title: Simulation of transient infrared spectra of a photoswitchable peptide.
abstract: In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.
authors.affiliation: Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany.
authors.forename: Maja
authors.initials: M
authors.lastname: Kobus
authors.forename: Martin
authors.initials: M
authors.lastname: Lieder
authors.forename: Phuong H
authors.initials: PH
authors.lastname: Nguyen
authors.forename: Gerhard
authors.initials: G
authors.lastname: Stock
mesh_terms: D008027:Light; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D055620:Optical Phenomena; D011487:Protein Conformation; D015203:Reproducibility of Results; D013055:Spectrophotometry, Infrared; D013997:Time Factors; D014867:Water
chemical_list: D009842:Oligopeptides; D014867:Water