Journal of Physical Chemistry A, Vol.108, No.16, 3439-3446, 2004
Acidity of a nucleotide base: Uracil
Experiment and calculations are used to show that the gas-phase acidity of uracil is comparable to that of HCl. The gas-phase acidity of uracil (denoted here by U) was bracketed by proton-transfer measurements involving U and various reference acids (denoted here by A) of known gas-phase acidity. Rate constants for proton transfer from the reference acid A to the conjugate anion of uracil, (U-H)(-), were measured in a selected-ion flow tube at 298 K. Rate constants for proton transfer from U to ions (A-H)(-) were measured at 467 K in a flowing-afterglow Langmuir probe apparatus. Here, (U-H) or (A-H) indicates a U or A molecule which is missing an H atom, respectively. The result is DeltaHdegreesacid(uracil) = 333 +/- 5 kcal mol(-1) and DeltaGdegrees(acid)(uracil) 326 +/- 5 kcal mol(-1) at 298 K, which agrees with earlier work. Thermal electron attachment to uracil was found to be too slow to permit measurement of a rate constant, consistent with the gas-phase acidity given above. G3 and G3(MP2) calculations are reported for uracil, and for the each of the (U-H) radicals and (U-H)(-) ions that result from H or H+ loss from each of the four hydrogen sites of U (on the N1, N3, C5, and C6 positions). From the calculated total energies we obtain the gas-phase acidity of uracil, the four U-H homolytic bond strengths, and the electron affinities of the four possible fragment radicals. We confirm earlier work that the most acidic site in uracil is at the N1 site; this site is where uracil becomes covalently bonded to a carbon of the ribose sugar in RNA. G3 calculations for the N1 site at 298 K give DeltaHdegrees(acid)(uracil) = 334.5 kcal mol(-1) and DeltaGdegrees(acid)(uracil) = 327.1 kcal mol(-1) at 298 K, in good agreement with the experiment. The weakest H-atom bond enthalpy (at the N1 site) is calculated to be 101.8 kcal mol(-1).