title: Influence of the nonlinearity and dipole strength on the amide I band of protein alpha-helices.
abstract: Vibrational energy storage and propagation are simulated in a fully atomic model of an alpha-helix by combining the AMBER force field for proteins with an extended version of the Davydov/Scott model for amide I vibrational transfer [A. Scott, Phys. Rep. 217, 1 (1992)]. Dipole-dipole interactions between transition dipole moments of amide I and its on-site energies are calculated from the corresponding three-dimensional atomic positions. The comparison of the theoretically calculated absorption line shapes with the experimentally measured ones leads to a putative value of the nonlinearity parameter of -30 pN.
authors.affiliation: CCMAR and FCT, University of Algarve, 8000 Faro, Portugal. lhansson@ualg.pt
authors.forename: Leonor
authors.initials: L
authors.lastname: Cruzeiro
mesh_terms: D000042:Absorption; D000577:Amides / Q000737:chemistry; D002244:Carbon / Q000737:chemistry; D002627:Chemistry, Physical / Q000379:methods*; D015233:Models, Statistical; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
chemical_list: D000577:Amides; D010455:Peptides; D011506:Proteins; C019529:polyalanine; D002244:Carbon; D010100:Oxygen