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Journal articles
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 using their far-IR/THz signatures. Both experimental and simulated IR spectra are well-resolved in the 100–800 cm−1 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 application to the more complex (Ac-Phe-OMe)1,2 peptidic systems shows that the complexity in assigning vibrational modes from MD simulations is reduced 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.
https://hal-univ-evry.archives-ouvertes.fr/hal-02082493
Contributor : Sana Bougueroua Connect in order to contact the contributor
Submitted on : Thursday, March 28, 2019 - 11:54:19 AM
Last modification on : Tuesday, January 4, 2022 - 6:09:09 AM
Contributor : Sana Bougueroua Connect in order to contact the contributor
Submitted on : Thursday, March 28, 2019 - 11:54:19 AM
Last modification on : Tuesday, January 4, 2022 - 6:09:09 AM
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