Neutron Inelastic Scattering, Optical Spectroscopies and Scaled Quantum Mechanical Force Fields for Analyzing the Vibrational Dynamics of Pyrimidine Nucleic Acid Bases. 1. Uracil

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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 uracil on the basis of an ab initio scaled quantum mechanical (SQM) force field. NIS, Raman, and IR spectra of polycrystalline uracil recorded at T = 15 K from native and N-deuterated species provide complementary data for analysing different groups of molecular vibrational modes. Solid-state spectra have been completed with various Raman (λexc = 257 nm, 514.5 nm, and 1.06 μm, and IR spectra in aqueous solutions. Both phases allowed effects of the environment on the vibrational modes, related to either strong (crystal) or weak (solution) hydrogen bondings, to be shown. In addition, the various laser excitations allowed the wavelength dependence of the Raman cross sections of in-plane characteristic modes to be observed. Due to the large NIS incoherent cross section of protons, the intense NIS bands are those arising from the vibrational modes containing hydrogen motions. The molecular fundamental wavenumbers calculated at the SCF+MP2 level, by using different types of molecular orbitals, have first been compared with the experimental wavenumbers taken from gas phase or Ar-matrix isolated uracil. Then the force field has been scaled in order to improve the agreement with experimental data from solid and aqueous phases. In the scaling procedure, the standard Pulay method was reliable for the in-plane vibrational modes, whereas it failed to scale successfully the out-of-plane vibrational modes. Consequently another scaling method, which consists of refining the nondiagonal elements of the internal force field matrix, has been used. On the basis of this procedure for out-of-plane modes, the simulation of the NIS intensity related to the C−H wagging motions could be performed without any particular difficulty. However some difficulties still exist for the N−H wagging motions which are largely perturbed by hydrogen bonding and packing effects in solid phase.

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