Protonation/deprotonation energetics of uracil, thymine, and cytosine in water from e.m.f./spectrophotometric measurements

Abstract

The protonation/deprotonation constants for uracil (U) (pK1 and pK2), thymine (T) (pK1) and cytosine (C) (pK1 and pK2) in water have been determined from emf measurements of Harned–Ehler type cells comprising H2 and Ag–AgI electrodes at five equidistant temperatures ranging from 15–35 °C. The pKa values were fitted in the temperature equation pKa = AT−1 + B + CT by the method of least squares and the standard free energies (ΔG0), entropies (ΔS0), and enthalpies (ΔH0) of protonation/deprotonation processes in water were evaluated using the values of the coefficients A, B, and C of the respective acids. The second step deprotonation constant for T was determined using precise spectrophotometric method. The results have been duly compared with the existing literature data and are also shown to derive important reflections on the sites of protonation/deprotonation in the light of pK values of some acids and bases of comparable functional groups and especially the entropies of protonation/deprotonation of the key DNA–RNA base molecules.