
Agent: [OH-]
Solvent: O
Solvent: CC(=O)N(C)C
Product: O=C(O)CSc1ccc(C(=O)c2ccccc2)cc1
Temperature: 107.5 °C
Yield: 80 %

Procedure:
55 g 4-chloro benzophenone and 24 g mercaptoacetic acid are added into a 500 ml three-neck flask, and are dissolved with 350 ml DME (dimethyl acetamide) to obtain a solution, and then 23 g solid sodium hydroxide is added into the solution. Heating the solution to reflux (105-110° C.), and starting to cool the solution when the content of 4-chloro benzophenone detected by HPLC is less than 1%. The reaction solution is added into 500 ml water, and then water insoluble substances are extracted with 100 ml methylbenzene. Concentrated hydrochloric acid is used to regulate the pH value of the aqueous phase to 3-4, then some solid substances precipitate, filtering to obtain crude products, and the weight after drying is 60 g; the dried crude products are recrystallized in dichloroethane to obtain 55.3 g white crystal, and the yield was 80%.
Reaction SMILES: [P:1]([Cl:5])(Cl)([Cl:3])=[O:2].[C:6]1([OH:12])[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1.C(N(CC)CC)C>C(OCC)C>[P:1]([Cl:5])([Cl:3])(=[O:2])[O:12][C:6]1[CH:11]=[CH:10][CH:9]=[CH:8][CH:7]=1
Reactant: Oc1ccccc1
Reactant: O=P(Cl)(Cl)Cl
Solvent: CCOCC
Solvent: CCN(CC)CC
Product: O=P(Cl)(Cl)Oc1ccccc1
Temperature: 25 °C

Procedure:
Phosphorus oxychloride (3.23 mL, 1 equiv) and phenol (g, 1 equiv) were stirred in anhydrous diethyl ether (25 mL). Anhydrous triethylamine was added (4.84 mL, 1 equiv) at −78° C. and the solution was allowed to warm to room temperature after 25 min. The triethylamine hydrochloride salt was filtered off and the solvent was removed under reduced pressure to give a clear pale yellow oil (g, %). (oil solidified in the freezer).
Reaction SMILES: [N+:1]1([O-:9])[C:2]([CH3:8])=[CH:3][CH:4]=[CH:5][C:6]=1[CH3:7].[N+:10]([O-])([OH:12])=[O:11]>S(=O)(=O)(O)O>[N+:10]([C:4]1[CH:3]=[C:2]([CH3:8])[N+:1]([O-:9])=[C:6]([CH3:7])[CH:5]=1)([O-:12])=[O:11]
Reactant: Cc1cccc(C)[n+]1[O-]
Reactant: O=[N+]([O-])O
Agent: O=S(=O)(O)O
Product: Cc1cc([N+](=O)[O-])cc(C)[n+]1[O-]

Procedure:
A mixture of 2,6-lutidine 1-oxide (20, 15 g, 110 mmol) and concentrated sulfuric acid (98%, 30 ml) and concentrated nitric acid (70%, 12 ml) is heated under reflux for 3 hours. The mixture is poured into a large excess of ice and extracted with chloroform (3×100 ml). The combined chloroform extracts are washed with aqueous sodium hydroxide and water and dried over magnesium sulfate. Removal of the solvent yields pure yellow solid 4-Nitro-2,6-lutidine 1-oxide (21). 1H NMR (300 MHz, CDCl3) δ 2.64 (s, 6H), 8.08 (s, 2H). MS, m/z 169 (M+1), 210 (M+MeCN).
Reaction SMILES: [CH2:1]=[CH:2][C:3]([N:5]1[CH2:10][C@H:9]([N:11]2[N:15]=[C:14]([C:16]3[CH:17]=[CH:18][C:19]([O:22][C:23]4[CH:24]=[CH:25][CH:26]=[CH:27][CH:28]=4)=[CH:20][CH:21]=3)[C:13]3=[C:29]([NH2:33])[N:30]=[CH:31][N:32]=[C:12]23)[CH2:8][CH2:7][CH2:6]1)=[O:4].[C:34]([O:37][CH2:38][O:39][C:40](ON1C(=O)CCC1=O)=[O:41])(=[O:36])[CH3:35].C(N(CC)CC)C>CN(C)C(=O)C>[C:34]([O:37][CH2:38][O:39][C:40](=[O:41])[NH:33][C:29]1[N:30]=[CH:31][N:32]=[C:12]2[N:11]([C@@H:9]3[CH2:8][CH2:7][CH2:6][N:5]([C:3](=[O:4])[CH:2]=[CH2:1])[CH2:10]3)[N:15]=[C:14]([C:16]3[CH:17]=[CH:18][C:19]([O:22][C:23]4[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=4)=[CH:20][CH:21]=3)[C:13]=12)(=[O:36])[CH3:35]
Reactant: C=CC(=O)N1CCC[C@@H](n2nc(-c3ccc(Oc4ccccc4)cc3)c3c(N)ncnc32)C1
Reactant: CC(=O)OCOC(=O)ON1C(=O)CCC1=O
Solvent: CC(=O)N(C)C
Solvent: CCN(CC)CC
Product: C=CC(=O)N1CCC[C@@H](n2nc(-c3ccc(Oc4ccccc4)cc3)c3c(NC(=O)OCOC(C)=O)ncnc32)C1
Temperature: 20 °C
Reaction time: 8 h

Procedure:
Alternatively, a mixture of ibrutinib (25 mg, 1.0 eq), (2,5-dioxopyrrolidin-1-yl)oxycarbonyloxymethyl acetate (1.5 eq), and triethylamine (3.0 eq) in N,N-dimethylacetamide (DMA) (1.0 mL) was stirred at 20° C. overnight. The reaction was then purified by reverse-phase (C-18) liquid chromatography using water and acetonitrile as eluents to yield compound (1).
Reaction SMILES: C(O[C:5](=[O:7])[CH3:6])(=O)C.[Br:8][C:9]1[CH:15]=[CH:14][C:13]([N+:16]([O-:18])=[O:17])=[CH:12][C:10]=1[NH2:11].O>C(O)(=O)C>[Br:8][C:9]1[CH:15]=[CH:14][C:13]([N+:16]([O-:18])=[O:17])=[CH:12][C:10]=1[NH:11][C:5](=[O:7])[CH3:6]
Reactant: CC(=O)OC(C)=O
Reactant: Nc1cc([N+](=O)[O-])ccc1Br
Solvent: O
Solvent: CC(=O)O
Product: CC(=O)Nc1cc([N+](=O)[O-])ccc1Br
Temperature: 25 °C
Reaction time: 8 h

Procedure:
Acetic anhydride (1.4 mL, 13.8 mmol) was added dropwise to a stirring solution of 2-bromo-5-nitroaniline (3 g, 13.8 mmol) in glacial acetic acid (30 mL) at 25° C. The reaction mixture was stirred at room temperature overnight, and then poured into water. The precipitate was collected via filtration, washed with water and dried under vacuum to provide N-(2-bromo-5-nitrophenyl)acetamide as an off white solid (3.6 g, 90%).
Reaction SMILES: [CH:1]1([N:6]2[CH2:12][C:11]([F:14])([F:13])[C:10](=[O:15])[N:9]([CH3:16])[C:8]3[CH:17]=[N:18][C:19]([NH:21][C:22]4[CH:30]=[CH:29][C:25]([C:26](O)=[O:27])=[CH:24][C:23]=4[O:31][CH3:32])=[N:20][C:7]2=3)[CH2:5][CH2:4][CH2:3][CH2:2]1.[CH3:33][N:34]1[CH2:39][CH2:38][CH:37]([NH2:40])[CH2:36][CH2:35]1.C(N(C(C)C)CC)(C)C>C(#N)C>[CH:1]1([N:6]2[CH2:12][C:11]([F:14])([F:13])[C:10](=[O:15])[N:9]([CH3:16])[C:8]3[CH:17]=[N:18][C:19]([NH:21][C:22]4[CH:30]=[CH:29][C:25]([C:26]([NH:40][CH:37]5[CH2:38][CH2:39][N:34]([CH3:33])[CH2:35][CH2:36]5)=[O:27])=[CH:24][C:23]=4[O:31][CH3:32])=[N:20][C:7]2=3)[CH2:5][CH2:4][CH2:3][CH2:2]1
Reactant: CN1CCC(N)CC1
Reactant: COc1cc(C(=O)O)ccc1Nc1ncc2c(n1)N(C1CCCC1)CC(F)(F)C(=O)N2C
Solvent: CC#N
Solvent: CCN(C(C)C)C(C)C
Product: COc1cc(C(=O)NC2CCN(C)CC2)ccc1Nc1ncc2c(n1)N(C1CCCC1)CC(F)(F)C(=O)N2C
Reaction time: 8 h

Procedure:
Combine 4-(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-ylamino)-3-methoxybenzoic acid (3.108 kg, 6.17 mol) and acetonitrile (14.56 kg) and adjust the temperature to about 0° C. Add N-methyl-4-aminopiperidine (0.775 k, 1.1 eq.). Diisopropylethylamine (1.595 kg) was added aver about 29 minutes at temperature of about 6 to 12° C., the temperature was adjusted to about 20 to 25° C. and the reaction mixture was stirred overnight. The solid was collected by filtration, rinsed with acetonitrile (4.47 kg) and dried under at stream of nitrogen for 1 hour, then in a vacuum oven at 40° C. for 2 days to give the title compound.
Reaction SMILES: [Br:1][C:2]1[N:3]=[C:4]([CH:10]2[CH2:15][CH2:14][N:13]([C:16]([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17])[CH2:12][CH2:11]2)[N:5]([CH2:7][CH2:8][OH:9])[CH:6]=1.CCN(CC)CC.[S:30](Cl)([CH3:33])(=[O:32])=[O:31]>C(Cl)Cl>[Br:1][C:2]1[N:3]=[C:4]([CH:10]2[CH2:15][CH2:14][N:13]([C:16]([O:18][C:19]([CH3:22])([CH3:21])[CH3:20])=[O:17])[CH2:12][CH2:11]2)[N:5]([CH2:7][CH2:8][O:9][S:30]([CH3:33])(=[O:32])=[O:31])[CH:6]=1
Reactant: CS(=O)(=O)Cl
Reactant: CC(C)(C)OC(=O)N1CCC(c2nc(Br)cn2CCO)CC1
Solvent: ClCCl
Solvent: CCN(CC)CC
Product: CC(C)(C)OC(=O)N1CCC(c2nc(Br)cn2CCOS(C)(=O)=O)CC1
Reaction time: 1 h

Procedure:
A solution of tert-butyl 4-(4-bromo-1-(2-hydroxyethyl)-1H-imidazol-2-yl)piperidine-1-carboxylate (22.0 g) and Et3N (24.5 ml) in DCM (250 ml) and cool to 0° C. Mesyl chloride (6.8 ml) was added dropwisely and the resulting mixture was stirred for 1 h. The reaction was quenched with saturated aqueous NaHCO3 and extracted with DCM. The organic layer was concentrated to give tert-butyl 4-(4-bromo-1-(2-((methylsulfonyl)oxy)ethyl)-1H-imidazol-2-yl)piperidine-1-carboxylate (28.0 g).