title: Modeling the vibrational dynamics and nonlinear infrared spectra of coupled amide I and II modes in peptides.
abstract: The amide vibrational modes play an important role in energy transport and relaxation in polypeptides and proteins and provide us with spectral markers for structure and structural dynamics of these macromolecules. Here, we present a detailed model to describe the dynamic properties of the amide I and amide II modes and the resulting linear and nonlinear spectra. These two modes have large oscillator strengths, and their mutual coupling plays an important role in their relaxation. Using first-principles calculations of NMA-d(7) and a dipeptide in a fluctuating bath described by molecular dynamics simulations, we model the frequencies of the local vibrations as well as the coupling between them. Both the coherent couplings and the fluctuations induced by contact with their environment are taken into account. We apply the resulting model of interacting fluctuating oscillators to study the collective vibrations and the partially coherent transport of vibrational energy through a model α-helix. We find that the instantaneous vibrations are delocalized over a few (up to four) amide units, while the coherences in the helix survive for 0.5-1 ps, leading to coherent transport on a similar time scale.
authors.affiliation: Centre for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Arend G
authors.initials: AG
authors.lastname: Dijkstra
authors.forename: Thomas la Cour
authors.initials: Tl
authors.lastname: Jansen
authors.forename: Jasper
authors.initials: J
authors.lastname: Knoester
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000577:Amides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D013055:Spectrophotometry, Infrared; D013997:Time Factors; D014732:Vibration
chemical_list: D000081:Acetamides; D000577:Amides; D010455:Peptides; C018595:N-methylacetamide