I am predicting pka values for several pharmaceutical compounds using MarvinView 5.9.2. The program predicts that sulfamethoxazole has a pKa around pH 7.7--however, several reports in the literature list its pKa around 5.8. Can anybody help me reconcile the difference between MarvinView's prediction and literature values? To be honest, the results from my sorption experiments support the pKa being at 7.7.
Thanks in advance,
In case it helps, here is how I am coming sulfamethoxazole pKa 7.7 values in MarvinView:
1. Open MarvinView 5.9.2
2. Paste Sulfamethoxazole SMILES into the window (e.g. Nc1ccc(cc1)S(=O)(=O)Nc1noc(C)c1)
3. Click on Tools/Protonation/pKa