Figure 3.

Computational scheme for constant‐pH binding free energy calculation. P _i circles on the left side represent possible multiple protonation states of a guest molecule, and blue circles on the right side represent complex formation. $\Delta G_1^{P_{\mathrm{i}}}$ is the free energy cost for constraining multiple protonation state to a single protonation state, P _i. $\Delta G_{\text{bind}}^{P_{\mathrm{i}}}$ is the binding free energy calculated with the fixed protonation state, P _i. $\Delta G_2^{P_{\mathrm{i}}}$ is the free energy change by freeing the protonation state P _i to multiple protonation states at a given pH condition.