title: Secondary Structure Dependence and Hydration Effect of the Infrared Intensity of the Amide II Mode of Peptide Chains.
abstract: Every vibrational mode to be used as a marker of the structural, dynamical, and/or interaction properties demands our good understanding of the relations between those properties and the spectral features. The present study is devoted to elucidating the effects of secondary structure variations and hydration on the infrared (IR) intensity of the amide II mode of peptide chains. It is shown that the IR intensity is significantly enhanced for the C5 (fully extended planar β-strand) conformation because of the interpeptide charge flux through the H···O interaction of the C5 ring, and there is a small cooperative effect giving rise to a larger enhancement for a consecutive C5 conformation. In contrast, the IR intensity is reduced for the α-helix conformation because of the partially canceling polarization effect of the hydrogen-bond accepting O atom in the N-H···O═C hydrogen bond and the absence of the interpeptide charge flux. With regard to the hydration effect, it is found that the IR intensity enhancement/reduction depends critically on the angular position of the hydrating water molecule, and is related to the presence/absence of the intermolecular charge flux and the polarization effect. It is suggested that, both for the secondary structure dependence and for the hydration effect, the geometrical relation between the vibrating N-H bond and the H···O interaction (of the C5 ring and/or the hydrogen bond) is an essential factor determining the enhancement/reduction of the IR intensity of the amide II mode.
authors.affiliation: Department of Chemistry, Faculty of Education, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan.|Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Torii
authors.affiliation: Department of Chemistry, Faculty of Education, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan.
authors.forename: Megumi
authors.initials: M
authors.lastname: Kawanaka
mesh_terms: D000577:Amides / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013055:Spectrophotometry, Infrared / Q000379:methods; D014867:Water / Q000737:chemistry*
chemical_list: D000577:Amides; D009842:Oligopeptides; D010455:Peptides; D014867:Water; C035647:glycyl-glycyl-glycine