Understanding the diffusion of small gases in porous organic cages using molecular dynamics

Holden, Daniel Understanding the diffusion of small gases in porous organic cages using molecular dynamics. Doctor of Philosophy thesis, University of Liverpool.

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Abstract

The aim of this thesis was to accurately simulate the dynamic nature of known porous organic cage molecules, with a view to understanding the diffusion of different gases through their pore structures. Initial calculations showed that, due to their unique chemical structure, no ‘off-the-shelf’ force field (FF) was accurate enough to describe their dynamic motion. Therefore, a cage specific force field, (CSFF), was developed to be transferable across the first three cage systems, CC1-CC3. CSFF was subsequently used to rationalise the ‘on’/‘off’ porosity observed in two different polymorphs of CC1. A combination of computational simulations, including simulated surface area calculations, grand canonical Monte Carlo (GCMC) adsorption isotherms, and molecular dynamics (MD) simulations, for hydrogen and nitrogen in CC1α and CC1β, helped to confirm experimental results, as well as to provide further insight into why the polymorphism of CC1 alters the porosity of the molecule. In addition, CSFF was used to study the diffusion of a range of gases through crystalline CC3. Seven gases were chosen: hydrogen, nitrogen, carbon dioxide, methane, sulfur hexafluoride, krypton and xenon. A detailed understanding of the diffusivity within CC3 was accomplished by combining MD simulations with new methodologies and techniques, for example analysis of the dynamic connectivity. This helped to rationalise why CC3 showed good experimental uptake of gas, as well as highlighting potential separation capabilities. In summary, the development of CSFF has made it possible to simulate the diffusion of small gases through porous organic imine cages, and it has been shown that this diffusion is dependent on the relative size of the gas to the cage window, assuming that there is a suitable diffusion pathway. Using MD simulations, we have unlocked phenomena such as gas selectivity, rare-event hopping and the diffusion of gases to regions previously thought inaccessible. This has aided the rationalisation of existing experimental observations, and is a significant step forward for a priori prediction of porous organic cage systems, and their properties. This work has also led to new experiments that were prompted by my simulations. Finally, a new way to visualise the connectivity of a system has been introduced. This is achieved by monitoring how the surface area evolves with respect to time, during a MD simulation. This suggests how the pore channels of various systems, previously thought too small for gas adsorption, are actually suitable candidates for separations.

Item Type:	Thesis (Doctor of Philosophy)
Additional Information:	Date: 2013-09 (completed)
Subjects:	?? QD ??
Divisions:	Faculty of Science and Engineering > School of Physical Sciences
Depositing User:	Symplectic Admin
Date Deposited:	12 Feb 2014 16:08
Last Modified:	16 Dec 2022 04:40
DOI:	10.17638/00014433
Supervisors:	Cooper, Andrew
URI:	https://livrepository.liverpool.ac.uk/id/eprint/14433