Here is the molecule
Here are some more molecules where we believe CXN calculated wrong tautomer and/or pKa.
If you feed CXN with the anionic form, it calculated a carbanion as the more stable form at pH7 [C-] just to be clear.
Benzimidazole (pKa is approx. 12.8) is only a substrucure of the attached molecule what is provided by you.
Its calculated pKa is approx. 7.0 at the "NH" nitrogen in the aromatic ring, this is why its major ionized form is anionic at pH 7-8.
Do you have literature pKa value for that molecule?
I was not able to reproduce the "C-" as the more stable form.
Could you provide more information about the version of the Marvin that you tried for predicting of the pKa, and/or tautomerization?
How do you use the pKa calcualtor? (commnad line or in Marvin GUI or other ?).