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  • Title: Time-domain calculations of the infrared and polarized Raman spectra of tetraalanine in aqueous solution.
    Author: Torii H.
    Journal: J Phys Chem B; 2007 May 17; 111(19):5434-44. PubMed ID: 17441760.
    Abstract:
    The IR and polarized (isotropic and anisotropic) Raman spectra are calculated for the amide I band of tetraalanine ((Ala)4) in aqueous solution by using a time-domain computational method, which includes the effects of the diagonal frequency modulations (of individual peptide groups), the off-diagonal (interpeptide) vibrational couplings, and structural dynamics. It is shown that the calculated band profiles, especially the existence of a large negative noncoincidence effect (i.e., large frequency separations between the IR, isotropic Raman, and anisotropic Raman bands, with the isotropic Raman being higher in frequency), are in reasonable agreement with the experimental results. This negative noncoincidence effect derives from two conditions: the positive coupling between the amide I vibrations of peptide groups and the angle larger than 90 degrees between the transition dipoles of the coupled vibrations. This result means that the dynamically changing structures mainly in the polyproline II and beta-type conformations containing some repeated interconversions obtained from the molecular dynamics calculation are consistent with the existence of a large negative noncoincidence effect, as far as the structures satisfy the above two conditions. It is also shown that the electric fields from solvent water molecules induce larger frequency shifts than those of intrachain interactions, with rapid underdamped oscillatory modulations ( approximately 43 fs) due to the librational motions of water molecules that give rise to motional narrowing effect on the spectra. The reason for the difference from the behavior seen for the O-H stretching mode of liquid water is discussed. The time-domain analysis of the mode identity shows that the system proceeds halfway to complete mode mixing with a similar time scale ( approximately 60 fs), suggesting the importance of the nonadiabatic effect, which is included in a natural way in the present computational method.
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