Three quantum chemistry methods (B3LYP, M05-2X and CBS-4B3*) have been used, in combination with SMD and CPCM continuum solvent models, to calculate the aqueous pK
values of common organic compounds (aliphatic alcohols, carboxylic acids, amines, phenols, benzoic acids and pyridines) by using an isodesmic reaction. Good precision is found for all the studied functional groups, resulting mean absolute deviations of 0.5–1 pK
units (equivalent to the best results obtained with thermodynamic cycles). It is worthy to note that no explicit water molecules were needed with the isodesmic reaction. In addition, the quality of the results is not strongly dependent on the combination of quantum chemistry method, solvent model and reference species. Therefore, the isodesmic reaction could be successfully used when dealing with gas-phase unstable species, with species that undergo large conformational changes between gas-phase and solution-phase or other difficult cases for the thermodynamic cycles.