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Développement de champs de forces polarisables et applications à la spectroscopie vibrationnelle

Abstract : Spectroscopy dissociation by absorption of infrared photons (IRPD) provides vibrational signatures of charged species in the gas phase, such as small peptides or hydrated ions in water clusters. The vibrational normal modes assignment to establish a relationship between the experimental spectrum and molecular structure is a delicate task and requires the use of molecular modeling.This manuscript presents a set of theoretical tools for calculation and assignment of vibrational spectra, based mainly on classical molecular dynamics and polarizable AMOEBA force field, and its application to gaseous ions of various sizes. Hydrated ions in water clusters M(H2O)n (n in 6-100 range) are characterized by a dynamic behavior, and their experimental spectrum can not be described by a single structure. The signature of peptides changes with temperature and dynamic anharmonicity effects. They can also be the site of proton transfer mechanisms, with a very characteristic vibrational signature.The potential energy surface of these systems is explored by classical molecular dynamics in individual trajectories or replica exchange to generate energetically stable structures. For smaller systems, quantum methods, as DFT and post-HF, are used to confirm the lowest energy structures, calculate their static IR and propose normal modes assignments. For larger systems, i.e ions in water drops of several tens of molecules, the simulation of IR spectra at finite temperature is based on the Fourier transform of the autocorrelation function of the dipole moment (DACF), calculated during a classical molecular dynamics trajectory. As this method does not allow direct access to the vibrational normal modes, we implemented a method of dynamic assigments, based on the Driven Molecular Dynamics (DMD) and coupled to the DACF. The combination AMOEBA /DACF / DMD was used to reproduce and assign the spectrum of the dipeptide Ace-Phe-Ala-NH2, and those of hydrated ions in water clusters.Finally, the vibrational signature of a proton transfer can not be described by quantum static methods or by classical dynamics. Its modeling required the development of a two states Empirical Valence Bond Model (EVB), coupled with AMOEBA polarizable force field. The two states EVB model was implemented in the software TINKER. It can reproduce the dynamic behavior of proton transfer in small peptides and deprotonated acids, as well as the spectroscopic signatures observed experimentally.An important part of the applications of these developments relates simple hydrated ions in nano-droplets, and in particular the sulfate ion of great environmental importance. We were able to reproduce satisfactorily, for the first time, the spectra of clusters containing up to 100 water molecules. The main contributor to this experimental spectroscopy is the team of E. Williams from the University of California of Berkeley. We have established cooperation with them to complete this work by modeling the IR spectra of hydrated sulfates ions [SO4(H2O) n=9-36]2-, for which they obtained experimental signatures.
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Submitted on : Tuesday, March 28, 2017 - 8:16:08 AM
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  • HAL Id : tel-01496879, version 1


Florian Thaunay. Développement de champs de forces polarisables et applications à la spectroscopie vibrationnelle. Chimie organique. Université Paris-Saclay, 2016. Français. ⟨NNT : 2016SACLX037⟩. ⟨tel-01496879⟩



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