title: Vibron-polaron in alpha-helices. II. Two-vibron bound states.
abstract: The two-vibron dynamics associated to amide-I vibrations in a three-dimensional (3D) alpha-helix is described according to a generalized Davydov model. The helix is modeled by three spines of hydrogen-bonded peptide units linked via covalent bonds. It is shown that the two-vibron energy spectrum supports both a two-vibron free states continuum and two kinds of bound states, called two-vibron bound states (TVBS)-I and TVBS-II, connected to the trapping of two vibrons onto the same amide-I mode and onto two nearest-neighbor amide-I modes belonging to the same spine, respectively. At low temperature, nonvanishing interspine hopping constants yield a three-dimensional nature of both TVBS-I and TVBS-II which the wave functions extend over the three spines of the helix. At biological temperature, the pairs are confined in a given spine and exhibit the same features as the bound states described within a one-dimensional model. The interplay between the temperature and the 3D nature of the helix is also responsible for the occurrence of a third bound state called TVBS-III which refers to the trapping of two vibrons onto two different spines. The experimental signature of the existence of bound states is discussed through the simulation of their infrared pump-probe spectroscopic response. Finally, the fundamental question of the breather-like behavior of two-vibron bound states is addressed.
authors.affiliation: Laboratoire de Physique Moléculaire, Unite Mixte de Recherche Centre National de la Recherche Scientifique 6624, Faculté des Sciences-La Bouloie, Université de Franche-Comté, 25030 Besançon Cedex, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Falvo
authors.forename: Vincent
authors.initials: V
authors.lastname: Pouthier
mesh_terms: D000162:Acoustics; D000465:Algorithms; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D011336:Probability; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013053:Spectrophotometry; D013696:Temperature
chemical_list: D010455:Peptides