Modelling molecular vibrations in extended hydrogen-bonded networks – crystalline bases of RNA and DNA and the nucleosides

Abstract

Crystalline bases of RNA and DNA and nucleosides provide a topical set of compounds showing extended hydrogen bond networks in up to three dimensions. In order to understand the structure and dynamics, such as molecular vibrations, in these systems, accurate potential energy calculations based on solid state molecular models are required. First-principles calculations based on density functional theory (DFT), which employ periodic boundary conditions have been shown in recent work on van der Waals solids and solids including hydrogen-bonded dimers and one-dimensional hydrogen-bonded chains to be most appropriate. Periodic calculations allow small molecular models based on the crystalline unit cell, which naturally include all features of any hydrogen bond network, to be constructed. Periodic DFT calculations of structure and molecular vibrations of the bases and nucleosides in the solid state, based on published crystallographic data, have been performed. The vibrational spectra are compared with recently published inelastic neutron scattering (INS) measurements and the analysis of this data based on single-molecule first-principles calculations. Solid state calculations are shown to be significantly better, offering a reliable description of vibrational modes of atoms involved in hydrogen bonds, without any refinement of calculated force constants.