Étude de la formation et des propriétés dynamiques, conformationelles et énergétiques d'assemblages supramoléculaires à base de nanotubes organiques et d'agrégats d'argent dans des brins d'ADN

Student thesis: Doc typesDoctor of Sciences

Abstract

The subject of our theoretically oriented Ph. D. thesis focuses on two types of supramolecular assemblies combining organic and inorganic materials: the first concerns complexes of organic molecules of various sizes and tubules formed by macrocycles, the second being a polynucleotide matrix allowing the formation of clusters of a few metallic atoms. In the first case, host molecules are cyclodextrins (CDs) assembled in tubules. The latter can accommodate various types of guest organic molecules, but more specifically, in the scope of our work, diphenylpolyenes (DPPs), styrene monomers, as well as a polystyrene oligomer. In the second case, the subject systems are polynucleotide strands complexing silver atoms, in the ionic, and then neutral state. The general goal of our work consists in the elucidation of structural, energetic, and dynamic properties of those complexes, with the help of theoretical methods based on “classical” force fields.

Regarding the first system of interest, we used the MMFF94 force field (FF), that we introduced ourselves in the Tinker simulation software source code. We first studied the organisation of CD tubules by three schemes: a structural examination of geometries from the Cambridge Structural Database, simulated annealing studies to evaluate the stability of tubular arrangements, and an incremental construction procedure of the tubules by molecular dynamics (MD). For β-CDs, the investigations pointed to a head-to-head configuration, while γ-CDs favoured a head-to-head+tail-to-head triplet. The position and interactions of water molecules inside the obtained tubular arrangements were studied as well. Various complexes for DPPs (DPB, DPH, and DPO) included in the β- and γ-CDs tubules were considered and compared based on structural, energetic, and dynamic criteria. Destabilisations of the arrangements are reported for perpendicular orientations of the DPPs and for the most heavily loaded tubules. Regarding assemblies between γ-CD and the two longest DPPs, various arrangements show similar stability. The same type of analyses was performed for the inclusion of styrene and polystyrene in the β- and γ-CDs tubules. These allowed us to correct assumptions formulated by experimentalists regarding the in situ polymerisation of styrene.

We next studied chromophore systems made of silver clusters stabilised by polynucleotide strands. To do so, classical interaction potentials relative to silver, neutral and cationic, were introduced in the AMBER FF. MD simulations allowed analysing the nature and force of the interactions between the various parts of the nucleic oligomers and the silver clusters, through averages of interaction energies. Conformational analyses were necessary to explore the flexibility of the supramolecular assemblies, specifically by radial distribution functions and Ramachandran-type maps.
Date of Award26 May 2014
Original languageFrench
Awarding Institution
  • University of Namur
SupervisorDaniel Vercauteren (Supervisor), Laurence Leherte (President), Benoît Champagne (Jury), Davide Bonifazi (Jury) & Aatto Laaksonen (Jury)

Keywords

  • Cyclodextrins
  • Computational Chemistry
  • DNA
  • Silver
  • Molecular Dynamics
  • Force Field

Cite this

Étude de la formation et des propriétés dynamiques, conformationelles et énergétiques d'assemblages supramoléculaires à base de nanotubes organiques et d'agrégats d'argent dans des brins d'ADN
Staelens, N. (Author). 26 May 2014

Student thesis: Doc typesDoctor of Sciences