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Sujet de stage / Master 2 Internship

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Excited states deactivation in model proteins chains: Non-adiabatic dynamics and ab initio methods

Contact: BRENNER Valerie, , valerie.brenner@cea.fr, +33 1 69 08 37 88
This internship focuses on the characterization of the deactivation excited states mechanisms in model proteins chains, capped peptides, and in particular, the determination of the performances for such systems of a quantum chemistry method dedicated to the excited states computation.
Possibility of continuation in PhD: Oui
Deadline for application:29/03/2019

Full description:
The proteins are endowed with mechanisms of excited-state deactivation following UV absorption. These mechanisms are of major importance for the photochemical stability of these species since they provide them a rapid and efficient way to dissipate the electronic energy in excess into vibration, thus avoiding photochemical processes to take place and then structural damages which affect the biological function of the system. In this context, an efficient modelling of the potential energy surfaces of excited states of model proteins should lead to better understanding the photophysical phenomena involved in the deactivation mechanisms. An efficient method for this modeling is the "Coupled Cluster" method of order 2 (CC2).1,2 However, this method is difficult to apply for large systems due to very long computation times and in non-adiabatic dynamics simulations for convergence problems. The main objective of this internship is then to test on a series of model proteins, capped peptides, the performances of an alternative quantum chemistry method to treat excited states, the ADC (2) method (Algebraic Diagrammatic Construction through Second Order).3 This theoretical work will be backed up by key gas phase experiments performed in the team, experiments using recent development of the spectroscopic techniques in gas phase.

[1] W. Y. Sohn, V. Brenner, E. Gloaguen and M. Mons, Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides. PCCP 2016, 18, 29969.
[2] N. Ben Amor, S. Hoyau, D. Maynau and V. Brenner, Low-lying excited states of models proteins: Performances of the CC2 method versus MRCI methods. J. Chem. Phys 2018, 148, 184105.
[3] (a) J. Schirmer, Beyond the random-phase approximation: a new approximation scheme for the polarization propagator. Physical Review A. 1982, 26, 2395. (b) A. B. Trofimov and J. Schirmer, An efficient polarization propagator approach to valence electron excitation spectra. Journal of Physics B. 1995, 28, 2299.
Technics/methods used during the internship:
During the course, the candidate will be trained in methods calculating excited states as well as to use quantum chemistry softwares: Turbomole (CC2 and ADC(2) methods) and NEWTON-X (Non-adiabatic dynamics).

Tutor of the internship


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