Bile salts are supramolecules with amphiphilic properties. Bile salts form aggregates in aqueous solutions. The primary aggregates of bile salts are hydrophobic and the secondary aggregates which form at higher concentrations are relatively hydrophilic. Among bile salts, sodium deoxycholate (NaDC) has been known to form hydrogels at pHs close to the neutral pH and within a certain concentration range. The aim of this work was to provide insight into the properties of a NaDC hydrogel as a supramolecular gel system through three different projects. Pyrene is a hydrophobic polycyclic aromatic compound which was used as a fluorescent probe and the guest for these projects. 1,1’-dioctadecyl-3,3,3’,3’-tetramethylindodicarbocyanine perchlorate (DiD) is another fluorescent compound which was used as another guest. The objective of the first project was to understand the mobility of a small guest molecule in NaDC gel in the presence of cucurbit[6]uril (CB[6]) compound as an additive for the gel. Cucurbit[n]urils are macrocyclic compounds with a hydrophobic cavity and two hydrophilic portals. The presence of CB[6] provides another binding site for pyrene in addition to the primary aggregates of the bile salts. The results showed that the mobility of the guest from water and CB[6] to the bile salts network happens when the temperature is raised. The release of the guest back into the water happens when the gel is cooled. The objective of the second project was to investigate the effect of surfaces with different hydrophilicity on the NaDC gel properties. The results of fluorescence correlation spectroscopy (FCS) experiments revealed that either the hydrophilicity of the surface does not affect the NaDC gel network or the FCS is insensitive to the structural changes induced by the hydrophilicity of the surface. These experiments depicted that the aggregates involved in the gel’s network are the same as those formed in the aqueous solutions. Moreover, results of the steady-state and time-resolved fluorescence experiments showed that the bulk gel properties are not affected by the hydrophilicity of the surface. The objective of the last project was to determine the effect of ions on NaDC gel properties. The results showed that cations with different charge density have different effects on the gel formation and properties. The presence of inorganic salts with a monovalent cation leads to the formation of a kinetically favored gel sample within a few hours after sample preparation. The extension of the network occurs overtime and a thermodynamically stable gel forms a couple of days after sample preparation. / Graduate / 2020-10-20

ZIF-8 is a flexible zeolitic imidazole-based metal−organic framework whose narrow pore apertures swing open by reorientation of imidazolate linkers and expand when probed with guest molecules. This work reports on the crystal size dependency of both structural transitions induced by N2 and Ar adsorption and dynamic adsorption behavior of n-butanol using well-engineered ZIF-8 crystals with identical surface area and micropore volume. It is found that the crystal downsizing of ZIF-8 regulates the structural flexibility in equilibrium adsorption and desorption of N2 and Ar. Adsorption kinetics of n-butanol in ZIF-8 are strongly affected by the crystal size, however, not according to a classical intracrystalline diffusion mechanism. Our results suggest that structural transitions and transport properties are dominated by crystal surface effects. Crystal downsizing increases the importance of such surface barriers.

The recently discovered cucurbit[n]uril are a range of macrocyclic hosts which have enormous potential in industrial, medical and academic applications. Cucurbit[n]uril have a rigid repeating structure of methylene bridged glycouril, which give cucurbit[n]uril their gourd like shape of a cavity with two carbonyl fringed portals. In this thesis the host-guest binding abilities of three cucurbit[n]uril (n = 6, 7, 8) have been examined for a range of potential guests. These guests ranged from simple alkyl amines through globular alkyl and carboranyl amines to bipyridyl systems. In total 45 guest molecules where examined. Most of the guests examined where either cationically charged, capable of hydrogen binding, contained a substantial molecular dipole, or a combination of these. Furthermore, all of the potential guests examined had some solubility in an acidified aqueous sodium sulfate solution within which the host-guest properties were examined. It was generally found that the larger guests did have selectivity for the larger hosts. However, when the host became too large weaker complexes would form and for the range of materials examined here cucurbit[7]uril was found to be the 'best' host system. In one example, p-xylene diamine, a 2:1 complex with cucurbit[8]uril was observed. While not the focus of this work a new rapid purification method was developed for the cucurbit[n]uril using different metal ions to either solubilise or precipitate the different cucurbit[n]uril. In the second part of this work these same guest molecules where used as potential templates in the synthesis of cucurbit[n]uril. Surprisingly the guests that bound strongly to an individual host did not seem to template the cucurbit[n]uril synthesis at all. Rather these strong binders inhibited the reaction such that little or no cucurbit[n]uril formed under the reaction conditions studied. However, several examples provided excellent template results. Indeed the results indicate that guests which bound with intermediate rates of exchange are the best templates and using templates under these conditions we have been able to produce cucurbit[7]uril as 46% by mass of the total cucurbit[n]uril product. This is the highest yield ever recorded for cucurbit[7]uril and it is the first example of cucurbit[7]uril being the major product of this condensation reaction. In an another example cucurbit[8]uril formed 18% of the product an increase of 150% over the standard reaction conditions. While studying both the template reactions and the host-guest binding properties of the cucurbit[n]uril a new supramolecular form, an 'inverse rotaxane' was discovered. Inverse rotaxanes are not held in place by large blocking groups, rather the molecular structure encapsulated by the cucurbit[n]uril host prevents decomplexation of the axle.

Most of the computer simulations of molecules in Metal-Organic Frameworks (MOFs) to be found in the literature are done with rigid framework. But, Molecular Dynamics (MD) simulations of the self-diffusivity, Ds, of ethane within the one-dimensional 4.5 Å channels of the MOF type Zn(tbip)(H2 tbip = 5-tert-butyl isophthalic acid) presented in this work have shown not only quantitative, but also qualitative, differences in the Ds values for fixed and flexible lattices. Particularly, the dependence of Ds upon the concentration of molecules, c, is strongly influenced by the lattice flexibility. The reasons for this influence are investigated with the aid of probability density plots, free energy landscapes and barriers, along with a determination of the structural changes accompanying increasing c. It is found that for flexible lattices, the tighter, more constrained parts of the channels become wider at higher c; this allows more molecules to diffuse in the central region of the channels. The investigations for Zn(tbip) have been extended to three equimolar mixtures of ethane/ethane, CO2/ethane and CO2/methanol. The simulations take into account the lattice flexibility. The diffusional characteristics are discussed in relation to molecule properties and lattice geometry. The results show that Zn(tbip) may be a useful material for separating methane/ethane and CO2/ethane mixtures at low concentrations, and CO2/methanol mixtures at high concentrations. The temperature and concentration dependence of the self-diffusivity of propane diffusion in Zn(tbip) have been investigated as well by performing normal MD and hyper-MD with bias potential simulations. The obtained temperature dependence of the self-diffusivities is analyzed using an Arrhenius relationship, yielding the activation energy to be 9.53 kJ/mol and the pre-exponential factor to be 4.48×10-9 m2s-1. Using this hyper-MD method, interesting mechanisms of the propane molecules able to pass each other and exchange their sites in the channels can be observed. Because of mutual hindrance of propane molecules, the propane self-diffusivities decrease with increasing concentration.

Most of the computer simulations of molecules in Metal-Organic Frameworks (MOFs) to be found in the literature are done with rigid framework. But, Molecular Dynamics (MD) simulations of the self-diffusivity, Ds, of ethane within the one-dimensional 4.5 Å channels of the MOF type Zn(tbip)(H2 tbip = 5-tert-butyl isophthalic acid) presented in this work have shown not only quantitative, but also qualitative, differences in the Ds values for fixed and flexible lattices. Particularly, the dependence of Ds upon the concentration of molecules, c, is strongly influenced by the lattice flexibility. The reasons for this influence are investigated with the aid of probability density plots, free energy landscapes and barriers, along with a determination of the structural changes accompanying increasing c. It is found that for flexible lattices, the tighter, more constrained parts of the channels become wider at higher c; this allows more molecules to diffuse in the central region of the channels. The investigations for Zn(tbip) have been extended to three equimolar mixtures of ethane/ethane, CO2/ethane and CO2/methanol. The simulations take into account the lattice flexibility. The diffusional characteristics are discussed in relation to molecule properties and lattice geometry. The results show that Zn(tbip) may be a useful material for separating methane/ethane and CO2/ethane mixtures at low concentrations, and CO2/methanol mixtures at high concentrations. The temperature and concentration dependence of the self-diffusivity of propane diffusion in Zn(tbip) have been investigated as well by performing normal MD and hyper-MD with bias potential simulations. The obtained temperature dependence of the self-diffusivities is analyzed using an Arrhenius relationship, yielding the activation energy to be 9.53 kJ/mol and the pre-exponential factor to be 4.48×10-9 m2s-1. Using this hyper-MD method, interesting mechanisms of the propane molecules able to pass each other and exchange their sites in the channels can be observed. Because of mutual hindrance of propane molecules, the propane self-diffusivities decrease with increasing concentration.