This comprehensive chapter examines the critical role of ionization in drug absorption, solubility, lipophilicity, and permeability. Beginning with the foundations of the Henderson–Hasselbalch equation and the pH-partition hypothesis, it explores the concept of “shift-in-the-pKa” and the accurate determination of ionization constants across thermodynamic scales. Detailed coverage of potentiometric and spectrophotometric methods—including cosolvent approaches, buffer considerations, and recent advances for sparingly soluble drugs—is complemented by discussion of prediction software and tabulated data resources. The chapter further analyzes octanol and membrane pKa in partition coefficient measurements, logD–pH profile interpretation, and key approximations for monoprotic molecules in both octanol and liposome systems. Practical guidance is provided for understanding apparent pKa values in solubility and permeability measurements, including Gibbs pKa, aggregation effects, flux-based analysis, and correction for aqueous boundary layer limitations using the pKaFLUX method. Mechanistic insights into membrane- and water layer–limited transport, as well as ionic-species transport in PAMPA, equip readers with the tools needed to interpret complex experimental data and apply ionization principles effectively in drug development.

‍