Molecular force fields of uracil and thymine, through neutron inelastic scattering experiments and scaled quantum mechanical calculations

Abstract

Abstract Neutron inelastic scattering (NIS) data have been obtained from polycrystalline samples of pyrimidine nucleic bases, i.e. uracil (U) and thymine (T). These spectra and those previously recorded by optical techniques (Raman scattering and infrared absorption) led us to carry out ab initio quantum mechanical calculations (SCF + MP2) in using split-valence gaussian sets with different d-orbital polarization functions for carbon, nitrogen and oxygen. The F x matrices (interatomic force constant matrices on the basis of cartesian coordinates) derived from these ab initio calculations have been then described in terms of internal molecular coordinates, allowing vibrational normal modes to be assigned in the framework of the so-called Wilson GF-matrix method. In addition, atomic displacements estimated from the normal mode calculations have been used to simulate the first-order NIS intensities by only considering the fundamentals of the internal molecular vibrational motions. For both molecules (U and T), the internal vibrational modes are located at higher wavenumbers than the lattice vibrational modes (external vibrational motions). In order to scale the calculated vibrational modes the so-called Pulay method has been used. A good agreement between calculated and experimental data (vibrational wavenumbers as well as NIS intensities) has been obtained for most of the internal vibrational modes.