Investigation of the molecular structure of the radical anions of some pyrimidine-type bases in aqueous solution by comparison of calculated hyperfine coupling constants with EPR results

Abstract

New results of DFT B3LYP calculations in aqueous solution are presented for the radical anions of uracil, thymine, 1-methylthymine, 1-methyluracil and 1,3-dimethyluracil. The most relevant molecular structure of the radical anions in water optimised with extended basis sets using either the Onsager or the CPCM self-consistent reaction field model is the boat conformation. The structure shows pyramidality at the radical centre C6 connected with a deviation of the C6–H atom from the molecular plane up to around 12°. Gas-phase structures, even optimised with extended basis sets, are not able to reproduce the large values of the hyperfine coupling (hfc) constant of the C6–H atom known from the experiments (about 35 MHz). Reliable values for this coupling require optimisations involving the solvent. The CPCM model appears to be superior to the Onsager model. Optimisations with inclusion of up to 10 water molecules, thus modelling hydrogen bonding with the solvent, confirm the results obtained with the continuum models.