Anharmonic vibrational frequency calculations of 5,6-dihydrouracil and its complex with water: testing improved semiempirical potentials for biological molecules

Abstract

The anharmonic vibrational spectra of the mutant nucleobase 5,6 dihydrouracil (DHU) and its complex with water are computed and the results are analysed with focus on the properties of the anharmonic coupling between different modes. A recently proposed potential surface is used, based on improving the potential from semiempirical PM3 electronic structure theory. This improved potential energy surface is obtained by a coordinate scaling that yields agreement for harmonic frequencies obtained through ab initio (MP2) or DFT methods. The improved PM3 potentials implemented herein give anharmonic frequencies that are in good agreement with experiment for isolated DHU. Similarly anharmonic frequencies for the DHU-water complex give good agreement when compared to experiments carried out on a remarkably similar model system; uracil-water. This supports the use of the improved PM3 potentials for the spectrochemical description of nucleobases and related molecules. The anharmonic frequencies for the scaled PM3 potential are computed by the vibrational self-consistent field (VSCF) method. The anharmonic coupling interaction between different vibrational modes are analyzed and characterized. For example, the CO out of plane bending mode in isolated DHU was observed to couple most strongly with the NH stretch mode at 3478 cm⁻¹. In the case of the DHU-H₂O complex, strong coupling was observed between the O–3H water stretch and the CO out of plane bending modes of DHU at 759 cm⁻¹. The results suggest insights into patterns of intramolecular vibrational energy transfer in DHU and DHU–H₂O.

Acknowledgement

We dedicate this paper to Professor John Simons in honour of his seminal contributions to spectroscopy of biological molecules. We are grateful to Prof. D. Michalska for helpful discussions and Dr. B. Brauer for her suggestions, bright ideas, and for kindly providing the ab initio scaling code.