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

Abstract

The protonatioddeprotonation constants for uracil (U) (pK, 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 HZ and Ag-AgI electrodes at five equidistant temperatures ranging from 15-35°C. The pKa values were fitted in the temperature equation pK, = AT-' + B + CT by the method of least squares and the standard free energies (AGO), entropies (AS0), and enthalpies (AH0) of protonatioddeprotonation 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 protonatioddeprotonation in the light of pK values of some acids and bases of comparable~functional groups and especially the entropies of protonatioddeprotonation of the key DNA-RNA base molecules.

Infrared Spectra of Protonated Uracil, Thymine and Cytosine

“…It is also likely that tautomer C1 is protonated in solution. In fact, several experimental and theoretical reports indicate that C1 is the preferred tautomer in solution, [8,36,39,53] and that protonation occurs at the N3 site [102,104,105] , with a pK value of 4.7 [103] (not far from that of our solution, namely, 5). Consequently, protonation in solution would lead to the C1_hb form, and therefore tautomerization has to take place to account for the major structure observed experimentally (i.e.…”

“…Note that data about protonated forms of uracil and thymine in solution are rather scarce. However, several reports seem to conclude that protonation of the three pyrimidic bases in solution should occur preferentially at N3 (Scheme 1), [102][103][104][105] thereby leading-in the particular case of U and T-to the forms represented by U1_hf and T1_hf (see the Supporting Information). Though minima in the gas phase, these forms are quite unstable and are not observed experimentally, their IR spectra (two strong absorptions bands at 1827 and 1867 cm À1 , n C=O ) being radically different from the experimental spectrum.…”

Surface-Enhanced Hyper-Raman Spectra of Adenine, Guanine, Cytosine, Thymine, and Uracil

“…Since the negatively charged forms of the molecules interact with the nanoparticle surface, we assume that the concentration of the anions at the surfaces at pH 7 is too small. These ions are only formed at very high solution pH values (the p K a values for uracil and thymine in water are 9.36 and 9.86, respectively 41 ) or upon lowering of the p K a by the contact with the silver surface. This is supported by citrate reduced silver nanoparticles, 13 but, as our results indicate, not by the hydroxylamine reduced silver nanoparticles.…”

Speciation studies of mono- and binuclear Pd(II) complexes involving mixed nitrogen–sulfur donor ligand and 4,4′-bipiperidine as a linker

“…The pyrimidines uracil, uridine, thymine, and thymidine have basic nitrogen donors (N3) in the measurable pH range [41] and as a consequence form 1 : 1 and 1 : 2 complexes with Pd(MMA) 2+ species. As a result of the high pK a values of pyrimidines (pK a > 9), complex formation predominates above pH 8.5.…”