Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: Cl[C:2]1[CH:7]=[CH:6][C:5]([Cl:8])=[CH:4][N:3]=1.[OH:9][C:10]1[CH:11]=[C:12]([CH:18]=[CH:19][CH:20]=1)[C:13]([O:15]CC)=[O:14]>>[Cl:8][C:5]1[CH:6]=[CH:7][C:2]([O:9][C:10]2[CH:11]=[C:12]([CH:18]=[CH:19][CH:20]=2)[C:13]([OH:15])=[O:14])=[N:3][CH:4]=1
Reactant: CCOC(=O)c1cccc(O)c1
Reactant: Clc1ccc(Cl)nc1
Product: O=C(O)c1cccc(Oc2ccc(Cl)cn2)c1

Procedure:
Prepared from 2,5-dichloropyridine and ethyl 3-hydroxybenzoate. 1H NMR (400 MHz, DMSO-d5) δ 13.17 (br. s., 1H), 8.22 (d, 1H), 8.00 (dd, 1H), 7.81 (dd, 1H), 7.60-7.64 (m, 1H), 7.58 (t, 1H), 7.43 (dd, 1H), 7.18 (d, 1H).
Reaction SMILES: C([O:3][C:4](=[O:38])[C@@H:5]([NH:15][C:16]([C:18]1[CH:37]=[CH:36][C:21]2[N:22]([CH:30]3[CH2:35][CH2:34][CH2:33][CH2:32][CH2:31]3)[C:23]([C:25]3[CH:29]=[CH:28][O:27][CH:26]=3)=[N:24][C:20]=2[CH:19]=1)=[O:17])[CH2:6][C:7]1[CH:12]=[CH:11][C:10]([C:13]#[N:14])=[CH:9][CH:8]=1)C.C(=O)([O-])[O-:40].[K+].[K+]>CC(C)=O.O>[C:13]([C:10]1[CH:11]=[CH:12][C:7]([CH2:6][C@H:5]([NH:15][C:16]([C:18]2[CH:37]=[CH:36][C:21]3[N:22]([CH:30]4[CH2:35][CH2:34][CH2:33][CH2:32][CH2:31]4)[C:23]([C:25]4[CH:29]=[CH:28][O:27][CH:26]=4)=[N:24][C:20]=3[CH:19]=2)=[O:17])[C:4]([OH:3])=[O:38])=[CH:8][CH:9]=1)(=[O:40])[NH2:14]
Reactant: CCOC(=O)[C@H](Cc1ccc(C#N)cc1)NC(=O)c1ccc2c(c1)nc(-c1ccoc1)n2C1CCCCC1
Reactant: O=C([O-])[O-]
Agent: [K+]
Solvent: O
Solvent: CC(C)=O
Product: NC(=O)c1ccc(C[C@H](NC(=O)c2ccc3c(c2)nc(-c2ccoc2)n3C2CCCCC2)C(=O)O)cc1

Procedure:
(S)-3-(4-Cyanophenyl)-2-{[1-(1-cyclohexyl-2-furan-3-yl-1H-benzoimidazol-5-yl)-methanoyl]-amino}-propionic acid ethyl ester from example 10 (0.120 g, 0.235 mmol) was dissolved in a mixture of acetone (5 mL) and water (3 mL). Urea-hydrogen peroxide complex (1.0 mmol, 0.094 g) and potassium carbonate (10 mg) were added and the mixture stirred until completion (HPLC). The reaction mixture was concentrated under reduced pressure, the residue was dissolved in DMSO (1.5 mL) and 5 N NaOH (0.2 mL) was added. After stirring for 30 min at room temperature, TFA (0.5 mL) was added and the product isolated by prep HPLC (18 mg).
Reaction SMILES: [ClH:1].O1CCOCC1.[N:8]1[CH:13]=[CH:12][CH:11]=[C:10]([CH2:14][CH2:15][CH:16]2[CH2:21][N:20](C(OC(C)(C)C)=O)[CH2:19][CH2:18][N:17]2[C:29]([O:31][CH2:32][C:33]2[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=2)=[O:30])[CH:9]=1>CO>[ClH:1].[ClH:1].[N:8]1[CH:13]=[CH:12][CH:11]=[C:10]([CH2:14][CH2:15][CH:16]2[CH2:21][NH:20][CH2:19][CH2:18][N:17]2[C:29]([O:31][CH2:32][C:33]2[CH:38]=[CH:37][CH:36]=[CH:35][CH:34]=2)=[O:30])[CH:9]=1
Reactant: CC(C)(C)OC(=O)N1CCN(C(=O)OCc2ccccc2)C(CCc2cccnc2)C1
Agent: Cl
Solvent: C1COCCO1
Solvent: CO
Product: O=C(OCc1ccccc1)N1CCNCC1CCc1cccnc1
Reaction time: 1 h
Yield: 58 %

Procedure:
4 M HCl in 1,4-dioxane (6 mL, 24 mmol) was added to a solution of 1-benzyl 4-tert-butyl 2-(2-(pyridin-3-yl)ethyl)piperazine-1,4-dicarboxylate (130.2 mg, 0.306 mmol) in MeOH (1 mL). After 1 h, the reaction mixture was concentrated under reduced pressure and purified by HPLC (5 to 50% MeCN/0.1% TFA in H2O/0.1% TFA gradient). The fractions containing the desired product were concentrated under reduced pressure. The material was dissolved in MeOH (1 mL) and 4 M HCl in 1,4-dioxane (0.015 mL) was added. The mixture was concentrated under reduced pressure to give 71.0 mg (58%) of the desired product. LC-MS: RT=3.50 min, [M+H]+=326.2.
Reaction SMILES: [Cl:1][C:2]1[CH:10]=[C:9]([C:11]#[C:12][CH2:13][O:14][CH3:15])[C:5]2[O:6][CH2:7][O:8][C:4]=2[C:3]=1[NH:16][C:17]1[C:26]2[C:21](=[CH:22][C:23]([O:31][CH2:32][CH2:33][CH2:34]Cl)=[CH:24][C:25]=2[O:27][CH:28]([CH3:30])[CH3:29])[N:20]=[CH:19][N:18]=1.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.[CH:55]([N:57]1[CH2:62][CH2:61][NH:60][CH2:59][CH2:58]1)=[O:56].[I-].[Na+]>COCCO.ClCCl>[Cl:1][C:2]1[CH:10]=[C:9]([C:11]#[C:12][CH2:13][O:14][CH3:15])[C:5]2[O:6][CH2:7][O:8][C:4]=2[C:3]=1[NH:16][C:17]1[C:26]2[C:21](=[CH:22][C:23]([O:31][CH2:32][CH2:33][CH2:34][N:60]3[CH2:61][CH2:62][N:57]([CH:55]=[O:56])[CH2:58][CH2:59]3)=[CH:24][C:25]=2[O:27][CH:28]([CH3:29])[CH3:30])[N:20]=[CH:19][N:18]=1
Reactant: COCC#Cc1cc(Cl)c(Nc2ncnc3cc(OCCCCl)cc(OC(C)C)c23)c2c1OCO2
Reactant: O=CN1CCNCC1
Agent: [I-]
Agent: [Na+]
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Solvent: COCCO
Solvent: ClCCl
Product: COCC#Cc1cc(Cl)c(Nc2ncnc3cc(OCCCN4CCN(C=O)CC4)cc(OC(C)C)c23)c2c1OCO2
Temperature: 110 °C
Reaction time: 24 h

Procedure:
A mixture N-[5-chloro-7-(3-methoxyprop-1-yn-1-yl)-1,3-benzodioxol-4-yl]-7-(3-chloropropoxy)-5-isopropoxyquinazolin-4-amine (0.320 g, as a 1:1.3 wt.:wt. mixture with triphenylphosphine) and N-formyl piperazine (0.69 ml) was dissolved in 2-methoxyethanol (7 ml), then sodium iodide (0.040 g) was added and the reaction mixture was then heated at 110° C. with stirring for 24 hours. The reaction mixture was then cooled to room temperature, diluted with dichloromethane (70 ml) and washed with water:brine (1:1) then water then brine and dried over magnesium sulfate before filtration and evaporation of solvents under reduced pressure. The residues so resulting were then purified by column chromatography on silica using increasingly polar mixtures of methanol in dichloromethane as eluent. There was thus obtained the title compound (0.086 g) as a white foam; NMR Spectrum: (CDCl3) 1.53 (d, 6H), 2.03 (quin, 2H), 2.47 (dt, 4H), 2.58 (t, 2H), 3.40 (t, 2H), 3.45 (s, 3H), 3.58 (t, 2H), 4.16 (t, 2H), 4.35 (s, 2H), 4.82 (sept, 1H), 6.10 (s, 2H), 6.49 (d, 1H), 6.83 (d, 1H), 7.06 (s, 1H), 8.03 (s, 1H), 8.51 (s, 1H), 9.41 (s, 1H); Mass Spectrum: M+H+ 596/598.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:13]=[CH:12][N:11]3[C:14](=[O:17])[NH:15][N:16]=[C:10]3[C:9]=2[C:18]2[CH:23]=[CH:22][N:21]=[CH:20][CH:19]=2)=[CH:4][CH:3]=1.Cl[CH2:25][C:26]1[C:27]([CH3:36])=[N:28][C:29]([C:32]([F:35])([F:34])[F:33])=[CH:30][CH:31]=1.C([O-])([O-])=O.[K+].[K+]>CN(C=O)C>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([C:8]2[CH:13]=[CH:12][N:11]3[C:14](=[O:17])[N:15]([CH2:25][C:26]4[C:27]([CH3:36])=[N:28][C:29]([C:32]([F:35])([F:33])[F:34])=[CH:30][CH:31]=4)[N:16]=[C:10]3[C:9]=2[C:18]2[CH:19]=[CH:20][N:21]=[CH:22][CH:23]=2)=[CH:4][CH:3]=1
Reactant: O=c1[nH]nc2c(-c3ccncc3)c(-c3ccc(Cl)cc3)ccn12
Reactant: Cc1nc(C(F)(F)F)ccc1CCl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CN(C)C=O
Product: Cc1nc(C(F)(F)F)ccc1Cn1nc2c(-c3ccncc3)c(-c3ccc(Cl)cc3)ccn2c1=O
Temperature: 80 °C
Reaction time: 5.5 h
Yield: 52.4 %

Procedure:
To a solution of 7-(4-chlorophenyl)-8-(pyridin-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one (162 mg, 0.50 mmol) and 3-(chloromethyl)-2-methyl-6-(trifluoromethyl)pyridine (137 mg, 0.65 mmol) in anhydrous DMF (1.5 mL) at room temperature was added anhydrous K2CO3 (105 mg, 0.75 mmol). The resulting yellow suspension was stirred at 80° C. for 5.5 h. Analysis by HPLC/MS indicated that starting 7-(4-chlorophenyl)-8-(pyridin-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one had been consumed. After cooling to room temperature, the reaction mixture was diluted with water and extracted with EtOAc (20 mL×3). The combined EtOAc extracts were washed with water, then saturated aqueous NaCl, dried (Na2SO4), filtered, and concentrated under reduced pressure. The crude product was purified using a silica gel cartridge (40 g) eluted with a gradient of ethyl acetate (0-70%) in hexanes to afford 130 mg (53%) of the title compound as a light brown foam. The product was further purified using preparative reverse phase HPLC (Phenomenex Luna 5 μm C-18 21.2×100 mm column eluted with a linear gradient of 50% to 90% B over 10 min (A=0.1% trifluoroacetic acid, 90% water, 10% methanol and B=0.1% trifluoroacetic acid, 90% methanol, 10% water) with flow rate at 20 mL/min and UV detection at 220 nm). The desired fractions were concentrated under reduced pressure. The resulting residue was dissolved in EtOAc, washed with saturated aqueous Na2CO3 once, water twice, then saturated aqueous NaCl, dried over Na2SO4 and evaporated. The residue was dissolved in acetonitrile, frozen and lyophilized to afford the title compound as a light yellow powder. HPLC/MS: retention time=2.80 min, [M+H]+=496.2. 1H NMR (CDCl3, 400 MHz): δ 8.56 (d, J=6.2 Hz, 2H), 7.87 (d, J=7.0 Hz, 1H), 7.68 (d, J=7.9 Hz, 1H), 7.49 (d, J=7.9 Hz, 1H), 7.27 (d, J=8.8 Hz, 2H), 7.17 (d, J=6.2 Hz, 2H), 7.05 (d, J=8.8 Hz, 2H), 6.66 (d, J=7.5 Hz, 1H), 5.23 (s, 2H), 2.75 (s, 3H).
Reaction SMILES: [F:1][C:2]1[CH:7]=[CH:6][C:5]([CH3:8])=[CH:4][C:3]=1[O:9][C:10]1[CH:15]=[CH:14][CH:13]=[CH:12][CH:11]=1.BrN1C(=[O:22])CCC1=O.C(OOC(=O)C1C=CC=CC=1)(=O)C1C=CC=CC=1.C[N+]1([O-])CCOCC1>C(Cl)(Cl)(Cl)Cl>[F:1][C:2]1[CH:7]=[CH:6][C:5]([CH:8]=[O:22])=[CH:4][C:3]=1[O:9][C:10]1[CH:11]=[CH:12][CH:13]=[CH:14][CH:15]=1
Reactant: O=C1CCC(=O)N1Br
Reactant: Cc1ccc(F)c(Oc2ccccc2)c1
Agent: C[N+]1([O-])CCOCC1
Agent: O=C(OOC(=O)c1ccccc1)c1ccccc1
Solvent: ClC(Cl)(Cl)Cl
Product: O=Cc1ccc(F)c(Oc2ccccc2)c1
Temperature: 0 °C
Reaction time: 20 h
Yield: 8.5 %

Procedure:
Combine 4-fluoro-1-methyl-3-phenoxybenzene (2.43 g, 12.0 mmol), N-bromosuccinimide (4.92 g, 27.6 mmol), benzoyl peroxide (408 mg, 1.68 mmol), and carbon tetrachloride (55 mL). Heat the mixture at reflux temperature for 6.5 h and cool to 0° C. for 64 h. Filter the solids and concentrate the filtrate. Dissolve the residue in chloroform and wash with ice cold sodium carbonate solution. Dry the chloroform solution over sodium sulfate, filter and concentrate under reduced pressure. Dissolve the residue in acetonitrile (50 mL) and add 4-methylmorpholine-4-oxide (4.6 g, 39.1 mmol) and powdered 4 Å sieves (200 mg). Stir at ambient temperature for 20 h, filter and concentrate. Purify by silica gel chromatography (5%, 30% ethyl acetate/hexanes) to give 220 mg (8%) of the title compound: MS (m/e): 216 (M+).
Reaction SMILES: C(OC([N:8]1[CH2:13][CH2:12][CH:11]([O:14][C:15]2[CH:16]=[CH:17][C:18]3[O:23][CH2:22][C:21](=[O:24])[NH:20][C:19]=3[CH:25]=2)[CH2:10][CH2:9]1)=O)(C)(C)C.[ClH:26]>ClCCl>[ClH:26].[NH:8]1[CH2:9][CH2:10][CH:11]([O:14][C:15]2[CH:16]=[CH:17][C:18]3[O:23][CH2:22][C:21](=[O:24])[NH:20][C:19]=3[CH:25]=2)[CH2:12][CH2:13]1
Reactant: CC(C)(C)OC(=O)N1CCC(Oc2ccc3c(c2)NC(=O)CO3)CC1
Agent: Cl
Solvent: ClCCl
Product: O=C1COc2ccc(OC3CCNCC3)cc2N1
Temperature: 40 °C
Reaction time: 18 h
Yield: 88 %

Procedure:
A mixture of 6-(1-(tert-butyloxycarbonyl)piperidin-4-yloxy)-4H-benzo[1,4]oxazin-3-one (3.78 g, 10.9 mmol), ethereal hydrogen chloride (50 mL) and dichloromethane (20 mL) was heated at 40° C. for 2 h, then allowed to stir at 20° C. for 18 h. The resulting colourless solid was collected by filtration to give the title compound (2.72 g, 88%).
Reaction SMILES: [C:1]([CH:5]1[CH2:10][CH2:9][CH2:8][CH:7]2[O:11][CH:6]12)([CH3:4])([CH3:3])[CH3:2].C(OC1(O)CCC(C(C)(C)C)CC1)(=O)C(C)=C.C(C1CCCCC1)(C)(C)C.ClC1C=C(C=CC=1)C(OO)=O>C(OC(=O)C)C>[C:1]([CH:5]1[CH2:10][CH2:9][CH:8]=[C:7]2[O:11][CH:6]12)([CH3:4])([CH3:2])[CH3:3]
Reactant: CC(C)(C)C1CCCC2OC21
Agent: C=C(C)C(=O)OC1(O)CCC(C(C)(C)C)CC1
Agent: CC(C)(C)C1CCCCC1
Agent: O=C(OO)c1cccc(Cl)c1
Solvent: CCOC(C)=O
Product: CC(C)(C)C1CCC=C2OC21
Reaction time: 2 h

Procedure:
4-t-butyl-2-epoxycyclohexane, an intermediate in the synthesis of 4-t-butylhydroxycyclohexyl methacrylate, is prepared by reacting a 4-t-butylcyclohexane with m-chloroperoxybenzoic acid in ethylacetate below 5° C. until mixing is complete, and then at room temperature for two hours. The reaction mixture is washed with aqueous NA2CO3, dried over MgSO4, and filtered. The theoretical reaction is: ##STR7##
Reaction SMILES: [NH2:1][C:2]1[CH:9]=[CH:8][CH:7]=[C:6]([O:10][CH:11]([CH2:15][CH2:16][CH3:17])[CH2:12][CH2:13][CH3:14])[C:3]=1[C:4]#[N:5].O=[C:19]([CH3:26])[CH2:20][C:21]([O:23][CH2:24][CH3:25])=[O:22]>>[CH2:24]([O:23][C:21]([C:20]1[C:19]([CH3:26])=[N:1][C:2]2[C:3]([C:4]=1[NH2:5])=[C:6]([O:10][CH:11]([CH2:15][CH2:16][CH3:17])[CH2:12][CH2:13][CH3:14])[CH:7]=[CH:8][CH:9]=2)=[O:22])[CH3:25]
Reactant: CCOC(=O)CC(C)=O
Reactant: CCCC(CCC)Oc1cccc(N)c1C#N
Product: CCCC(CCC)Oc1cccc2nc(C)c(C(=O)OCC)c(N)c12

Procedure:
Prepared as in Example 2a from 2-amino-6-(heptan-4-yloxy)benzonitrile (Example 23b) and ethyl 3-oxobutanoate as a pale yellow solid (65%). 1H NMR (400 MHz, DMSO-d6) δ 0.87 (t, J=7.2 Hz, 6H), 1.31 (t, J=7.2 Hz, 3H), 1.47-1.33 (m, 4H), 1.77-1.59 (m, 4H), 2.54 (s, 3H), 4.30 (q, J=7.2 Hz, 2H), 4.67-4.64 (m, 1H), 6.92 (d, J=7.6 Hz, 1H), 7.19 (dd, J=0.8, 8.4 Hz, 1H), 7.49 (t, J=8.0 Hz, 1H), 8.13 (brs, 2H). MS 345 (MH+).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([C@@H:12]([CH2:31][CH:32]2[CH2:36][CH2:35][CH2:34][CH2:33]2)[C:13]([NH:15][C:16]2[CH:20]=[CH:19][N:18]([CH2:21][C:22]3[CH:30]=[CH:29][C:25]([C:26](O)=[O:27])=[CH:24][CH:23]=3)[N:17]=2)=[O:14])[CH:5]=[CH:6][C:7]=1[S:8]([CH3:11])(=[O:10])=[O:9].C(Cl)(=O)C(Cl)=O.N1C(C)=CC=CC=1C.[NH2:51][CH2:52][CH2:53][CH2:54][OH:55]>C(Cl)Cl>[Cl:1][C:2]1[CH:3]=[C:4]([C@@H:12]([CH2:31][CH:32]2[CH2:33][CH2:34][CH2:35][CH2:36]2)[C:13]([NH:15][C:16]2[CH:20]=[CH:19][N:18]([CH2:21][C:22]3[CH:23]=[CH:24][C:25]([C:26]([NH:51][CH2:52][CH2:53][CH2:54][OH:55])=[O:27])=[CH:29][CH:30]=3)[N:17]=2)=[O:14])[CH:5]=[CH:6][C:7]=1[S:8]([CH3:11])(=[O:9])=[O:10]
Reactant: CS(=O)(=O)c1ccc([C@@H](CC2CCCC2)C(=O)Nc2ccn(Cc3ccc(C(=O)O)cc3)n2)cc1Cl
Reactant: NCCCO
Agent: O=C(Cl)C(=O)Cl
Solvent: Cc1cccc(C)n1
Solvent: ClCCl
Product: CS(=O)(=O)c1ccc([C@@H](CC2CCCC2)C(=O)Nc2ccn(Cc3ccc(C(=O)NCCCO)cc3)n2)cc1Cl
Temperature: 25 °C
Reaction time: 0.33 h
Yield: 29.8 %

Procedure:
4-{3-[2-(R)-(3-Chloro-4-methanesulfonyl-phenyl)-3-cyclopentyl-propionylamino]-pyrazol-1-ylmethyl}-benzoic acid (prepared in example 45, 40 mg, 0.08 mmol) was suspended in methylene chloride (1 mL) and a 2.0 M solution of oxalyl chloride in methylene chloride (38 μL, 0.08 mmol) was added and the reaction stirred at 25° C. for 20 min. The solution was chilled to 0° C. and 2,6-lutidine (18 μL, 0.15 mmol) was added. The reaction continued to stir at 0° C. for 20 min. 3-Amino-propan-1-ol (7 μL, 0.09 mmol) was added, the ice bath was removed and the reaction continued to stir at 25° C. for 16 h. The reaction was diluted with methylene chloride (10 mL), washed with water (2×4 mL), saturated aqueous brine solution (1×4 mL), dried over magnesium sulfate and concentrated in vacuo to a beige foam. Purification by reverse phase preparative HPLC (Column: Thomson C18 ODSA, 5 micron, 50×21.2 mm ID; 30% acetonitrile/water to 100% acetonitrile/water; 30 mL/min flow rate for 15 min run) followed by preparative thin layer chromatography (Merck Silica gel 60 F254, 500 μm, 20×20 cm; 100% ethyl acetate) afforded 4-{3-[2-(R)-(3-chloro-4-methanesulfonyl-phenyl)-3-cyclopentyl-propionylamino]-pyrazol-1-ylmethyl}-N-(3-hydroxy-propyl)-benzamide (14 mg, 32%) as a white waxy solid: ESI-LRMS m/e calcd for C29H35ClN4O5S [M+] 586.2, found 587.29 [M+H+]; 1H NMR (400 MHz, CDCl3) δ ppm 1.08-1.22 (m, 2H, CH2), 1.43-1.93 (m, 10H, 5×CH2), 2.15-2.31 (m, 1H, CH), 3.26 (s, 3H, SO2CH3), 3.57-3.67 (m, 3H, CH2 and CH), 3.73 (t, J=5.5 Hz, 2H, CH2), 5.18 (s, 2H, NCH2), 6.74 (d, J=2.3 Hz, 1H, Ar), 6.82 (brm, 1H, NH), 7.12 (d, Jo=8.1 Hz, 2H, Ar), 7.36 (d, J=2.3 Hz, 1H, Ar), 7.43 (dd, Jo=8.1, Jm=1.6 Hz. 1H, Ar), 7.59 (d, Jm=1.6 Hz, 1H, Ar), 7.67 (d, Jo=8.1 Hz, 2H, Ar), 8.04 (d, Jo=8.1 Hz, 1H, Ar), 8.32 (s, 1H, NH).
Reaction SMILES: C1C=[C:9]2[C:4]([CH:5]=[C:6]([CH2:11][C@H:12]([NH2:16])[C:13]([OH:15])=[O:14])[CH:7]=[CH:8]2)=CC=1.C([O-])(=O)CC[C@H](NC(C1C=CC(NCC2CNC3N=C(NC(C=3N=2)=O)N)=CC=1)=O)C(O)=[O:22]>>[NH2:16][C@H:12]([C:13]([OH:15])=[O:14])[CH2:11][C:6]1[CH:7]=[CH:8][C:9]([OH:22])=[CH:4][CH:5]=1
Reactant: Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@@H](CCC(=O)[O-])C(=O)O)cc1)CN2
Reactant: N[C@@H](Cc1ccc2ccccc2c1)C(=O)O
Product: N[C@@H](Cc1ccc(O)cc1)C(=O)O

Procedure:
An L-3-(2-naphthyl)-alanine mutant of mouse dihydrofolate reductase (DHFR) was generated and characterized to confirm the ability of the mtRNACUATyr/SS 12-TyrRS pair to site-specifically incorporate L-3-(2-naphthyl)-alanine in response to an amber stop codon. The Tyr163 codon of the mouse DHFR gene was mutated to TAG, and a His6 tag was added to the COOH-terminus of DHFR to facilitate protein purification using Ni2+ affinity chromatography. As a positive control, wild-type M. jannaschii TyrRS was coexpressed with the mtRNACUATyr resulting in efficient suppression of the TAG codon with tyrosine (FIG. 4). When SS12-TyrRS was coexpressed with the mu tRNACUATyr in the presence of 1 mM L-3-(2-naphthyl)-alanine, full-length mouse DHFR was also generated (with yield of 2.2 mg/L in liquid GMML minimal medium). In the absence of either L-3-(2-naphthyl)-alanine, mtRNACUATyr, or SS12-TyrRS, no full length DHFR was produced. A penta-His antibody was used to detect the His6 tag at the COOH-terminus of DHFR in a Western blot. No DHFR could be detected in the absence of each of the above three components.
Reaction SMILES: Cl.[CH2:2]([O:4][C:5](=[O:8])[CH2:6][NH2:7])[CH3:3].S([O-])([O-])(=O)=O.[Mg+2].[CH2:15]([O:17][C:18](=[O:34])[C:19]1[CH:24]=[CH:23][C:22]([O:25][C:26]2[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=2)=[CH:21][C:20]=1[CH:32]=O)[CH3:16]>ClCCl.C(N(CC)CC)C>[CH2:15]([O:17][C:18](=[O:34])[C:19]1[CH:24]=[CH:23][C:22]([O:25][C:26]2[CH:31]=[CH:30][CH:29]=[CH:28][CH:27]=2)=[CH:21][C:20]=1[CH:32]=[N:7][CH2:6][C:5]([O:4][CH2:2][CH3:3])=[O:8])[CH3:16]
Reactant: CCOC(=O)CN
Reactant: CCOC(=O)c1ccc(Oc2ccccc2)cc1C=O
Agent: Cl
Agent: O=S(=O)([O-])[O-]
Agent: [Mg+2]
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CCOC(=O)CN=Cc1cc(Oc2ccccc2)ccc1C(=O)OCC
Temperature: 25 °C
Reaction time: 15 h
Yield: 101.4 %

Procedure:
To a dried flask with glycine ethyl ester hydrochloride salt (62 mg) was added anhydrous dichloromethane (2 mL), followed by triethylamine (124 μL). Then magnesium sulfate (pre-dried on high vacuum by heat gun, 100 mg) was added, followed by addition of a dichloromethane (1 mL) solution of 2-formyl-4-phenoxy-benzoic acid ethyl ester (120 mg). The flask of 2-formyl-4-phenoxy-benzoic acid ethyl ester was further rinsed with 0.5 mL of dichloromethane. The resulting mixture was stirred at room temperature under nitrogen for 15 h. The mixture was filtered and rinsed with dichloromethane. After removal of solvent, the reaction was diluted with ether (15 mL) and washed with brine twice and dried. Filtration and removal of solvent gave the title compound 160 mg as an oil with good purity. 1H NMR (200 MHz, CDCl3) δ 9.02 (d, J=1.2, 1H), 7.94 (d, J=8.6 Hz, 1H), 7.63 (d, J=2.4, 1H), 7.40-7.32 (m, 2H), 7.20-7.11 (m, 1H), 7.06-6.97 (m, 3H), 4.41 (s, 2H), 4.35 (q, J=7.0 Hz, 2H), 4.21 (q, J=7.4 Hz, 2H), 1.39 (t, J=7.0 Hz, 3H), 1.28 (t, J=7.0 Hz, 3H).
Reaction SMILES: [C:1]([O:5][C:6]([NH:8][CH:9]([CH2:13][C:14]1[CH:19]=[CH:18][C:17]([C:20]#[N:21])=[CH:16][CH:15]=1)[C:10]([OH:12])=O)=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH:22]([NH:25][CH:26]([CH3:28])[CH3:27])([CH3:24])[CH3:23].C(N(CC)CC)C.F[P-](F)(F)(F)(F)F.Br[P+](N1CCCC1)(N1CCCC1)N1CCCC1>C(Cl)Cl>[C:1]([O:5][C:6]([NH:8][CH:9]([CH2:13][C:14]1[CH:19]=[CH:18][C:17]([C:20]#[N:21])=[CH:16][CH:15]=1)[C:10]([N:25]([CH:26]([CH3:28])[CH3:27])[CH:22]([CH3:24])[CH3:23])=[O:12])=[O:7])([CH3:2])([CH3:3])[CH3:4]
Reactant: CC(C)(C)OC(=O)NC(Cc1ccc(C#N)cc1)C(=O)O
Reactant: CC(C)NC(C)C
Agent: Br[P+](N1CCCC1)(N1CCCC1)N1CCCC1
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(CC)CC
Solvent: ClCCl
Product: CC(C)N(C(=O)C(Cc1ccc(C#N)cc1)NC(=O)OC(C)(C)C)C(C)C
Temperature: 0 °C
Reaction time: 2 h
Yield: 31.1 %

Procedure:
A mixture of 1 g of 2-(tert-butoxycarbonylamino)-3-(4-cyanophenyl)propionic acid and 0.540 g of diisopropylamine in 10 ml of DCM is cooled to 0° C., 0.960 ml of triethylamine is added, followed by addition of 1.76 g of bromotripyrrolidinophosphonium hexafluorophosphate, and the mixture is stirred for 2 hours and allowed to warm to RT. The reaction mixture is concentrated under vacuum, the residue is extracted with EtOAc, the organic phase is washed with water, with 5% KHSO4 solution, with water, with saturated NaHCO3 solution and with saturated NaCl solution and dried over Na2SO4, and the solvent is evaporated off under vacuum. The residue is chromatographed on silica gel, eluting with a heptane/EtOAc mixture (80/20; v/v). 0.4 g of the expected product is obtained; m.p.=172° C.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:21]=[CH:22][C:23]=1[O:24][CH2:25][C:26]1[N:27]([CH3:37])[CH:28]=[C:29]([C:31]2[CH:36]=[CH:35][CH:34]=[CH:33][CH:32]=2)[N:30]=1)[CH2:6][O:7][C:8]1[C:12]([CH:13]=O)=[CH:11][N:10]([C:15]2[CH:20]=[CH:19][CH:18]=[CH:17][CH:16]=2)[N:9]=1.[CH2:38]([P:47](=[O:54])([O:51][CH2:52][CH3:53])[O:48][CH2:49][CH3:50])P(=O)(OCC)OCC.CN(C)C=O.[H-].[Na+]>O>[CH3:1][O:2][C:3]1[CH:4]=[C:5]([CH:21]=[CH:22][C:23]=1[O:24][CH2:25][C:26]1[N:27]([CH3:37])[CH:28]=[C:29]([C:31]2[CH:32]=[CH:33][CH:34]=[CH:35][CH:36]=2)[N:30]=1)[CH2:6][O:7][C:8]1[C:12](/[CH:13]=[CH:38]/[P:47](=[O:54])([O:48][CH2:49][CH3:50])[O:51][CH2:52][CH3:53])=[CH:11][N:10]([C:15]2[CH:16]=[CH:17][CH:18]=[CH:19][CH:20]=2)[N:9]=1
Reactant: COc1cc(COc2nn(-c3ccccc3)cc2C=O)ccc1OCc1nc(-c2ccccc2)cn1C
Reactant: CCOP(=O)(CP(=O)(OCC)OCC)OCC
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Solvent: O
Product: CCOP(=O)(/C=C/c1cn(-c2ccccc2)nc1OCc1ccc(OCc2nc(-c3ccccc3)cn2C)c(OC)c1)OCC
Reaction time: 15 h
Yield: 70.2 %

Procedure:
To a mixture of 3-({3-methoxy-4-[(1-methyl-4-phenyl-1H-imidazol-2-yl)methoxy]benzyl}oxy)-1-phenyl-1H-pyrazole-4-carbaldehyde (0.65 g), tetraethyl methylenediphosphonate (0.40 g) and N,N-dimethylformamide (30 mL) was added sodium hydride (60% in oil, 0.060 g) at room temperature, and the mixture was stirred at the same temperature for 15 hrs. Water was poured into the reaction mixture, and the mixture was extracted with ethyl acetate. The organic layer was washed with saturated brine, dried over anhydrous magnesium sulfate and concentrated. The residue was subjected to silica gel column chromatography to give diethyl (E)-2-[3-({3-methoxy-4-[(1-methyl-4-phenyl-1H-imidazol-2-yl)methoxy]benzyl}oxy)-1-phenyl-1H-pyrazol-4-yl]ethenylphosphonate as colorless crystals (0.58 g, yield 71%) from a fraction eluted with ethyl acetate-hexane (8:1, v/v). Recrystallization from ethyl acetate-hexane gave colorless prism crystals. melting point: 144-145° C.
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:42]=[C:41]([O:43][CH3:44])[CH:40]=[CH:39][C:4]=1[CH2:5][NH:6][CH:7]([CH2:21][CH2:22][CH2:23][C:24]1[CH:29]=[CH:28][C:27]([O:30][CH2:31][C@@H:32]2[CH2:36][O:35]C(C)(C)[O:33]2)=[CH:26][CH:25]=1)[CH2:8][NH:9][C:10]([C:12]1[C:17]([NH2:18])=[N:16][C:15]([NH2:19])=[C:14]([Cl:20])[N:13]=1)=[O:11].C(O)(C(F)(F)F)=O>C(Cl)Cl>[OH:33][C@@H:32]([CH2:36][OH:35])[CH2:31][O:30][C:27]1[CH:26]=[CH:25][C:24]([CH2:23][CH2:22][CH2:21][CH:7]([NH:6][CH2:5][C:4]2[CH:39]=[CH:40][C:41]([O:43][CH3:44])=[CH:42][C:3]=2[O:2][CH3:1])[CH2:8][NH:9][C:10]([C:12]2[C:17]([NH2:18])=[N:16][C:15]([NH2:19])=[C:14]([Cl:20])[N:13]=2)=[O:11])=[CH:29][CH:28]=1
Reactant: COc1ccc(CNC(CCCc2ccc(OC[C@@H]3COC(C)(C)O3)cc2)CNC(=O)c2nc(Cl)c(N)nc2N)c(OC)c1
Solvent: O=C(O)C(F)(F)F
Solvent: ClCCl
Product: COc1ccc(CNC(CCCc2ccc(OC[C@@H](O)CO)cc2)CNC(=O)c2nc(Cl)c(N)nc2N)c(OC)c1
Temperature: 25 °C
Reaction time: 72 h

Procedure:
To a solution of 3,5-diamino-6-chloro-pyrazine-2-carboxylic acid {2-(2,4-dimethoxy-benzylamino)-5-[4-((R)-2,2-dimethyl-[1,3]dioxolan-4-ylmethoxy)-phenyl]-pentyl}-amide (391 mg, 0.62 mmol) in DCM (3 mL) is added TFA (3 mL) and the reaction is stirred at RT for 72 h. The solvent is removed in vacuo and the residue is diluted with water (20 mL) and EtOAc (20 mL). The layers are separated and the aqueous phase is neutralised with aqueous sodium hydroxide and then extracted with EtOAc (2×20 mL). The EtOAc extracts are combined and dried (MgSO4), filtered and the solvent is removed in vacuo. Chromatography (SiO2, MeOH:DCM, 1:9) affords the title compound as a colourless solid as a mixture of diastereoisomers. [M+H]+ 589. 1H NMR (400 MHz, CDCl3) δ 7.63 (1H, br), 7.05 and 7.04 (1H, 2×d), 6.98 and 6.97 (2H, 2×d), 6.73 and 6.71 (2H 2×d), 6.36 and 6.35 (1H, 2×d), 6.34 and 6.30 (1H, 2×s), 5.15 (2H, br), 4.08-3.59 (8H, m), 3.71 (3H, s), 3.65 (3H, s), 3.50-3.41 (2H, m) 2.55 and 2.49 (2H, 2×t), 1.80-1.29 (4H, m).