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A solution of mixture of 2-(methoxycarbonyl)-3-methylpyrazine 1-oxide compound with 3-(methoxycarbonyl)-2-methylpyrazine 1-oxide (1:1) (5.1 g, 15.17 mmol) in toluene (50 mL) was cooled to 0° C. To the mixture was added phosphorus oxychloride (2.78 ml, 30.3 mmol) under nitrogen followed by n,n′-dimethylformamide (0.117 ml, 1.517 mmol). The reaction mixture was stirred at room temperature for 4 h and then was heated to 65° C. for 18 h. The mixture was cooled to room temperature, diluted with EtOAc and washed with saturated NaHCO3 solution. The aqueous layer was back-extracted with EtOAc. The combined organic extracts were dried (MgSO4), filtered and concentrated in vacuo. The mixture was purified with ISCO (0% to 50% EtOAc/Hexanes) to afford both isomers: methyl 5-chloro-3-methylpyrazine-2-carboxylate (0.68 g, 48.1% yield) and methyl 6-chloro-3-methylpyrazine-2-carboxylate (1.5 g, 106% yield).

1. temperaturewas heated to 65° C. for 18 h
2. temperatureThe mixture was cooled to room temperature
3. washwashed with saturated NaHCO3 solution
4. extractionThe aqueous layer was back-extracted with EtOAc
5. dry with materialThe combined organic extracts were dried (MgSO4)
6. filtrationfiltered
7. concentrationconcentrated in vacuo
8. customThe mixture was purified with ISCO (0% to 50% EtOAc/Hexanes)
9. customto afford both isomers