Nitrosubstituted aromatic molecules as universal nucleobases: Computational analysis of stacking interactions

MP2 stacking interactions between nitrosubstituted rings (3-nitropyrrole, 5-nitroindole, 4-nitropyrazole, 4-nitroimidazole), the corresponding unsubstituted rings and natural nucleobases were investigated. Although the enhancement in stacking provided by the nitro group decreases with an increase in the size of the aromatic ring, the largest stacking interactions were found for 5-nitroindole dimers. Nevertheless, the stacking interactions of nitrosubstituted rings cannot compensate for the loss of hydrogen-bonding interactions upon incorporation into DNA. The calculated stacking energies help explain experimentally observed behaviors of these molecules, and suggest that ring composition and size, in addition to external substituents, should be considered when designing novel universal nucleobases.