Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH3:1][C:2]1([CH2:5][OH:6])[CH2:4][CH2:3]1.[CH3:7][S:8](Cl)(=[O:10])=[O:9]>C(Cl)Cl>[CH3:7][S:8]([O:6][CH2:5][C:2]1([CH3:1])[CH2:4][CH2:3]1)(=[O:10])=[O:9]
Reactant: CC1(CO)CC1
Reactant: CS(=O)(=O)Cl
Solvent: ClCCl
Product: CC1(COS(C)(=O)=O)CC1
Temperature: 0 °C
Reaction time: 2 h
Yield: 96 %

Procedure:
Treat a cooled solution (0° C.) of 1-methylcyclopropanemethanol (2.0 g, 23.22 mmol) in DCM (75 mL) with TEA (2.58 g, 25.5 mmol) and add methanesulfonyl chloride (2.93 g, 25.5 mmol) dropwise. Stir the mixture at 0° C. for 2 h, wash with H2O then brine, dry over Na2SO4 and concentrate to dryness to afford the title compound (3.66 g, 96%) as an oil. 1H NMR (400 MHz, DMSO-d6): δ 3.60 (s, 3H), 2.10 (m, 2H), 0.72 (s, 3H), 0.14 (m, 2H), 0.01 (m, 2H).
Reaction SMILES: [S:1]1[CH:5]=[CH:4][CH:3]=[C:2]1[CH2:6][O:7][C:8]1[CH:9]=[C:10]([CH:16]=[CH:17][CH:18]=1)[C:11]([O:13]CC)=O.[C:19](#[N:21])[CH3:20]>>[O:13]=[C:11]([C:10]1[CH:16]=[CH:17][CH:18]=[C:8]([O:7][CH2:6][C:2]2[S:1][CH:5]=[CH:4][CH:3]=2)[CH:9]=1)[CH2:20][C:19]#[N:21]
Reactant: CC#N
Reactant: CCOC(=O)c1cccc(OCc2cccs2)c1
Product: N#CCC(=O)c1cccc(OCc2cccs2)c1

Procedure:
Condensation between ethyl 3-(thiophen-2-ylmethoxy)benzoate and acetonitrile gave after flash column chromatography 3-oxo-3-(3-(thiophen-2-ylmethoxy)phenyl)propanenitrile as a pale yellow solid. Yield (2.60 g, 83%); 1H NMR (400 MHz, CDCl3): δ 7.52 (s, 1H), 7.48-7.41 (m, 2H), 3.73 (d, J=3.2 Hz, 2H), 7.27 (s, 1H), 7.15 (d, J=4.8 Hz, 1H), 5.13 (s, 2H), 4.05 (s, 2H); MS: m/z 258.0.
Reaction SMILES: [CH2:1]([N:8]=[C:9]=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[C:11]1([C:17]2([CH2:27][OH:28])[C:21]3[CH2:22][NH:23][CH2:24][CH2:25][C:20]=3[C:19](=[O:26])[O:18]2)[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=1>ClCCl>[CH2:1]([NH:8][C:9]([N:23]1[CH2:24][CH2:25][C:20]2[C:19](=[O:26])[O:18][C:17]([CH2:27][OH:28])([C:11]3[CH:16]=[CH:15][CH:14]=[CH:13][CH:12]=3)[C:21]=2[CH2:22]1)=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: O=C=NCc1ccccc1
Reactant: O=C1OC(CO)(c2ccccc2)C2=C1CCNC2
Solvent: ClCCl
Product: O=C1OC(CO)(c2ccccc2)C2=C1CCN(C(=O)NCc1ccccc1)C2
Temperature: 25 °C
Reaction time: 1 h
Yield: 51 %

Procedure:
Benzyl isocyanate (0.069 g, 0.52 mmol) was added to a solution of 3-phenyl-3-hydroxymethyl-4,5,6,7-tetrahydrofuro[3,4-c]pyridin-1(3H)-one (0.128 g, 0.52 mmol prepared in a manner analogous to compound 2) in dichloromethane (10 mL) and was stirred at room temperature for 1 h. The solvent was removed and the resulting residue was purified on silica to give the desired product (0.101 g, 51%). 1H NMR (300 MHz, CHLOROFORM-d) δ ppm 2.18-2.47 (m, 2H), 3.19-3.31 (m, 1H), 3.63 (dt, J=13.75, 4.99 Hz, 1H), 3.94-4.07 (m, 3H), 4.07-4.18 (m, 1H), 4.35 (d, J=5.65 Hz, 2H), 4.47 (d, J=18.84 Hz, 1H), 5.50 (t, J=5.65 Hz, 1H), 7.15-7.25 (m, 4H), 7.27-7.42 (m, 6H).
Reaction SMILES: O=[CH:2][C@@H:3]([C@H:5]([C@@H:7]([C@@H:9]([CH2:11]O)O)O)O)O.[NH2:13][C@H:14]([C:16]([OH:18])=[O:17])[CH3:15]>>[NH2:13][C@@H:14]([C:16]([OH:18])=[O:17])[CH2:15][C:2]1[CH:11]=[CH:9][CH:7]=[CH:5][CH:3]=1.[NH2:13][C@H:14]([C:16]([OH:18])=[O:17])[CH2:15][C:2]1[CH:11]=[CH:9][CH:7]=[CH:5][CH:3]=1
Reactant: O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
Reactant: C[C@H](N)C(=O)O
Product: N[C@@H](Cc1ccccc1)C(=O)O
Product: N[C@H](Cc1ccccc1)C(=O)O
Reaction time: 12 h

Procedure:
The amount of glucose fed was 2021 g over 52 hours. The fermentation medium included a D-, L-alanine feed whereby a total of 1400 mls of 167 g/l D-, L-alanine was fed at a rate of 1.9 ml/min starting 12 hrs from the beginning of the fermentation. In addition, L-phenylalanine was fed at the same concentration and rate as the D-, L-alanine. The fermentation resulted in 13.66 g/l of D-phenylalanine and 0.87 g/l L-phenylalanine being produced.
Reaction SMILES: N1C(C)=CC(C)=CC=1C.[Br:10][CH2:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][OH:21].[C:22](Cl)(=[O:26])[C:23]([CH3:25])=[CH2:24]>ClCCl>[Br:10][CH2:11][CH2:12][CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][O:21][C:22](=[O:26])[C:23]([CH3:25])=[CH2:24]
Reactant: OCCCCCCCCCCBr
Reactant: C=C(C)C(=O)Cl
Solvent: ClCCl
Solvent: Cc1cc(C)nc(C)c1
Product: C=C(C)C(=O)OCCCCCCCCCCBr
Temperature: 0 °C
Reaction time: 15 h
Yield: 69.9 %

Procedure:
2,4,6-Collidin (12.3 ml, 92.7 mmol, 1.1 eq.) was added to a solution of 10-bromodecanol (20.0 g, 84.3 mmol) in anhydrous dichloromethane (200 ml). After cooling the mixture to 0° C. methacrylic acid chloride (16.5 ml, 168.6 mmol, 2 eq.) was slowly added dropwise and the reaction mixture was stirred for 1 h at 0° C. and at for 15 h room temperature. The reaction mixture was then washed with water (100 ml) and cold 1N HCl (100 ml). The combined organic phases were dried with anhydrous sodium sulphate. After removal of the solvent under reduced pressure the obtained crude product was purified by column chromatography (eluent: hexane/dichloromethane 8:2). 18.0 g (70% yield) of the product was obtained as a colorless liquid.
Reaction SMILES: [CH3:1][S:2](Cl)(=[O:4])=[O:3].[OH:6][CH2:7][CH2:8][CH2:9][C:10]1[NH:11][C:12]2[CH:13]=[CH:14][C:15]([N+:23]([O-:25])=[O:24])=[C:16]([C:19]([O:21][CH3:22])=[O:20])[C:17]=2[CH:18]=1>N1C=CC=CC=1.C(Cl)Cl>[CH3:1][S:2]([O:6][CH2:7][CH2:8][CH2:9][C:10]1[NH:11][C:12]2[CH:13]=[CH:14][C:15]([N+:23]([O-:25])=[O:24])=[C:16]([C:19]([O:21][CH3:22])=[O:20])[C:17]=2[CH:18]=1)(=[O:4])=[O:3]
Reactant: CS(=O)(=O)Cl
Reactant: COC(=O)c1c([N+](=O)[O-])ccc2[nH]c(CCCO)cc12
Solvent: ClCCl
Solvent: c1ccncc1
Product: COC(=O)c1c([N+](=O)[O-])ccc2[nH]c(CCCOS(C)(=O)=O)cc12
Temperature: 25 °C
Reaction time: 4 h
Yield: 99.8 %

Procedure:
Methanesulfonyl chloride (0.176 g) was added to a solution of methyl 2-(3-hydroxypropyl)-5-nitro-1H-indole-4-carboxylate (Intermediate 21, 0.360 g) in pyridine (1 mL) and DCM (10 mL) and the reaction mixture was stirred at room temperature for 4 hours. The mixture was diluted with DCM, washed with aqueous citric acid (5%), aqueous sodium bicarbonate and brine, dried (MgSO4) and filtered. The filtrate was concentrated in vacuo and the residue was dissolved in toluene and evaporated to dryness, four times to give methyl 2-(3-methanesulfonyloxypropyl)-5-nitro-1H-indole-4-carboxylate (0.460 g) as an orange gum.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[CH:4][C:5]2[CH2:11][CH2:10][CH:9]([NH:12][CH2:13][CH2:14][OH:15])[CH2:8][CH2:7][C:6]=2[C:16]=1[O:17][CH3:18].Cl[C:20]1[N:25]=[C:24]([NH:26][C:27]2[CH:32]=[CH:31][C:30]([N:33]3[CH2:38][CH2:37][O:36][CH2:35][CH2:34]3)=[CH:29][C:28]=2[O:39][CH3:40])[C:23]([Cl:41])=[CH:22][N:21]=1>>[Cl:41][C:23]1[C:24]([NH:26][C:27]2[CH:32]=[CH:31][C:30]([N:33]3[CH2:34][CH2:35][O:36][CH2:37][CH2:38]3)=[CH:29][C:28]=2[O:39][CH3:40])=[N:25][C:20]([NH:1][C:2]2[CH:3]=[CH:4][C:5]3[CH2:11][CH2:10][CH:9]([NH:12][CH2:13][CH2:14][OH:15])[CH2:8][CH2:7][C:6]=3[C:16]=2[O:17][CH3:18])=[N:21][CH:22]=1
Reactant: COc1cc(N2CCOCC2)ccc1Nc1nc(Cl)ncc1Cl
Reactant: COc1c(N)ccc2c1CCC(NCCO)CC2
Product: COc1cc(N2CCOCC2)ccc1Nc1nc(Nc2ccc3c(c2OC)CCC(NCCO)CC3)ncc1Cl
Yield: 38 %

Procedure:
In an analogous manner to Experimental 691, part c, 2-(2-amino-1-methoxy-6,7,8,9-tetrahydro-5H-benzocyclohepten-7-ylamino)-ethanol and (2,5-Dichloro-pyrimidin-4-yl)-(2-methoxy-4-morpholin-4-yl-phenyl)-amine were combined to yield 2-{2-[5-Chloro-4-(2-methoxy-4-morpholin-4-yl-phenylamino)-pyrimidin-2-ylamino]-1-methoxy-6,7,8,9-tetrahydro-5H-benzocyclohepten-7-ylamino}-ethanol (146.19 mg, 38% yield) as a beige foam. 1H-NMR (CDCl3) δ 8.25 (d, J=7.5 Hz, 1H), 8.03 (m, 2H), 7.54 (s, 1H), 7.37 (s, 1H), 6.83 (d, J=6.9 Hz, 1H), 6.54 (m, 2H), 3.91 (br s, 6H), 3.72 (s, 3H), 3.63 (s, 2H), 3.17 (m, 5H), 2.85 (m, 4H), 2.68 (m, 1H), 2.47 (m, 1H), 2.14 (m, 2H), 1.31 (m, 3H). LC/MS (ESI+)=569 (M+H).
Reaction SMILES: [O:1]1[CH:6]([C:7]([OH:9])=[O:8])[CH:2]1[C:3]([OH:5])=O.[CH2:10]([K])[CH3:11].C(Cl)(=O)C(Cl)=O.[CH:19]1([NH2:24])[CH2:23][CH2:22][CH2:21][CH2:20]1>>[CH:19]1([NH:24][C:3](=[O:5])[CH:2]2[O:1][CH:6]2[C:7]([O:9][CH2:10][CH3:11])=[O:8])[CH2:23][CH2:22][CH2:21][CH2:20]1
Reactant: O=C(O)C1OC1C(=O)O
Reactant: NC1CCCC1
Reactant: CC[K]
Agent: O=C(Cl)C(=O)Cl
Product: CCOC(=O)C1OC1C(=O)NC1CCCC1
Yield: 62.6 %

Procedure:
Following the procedure of Example 1, monoethyl potassium epoxysuccinate (1.0 g) was successively treated with oxalyl chloride (0.75 g) and cyclopentylamine (0.86 g) to give 0.71 g of ethyl N-cyclopentyl-2,3-epoxysuccinamate (Compound No. 18) as colorless needles melting at 94°-97° C.
Reaction SMILES: [CH2:1]([O:8][C:9]([NH:11][C@H:12]([C:25]1[NH:26][C:27]([C:30]2[CH:39]=[CH:38][C:37]3[C:32](=[CH:33][CH:34]=[C:35]([O:40][CH3:41])[CH:36]=3)[CH:31]=2)=[CH:28][N:29]=1)[CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][C:18]([O:20]C(C)(C)C)=[O:19])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[C:42]([OH:48])([C:44]([F:47])([F:46])[F:45])=[O:43].C1(C)C=CC=CC=1.CCOCC>C(Cl)Cl>[F:45][C:44]([F:47])([F:46])[C:42]([O-:48])=[O:43].[CH2:1]([O:8][C:9]([NH:11][C@H:12]([C:25]1[NH:26][C:27]([C:30]2[CH:39]=[CH:38][C:37]3[C:32](=[CH:33][CH:34]=[C:35]([O:40][CH3:41])[CH:36]=3)[CH:31]=2)=[CH:28][NH+:29]=1)[CH2:13][CH2:14][CH2:15][CH2:16][CH2:17][C:18]([OH:20])=[O:19])=[O:10])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1
Reactant: COc1ccc2cc(-c3cnc([C@H](CCCCCC(=O)OC(C)(C)C)NC(=O)OCc4ccccc4)[nH]3)ccc2c1
Reactant: O=C(O)C(F)(F)F
Solvent: ClCCl
Solvent: CCOCC
Solvent: Cc1ccccc1
Product: COc1ccc2cc(-c3c[nH+]c([C@H](CCCCCC(=O)O)NC(=O)OCc4ccccc4)[nH]3)ccc2c1
Product: O=C([O-])C(F)(F)F
Temperature: 25 °C
Reaction time: 2 h

Procedure:
To a stirred solution of E1 in DCM (0.2 M) cooled to 0° C. TFA (70 eq.) was slowly added. The reaction mixture was stirred at room temperature for 2 h. Then, solvent was evaporated under reduced pressure to afford an oily residue that was co-evaporated first with toluene then with Et2O to give the title compound as a pale red solid which was used as such in the next step. MS (ES+) C29H31N3O5: 502 (M+H)+.
Reaction SMILES: [CH3:1][O:2][C:3]1[C:10]([O:11][CH3:12])=[C:9]([O:13][CH3:14])[C:8]([O:15][CH3:16])=[CH:7][C:4]=1[CH:5]=[O:6].C(Cl)[Cl:18]>>[Cl:18][C:7]1[C:8]([O:15][CH3:16])=[C:9]([O:13][CH3:14])[C:10]([O:11][CH3:12])=[C:3]([O:2][CH3:1])[C:4]=1[CH:5]=[O:6]
Reactant: COc1cc(C=O)c(OC)c(OC)c1OC
Reactant: ClCCl
Product: COc1c(Cl)c(C=O)c(OC)c(OC)c1OC
Reaction time: 1 h
Yield: 97 %

Procedure:
According to a general aryl chlorination procedure by Lopez-Alvarado,39 19 (0.767 g, 3.39 mmol) was dissolved in CH2Cl2 (10.0 mL) at room temperature and then SO2Cl2 (neat, 0.31 mL, 3.7 mmol) was added at room temperature. The reaction was stirred for 1 hour and monitored by 1H NMR for completion. The reaction was then diluted with CH2Cl2, washed with brine, dried over MgSO4, filtered, and condensed. The resulting oil was then purified by flash column chromatography (1:4 Et2O:hexanes) to provide 20 (0.861 g, 3.30 mmol, 97%) as a colorless oil.
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([N:8]2[C:12]([CH:13]([CH3:15])[CH3:14])=[C:11]([NH2:16])[CH:10]=[N:9]2)=[CH:4][CH:3]=1.[CH3:17][C:18]1[N:22]([CH:23]([CH3:27])[C:24](O)=[O:25])[N:21]=[C:20]([C:28]([F:31])([F:30])[F:29])[N:19]=1.C(N(C(C)C)CC)(C)C.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F>CN(C=O)C.O>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([N:8]2[C:12]([CH:13]([CH3:14])[CH3:15])=[C:11]([NH:16][C:24](=[O:25])[CH:23]([N:22]3[C:18]([CH3:17])=[N:19][C:20]([C:28]([F:29])([F:30])[F:31])=[N:21]3)[CH3:27])[CH:10]=[N:9]2)=[CH:6][CH:7]=1
Reactant: Cc1nc(C(F)(F)F)nn1C(C)C(=O)O
Reactant: CC(C)c1c(N)cnn1-c1ccc(Cl)cc1
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: O
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: Cc1nc(C(F)(F)F)nn1C(C)C(=O)Nc1cnn(-c2ccc(Cl)cc2)c1C(C)C
Temperature: 25 °C
Reaction time: 1 h
Yield: 24.8 %

Procedure:
To a solution of 1-(4-chlorophenyl)-5-isopropylpyrazol-4-amine (0.054 g, 0.23 mmol) in DMF (1.0 mL) was added 2-[5-methyl-3-(trifluoromethyl)-1,2,4-triazol-1-yl]propanoic acid (0.051 g, 0.23 mmol), followed by diisopropylethylamine (0.059 g, 0.46 mmol) and HATU (0.105 g, 0.28 mmol). After stirring at room temperature for 1 h, the reaction was diluted with water and the aqueous layer was extracted with ethyl acetate (2×5 mL). The combined organic layers were washed with brine, dried (Na2SO4), filtered, and concentrated in vacuo. The resulting crude product was purified by reverse phase HPLC (C18 column, acetonitrile-H2O with 0.1% TFA as eluent) to give the title compound as a white solid (0.025 g, 0.057 mmol, 25%). 1H NMR (400 MHz, CDCl3) δ 8.25 (s, 1H), 8.03 (d, J=0.6 Hz, 1H), 7.49-7.41 (m, 2H), 7.32-7.23 (m, 2H), 5.12 (q, J=7.2 Hz, 1H), 3.02 (m, 1H), 2.61 (s, 3H), 1.92 (d, J=7.2 Hz, 3H), 1.27 (d, J=7.2 Hz, 3H), 1.10 (d, J=7.2 Hz, 3H); MS: (ES) m/z calculated for C19H20ClF3N6O [M+H]+ 441.1, found 440.9.
Reaction SMILES: [CH2:1]([O:3][C:4](=[O:28])[CH:5]([O:24][CH:25]([CH3:27])[CH3:26])[CH2:6][C:7]1[CH:12]=[C:11]([CH2:13][NH:14][C:15]([O:17][C:18]([CH3:21])([CH3:20])[CH3:19])=[O:16])[C:10]([OH:22])=[C:9](Br)[CH:8]=1)[CH3:2].[I:29]N1C(=O)CCC1=O>C(#N)C.C(OCC)(=O)C>[CH2:1]([O:3][C:4](=[O:28])[CH:5]([O:24][CH:25]([CH3:27])[CH3:26])[CH2:6][C:7]1[CH:12]=[C:11]([CH2:13][NH:14][C:15]([O:17][C:18]([CH3:21])([CH3:20])[CH3:19])=[O:16])[C:10]([OH:22])=[C:9]([I:29])[CH:8]=1)[CH3:2]
Reactant: CCOC(=O)C(Cc1cc(Br)c(O)c(CNC(=O)OC(C)(C)C)c1)OC(C)C
Reactant: O=C1CCC(=O)N1I
Solvent: CCOC(C)=O
Solvent: CC#N
Product: CCOC(=O)C(Cc1cc(I)c(O)c(CNC(=O)OC(C)(C)C)c1)OC(C)C
Temperature: 25 °C
Reaction time: 60 h
Yield: 35.9 %

Procedure:
253 mg of 3-(3-bromo-5-[(t-butoxycarbonyl)amino]methyl-4-hydroxyphenyl)-2-isopropoxypropionic acid ethyl ester was dissolved in 3 ml of acetonitrile, and 157 mg of N-iodosuccinimide was added. After stirring for 2.5 days at room temperature, the reaction mixture was diluted with ethyl acetate. The organic layer was washed with water and saturated sodium thiosulfate water, and dried over anhydrous magnesium sulfate, and the solvent was evaporated. The residue was purified by silica gel column chromatography, and 100 mg of 3-(3-iodo-5-[(t-butoxycarbonyl)amino]methyl-4-hydroxyphenyl)-2-isopropoxypropionic acid ethyl ester was obtained from fractions eluted with hexane-ethyl acetate (4:1).
Reaction SMILES: [H-].[K+].[Cl:3][C:4]1[C:5]([Cl:25])=[CH:6][C:7]2[C:8]3[CH2:17][CH2:16][N:15]([C:18]([O:20][C:21]([CH3:24])([CH3:23])[CH3:22])=[O:19])[CH2:14][CH2:13][C:9]=3[NH:10][C:11]=2[CH:12]=1.Br[CH2:27][CH2:28][CH2:29][C:30]1[CH:35]=[CH:34][CH:33]=[CH:32][CH:31]=1>CN(C=O)C>[Cl:3][C:4]1[C:5]([Cl:25])=[CH:6][C:7]2[C:8]3[CH2:17][CH2:16][N:15]([C:18]([O:20][C:21]([CH3:22])([CH3:24])[CH3:23])=[O:19])[CH2:14][CH2:13][C:9]=3[N:10]([CH2:27][CH2:28][CH2:29][C:30]3[CH:35]=[CH:34][CH:33]=[CH:32][CH:31]=3)[C:11]=2[CH:12]=1
Reactant: CC(C)(C)OC(=O)N1CCc2[nH]c3cc(Cl)c(Cl)cc3c2CC1
Reactant: BrCCCc1ccccc1
Agent: [H-]
Agent: [K+]
Solvent: CN(C)C=O
Product: CC(C)(C)OC(=O)N1CCc2c(n(CCCc3ccccc3)c3cc(Cl)c(Cl)cc23)CC1
Reaction time: 5 h
Yield: 79.2 %

Procedure:
Potassium hydride (45 mg, 1.1 mmol) was added to a solution of tert-butyl 8,9-dichloro-1,4,5,6-tetrahydroazepino[4,5-b]indole-3(2H)-carboxylate (0.20 g, 0.56 mmol) in DMF (1.0 mL). After 15 nm, 1-bromo-3-phenylpropane (0.13 mL, 0.86 mmol) was added. After 5 h, the reaction was quenched with saturated aqueous NH4Cl (10 mL) and extracted with CH2Cl2 (3×10 mL). The combined organic extracts were washed with brine, dried over Na2SO4, decanted, and concentrated. The crude product was purified by column chromatography (Biotage, 40S) with heptane/EtOAc (3:1) to give 0.21 g (78%) of a yellow solid: mp 119-124° C.; IR (diffuse reflectance) 2980, 2973, 2941, 2932, 1686, 1478, 1462, 1417, 1365, 1247, 1178, 1160, 1112, 855, 699cm−1; MS (EI) m/z 472 (M+), 416, 227, 226, 224, 211, 188, 153, 115, 90, 56; Anal. Calcd for C26H30Cl2N2O2: C, 65.96; H, 6.39; N, 5.92; found: C, 66.01; H, 6.47; N, 5.82.
Reaction SMILES: F[C:2]1[CH:9]=[CH:8][CH:7]=[C:6]([I:10])[C:3]=1[C:4]#[N:5].C(=O)(O)O.[NH2:15][C:16]([NH2:18])=[NH:17]>CC(N(C)C)=O>[I:10][C:6]1[CH:7]=[CH:8][CH:9]=[C:2]2[C:3]=1[C:4]([NH2:5])=[N:17][C:16]([NH2:18])=[N:15]2
Reactant: N=C(N)N
Reactant: N#Cc1c(F)cccc1I
Agent: O=C(O)O
Solvent: CC(=O)N(C)C
Product: Nc1nc(N)c2c(I)cccc2n1
Temperature: 165 °C
Yield: 19.5 %

Procedure:
2-Fluoro-6-iodobenzonitrile (700 mg; 2.83 mmol) is dissolved in dimethylacetamide (5 mL) with guanidine carbonate (766 mg; 4.25 mmol). The vessel is purged with N2, sealed, and heated to 165° C. for 5 hours. After cooling to room temperature, the reaction mixture is placed in the freezer overnight. The precipitate which has formed is removed by filtration and purified by recrystallization from 50% EtOH/water. The resulting solids are filtered and dried at room temperature to yield 158 mg of 5-iodoquinazoline-2,4-diamine.
Reaction SMILES: [Cl:1][C:2]1[C:3]([N:8]2[C:12]([C:13](Cl)=[O:14])=[CH:11][C:10]([C:16]([F:19])([F:18])[F:17])=[N:9]2)=[N:4][CH:5]=[CH:6][CH:7]=1.[NH2:20][C:21]1[C:29]([CH3:30])=[CH:28][CH:27]=[CH:26][C:22]=1[C:23](O)=[O:24].C(N(CC)CC)C.CS(Cl)(=O)=O>C(#N)C.O>[Cl:1][C:2]1[C:3]([N:8]2[C:12]([C:13]3[O:14][C:23](=[O:24])[C:22]4[CH:26]=[CH:27][CH:28]=[C:29]([CH3:30])[C:21]=4[N:20]=3)=[CH:11][C:10]([C:16]([F:19])([F:18])[F:17])=[N:9]2)=[N:4][CH:5]=[CH:6][CH:7]=1
Reactant: Cc1cccc(C(=O)O)c1N
Reactant: O=C(Cl)c1cc(C(F)(F)F)nn1-c1ncccc1Cl
Agent: CS(=O)(=O)Cl
Solvent: O
Solvent: CCN(CC)CC
Solvent: CC#N
Product: Cc1cccc2c(=O)oc(-c3cc(C(F)(F)F)nn3-c3ncccc3Cl)nc12
Temperature: 25 °C
Reaction time: 0.17 h
Yield: 44.6 %

Procedure:
To a solution of 2.0 g of 1-(3-chloro-2-pyridinyl)-3-trifluoromethyl-1H-pyrazole-5-carbonyl chloride in 50 ml of acetonitrile, 0.98 g of 2-amino-3-methylbenzoic acid was added. The mixture was stirred at room temperature for 10 minutes and then, 0.9 ml of triethylamine was added thereto. The mixture was stirred at room temperature for 20 minutes and then, 1.8 ml of triethylamine was further added thereto. After the mixture was stirred at room temperature for 20 minutes, 0.56 ml of methanesulfonyl chloride was added and the mixture was stirred at room temperature for 3 hours. Water was poured into the reaction mixture, and the mixture was extracted with ethyl acetate two times. The organic layers were combined, washed with an aqueous saturated sodium chloride solution, dried over anhydrous magnesium sulfate, and concentrated under reduced pressure. The resulting residue was subjected to silica gel column chromatography to obtain 1.17 g of 2-[1-(3-chloro-2-pyridinyl)-3-trifluoromethyl-1H-pyrazol-5-yl]-8-methyl-4H-3,1-benzoxazine-4-one of the formula:
Reaction SMILES: C1N=C2N([C@@H]3[O:14][C@H](COP(OP(OP(O)(O)=O)(O)=O)(O)=O)[C@@H](O)C3)C=NC2=C(N)N=1.P(OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C[C@@H]1O)(OP(OP(O)(O)=O)(O)=O)(=O)O.P(OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O)(OP(OP(O)(O)=O)(O)=O)(=O)O.[CH:90]1[C:96](=[O:97])[NH:95][C:93](=[O:94])[N:92]([C@@H:98]2[O:102][C@H:101]([CH2:103][O:104]P(OP(OP(O)(O)=O)(O)=O)(O)=O)[C@@H:100]([OH:117])[CH2:99]2)[CH:91]=1.C1(O)C=CC=CC=1>>[C@@H:98]1([N:92]2[CH:91]=[CH:90][C:96](=[O:97])[NH:95][C:93]2=[O:94])[O:102][C@H:101]([CH2:103][OH:104])[C@@H:100]([OH:117])[C@H:99]1[OH:14]
Reactant: O=c1ccn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O2)c(=O)[nH]1
Reactant: Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O1
Agent: Nc1ccn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O2)c(=O)n1
Agent: Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O2)c(=O)[nH]1
Solvent: Oc1ccccc1
Product: O=c1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[nH]1

Procedure:
The subtracter-amplicon was diluted to 10 μg/ml, and four PCR reactions were set up on ice to generate subtracter U-DNA for the control set. Each 50 μl reaction contained 2 μl diluted ligation, 1 μl 4 μg/μl S-hpa-24mer oligo, 2 μl dNTPs (10 mM dATP, 10 mM dCTP, 10 mM dGTP, and 30 mM dUTP), 5 μl 10× PCR buffer, 1 μl 3.5 U/μl Taq DNA polymerase and ddH2O. The S-hpa-12mer was melted away (5 min, 72° C.), and ends filled in with Taq DNA polymerase (7 min, 72° C.). Twenty-one cycles of amplification were performed (1 min, 95° C.; 3 min, 72° C.), and the products were phenol-extracted, isopropanol-precipitated and resuspended in 20 μl 10 mM Tris-buffer each (Sambrook et. al., "Molecular Cloning, 2nd Edition", p10.49 (1989)). The S-adaptors were then removed with Hpa2-restriction, and the restricted products (subtracters) were phenol-extracted, isopropanol-precipitated, combined and resuspended in a total 16 μl EEx3 buffer (30 mM EPPS, pH 8.0 at 20° C.; 3mM EDTA). 6 μl (9 μg) subtracters were measured on a 2.5% TBE-agarose gel.
Reaction SMILES: COCC([Cl:6])=O.[Cl:7][C:8]1[CH:9]=[C:10]([N:14]2C(N)COC2=O)[CH:11]=[CH:12][CH:13]=1.[N:21]1C=CC=CC=1>C(Cl)Cl>[ClH:6].[Cl:7][C:8]1[CH:9]=[C:10]([NH:14][NH2:21])[CH:11]=[CH:12][CH:13]=1
Reactant: COCC(=O)Cl
Reactant: NC1COC(=O)N1c1cccc(Cl)c1
Reactant: c1ccncc1
Solvent: ClCCl
Product: Cl
Product: NNc1cccc(Cl)c1

Procedure:
Methoxyacetyl chloride (2.5 g) was added dropwise to a stirred solution of the intermediate prepared as described in point (B) (5 g) and pyridine (1.7 g) in CH2Cl2 (40 ml).
Reaction SMILES: [C:1]([Si:5]([CH3:14])([CH3:13])[O:6][CH2:7][C:8]([CH3:12])([CH3:11])[CH2:9][OH:10])([CH3:4])([CH3:3])[CH3:2].C(N(CC)CC)C.[CH3:22][S:23](Cl)(=[O:25])=[O:24].O>ClCCl>[C:1]([Si:5]([CH3:14])([CH3:13])[O:6][CH2:7][C:8]([CH3:12])([CH3:11])[CH2:9][O:10][S:23]([CH3:22])(=[O:25])=[O:24])([CH3:4])([CH3:3])[CH3:2]
Reactant: CS(=O)(=O)Cl
Reactant: CC(C)(CO)CO[Si](C)(C)C(C)(C)C
Solvent: ClCCl
Solvent: O
Solvent: CCN(CC)CC
Product: CC(C)(CO[Si](C)(C)C(C)(C)C)COS(C)(=O)=O
Temperature: 0 °C
Reaction time: 2 h
Yield: 87 %

Procedure:
To the solution of 3-(tert-butyl-dimethyl-silanyloxy)-2,2-dimethyl-propan-1-ol (20.4 g, 93 mmol) and triethylamine (26 g, 186 mmol) in dichloromethane (200 mL) at 0° C. was added a dichlormethane solution (20 mL) of methanesulfonyl chloride (Aldrich) (8.69 mL, 112 mmol). The reaction mixture was stirred at 0° C. for 2 h. Water was added. Organic layer was separated, the aqueous layer was extracted with dichlormethane. The combined organic layers were washed with diluted aqueous HCl solution, saturated aqueous NaHCO3 solution, brine, dried over MgSO4, and concentrated to give methanesulfonic acid 3-(tert-butyl-dimethyl-silanyloxy)-2,2-dimethyl-propyl ester as a yellow oil (24 g, 87%).
Reaction SMILES: [Cl:1][C:2]1[CH:18]=[CH:17][C:5]([O:6][C:7]2[C:12]([CH3:13])=[CH:11][C:10]([N+:14]([O-])=O)=[CH:9][N:8]=2)=[C:4]([CH3:19])[CH:3]=1.[H][H]>C(O)C.[OH-].[OH-].[Pd+2]>[Cl:1][C:2]1[CH:18]=[CH:17][C:5]([O:6][C:7]2[C:12]([CH3:13])=[CH:11][C:10]([NH2:14])=[CH:9][N:8]=2)=[C:4]([CH3:19])[CH:3]=1
Reactant: [H][H]
Reactant: Cc1cc(Cl)ccc1Oc1ncc([N+](=O)[O-])cc1C
Agent: [Pd+2]
Agent: [OH-]
Solvent: CCO
Product: Cc1cc(Cl)ccc1Oc1ncc(N)cc1C

Procedure:
2-(4-chloro-2-methyl-phenoxy)-3-methyl-5-nitropyridine (5.8 g, 20.8 mmol) was dissolved in 95% ethanol (50 mL) and treated with 20% palladium hydroxide on carbon (350 mg). The reaction mixture was shaken in a hydrogen atmosphere (40 psi) for 1 hour. The solution was filtered through celite and concentrated in vacuo followed by chromatography on SiO2 using 1:1 ethyl acetate/hexanes as eluant. MS (m/z): 248/250 (M+H)+; C13H13N2OCl requires 248.7.