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Sujet de stage / Master 2 Internship

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Sulfur-assisted molecular folding : characterisation of the intramolecular interactions of foldamers by atomic scale modelling

Contact: MONS Michel, , michel.mons@cea.fr, +33 1 69 08 20 01
Summary:
The aim of the internship will be to characterize the intramolecular H-bonding in a series of building blocks of foldamers, all of them containing a S heteroatom. For each of them, their conformational landscape will be explored, in order to detect the emergence of original folding properties.
Possibility of continuation in PhD: Oui
Deadline for application:29/03/2019

Full description:
The "BioMolecular Structures” group at LIDYL is involved in an ARN-funded project aiming at optimizing the design of foldamers, that is, polymers adopting various secondary structures, such as helices or ribbons. The approach is articulated in three levels, each of which comprises: i) a theoretical modeling characterizing the systems, ii) their synthesis and iii) their experimental characterization, in particular using laser spectroscopy.
The first level will deal with the building blocks of these foldamers and the hydrogen bonds which stabilize them. The second will deal with the dimers of these elementary bricks, in particular to document their flexibility and to understand how the internal H bonds to the elementary bricks control it. Finally, in a third stage, oligomers of larger size will be considered.
The objective of the internship, focused on the first level, will consist in characterizing the intramolecular H bonds in a series of foldamer building blocks, all containing a S heteroatom. For each of them, the conformational landscape will be explored, using an energetic description based on the force field methods, then refined at the quantum chemistry level. The infrared spectrum of each of the most stable molecular conformations will be obtained by quantum chemistry, in the perspective of a comparison with spectra obtained by laser spectroscopy in the laboratory.
During the course, the candidate will be trained to use several softwares dedicated to :
- calculation of molecular structures, at the force field (AMBER, TINKER) and quantum chemistry (TURBOMOLE) levels,
- calculation of the frequencies of the vibration modes of the molecules (Turbomole).
- visualization of structures (Discovery Studio) and of intramolecular interactions (NCI-plot)
Technics/methods used during the internship:
During the course, the candidate will be trained to use several softwares dedicated to : - calculation of molecular structures, at the force field (AMBER, TINKER) and quantum chemistry (TURBOMOLE) levels, - calculation of the frequencies of the vibration modes of the molecules (Turbomole). - visualization of structures (Discovery Studio) and of intramolecular interactions (NCI-plot)

Laboratory
Tutor of the internship

 

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