Computational assessment and visualization of guest inclusion in porous crystalline materials.
Date
2020-11
Authors
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Publisher
Stellenbosch : Stellenbosch University
Abstract
ENGLISH ABSTRACT: Host-guest systems are a central feature of supramolecular chemistry and an improved understanding of guest inclusion phenomena (i.e., transport and accommodation) may lead to the development of improved functional porous materials. However, the generally greater degree of thermal motion of guest molecule(s) relative to the host often impedes their accurate modelling in crystal structures. Furthermore, activation, the act of removing the guest to yield the empty apohost phase, often results in a loss of single crystallinity. Physical stimuli such as temperature, light, mechanical pressure, gas and liquid sorption, and electric and magnetic fields can induce structural transformations; however, the scarcity of in situ or in operando single-crystal X-ray diffraction (SCXRD) data encumbers the direct elucidation of underlying mechanisms. The work presented in this thesis contribute to the collective understanding of inclusion and dynamic phenomena in the solid state. Results are presented as two manuscripts, both of which have been submitted for peer review. The first manuscript describes the systematic derivation of a fractional occupancy factor θ that allows for “back-of-the-envelope” estimation of host/guest ratios in crystal structures. A common method of evaluating guest-occupiable space involves in silico sampling of free space by means of a spherical probe in van der Waals contact with the host structure. In addition to discussing caveats pertaining to reporting guest-occupiable space, we propose the terms probe-traversable volume (PTV) and probe-accessible volume (PAV) to refer to the regions mapped out by the center and surface of the probe, respectively. High-throughput analysis of close to 40 000 solvates yielded a weighted mean θ value of 51.1(4)%, where θ is the ratio of the molecular volume of the solvent to the PAV. The utility of our methodology is demonstrated through application to case studies encompassing 0D organic and organometallic, as well as metal-organic framework (MOF) materials. As part of an ongoing investigation in our group, the second manuscript reports on a combined theoretical and in situ SCXRD structural analysis of a flexible MOF subjected to methane, ethane, propane and butane gas pressures. Whereas subnetwork displacement is induced by sorption of ethane, distinctly stepped sorption isotherms for propane and butane are associated only with linker rotation; i.e., true gate opening. A turnstile mechanism is elucidated whereby neighboring pockets are temporarily fused to allow diffusion of guest molecules through the seemingly nonporous system.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.
Description
Thesis (PhD)--Stellenbosch University, 2020.