Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [N+:1]([C:4]1[CH:9]=[CH:8][CH:7]=[CH:6][C:5]=1B(O)O)([O-:3])=[O:2].[F:13][C:14]([F:33])([F:32])[C:15]1[CH:16]=[C:17]([CH:29]=[CH:30][CH:31]=1)[CH2:18][NH:19][C:20](=[O:28])[C:21]1[CH:26]=[CH:25][N:24]=[C:23](Br)[CH:22]=1.C(=O)([O-])[O-].[Na+].[Na+]>COCCOC.O.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>[F:32][C:14]([F:13])([F:33])[C:15]1[CH:16]=[C:17]([CH:29]=[CH:30][CH:31]=1)[CH2:18][NH:19][C:20](=[O:28])[C:21]1[CH:22]=[CH:23][N:24]=[C:25]([C:5]2[CH:6]=[CH:7][CH:8]=[CH:9][C:4]=2[N+:1]([O-:3])=[O:2])[CH:26]=1
Reactant: O=C(NCc1cccc(C(F)(F)F)c1)c1ccnc(Br)c1
Reactant: O=[N+]([O-])c1ccccc1B(O)O
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: COCCOC
Solvent: O
Product: O=C(NCc1cccc(C(F)(F)F)c1)c1ccnc(-c2ccccc2[N+](=O)[O-])c1
Temperature: 80 °C
Reaction time: 1.5 h
Yield: 83.3 %

Procedure:
Into a 250-mL 3-necked round bottom flask purged and maintained with an inert atmosphere of nitrogen, was placed a solution of 2-nitrophenylboronic acid (500 mg, 2.99 mmol, 1.00 equiv) in ethylene glycol dimethyl ether (30 mL), N-(3-(trifluoromethyl)benzyl)-2-bromoisonicotinamide 21a (1.08 g, 3.01 mmol, 1.00 equiv), Pd(PPh3)4 (334.7 mg, 0.30 mmol, 0.10 equiv), and a solution of sodium carbonate (1.6 g, 15.09 mmol, 5.00 equiv) in water (4 mL). The resulting solution was stirred for 1.5 h at 80° C. The reaction progress was monitored by TLC (ethyl acetate/petroleum ether=1:1). The resulting solution was diluted with 50 mL of water. The resulting solution was extracted with 2×100 mL of ethyl acetate and the organic layers combined and dried over magnesium sulfate. The solids were filtered out. The resulting mixture was concentrated under vacuum. The residue was applied onto a silica gel column and eluted with petroleum ether/EtOAc (20:1-5:1). The product was obtained as 1.0 g (83%) of a light yellow solid.
Reaction SMILES: [Si]([O:8][C@@H:9]1[C@@:26]2([CH3:27])[C:13](=[CH:14][CH:15]=[C:16]3[C@@H:25]2[CH2:24][CH2:23][C@@:21]2([CH3:22])[C@H:17]3[CH2:18][CH:19]=[C:20]2[CH2:28][O:29][CH2:30][CH2:31][CH2:32][C:33]([O:36][Si](CC)(CC)CC)([CH3:35])[CH3:34])[CH2:12][C@@H:11]([O:44][Si](C(C)(C)C)(C)C)[CH2:10]1)(C(C)(C)C)(C)C.O1CCCC1.[F-].C([N+](CCCC)(CCCC)CCCC)CCC>O1CCCC1.C(OCC)(=O)C>[OH:8][C@@H:9]1[C@@:26]2([CH3:27])[C:13](=[CH:14][CH:15]=[C:16]3[C@@H:25]2[CH2:24][CH2:23][C@@:21]2([CH3:22])[C@H:17]3[CH2:18][CH:19]=[C:20]2[CH2:28][O:29][CH2:30][CH2:31][CH2:32][C:33]([OH:36])([CH3:35])[CH3:34])[CH2:12][C@@H:11]([OH:44])[CH2:10]1
Reactant: CC[Si](CC)(CC)OC(C)(C)CCCOCC1=CC[C@H]2C3=CC=C4C[C@@H](O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@]4(C)[C@H]3CC[C@]12C
Agent: CCCC[N+](CCCC)(CCCC)CCCC
Agent: [F-]
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: CC(C)(O)CCCOCC1=CC[C@H]2C3=CC=C4C[C@@H](O)C[C@H](O)[C@]4(C)[C@H]3CC[C@]12C
Yield: 36.8 %

Procedure:
To a solution of 1α,3β-bis(tert-butyldimethylsilyloxy)-17-(4-triethylsilyloxy-4-methylpentyloxymethyl)androsta-5,7,16-triene (278.7 mg, 0.367 mmol) in tetrahydrofuran (2 ml), was added a 1M tetra-n-butylammonium fluoride tetrahydrofuran solution (3.3 ml, 3.3 mmol), followed by reflux under heating for 14 hours. The reaction solution was diluted with ethyl acetate, washed with 5% hydrochloric acid, a saturated aqueous sodium bicarbonate solution and saturated brine in that order, the organic layer was dried over anhydrous magnesium sulfate and evaporated under reduced pressure to remove the solvent. The thus obtained residue was purified by column chromatography (dichloromethane:ethanol=10:1) and preparative thin layer chromatography (4 sheets (each 0.5 mm thickness), dichloromethane:ethanol=20:1, developed twice, and then dichloromethane:ethanol=10:1, developed twice) to give the titled compound (56.3 mg, 37%) as a colorless foam.
Reaction SMILES: [OH:1][C:2]1[C:11]2[C:6](=[CH:7][C:8]([O:12][C:13]3[CH:18]=[C:17]([F:19])[CH:16]=[C:15]([F:20])[CH:14]=3)=[CH:9][CH:10]=2)[C:5]([CH3:21])=[N:4][C:3]=1[C:22](OC)=[O:23].[NH2:26][CH2:27][C:28]([OH:30])=[O:29].C[O-].[Na+]>CO>[OH:1][C:2]1[C:11]2[C:6](=[CH:7][C:8]([O:12][C:13]3[CH:18]=[C:17]([F:19])[CH:16]=[C:15]([F:20])[CH:14]=3)=[CH:9][CH:10]=2)[C:5]([CH3:21])=[N:4][C:3]=1[C:22]([NH:26][CH2:27][C:28]([OH:30])=[O:29])=[O:23]
Reactant: COC(=O)c1nc(C)c2cc(Oc3cc(F)cc(F)c3)ccc2c1O
Reactant: NCC(=O)O
Agent: C[O-]
Agent: [Na+]
Solvent: CO
Product: Cc1nc(C(=O)NCC(=O)O)c(O)c2ccc(Oc3cc(F)cc(F)c3)cc12
Temperature: 110 °C

Procedure:
A pressure glass reaction flask which included top threads for a screw cap lid can be fitted with a magnetic stirrer, charged with 7e, glycine (about 3 molar equivalents), methanol, and a sodium methoxide solution (with 1.2 molar eqivalents NaOCH3) and sealed. The reaction can then be heated to 110° C. for at least 6 h during which time the reaction forms a yellow suspension. The reaction can then be cooled to 20-25° C. and evaluated by HPLC. The reaction can be continued until less than 1% 7e remains as determined by HPLC, filtered, washed with methanol, dried under vacuum, dissolved in water and extracted with ethyl acetate to remove impurities to below 0.1%. The ethyl acetate can be removed and an acetic acid solution (with 3 molar eqivalents acetic acid) can be added over one hour. The suspension can be stirred at room temperature for at least 3 hours, filtered, and the solid washed with water (3×), cold acetone (5-10° C., 2×) and evaluated for impurities by HPLC. If acetone removable impurities are present, the flask can be charged with acetone and refluxed for at least 8 h, slowly cooled to 5-10° C., stirred for at least 2-3 h, filtered, washed with cold acetone (5-10° C., 3×) and dried under vacuum to obtain 2-[4-hydroxy-1-methyl-7-(3,5-difluoro-phenoxy)-isoquinoline-3-carboxamido]acetic acid.
Reaction SMILES: B(Br)(Br)Br.Cl[C:6]1[N:7]([C:15]2[CH:20]=[C:19]([O:21]C(C)C)[C:18]([Cl:25])=[CH:17][C:16]=2[Cl:26])[N:8]=[C:9]2[C:14]=1[CH2:13][CH2:12][CH2:11][CH2:10]2.O.CCOCC>ClCCl>[Cl:26][C:16]1[CH:17]=[C:18]([Cl:25])[C:19]([OH:21])=[CH:20][C:15]=1[N:7]1[CH:6]=[C:14]2[C:9]([CH2:10][CH2:11][CH2:12][CH2:13]2)=[N:8]1
Reactant: CC(C)Oc1cc(-n2nc3c(c2Cl)CCCC3)c(Cl)cc1Cl
Agent: BrB(Br)Br
Solvent: ClCCl
Solvent: CCOCC
Solvent: O
Product: Oc1cc(-n2cc3c(n2)CCCC3)c(Cl)cc1Cl
Temperature: -78 °C
Yield: 97.9 %

Procedure:
To a solution of 2.78 g boron tribromide in 5 ml of dichloromethane was added a solution of 3.10 g of 3-chloro-2-(2,4-dichloro-5-isopropoxyphenyl)-4,5,6,7-tetrahydro-2H-indazole VII-1 in 35 ml of dichloromethane under cooling at -78° C. in 15 minutes. The resultant mixture was stirred at -78° C. for 0.5 hours and at room temperature for 1.5 hours and mixed with water and ether at 0° C. The mixture was basified, and the aqueous layer was separated and acidified and shaken with ether. The extract was dried, concentrated and the residue was purified by silica gel chromatography, whereby 2.39 g of the titled compound II-1 was obtained.
Reaction SMILES: S(Cl)([Cl:3])=O.N[C@H](C(O)=O)[C@@H](C)O.[ClH:13].[CH3:14][O:15][C:16](=[O:22])[C@H:17]([C@@H:19]([CH3:21])O)[NH2:18]>CO>[ClH:3].[CH3:14][O:15][C:16](=[O:22])[CH:17]([NH2:18])[CH:19]([Cl:13])[CH3:21]
Reactant: COC(=O)[C@@H](N)[C@@H](C)O
Reactant: O=S(Cl)Cl
Agent: C[C@@H](O)[C@H](N)C(=O)O
Agent: Cl
Solvent: CO
Product: COC(=O)C(N)C(C)Cl

Procedure:
Using thionyl chloride and methanol, threonine was derivatized into threonine methyl ester hydrochloride, which was then treated with thionyl chloride to give α-amino-β-chlorobutyric acid methyl ester hydrochloride. This was then converted to α-amino-β-chloropropionic acid hydrochloride by hydrolyzing with hydrochloric acid. The α-amino-β-chloropropionic acid hydrochloride was crystallized and isolated by the same technique as mentioned in Example 8.
Reaction SMILES: [Cl:1][C:2]1[N:3]([C:11]2[CH:16]=[CH:15][C:14]([O:17][CH2:18][CH2:19]Cl)=[CH:13][CH:12]=2)[N:4]=[C:5]2[C:10]=1[CH:9]=[CH:8][CH:7]=[CH:6]2.[CH3:21][NH2:22]>C(#N)C>[ClH:1].[Cl:1][C:2]1[N:3]([C:11]2[CH:16]=[CH:15][C:14]([O:17][CH2:18][CH2:19][NH:22][CH3:21])=[CH:13][CH:12]=2)[N:4]=[C:5]2[C:10]=1[CH:9]=[CH:8][CH:7]=[CH:6]2
Reactant: CN
Reactant: ClCCOc1ccc(-n2nc3ccccc3c2Cl)cc1
Solvent: CC#N
Product: CNCCOc1ccc(-n2nc3ccccc3c2Cl)cc1
Product: Cl
Temperature: 60 °C
Reaction time: 16 h
Yield: 179.2 %

Procedure:
A mixture of the product from Step 1 (0.1 g, 0.33 mmol), methylamine (40% in water, 3 mL, 81 mmol) in acetonitrile (2 mL) was heated to 60° C. for 7 h, and then room temperature for 16 h. The mixture was extracted with ethyl acetate. The combined organic portions were acidified with 10% HCl to pH to 1, and stirred at 0° C. for 1 h. The product was collected on a filter, washed with 1N HCl, water and hexane. After dried under vacuum, the title compound (100 mg, 91%) was obtained as hydrochloride salt; MS (APCI) m/z 302 (M+1, 100).
Reaction SMILES: [CH3:1][N:2]1[C:6]([CH3:7])=[C:5]([C:8](Cl)=[O:9])[C:4]([CH3:11])=[N:3]1.[CH2:12]([C:16]1[CH:17]=[C:18]([CH:20]=[CH:21][C:22]=1[CH:23]([C:28]([F:31])([F:30])[F:29])[C:24]([F:27])([F:26])[F:25])[NH2:19])[CH:13]([CH3:15])[CH3:14].C(N(CC)CC)C>O1CCCC1.C(OCC)(=O)C>[CH2:12]([C:16]1[CH:17]=[C:18]([NH:19][C:8]([C:5]2[C:4]([CH3:11])=[N:3][N:2]([CH3:1])[C:6]=2[CH3:7])=[O:9])[CH:20]=[CH:21][C:22]=1[CH:23]([C:28]([F:29])([F:30])[F:31])[C:24]([F:25])([F:26])[F:27])[CH:13]([CH3:15])[CH3:14]
Reactant: Cc1nn(C)c(C)c1C(=O)Cl
Reactant: CC(C)Cc1cc(N)ccc1C(C(F)(F)F)C(F)(F)F
Solvent: C1CCOC1
Solvent: CCOC(C)=O
Solvent: CCN(CC)CC
Product: Cc1nn(C)c(C)c1C(=O)Nc1ccc(C(C(F)(F)F)C(F)(F)F)c(CC(C)C)c1
Yield: 82.7 %

Procedure:
1,3,5-Trimethylpyrazole-4-carbonyl chloride (2.09 g, 10.0 mmol), 3-isobutyl-4-[2,2,2-trifluoro-1-(trifluoromethyl)ethyl]aniline (2.0 g, 6.69 mmol), and triethylamine (1.35 g, 13.4 mmol) were dissolved in tetrahydrofuran (60 ml), and the mixture was heated under reflux for 5 hr. The reaction mixture was diluted with ethyl acetate, and washed with water. The organic layer was dried over anhydrous magnesium sulfate and concentrated under reduced pressure, and the obtained residue was purified by silica gel column chromatography (hexane:ethyl acetate=1:3) to give the desired compound (2.41 g).
Reaction SMILES: [F:1][C:2]([F:17])([F:16])[CH2:3][O:4][C:5]1[C:10]([Cl:11])=[CH:9][CH:8]=[CH:7][C:6]=1[CH2:12][C:13]([OH:15])=O.[C:18]([CH:21]1[CH2:26][N:25]([C:27]2[CH:32]=[CH:31][CH:30]=[CH:29][C:28]=2[CH3:33])[CH2:24][CH2:23][NH:22]1)(=[O:20])[NH2:19].C1C=CC2N(O)N=NC=2C=1.C(Cl)CCl.CCN(C(C)C)C(C)C>CN(C=O)C>[Cl:11][C:10]1[C:5]([O:4][CH2:3][C:2]([F:1])([F:17])[F:16])=[C:6]([CH2:12][C:13]([N:22]2[CH2:23][CH2:24][N:25]([C:27]3[CH:32]=[CH:31][CH:30]=[CH:29][C:28]=3[CH3:33])[CH2:26][CH:21]2[C:18](=[O:20])[NH2:19])=[O:15])[CH:7]=[CH:8][CH:9]=1
Reactant: O=C(O)Cc1cccc(Cl)c1OCC(F)(F)F
Reactant: Cc1ccccc1N1CCNC(C(N)=O)C1
Agent: On1nnc2ccccc21
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCCl
Solvent: CN(C)C=O
Product: Cc1ccccc1N1CCN(C(=O)Cc2cccc(Cl)c2OCC(F)(F)F)C(C(N)=O)C1
Temperature: 25 °C
Reaction time: 14 h

Procedure:
To a stirred solution of 2-(2,2,2-trifluoroethoxy)-3-chlorophenylacetic acid (0.14 g, 0.53 mmol) from Step 4 above, 2-carbamoyl-4-(2-methylphenyl)piperazine (0.12 g, 0.53 mmol) from Step 4 of Example 1, and HOBT (0.08 g, 0.53 mmol) in DMF (5 mL) was added EDC (0.15 g, 0.8 mmol) and DIEA (0.14 mL, 0.8 mmol). The mixture was stirred at ambient temperature for 14 h. The solvent was removed under reduced pressure and the residue was purified by preparative reverse phase HPLC using a H2O:CH3CN gradient containing 0.1% TFA. The product-containing fractions were lyophilized to give the title compound as an amorphous powder.
Reaction SMILES: N1C=C[CH:4]=[CH:3][CH:2]=1.[NH2:7]/[C:8](=[C:14](\Cl)/[C:15]([O:17][CH2:18][CH3:19])=[O:16])/[C:9]([O:11][CH2:12][CH3:13])=[O:10].[CH3:21][O:22]C(C=C)=O>C(O)(=O)C>[CH3:21][O:22][C:3]1[CH:4]=[C:14]([C:15]([O:17][CH2:18][CH3:19])=[O:16])[C:8]([C:9]([O:11][CH2:12][CH3:13])=[O:10])=[N:7][CH:2]=1
Reactant: c1ccncc1
Reactant: CCOC(=O)/C(N)=C(/Cl)C(=O)OCC
Reactant: C=CC(=O)OC
Solvent: CC(=O)O
Product: CCOC(=O)c1cc(OC)cnc1C(=O)OCC

Procedure:
83 g (1.05 mol) of pyridine were added to 221.5 (1.0 mol) of diethyl 2-amino-3-chloromaleate in 250 ml of glacial acetic acid at 80° C. while stirring. 90 g (1.05 mol) of methoxyacrolein were then added at 120° C. in the course of 30 minutes, gentle refluxing being established without heating. The reaction mixture was stirred for 3 hours at 120° C. and then evaporated down under reduced pressure, water was added to the residue and the mixture was extracted with methylene chloride. After filtration of active carbon, drying, filtration over neutral alumina with suction and evaporating down under reduced pressure, 190 g (75% of theory) of the title compound were obtained as a pale yellow syrup.
Reaction SMILES: [C:1]([CH2:4][CH2:5][CH2:6][CH2:7][CH2:8][CH2:9][CH:10]1[CH:14]([CH2:15][N+:16]([O-:18])=[O:17])[CH2:13][CH2:12][C:11]1=[O:19])([OH:3])=[O:2].[C:20]1([CH3:30])C=CC(S(O)(=O)=O)=CC=1.[OH2:31]>C1C=CC=CC=1.C(O)CO>[CH2:30]1[CH2:20][O:31][C:10]2([CH2:9][CH2:8][CH2:7][CH2:6][CH2:5][CH2:4][C:1]([OH:3])=[O:2])[CH:14]([CH2:15][N+:16]([O-:18])=[O:17])[CH2:13][CH2:12][CH:11]2[O:19]1
Reactant: Cc1ccc(S(=O)(=O)O)cc1
Reactant: O=C(O)CCCCCCC1C(=O)CCC1C[N+](=O)[O-]
Reactant: O
Solvent: OCCO
Solvent: c1ccccc1
Product: O=C(O)CCCCCCC12OCCOC1CCC2C[N+](=O)[O-]
Reaction time: 16 h

Procedure:
The solution of 2-(6-carboxyhexyl)-3-nitromethyl-cyclopentan-1-one, methyl ester (14 g.) in benzene (200 ml.), ethylene glycol (16.1 ml.), p-toluenesulphonic acid (0.315 g.), is heated to boiling for 16 hours. The reaction water is separated in a Marcusson apparatus. The mixture is washed with an aqueous saturated NaHCO3 -solution (50 ml.), then with water to neutrality, dried over sodium sulphate and the solvent is evaporated in vacuo. From the oily residue, by chromatography on silica (300 g.) and elution with benzene/ethyl acetate (6:1), 13 g. of 1-ethylenedioxy-2-(6-carboxyhexyl)-3-nitromethyl-cyclopentane, methyl ester, are obtained.
Reaction SMILES: [CH3:1][C@:2]12[CH2:19][CH2:18][C@H:17]3[C@@H:7]([CH2:8][CH2:9][C:10]4[C@:15]3([CH3:16])[CH:14]=[CH:13][C:12](=[O:20])[CH:11]=4)[C@@H:6]1[CH2:5][CH2:4][C:3]2=[O:21].[CH3:22][Al](C)C.O>O1CCOCC1.C1(C)C=CC=CC=1.[Cu]Br>[CH3:22][C@@H:14]1[C@@:15]2([CH3:16])[C:10]([CH2:9][CH2:8][C@@H:7]3[C@@H:17]2[CH2:18][CH2:19][C@@:2]2([CH3:1])[C@H:6]3[CH2:5][CH2:4][C:3]2=[O:21])=[CH:11][C:12](=[O:20])[CH2:13]1
Reactant: C[Al](C)C
Reactant: C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@]2(C)C(=O)CC[C@@H]12
Agent: [Cu]Br
Solvent: Cc1ccccc1
Solvent: O
Solvent: C1COCCO1
Product: C[C@H]1CC(=O)C=C2CC[C@@H]3[C@H](CC[C@]4(C)C(=O)CC[C@@H]34)[C@]21C
Temperature: 25 °C
Reaction time: 1.5 h

Procedure:
14.2 g (50 mmol) of androsta-1,4-diene-3,17-dione is dissolved under nitrogen atmosphere in 100 ml of anhydrous dioxane. 716 mg (5 mmol) of copper(I) bromide is added and the solution is heated to 25° C. Then 47 ml (55 mmol) of a 10% solution of trimethyl aluminum in toluene is added to the reaction so that the temperature does not rise above 35° C. Then it is stirred for 1.5 hours more at 35° C. For the hydrolysis, 2.5 ml of water mixed with 10 ml of dioxane is added to the reaction and the solution is stirred for 15 minutes more. The inorganic solid is suctioned off and washed again with 30 ml of dioxane. After concentration by evaporation of the dioxane solution, 17 g of crude product is obtained, that is chromatographed on silica gel with an hexane/ethyl acetate mixtures as eluent. After concentration by evaporation of the fractions and recrystallization from diisopropyl ether, 11.66 g of 1α-methylandrost-4-ene-3,17-dione (77% of theory) of a melting point of 154° C. is obtained.
Reaction SMILES: [OH:1][C:2]1[C:11]2[C:10]([CH3:13])([CH3:12])[CH2:9][CH2:8][C:7]([CH3:15])([CH3:14])[C:6]=2[CH:5]=[C:4]([CH:16]=[O:17])[CH:3]=1.[H-].[Na+].[CH3:20][O:21][CH2:22][CH2:23]Cl>CN(C=O)C>[CH3:13][C:10]1([CH3:12])[CH2:9][CH2:8][C:7]([CH3:15])([CH3:14])[C:6]2[CH:5]=[C:4]([CH:16]=[O:17])[CH:3]=[C:2]([O:1][CH2:23][CH2:22][O:21][CH3:20])[C:11]1=2
Reactant: COCCCl
Reactant: CC1(C)CCC(C)(C)c2c(O)cc(C=O)cc21
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: COCCOc1cc(C=O)cc2c1C(C)(C)CCC2(C)C
Reaction time: 1 h
Yield: 95 %

Procedure:
34 g (148 mmol) of 4-hydroxy-5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalene-2-carbaldehyde are dissolved in 400 mL of anhydrous DMF. 7.2 g (178 mmol) of 60% sodium hydride are then added portionwise, and the reaction medium is stirred for 1 hour. 16.5 mL (178 mmol) of 2-methoxyethyl chloride are added dropwise, and the medium is stirred at room temperature for 2 hours and then hydrolysed and extracted with ethyl ether. The organic phase is washed with 1N sodium hydroxide solution and then three times with water. The residue obtained is purified by chromatography (eluent:heptane). A yellow oil is obtained (m=42.7 g; yield=95%).
Reaction SMILES: [Br:1][C:2]1[CH:10]=[C:9]([CH3:11])[CH:8]=[CH:7][C:3]=1[C:4](O)=[O:5].C[N:13](C=O)C>C1(C)C=CC=CC=1.S(Cl)(Cl)=O>[Br:1][C:2]1[CH:10]=[C:9]([CH3:11])[CH:8]=[CH:7][C:3]=1[C:4]([NH2:13])=[O:5]
Reactant: CN(C)C=O
Reactant: Cc1ccc(C(=O)O)c(Br)c1
Solvent: Cc1ccccc1
Solvent: O=S(Cl)Cl
Product: Cc1ccc(C(N)=O)c(Br)c1
Temperature: 50 °C
Reaction time: 3 h
Yield: 99 %

Procedure:
To a suspension of 2-bromo-4-methylbenzoic acid (15.0 g, 69.8 mmol) in toluene (60 mL), thionyl chloride (10.3 mL) and DMF (0.10 mL) were added and stirred at 50° C. for 3 h. After cooling to room temperature, the excess thionyl chloride was removed in vacuo. The residue was dissolved in toluene (50 mL), and the mixture was added to the solution of ammonia (25%, 60 mL). The white precipitate was filtered over Celite and dried in vacuo to afford 2-bromo-4-methylbenzamide (14.8 g, 99%).
Reaction SMILES: [Cl:1][C:2]1[C:10]([Cl:11])=[CH:9][C:5]2[N:6]=[CH:7][NH:8][C:4]=2[CH:3]=1.F[C:13]1[CH:20]=[CH:19][C:16]([CH:17]=[O:18])=[CH:15][CH:14]=1.C(=O)([O-])[O-].[K+].[K+].O>CS(C)=O>[Cl:11][C:10]1[C:2]([Cl:1])=[CH:3][C:4]2[N:8]([C:13]3[CH:20]=[CH:19][C:16]([CH:17]=[O:18])=[CH:15][CH:14]=3)[CH:7]=[N:6][C:5]=2[CH:9]=1
Reactant: O=Cc1ccc(F)cc1
Reactant: Clc1cc2nc[nH]c2cc1Cl
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CS(C)=O
Solvent: O
Product: O=Cc1ccc(-n2cnc3cc(Cl)c(Cl)cc32)cc1
Temperature: 100 °C
Yield: 61.8 %

Procedure:
A mixture of 5,6-dichlorobenzimidazole (94 mg, 0.50 mmol), 4-fluorobenzaldehyde (0.064 mL, 0.60 mmol), and potassium carbonate (83 mg, 0.60 mmol) in dimethylsulfoxide (3 mL) was heated at 100° C. for 3 h. The mixture was cooled to room temperature, and water was added. The precipitated product was collected by filtration and washed with water and ethanol to afford 5,6-dicloro-1-(4-formylphenyl)benzimidazole (90 mg, 62%).
Reaction SMILES: [NH2:1][C@@H:2]([CH2:6][CH2:7][C@H:8]([NH2:30])[CH2:9][C@@H:10]1[C@@H:14]([OH:15])[C@@H:13]([O:16]CC#C)[C@H:12]([N:20]2[CH:28]=[N:27][C:26]3[C:21]2=[N:22][CH:23]=[N:24][C:25]=3[NH2:29])[O:11]1)[C:3]([OH:5])=[O:4]>CO.O.CC(O)=O>[CH:23]1[N:24]=[C:25]([NH2:29])[C:26]2[N:27]=[CH:28][N:20]([C@@H:12]3[O:11][C@H:10]([CH2:9][C@@H:8]([NH2:30])[CH2:7][CH2:6][C@H:2]([NH2:1])[C:3]([OH:5])=[O:4])[C@@H:14]([OH:15])[C@H:13]3[OH:16])[C:21]=2[N:22]=1
Reactant: C#CCO[C@@H]1[C@H](O)[C@@H](C[C@@H](N)CC[C@H](N)C(=O)O)O[C@H]1n1cnc2c(N)ncnc21
Solvent: CO
Solvent: CC(=O)O
Solvent: O
Product: Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@H](N)C(=O)O)[C@@H](O)[C@H]1O

Procedure:
The title detection analyte compound was prepared from Compound 7 (Example 1, Step 3a) by coupling with 6-carboxyfluorescein-PEG3 azide (Berry & Associates, CAS #412319-45-0, Catalog No. FF6110) using the click chemistry methods reported herein; LC/MS (Gemini C18, 3μ, 2.0×50 mm, 400 μL/min, A: 90/10/0.01 H2O/MeOH/HOAc, B 90/10/0.01 MeOH/H2O/HOAc 0-6 min 0-100% B, 6-9 hold at 100% B, 9.1-15 min re-equilibrate at 0% B) 4.3 min (100% purity), ESI+ m/z 498 (z=2; expected molecular mass: 996).
Reaction SMILES: C[Si](C)(C)[C:3]1[C:7]([C:8]2[CH:9]=[CH:10][C:11]3[S:16][C:15]4[N:17]=[CH:18][CH:19]=[N:20][C:14]=4[N:13]([CH2:21][O:22][CH3:23])[C:12]=3[CH:24]=2)=[CH:6][NH:5][N:4]=1.[F-].C([N+](CCCC)(CCCC)CCCC)CCC.C(OCC)(=O)C.Cl>O1CCCC1>[NH:5]1[CH:6]=[C:7]([C:8]2[CH:9]=[CH:10][C:11]3[S:16][C:15]4[N:17]=[CH:18][CH:19]=[N:20][C:14]=4[N:13]([CH2:21][O:22][CH3:23])[C:12]=3[CH:24]=2)[CH:3]=[N:4]1
Reactant: COCN1c2cc(-c3c[nH]nc3[Si](C)(C)C)ccc2Sc2nccnc21
Agent: CCCC[N+](CCCC)(CCCC)CCCC
Agent: Cl
Agent: [F-]
Solvent: CCOC(C)=O
Solvent: C1CCOC1
Product: COCN1c2cc(-c3cn[nH]c3)ccc2Sc2nccnc21
Reaction time: 0.08 h
Yield: 39.8 %

Procedure:
5 ml of a solution of 130 mg of 8-(3-trimethylsilyl-pyrazol-4-yl)-10-methoxymethyl-10H-pyrazino(2,3-b][1,4]-benzothiazine in tetrahydrofuran was stirred at room temperature and 1.1 ml of a 1M solution of tetrabutylammonium fluoride in tetrahydrofuran was added thereto. After stirring for 5 minutes, the reaction mixture was distributed into ethyl acetate and 1 N hydrochloric acid. The organic layer was extracted, washed with water and dried over anhydrous sodium sulfate. After distilling off the solvent under reduced pressure, the obtained residue was purified by silica gel column chromatography (eluted with dichloromethane/methanol) to thereby give 42 mg of the title compound as yellow crystals.
Reaction SMILES: [NH2:1][C@@H:2]([CH:15]([CH3:17])[CH3:16])[C:3]([NH:5][C@@H:6]([CH3:14])[C:7]([O:9][C:10]([CH3:13])([CH3:12])[CH3:11])=[O:8])=[O:4].[C:18]1(=[O:33])[N:22]([C:23]2[CH:31]=[CH:30][C:26]([C:27](O)=[O:28])=[CH:25][CH:24]=2)[C:21](=[O:32])[CH:20]=[CH:19]1.CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.[B-](F)(F)(F)F.CCN(C(C)C)C(C)C>ClCCl>[O:32]=[C:21]1[CH:20]=[CH:19][C:18](=[O:33])[N:22]1[C:23]1[CH:31]=[CH:30][C:26]([C:27]([NH:1][C@@H:2]([CH:15]([CH3:17])[CH3:16])[C:3]([NH:5][C@@H:6]([CH3:14])[C:7]([O:9][C:10]([CH3:11])([CH3:13])[CH3:12])=[O:8])=[O:4])=[O:28])=[CH:25][CH:24]=1
Reactant: O=C(O)c1ccc(N2C(=O)C=CC2=O)cc1
Reactant: CC(C)[C@H](N)C(=O)N[C@@H](C)C(=O)OC(C)(C)C
Agent: CN(C)C(On1nnc2ccccc21)=[N+](C)C
Agent: F[B-](F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: ClCCl
Product: CC(C)[C@H](NC(=O)c1ccc(N2C(=O)C=CC2=O)cc1)C(=O)N[C@@H](C)C(=O)OC(C)(C)C
Temperature: 25 °C
Reaction time: 16 h
Yield: 52.2 %

Procedure:
To a mixture of the 97 (100 mg, 0.41 mmol) and 4-maleimidobenzoic acid (101) (98 mg, 0.45 mmol) was added dichloromethane (5 mL), followed by TBTU (157 mg, 0.49 mmol) and DIPEA (212 uL, 1.23 mmol). The mixture was stirred at an ambient temperature for 16 h and then purified on a 2 mm radial chromatotron plate eluting with 50% ethyl acetate in hexanes to give 95 mg (51%) of 100: 1H-NMR (400 MHz, CDCl3) δ 7.85 (d, J=6.6 Hz, 2H), 7.42 (d, J=6.6 Hz, 2H), 6.81 (s, 2H), 6.38 (bs, 1H), 4.43 (m, 2H), 2.14 (sept, J=6.6 Hz, 1H), 1.41 (s, 9H), 1.31 (d, J=7.0 Hz, 3H), 0.98 (m, 6H); MS (ES−) m/z 441.90 [M−H]−.