The journal of physical chemistry. A

Zooming into pi-stacked manifolds of nucleobases: ionized states of dimethylated uracil dimers.

PMID 20055394


The electronic structure of 1,3-dimethyluracil and its dimer is characterized by ab initio calculations. The methylation eliminates the H-bonded isomers and allows one to focus on the pi-stacked manifold. In the neutral species, methylation increases the binding energy by 3-4 kcal/mol and reduces the lowest ionization energy (IE) by 0.6 eV. Other valence IEs are also red-shifted and the relative state ordering is the same as in uracil; however, the magnitude of the effect varies from 0.37 to 0.86 eV. The largest shifts are observed for the states with large contributions from lone pairs of nitrogens, which are primary substitution sites. The effect of stacking interactions on IEs is similar in methylated and non-methylated dimers: the lowest IE is red-shifted by 0.37 and 0.35 eV relative to the respective monomers. The splittings between other pairs of dimer states derived from the in-phase and out-of-phase combinations of the monomers' states are also similar to non-methylated uracil dimers, except for the states that include a large weight of nitrogen lone pairs. Because of the nonuniform effect on both monomers' levels and the shifts, the relative order of the ionized states in the dimer changes, relative to that of the non-methylated uracil dimer. The ionized stacked isomers show two different relaxation patterns--several isomers form structures with the delocalized hole stabilized by the orbital overlap, whereas others relax to the structures with the localized hole stabilized by electrostatic interactions. Electronic spectra of the ionized species at the neutral and cation geometries are presented and discussed.

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1,3-Dimethyluracil, 99%