Neutron Inelastic Scattering, Optical Spectroscopies, and Scaled Quantum Mechanical Force Fields for Analyzing the Vibrational Dynamics of Pyrimidine Nucleic Acid Bases. 2. Thymine

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Abstract

As in the case of uracil, a complete set of vibrational spectra of thymine and its N-deuterated species, 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 on the basis of an ab initio scaled quantum mechanical (SQM) force field. NIS, Raman, and IR spectra of polycrystalline thymine recorded at T = 15 K provide complementary data for analyzing different groups of molecular vibrational modes. Solid-state spectra have been supplemented with FT Raman (λexc = 1.06 μm) and IR spectra of aqueous solutions. The spectra from both phases allowed us to analyze the effects of the environment related to strong (crystal) or weak (solution) hydrogen bondings. 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 the gas phase of thymine. Then the force field has been scaled in order to improve the agreement with experimental data from solid and aqueous phases. The scaling procedure is similar to that established in the case of uracil. We have used the Pulay method in order to improve the wavenumbers and NIS intensities corresponding to the bond stretchings and angular bendings as well as those related to the methyl group vibrational motions. The majority of these scaling factors lie close to unity (between 0.8 and 1.1), except for the methyl torsion, for which a large value of 1.4 was needed. The other force constants related to the ring torsional and wagging motions have been scaled by the least-squares refinement of the off-diagonal force constant expressed in terms of internal coordinates.

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