Raman and Infrared Spectra of Thymine. A Matrix Isolation and DFT Study

TLDR

The authors use the measured Raman and infrared spectra of thymine isolated in an argon matrix to assign its vibrational modes. They record the Raman spectrum with an FTRA instrument at 1.064 µm to avoid resonance effects, complement it with infrared data, and employ B3LYP/6‑31G(d,p) DFT calculations—refining them with effective force constants to account for anharmonicity—to predict spectra and intensity distributions. The computed spectra agree surprisingly well with experiment, with remaining differences traced to the harmonic approximation; the analysis yields an unambiguous vibrational assignment and shows that PEDs, IDs, and RIDs are valuable tools, while Raman spectra of isolated and polycrystalline thymine are similar but their infrared spectra differ.

Abstract

The Raman spectrum has been measured for thymine isolated in an Ar matrix using an FTRA instrument with infrared excitation at 1.064 μm, thereby avoiding complications due to resonance Raman and fluorescence effects. This spectrum is used, together with the newly measured infrared spectrum, to establish the assignment of the vibrational spectra of isolated thymine. The assignment is assisted by DFT calculations made at the B3LYP/6-31G(d,p) level of theory, using GAUSSIAN 98W. The calculated spectra, including the Raman spectrum, are in surprisingly good agreement with the experimental spectra. The discrepancies that are observed for some parts of the spectrum result primarily from the failure of the harmonic approximation made in the calculation. The effect of the neglect of anharmonicity has been investigated by determining a set of effective force constants that reproduce the experimental frequencies and intensity patterns in the infrared and Raman spectra and by examining how the predicted spectra (intensities, frequencies, potential energy distributions (PEDs), infrared intensity distributions (IDs), and Raman intensity distributions (RIDs)) change. The final results provide an unambiguous assignment of the vibrational spectra for thymine isolated in an Ar matrix and illustrate that the concepts of PEDs, IDs, and RIDs are useful for the interpretation of the vibrational spectra of molecules the size of the pyrimidine bases. Comparison of the Raman spectrum of thymine isolated in the Ar matrix with that of a polycrystalline sample indicates that they are quite similar, in marked contrast to the differences in the corresponding infrared spectra.