Structural and vibrational analysis of indolyl radical and indolyl radical cation from density functional methods

Electronic and structural properties of indole are the foundation for analyses of proteins based on the photochemistry and photophysics of the aromatic amino acid tryptophan. As the physiological importance of tryptophyl radicals and radicals of tryptophyl derivatives becomes apparent, the need for detailed information concerning indolyl radical and indolyl radical cation grows. Because of the high reactivity and very short life-span of these species, they are ideal targets for computational examination and prediction of properties to guide experimentalists. We have applied relatively new density functional based methods (SVWN, BLYP and B3LYP) to test their applicability and accuracy for this type of molecule. Although available experimental evidence for comparisons is scarce, our calculations exhibit excellent agreement with photochemically induced dynamic nuclear polarization (p-CIDNP), time-resolved resonance Raman (TR(3)), and difference Fourier transform infrared spectroscopic (FTIR) experiments. We compare the geometries and vibrational modes of the radicals to the closed shell indole, to each other, and to available tryptophyl radical experimental information. We present the first complete set of assigned vibrational modes for indolyl radical and indolyl radical cation to further the applicability of vibrational spectroscopy for characterizing tryptophan radicals in proteins.