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

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 (λ exc ) 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.

Spontaneous self-association of adenine and uracil in polycrystals from low temperature FTIR spectra in the range below 1000cm−1

“…1), the bands at 873 and 826 cm −1 were assigned to out of plane bending modes of the N3H and N1H groups, respectively [6]. All the remaining bands observed in this spectrum have major contributions from skeletal modes (νC4 C5: 784 cm −1 ; γC2 O: 761 cm −1 ; γC4 O: 750 cm −1 ; δ ring : 590 cm −1 ; δC2 O: 567/565 cm −1 ; δ ring : 549 cm −1 and γ ring : 532 cm −1 [15,16]). In the spectrum of the mixture (trace 2), it can be seen that the component of deconvolution at ca.…”

“…1). For both molecules, the bands appearing at these frequencies have been assigned to vibrations with dominant contributions from skeletal coordinates [6,[13][14][15][16] and are expected not to change appreciably their intensity upon local environment changes due to the base pairing. A possible explanation for this result is that these modes have effectively appreciable contributions either from the N3H (in uracil) or the NH 2 coordinates (in adenine).…”

Calculation and analysis of vibrational spectra of adenine–thymine, guanine–cytosine, and adenine–uracil complementary pairs in the condensed state

“…We used the fragment method in [23] to calculate the frequencies of the normal vibrations for the complementary pairs adenine-thymine (Ade-Thy), guanine-cytosine (Gua-Cyt), adenine-uracil (Ade-Ura) corresponding to the Watson-Crick structure, and the pair Ade-Ura formed according to the Hoogsteen model. As the initial force fields of the fragments Ade, Thy, Ura, Gua, and Cyt, we used the force fields taking into account the effect of a hydrogen bond on the IR and Raman spectra of the considered nucleic acid bases in solid and liquid (i.e., condensed) phase states [24][25][26][27][28]. Such a calculation method will allow us to compare the vibrational spectra of the complementary pairs with the spectra of the individual nucleic acid bases in condensed states, and to determine the effect of hydrogen bonds on the vibrational spectra of the pairs.…”

A Theoretical Study of NBO Analysis and Solvation Effects on Tautomerism Stability of 4,8-dioxygenated 1,5-naphthyridine

“…The density functional theory (DFT) method where electron correlation is taken into account by means of non-local exchange and correlation functional is emerging as a cost-effective alternativ sophisticated MP2 computations [11][12][13][14][15][16][17] . In the case of uracil, the DFT method is shown to provide a similar vibrational mode to those obtained at the MP2 level 18,19 . DFT studies have been investigated by chemists during last decades by chemist.…”