pKa shifts for protonation-dependent degrees of freedom

Conventional pKa calculations neglect the entropic contributions to the change in free energy for transferring the model compound from the solvent into the protein. This Letter shows that, for molecules containing internal degrees of freedom with protonation-dependent conformational space, this method may fail and introduce an error of about 1 kT ≈ 0.5ΔpKa units at room temperature for each of these degrees of freedom.