I'm trying to find the major microspecies of symmetrical molecules. However, at a given pH the major microspecies tool only gives me the protonated atoms on one "side" of the molecule but not on the other side. If my molecule is symmetrical (one side is the mirror image of the other), shouldn't the same atoms in each side of the molecule be protonated? Is there anything I should be doing different for symmetrical molecules?
When you protonate (or deprotonate) one group in a compound, it changes the basicity (or acidity) of other groups in the compound. So no, you do not expect both sides to be protonated (or deprotonated).
Thanks for the reply!
Could you recommend a good source to read on this topic, please?
Please look at this site , "http://en.wikipedia.org/wiki/Acid_dissociation_constant"
Phosphoric acid has 3 identical "OH" groups; its "pH-%" distribution provided under the section of the "Polyprotic acids".