In summary, titration curves and pK a values may exhibit diverse pH-dependent behaviors due to the coupling of titratable sites. The pK a s of such coupled site residues may be difficult to resolve, and even if a curve is resolved, a singular pK a may overlook unique functionally relevant microstates. Probing these states and the microscopic pK a values between them using free energy calculations based on a rigorous formalism may be a worthwhile approach to provide additional insight into this key biophysical phenomenon. In this work, we derive a formalism to quantify individual site pK a s in coupled residues starting from double free energy differences. This is particularly convenient, as such ∆∆G values can be efficiently computed by means of alchemical free energy calculations. Moreover, we demonstrate how such ∆∆G values can be used to extract relevant coupling insights within an existing framework based on ligand binding partition functions.