Neutron inelastic scattering, optical spectroscopies and scaled quantum mechanical force fields for analyzing the vibrational dynamics of pyrimidine nucleic acid bases: 3. Cytosine

Neutron inelastic scattering (NIS), Raman scattering (R), and infrared absorption (IR) spectra of cytosine and its N-deuterated species in solid phase were recorded at 15 K. These spectra were completed by the room temperature Raman and IR spectra from both solid samples and aqueous solutions. NIS spectra are sensitive to the modes in which the hydrogen displacements are involved. The evolution of the vibrational spectra in going from solid phase to solution is discussed. To analyze the structural and vibrational features of an isolated cytosine, we resorted to the quantum mechanical calculations performed at SCF or MP2 levels of theory, with double-zeta form basis sets enlarged or not by adequate polarization functions. The energetically most favorable tautomers, e.g. amino-oxo (a-o) and amino-hydroxy (a-h) forms have been analyzed in this framework. MP2 calculations have shown that the a-h tautomeric form has a lower energy than the well-known a-o form. However, taking into account the small energy difference between the above tautomers, all of them have been considered in assigning the vibrational modes observed in gas phase or in Ar matrix. It turns out that the conformation of the amino group in cytosine deduced from the calculations depends strongly on the extension of the basis functions used. At MP2 level, as soon as the d-polarization functions have been added to the basis sets the NH2 group prefers a pyramidal conformation. It has been verified that the inversion of the nitrogen located at the top of this pyramid does not correspond to a double minima and that the planar geometry of this chemical group, leading to an overall C-s symmetry for cytosine, corresponds to a transition state. However, as the calculations show, the preferred amino group pyramid orientation (upward or downward with respect to the cytosine ring) also depends on the extension of the basis sets used. The addition of p-polarization functions on hydrogen orbitals leads to the inversion of the NH2 orientation. In condensed phase, experimental evidence is in favor of the predominance of the a-o form. In order to assign the vibrational modes observed in the condensed phase, where intermolecular interactions are important, the ab initio force field of the a-o tautomer has been scaled. Although, in many cases this scaling improves the agreement between the experimental and calculated results (wavenumbers and NIS intensities), some crucial problems still exist. Indeed, as has been confirmed by the comparison between the experimental and calculated NIS intensities, the scaled theoretical force field overestimates the coupling between N1-H (or NH2) wagging and torsional motions, whereas the coupling between C-H waggings and skeletal torsional motions is largely underestimated. Similar effects have also been observed in the other two pyrimidine bases (Aamouche, A. et al. J Phys. Chem. 1996, 100, 5224; J. Phys. Chem. A 1997, 101, 1808). Recently, it has been shown that an implicit introduction of intermolecular hydrogen bonds by taking into consideration supermolecular models allows to solve partly the above-mentioned problems without a crucial need to scale the molecular force field (Ghomi, M. et al. J. Mel. Struct. 1997, 411, 323).