By combining gas phase IR-UV ion dip spectroscopy experiments with DFT-based molecular dynamics simulations for theoretical anharmonic spectroscopy, the 3D structures of (Ac-Phe-OMe)_1,2 peptides are revealed, here using the far-IR/THz signatures (100-800 cm^-1).
Beyond the experiment/theory agreement, this talk presents a 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.
As will be detailed in the talk, our strategy for assigning the vibrational modes to the active IR bands is organized over two steps: one step consists in reconstructing the exact theoretical IR spectrum (calculated through the Fourier transform of the time correlation function of the dipole moment of the system) in terms of the spectra of the APT weighted-internal coordinates velocities; the second step consists in applying Graph Theory algorithms to transform these spectral data into graphs where the vertices are the internal coordinates that participate to the modes (self-terms) and the edges represent the internal coordinates cross-terms in the spectrum reconstruction.
The graphs hence obtained immediately show how many motions are participating to each given vibrational mode, whether the mode results in localized or delocalized/collective motions, how many coupled motions participate to the mode(s) together with the percentage of participation of each of the motions into the final mode(s). Similarities between graphs can be easily obtained, hence providing similarities in between vibrational modes. This is especially useful when assigning the vibrational modes of dimers (here the (Ac-Phe-OMe)2 sheet peptidic model), providing the similarities/disimilarities in the modes in going from the monomer to the dimer. This is highly important for rapid and definitive structural assignments.

Prof Marie Gaigeot

Prof, LAMBE UMR8587, Universite d'Evry val d'Essonne

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