Molecular dynamics modeling of imogolite formation mechanisms

Full description

Imogolite is a nanotubular clay mineral that can be synthesized in large quantities in the laboratory. Over the years, numerous modifications of this type of nanotube have been discovered, and this family of materials now constitutes a nanoplatform with multiple potential applications [1]. These structures have been the subject of various experimental studies at NIMBE, notably characterized by complementary spectroscopies such as SAXS or Nuclear Magnetic Resonance (NMR) [2].

Imogolite is formed by the folding of an aluminum hydroxide monolayer due to the asymmetric tension exerted by silicon on one of the monolayer’s surfaces. Different folding modes characterize natural and synthetic imogolites, as suggested by the most recent studies coupling small-angle X-ray scattering and cryo-microscopy [3]. A detailed understanding of these folding modes is currently at the heart of our concerns. It is known that all nanotubes are formed from crystallization intermediates called proto-imogolites. These are 3-5 nm nanoparticles with the same local structure as the final nanotube, but too small to form a complete circumference. The protoimogolites are also curved in the form of nanotubes. We suggest that nanotubes are formed by self-assembly of these protoimogolites, and that there is a link between the folding of protoimogolites and nanotubes. We also believe that interaction with the solvent plays a key role in the role in defining the curvature and chirality of proto-imogolites and final nanotubes.

The aim of this internship is to simulate the proto-imogolite folding by means of Molecular Dynamics (MD) simulations, using classical force fields developed for modeling clay systems, in addition to ab-initio (or DFT) simulations. We would like to test the impact of solvent (hydrogen bond network) and temperature on the folding of numerical models of proto-imogolites. We want to determine the final curvature and its direction relative to the imogolite crystal axes as a function of proto-imogolite size.

The internship will focus on producing numerical models of proto-imogolites (OH and CH3) of various shapes and sizes, paying particular attention to the management of edge effects. These numerical models will be relaxed in the presence of water. The mean curvature and direction of curvature will be determined using molecular dynamics simulation trajectories. This internship is closely linked with experimentalists, but will mainly use numerical tools. We are looking for a student in computational chemistry with skills or wishing to train in molecular dynamics. The internship will last 5-6 months and could start as early as March 2025.

The internship will take place at CEA Paris-Saclay, in the NIMBE research unit ( https://iramis.cea.fr/nimbe) under the supervision of Antoine Thill and Thibault Charpentier to whom applications should be addressed.

Location

CEA Saclay, (91) Essonne, France

Internship conditions

• Internship duration: 6 months
• Level of study: Bac+5
• Training: Master 2
• Continuation in PhD thesis: Yes
• Application deadline: 3 mars 2025

Useful methods and technics: Computational chemistry, molecular dynamics, DFT

Computer languages and software: Python

Supervisor

Thibault Charpentier
Phone: +33 1 69 08 23 56
Email :

Head of the laboratory NIMBE / LIONS

Antoine Thill
Phone: +33 1 69 08 99 82