2D sketch for multiple ionization states

User 1f9031b389

04-11-2008 23:18:09

I am trying your demo of web-based pKa calculator. I have a question and need your help to resolve it.

I tried two molecules,

(1). c1ccc2cc(ccc2c1)S(=O)(=O)NCC(=O)N[C@H](Cc3ccc(cc3)C(=[NH2+])N)C(=O)N4CCCCC4;

(2). c1cc(ccc1C[C@@H](C(=O)NCCOCCOCC(=O)N)NC(=O)CSc2ccc(cc2)Cl)NC(=[NH2+])N;

I just simply copy the smiles string and paste on the web window and then go to tool/Protonation/pKa, choose default parameters and click OK. I got two different types of charts, one with the 2D structural sketch and another without it. I need the 2D sketch. My simple question is why it is not consistent and how to get the 2D sketch for the second molecule? Thanks.

ChemAxon 990acf0dec

05-11-2008 23:52:32

We could reproduce the problem, thank you for the bug report. We are investigating this issue an come back with more info soon.

ChemAxon e08c317633

06-11-2008 10:14:08

If there are 8 or less ionizable atoms in the molecule, then microspecies distribution is show on the distribution chart, otherwise macrospecies distribution is show. Images of microspecies are displayed only on the microspecies distribution chart; on macrospecies distribution chart the formal charges of the macrospecies are shown.

The first molecule has 7 ionizable atoms, so the microspecies distribution chart is displayed. The second molecule has 8 ionizable atoms in the molecule, but a pre-filtering algorithm in pKa calculator predicts more then 8 ionizable atoms, so the macrospecies distribution chart is displayed.

We will rename the option "Show microspecies distribution" to "Show distribution chart", and there will be options for choosing microspecies or macrospecies distribution.

Till then you can do the following: set the "Min basic pKa" to "-4" on the options panel. In this case the microspecies distribution chart will be displayed.


User 1f9031b389

06-11-2008 20:59:03

Thanks a lot.