Electron Affinities of the DNA and RNA Bases

Abstract

Adiabatic electron affinities (AEAs) for the DNA and RNA bases are predicted by using a range of density functionals with a double-zeta plus polarization plus diffuse (DZP++) basis set in an effort to bracket the true EAs. Although the AEAs exhibit moderate fluctuations with respect to the choice of functional, systematic trends show that the covalent uracil (U) and thymine (T) anions are bound by 0.05-0.25 eV while the adenine (A) anion is clearly unbound. The computed AEAs for cytosine (C) and guanine (G) oscillate between small positive and negative values for the three most reliable functional combinations (BP86, B3LYP, and BLYP), and it remains unclear if either covalent anion is bound. AEAs with B3LYP/TZ2P++ single points are 0.19 (U), 0.16 (T), 0.07 (G), -0.02 (C), and -0.17 eV (A). Favorable comparisons are made to experimental estimates extrapolated from photoelectron spectra data for the complexes of the nucleobases with water. However, experimental values scaled from liquid-phase reduction potentials are shown to overestimate the AEAs by as much as 1.5 eV. Because the uracil and thymine covalent EAs are in energy ranges near those of their dipole-bound counterparts, preparation and precise experimental measurement of the thermodynamically stable covalent anions may prove challenging.

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

“…This supposition is based on the electron affinities of isolated nucleobases. Indeed, the adiabatic gas-phase electron affinities of the valence anions of canonical tautomers of nucleic bases, calculated at the B3LYP/DZP++ level, diminish in the following sequence [81]: U>T>C>G>A, and for pyrimidines compare very well with the values extrapolated from photoelectron spectra of nucleobase•(H 2 O) n clusters [82]. This AEA sequence therefore suggests that thymine and cytosine molecules are primary targets for the formation of nucleic base anions in DNA.…”

“…The excess electron attachment to this trimer leads to an anionic structure with an unpaired electron localized primarily on thymine and characterized by a VDE of 0.37 eV. This localization of the unpaired electron is consistent with the sequence of electron affinities of isolated NBs: T>A [81]. The anionic structure is, however, only a local minimum on the potential energy surface of the anionic trimer.…”

Low-energy electron collisions with gas-phase uracil

“…The resulting nuclear coordinates are listed in Table I. For the elastic scattering calculations, we made an extensive exploration of the use of different basis sets and different treatments of polarization. Uracil presents unusual numerical difficulties not only because of its size and low symmetry but also because of its large dipole moment, ϳ4 − 5 debye, [36][37][38] which is sufficient to form at least one dipolebound anion state 36,[39][40][41][42][43][44] and which will strongly influence the scattering cross section at low energies. Indeed, the fixed-nuclei elastic scattering cross section for a polar molecule is formally divergent.…”

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

“…[36] Experimental Reference PS 0.15 ± 0.12 [117] More accurate functionals are constructed by combining GGAs with HF (exact) exchange in an appropriate proportion. This is the case for the hybrid B3LYP functional [124,125], which has proved itself to be particularly reliable for predicting AEAs of DNA components [122]. A further step up is to combine the hybrid exchange with a meta-GGA that includes not only the gradient of the density, but also the kinetic energy density (laplacian).…”