Ionization of DNA Nucleotides in Explicit Solution

TL;DR

This study uses simulations to explore how DNA nucleotides ionize in water, showing that the surrounding water significantly affects the process.

Contribution

The study reveals that explicit water environments significantly impact ionization energies of DNA nucleotides, differing from implicit solvent model predictions.

Findings

QM/MM simulations show that water environments reduce vertical ionization energies of DNA nucleotides by ~0.70 eV.

Bulk-water polarization drives hole transfer from water to nucleobases, increasing ionization energies.

Structural relaxations after ionization release minimal energy, mainly from electron density redistribution in water and nucleobases.

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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