Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

Abstract

In this work, DNA base monomers, 15 B-form stacking dimers and two G-quadruplex stacking dimers were studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal vibrational signatures for structural aspect of the base monomers and dimers. It was found that from isolated base monomers to stacking dimers, particularly those containing guanine, the interaction between the C＝O stretching is very strong, as depicted by the significant changes of their vibrational frequencies and anharmonicities. Such changes can be manifested well in simulated 1D IR and 2D IR spectra. Delocalization degree of the C＝O vibrational modes in stacking dimers, represented by the potential energy distribution and the contribution to the diagonal anharmonicity composition from the vibrators, was found to have significant variations in comparison with isolated bases, which resulted from the influences of the C＝ O stretching and the nearby vibrations of stacking bases.