Thesis (PhD (Chemistry and Polymer Science))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: The primary objective of the work was to prepare and investigate new porous materials using the principles of crystal engineering. Both organic and metal-organic systems were studied and the work can best be divided into two separate sections: 1. The crystal engineering of Dianin’s Compound, a well-known organic host. 2. The design and synthesis of a series of related porous coordination compounds consisting of discrete, dinuclear metallocycles. The first section discusses the synthetic modification of Dianin’s compound in order to engineer a new clathrate host with an altered aperture size. Although this study ultimately failed to isolate the host material in its porous guest-free form, the work led to the discovery of a chiral host framework that aligns guest molecules in a polar fashion, and consequently displays non-linear optical properties. These findings are unprecedented in the long history of crystal engineering of Dianin’s compound and its analogues. This section also describes desorption studies of the new inclusion compound, as well as the known thiol analogue of Dianin’s compound. Systematic characterisation of these desorbed phases has raised interesting fundamental questions about desolvation processes in general. The second section constitutes the major portion of the work. A series of related isostructural coordination metallocycles were synthesised and their structure-property relationships were investigated using a variety of complementary techniques. These metallocyclic compounds all crystallise as solvates in their as-synthesised forms, and different results are obtained upon desolvation of the materials. In each case, desolvation occurs as a single-crystal to single-crystal transformation and three new “seemingly nonporous” porous materials were obtained. A single-crystal diffraction study under various pressures of acetylene and carbon dioxide was conducted for one of the porous metallocycles. This enabled the systematic study of the host deformation with increasing equilibrium pressure (i.e. with increasing guest occupancy). The observed differences in the sorption behaviour for acetylene and carbon dioxide are discussed and rationalised. Gravimetric gas sorption isotherms were also recorded for the three different porous materials and the diffusion of bulkier molecules through the host was also investigated structurally. Finally, a possible gas transport mechanism is postulated for this type of porous material (i.e. seemingly nonporous), and this is supported by thermodynamic and kinetic studies, as well as molecular mechanics and statistical mechanics simulations. / AFRIKAANSE OPSOMMING: Die primêre doel van die werk was om nuwe poreuse materiale te berei en deur die toepassing van beginsels van kristalmanipulasie (E. crystal engineering) te ondersoek. Beide organiese- en metaal-organiese sisteme is bestudeer en die werk kan in twee kategorieë verdeel word: 1. Die kristalmanipulasie van Dianin se verbinding, ’n bekende organiese gasheer. 2. Die ontwerp en sintese van ’n reeks verwante poreuse koördinasieverbindings wat uit diskrete, binukleêre metallosiklieseverbindings bestaan. Die eerste deel handel oor die sintetiese verandering van Dianin se verbinding om ’n nuwe klatraatgasheer met ’n veranderde spleetgrootte te vorm. Alhoewel hierdie studie nie daarin geslaag het om die gasheer in sy poreuse “gas(E. guest)-vrye” vorm te isoleer nie, het die werk ’n nuwe chirale gasheerraamwerk aan die lig gebring. Die chirale gasheerraamwerk rig gas(E. guest)molekules in eendimensionele kolomme op ’n polêre wyse en gevolglik vertoon die materiaal nie-linieêre optiese eienskappe. Hierdie resultaat is ongekend in die lang geskiedenis van kristalmanipulasie van Dianin se verbindings en sy analoë. Hierdie afdeling beskryf ook die desorpsiestudies van die nuwe gasheer, en die tiol-afgeleide van Dianin se verbinding. Die sistematiese karakterisering van hierdie fases na desorpsie het fundamentale vrae na vore gebring oor desorpsieprosesse oor die algmeen. Die tweede afdeling maak die grootste gedeelte van die werk uit. ’n Reeks verwante isostrukturele ringvormige koördinasieverbindings is gesintetiseer en hul struktuureienskap verhoudings is deur ’n verskeidenheid komplementêre tegnieke ondersoek. Hierdie metallosiklieseverbindings kristalliseer almal in gesolveerde toestand vanaf sintese en verskillende resultate word verkry wanneer die verbinding desorpsie ondergaan. In alle gevalle vind gas(E. guest)desorpsie as enkel-kristal na enkel-kristal omsettings plaas en drie nuwe ‘oënskynlik nie-poreuse’ poreuse materiale is bekom. ’n Enkelkristal diffraksiestudie onder verskeie gasdrukke is met asetileen en koolstofdioksied uitgevoer vir een van die poreuse metallosiklieseverbindings. Dit het die geleentheid geskep om die mate waartoe die gasheer as gevolg van verhoogde ewewigsdruk vervorm (en dus toename in gasheerbesetting), sistematies te bestudeer. Die waargenome verskille in sorpsie-optrede vir asetileen en koolstofdioksied word bespreek en verklaar. Gravimetriese gassorpsie isoterme is ook vir die drie poreuse materiale verkry en die diffusie van groter molekules deur die gasheer is struktureel ondersoek. Laastens word ’n moontlike gasoordragmeganisme vir hierdie tipe poreuse (i.e. oënskynlik nie-poreuse) materiale gepostuleer. Hierdie bespreking word deur termodinamiese en kinetiese studies aangevul, sowel as molekulêre-meganika en statisties-meganiese studies.

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General anisotropic constitutive laws and relevant dynamic equations of motion for porous media are described. The accuracy of various discretization algorithms in space and in time was surveyed. Results of these models and algorithms were compared to the exact solutions. Appropriate models and algorithms for further studies of spinal motion segments were then determined. Poroelastic axisymmetric finite element models, simulating spinal motion segments were analyzed and studied. Material properties of the intervertebral disc were derived by fitting experimental data based on porous medium theory using one-dimensional mathematical models. Structural models for the normal and degenerative processes were simulated for investigation of nutritional supply routes in the disc. Detailed structural anaalyses and failure conditions in various spinal motion segments were studied. Results of finite element analyses were consistent with the experimental observations. Nonlinear elastic material behavior of the solid skeleton was assumed and relevant formulas in creep were derived and examined. Preliminary results indicated that the nonlinear poroelastic material law used here may be useful in future analysis of the disc in finite element models of spinal motion segments.

Inorganic and metal-organic framework materials possessing accessible and permanent pores are receiving tremendous attention. Among them, zeolites are the most famous class due to their wide applications on petrochemistry and gas separation. Besides zeolites, the other oxide framework materials are also intensively investigated because of their diverse structures and compositions. Metal-organic frameworks are built from metal clusters and organic linkers. By rational designing the reagent, the network with desired topology and functionality can be synthesized. For all of the framework materials mentioned above, to explore novel framework structures is important for improving properties and discovering new applications. This thesis includes the synthesis of zeolites and structure characterization for various types of inorganic framework materials. The zeolite synthesis conditions was exploited. With the optimized condition, the zeolite ITQ-33 was synthesized as single crystals. From the single crystal X-ray diffraction data, the disorder in the structure is discovered and explained. Following the topic of disorder and twinning, we proposed a novel method of solving structure of pseudo-merohedric twinning crystal by using an example of a metal-organic complex crystal. Then we also showed methods for solving structures of high complexity and nano-crystal by using mainly powder X-ray diffraction and transmission electron microscopy. Four examples were shown in chapter 4 including open-framework germanates and metal-organic frameworks. / <p>At the time of the doctoral defence the following paper was unpublished and a status as follows: Paper  4: Manuscript</p>

Molecularly imprinted polymers (MIPs) are a novel, promising family of porous materials with potential applications ranging from separations, chemical sensing and catalysis to drug delivery and artificial immunoassays. The unique feature of these materials is their biomimetic molecular recognition functionality. Molecular recognition is the biological phenomenon of specific, selective and strong association between a substrate and a ligand. In man made MIPs this functionality is implemented via templated synthesis protocol. MIPs are synthesized in the presence of additional template molecules which form complexes with functional monomers in the pre‐polymerization mixture. After polymerization, the template is removed, leaving cavities in the structure which are complementary in shape and interaction patterns to the template molecules. These cavities act as mimics of biological receptors and are able to recognize and rebind template molecules. Although the imprinting concept is simple in principle, synthesis of MIPs with precisely controlled characteristics and performance remains a challenging task. Composition, polymerization conditions, template removal process and application conditions all affect the properties of MIPs. The material is affected at different scales, but crucially at the microscopic level, the number, fidelity and accessibility of binding sites are dependent on all the factors mentioned. The full potential of these materials can only be achieved if researchers can control and optimize the properties of MIPs through detailed understanding of adsorption and molecular recognition processes in these materials. The objective of this work is to, using computer simulations and statistical mechanics; develop a fundamental description of MIP formation and function, and to link morphological features of the model materials to their molecular recognition capabilities. In general, molecular simulations employed in this study should allow easier and more efficient exploration of a vast number of factors influencing the behaviour of MIPs. At the heart of the approach developed in this thesis is a computational strategy that imitates all the stages of MIP formation and function. First, the model simulates the pre‐polymerization mixture, allowing the formation of template‐functional monomer complexes. (This stage is implemented via canonical Monte Carlo simulation). Complexes can have different structures, depending on the chemical nature of template and functional monomer; therefore complexes can have a range of association constants. The distribution of template‐functional monomer complexes also translates into a distribution of binding sites of different specificity after template removal. In the second stage of the process, adsorption simulations (grand canonical Monte Carlo) are performed for a variety of model MIPs prepared to assess the role of various processing conditions such as composition, density and binding sites degeneration. This strategy was first applied to a simplified description of MIP species in order to identify the minimal model capable of molecular recognition and thus shed the light on the very nature of this phenomenon. In the developed model, the molecular species are constructed from hard spheres, featuring small interaction sites on their surfaces. The bond between two interaction sites has the strength and topological features of a typical hydrogen bond. The model exhibits molecular recognition, being able to preferentially adsorb template molecules. The associations between template and functional monomers were analyzed and classified to describe the distribution of binding sites and their heterogeneity. Using this model, several experimental trends typically observed in MIP studies could be explained, such as maximum in the selectivity as a function of monomer concentration. Using this model, we were also able to explore hypothetical, alternative protocols for MIP synthesis in order to improve their performance. These include the use of alternative templates and the post‐synthetic surface modifications of MIPs. The general strategy to modelling MIP, employed in this thesis, was then applied to a more detailed description of MIPs with realistic force field potentials for all the species involved. This more elaborate model is simulated with a combination of molecular dynamics (MD) and Monte Carlo techniques. This detailed model provided a wealth of information on various types of complexes observed in the pre‐polymerization mixture. Specifically, it revealed the relative weight of different interactions in the complex and their role in the binding energy of adsorbates. These simulations also provided the comparison of the relative contribution of different types of interactions (van der Waals, Coulombic) involved in a molecular recognition process. We believe the insights gained in this work will contribute to the development of rational MIP design strategies. In the discussion of the results of the thesis we speculate on how these models can be further developed in order to generate quantitative predictions and what type of systems it would be interesting and important to investigate in the future.

Phonon transport analysis in nano- and micro-porous materials is critical to their energy-related applications. Assuming diffusive phonon scattering by pore edges, the lattice thermal conductivity can be predicted by modifying the bulk phonon mean free paths with the characteristic length of the nanoporous structure, i.e., the phonon mean free path (Lambda(pore)) for the pore-edge scattering of phonons. In previous studies (Jean et al., 2014), a Monte Carlo (MC) technique have been employed to extract geometry determined Lambda(pore) for nanoporous bulk materials with selected periods and porosities. In other studies (Minnich and Chen, 2007; Machrafi and Lebon, 2015), simple expressions have been proposed to compute Lambda(pore). However, some divergence can often be found between lattice thermal conductivities predicted by phonon MC simulations and by analytical models using Lambda(pore). In this work, the effective Lambda(pore) values are extracted by matching the frequency-dependent phonon MC simulations with the analytical model for nanoporous bulk Si. The obtained Lambda(pore) values are usually smaller than their analytical expressions. These new values are further confirmed by frequency-dependent phonon MC simulations on nano porous bulk Ge. By normalizing the volumetric surface area A and Lambda(pore) with the period length p, the same curve can be used for bulk materials with aligned cubic or spherical pores up to dimensionless p.A of 1.5. Available experimental data for nanoporous Si materials are further analyzed with new Lambda(pore) values. In practice, the proposed model can be employed for the thermal analysis of various nanoporous materials and thus replace the time-consuming phonon MC simulations.

L’objectif du travail de thèse a été la mise en place de deux modélisations multi-physiques fondées sur des fondements théoriques communs mais appliquées à deux domaines de la recherche scientifique très différents: i) l’étude du comportement du béton au jeune âge pour la prévention de la fissuration précoce- ii) l’analyse des phénomènes physiques, chimiques et biologiques qui gouvernent la croissance et l’évolution de la tumeur cancéreuse. Le développement d’un outil numérique pour la modélisation du béton au jeune âge est très important pour la conception de structures durables. Le modèle développé pendant la thèse doctorale a été implanté sur le code aux éléments finis Cast3M, puis validé expérimentalement. Il permet de multiples applications: étude des sollicitations et des phénomènes de fissuration au jeune âge, gradients thermiques et hydriques, prédiction du retrait endogène et de dessiccation, étude de l’inhibition de l’hydratation causée par le séchage, prédiction du fluage et de la redistribution des contraintes associées, étude des réparations. Les équations qui gouvernent le comportement thermo-hydro-chemo-mécanique du béton au jeune âge ont plusieurs analogies formelles avec celles qui sont typiquement à la base de la modélisation de la croissance des tumeurs cancéreuses. L'élargissement de l'analyse numérique dans le domaine médical est d’un grand intérêt social en complément de l’intérêt scientifique. Les équations utilisées pour le béton ont été réadaptées, et le modèle mathématique obtenu a été implanté dans Cast3M. Les premiers résultats du modèle ont été satisfaisants et qualitativement très proches des données expérimentales de la littérature dans ce domaine. / The aim of the PhD thesis has been the development of two multi-physics models based on common theoretical basis, but applied to two very different areas: i) the study of the behavior of concrete at early age, essentially for the prevention of early cracking and related issues- ii) the analysis of physical, chemical and biological processes that govern growth and development of cancer. The development of a numerical tool to model concrete at early age is of great importance for the design of durable and sustainable structures. The model has been implemented on the finite element code CAST3M (developed by CEA), also it was validated and nowadays allows multiple applications: study of stresses and cracking phenomena in young concrete, thermal and hygral gradients, autogenous and drying shrinkage, inhibition of hydration caused by drying, creep, stress redistribution, study repairs, etc.. In the fight against cancer, it is clear that the advance of medical strategies based on numerical analysis have a critical scientific interest and can have a great social impact. The equations which govern the thermo-hydro-chemo-mechanical behavior of concrete at early age have may formal analogies with those used to model tumor growth. Hence, these equations have been readapted and a novel mathematical model for tumor growth has been developed. The model was implemented in Cast3M and the first numerical results have been encouraging since very close to the experimental data present in the literature.

Thesis advisor: Chia-Kuang (Frank) Tsung / Exchange reactions have enabled a new level of control in the rational, stepwise preparation of metal-organic framework (MOF) materials. However, their full potential is limited by a lack of understanding of the molecular mechanisms by which they occur. This dissertation describes our efforts to understand this important class of reactions in two parts. The first reports our use of a linker exchange process to encapsulate guest molecules larger than the limiting pore aperture of the MOF. The concept is demonstrated, along with evidence for guest encapsulation and its relation to a dissociative linker exchange process. The second part describes our development of the first quantitative kinetic method for studying MOF linker exchange reactions and our application of this method to understand the solvent dependence of the reaction of ZIF-8 with imidazole. This project involved the collection of the largest set of rate data available on any MOF linker exchange reaction. The combination of this dataset with small molecule encapsulation experiments allowed us to formulate a mechanistic model that could account for all the observed kinetic and structural data. By comparison with the kinetic behavior of complexes in solution, we were able to fit the kinetic behavior of ZIF-8 into the broader family of coordination compounds. Aside from the specific use that our kinetic data may have in predicting the reactivity of ZIF linker exchange, we hope that the conceptual bridges made between MOFs and related metal−organic compounds can help reveal underlying patterns in behavior and advance the field. / Thesis (PhD) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

A dissertation submitted to the Faculty of Science,University of the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science. December 2016. / This research is concerned with the analysis of a two-dimensional Newtonian fluid-driven fracture in a permeable rock. The fluid flow in the fracture is laminar and the fracture is driven by the injection of a Newtonian fluid into it. Most of the problems in litera- ture involving fluid flow in permeable rock formation have been modeled with the use of Darcy's law. It is however known that Darcy's model breaks down for flows involv- ing high fluid velocity, such as the flow in a porous rock formation during hydraulic fracturing. The Forchheimer flow model is used to describe the non-Darcy fluid flow in the porous medium. The objective of this study is to investigate the problem of a fluid-driven fracture in a porous medium such that the flow in the porous medium is non-Darcy. Lubrication theory is applied to the system of partial di erential equations since the fracture that is considered is thin and its width slowly varies along its length. For this same reason, Perkins-Kern-Nordgren approximation is adopted. The theory of Lie group analysis of differential equations is used to solve the nonlinear coupled sys- tem of partial differential equations to obtain group invariant solutions for the fracture half-width, leak-o depth and length of the fracture. The strength of fluid leak-off at the fracture wall is classi ed into three forms, namely, weak, strong and moderate. A group invariant solution of the traveling wave form is obtained and an exact solution for the case in which there is weak fluid leak-off at the interface is found. A dimensionless parameter, F0, termed the Forchheimer number was obtained and investigated. Nu- merical results are obtained for both the case of Darcy and non-Darcy flow. Computer generated graphs are used to illustrate the analytical and numerical results. / MT2017

Colloid detachment and mobilization can be of significant interest to those studying colloid behavior in the environment. The transport of pathogens such as viruses, bacteria, and protozoa can cause health problems in animals and humans. The transport of organics, radionuclides, and other hydrophobic contaminants can be enhanced by adsorption to mobilized colloid surfaces. Research has been done by others quantifying the detachment of colloids from smooth porous media. Real surfaces in the environment and engineered systems are rough. Glass beads were chemically roughened by procedures similar to those from Shellenberger and Logan (2002) and It et al. (2001) using chromic acid and a citric acid/ammonium fluoride solution. Surface asperities were measured using Atomic Force Microscopy (AFM), and the roughness was defined by three parameters: Root Mean Square (RMS) roughness, peak to valley height (P/V height), and peak to peak distance (λ). Detachment from the chemically etched porous media was measured in column tests. The controlling roughness parameter between the two batches of beads was found to be λ. A theoretical model to predict the effect of roughness on detachment was developed. Using a moment balance around the downstream point of contact, the parameters incorporated into the model were particle diameter, P/V height, and λ. The model predicted the shear required for colloid detachment in column tests. Surface roughness was found to significantly inhibit colloid detachment.