However, unlike many alternative approaches, the alchemical method described here allows for the resolution of conditional pK a values. The consideration of such values may not only improve the estimates but also allow one to determine the pH-dependent pK a of a residue. Recently, we derived a formalism to conveniently combine double free energy differences from alchemical calculations in order to account for coupling between residues when predicting the pK a . In this work, we selected 18 residues, including several acidic dyads across the dataset, for which the deviation from experiment was > 1 pK. We further calculated the pK a values of these residues by taking into account possible couplings with the protonatable residues in their neighbourhood. For neighbouring residues containing a histidine, standard pK a calculations (i.e., without accounting for multiple histidine protonation states) were performed in the presence of doubly protonated histidine. For pairs of nearby (i.e., < 0.5 nm) acidic residues, we applied the aforementioned thermodynamic formalism, while in the case of apparent triads, an assessment of the most probable deprotonation event was first determined, followed by an application of the formalism on the remaining dyad.