Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [O:1]([CH:9]1[CH2:13][C:12](=[O:14])[CH:11]=[CH:10]1)[Si:2]([C:5]([CH3:8])([CH3:7])[CH3:6])([CH3:4])[CH3:3].[I-].[Li+].[H-].[Al+3].[Li+].[H-].[H-].[H-]>C(OCC)C>[Si:2]([O:1][C@@H:9]1[CH2:13][C@H:12]([OH:14])[CH:11]=[CH:10]1)([C:5]([CH3:8])([CH3:7])[CH3:6])([CH3:4])[CH3:3]
Reactant: CC(C)(C)[Si](C)(C)OC1C=CC(=O)C1
Agent: [Al+3]
Agent: [H-]
Agent: [I-]
Solvent: CCOCC
Product: CC(C)(C)[Si](C)(C)O[C@H]1C=C[C@@H](O)C1
Temperature: -78 °C
Reaction time: 1.5 h
Yield: 80.4 %

Procedure:
A mechanically stirred solution of 4-tert-butyldimethylsiloxy-2-cyclopentenone (1.01 g, 4.76 mmol) in anhydrous ethyl ether (20 mL) under an atmosphere of argon is treated with lithium iodide (3.20 g, 23.9 mmol). The mixture is cooled to -78° C. and treated with lithium aluminum hydride (184 mg, 4.85 mmol) in one portion. The reaction is then stirred for 90 minutes. It is then quenched by slow addition of aqueous sodium hydroxide (1N, 23 mL) at a rate that maintains the temperature of the reaction below 20° C. The resulting suspension is then filtered through a pad of diatomaceous earth and the pad is subsequently rinsed with ether. The filtrate phases are separated and the aqueous phase is extracted with ether (20 mL). The organic phase and organic extract are combined, rinsed with aqueous sodium hydroxide (1N, 20 mL), brine (20 mL), dried over anhydrous magnesium sulfate, filtered and concentrated under vacuum (40° C., 20 mmHg). The residue is then purified by Kugelrohr distillation (60°-80° C., 1 mmHg) to provide the title compound (820 mg, 80% yield) as a colorless oil; cis/trans/l-2+l-4 addition, 88.5/3.3/8.2.
Reaction SMILES: [O:1]([CH:9]1[CH2:13][C:12](=[O:14])[CH:11]=[CH:10]1)[Si:2]([C:5]([CH3:8])([CH3:7])[CH3:6])([CH3:4])[CH3:3].[I-].[Li+].[H-].[Al+3].[Li+].[H-].[H-].[H-].COC(C)(C)C>C1(C)C=CC=CC=1>[Si:2]([O:1][C@@H:9]1[CH2:13][C@H:12]([OH:14])[CH:11]=[CH:10]1)([C:5]([CH3:8])([CH3:7])[CH3:6])([CH3:4])[CH3:3]
Reactant: CC(C)(C)[Si](C)(C)OC1C=CC(=O)C1
Agent: [Al+3]
Agent: [H-]
Agent: [I-]
Solvent: COC(C)(C)C
Solvent: Cc1ccccc1
Product: CC(C)(C)[Si](C)(C)O[C@H]1C=C[C@@H](O)C1
Temperature: -20 °C
Reaction time: 0.08 h
Yield: 73.9 %

Procedure:
A mechanically stirred solution of 4-tert-butyldimethylsiloxy-2-cyclopentenone (50.2 g, 236 mmol) in anhydrous toluene (1 L) under an atmosphere of argon is treated with lithium iodide (160 g, 1.20 mol). The mixture is cooled to -20° C. and treated with lithium aluminum hydride (9.0 g, 237 mmol) in one portion. The reaction is then stirred for 5 minutes and anhydrous tert-butyl methyl ether (200 mL) is added at a rate that maintains the temperature of the reaction at or below -15° C. (total addition time is approximately 3 minutes). The reaction is stirred for one hour at -20° C. and then it is quenched by slow addition of aqueous sodium hydroxide (1N, 250 mL) at a rate that maintains the temperature of the reaction below 20° C. The resulting suspension is then filtered through a pad of diatomaceous earth and the pad is subsequently rinsed with toluene (400 mL). The filtrate phases are separated and the aqueous phase is extracted with toluene (300 mL). The organic phase and organic extract are combined, rinsed with aqueous sodium hydroxide (1N, 300 mL), brine (300 mL), dried over anhydrous magnesium sulfate, filtered and concentrated under vacuum (40° C., 20 mmHg). The residue is then purified by Kugelrohr distillation (60°-80° C., 1 mmHg) to provide the title compound (37.4 g, 74% yield) as a colorless oil; cis/trans/l-2+l-4 addition, 95.3/2.1/2.6; Rf =0.20, 20% ethyl acetate/hexane, GC retention time for the title compound is 13.95 minutes, while CC retention times for the byproducts corresponding to compounds 3 (trans) and 4 (l-2+l-4 addition) in Scheme I wherein Pg is a TBDMS group are 14.45 min. and 14.06 min. respectively; for the title compound, 1H NMR (CDCl3) δ 5.93 (dt, J=5.5, 1.7 Hz, 1 H), 5.84 (dt, J=5.5, 1.6 Hz, 1 H), 4.63-4.68 (m, 1 H), 4.52-4.62 (m, 1 H), 2.76-2.86 (bs, 1 H), 2.69 (dt, J=13.8, 7.1 Hz, 1 H), 1.52 (dt, J=13.8, 4.7 Hz, 1 H), 0.90 (s, 9 H), 0.09 (s, 6 H); 13C NMR (CDCl3) δ 136.7, 135.6, 75.1, 75.0, 44.5, 25.9, 18.1; IR (neat) νmax 3373, 2957, 2932 cm-1 ; MS (EI) m/e (% relative intensity) 157 (M+ -57).
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]([CH:7]=[CH:8][CH:9]=1)[CH:5]=[O:6].[CH:10]#[C:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH3:21]>C(N(CC)CC)C.C(OCC)(=O)C.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.[Cu]I>[C:10]([C:2]1[CH:3]=[C:4]([CH:7]=[CH:8][CH:9]=1)[CH:5]=[O:6])#[C:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH3:21]
Reactant: O=Cc1cccc(Br)c1
Reactant: C#CCCCCCCCCCC
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: [Cu]I
Solvent: CCOC(C)=O
Solvent: CCN(CC)CC
Product: CCCCCCCCCCC#Cc1cccc(C=O)c1
Temperature: 25 °C
Yield: 97.3 %

Procedure:
To a solution of 3-bromobenzaldehyde (26.5 g) and (25.0 g) 1-dodecyne in triethylamine (105 ml) was added bis(triphenylphosphine)palladium(II) chloride (1.73 g) followed by copper(I) iodide (0.24 g). The resultant mixture was stirred in the dark at 55° C. for 7 hrs, under nitrogen. After cooling to room temperature, the reaction mixture was diluted with ethyl acetate and filtered. The filtrate was washed with water and saturated sodium chloride solution, dried over anhydrous magnesium sulfate, filtered, and concentrated to yield 37.7 g 3-(1-dodecynyl)benzaldehyde. The filtrate was an oil.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][C:5]([NH:8][C:9]2[CH:14]=[CH:13][C:12](Br)=[CH:11][CH:10]=2)=[CH:4][CH:3]=1.[C:16]1(B(O)O)[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1.C(=O)([O-])[O-].[K+].[K+]>C([O-])(=O)C.[Pd+2].C([O-])(=O)C.COCCOC>[C:2]1([C:2]2[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=2)[CH:7]=[CH:6][C:5]([NH:8][C:9]2[CH:14]=[CH:13][C:12]([C:16]3[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=3)=[CH:11][CH:10]=2)=[CH:4][CH:3]=1
Reactant: Brc1ccc(Nc2ccc(Br)cc2)cc1
Reactant: OB(O)c1ccccc1
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: O=C([O-])[O-]
Solvent: COCCOC
Product: c1ccc(-c2ccc(Nc3ccc(-c4ccccc4)cc3)cc2)cc1
Reaction time: 7 h
Yield: 143.8 %

Procedure:
In a nitrogen atmosphere, an ethylene glycol dimethyl ether (20 mL) solution containing 9.5 g (29 mmol) of N,N-bis(4-bromophenyl)amine, 7.9 g (65 mmol) of phenyl boronic acid, 0.15 g (0.646 mmol) of palladium acetate, and 1.4 g (4.5 mmol) of tris(o-thryl)phosphine, to which 95 mL of a potassium carbonate solution (2.0 mol/L) is added, is rectified at 90° C. for seven hours. After completion of reaction, the reaction mixture is filtrated, and the obtained solid is recrystallized with chloroform and hexane to obtain 6.7 g (yield: 72%) of N,N-di(4-biphenylyl)amine which is an object as a white powdered solid.
Reaction SMILES: [CH:1]1([CH2:7][O:8][C:9]2[C:10]([NH2:15])=[N:11][CH:12]=[CH:13][CH:14]=2)[CH2:6][CH2:5][CH2:4][CH2:3][CH2:2]1.Cl[CH:17]([C:23](=O)[CH3:24])[C:18]([O:20][CH2:21][CH3:22])=[O:19].C(N(CC)CC)C.O>C1(C)C=CC=CC=1.CCCCCC.C(OCC)(=O)C>[CH:1]1([CH2:7][O:8][C:9]2[C:10]3[N:11]([C:17]([C:18]([O:20][CH2:21][CH3:22])=[O:19])=[C:23]([CH3:24])[N:15]=3)[CH:12]=[CH:13][CH:14]=2)[CH2:2][CH2:3][CH2:4][CH2:5][CH2:6]1
Reactant: CCOC(=O)C(Cl)C(C)=O
Reactant: Nc1ncccc1OCC1CCCCC1
Solvent: CCN(CC)CC
Solvent: CCOC(C)=O
Solvent: Cc1ccccc1
Product: CCOC(=O)c1c(C)nc2c(OCC3CCCCC3)cccn12
Reaction time: 8 h

Procedure:
To a solution of 5.8 g of 3-(cyclohexylmethoxy)pyridin-2-amine in 100 ml of toluene were added 4.3 ml of ethyl 2-chloro-3-oxobutanoate and 4.3 ml of triethylamine, followed by stirring overnight under heating to reflux. To the reaction mixture were added 1 ml of ethyl 2-chloro-3-oxobutanoate and 1 ml of triethylamine, followed by stirring for 6.5 hours under heating to reflux. To the reaction mixture was added water, followed by extraction with ethyl acetate. The organic layer was dried over anhydrous sodium sulfate and the solvent was then evaporated under reduced pressure. The obtained residue was purified by silica gel column chromatography. To the purified product thus obtained were added ethyl acetate and hexane, followed by heating and stirring, and then stirring under ice-cooling. The resulting solid was collected by filtration to obtain 4.0 g of ethyl 8-(cyclohexylmethoxy)-2-methylimidazo[1,2-a]pyridine-3-carboxylate.
Reaction SMILES: N(C1N(CC(C)C)C(=O)N(C)C(=O)C=1)N.ClC1C=C2C(=CC=1)NC=C2C=O.C(C1C=C(C=O)N(C)C=1)(=O)C.[C:39]([C:42]1[CH:43]=[C:44]([C:48]2[N:49]([CH2:64][C:65]3[C:73]4[C:68](=[CH:69][CH:70]=[C:71]([Cl:74])[CH:72]=4)[NH:67][CH:66]=3)[N:50]=[C:51]3[C:56]=2[C:55](=[O:57])[N:54]([CH3:58])[C:53](=[O:59])[N:52]3[CH2:60][CH:61]([CH3:63])[CH3:62])[N:45]([CH3:47])[CH:46]=1)(=O)[CH3:40].Cl.[CH3:76][O:77][NH2:78]>C(N(CC)CC)C>[Cl:74][C:71]1[CH:72]=[C:73]2[C:68](=[CH:69][CH:70]=1)[NH:67][CH:66]=[C:65]2[CH2:64][N:49]1[C:48]([C:44]2[N:45]([CH3:47])[CH:46]=[C:42](/[C:39](=[N:78]/[O:77][CH3:76])/[CH3:40])[CH:43]=2)=[C:56]2[C:51]([N:52]([CH2:60][CH:61]([CH3:62])[CH3:63])[C:53](=[O:59])[N:54]([CH3:58])[C:55]2=[O:57])=[N:50]1
Reactant: CON
Reactant: CC(=O)c1cc(-c2c3c(=O)n(C)c(=O)n(CC(C)C)c3nn2Cc2c[nH]c3ccc(Cl)cc23)n(C)c1
Agent: CC(=O)c1cc(C=O)n(C)c1
Agent: CC(C)Cn1c(NN)cc(=O)n(C)c1=O
Agent: Cl
Solvent: CCN(CC)CC
Product: CO/N=C(\C)c1cc(-c2c3c(=O)n(C)c(=O)n(CC(C)C)c3nn2Cc2c[nH]c3ccc(Cl)cc23)n(C)c1

Procedure:
This compound was made in two steps following the procedure described above, stating with 6-hydrazino-1-isobutyl-3-methylpyrimidine-2,4(1H,3H)-dione, and condensing first 5-chloro-1H-indole-3-carbaldehyde, followed by 4-acetyl-1-methyl-1H-pyrrole-2-carbaldehyde. To the isolated 3-(4-acetyl-1-methyl-1H-pyrrol-2-yl)-2-[(5-chloro-1H-indol-3-yl)methyl]-7-isobutyl-5-methyl-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione was added 4 equivalents of methoxyamine hydrochloride, triethylamine and heated at 80° C. in N,N′dimethylacetamide for 4 h. A second peak, an isomer was isolated purification by semi-prep RPHPLC eluting with water/acetonitrile/trifluoroacetic acid mixtures. 536.2 (M+H).
Reaction SMILES: [NH2:1][C:2]1[C:32]([Cl:33])=[CH:31][C:5]([C:6]([NH:8][CH2:9][CH:10]2[CH2:15][CH2:14][N:13]([CH2:16][CH2:17][CH2:18][CH2:19][N:20]3C(=O)C4C(=CC=CC=4)C3=O)[CH2:12][CH2:11]2)=[O:7])=[C:4]([O:34][CH3:35])[CH:3]=1.O.NN>>[NH2:1][C:2]1[C:32]([Cl:33])=[CH:31][C:5]([C:6]([NH:8][CH2:9][CH:10]2[CH2:11][CH2:12][N:13]([CH2:16][CH2:17][CH2:18][CH2:19][NH2:20])[CH2:14][CH2:15]2)=[O:7])=[C:4]([O:34][CH3:35])[CH:3]=1
Reactant: COc1cc(N)c(Cl)cc1C(=O)NCC1CCN(CCCCN2C(=O)c3ccccc3C2=O)CC1
Agent: NN
Solvent: O
Product: COc1cc(N)c(Cl)cc1C(=O)NCC1CCN(CCCCN)CC1
Yield: 100.4 %

Procedure:
4-Amino-5-chloro-N-(1-(4-(2,3-dihydro-1,3-dioxo-1H-isoindol-2-yl)butyl)piperidin-4-ylmethyl)-2-methoxybenzamide (9.3 g) as starting compound and hydrazine monohydrate (1.4 ml) were reacted and treated in the same manner as in Example 117 to give 6.9 g of 4-amino-N-(1-(4-aminobutyl)piperidin-4-ylmethyl)-5-chloro-2-methoxybenzamide. m.p. 104°-107° C.
Reaction SMILES: [NH:1]1[C:9]2[C:4](=[CH:5][CH:6]=[CH:7][CH:8]=2)[CH:3]=[C:2]1[C:10]([O:12][CH2:13][CH3:14])=[O:11].[OH-].[Na+]>FC(F)(F)C(O)=O.CCOCC.[Pt]=O>[NH:1]1[CH:9]2[CH:4]([CH2:5][CH2:6][CH2:7][CH2:8]2)[CH2:3][CH:2]1[C:10]([O:12][CH2:13][CH3:14])=[O:11]
Reactant: CCOC(=O)c1cc2ccccc2[nH]1
Agent: O=[Pt]
Agent: [Na+]
Agent: [OH-]
Solvent: CCOCC
Solvent: O=C(O)C(F)(F)F
Product: CCOC(=O)C1CC2CCCCC2N1

Procedure:
Dissolve 27.0 g of ethyl indole-2-carboxylate in 250 ml of trifluoroacetic acid. Add 2.05 g of platinum oxide, hydrogenate the mixture at 50 lb/in2 at room temperature. Filter the mixture and concentrate the filtrate in vacuo to give a residue. Suspend the residue in ether and treat with cold dilute sodium hydroxide solution. Dry the organic layer over magnesium sulfate and concentrate it to give ethyl octahydroindole-2-carboxylate, a pale yellow oil.
Reaction SMILES: [CH2:1]([O:8][C:9]1[CH:14]=[CH:13][C:12]([CH2:15][CH:16]([O:22]S(C)(=O)=O)[C:17]([O:19][CH2:20][CH3:21])=[O:18])=[CH:11][CH:10]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[Cl:27][C:28]1[CH:33]=[CH:32][C:31](O)=[CH:30][CH:29]=1.C(=O)([O-])[O-].[K+].[K+]>CN(C)C=O>[CH2:1]([O:8][C:9]1[CH:14]=[CH:13][C:12]([CH2:15][CH:16]([O:22][C:31]2[CH:32]=[CH:33][C:28]([Cl:27])=[CH:29][CH:30]=2)[C:17]([O:19][CH2:20][CH3:21])=[O:18])=[CH:11][CH:10]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: CCOC(=O)C(Cc1ccc(OCc2ccccc2)cc1)OS(C)(=O)=O
Reactant: Oc1ccc(Cl)cc1
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: CCOC(=O)C(Cc1ccc(OCc2ccccc2)cc1)Oc1ccc(Cl)cc1
Temperature: 70 °C
Reaction time: 16 h
Yield: 62.6 %

Procedure:
To a solution of ethyl 3-(4-benzyloxyphenyl)-2-methanesulfonyloxypropionate (8.82 g) obtained from Reference example 24(b) and 4-chlorophenol (3.00 g) in N,N-dimethylformamide (110 ml) was added potassium carbonate (6.44 g), and the mixture was stirred at 70° C. for 16 hours. The reaction solution was partitioned between ethyl acetate and water, and then the ethyl acetate layer was dried over anhydrous magnesium sulfate and concentrated under reduced pressure. The residue was purified by chromatography on a silica gel column (eluant; hexane/ethyl acetate=9/1) to afford the target compound (5.99 g) as colorless crystals.
Reaction SMILES: [OH:1][C:2]1[CH:9]=[CH:8][C:5]([CH:6]=[O:7])=[CH:4][CH:3]=1.[CH2:10](Br)[CH:11]([CH3:13])[CH3:12].[I-].[Na+]>>[CH2:10]([O:1][C:2]1[CH:9]=[CH:8][C:5]([CH:6]=[O:7])=[CH:4][CH:3]=1)[CH:11]([CH3:13])[CH3:12]
Reactant: CC(C)CBr
Reactant: O=Cc1ccc(O)cc1
Agent: [I-]
Agent: [Na+]
Product: CC(C)COc1ccc(C=O)cc1
Yield: 100.6 %

Procedure:
The compound was synthesized as in Example 24.1, using 4-hydroxybenzaldehyde (200 mg, 1.64 mmol) and isobutyl bromide (449 mg, 1.97 mmol) in place of 1-chloro-3,3-dimethylbutane (no sodium iodide was used) to give 4-isobutoxybenzaldehyde (294 mg, quant. crude) as a yellow oil that was used without further purification or characterization.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:12][C@H:11]([S:13][CH2:14][C:15]2[CH:20]=[CH:19][C:18]([O:21][CH3:22])=[CH:17][CH:16]=2)[CH2:10][C@H:9]1[C:23]([OH:25])=O)=[O:7])([CH3:4])([CH3:3])[CH3:2].CN1CCOCC1.OC1C2N=NNC=2C=CC=1.CCN=C=NCCCN(C)C.Cl.[CH3:55][NH:56][O:57][CH3:58]>C(Cl)Cl>[C:1]([O:5][C:6]([N:8]1[CH2:12][C@H:11]([S:13][CH2:14][C:15]2[CH:20]=[CH:19][C:18]([O:21][CH3:22])=[CH:17][CH:16]=2)[CH2:10][C@H:9]1[C:23](=[O:25])[N:56]([O:57][CH3:58])[CH3:55])=[O:7])([CH3:4])([CH3:3])[CH3:2]
Reactant: COc1ccc(CS[C@@H]2C[C@@H](C(=O)O)N(C(=O)OC(C)(C)C)C2)cc1
Reactant: CNOC
Agent: CCN=C=NCCCN(C)C
Agent: Cl
Agent: Oc1cccc2[nH]nnc12
Solvent: ClCCl
Solvent: CN1CCOCC1
Product: COc1ccc(CS[C@@H]2C[C@@H](C(=O)N(C)OC)N(C(=O)OC(C)(C)C)C2)cc1
Temperature: 25 °C
Reaction time: 3 h
Yield: 10.7 %

Procedure:
30 g (81.6 mmol) (2S,4R)-4-(4-Methoxy-benzylsulfanyl)-pyrrolidine-1,2-dicarboxylic acid 1-tert-butyl ester in 800 ml CH2Cl2 were treated with 62.8 ml (571.2, 7 eq) NMM, 2.19 g (16.24 mmol, 0.2 eq) hydroxybenzotriazole, 37.5 g (195.84 mmol, 2.4 eq) EDCI and 17.5 g (179.52 mmol, 2.2 eq) N,O-dimethylhydroxylamine-hydrochloride. The solution was stirred for 3 h at RT, concentrated and dissolved in 500 ml 1M KHSO4 solution and 500 ml EtOAc were added. The organic layer was separated and washed with brine, dried over Na2SO4 and evaporated. The crude product was purified by flash chromatography on silica gel with EtOAc:hexane 1:1 as eluent yielding 3.6 g (62.4%) (2S,4R)-4-(4-Methoxy-benzylsulfanyl)-2-(methoxy-methyl-carbamoyl)-pyrrolidine-1-carboxylic acid tert-butyl ester as light yellow oil, MS: 411 (MH+).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([CH:6]=[C:7]([F:9])[CH:8]=1)[NH2:5].[Br:10]N1C(=O)CCC1=O>CC#N>[Br:10][C:8]1[C:7]([F:9])=[CH:6][C:4]([NH2:5])=[CH:3][C:2]=1[Cl:1]
Reactant: O=C1CCC(=O)N1Br
Reactant: Nc1cc(F)cc(Cl)c1
Solvent: CC#N
Product: Nc1cc(F)c(Br)c(Cl)c1
Temperature: 25 °C
Reaction time: 2 h
Yield: 74.3 %

Procedure:
To a cooled (0° C.) solution of 3-chloro-5-fluoroaniline (5.0 g, 33 mmol) in MeCN (50 ml) was added a suspension of N-bromosuccinimide (5.9 g, 33 mmol) in MeCN (10 ml). After being stirred for 2 h at RT the reaction was quenched by adding 10% NaHSO3 (50 ml). The mixture was concentrated to about half of the volume, diluted with water (50 ml) and extracted with EtOAc (3×50 ml). Combined organic phases were dried over Na2SO4 and evaporated to give crude product, which was purified by CombiFlash (column: silica, eluent: 0-100% EtOAc in heptane) to yield 5.5 g (74%) of the title compound. 1H-NMR (400 MHz; d6-DMSO): δ 5.88 (bs, 2H), 6.45 (dd, 1H), 6.64 (m, 1H).
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[CH2:13][CH2:12][N:11]([C:14]2[N:19]=[CH:18][C:17]([C:20]([OH:22])=O)=[CH:16][N:15]=2)[CH2:10][CH2:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].C(N=C=NCCCN(C)C)C.OC1C2N=NNC=2C=CC=1.C(N(CC)CC)C.[CH3:51][NH:52][O:53][CH3:54]>ClCCl>[CH3:54][O:53][N:52]([CH3:51])[C:20]([C:17]1[CH:16]=[N:15][C:14]([N:11]2[CH2:10][CH2:9][N:8]([C:6]([O:5][C:1]([CH3:4])([CH3:2])[CH3:3])=[O:7])[CH2:13][CH2:12]2)=[N:19][CH:18]=1)=[O:22]
Reactant: CC(C)(C)OC(=O)N1CCN(c2ncc(C(=O)O)cn2)CC1
Reactant: CNOC
Agent: CCN=C=NCCCN(C)C
Agent: Oc1cccc2[nH]nnc12
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CON(C)C(=O)c1cnc(N2CCN(C(=O)OC(C)(C)C)CC2)nc1
Temperature: 25 °C
Reaction time: 1 h
Yield: 71.1 %

Procedure:
To a suspension of 2-(4-(tert-butoxycarbonyl)piperazin-1-yl)pyrimidine-5-carboxylic acid (13.8 g, 44.8 mmol), 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (12.8 g, 67.2 mmol) and hydroxybenzotriazole (7.2 g, 53.7 mmol) in dichloromethane (200 mL) was added triethylamine (25 mL, 179.2 mmol). The mixture was stirred at room temperature for 1 hour, and then N,O-dimethylhydroxylamine (5 g, 53.7 mmol) was added. The reaction mixture was stirred for another 3 hours. LCMS showed the reaction was completed. The reaction mixture was directly washed with water (100 mL), and the organic layer was dried over sodium sulfate, filtered and concentrated. The residue was purified by silica gel chromatography (petroleum ether:ethyl acetate=1:1) to give tert-butyl 4-(5-(methoxy(methyl)carbamoyl)pyrimidin-2-yl)piperazine-1-carboxylate (11.2 g, 67%) as a white solid. MS (ES+) C16H25N5O4 requires: 351, found: 296 [M-56+H]+.
Reaction SMILES: [NH:1]1[CH2:5][CH2:4][CH2:3][CH2:2]1.C(N(CC)CC)C.[Cl:13][CH2:14][C:15](Cl)=[O:16]>ClCCl>[Cl:13][CH2:14][C:15]([N:1]1[CH2:5][CH2:4][CH2:3][CH2:2]1)=[O:16]
Reactant: C1CCNC1
Reactant: O=C(Cl)CCl
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: O=C(CCl)N1CCCC1
Temperature: 25 °C
Reaction time: 2 h
Yield: 94.8 %

Procedure:
To a solution of pyrrolidine (5 g, 0.07 mol) in dichloromethane (100 ml) at 0° C. was added triethylamine (11.8 ml, 0.084 mol) followed by dropwise addition of chloroacetyl chloride (6.2 ml 0.077 mol) in dichoromethane (20 ml), stirred for 2 hrs, left to warm to room temperature. The reaction was washed with water (2×100 ml), brine (1×100 ml), the organic layers were dried (MgSO4), filtered and evaporated to give the required product (9.8 g) which was used without purification.
Reaction SMILES: Br[C:2]1[C:3]([F:21])=[C:4]([F:20])[C:5]([NH:12][C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=2[F:19])=[C:6]([CH:11]=1)[C:7]([O:9][CH3:10])=[O:8].P.[CH3:23][O:24][C:25]1[CH:30]=[CH:29][C:28]([CH2:31][SH:32])=[CH:27][CH:26]=1>[Pd]>[F:20][C:4]1[C:5]([NH:12][C:13]2[CH:18]=[CH:17][CH:16]=[CH:15][C:14]=2[F:19])=[C:6]([CH:11]=[C:2]([S:32][CH2:31][C:28]2[CH:29]=[CH:30][C:25]([O:24][CH3:23])=[CH:26][CH:27]=2)[C:3]=1[F:21])[C:7]([O:9][CH3:10])=[O:8]
Reactant: COc1ccc(CS)cc1
Reactant: COC(=O)c1cc(Br)c(F)c(F)c1Nc1ccccc1F
Agent: [Pd]
Agent: P
Product: COC(=O)c1cc(SCc2ccc(OC)cc2)c(F)c(F)c1Nc1ccccc1F

Procedure:
To a solution of methyl 5-bromo-3,4-difluoro-2-((2-fluorophenyl)amino)benzoate in appropriate solvent is added base under nitrogen atmosphere, followed by Pd catalyst, phosphine ligand and (4-methoxyphenyl)methanethiol. The reaction is generally carried out at high temperature (80-130° C., prefer 90-110° C.) and normally complete within several hours (8-24 h, prefer 12-18 h). Methyl 3,4-difluoro-2-((2-fluorophenyl)amino)-5-((4-methoxybenzyl)thio)benzoate is obtained after conventional workup.
Reaction SMILES: Br[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][C:3]=1[CH2:8][C:9]([CH:11]1[CH2:16][CH2:15][N:14]([CH2:17][C:18]2[C:23]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[N:22][CH:21]=[CH:20][N:19]=2)[CH2:13][CH2:12]1)=[O:10].[OH-].[Na+].C(OCC)(=O)C.[CH3:37][N:38](C)C=O>[C-]#N.[Zn+2].[C-]#N.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:25]([O:24][C:23]1[C:18]([CH2:17][N:14]2[CH2:15][CH2:16][CH:11]([C:9](=[O:10])[CH2:8][C:3]3[CH:4]=[CH:5][CH:6]=[CH:7][C:2]=3[C:37]#[N:38])[CH2:12][CH2:13]2)=[N:19][CH:20]=[CH:21][N:22]=1)([CH3:28])([CH3:27])[CH3:26]
Reactant: CC(C)(C)Oc1nccnc1CN1CCC(C(=O)Cc2ccccc2Br)CC1
Reactant: CN(C)C=O
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: [C-]#N
Agent: [Na+]
Solvent: CCOC(C)=O
Product: CC(C)(C)Oc1nccnc1CN1CCC(C(=O)Cc2ccccc2C#N)CC1
Temperature: 100 °C
Reaction time: 8 h
Yield: 34 %

Procedure:
After dissolving 298 mg of 2-(2-bromophenyl)-1-[1-(3-tert-butoxy-2-pyrazinylmethyl)piperidin-4-yl]ethanone in 2 ml of N,N-dimethylformamide, 235 mg of zinc cyanide and 77 mg of tetrakis(triphenylphosphine)palladium(0) were added and the mixture was stirred overnight at 100° C. A 1N sodium hydroxide solution was added to the reaction mixture and extraction was performed with ethyl acetate. The organic layer was washed with saturated brine and dried over anhydrous magnesium sulfate, and then the solvent was distilled off under reduced pressure. The residue was purified by silica gel column chromatography (solvent: n-hexane/ethyl acetate) to obtain the title compound (90 mg, 34% yield).
Reaction SMILES: C(O)(C(F)(F)F)=O.[N:8]([CH2:11][C@H:12]1[O:16][C:15](=[O:17])[N:14]([C:18]2[CH:23]=[CH:22][C:21]([C:24]([O:26]C(C)(C)C)=[O:25])=[C:20]([F:31])[CH:19]=2)[CH2:13]1)=[N+:9]=[N-:10]>ClC(Cl)C>[N:8]([CH2:11][C@H:12]1[O:16][C:15](=[O:17])[N:14]([C:18]2[CH:23]=[CH:22][C:21]([C:24]([OH:26])=[O:25])=[C:20]([F:31])[CH:19]=2)[CH2:13]1)=[N+:9]=[N-:10]
Reactant: CC(C)(C)OC(=O)c1ccc(N2C[C@@H](CN=[N+]=[N-])OC2=O)cc1F
Solvent: O=C(O)C(F)(F)F
Solvent: CC(Cl)Cl
Product: [N-]=[N+]=NC[C@@H]1CN(c2ccc(C(=O)O)c(F)c2)C(=O)O1
Reaction time: 1 h
Yield: 99 %

Procedure:
60% TFA in dichloroethane (10 ml) was added to 5-(S)-azidomethyl-3-[4′-tert-butoxycarbonyl-3′-fluorophenyl]oxazolidine-2-one (2.00 g, 5.95 mmol; prepared as described for Example 2) and the solution kept at r.t. for 1 h. Solvent was removed under vacuum to afford 5-(S)-azidomethyl-3-[4′-carboxy-3′-fluorophenyl]oxazolidine-2-one (1.65 g, 5.89 mmol, 99%). This intermediate was dissolved in DMF (15 ml), and pentafluorophenyl trifluoroacetate (1.21 ml, 7.06 mmol) and pyridine (1.91 ml, 23.6 mmol) were added with stirring. The mixture was stirred at r.t. for 3 h, most of the solvent removed under vacuum, and the residue triturated with water. The resulting precipitate was filtered, washed with water, ether, and dried under vacuum. White crystals. Yield g (2.53 g, 93%). MS (m/z): [M+H]+=463.
Reaction SMILES: [CH3:1][N:2]1[CH2:6][CH2:5][CH:4]([C:7](=O)[C:8]2[CH:13]=[CH:12][CH:11]=[N:10][CH:9]=2)C1=O.[OH-].[K+].[BH4-].[K+]>Cl>[N:10]1[CH:9]=[C:8]([CH:7]2[CH2:4][CH2:5][CH2:6][N:2]2[CH3:1])[CH:13]=[CH:12][CH:11]=1
Reactant: CN1CCC(C(=O)c2cccnc2)C1=O
Agent: Cl
Agent: [BH4-]
Agent: [K+]
Product: CN1CCCC1c1cccnc1
Temperature: 100 °C
Reaction time: 2 h
Yield: 67.8 %

Procedure:
1-methyl-3-nicotinoyl-2-pyrrolidone (20.4 g, 0.1 mol) was dissolved in a 6N hydrochloric acid (150 mL) The solution was heated to 100° C. to react for 24 h and then cooled to room temperature. The pH of the solution was adjusted to 7 by using KOH under an ice bath, and then potassium borohydride (5.3 g, 0.1 mol) was added therein and the temperature was back to room temperature for 2 h. 200 mL Distilled water was added and the mixture was then stream-distilled. The distilled water phase was extracted with 300 mL petroleum ether, and the resultant petroleum ether was concentrated till dry to give a colorless oily product (11.0 g). HPLC purity 99.2%; 1H NMR (CDCl3, 300 MHz) δ: 8.52 (d, 1H), 8.48 (dd, 1H), 7.69 (dt, 1H), 7.25 (dd, 1H), 3.23 (t, 1H), 3.07 (t, 1H), 2.29 (m, 1H), 2.16 (s, 3H), 1.90-2.04 (m, 2H), 1.65-1.88 (m, 2H), ESI-MS 163.4 (M+H).