Hydrogen Atom Loss in Pyrimidine DNA Bases Induced by Low-Energy Electrons: Energetics Predicted by Theory

In addition to inducing DNA strand breaks, low-energy electrons (LEEs) also have been shown to induce
fragmentation of pyrimidine bases (uracil, thymine, and cytosine) in the gas and condensed phases. Loss of
a hydrogen atom from a DNA base−electron adduct initiates chemical modification of the base, which can
cause permanent damage to the base as well as to DNA. Thus, the energetics of hydrogen atom loss reactions
from anionic bases is crucial to understanding the mechanism of LEE-induced damage to DNA and its
component bases. Following our previous report on LEE interactions with uracil [J. Phys. Chem. B 2004,
108, 5472−5476], in this work we investigate LEE interactions with thymine and cytosine. The adiabatic
potential energy surface along each N−H or C−H bond is explored up to 3 Å at the DFT level. The changes
in energy, enthalpy, and free energy (ΔE, ΔH, and ΔG) for a complete separation of an H atom or a methyl
(amino) group from the anionic base as well as bond dissociation energies of neutral bases are calculated at
the CBS-Q level. The electron affinities of the DNA base thymine and cytosine and their H-deleted neutral
fragments are also calculated. All N−H bonds are more susceptible to LEE-induced fragmentation than C−H
bonds, with N1−H as the most vulnerable site. Since N1 is the site of the glycosidic bond between the
deoxyribose and the base in DNA, the vulnerable nature of this site toward bond rupture suggests that LEEs
are likely to induce base release in DNA. Investigations along these lines are under way.