Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble.

Autor: Kotobi A; Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany., Schwob L; Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. lucas.schwob@desy.de., Vonbun-Feldbauer GB; Hamburg University of Technology, Institute of Advanced Ceramics, Hamburg, Germany., Rossi M; Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany., Gasparotto P; Scientific Computing Division, Paul Scherrer Institute, Villigen, Switzerland., Feiler C; Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany., Berden G; Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands., Oomens J; Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Nijmegen, The Netherlands., Oostenrijk B; Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.; The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany., Scuderi D; Institut de Chimie Physique, CNRS UMR8000, Université Paris-Saclay, Orsay, France., Bari S; Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. sadia.bari@desy.de.; The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany. sadia.bari@desy.de.; Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands. sadia.bari@desy.de., Meißner RH; Helmholtz-Zentrum Hereon, Institute of Surface Science, Geesthacht, Germany. robert.meissner@tuhh.de.; Hamburg University of Technology, Institute of Polymers and Composites, Hamburg, Germany. robert.meissner@tuhh.de.
Jazyk: angličtina
Zdroj: Communications chemistry [Commun Chem] 2023 Mar 03; Vol. 6 (1), pp. 46. Date of Electronic Publication: 2023 Mar 03.
DOI: 10.1038/s42004-023-00835-3
Abstrakt: Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.
(© 2023. The Author(s).)
Databáze: MEDLINE
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