Acidity of a Nucleotide Base: Uracil

Abstract

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 (DeltaH acid(uracil)) = 333 +/- 5 kcal and DeltaG(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. 63 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, CS, 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 DeltaH acid(uracil) = 334.5 kcal mol(-1) and DeltaG acid(uracil) = 327.1 kcal mol at 298 K, in good agreement with the experiment. The weakest H-atom bond enthalpy (at the NI site) is calculated to be 101.8 kcal mol.

Open PDF

Document Details

Document Type
Technical Report
Publication Date
Jan 01, 2004
Accession Number
ADA423114

Entities

People

  • A. E. Miller
  • Albert A Viggiano
  • S. T. Arnold
  • T. M. Miller

Organizations

  • Air Force Research Laboratory

Tags

Communities of Interest

  • Energy and Power Technologies

DTIC Thesaurus Topics

  • Acids
  • Afterglows
  • Agreements
  • Air Force
  • Air Force Research Laboratories
  • Chemical Reaction Properties
  • Chemical Reactions
  • Chemistry
  • Deoxyribonucleic Acids
  • Electron Density
  • Electrons
  • Langmuir Probes
  • Measurement
  • Molecules
  • Nucleic Acids
  • Physical Chemistry
  • Ribonucleic Acids

Readers

  • Combustion science or combustion engineering.
  • Materials Science and Engineering.
  • Molecular Photonics/Laser Physics

Technology Areas

  • Microelectronics