title: Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details.
abstract: Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call local mode analysis (LMA) for calculating IR spectra and assigning spectral IR-bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory. Through LMA the decoding of IR spectra no longer requires several simulations or optimizations. The novel approach correlates the motions of atoms of a single simulation with the corresponding IR bands and provides direct access to the structural information encoded in IR spectra. Either the contributions of a particular atom or atom group to the complete IR spectrum of the molecule are visualized, or an IR-band is selected to visualize the corresponding structural motions. Thus, LMA decodes the detailed information contained in IR spectra and provides an intuitive approach for structural biologists and biochemists. The unique feature of LMA is the bidirectional analysis connecting structural details to spectral features and vice versa spectral features to molecular motions.
authors.affiliation: Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Massarczyk
authors.affiliation: Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.|Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.|Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS) , Shanghai 200031, China.
authors.forename: T
authors.identifier: 0000-0003-2693-9561
authors.initials: T
authors.lastname: Rudack
authors.affiliation: Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Schlitter
authors.affiliation: Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Kuhne
authors.affiliation: Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.
authors.forename: C
authors.identifier: 0000-0002-3599-9657
authors.initials: C
authors.lastname: Kötting
authors.affiliation: Department of Biophysics, Ruhr-University , 44801 Bochum, Germany.|Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS) , Shanghai 200031, China.
authors.forename: K
authors.initials: K
authors.lastname: Gerwert
mesh_terms: D000081:Acetamides / Q000737:chemistry; D011789:Quantum Theory; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: D000081:Acetamides; D014867:Water; C018595:N-methylacetamide