ArticleMolecules (Basel, Switzerland)2025
Ionization of DNA Nucleotides in Explicit Solution.
Article in Molecules (Basel, Switzerland), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
QM/MM simulations were performed to investigate the ionizations of four DNA nucleotides in the explicit solution. The vertical ionization energies (VIEs) and adiabatic ionization energies (AIEs) were averaged over 40 snapshots to calculate mean values. The QM/MM VIEs (6.92-7.63 eV) were ~0.70 eV lower than those of the corresponding nucleosides. This suggests that the water environment cannot fully screen the effect of the phosphate group on ionizations. The result is inconsistent with computations using implicit solvent models. The distributions of holes in both adiabatic and vertical ionizations suggest that bulk-water polarization drives the hole transfer from first-shell water to nucleobases, resulting in increases in VIEs and AIEs. Moreover, we computed the released energies in the structural relaxations after ionizations. The results indicate that the minimal energies are released by the structural relaxations of both the bulk-water and the QM region. The redistributions of the electron density on first-shell water molecules and nucleobases produce the primary contributions to released energies.
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