Quantum chemical calculations of energies, electronic structures, and molecular geometries of 3,5,6-trimethylthieno[2,3-d]pyrimidin-4-one (1), tricyclic 2,3-tri-, 2,3-tetra-, and 2,3-pentamethylene-substituted 5,6-dimethylthieno[2,3-d]pyrimidin-4-ones (2-4), carboxylic acids 5-8 resulting from oxidation of compounds 1-4 at the methyl group in position 5 of thienopyrimidine, methyl esters of these acids (9-12), and products of ipso-nitration of esters (13-16) were performed in terms of the HF and DFT (B3LYP) approximations with the 3-21G basis set. Also, calculations for mixed anhydrides of nitric acid and carboxylic acids 17-20 were carried out. The possible causes of differences in the behaviors of 3-unsubstituted and 3-substituted thieno[2,3-d]pyrimidin-4-ones were discussed.