One of the largest problems in current medicine is the shortage of organs for transplant due to technological limitations in the storage of organs for any length of time. A possible solution to this problem would involve cryopreservation. However, current cryopreservatives such as sucrose or DMSO have concerning cytotoxic issues that limit their possible applications. A major cause of cryoinjury is the uncontrolled recrystallization of inter and intra-cellular ice crystals that occurs during the thawing process leading to mechanical damage and dehydration. The Ben lab has thus been interested in the design of compounds that are capable of inhibiting this process but do not possess other undesirable properties found in the native compounds. These synthetic analogues have been shown to increase cellular viability post-thaw. A series of mixed α/β glycopeptides are prepared and analyzed for antifreeze properties. The results of this study imply that it is not the gross conformation of the glycopeptide that is responsible for activity, but rather that intramolecular relationships may be responsible for disrupting the reorganization of ice. A technique was devised for the incorporation of triazoles into the analogues to investigate the importance of the linker and to greatly simplify the synthesis of a library of glycoconjugates. It was found that the IRI activity of glycopeptides is very sensitive to the distance between carbohydrate and peptide backbone. The electron density at the anomeric oxygen is an important parameter with respect to intramolecular networks. A series of substituted galactosides is presented that modify the electronics of the anomeric oxygen. The results demonstrate that decreasing electron density at this position appears to improve IRI activity in a predictable manner. To better understand the remarkable IRI activity of a key analogue, it was systematically truncated. This study led to the serendipitous discovery of a series of very highly IRI active analogues that do not contain a peptide backbone. These compounds represent the first non-glycopeptides that can show very significant IRI activity even at very low concentrations. The final portion of the thesis reports the efforts towards the preparation of a carbasugar analogue of AFGP-8.

Experimental methods based on the magnetic resonance phenomenon belong to the most widely used experimental techniques for investigations of molecular and electronic structure. The difficulty with such experiments, usually a proper interpretation of data obtained from high-resolution spectra, opens new challenges for pure theoretical methods. One of these methods is density functional theory (DFT), that now has an advanced position among a whole variety of computational techniques. This thesis constitutes an effort in this respect, as it presents theory and discusses calculations of electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) parameters of paramagnetic molecules. It is known that the experimental determination of the magnetic resonance parameters of such molecules, especially in the case of NMR, is quite complicated and requires special techniques of spectral detection. On the other hand, paramagnetics play an important role in many areas, such as molecular magnets, active centers in biological systems, and defects in inorganic conductive materials. Therefore, they have spurred great interest among experimentalists, motivating us to facilitate the interpretation of spectral data through theoretical calculations. This thesis describes new methodologies for the determination of magnetic properties of paramagnetic molecules in the framework of DFT, which have been developed in our laboratory, and their applications in calculations of a wide range of molecular systems. The first two papers of this thesis deal with the theoretical determination of NMRparameters, such as nuclear shielding tensors and chemical shifts, in paramagnetic nitroxides that form core units in molecular magnets. The developed methodology is aimed to realize a high calculational accuracy for these systems. The effects of hydrogen bonding are also described in that context. Our theory for the evaluation of nuclear shielding tensors in paramagnetic molecules is consistent up to second order in the fine structure constant and considers orbital, fully anisotropic dipolar, and isotropic contact contributions to the shielding tensor. The next projects concern electron paramagnetic resonance. The well-known EPR parameters, such as the g-tensors and the hyperfine coupling constants are explored. Calculations of electronic g-tensors were carried out in the framework of a spin-restricted open-shell Kohn-Sham method combined with the linear response theory recently developed in our laboratory and allowing us to avoid by definition the spin-contamination problem. The inclusion of solvent effects, described by the polarizable continuum model, extends the possibility to treat molecular systems often investigated in solution. For calculations of the hyperfine coupling constants a so-called restricted-unrestricted approach to account for the spin polarization effect has been developed in the context of DFT. To examine the validity of the approximations implicit in this scheme, the neglect ii of singlet operators, a generalized RU methodology was implemented, which includes a fully unrestricted treatment with both singlet and triplet operators. The small magnitude of the changes in hyperfine coupling constants confirms the validity of the original scheme. / QC 20100923

The generation of nanostructured assemblies with complex (three-dimensional, 3D) self-assembled morphologies and with complex (multicomponent) tailorable inorganic compositions is of considerable technological and scientific interest. This research demonstrates self-assembled 3D organic templates of biogenic origin can be converted into replicas comprised of numerous other functional nanocrystalline inorganic materials. Nature provides a spectacular variety of biologically-assembled 3D organic structures with intricate, hierarchical (macro-to-micro-to-nanoscale) morphologies. Morphology-preserving chemical conversion of such readily available, structurally complex templates will provide a framework for chemical conversion of synthetic organic templates and, potentially, production of organic/inorganic composites. Four research thrusts are detailed in this dissertation. First, chemical conversion of a nanostructured bioorganic template into a multicomponent oxide compound (tetragonal BaTiO₃ via layer-by-layer surface sol-gel coating and subsequent morphology-preserving microwave hydrothermal processing was demonstrated. Second, photoluminescence was imparted to bioorganic template structures through morphology-preserving chemical conversion to exhibit both the dramatic change in properties such processing can provide, and the potential utility of chemically transformed templates in anti-counterfeiting / authentication applications. Third, the reaction mechanism(s) for morphology-preserving microwave hydrothermal conversion of TiO₂ to BaTiO₃, were studied with the aid of Au inert markers on single crystal rutile TiO₂. Finally, constructive coating techniques (SSG) and moderate temperature (< 500C) heat treatments were utilized to modify and replicate structural color and were coupled with deconstructive focused ion beam microsurgery to prepare samples for microscale structure/property interrogation. Specifically, the effects of coating thickness and coating composition on reflection spectra of structurally colored templates were examined. Also, the effects of the replacement of natural material with higher index of refraction inorganic materials on optical properties were studied. The three processing research thrusts constituting chapters 1, 2 and 4 take advantage of moderate temperature processing to ensure nanocrystalline materials, either for shape preservation or to prevent scattering in optical applications. The research thrust presented in chapter 3 examines hydrothermal conversion of TiO₂ to BaTiO₃, not only to identify the reaction mechanism(s) involved in hydrothermal conversion under morphology-preserving conditions, but also to introduce inert marker experiments to the field of microwave hydrothermal processing.

The development of novel imidazopyridines, which includes both tetrahydroimidazo[1,5-a]pyridine (rIMP) and imidazo[1,5-a]pyridine (IMP) was investigated using conventional and microwave induced procedures that afforded compounds at high yield of 88-96%. rIMP was synthesized using a two-step procedure that involved the microwave synthesis of IMP, then the reduction of the pyridine moiety of the fused imidazopyridine rings using 10% Pd/C and hydrazine monohydrate. The microwave synthesis of imidazopyridines involved the one pot reaction of 2-benzoylpyridine, substituted benzaldehyde and ammonium formate in acetic acid under open vessel microwave conditions, which resulted in products within 40 minutes. Novel PEG-IMP development, involved the synthesis of ethylene glycol tethered benzaldehydes and IMPs using traditional Williamson etherification synthesis, which afforded products at a high yield of 92-95%. We have then shown IMP and rIMP roles in its antiproliferative property towards PCa cells, specificity in inhibiting PI3K isoforms, and structural motif’s interaction with different residues in the kinase binding domain of the class I PI3K isoforms. The antiproliferative property towards PC3 cells shows increased activity with compounds containing pyridyl group on carbon 3 of the imidazo[1,5-a]pyridine parent moiety with signs of toxicity to PC3 within 24 hours of incubation and at 1 μM of the parent compound. Furthermore, the IMPs were tested against five prostate cellular lines: PC3, RWPE1, D145, LNCaP and LNCaP C81. IMPs showed little activity towards RWPE1 and increased activity towards PC3 cells. We determined that functionalizing the phenyl group at position 1 increased the efficacy of rIMP compared to the IMP. After showing increased toxicity to PC3 cells, it was important to investigate the mechanism in which IMP pose toxicity towards PC3 cells. The biochemical assay showed that rIMP was more effective in inhibiting PI3Kα isoform compared to both pan inhibitor wortmannin and IMP. Both IMP and rIMP inhibited more than 60% of PI3Kγ isoform activity at nanomolar concentrations. After showing IMPs affinity to PI3K isoforms, we investigated the binding interactions rIMP and IMP towards the PI3K isoforms using MOE molecular modeling software.

M. Tech. (Department of Chemistry, Faculty of Applied and Computer Sciences) -- Vaal University of Technology / The widespread use of phenols and phenolic derivatives in industrial applications has resulted in their discharge as part of industrial wastewater. These chemicals are toxic and need to be removed from the aqueous environment. Amongst the available pollutant removal technologies, adsorption has been widely used due to its simplicity, ease of operation, cost-effectiveness and ability to sequester pollutants at very low concentrations. Different adsorbents have been applied for removal of phenols and their derivatives. Use of agricultural waste as adsorbents seems to offer a much cheaper alternative in pollutant removal. This study examines the synthesis of a hydrophobic biomaterial composite by cross-linking of Fenton treated pine cone and applying the prepared adsorbent for 2-nitrophenol removal from aqueous solution. Pine cone biomass, in its raw and modified forms was tested for its ability to remove 2-nitrophenol from simulated industrial wastewater. The experimental procedure is divided into two main parts: (1) pine cone modification using Fenton’s reagent and 1.6-hexamethylene diisocyanate and (2) application of the prepared hydrophobic adsorbent for 2-nitrophenol removal from wastewater. Fenton’s reagent was used to remove pigments, extractives and other soluble organic compounds from the raw pine. FTIR spectroscopy showed an increase in magnitude of oxygenated surface groups which resulted in a decrease in pHpzc. The effect of Fenton treatment on further modification of the pine biomass via cross-linking using 1.6-hexamethylene diisocyanate was investigated. Optimum reaction variables for the cross-linking using dibutyltin dilaurate as catalyst under an inert nitrogen gas atmosphere in anhydrous hexane solvent were determined using FTIR spectroscopy. Success of the cross-linking procedure was confirmed by use of analytical techniques (XRD, TGA, SEM, EDX and BET surface area) and weight percent gain calculations. Pine and modified pine biomass were tested for their ability to sequester 2-nitrophenol via batch adsorption technique. The effect of pine modification on affinity for the biosorbate was investigated. The mechanism of the adsorption process was determined via use of kinetic, diffusion and equilibrium isotherm models. Two error functions (coefficient of determination and percent variable error) were employed to substantiate the model showing a good fit to the experimental adsorption data. The experimental adsorption kinetic data was fit to the pseudo-first-order and pseudo-second-order kinetic models. Due to the large size of the pollutant molecules diffusion process analysis was also conducted. The effect of pine modification on kinetic and diffusion parameters was determined. The experimental equilibrium adsorption data was fit to the Freundlich, Redlich-Peterson and Hill isotherm models. The initial shapes of the adsorption isotherms for 2-nitrophenol adsorption onto pine and modified pine biomass determined the type of equilibrium isotherm models to fit the experimental data to. Thermodynamic parameters were calculated to determine the spontaneity, feasibility and energy changes associated with the adsorption process. The degree of disorder at the solid/liquid interface after the adsorption was determined. The effect of temperature on the adsorption process was used to show whether the adsorption is physical or chemical. The effect of pine modification on equilibrium isotherm parameters was determined. The study is divided into seven chapters: Chapter 1: The chapter covers the introduction, problem statement, aim and objectives of the research. It gives an insight into the research project. Chapter 2: The literature review of pollutants in industrial wastewater and methods of their removal is dealt with in this chapter. Adsorption is introduced as an alternative technique for pollutant removal from aqueous systems. An in-depth review of various adsorbents (including pine cone), their merits and limitations are also discussed together with methods of modifying and use of modified adsorbents. Equilibrium, kinetic and thermodynamic models used to treat adsorption experimental data are presented. Chapter 3: The experimental procedures on the synthesis, characterization and application of the hydrophobic biosorbent in the removal of 2-nitrophenol from aqueous solution are presented. Kinetic and equilibrium experiments are described in detail. Chapter 4: It describes the first part of the results and discussions. The chapter focuses on optimization of reaction variables and characterization (using various analytical techniques) of the hydrophobic biomaterial composite. Chapter 5 The chapter discusses the second part of the results. It focuses on magnitude of surface charge, pHpzc and kinetic studies. Fitting of the adsorption experimental data to kinetic and diffusion models is presented together with the error functions. Chapter 6 The chapter discusses part three of the results on equilibrium studies. The adsorption experimental data is fitted to equilibrium isotherm equations and error determination is presented. Thermodynamic parameters are calculated and interpreted. Chapter 7: Conclusion and recommendations are presented. The optimum reaction variables for cross-linking of Raw and Fenton treated pine cone were determined using FTIR analysis and found to be: 0.2 g pine biomass, 3.5 cm3 1.6-hexamethylene diisocyanate cross-linker, 50 cm3 anhydrous hexane solvent, 1.5 cm3 dibutyltin dilaurate catalyst, temperature of 50 °C and a reaction time of 4 hours. The pine surface showed an increase in phenolic, lactonic and carboxylic acid groups due to the modification. The pHpzc showed a decrease due to modification of the pine cone biomass. The pHpzc values for the pine and modified pine cone biomass were found to be: Raw = 7.49, Raw-HMDI modified = 6.68, Fenton treated pine = 5.40 and Fenton-HMDI modified = 6.12. The optimum pH for the adsorption of 2-nitrophenol onto raw pine and modified pine cone biomass was determined to be 6. The optimum adsorbent dosage was determined as 1.5 g/dm3. The adsorption kinetics show a good fit with the pseudo-second-order model. This suggests that surface adsorption is the controlling step in the adsorption of 2-nitrophenol onto pine cone biomass. The analysis of diffusion processes showed that the initial rapid stage during the adsorption is due to external mass transfer processes. The adsorption experimental data also showed that pore diffusion was rate-limiting amongst the diffusion processes. Pine modification using Fenton’s reagent and 1.6-hexamethylene diisocyanate increased magnitude of kinetic and diffusion parameters. Experimental data for 2-nitrophenol adsorption onto pine and modified pine cone biomass showed better correlation with the Redlich-Peterson and Hill isotherm models and poor correlation with the Freundlich isotherm model. This suggests that the mechanism does not show complete multilayer coverage with cooperative phenomena between adsorbate molecules. Thermodynamic parameters showed that the adsorption is feasible, spontaneous, and exothermic and results in a decrease in degree of disorder at the solid/liquid interface. An increase in temperature resulted in a decrease in adsorption capacity showing that the adsorption is physical. Pine modification using Fenton’s reagent and 1.6-hexamethylene diisocyanate increased magnitude of kinetic, diffusion and isotherm parameters. The kinetic and equilibrium results show that the adsorption of 2-nitrophenol onto pine cone biomass follows the order: Fenton treated-HMDI > Fenton treated > Raw-HMDI > Raw. Hence, it can be concluded that Fenton treatment and HMDI cross-linking modification did increase the adsorptive capabilities of the pine cone biomass. / VUT Research Directorate

M. Tech. (Department of Chemical Engineering, Faculty of Engineering and Technology), Vaal University of Technology / Fenton oxidation is classified into two processes, homogeneous and heterogeneous. Homogeneous Fenton oxidation process, have been shown to be efficient in the degradation of organic pollutants. However, it was shown to have limitations which can be addressed by the heterogeneous Fenton oxidation. Despite the high efficiency of the heterogeneous Fenton oxidation process in the degradation of recalcitrant organic pollutants, the currents synthesis trends of the heterogeneous Fenton catalyst have been proven to be time and energy constraining, since it involves the multi-step were the activated carbon have to be prepared first then co-precipitate the iron oxide on the activated carbon. However, as much as the heterogeneous Fenton catalyst has been proven to have high catalytic activity towards degradation of organic pollutants, these catalysts have some limitations, such limitations include metal ions being leached from the catalyst support into the treated water causing catalyst deactivation and a secondary pollution to the treated water. In this thesis, these catalysts have been applied in the degradation of recalcitrant organic pollutants such as methylene blue and phenols. This study focuses on the single step synthesis of iron oxide nanoparticles supported on activated carbon, were carbonaceous material is impregnated with iron salt then pyrolysed via microwave heating. Microwave power and the amount of iron salt were optimized. The prepared activated carbon-iron oxide composites were applied to the degradation of 2-nitrophenol (2-NP) and methylene blue (MB). Methylene blue was used as a model compound due to the fact that it is easier to monitor the degradation process with UV-Vis as compared to 2-nitrophenol . 2-nitrophenol the additional step for the adjustment of pH is required since nitrophenols are colorless in color at lower pH. The characterization showed that the microwave power and the amount of the iron precursor have an influence on the porosity and surface functional groups of the activated carbon. Further it was vi observed that microwave power and iron precursor influnces the amount of iron oxide formed on the surface of the support. It was also observed that the activated carbon-iron oxide composite have the catalytic effects on the Fenton oxidation process of MB and 2-NP. The parameters such as H2O2, pH, catalyst dose, initial concentration, temperature affect the degradation of both MB and 2-NP. Kinetics studies showed that Fenton is a surface driven reaction since the results fitted the pseudo first order model. The thermodynamics parameters also showed that the reaction is endothermic, spontaneous and is randomized. This implies that the reaction of the degradation of MB and 2-NP is feasible and the catalysts prepared have high catalytic activity. MB and 2-NP were degraded to smaller organic molecules (carboxylic acids). The stability of the catalyst observed to decrease as the number of cycles increased, this is due to the leaching of iron ions from the support material. Hence it was concluded that the activated carbon-iron oxide composite was successfully synthesized and had the high catalytic activity for the degradation of MB and 2-NP.

Combined thermodynamic/kinetic events amount to a kinetically controlled Dynamic Combinatorial Resolution (DCR) process, where the lability of themolecules/aggregates are used to generate dynamics, and the species experiencing the lowest activation energy is selected via kinetic process. Bothinter- and intramolecular processes can be performed using this concept,resulting in complete resolution and associated amplification of the selected species. When intermolecular processes are resolved using this method, an additional advantage is that only a catalytic amount of selector is required tocontrol the system.In this thesis, the Henry and Strecker reactions were developed as efficient C–C bond-forming routes to single and multi-level dynamic covalent systems.These methods efficiently provided a vast variety of substrates from smallnumbers of starting compounds. These dynamic systems, generated underthermodynamic control at mild conditions, were coupled in one-pot processes with kinetically controlled lipase-mediated transacylation. The enzym emediated resolution of the dynamic nitroaldol system led to enantiomericallypure β-nitroacetates in high yield. Furthermore, combination of multi-leveldynamic Strecker systems and lipase-mediated acylation resulted in theresolution of specific α-aminonitriles from the pool.In addition, the asymmetric synthesis of discrete β-nitroalkanol derivatives wassimply achieved, resulting in high yields and high enantiomeric purities through the direct one-pot procedure. Moreover, racemase type activity oflipase enzyme through N-substituted α-aminonitrile structure has been discovered. By use of control experiments together with molecular modeling,the mechanism of the racemization process has been established. Asymmetric synthesis of N-methyl α-aminonitriles was also performed through the dualfunction of lipase, resulting in high yield and good enantio selectivity. / <p>QC 20100818</p>

This thesis is based on six original research publications describing synthesis, structure and physicochemical and biochemical analysis of chemically modified oligonucleotides (ONs) in terms of their potential diagnostic and therapeutic applications. Synthesis of two types of bicyclic conformationally constrained nucleosides, North-East locked 1',2'-azetidine and North locked 2',4'-aza-ENA, is described. Study of the molecular structures and dynamics of bicyclic nucleosides showed that depending upon the type of fused system they fall into two distinct categories with their respective internal dynamics and type of sugar conformation. The physicochemical properties of the nucleobases in the conformationally constrained nucleosides found to be depended on the site and ring-size of the fused system. The incorporation of azetidine modified nucleotide units into 15mer ONs lowered the affinity toward the complementary RNA. However, they performed better than previously reported isosequential 1',2'-oxetane modified analogues. Whereas aza-ENA-T modification incorporated into ONs significantly enhanced affinity to the complementary RNA. To evaluate the antisense potential of azetidine-T and aza-ENA-T modified ONs, they were subjected to RNase H promoted cleavage as well as tested towards nucleolytic degradation. Kinetic experiments showed that modified ONs recruit RNase H, however with lower enzyme efficiency due to decreased enzyme-substrate binding affinity, but with enhanced turnover number. Both, azetidine-T and aza-ENA-T modified ONs demonstrated improved 3'-exonuclease stability in the presence of snake venom phosphodiesterase and human serum compared to the unmodified sequence. Oligodeoxynucleotides (ODNs) containing pyrene-functionalized azetidine-T (Aze-pyr X) and aza-ENA-T (Aza-ENA-pyr Y) modifications showed different fluorescence properties. The X modified ODNs hybridized to the complementary DNA and RNA showed variable increase in the fluorescence intensity depending upon the nearest-neighbor at the 3'-end to X modification (dA &gt; dG &gt; dT &gt; dC) with high fluorescence quantum yield. However, the Y modified ODNs showed a sensible enhancement of the fluorescence intensity only with complementary DNA. Also, the X modified ODN showed decrease (~37-fold) in the fluorescence intensity upon duplex formation with RNA containing a G nucleobase mismatch opposite to the modification site, whereas a ~3-fold increase was observed for the Y modified probe.

This thesis deals with the design, formation and evaluation of dynamic systems constructed by means of sulfur-containing reversible reactions, in organic and aqueous media and under mild conditions. In a first part, the synthesis of thioglycoside derivatives, constituting the biologically relevant starting components of the dynamic systems, is described. In addition, the pD-profile of the mutarotation process in aqueous media for a series of 1-thioaldoses is reported and revealed an astonishing beta-anomeric preference for all the carbohydrate analogs under acidic or neutral conditions. In a second part, the phosphine-catalyzed or -mediated disulfide metathesis for dynamic system generation in organic or aqueous media is presented, respectively. The direct in situ 1H STD-NMR resolution of a dynamic carbohydrate system in the presence of a target protein (Concanavalin A) proved the suitability and compatibility of such disulfide metathesis protocols for the discovery of biologically relevant ligands. In a third part, hemithioacetal formation is demonstrated as a new and efficient reversible reaction for the spontaneous generation of a dynamic system, despite a virtual character of the component associations in basic aqueous media. The direct in situ 1H STD-NMR identification of the best dynamic beta-galactosidase inhibitors from the dynamic HTA system was performed and the results were confirmed by inhibition studies. Thus, the HTA product formed from the reaction between 1-thiogalactopyranose and a pyridine carboxaldehyde derivative provided the best dynamic inhibitor. In a fourth and final part, a dynamic drug design strategy, where the best inhibitors from the aforementioned dynamic HTA system were used as model for the design of non-dynamic (or “static”) beta-galactosidase inhibitors, is depicted. Inhibition studies disclosed potent leads among the set of ligands. / QC 20100621

This thesis is divided into six parts, all centered around the development of dynamic (i.e., reversibly interacting) systems of molecules and their applications in dynamic combinatorial chemistry (DCC) and organic synthesis. Part one offers a general introduction, as well as a more detailed description of DCC, being the central concept of this thesis. Part two explores the potential of the nitroaldol reaction as a tool for constructing dynamic systems, employing benzaldehyde derivatives and nitroalkanes. This reaction is then applied in part three where a dynamic nitroaldol system is resolved by lipase-catalyzed transacylation, selecting two out of 16 components. In part four, reaction and crystallization driven DCC protocols are developed and demonstrated. The discovery of unexpected crystalline properties of certain pyridine β-nitroalcohols is used to resolve a dynamic system and further expanded into asynthetic procedure. Furthermore, a previously unexplored tandem nitroaldol-iminolactone rearrangement reaction between 2-cyanobenzaldehyde and primarynitroalkanes is used for the resolution of dynamic systems. It is also coupled with diastereoselective crystallization to demonstrate the possibility to combine several selection processes. The mechanism of this reaction is investigated and a synthetic protocol is developed for asymmetric synthesis of 3-substituted isoindolinones. Part five continues the exploration of tandem reactions by combining dynamic hemithioacetal or cyanohydrin formation with intramolecular cyclization to synthesize a wide range of 3-functionalized phthalides. Finally, part six deals with the construction of a laboratory experiment to facilitate the introduction of DCC in undergraduate chemistry education. The experiment is based on previous work in our group and features an acetylcholinesterase-catalyzed resolution of a dynamic transthioacylation system. / QC 20100628