Ionization and Electron Attachment for Nucleobases in Water

Abstract

We used a combined quantum mechanical/mechanical molecular (QM/MM) method to investigate ionization and electron attachment for nucleobases in water. We first explored the snapshot number and QM-region size to get converged results. The computations of 20 snapshots can get converged physical quantities and converged QM regions contain about 100 atoms. We computed the vertical ionization energies (VIEs), adiabatic ionization energies, vertical electron affinities, adiabatic electron affinities, and vertical detachment energies of five bases in the explicit aqueous solvent. The computational VIEs of cytosine and thymine agree well with the experimental values in aqueous solutions. The results of the five physical quantities indicate that the QM-region polarization by bulk water evidently affects the ionization and electron attachment. Holes or excess electrons do not entirely localize on nucleobases in the ionization and electron attachment. The QM-region polarization and the movements of the QM atoms induce a drastic decrease (∼2.1 eV for cation and ∼2.9 eV for anion) of the cationic and anionic energies in structural relaxations. The potential energy surfaces of the cation and anion would become very steep near the equilibrium structure.

Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches

“…The relative order of the one-electron oxidation potentials previously determined by experiments and theory 1,2,4,5,17,18,26,28,30,31 is successfully reproduced by our calculations using both static and dynamic approaches: G < A < T < C < U. Thus, guanine is the most oxidizable nucleobase followed by adenine, i.e., purine molecules are proner than pyrimidines to transfer an electron to a sacrificial agent present in the environment.…”

“…Table 1: Experimental [3][4][5][17][18][19][20][21][22][23] and theoretical 1,2,[24][25][26][27][28][29][30] ranges provided by the literature for one-electron oxidation potentials of the nucleobases in aqueous solution.…”

Interactions of Solvated Electrons with Nucleobases: The Effect of Base Pairing

“…The most popular multi‐level approach is QM/MM method, where the solute is treated using QM, and the surrounding water molecules are treated with molecular mechanics (MM). A limited number of QM/MM based explicit solvation studies on the electron attachment to the genetic material has been reported in recent times. However, they are mostly restricted to nucleobases.…”

Damage Induced to DNA and Its Constituents by 0–3 eV UV Photoelectrons†

“…Table 2 provides the ionization energies of water ( 33) and known fundamental components of histone proteins and DNA (34)(35)(36)(37)(38)(39)(40)(41)(42)(43), along with the longest UV wavelength capable of ionizing each of these molecules. Ionization of DNA can occur by creation of a cation (hole) or electron photodetachment from a negatively charged group.…”

“…1, there is a volume within and around DNA, containing a considerable number of LEPEs capable of damaging the genome. This number depends on the photoelectron energy and corresponding photoionization CSs (33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43).…”