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Doctor of Philosophy / Department of Chemistry / Eric A. Maatta / The thesis focuses on the design and synthesis of novel organoimido delivery reagents capable of forming bimetallic polyoxometalate (POM) hybrids, and their use in the assembly of bimetallic hexamolybdate derivatives. These delivery reagents have been designed thoughtfully and separate organic moieties have been selected for coordinating to both the POM cluster and the second metal atom. A series of three ligands [4-aminopiperidine, 4-(4-aminophenyl) piperazine, and 4-(4-aminophenyl) piperidine] were selected and used to synthesize the dithiocarbamate metal-coordinating ligands, which in turn were used for preparing the corresponding metal (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, Ag) complexes. All the complexes were characterized by infrared spectroscopy (IR). Reported routes were followed for the covalent grafting of these metal complexes onto hexamolybdate. But, the poor solubility of these metal complexes was found to be a major stumbling block in our endeavors to synthesize the dithiocarbamate based polyoxometalate hybrids. The observed poor solubility of metal dithiocarbamate complexes was overcome by synthesizing [potassium(I) tris(3,5-diphenylpyrazole)borate] and [potassium(I) tris(3,5-dimethylpyrazole)borate] via thermal dehydrogenative condensation between tetrahydroborate and the respective pyrazole molecule. A series of corresponding transition metal (M = Co, Ni, Cu, Mn) complexes of tris(3,5-diphenylpyrazole)borate and tris(3,5-dimethylpyrazole)borate were synthesized, and characterized by IR and UV-visible spectroscopy, and single crystal X-ray diffraction. The single crystal structure of [manganese(II) (tris(3,5-dimethylpyrazole)borate)2] turned out to an outlier as it displayed the formation of a bis-complex, thus having no substitutable anion for further reaction with dithiocarbamates. Thereafter, a series of metal dithiocarbamate complexes of these [hydrotris(pyrazolyl)borates] (M = Co, Ni, Cu ) were prepared using [sodium 4-aminopiperidyldithiocarbamate] and were characterized by IR and UV-visible spectroscopy. A remarkable improvement in the solubility of these metal dithiocarbamates in organic solvents was observed. Furthermore, attempts to covalently graft these complexes onto hexamolybdate cluster were undertaken, and found to be unsuccessful possibly due to the strong oxidizing nature of PPh[subscript]3Br[subscript]2 and hexamolybdate. Although, we were able to successfully tailor the solubility of the dithiocarbamate complexes to suit our needs, our efforts to achieve the primary goal of synthesizing dithiocarbamate based polyoxometalate hybrids have so far been unsuccessful. A series of three pyridyl based ligands i.e., 3,5-di(pyridin-2-yl)-4H-1,2,4-triazol-4-amine, 4-(pyridin-4-ylethynyl)aniline and 4-(pyridin-3-ylethynyl)aniline were synthesized and characterized. Covalent attachment of these ligands to hexamolybdate were attempted following various well-known routes. Although, no evidence of covalent attachment of 3,5-di(pyridin-2-yl)-4H-1,2,4-triazol-4-amine to hexamolybdate was observed, the covalent grafting of 4-(pyridin-4-ylethynyl)aniline and 4-(pyridin-3-ylethynyl)aniline to hexamolybdate cluster was successfully achieved. Characterization of these novel organic-inorganic hybrids was done using IR and NMR spectroscopy as analytical tools. Attempts have been undertaken to obtain single crystals of these hybrids. Also, a novel route involving halogen bonding as a purification and separation technique for pyridyl functionalized hexamolybdate hybrids is also being explored. The novel acetylacetonate moiety has been explored as an imidodelivery reagent for synthesizing hexamolybdate covalent hybrids, wherein [3-(4-((4-aminophenyl)ethynyl)phenyl)-4-hydroxypent-3-en-2-one] ligand has been successfully synthesized and characterized. Traditional methods along with unconventional methods such as heating at elevated temperatures and microwave reaction conditions, have so far proved to be unsuccessful in the synthesis of the hybrids. A series of the corresponding metal complexes have been synthesized and characterized, where the ligand and its corresponding copper(II) complex have been characterized by single crystal XRD. In the crystal structure of the copper complex, the metal ion sits in a slightly distorted square-planar pocket, where no coordination to the -NH[subscript]2 group is observed, which highlights the potential of using it as an imidodelivery reagent.

Mercury and arsenic are widespread contaminants in aqueous environments throughout the world. The elements arise from multiple sources including mercury from coal-fired power plants and wells placed in natural geological deposits of arseniccontaining minerals. Both elements have significant negative health impacts on humans as they are cumulative toxins that bind to the sulfhydryl groups in proteins, disrupting many biological functions. There are currently no effective, economical techniques for removing either mercury or arsenic from aqueous sources. This thesis will demonstrate a superior removal method for both elements by formation of covalent bonds with the sulfur atoms in N,N’-Bis(2-mercaptoethyl)isophthalamide (commonly called “B9”). That B9 can precipitate both elements from water is unusual since aqueous mercury exists primarily as a metal(II) dication while aqueous arsenic exists as As(III) and As(V) oxyanions.

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Non-covalent interactions underpin the whole of chemistry and biology, but their study is extremely difficult in complicated biological systems. This thesis presents the application of synthetic molecular balances for gaining fundamental insights into the physicochemical phenomena that govern molecular recognition processes. Chapter 1 reviews the use of small synthetic molecules that exist in two conformational states via slow rotation of a bond, in the quantification of non-covalent interactions. Chapter 2 presents a new molecular torsion balance, based on a slowly rotating tertiary formyl amide for the study of non-covalent interactions. The incorporation of a fluorine atom in one of the rings allows the quantification of solvent effects in a wide range of solvents. Intramolecular electrostatic interactions and intermolecular solvation effects (but not solvophobic effects) are shown to be important in determining the position of the conformational equilibria. Correlations with calculated molecular properties show that solvent effects are fully dissected, revealing the idealistic behavior of the system in the gas phase. Chapter 3 discusses through-space substituent effects on the properties of aromatic rings. Electronic communication between both electron-rich and electron-deficient substituents with the electron density of an adjacent aromatic ring is predicted by molecular electrostatic potential calculations. The effect is confirmed to occur experimentally and is quantified using synthetic molecular balances. Chapter 4 describes the work done towards the investigation of solvent bridging interactions in molecular torsion balances. No experimental evidence of bridging interactions was observed. This might be attributed to the entropic penalty associated with this binding mode, or the non-ideal geometry of the potential bridging sites. Chapter 5 outlines a steric blocking effect observed in certain balances with bulky substituents in chloroform and dichloromethane. Chapter 6 presents synthetic procedures and compound characterisation including a thorough analysis of NMR data obtained in this study.

A novel electrochemical probe has been designed, built, and used to characterize the distribution in solution potential within the metal capillary and Taylor cone of the electrospray (ES) device. Results show that the measured potential difference increases as the internal probe travels toward the ES capillary exit, with values rising sharply as the base of the Taylor cone is penetrated. Higher conductivity solutions exhibit potentials of higher magnitude at longer distances away from the counter electrode, but these same solutions show lower potentials near the ES capillary exit. Removal of easily oxidizable species from the solution causes the measured potential difference to have nonzero values at distances further within the capillary, and the values measured at all points are raised. The influence of the diameter of the spray tip employed for nano-electrospray mass spectrometry (nano-ES-MS) upon mass spectral charge state distributions was investigated. A detailed comparison of charge state distributions obtained for nanospray capillaries of varying diameters was undertaken while systematically varying experimental parameters such as sample flow rate, analyte concentration, solvent composition, and electrospray current. The general tendency to obtain higher charge states from narrow diameter capillaries was conserved throughout, but tips with smaller orifices were more sensitive to sample flow rate, while tips with larger orifices were more sensitive to analyte concentration and pH of the solution. Electrospray mass spectrometry (ES-MS) has been employed to study noncovalent associations between lipids and fusion peptides. Detailed binding specificities between selected phospholipids and model fusion peptides were investigated. Strong evidence has been compiled to demonstrate the importance of the initial hydrophobic interaction to the observation of lipid-peptide binding by ES-MS. Initial hydrophobic interactions in solution contributed heavily to the formation of these peptide-lipid complexes, particularly for [peptide+PC] complexes, whereas electrostatic interactions played a larger role for [peptide+PG] complexes. The influence of solution pH and degree of unsaturation of lipids upon the binding strength of [peptide+PC] complexes were also investigated. These experiments help to establish ES-MS as a viable new biotechnology tool capable of providing valuable information regarding the strength of hydrophobically driven, noncovalent interactions.

Thesis advisor: Eranthie Weerapana / Thesis advisor: Jianmin Gao / Proteins are composed of the 20 naturally occurring amino acids and are further modified by a variety of post-translational modifications (PTMS). Naturally occurring amino acids are diverse in structure and function. Catalytic amino acids, or nucleophilic amino acids, are of particular interest because of their contribution to chemical transformations in the cell. Synthetic covalent modification is a means to further functionalize or diversify proteins. These modifications, or enhancements, allow for improved understanding of protein structure, function and activity. For instance, isotope labeling of amino acid side chains in NMR studies enable investigators to study protein dynamics upon substrate or ligand binding. Fluorescence labeling is particularly useful to investigate protein cellular localization. Covalent modification is a useful tool to investigate the relative level of activity for protein known to be regulated by PTMs. An important feature of covalent modification reactions is site specificity, as this dictates the location, number of modifications, and protein targets. Tyrosine is of particular interest because it is both nucleophilic and aromatic. These characteristics contribute to the existence of tyrosine residues in both the protein surface and hydrophobic cores. Tyrosine is incorporated into proteins at a relatively low frequency. Unlike lysine, which is ubiquitous on protein surfaces, the low number of potential sites for general tyrosine modifications makes it an attractive site for surface bioconjugation modifications. A low number of surface modifications is less likely to perturb native protein function. Bioconjugation reactions give access to functionalizing the surface of proteins with moieties such as fluorophores, PEG, peptides, or drugs. Tyrosine is an attractive target for modifications because it is found in the active sites of a variety of enzymes such as sialidases, glutathione-S transferases, corticosteroid 11-beta-dehydrogensase, DNA topoisomerase, and ferredoxin-NADP+ reductase. Provided here is a survey of the known non-selective and selective synthetic chemical modification reactions for tyrosine. To investigate nucleophilic amino acids, Activity Based Protein Profiling (ABPP) may be implemented to investigate the role of these residues. ABPP utilizes small molecule covalent probes as a tool to selectively target enzymes in their active state. To investigate a protein of interest (POI) (or class of proteins) by ABPP, it is necessary to use a small molecule covalent probe that selectively reacts with the POI over other proteins within the proteome. Due to this requirement, it is necessary to expand the current ABPP probe toolbox to increase the coverage of what proteins in the proteome may be studied. Inspired by findings in the literature, our lab sought to explore the utility of various aryl halides for implementation in ABPP probes to overcome this limitation. This study revealed dichlorotriazine as a biologically relevant and reactive electrophile. A focus was placed on a dichlorotriazine containing probe library (LAS1-LAS20). LAS17 was discovered to be a potent and selective inhibitor of human glutathione S-transferase pi (GSTP1). Further studies revealed GSTP1 as a novel therapeutic target for the treatment of triple negative breast cancer. Other studies revealed several members of the dichlorotriazine library were found to covalently modify purified recombinant human aldolase A (ALDOA) in the presence of a complex cellular background. Additionally, LAS9 was identified as an inhibitor of ALDOA retro aldol condensation activity in vitro. Lastly, the final chapter highlights two collaborations in which tandem mass spectrometry experiments aid in the characterization of experimental data. In the first collaboration, a quantitative cysteine reactivity profiling method was used to characterize the selectivity of a cysteine reactive covalent NRF2-inducing small molecule, MIND4-17. In the second collaboration, analysis of tryptic mass spectrometry data enabled high resolution characterization of peptide sequencing for superfolder green fluorescent protein (sfGFP) expressed from observed internal nonsense suppression. Identification of the misincorporated amino acid facilitated the elucidation of the cross-talk mechanism. / Thesis (PhD) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

The work presented in this dissertation attempts to form an understanding of the importance of polymer connectivity and nanoparticle shape and curvature on the formation of non-covalent interactions between polymer and nanoparticles by monitoring the dispersion of nanoparticles in copolymers containing functionalities that can form non-covalent interactions with carbon nanoparticles. The first portion of this study is to gain a fundamental understanding of the role of electron donating/withdrawing moieties on the dispersion of the fullerenes in copolymers. UV- Vis spectroscopy and x-ray diffraction were used to quantify the miscibility limit of C60 fullerene with the incorporation of electron donor-acceptor interactions (EDA) between the polymer and fullerene. The miscibility and dispersion of the nanoparticles in a polymer matrix are interpreted to indicate the extent of intermolecular interactions, in this case non-covalent EDA interactions. Experimental data indicate that the presence of a minority of interacting functional groups within the polymer chains leads to an optimum interaction between polymer and fullerene. This is further affirmed by density functional theory (DFT) calculations that specify the binding energy between interacting monomers and fullerenes. The second portion focuses on the impact of sample preparation on the dispersion of graphene nanocomposites. Visualization and transparency are used to quantify the dispersion of graphene in the polymer matrix. In addition, differential scanning Calorimetry (DSC) also provides insight into the efficiency of the preparation process in forming a homogeneous sample, where rapid precipitation and solvent evaporation are studied. Examining the change in glass transition temperature, Tg, with nanoparticle addition also provides insight into the level of interaction and dispersion in the graphene nanocomposites. The approach of utilizing non-covalent interactions to enhance the dispersion of polymer nanocomposites is realized by varying the functional group in the copolymer chains, while the impact of nanoparticle shape is also examined. The optimum enhancement of dispersion is interpreted in terms of the improvement of interaction between polymer and nanocomposites. This interpretation leads to the conclusion that chain connectivity and the ability of the polymer to conform to the nanoparticle shape are two important factors that govern the formation of non-covalent interactions in polymer nanocomposites.

I present the characterization and applications of a technique to modify the surface of the conducting polymer, polypyrrole, via a novel, 12-amino acid peptide, THRTSTLDYFVI (T59). This peptide non-covalently binds to the chlorine-doped conducting polymer polypyrrole, allowing it to be used in tethering molecules to polypyrrole for uses such as a scaffold for the treatment of peripheral nerve injury or in surface coatings of neural recording electrodes. I have quantified the binding of this peptide as well as investigating the mechanism of the binding. The equilibrium constant of the binding interaction of PPyCl and the T59 peptide was found through a binding assay to be 92.6 nM, and the off rate was found to be approximately 2.49 s⁻¹, via AFM force spectroscopy. The maximum observed surface density of the peptide was 1.27 +/- 0.42 femtomoles/cm². Furthermore, my studies suggest that the eighth residue, aspartic acid, is the main contributor of the binding, by interacting with the partially positive charge on the backbone of polypyrrole. I have demonstrated practical applications of the technique in the successful modification of a PPyCl surface with the laminin fragment IKVAV, as well as the so-called stealth molecule poly(ethylene glycol) (PEG). A subcutaneous implant study was performed to confirm that the T59 peptide did not induce any significant reaction in vivo. Significantly, the conductivity of a PPyCl surface was unaffected by this surface modification technique. / text

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第13840号 / 工博第2944号 / 新制||工||1435(附属図書館) / 26056 / UT51-2008-C756 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 榊 茂好, 教授 川﨑 昌博, 教授 田中 庸裕 / 学位規則第4条第1項該当