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  • Title: Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water.
    Author: Hahn S, Ham S, Cho M.
    Journal: J Phys Chem B; 2005 Jun 16; 109(23):11789-801. PubMed ID: 16852448.
    Abstract:
    Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the beta hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) beta hairpin are directly compared with those of the realistic 16-residue (GB1) beta hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 beta hairpin are the same. The simulated IR spectrum of the GB1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.
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