Low‐frequency intra‐ and intermolecular vibration modes of H‐bonded nucleobases in oligonucleotide double helixes and hydrated nucleotide duplex: Application of the PM3 method

To understand the physical mechanisms of the structural–dynamic organization of the DNA double helix, it is important to investigate the spectrum of vibration modes of Watson–Crick base pairs with different models of H‐bonding complexes. Using the PM3 technique, we calculate the energy of low‐frequency intra‐ and inter‐molecular vibration modes of isolated canonical nucleoside and nucleotide pairs and analyze the dependence on the elongation of oligonucleotide double helix. The vibration spectrum of hydrated duplex [d(ApA) · d(TpT)]−2 · 47H2O was also calculated to elucidate the role of water in formation of the DNA spectrum. The results are compared with the available experimental data and analytical estimations.