benzimidazole should not be anionic at pH 7-8.

User cd46b9a398

25-09-2012 20:10:16

Here is the molecule


Cn1cc(cn1)CN(C)C(=O)CS(=O)(=O)c2[nH]c3ccccc3n2 66206150



Here are some more molecules where we believe CXN calculated wrong tautomer and/or pKa. 


c1ccc(cc1)C(=O)CSc2nc(c3c(n2)[n-]c(n3)C#N)N ZINC01237420

Cc1c(c(c(c(c1O)/C(=C\C(=O)c2ccccc2)/[O-])O)C=O)O ZINC29482909

c1ccc2c(c1)CCN2C(=O)CSc3c4c(nc[nH]4)ncn3 ZINC13578887

Cn1cc(cn1)CN(C)C(=O)CS(=O)(=O)c2[nH]c3ccccc3n2 ZINC66206150

CCn1c2ccccc2c(=O)c(c1[O-])C(=O)NCCc3ccccc3 ZINC13116859

Cn1c2ccccc2c(=O)c(c1[O-])C3=NO[C@H](C3)/C=C/c4ccccc4 ZINC03846596

c1ccc(cc1)NC(=O)CSc2[nH]c(=O)n(n2)c3ccccc3 ZINC32871476

c1ccc(cc1)C(=O)CSc2nc(c(nn2)Cc3cccnc3)[O-] ZINC36646243

If you feed CXN with the anionic form, it calculated a carbanion as the more stable form at pH7 [C-] just to be clear.


User 851ac690a0

25-09-2012 21:56:12



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 ?).