I have been using JCChemicalTerms(molecule,majorMicrospecies("7.2")) to calculate the formula for many compounds at pH 7.2. However, upon doing a pKa calculation in Marvin, the microspecies predicted to dominate at pH 7.2 is often different from what JCChemicalTerms gave in the previously mentioned method.
So I'm wondering: which method should I trust??
This actually happens for many compounds, and I attached the sdf file for two of them. Both compounds are documented in PubChem.