Solvent Effects in Calculated Vibrational Raman Optical Activity Spectra of α-Helices

Abstract

We study the influence of solvation effects on vibrational Raman optical activity spectra of α-helices by means of quantum chemical calculations. Solvent effects are considered in the calculations via the conductor-like screening model COSMO and, in addition, via explicit water molecules. The so-called external type of hydration is employed. In this hydration pattern, the water molecules form hydrogen bonds to the carbonyl groups of the α-helical (Ala)20 model. It is found that the amide I bands are significantly shifted to lower wavenumbers if solvent effects are incorporated into the calculations. These computational results, obtained within the static picture employed in this work, suggest that the amide I bands may serve as a signature for the hydration of α-helices.

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra

“…Caution must however be exerted in making such assignments as the database spectra only represent the conformational sensitivity of the spectral patterns. The database does not directly include the effect of explicit hydration which has only limitedly been studied theoretically 74 nor is the effect of different amino acid compositions included, which has been proposed by Kessler et al to affect the intensity ratio of the two α-helical bands 14 . Kessler and co-workers suggested that the difference in the intensity ratio might be explained by a difference in the content of aromatic residues as these couple to main chain Cα-H bending.…”

Raman spectra from ab initio molecular dynamics and its application to liquid S-methyloxirane

“…Another possibility is the combination of continuum solvation models with micro-solvation including explicit solvent molecules. Although this approach improves the agreement between computational and experimental data, [5][6][7][8] it does not account for dynamic effects. This problem can, to some extend, be overcome by taking molecular structures from snapshots of molecular dynamics (MD) runs.…”

Molecules‐in‐molecules fragment‐based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides

“…The two positive peaks approximately at 1304 and 1340 are reproduced as a shoulder at 1300 and a strong peak at 1330 cm −1 in the MIM calculations. Explicit solvent interactions appear to be needed to reproduce the relative intensities of the two split modes . Similarly, the amide II region shows a couplet around 1460 cm −1 that is reproduced very well in the MIM calculations.…”

“…In order to understand the factors that influence and control the secondary folded structures, it is important to evaluate the relative energies and properties of various abundant secondary structures in proteins . Alanine polypeptides are the simplest chiral amino acids, primarily used to model dynamics of secondary structure formation in proteins . Therefore, understanding the balance between various conformational isomers and the associated structural transformations of polyalanine has become an intensely studied research area …”

“…In addition, the missing long-range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM-VCD and MIM-ROA fragment-based methods to explore the evolution of the chiroptical spectroscopic characteristics of 3 10 -helix, α-helix, β-hairpin, γ-turn, and β-extended conformers of gas phase polyalanine (chain length n = [6][7][8][9][10][11][12][13][14]. The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size.…”