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Conformational assignment of gas phase peptides and their H-Bonded complexes using far-IR/THz: IR- UV ion dip experiment, DFT-MD spectroscopy, and Graph Theory for modes assignment.

Abstract

The combined approach of gas phase IR-UV ion dip spectroscopy experiments and DFT-based molecular dynamics simulations for theoretical spectroscopy reveals the 3D structures of (Ac-Phe-OMe)$_{1,2}$ peptides %and the dimeric $\beta$-sheet using the far-IR/THz signatures. Both experimental and simulated IR spectra are well-resolved in the 100-800~\cm \ domain, allowing an unambiguous assignment of the conformers, that could not be achieved in other more congested spectral domains. We also present and make proofs-of-principles for our newly developed theoretical method for the assignment of (anharmonic) vibrational modes from MD simulations based on Graph Theory coupled to APT weighted-internal coordinates velocities DOS spectra. The principles of the method are reviewed, applications to the simple gas phase water and NMA (N-Methyl-Acetamide) molecules are presented, and the application to the more complex (Ac-Phe-OMe)$_{1,2}$ peptidic systems shows that the complexity in assigning vibrational modes from MD simulations is released with the graphs. Our newly developed graph-based methodology is furthermore shown to allow an easy comparison between the vibrational modes of isolated monomer(s) and their complexes, as illustrated by the (Ac-Phe-OMe)$_{1,2}$ peptides.

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Publication details

The article was received on 27 Nov 2018, accepted on 09 Jan 2019 and first published on 09 Jan 2019


Article type: Paper
DOI: 10.1039/C8FD00211H
Citation: Faraday Discuss., 2019, Accepted Manuscript
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    Conformational assignment of gas phase peptides and their H-Bonded complexes using far-IR/THz: IR- UV ion dip experiment, DFT-MD spectroscopy, and Graph Theory for modes assignment.

    D. Galimberti, S. Bougueroua, J. Mahé, M. Tommasini, A. Rijs and M. Gaigeot, Faraday Discuss., 2019, Accepted Manuscript , DOI: 10.1039/C8FD00211H

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