1. To a stirred solution of methyl 3-aminothiophene-2-carboxylate (45a, 1.57 g, 10.0 mmol) in ethanol (EtOH, 10 mL) was sequentially added trifluoroacetamidine (2.24 g, 20.0 mmol) and trifluoroacetic acid (1.54 mL, 20.0 mmol) at 45 °C.
2. The reaction mixture was transferred to a microwave reactor, heated to 150 °C and kept for 1 hour.
3. After completion of the reaction, it was cooled to room temperature and the solid was collected by filtration to afford 2-(trifluoromethyl)thieno[3,2-d]pyrimidin-4(3H)-one (45b, 0.61 g).
4. 2-(Trifluoromethyl)thieno[3,2-d]pyrimidin-4(3H)-one (45b, 0.61 g, 2.77 mmol) was suspended in phosphorus oxychloride (POCl3) and refluxed for 3 h under nitrogen protection.
5. At the end of the reaction, POCl3 was removed by concentration under reduced pressure.
6. The residue was partitioned between ethyl acetate and saturated sodium bicarbonate (NaHCO3) solution and the organic phase was dried and concentrated to afford 4-chloro-2-trifluoromethylthieno[3,2-d]pyrimidine (45c, 0.58 g, 88% yield).