title: Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins.
abstract: In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.
authors.affiliation: Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Anna S
authors.initials: AS
authors.lastname: Bondarenko
authors.affiliation: Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Thomas L C
authors.initials: TL
authors.lastname: Jansen
mesh_terms: D000577:Amides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D000577:Amides; D011506:Proteins