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

Area of Science:

• Spectroscopy
• Computational Chemistry
• Molecular Physics

Background:

• 1-methylthymine (1-MeT) is a derivative of thymine, a fundamental component of DNA.
• Understanding its vibrational properties is crucial for molecular recognition and DNA damage studies.
• Previous vibrational assignments for 1-MeT were ambiguous.

Purpose of the Study:

• To present the first infrared spectra of 1-methylthymine (1-MeT) in argon and nitrogen cryogenic matrices.
• To perform a comprehensive vibrational analysis of 1-MeT using advanced computational methods.
• To clarify ambiguities in previous vibrational spectral assignments of 1-MeT.

Main Methods:

• Matrix isolation infrared spectroscopy.
• Density Functional Theory (DFT) calculations using the B3LYP functional.
• Second-order Møller–Plesset perturbation theory (MP2) and Hartree-Fock (HF) methods.
• D95V** basis set for calculations.
• Normal coordinate analysis and potential energy distribution (PED) calculations.

Main Results:

• Experimental infrared spectra of 1-MeT in Ar and N2 matrices were obtained.
• Theoretical calculations provided accurate predictions of vibrational frequencies, intensities, and Raman activities.
• The B3LYP method demonstrated superior accuracy in predicting frequencies compared to MP2 and HF methods.
• MP2 and HF methods showed specific systematic deviations in predicting certain vibrational modes.
• Frequency shifts between matrix isolation and solid-state spectra provided insights into intermolecular hydrogen bonding.

Conclusions:

• The study provides a complete and unambiguous vibrational assignment for 1-methylthymine.
• The B3LYP method is recommended for accurate frequency predictions of uracil derivatives.
• The findings clarify previous spectral assignments and offer insights into intermolecular interactions in crystalline 1-MeT.