I got very bad results on a pKa calculation with Jaguar. What did I do wrong in my setup?

You may have computed the pKa for the wrong acid/base couple. For instance if you are working with Et-NH2 and you pick an H, instead of computing the pKa for Et-NH3+/Et-NH2 you will compute the pKa for Et-NH2/Et-NH-. The pKa atom should be the acidic hydrogen atom in an acid, or the basic atom in a base. You can use the conjugate acid or base as input, but you should chose the hydrogen for a conjugate acid such as an ammonium ion or the heavy atom for the conjugate base such as a carboxylate.

Keywords: Jaguar, pKa, wrong value, set up, picked pKa atom

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