carbonate ion

When carbonate (CO3(2-)) is submitted to the pKa plugin, why does the plugin return a value of 6.05 for one O and 10.64 for the other O? Shouldn't it return the same value for both O atoms? And yes, I know that carbonic acid has a first and second pKa, but the two O atoms of CO3(2-) have the same protonation state.





Again, this nonsensical sort of behavior would be easily rectified if you calculated the pKa values of the compound in the protonation state in which it is submitted. So if I submit HCO3(-), you can give the acidic pKa (my definition) of the OH as 10.64 and the basic pKa (my definition) of the O(-) as 6.05. But if H2CO3 is submitted, the acidic pKa (my definition) of both O atoms is 6.05, and if CO3(2-) is submitted, the basic pKa (my definition) of both O atoms is 10.64.





I do note that when I submit H2CO3 in micro mode, the plugin returns 6.35 for both OH atoms. But when I submit CO3(2-), the plugin returns, "No ionizable atoms."

Hi,





My suspect is that you use an older version.


Do you see the 'acid/base prefix button on the option panel on the pKa calculator ? See attached picture.














Jozsi

Yes, you're right, we haven't yet upgraded to JChem 3.2; we are still using a prerelease version from August. I'll see if we can upgrade soon, and I won't post any complaints until then.

bobgr wrote:

Yes, you're right, we haven't yet upgraded to JChem 3.2; we are still using a prerelease version from August. I'll see if we can upgrade soon, and I won't post any complaints until then.

Hi,





This new pKa option will be included only in JChem 3.2.1. release. It will be released this week. Sorry for the wrong information.





Zsolt