Browsing by Author "Van Heerden, Dewald Pepler"

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    Computational assessment and visualization of guest inclusion in porous crystalline materials.
    (Stellenbosch : Stellenbosch University, 2020-11) Van Heerden, Dewald Pepler; Barbour, Leonard J.; Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science.
    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.
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    Evaluation of gas sorption techniques and computational methods utilized in the analysis of porous compounds
    (Stellenbosch : Stellenbosch University, 2014-12) Van Heerden, Dewald Pepler; Barbour, Leonard J.; Esterhuysen, Catharine; Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science.
    ENGLISH ABSTRACT: A recently proposed mechanism responsible for anomalous thermal expansion in a metal-organic framework (compound 1) is examined through theoretical calculations. A mechanistic model that reproduces the convergent expansion of the material’s coordination spiral is developed. In order to decide on a suitable theoretical method, specifically at the Density Functional Theory (DFT) level of theory, a tricyclicorthoamide that presents a unique nearly-eclipsed methyl group in the solid state (compound 2) is investigated. Since the anhydrous solid form of this molecule presents with the expected staggered conformation, the nearly-eclipsed conformation is ascribed to the presence of water molecules in the trihydrate form. An evaluation of the potential energy profile for rotation of the methyl group by the ab initio wave function methods HF, MP2 and CCSD revealed the global minimum to indeed be the nearly-eclipsed conformation (𝜔ℎ𝑐𝑐𝑛 ≈ 10°) with a barrier to rotation (Δ𝐸𝑟𝑜𝑡) of 1.24 kcal.mol-1 located at ~85° at the MP2/6-31+G(d) level of theory. The CCSD potential energy profiles also feature a local minimum at ~55° that is ascribed to a dispersive intramolecular interaction. Since the Kohn-Sham implementation of DFT functionals ignores the dynamic electron correlation required to describe dispersion, semi-empirical dispersion-correction schemes to the density-dependent energy are evaluated. The mechanistic model describing the thermal expansion of 1 is evaluated with the B3LYP (hybrid GGA) and M06 (hybrid meta-GGA) density functionals augmented by the GD2 and GD3 dispersion correction schemes, respectively, in addition to the dispersion-corrected ωB97XD (LC-hybrid GGA) functional in conjunction with various basis sets. The resulting energy trends are found to compare favorably to the four energies obtained by periodic DFT evaluations of the 100, 190, 280 and 370 K crystal structures of 1. The thermodynamic data for carbon dioxide adsorption measured on a previously constructed in-house volumetric isosteric sorption technique (SIT) device are compared to those obtained through conventional gravimetric instrumentation. Two metallocyclic compounds (3 and 4) that maintain their crystallinity upon generation of the porous apohost, are evaluated. A comparison of the various methodologies that exist in the literature to determine isosteric heats of adsorption (𝑄𝑠𝑡) from adsorption isotherms are presented. In particular, the temperature-dependent dual-site Langmuir and virial-type isotherm equations are compared for the first time and found to be complementary. The 𝑄𝑠𝑡 values at zero occupancy are determined to be 29.2 and 35.5 kJ.mol-1 for compounds 3 and 4, respectively, and trends in 𝑄𝑠𝑡 as a function of occupancy plots are accounted for.