Effect of molecular environment on the vibrational dynamics of pyrimidine bases as analysed by NIS, optical spectroscopy and quantum mechanical force fields

Abstract

A complete set of vibrational spectra, obtained from several spectroscopic techniques, i.e. neutron inelastic scattering (NIS), Raman scattering and infrared absorption (IR), has been used in order to assign the vibrational modes of pyrimidine bases (uracil, thymine, cytosine) and their N-deuterated species. The spectra of solid and aqueous samples allowed us to analyse the effects of hydrogen bonding in crystal and in solution. In a first step, to assign the observed vibrational modes, we have resorted to harmonic quantum mechanical force field, calculated at SCF + MP2 level using double-zeta 6-31G and D95V basis sets with non-standard exponents for d-orbital polarisation functions. In order to improve the agreement between the experimental results obtained in condensed phases and the calculated ones based on isolated molecules, the molecular force field has been scaled. In a second step, to estimate the effect of intermolecular interactions on the vibrational dynamics of pyrimidine bases, we have undertaken additional calculations with the density functional theory (DFT) method using B3LYP functionals and polarised 6-31G basis sets. Two theoretical models have been considered: 1. 1. a uracil embedded in a dielectric continuum ( ε = 78), and 2. 2. a uracil H-bonded to two water molecules (through N1 and N3 atoms).