An analytical derivative procedure for the calculation of vibrational Raman optical activity spectra

Amide I Raman optical activity of polypeptides: fragment approximation

Vibrational optical activity (VOA) is an important property used to determine the absolute configuration of a chiral molecule in condensed phases. In particular, vibrational circular dichroism and Raman optical activity (ROA) are two representative VOA measurement techniques that have been extensively used to study structures and dynamics of biomolecules. Recently, the amide I vibrational circular dichroism of polypeptides was theoretically described by using fragment approximation methods, which are based on the assumption that amide I VOA can be described as a linear combination of those of constituent fragment peptide units. Here, we develop a fragment approximation theory applicable to numerical simulations of Raman and Raman optical activity spectra for the amide I vibrations in polypeptides. For an alanine dipeptide and pentapeptide analogs, we carried out density functional theory calculations of polarizability, magnetic dipole-, and electric quadrupole-ROA tensors. Numerically simulated spectra using the fragment approximation are directly compared to density functional theory results. Furthermore, the simulated ROA spectra of alanine-based right-handed alpha-helix and polyproline II polypeptides are directly compared to the previously reported experimental results. The agreements were found to be excellent, which suggests that the fragment approximation method developed for the numerical simulation of ROA spectrum of polypeptide in solution is valid and useful.

Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N'-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (alpha(R)) and left-handed (alpha(L)) helical conformations. The computed ROA spectra based on MC-sampled alpha(R) and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the alpha(L)- and beta-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the alpha(R) and PPII conformations but no substantial population of alpha(L)- or beta-structures, despite sampling alpha(L)- and beta-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.