Vibrational spectra of 1-methylthymine: matrix isolation, solid state and theoretical studies.

Barbara Morzyk-Ociepa, Maciej J Nowak, Danuta Michalska

Index: Spectrochim. Acta. A. Mol. Biomol. Spectrosc. 60(8-9) , 2113-23, (2004)

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Abstract

The infrared spectra of 1-methylthymine (1-MeT) in argon and nitrogen cryogenic matrices are presented, for the first time. The molecular structure, conformations, vibrational frequencies, infrared intensities and Raman scattering activities of 1-MeT have been calculated by the DFT(B3LYP), MP2 and HF methods using the D95V** basis set. The theoretically predicted intensity pattern of the IR and Raman bands has proved to be of great help in assigning the experimental spectra. Rigorous normal coordinate analysis has been performed, at each level of theory. The unequivocal and complete vibrational assignment for 1-MeT has been made on the basis of the calculated potential energy distribution (PED). Comparison of the experimental matrix isolation spectra with the theoretical results has revealed that the B3LYP method is superior to both the MP2 and HF methods in predicting the frequencies of uracil derivatives. The MP2 method consistently underestimates the frequencies of the out-of-plane gamma(C=O) and gamma(C-H) bending modes, while the HF method yields the reverse order of the frequencies of two nu(C=O) stretching vibrations. Investigation of the frequency shift of several bands, on passing from matrix isolation to solid state spectra, has provided information on the strength of intermolecular hydrogen bonding in the crystal of 1-MeT. Several ambiguities in the earlier assignments of the vibrational spectra of polycrystalline 1-MeT have been clarified.