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Énergétique et spectroscopie de polypeptides par dynamique moléculaire : champ de force de seconde génération et chimie quantique

Abstract : InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy allows obtaining the vibrational signatures of charged species in the gas phase. The assignment of vibrational modes to establish a relationship between a spectrum and a molecular structure is however non trivial and requires extensive molecular modeling. This thesis describes a complete methodology for the calculation of vibrational spectra and its application to peptides attached to a sodium cation. We start with the efficient exploration of the complex conformational space of these systems, using replica-exchange molecular dynamics, in order to select the most likely structures. We have used the polarizable force field AMOEBA for the cation-peptide complexes, and (re)optimized parameters whenever required, in particular for improving the calculation of vibrational spectra of model compounds. Simulation of spectra for the structures selected has been performed using DFT and MP2 quantum chemical methods.This involved evaluating the performance of several density functionals, with or without a correction for dispersion interactions. We then describe the Fourier transform of the Dipole moment Auto-Correlation Function (DACF) computed along a classical molecular dynamics trajectory as a means of simulating infrared spectra including temperature and anharmonic coupling effects that are necessary for a full comparison with experiment. We discuss the relevance of the DACF/AMOEBA combination to model IRMPD spectra. This set of methods has been applied to the structure, energetics and infrared spectroscopy of poly-glycines containing two to eight residues, attached to a sodium cation. The computed spectra for the lowest energy structures allow for the assignment of experimental bands, thus establishing the structures of these complexes. Peptide folding around the sodium ion is achieved via the amide oxygens. When the ion coordination becomes saturated, peptide structuration is completed with turns.
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https://pastel.archives-ouvertes.fr/pastel-00528244
Contributor : David Semrouni <>
Submitted on : Thursday, October 21, 2010 - 1:22:33 PM
Last modification on : Wednesday, March 20, 2019 - 12:12:02 PM
Long-term archiving on: : Friday, October 26, 2012 - 11:50:09 AM

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David Semrouni. Énergétique et spectroscopie de polypeptides par dynamique moléculaire : champ de force de seconde génération et chimie quantique. Chimie théorique et/ou physique. Ecole Polytechnique X, 2010. Français. ⟨pastel-00528244⟩

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