Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]2[C:10]([C:11]3[CH:16]=[CH:15][CH:14]=[C:13]([F:17])[N:12]=3)=[N:9][N:8]([CH:18]3[CH2:23][CH2:22][CH2:21][CH2:20][O:19]3)[C:5]2=[CH:6][N:7]=1.[N:24]1[CH:29]=[CH:28][CH:27]=[C:26](B2OC(C)(C)C(C)(C)O2)[CH:25]=1.C(=O)([O-])[O-].[Cs+].[Cs+]>O.C(#N)C.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.C1C=CC(P(C2C=CC=CC=2)[C-]2C=CC=C2)=CC=1.Cl[Pd]Cl.[Fe+2]>[F:17][C:13]1[N:12]=[C:11]([C:10]2[C:4]3[C:5](=[CH:6][N:7]=[C:2]([C:26]4[CH:25]=[N:24][CH:29]=[CH:28][CH:27]=4)[CH:3]=3)[N:8]([CH:18]3[CH2:23][CH2:22][CH2:21][CH2:20][O:19]3)[N:9]=2)[CH:16]=[CH:15][CH:14]=1
Reactant: CC1(C)OB(c2cccnc2)OC1(C)C
Reactant: Fc1cccc(-c2nn(C3CCCCO3)c3cnc(Br)cc23)n1
Agent: Cl[Pd]Cl
Agent: [Fe+2]
Agent: O=C([O-])[O-]
Solvent: CC#N
Solvent: O
Product: Fc1cccc(-c2nn(C3CCCCO3)c3cnc(-c4cccnc4)cc23)n1
Temperature: 95 °C

Procedure:
A mixture of 1.356 g (3.60 mmol) of 5-bromo-3-(6-fluoropyridin-2-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-c]pyridine, 3.445 g, (16.80 mmol) of 3-pyridineboronic acid pinacol ester and 0.457 g (0.560 mmol) of 1,1′bis(diphenylphosphino)ferrocenepalladium (II) chloride and 7.2 ml of 1.0 M of Cesium Carbonate in water in 60 ml of Acetonitrile was degassed an heated in a sealed glass vial at 95° C. for 2 hours. The mixture was filtered through Celite and the filtrate concentrated in vacuum. The residue was redissolved in dichloromethane, the organic layer washed with water, brine, dried over MgSO4 and concentrated. The crude residue was purified on a 80 g silica gel column eluting with 3-4% of methanol in dichloromethane. Pooled fractions were concentrated. The residue was triturated with 7 ml of cold methanol and filtered to give 3-(6-Fluoropyridin-2-yl)-5-(pyridin-3-yl)-1-(tetrahydro-2H-pyran-2-yl)-1H-pyrazolo[3,4-c]pyridine. Yield 1.147 g (85%). ESI MS m/z=376.1 (M+1)
Reaction SMILES: [Br:1][C:2]1[CH:7]=[CH:6][C:5](Br)=[CH:4][CH:3]=1.[CH3:9][PH:10](=[O:12])[CH3:11].CC#N>[Pd].C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.C(N(CC)CC)C>[Br:1][C:2]1[CH:7]=[CH:6][C:5]([P:10](=[O:12])([CH3:11])[CH3:9])=[CH:4][CH:3]=1
Reactant: Brc1ccc(Br)cc1
Reactant: C[PH](C)=O
Agent: [Pd]
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: CC#N
Solvent: CCN(CC)CC
Product: CP(C)(=O)c1ccc(Br)cc1
Yield: 25.7 %

Procedure:
A solution of 1,4-dibromobenzene (2.35 g, 10 mmol), dimethylphosphine oxide (0.78 g, 10 mmol), and tetrakis(triphenylphosphine) palladium (0) (0.5 g) in nitrogen-purged CH3CN (20 mL) and triethylamine (5 mL) was heated at reflux for overnight. Then, the reaction mixture was concentrated and the residue was chromatographed on silica gel (0˜20 percent MeOH/DCM) to afford the product (600 mg, 26%) as a colorless solid; 1H NMR (CD3OD): δ 7.80-7.70 (m, 4H), 1.75 (d, 6H).
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([CH3:8])[C:3]=1[NH:9][C:10]([CH2:12][N:13]1[CH2:18][CH2:17][C:16](=O)[CH2:15][CH2:14]1)=[O:11].[Cl-].[O:21]1[C:26]2[CH:27]=[CH:28][CH:29]=[CH:30][C:25]=2[O:24][CH2:23][CH:22]1[CH:31]([OH:34])[CH2:32][NH2:33].N1CCCCC1.C([BH3-])#N.[Na+]>>[O:21]1[C:26]2[CH:27]=[CH:28][CH:29]=[CH:30][C:25]=2[O:24][CH2:23][CH:22]1[CH:31]([OH:34])[CH2:32][NH:33][CH:16]1[CH2:17][CH2:18][N:13]([CH2:12][C:10]([NH:9][C:3]2[C:2]([CH3:1])=[CH:7][CH:6]=[CH:5][C:4]=2[CH3:8])=[O:11])[CH2:14][CH2:15]1
Reactant: Cc1cccc(C)c1NC(=O)CN1CCC(=O)CC1
Reactant: NCC(O)C1COc2ccccc2O1
Agent: [BH3-]C#N
Agent: [Cl-]
Agent: [Na+]
Solvent: C1CCNCC1
Product: Cc1cccc(C)c1NC(=O)CN1CCC(NCC(O)C2COc3ccccc3O2)CC1

Procedure:
Substituting into the procedure of Example 1, 1-[(2,6-dimethylphenyl)aminocarbonylmethyl]-4-piperidone for the corresponding chloride and [2-(1,4-benzodioxan-2-yl)-2-hydroxyethyl]amine or amine hydrochloride, rather than the corresponding piperidine and adding 75 g of sodium cyanoborohydride, one obtains 4-{[2-(1,4-benzodioxan-2-yl)-2-hydroxyethyl]amino}-1-[(2,6-dimethylphenyl)aminocarbonylmethyl]piperidine compound.
Reaction SMILES: [Br-].[CH2:2]([C:5]1[CH:30]=[CH:29][C:8]([CH2:9][P+](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=[CH:7][CH:6]=1)[CH2:3][CH3:4].CC(C)([O-])C.[K+].[CH:37]([CH:39]1[CH2:44][CH2:43][C:42](=[O:45])[CH2:41][CH2:40]1)=O.O>C1COCC1>[CH2:2]([C:5]1[CH:30]=[CH:29][C:8]([CH:9]=[CH:37][CH:39]2[CH2:44][CH2:43][C:42](=[O:45])[CH2:41][CH2:40]2)=[CH:7][CH:6]=1)[CH2:3][CH3:4]
Reactant: O=CC1CCC(=O)CC1
Reactant: CCCc1ccc(C[P+](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: CC(C)(C)[O-]
Agent: [Br-]
Agent: [K+]
Solvent: O
Solvent: C1CCOC1
Product: CCCc1ccc(C=CC2CCC(=O)CC2)cc1
Temperature: 25 °C
Reaction time: 1 h
Yield: 72.3 %

Procedure:
Suspension of 114 g of 4-n-propylbenzyltriphenyl phosphonium bromide in 500 ml of THF was stirred under nitrogen gas stream and 32.3 g of potassium-t-butoxide was added thereto at room temperature. After stirred at room temperature for 1 hour, a solution of 31.2 g of 4-formylcyclohexanone in 200 ml of THF was added dropwise to the suspension. After stirred at room temperature for 2 hours, 1 l of water was added thereto and then it was extracted with 1 l of ethyl acetate. Organic layer was washed with water and dried over anhydrous magnesium sulfate, the solvent was distilled off under a reduced pressure, and then 500 ml of heptane was added thereto. Precipitate thus separated was filtered off and purified by a column chromatography over a silica gel by using ethyl acetate/heptane (1/5) as an eluent, and the solvent was distilled off under a reduced pressure to obtain 42 g of 4-(2-(4-n-propylphenyl)ethenyl)cyclohexanone.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:47]=[CH:46][CH:45]=[CH:44][C:4]=1[CH2:5][O:6][CH2:7][CH2:8][CH2:9][O:10][C:11]1[CH:16]=[CH:15][C:14]([CH:17]2[CH2:22][CH2:21][N:20]([C:23]([O:25][C:26]([CH3:29])([CH3:28])[CH3:27])=[O:24])[CH2:19][CH:18]2[O:30][CH2:31][CH2:32]OS(C2C=CC(C)=CC=2)(=O)=O)=[CH:13][CH:12]=1.[NH:48]1[C:56]2[C:51](=[CH:52][CH:53]=[CH:54][CH:55]=2)[C:50]([CH2:57][CH2:58][NH:59][C:60](=[O:62])[CH3:61])=[CH:49]1.[H-].[Na+].C(=O)(O)[O-].[Na+]>CN(C)C=O>[C:60]([NH:59][CH2:58][CH2:57][C:50]1[C:51]2[C:56](=[CH:55][CH:54]=[CH:53][CH:52]=2)[N:48]([CH2:32][CH2:31][O:30][CH:18]2[CH:17]([C:14]3[CH:13]=[CH:12][C:11]([O:10][CH2:9][CH2:8][CH2:7][O:6][CH2:5][C:4]4[CH:44]=[CH:45][CH:46]=[CH:47][C:3]=4[O:2][CH3:1])=[CH:16][CH:15]=3)[CH2:22][CH2:21][N:20]([C:23]([O:25][C:26]([CH3:27])([CH3:29])[CH3:28])=[O:24])[CH2:19]2)[CH:49]=1)(=[O:62])[CH3:61]
Reactant: COc1ccccc1COCCCOc1ccc(C2CCN(C(=O)OC(C)(C)C)CC2OCCOS(=O)(=O)c2ccc(C)cc2)cc1
Reactant: CC(=O)NCCc1c[nH]c2ccccc12
Agent: O=C([O-])O
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: COc1ccccc1COCCCOc1ccc(C2CCN(C(=O)OC(C)(C)C)CC2OCCn2cc(CCNC(C)=O)c3ccccc32)cc1
Temperature: 25 °C
Reaction time: 20 h

Procedure:
A suspension of 0.20 g of tert-butyl 4-{4-[3-(2-methoxybenzyloxy)propoxy]phenyl}-3-[2-(toluene-4-sulphonyloxy)ethoxy]piperidine-1-carboxylate (Example 14b) and 0.067 g of N-[2-(1H-indol-3-yl)ethyl]acetamide in 7 ml of N,N-dimethylformamide is admixed at 0° C. with 0.024 g of sodium hydride dispersion (60%) and stirred at room temperature over 20 hours. The reaction mixture is poured onto saturated aqueous sodium bicarbonate solution and extracted with ethyl acetate (2×). The combined organic phases are washed with brine, dried over sodium sulphate and concentrated by evaporation. The title compound is obtained as a yellow oil from the residue by means of flash chromatography (SiO2 60F). Rf=0.35 (EtOAc); Rt=5.69.
Reaction SMILES: [Na].C[CH:3]([CH3:9])[CH:4]([CH:7]=O)[C:5]#[N:6].Cl.[NH2:11][C:12]1[S:13][CH:14]=[CH:15]C=1>CO>[S:13]1[C:12]2=[N:11][CH:7]=[C:4]([C:5]#[N:6])[CH:3]=[C:9]2[CH:15]=[CH:14]1
Reactant: CC(C)C(C#N)C=O
Reactant: Nc1cccs1
Agent: Cl
Agent: [Na]
Solvent: CO
Product: N#Cc1cnc2sccc2c1
Temperature: 80 °C
Yield: 24 %

Procedure:
3,3-Dimethyl-2-formyl propionitrile sodium (3.33 g, 20.2 mmol) can readily be prepared from the method described by Bertz, S. H., et al., J. Org. Chem., 47, 2216-2217 (1982). 3,3-Dimethyl-2-formyl propionitrile sodium is dissolved in MeOH (40 mL), and concentrated HCl (4 mL) and the hexachlorostannate salt of 2-aminothiophene (10.04 g, 19.1 mmol) in MeOH (130 mL) is slowly added drop-wise to the mixture. Following addition, the mixture is heated to reflux in an oil bath (80° C.) for 4 h, and then MeOH (10 mL) and concentrated HCl (10 mL) are added. The reaction continued refluxing for another 20 h. The solution is cooled to rt, and the reaction is concentrated in vacuo. The purple residue is dissolved in H2O (60 mL), and the slurry is filtered. The cake is pulverized and stirred vigorously with 5% MeOH/CHCl3 (105 mL) while heating to 55° C. The mixture is cooled and filtered, and the organic layer is concentrated to a green oil. The crude material is chromatographed over 130 g slurry-packed silica, eluting with 30% EtOAc/hexane to afford thieno[2,3-b]pyridine-5-carbonitrile (C105) as a pale yellow solid (24% yield). HRMS (FAB) calculated for C8H4N2S+H: 161.0173, found 161.0173 (M+H).
Reaction SMILES: [CH3:1][O:2][C:3]([C:5]1[N:6]=[CH:7][C:8]2[C:13]([C:14]=1[OH:15])=[CH:12][CH:11]=[C:10]([C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1)[CH:9]=2)=[O:4].CC1C=C(C)[N:26]=[C:25](C)C=1.CC1C([IH+])=C(C)N=C(C)C=1.F[P-](F)(F)(F)(F)F.C([Cu])#N.Cl>C(Cl)Cl.O.CN(C=O)C>[CH3:1][O:2][C:3]([C:5]1[N:6]=[C:7]([C:25]#[N:26])[C:8]2[C:13]([C:14]=1[OH:15])=[CH:12][CH:11]=[C:10]([C:16]1[CH:21]=[CH:20][CH:19]=[CH:18][CH:17]=1)[CH:9]=2)=[O:4]
Reactant: COC(=O)c1ncc2cc(-c3ccccc3)ccc2c1O
Reactant: Cc1cc(C)nc(C)c1
Agent: N#C[Cu]
Agent: Cc1cc(C)c([IH+])c(C)n1
Agent: Cl
Solvent: ClCCl
Solvent: O
Solvent: CN(C)C=O
Product: COC(=O)c1nc(C#N)c2cc(-c3ccccc3)ccc2c1O
Temperature: 25 °C
Reaction time: 16 h
Yield: 50.1 %

Procedure:
A mixture of 4-hydroxy-7-phenyl-isoquinoline-3-carboxylic acid methyl ester (170 mg, 0.61 mmol) and bis(2,4,6-trimethylpyridine)iodine(I) hexafluorophosphate (783 mg, 1.52 mmol) in CH2Cl2 (10 mL) was stirred at r.t. for 16 h, then diluted with CH2Cl2 (50 mL). The resulting mixture was washed with 5% sodium thiosulfate and 1 M HCl. The organic layer was dried over MgSO4 and concentrated. To the residue were added CuCN (102 mg, 1.14 mmol) and anhydrous DMF (6 mL), and the resulting mixture was refluxed for 20 min. After cooling to r.t., the reaction mixture was poured into a mixture of CH2Cl2 (100 mL) and water (100 mL). 4 M HCl was added with vigorous stirring until no solid was observed. The aqueous layer was extracted with additional CH2Cl2, and the organic layers were combined, dried over MgSO4 and concentrated. The crude product was purified by column chromatography (20-100% CH2Cl2/hexanes) to give 93 mg of the title compound as a light brown solid. MS: (+) m/z 305.06 (M+1).
Reaction SMILES: [CH2:1]([O:8][CH2:9][CH2:10][CH2:11][C:12]1[CH:13]=[N+:14]([O-])[CH:15]=[CH:16][CH:17]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.P(Br)(Br)(Br)=O.C(=O)(O)[O-].[Na+].BrC1C=CC(CCCOCC2C=CC=CC=2)=CN=1.BrC1C(CCCOCC2C=CC=CC=2)=CC=CN=1.C(N1CCN(C2C3C(=CC=CC=3)C=C(Br)N=2)CC1)C>C(Cl)Cl.O>[CH2:1]([O:8][CH2:9][CH2:10][CH2:11][C:12]1[CH:13]=[N:14][CH:15]=[CH:16][CH:17]=1)[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: [O-][n+]1cccc(CCCOCc2ccccc2)c1
Agent: Brc1ccc(CCCOCc2ccccc2)cn1
Agent: Brc1ncccc1CCCOCc1ccccc1
Agent: CCN1CCN(c2nc(Br)cc3ccccc23)CC1
Solvent: ClCCl
Solvent: O
Product: c1ccc(COCCCc2cccnc2)cc1
Reaction time: 2 h
Yield: 7.7 %

Procedure:
3-(3-Benzyloxypropyl)pyridine N-oxide (4.546 g) was dissolved in methylene chloride, phosphorus oxybromide (11.47 g) was added thereto under ice-cooling, and the mixture was stirred for 2 hr. Then, it was further stirred at room temperature for 2 hr. The reaction mixture was poured into warm water, and then it was neutralized by adding sodium bicarbonate thereto. The mixture was extracted with ethyl acetate. The resulting organic layer was washed with water, dried (over MgSO4) and evaporated. The resulting residue was purified by silica gel column chromatography (ethyl acetate/hexane system), to give a mixture of 2-bromo-5-(3-benzyloxypropyl)pyridine and 2-bromo-3-(3-benzyloxypropyl)pyridine (1:1) as a brown oil (2.203 g). The resulting mixture (1.111 g) and 1-(1-ethylpiperazin-4-yl)-3-bromoisoquinoline (662 mg) were treated in the same manner as in Example 167-2, to give the title compound as a yellow oil (326 mg, yield; 33%).
Reaction SMILES: [H-].[Na+].[CH3:3][C:4]1[CH:10]=[CH:9][CH:8]=[C:7]([CH3:11])[C:5]=1[NH2:6].[CH3:12][O:13][C:14]([C:16]1[CH:22]=[CH:21][C:19](=O)[O:18][CH:17]=1)=[O:15].[Cl-].[NH4+]>O1CCCC1>[CH3:3][C:4]1[CH:10]=[CH:9][CH:8]=[C:7]([CH3:11])[C:5]=1[N:6]1[C:19](=[O:18])[CH:21]=[CH:22][C:16]([C:14]([O:13][CH3:12])=[O:15])=[CH:17]1
Reactant: Cc1cccc(C)c1N
Reactant: COC(=O)c1ccc(=O)oc1
Agent: [Cl-]
Agent: [H-]
Agent: [NH4+]
Solvent: C1CCOC1
Product: COC(=O)c1ccc(=O)n(-c2c(C)cccc2C)c1
Temperature: 60 °C
Reaction time: 4 h
Yield: 33.5 %

Procedure:
To a suspended solution of sodium hydride (60% in oil, 14.5 g) in tetrahydrofuran (240 mL) were added 2,6-dimethylaniline (29.3 g) and methyl coumalate (18.6 g) and the mixture was stirred at 60° C. for 4 hours. To the reaction mixture was added an aqueous solution of ammonium chloride and the mixture was extracted with ethyl acetate. The obtained organic layer was dried and concentrated. The obtained residue was purified by column chromatography on silica gel (hexane:ethyl acetate=3:2) to give the title compound (10.4 g) having the following physical data.
Reaction SMILES: [C:1]([C:4]1[CH:15]=[CH:14][C:7]([O:8][CH2:9][CH2:10][CH2:11][CH2:12]Br)=[C:6]([CH2:16][CH2:17][CH3:18])[C:5]=1[OH:19])(=[O:3])[CH3:2].[C-:20]#[N:21].[Na+]>CN(C)C=O>[C:1]([C:4]1[CH:15]=[CH:14][C:7]([O:8][CH2:9][CH2:10][CH2:11][CH2:12][C:20]#[N:21])=[C:6]([CH2:16][CH2:17][CH3:18])[C:5]=1[OH:19])(=[O:3])[CH3:2]
Reactant: [C-]#N
Reactant: CCCc1c(OCCCCBr)ccc(C(C)=O)c1O
Agent: [Na+]
Solvent: CN(C)C=O
Product: CCCc1c(OCCCCC#N)ccc(C(C)=O)c1O
Temperature: 25 °C

Procedure:
A solution of 30.0 g. (91.1 mmoles) of 4-(4-acetyl-3-hydroxy-2-propylphenoxy)butyl bromide and 4.91 g. (100.2 mmoles) of sodium cyanide in 225 ml. of dimethylformamide was heated to 75°-85° C. for about 17 hours. The reaction mixture was cooled to room temperature, filtered, and evaporated in vacuo at 75° C. Cold 0.1N hydrochloric acid was added to the residue, and the residue was extracted into ethyl acetate. The ethyl acetate layer was twice washed with 0.1N hydrochloric acid, dried over sodium sulfate, and evaporated in vacuo to yield 21.02 g. of 5-(4-acetyl-3-hydroxy-2-propylphenoxy)pentane nitrile as a dark amber oil which crystallized as it cooled.
Reaction SMILES: C(OC([NH:8][CH2:9][C:10]#[C:11][C:12]1[C:17]([C@H:18]2[CH2:22][CH2:21][CH2:20][N:19]2[C:23]2[CH:28]=[CH:27][N:26]3[N:29]=[CH:30][C:31]([C:32]([O:34][CH2:35][CH3:36])=[O:33])=[C:25]3[N:24]=2)=[CH:16][C:15]([F:37])=[CH:14][N:13]=1)=O)(C)(C)C>CO.O[Pd]O>[NH2:8][CH2:9][CH2:10][CH2:11][C:12]1[C:17]([C@H:18]2[CH2:22][CH2:21][CH2:20][N:19]2[C:23]2[CH:28]=[CH:27][N:26]3[N:29]=[CH:30][C:31]([C:32]([O:34][CH2:35][CH3:36])=[O:33])=[C:25]3[N:24]=2)=[CH:16][C:15]([F:37])=[CH:14][N:13]=1
Reactant: CCOC(=O)c1cnn2ccc(N3CCC[C@@H]3c3cc(F)cnc3C#CCNC(=O)OC(C)(C)C)nc12
Agent: O[Pd]O
Solvent: CO
Product: CCOC(=O)c1cnn2ccc(N3CCC[C@@H]3c3cc(F)cnc3CCCN)nc12
Reaction time: 6 h
Yield: 107.8 %

Procedure:
To (R)-ethyl 5-(2-(2-(3-(tert-butoxycarbonylamino)prop-1-ynyl)-5-fluoropyridin-3-yl)pyrrolidin-1-yl)pyrazolo[1,5-a]pyrimidine-3-carboxylate (160 mg, 0.315 mmol) in MeOH (10 mL) was added dihydroxypalladium (101 mg, 0.144 mmol). The reaction mixture was stirred under a hydrogen balloon for 6 hours, then filtered through a pad of Celite® and washed with MeOH (30 mL). The filtrate was concentrated and the resultant residue was treated with 4 M HCl in dioxane (3 mL). After stirring for 30 minutes, the solution was concentrated to afford the product as an HCl salt (140 mg, 108% yield). MS (apci) m/z=413.0 (M+H).
Reaction SMILES: [CH:1]1[C:6]([C@@H:7](O)[C@H:8]([NH:11]C(C(Cl)Cl)=O)[CH2:9][OH:10])=[CH:5][CH:4]=[C:3]([N+]([O-])=O)[CH:2]=1.CC(S[C@@H]1[O:30][C@H](CO)[C@H](O)[C@H](O)[C@H]1O)C>>[NH2:11][C@H:8]([C:9]([OH:10])=[O:30])[CH2:7][C:6]1[CH:1]=[CH:2][CH:3]=[CH:4][CH:5]=1
Reactant: O=C(N[C@H](CO)[C@H](O)c1ccc([N+](=O)[O-])cc1)C(Cl)Cl
Reactant: CC(C)S[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
Product: N[C@@H](Cc1ccccc1)C(=O)O
Reaction time: 12 h

Procedure:
Both PAL and TAL activities were also investigated according to whole cell assays. Seed cultures consisting of 5 ml of LB broth containing 34 mg/L chloramphenicol were prepared of E. coli BL21(DE3) strains that were individually transformed with each of pSpalAv, pSpalNp, pSencPSm, pSpal1At, and pSpal2At. These cultures were grown for 12 hours at 30° C. while agitating at 250 rpm. 1 mL of each culture was then used to inoculate 3×250 mL cultures flasks containing 50 mL of LB supplemented with 34 mg/L chloramphenicol. All cultures were then grown at 30° C. while agitating at 250 rpm until an OD600 of 0.6 was reached, at which point the cultures were induced by IPTG addition to a final concentration of 0.2 mM. Cultures were then grown for an additional 6 h before the cells were then collected by centrifugation in 50 ml Falcon tubes for 5 min at 1400×g and washed once with pH7 PBS (phosphate buffered saline) buffer. The entire cell pellet was then resuspended in 10 ml pH7 PBS buffer before the appropriate substrate, L-phenylalanine or L-tyrosine, was added at a final concentration of 1 g/L. The results for L-phenylalanine addition are shown in FIG. 2. For all strains tested the addition of L-tyrosine did not result in the formation of p-coumaric acid, indicating that no TAL activity was displayed by these recombinant strains.
Reaction SMILES: [C:1]([O:4][CH2:5][C:6]([CH2:18][CH2:19][C:20]1([CH2:26][CH2:27][N:28]2[CH2:33][CH2:32][CH:31]([NH:34][C:35]3[CH:40]=[CH:39][C:38]([CH3:41])=[CH:37][CH:36]=3)[CH2:30][CH2:29]2)[CH2:25][CH2:24][CH2:23][CH2:22][CH2:21]1)([CH2:12][CH2:13][O:14][C:15](=[O:17])[CH3:16])[CH2:7][O:8][C:9](=[O:11])[CH3:10])(=[O:3])[CH3:2].C(N(CC)CC)C.[O:49]1[CH:53]=[CH:52][CH:51]=[C:50]1[C:54](Cl)=[O:55].C(O)(=O)CC(CC(O)=O)(C(O)=O)O>ClCCl>[C:1]([O:4][CH2:5][C:6]([CH2:18][CH2:19][C:20]1([CH2:26][CH2:27][N:28]2[CH2:33][CH2:32][CH:31]([N:34]([C:35]3[CH:40]=[CH:39][C:38]([CH3:41])=[CH:37][CH:36]=3)[C:54]([C:50]3[O:49][CH:53]=[CH:52][CH:51]=3)=[O:55])[CH2:30][CH2:29]2)[CH2:25][CH2:24][CH2:23][CH2:22][CH2:21]1)([CH2:12][CH2:13][O:14][C:15](=[O:17])[CH3:16])[CH2:7][O:8][C:9](=[O:11])[CH3:10])(=[O:3])[CH3:2]
Reactant: O=C(Cl)c1ccco1
Reactant: CC(=O)OCCC(CCC1(CCN2CCC(Nc3ccc(C)cc3)CC2)CCCCC1)(COC(C)=O)COC(C)=O
Agent: O=C(O)CC(O)(CC(=O)O)C(=O)O
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(=O)OCCC(CCC1(CCN2CCC(N(C(=O)c3ccco3)c3ccc(C)cc3)CC2)CCCCC1)(COC(C)=O)COC(C)=O
Reaction time: 17 h

Procedure:
To a solution of 2-(acetoxymethyl)-2-[2-[1-[2-[4-(p-toluidino)piperidin-1-yl]ethyl]cyclohexyl]ethyl]-1,4-diacetoxybutane (synthesized in Example 13) (324 mg) dissolved in dichloromethane (4 mL) was added triethylamine (0.16 mL). 2-Furoyl chloride (0.084 mL) was added to the solution under ice cooling, and the temperature was then allowed to rise to room temperature. The solution was stirred for 17 hours. A 10% aqueous citric acid solution was added to the solution and the solution was extracted with chloroform. The organic layer was dried over anhydrous magnesium sulfate, filtered and concentrated under reduced pressure. The residue was purified by chromatography [NH silica gel, hexane-ethyl acetate (1:1)] to give the title compound (356 mg).
Reaction SMILES: [C:1]1([C:7]([F:10])([F:9])[F:8])[CH:6]=[CH:5][CH:4]=[CH:3][CH:2]=1.O=O>>[F:8][C:7]([CH:1]1[CH:2]=[CH:3][CH:4]=[CH:5][CH2:6]1)([F:10])[F:9]
Reactant: FC(F)(F)c1ccccc1
Agent: O=O
Product: FC(F)(F)C1C=CC=CC1
Reaction time: 2 h

Procedure:
8 liters of YEM in a fermenter were inoculated with a 20 h shake culture of P. putida NCIB 12190 (stock slant derived from a shake culture grown on benzene) grown on the same medium (50 ml). The organism was grown at 500 rpm; 500 ml air/min for 20 h, with a continuous feed of concentrated nutrient (disodium succinate (320 g) and (NH4)2SO4 (64 g) in 1 liter of 0.025M potassium phosphate buffer pH 7.2) at 40 ml/h, reach a dry cell weight of 2.8 g/l. The aeration was then increased (550 rpm; 750 ml air/min) for 1 hr giving an oxygen tension of 20-30% air-saturated. Benzotrifluoride was then added at 50 μl/min via an HPLC pump. Using these settings no product was found in the reaction mixture by GLC. It was thus concluded that the combination of low substrate solubility and high aeration was stripping substrate into the exhaust gas before a high enough concentration could be reached for the reaction to occur. To reduce this effect while still maintaining an adequate oxygen tension (>30%) the stirrer speed was raised to 650 rpm while aeration was reduced to 300 ml/min. 5 g of substrate was added batchwise while still maintaining a flow of 50 μl/min. Product formation commenced immediately as judged by GLC and reached-0.3 g/l after 60 min. Further additions of substrate (5 ml) were made at approximately 2 h intervals while maintaining the continuous addition (50 μl/min). The product concentration reached 1.25 g/l after approximately 6 h at which point the run was terminated. The product was adsorbed onto charcoal followed by stripping in a Soxhlet apparatus (Et2O:MeOH 3:1). Evaporation of the solvent yielded about 60 ml of aqueous solution of trifluoromethylcyclohexa-3,5-diene which crystallised upon addition of a trace of NaCl. Recrystallisation from Et2O:petrol 1:4 yielded approximately 12 g (=1.5 g/l) of pure trifluoromethylcyclohexa-3,5-diene.
Reaction SMILES: FC(F)(F)S(O[C:7]1[CH:8]=[C:9]2[C:14](=[CH:15][CH:16]=1)[CH:13]([C:17]([O:19][CH2:20][CH3:21])=[O:18])[N:12]([C:22]([O:24][C:25]([CH3:28])([CH3:27])[CH3:26])=[O:23])[CH2:11][CH2:10]2)(=O)=O.[CH3:31][N:32](C=O)C>C(OCC)(=O)C.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-]#N.[Zn+2].[C-]#N>[C:31]([C:7]1[CH:8]=[C:9]2[C:14](=[CH:15][CH:16]=1)[CH:13]([C:17]([O:19][CH2:20][CH3:21])=[O:18])[N:12]([C:22]([O:24][C:25]([CH3:27])([CH3:26])[CH3:28])=[O:23])[CH2:11][CH2:10]2)#[N:32]
Reactant: CN(C)C=O
Reactant: CCOC(=O)C1c2ccc(OS(=O)(=O)C(F)(F)F)cc2CCN1C(=O)OC(C)(C)C
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: [C-]#N
Agent: [Zn+2]
Solvent: CCOC(C)=O
Product: CCOC(=O)C1c2ccc(C#N)cc2CCN1C(=O)OC(C)(C)C
Temperature: 100 °C
Reaction time: 8 h
Yield: 91 %

Procedure:
A mixture of 1-ethyl 2-tert-butyl 6-(((trifluoromethyl)sulfonyl)oxy)-3,4-dihydroisoquinoline-1,2(1H)-dicarboxylate (7.44 g, 16.41 mmol), Pd(PPh3)4 (0.948 g, 0.82 mmol), zinc cyanide (2.119 g, 18.05 mmol) and DMF (100 mL) was stirred overnight at 100° C. The reaction mixture was diluted with ethyl acetate, and filtered. The filtrate was washed with water and brine, and dried over magnesium sulfate, and the solvent was evaporated under reduced pressure. The obtained residue was purified by silica gel column chromatography (solvent gradient; 3→60% ethyl acetate/hexane) to give 1-ethyl 2-tert-butyl 6-cyano-3,4-dihydroisoquinoline-1,2(1H)-dicarboxylate (4.92 g, 14.89 mmol, 91%) as a colorless oil.