This thesis describes optical microscopical and spectroscopical studies of 2D materials, including graphite/graphene and multilayer/single layer MoS2, under strong charge transfer doping. Under this conceptually unifying umbrella lie many aspects of materials behaviors unique to each of the systems. The strong chemical doping results from intercalation and surface adsorption, and changes the electronic properties of the host 2D materials drastically. Associated with the significant electronic change, aspects such as mass transport, surface reaction, and phase transformation are covered in the following chapters. The first chapter introduces representative members of the 2D materials family, graphene and molybdenum disulphide (MoS2). It briefly reviews the history, discovery and unique properties of each materials class. The other part of the introduction focuses on the main methods utilized in the study of these materials. A concise survey of Raman spectroscopy and optical reflectance contrast spectroscopy will be presented. The second chapter investigates the intercalation process of Li into bulk graphite. This is a revisit of an extensively studied subject, with a new set of experiments and theories. Here we show that the daunting technical difficulties of disentangling complex electrochemical systems can be cleanly addressed with optical methods with well defined samples. Measuring and understanding the intrinsic transport of Li in graphite electrodes has been a difficult task. The challenge is well recognized to stem from a multitude of simultaneous electrochemical processes as well as systematic heterogeneities in the sample. We distinguish the Li intercalation process in graphite from all other processes, combining optical reflectance microscopy and Raman spectroscopy. The heterogeneity problem is circumvented by using lithography to tailor a single crystal into a defined geometry. We apply two levels of theoretical models to interpret the intrinsic information revealed in our data. Concentration dependent diffusion coefficients are measured, in agreement with theoretical results. The effects of sample geometry and electrode reaction kinetics on the overall intercalation are elucidated. The third chapter presents the study of lithiation on single and few layer graphene. Raman spectroscopy reveals a high doping level similar in strength to that of the bulk intercalated compound. The optical reflectance imaging, however, shows a different observation from the bulk case. We directly visualize the surface film formation and associated strong doping. The lithiation in single and few layer graphene progresses differently from the bulk graphite, since certain stages of the intercalation compound cannot be sustained by a single or few layer sample. The realization of strong charge transfer doping in lithiated single and few layer graphene could lead to discoveries of interesting physics. The direct visualization of surface film formation could have important implications in the design of electrochemical energy storage systems. The fourth chapter explores the structural effect of strong charge transfer doping in bulk and multilayer MoS2 with optical methods. MoS2, as a representative material of the transition metal dichalcogenide family, possesses different structural polymorphs. Strong charge transfer doping induces a structural phase change, which goes from the usual thermodynamically stable semiconducting 2H phase into the metallic 1T/1T' phase. The metallic 1T/1T' structure can remain a metastable phase without the stabilization of intercalants. We optically induce the 1T/1T' to 2H phase change and measure the temperature dependent kinetics of the structural phase transformation with in situ Raman spectroscopy. We demonstrate a photolithography technique, which efficiently patterns in-plane coherent heterojunctions between 1T/1T' and 2H MoS2. The fifth and final chapter describes the study of the structural change in single layer MoS2. More spectroscopic methods are employed for characterization, such as photoluminescence spectroscopy and second harmonic generation. The results indicate that the structural change occurs in single layer MoS2 after reaction with n-butyl lithium. The structural change can be reversed by thermal and laser annealing, similar to the case of bulk and multilayer MoS2. The annealed MoS2 exhibits reduced crystallinity. Future directions to further this work are outlined in the last section.

In this thesis, the adsorption of single-wall carbon nanotubes (SWCNTs) at the liquid/liquid interface, and the subsequent electrochemical investigation of the electrical properties of the adsorbed nanotubes have been studied. Prior to the adsorption of the nanotube, the stability of dispersion of SWCNTs in non-aqueous solvents was assessed by determining the onset of aggregation of the SWCNTs when organic electrolyte was introduced. It was found that electrostatic repulsion between the SWCNTs contributes significantly to the stability of the SWCNTs in non-aqueous solvents. Similar result was also found when the aggregation kinetics of molybdenum disulphide (MoS2) dispersion in non-aqueous media was studied using the same organic electrolyte. The formation of nanomaterial-polymer composites by deliberate electrochemical oxidation of pyrrole and the sonochemical polymerisation of the organic solvent was also studied. Electrolyte addition was shown to be a promising way to separate the 2D material from the sonopolymer.

The ability to safely delivery efficacious amounts of nucleic acids to cells and tissues remains an important goal for the gene therapy field. Viruses are very efficient at delivering DNA, but safety concerns limit their clinical use. Nonviral vectors are not as efficient at DNA delivery, but have a better safety profile. Limiting the efficaciousness of nonviral vectors are the numerous extra and intracellular barriers that must be overcome for successful DNA delivery in vivo. While single polymers can successfully transfect immortalized cell lines in vitro, multicomponent gene delivery systems are required for delivery in vivo. Key in the development of multicomponent systems is their syntheses. Optimization of a nonviral gene delivery system requires the development of methodologies that incorporate the different components in a controlled fashion, generating homogeneous gene delivery vectors. Such syntheses ensure every polymer has the different components required for successful delivery. The amount of each component and location within the gene delivery system can also be varied systemically, allowing optimization of the vector. The overall scope of this thesis is to develop a chemical method to iteratively couple gene delivery peptides through reducible disulfide bonds. The synthesis of such polypeptides allows the triggered disassembly of a polypeptide polyplexed with DNA upon cellular uptake. To synthesize homogeneous gene delivery polypeptides, a novel iterative reducible ligation strategy was developed, based upon the use of a thiazolidine masked cysteine. Initial studies demonstrated that a thiazolidine could be unmasked to a cysteine in the presence of a disulfide bond without side reaction, though the reported thiazolidine hydrolysis conditions of aqueous methoxyamine were insufficiently robust for high yielding ligations. Discovery of a novel silver trifluoromethanesulfonate hydrolysis led to an efficient process for generating reducible polypeptides, as evidenced in the synthesis of a 4 component polypeptide. Due to the success of the thiazolidine mediated iterative ligation strategy, cysteines were replaced by penicillamines to produce more stable disulfide bonds. The mild thiazolidine hydrolysis and subsequent peptide conjugation reactions led to attempt the iterative ligation strategy on a solid support, eliminating purification steps that lowered the yields in the solution phase methodology. Initial progress at generating gene delivery peptides that could be incorporated into the synthetic strategy included the generation of a tri-orthogonal cysteine protecting scheme that allowed a third cysteine to be derivatized with a targeting ligand or stealthing polymer. Due to the use of terminal cysteines in the iterative ligation strategy, a PEG stealthing polymer could be placed in the center of a polyacridine gene delivery peptide with only a small decrease in the ability to condense and protect DNA during systemic circulation. A convergent synthesis was also developed that was able to synthesize large polypeptides in fewer linear steps. The synthetic methodology of thiazolidine mediated iterative reducible ligation developed in this thesis is important in the gene therapy field as it allows the construction of polypeptides that can be systemically optimized, potentially resulting in highly efficacious nonviral gene delivery.

Of the 20 standard amino acids, cysteines are the only amino acids that have a reactive sulphur atom, thus enabling two cysteines to form strong covalent bonds known as disulfide bonds. Even though almost all proteins have cysteines, not all of them have disulfide bonds. Disulfide bonds provide structural stability to proteins and hence are an important constraint in determining the structure of a protein. As a result, disulfide bonds are used to study various protein properties, one of them being protein folding. Protein structure prediction is the problem of predicting the three-dimensional structure of a protein from its one-dimensional amino acid sequence. Ab initio methods are a group of methods that attempt to solve this problem from first principles, using only basic physico-chemical properties of proteins. These methods use structure libraries of short amino acid fragments in the process of predicting the structure of a protein. The protein structures from which these structure libraries are created are not classified in any other way apart from being non-redundant. In this thesis, we investigate the structural dissimilarities of short amino acid fragments when occurring in proteins with disulfide bonds and when occurring in those proteins without disulfide bonds. We are interested in this because, as mentioned earlier, the protein structures from which the structure libraries of ab initio methods are created, are not classified in any form. This means that any significant structural difference in amino acids and short fragments when occurring in proteins with and without disulfide bonds would remain unnoticed as these structure libraries have both fragments from proteins with disulfide bonds and without disulfide bonds together. Our investigation of structural dissimilarities of amino acids and short fragments is done in four phases. In phase one, by statistically analysing the phi and psi backbone dihedral angle distributions we show that these fragments have significantly different structures in terms of dihedral angles when occurring in proteins with and without disulfide bonds. In phase two, using directional statistics we investigate how structurally different are the 20 different amino acids and the short fragments when occurring in proteins with and without disulfide bonds. In phase three of our work, we investigate the differences in secondary structure preference of the 20 amino acids in proteins with and without disulfide bonds. In phase four, we further investigate and show that there are significant differences within the same secondary structure region of amino acids when they occur in proteins with and without disulfide bonds. Finally, we present the design and implementation details of a dihedral angle and secondary structure database of short amino acid fragments (DASSD) that is publicly available. Thus, in this thesis we show previously unknown significant structure differences in terms of backbone dihedral angles and secondary structures in amino acids and short fragments when they occur in proteins with and without disulfide bonds.

<p>Hedgehog related genes have been shown to play a major role in development in all deuterostomes. In C.elegans, such genes have been found where the similarity is restricted to the C-terminal domain. This work has focused on the hedgehog related C.elegans proteins called ground (grd), ground-like (grl), and wart (wrt) which appear to form a unique structural family.These proteins are cysteine rich and have conserved cysteine patterns which, together with thethought that they are secreted, are expected to be in disulfide form. Since the extracellular environment is very oxidizing and due to the conserved cysteine pattern, disulfide bonds are thought to play a big part in the folding and stabilization of these proteins. The stability of the protein and the formation of a disulfide bond are related through a thermodynamic cycle, which insures that the stabilization of the protein by the disulfide is reflected by the identical stabilization of the disulfide by the protein. Practically, there are numerous parameters that can be used to try to achieve the correct disulfide bonds and folding, when doing in vitro trials, some of which were used in this project. C.elegans proteins grd-5, grd-13, grl-24, wrt-3 and wrt-5 were studied in this project. All of the proteins were expressed and purified with success, with theexception of grl-24. All constructs formed inclusion bodies. Some refolding attempts were performed on grd-13 and wrt-3. The presence of a disulfide bond in refolded grd-13 was demonstrated using chemical fragmentation. In general, these attempts did not give correctly folded proteins but provide a foundation to continue experiments aimed at producing a native-like protein for structural and functional studies.</p>

Hedgehog related genes have been shown to play a major role in development in all deuterostomes. In C.elegans, such genes have been found where the similarity is restricted to the C-terminal domain. This work has focused on the hedgehog related C.elegans proteins called ground (grd), ground-like (grl), and wart (wrt) which appear to form a unique structural family.These proteins are cysteine rich and have conserved cysteine patterns which, together with thethought that they are secreted, are expected to be in disulfide form. Since the extracellular environment is very oxidizing and due to the conserved cysteine pattern, disulfide bonds are thought to play a big part in the folding and stabilization of these proteins. The stability of the protein and the formation of a disulfide bond are related through a thermodynamic cycle, which insures that the stabilization of the protein by the disulfide is reflected by the identical stabilization of the disulfide by the protein. Practically, there are numerous parameters that can be used to try to achieve the correct disulfide bonds and folding, when doing in vitro trials, some of which were used in this project. C.elegans proteins grd-5, grd-13, grl-24, wrt-3 and wrt-5 were studied in this project. All of the proteins were expressed and purified with success, with theexception of grl-24. All constructs formed inclusion bodies. Some refolding attempts were performed on grd-13 and wrt-3. The presence of a disulfide bond in refolded grd-13 was demonstrated using chemical fragmentation. In general, these attempts did not give correctly folded proteins but provide a foundation to continue experiments aimed at producing a native-like protein for structural and functional studies.

Momentum vectors of fragment ions produced by the Coulomb explosion of CO2z+ (z = 3 - 6) and CS2z+ (z = 3 - 13) in an intense laser field (~50 fs, 1 x 1015 W/cm2) are determined by the triple coincidence imaging technique. The molecular structure from symmetric and asymmetric explosion channels is reconstructed from the measured momentum vectors using a novel simplex algorithm that can be extended to study larger molecules. Physical parameters such as bend angle and bond lengths are extracted from the data and are qualitatively described using an enhanced ionization model that predicts the laser intensity required for ionization as a function of bond length using classical, over the barrier arguments. As a way of going beyond the classical model, molecular ionization is examined using a quantum-mechanical, wave function modified ADK method. The ADK model is used to calculate the ionization rates of H2, N2, and CO2 as a function of initial vibrational level of the molecules. A strong increase in the ionization rate, with vibrational level, is found for H2, while N2 and CO2 show a lesser increase. The prospects for using ionization rates as a diagnostic for vibrational level population are assessed.

Momentum vectors of fragment ions produced by the Coulomb explosion of CO2z+ (z = 3 - 6) and CS2z+ (z = 3 - 13) in an intense laser field (~50 fs, 1 x 1015 W/cm2) are determined by the triple coincidence imaging technique. The molecular structure from symmetric and asymmetric explosion channels is reconstructed from the measured momentum vectors using a novel simplex algorithm that can be extended to study larger molecules. Physical parameters such as bend angle and bond lengths are extracted from the data and are qualitatively described using an enhanced ionization model that predicts the laser intensity required for ionization as a function of bond length using classical, over the barrier arguments. As a way of going beyond the classical model, molecular ionization is examined using a quantum-mechanical, wave function modified ADK method. The ADK model is used to calculate the ionization rates of H2, N2, and CO2 as a function of initial vibrational level of the molecules. A strong increase in the ionization rate, with vibrational level, is found for H2, while N2 and CO2 show a lesser increase. The prospects for using ionization rates as a diagnostic for vibrational level population are assessed.

The formation of aberrant disulfide bonds is a structural consideration for the manufacturing of the extracellular domain of human CD83 (hCD83ext), a potential therapeutic protein. In certain instances, hCD83ext protein products, even when stored frozen, tend to dimerize or even multimerize through the formation of aberrant intermolecular disulfide bonds. Herein, we discovered an analytical inconsistency and applied a modified sample preparation protocol for proper structural analysis of hCD83ext products which are heterologously expressed in Escherichia coli and subsequently purified. In addition, a mutant derivative with the Cys100Ser mutation was identified as an improved version which did not form dimers or multimers. The identification of this mutant variant as a more potent therapeutic protein than other hCD83ext species demonstrated that the structural variation associated with disulfide bond formation can be a critical issue for rigorous control of the quality and bioactivity of therapeutic proteins. The application of this mutant variant for protein therapeutic is currently under exploration. As a comparative study, the hCD83ext was expressed as a glutathione-S-transferase (GST) fusion in two E. coli B strains, i.e. BL21 and Origami B having a reductive and oxidative cytoplasm. The final therapeutic products of hCD83ext produced by the two expression hosts exhibited significant differences in protein conformation and molecular properties, which presumably resulted from different disulfide patterns. The study highlights the importance of developing proper host/vector systems and biomanufacturing conditions for the production of recombinant therapeutic proteins with a consistent product quality. Cys27 in the hCD83ext was identified as a target for molecular manipulation. Two E. coli strains of BL21(DE3) and Origami B(DE3) were used as the expression host to produce the Cys27 mutants. It was observed that Cys27 was involved in the in vivo formation of intramolecular disulfide bonds when hCD83ext was expressed in Origami B(DE3). The Origami-derived protein products had a higher tendency than the BL21-derived counterparts for multimerization via the in vitro formation of intermolecular disulfide bonds. Various analyses were conducted to identify the structural differences among these mutant variants. Most importantly, molecular stability was enhanced by the Cys27 mutations since the Cys27 mutants derived from either BL21 or Origami were much less susceptible to degradation compared to wild-type hCD83ext. This study highlights the implications of aberrant disulfide bond formation on the production of therapeutic proteins. To address an inconsistent bioactivity issue that is primarily due to the aberrant formation of disulfide bonds associated with the presence of five cysteine residues, i.e. AA 27, 35, 100, 107, and 129, the molecular role that each cysteine plays upon the formation of intramolecular or intermolecular disulfide bonds was characterized, using various hCD83ext mutant variants derived by two E. coli expression hosts, i.e. BL21(DE3) and Origami B(DE3). Among the five cysteines, Cys100 and Cys129 can act as a bridging cysteine for in vitro multimerization via the formation of intermolecular disulfide bonds. The multimerization can be alleviated to some extent with less free Cys129 residues, associated with the possible formation of Cys27-Cys129 intramolecular disulfide bond. As a result, introducing the Cys27 mutation can increase the multimerization presumably via freeing more Cys129 residues. In addition, protein stability can be improved in the presence of the Cys27 mutation. The formation of the Cys27-Cys129 intramolecular disulfide bond appears to be more effective in the presence of the Cys100 mutation, resulting in the suppression of multimerization. The two conserved cysteine residues, i.e. Cys35 and Cys107, can be potentially linked to form an intramolecular disulfide bond, particularly when the protein is produced in Origami B(DE3).

Thesis (Ph. D.)--York University, 2000. Graduate Programme in Chemistry. / Typescript. Includes bibliographical references (leaves 370-416). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pNQ59143