Effects of Hydrogen Bonding on Vibrational Normal Modes of Pyrimidine

Abstract

The effects of weak intermolecular interactions on 10 vibrational normal modes of pyrimidine are investigated by Raman spectroscopy and electronic structure computations. Hydrogen-bonded networks of water induce a shift to higher energy in certain normal modes of pyrimidine with increasing water concentration, while other modes are relatively unaffected. Pyrimidine molecules also exhibit weak C-H...N interactions and shifted normal modes upon crystallization. The selective nature of the shifting of normal modes to higher energy allows for definitive assignments of the nearly degenerate nu(8a) and nu(8b) modes with polarized Raman spectroscopy. Natural bond orbital (NBO) analyses indicate that when water molecules donate hydrogen bonds to the nitrogen atoms of pyrimidine, there is significant charge transfer from pyrimidine to water, much of which can be accounted for by substantial decreases in the populations of the nitrogen lone pair orbitals. Despite the overall decrease of electron density in pyrimidine upon complexation with water, there are concomitant changes in NBO populations that polarize the pi-electron system toward the proton acceptor N atoms, as well as contractions of the bonds associated with the N-C-N and C-C-C regions of the pyrimidine ring.