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Green hydrogen generation is currently a leading topic of research in the field of renewables and sustainable energy. The development of synthetic hydrogenase mimetics as catalysts for hydrogen evolution has emerged as a promising approach due to their relatively low cost and sustainability. Mimetics of the [2Fe-2S] active site, which are originally based on the active site of the [FeFe]-hydrogenase enzyme, have been shown to efficiently reduce protons to molecular hydrogen and help highlight interesting synthetic and spectroscopic insights into the improvement of catalytic capabilities of this class of complexes. These synthetic mimetics are typically defined by the composition and connectivity of the thiolato ligands to both each other and the [2Fe-2S] catalytic core. This dissertation focuses primarily on the effects that differences in the architecture of the thiolate attachments have on catalytic performance and mechanism for both molecular and metallopolymer type [2Fe-2S] catalysts.The complexes discussed in this dissertation underwent new electrochemical and spectroscopic experimentation that defined differences in their catalytic behavior. New spectroelectrochemical equipment and methodology were developed to make the first in situ spectroelectrochemical observations of the initially reduced and protonated catalytic intermediates for aryl dithiolate [2Fe-2S] catalysts in the presence of weak acids. These structural assignments were supported by improved DFT computations and led to the first refinement of the mechanistic paradigm for aryl dithiolate [2Fe-2S] catalysts in the presence of weak acids. Comparisons of new and existing aryl dithiolate [2Fe-2S] active sites in both the organic molecular and aqueous metallopolymer phases revealed the influence of metallopolymer system factors on active site catalytic behavior. These studies also highlighted limitations in the predictive power of [2Fe-2S] molecular system studies to predict catalytic properties of [2F

Capillary electrophoresis (CE) is a widely employed technique in life sciences, with applications in environmental, clinical, pharmaceutical, and food analysis. Among its various modes, capillary zone electrophoresis (CZE) stands out as the most commonly used due to its efficiency in achieving rapid separation. The flat flow profile within small-diameter capillaries further enhances separation efficiency, making it particularly effective for analyzing large biomarkers, as well as charged biomolecules such as proteins and signaling molecules. While UV detection is frequently utilized, techniques like laser-induced fluorescence (LIF) offer increased sensitivity. However, limitations arise from the ultra-small sample injection volume and the short optical path length, which can be mitigated by employing on-capillary preconcentration techniques, such as transient capillary isotachophoresis (tITP). Furthermore, CE-based flow-gated online injections prove indispensable for achieving high temporal resolution in monitoring time-sensitive reactions, enabling the study of dynamic processes and kinetics in a range of systems.The dissertation focuses on advancing the analysis of trace compounds by utilizing CZE, tITP-CZE, and flow-gated methods. It explores the quantitative analysis of intracellular nitroxyl (HNO) delivery, employing a fluorescent thiol-based trapping agent that eliminates the need for additional labeling steps. Through the use of CZE-LIF, HNO can be detected with good sensitivity, allowing for precise differentiation from other signals. It further introduces an analytical process that combines preconcentration through counterflow tITP within a monolith with CZE separation. Counterflow tITP-CZE addresses challenges such as flow dispersion and provides a stable porous medium for effective analyte preconcentration. Moreover, the addition of tITP-CZE in a flow-gated online injection system holds promise for the analysis of trace compounds and immunoassays, with fl

Linear oligopyrroles are degradation products of heme, which is converted in the presence of heme oxygenase to bile pigments, such as biliverdin and bilirubin. These tetrapyrrolic oligopyrroles are ubiquitously present in biological systems and find applications in the fields of catalysis and sensing. These linear tetrapyrrolic scaffolds are further degraded into linear tripyrrolic and dipyrrolic fragments. Although these lower oligopyrroles are abundantly present, their coordination chemistry requires further characterization. This dissertation focuses mainly on two classes of bioinspired linear oligopyrroles, propentdyopent and tripyrrindione, and their transition metal complexes, which present a rich ligand-based redox chemistry. Chapter 1 offers an overview of heme degradation to different classes of linear oligopyrroles and properties of their transition metal complexes. Chapter 2 is focused on the tripyrrin-1,14-dione scaffold of the urinary pigment uroerythrin, which coordinates divalent transition metals palladium and copper with square planar geometry. Specifically, the tripyrrin-1, 14-dione ligand binds Cu(II) and Pd(II) as a dianionic organic radical under ambient conditions. The electrochemical study confirms the presence of ligand based redox chemistry, and one electron oxidation or reduction reactions do not alter the planar geometry around the metal center. The X-Ray analysis and the electron paramagnetic resonance (EPR) studies of the complexes in the solid and solution phase reveals intermolecular interactions between the ligand based unpaired electrons and therefore formation of neutral π-π dimers. In Chapter 3, the antioxidant activity and the fluorescence sensor properties of the tripyrrin-1,14-dione ligand in the presence of superoxide are described. We found that the tripyrrindione ligand undergoes one-electron reduction in the presence of the superoxide radical anion (O2●–) to form highly fluorescent H3TD1●– radical anion, which emits at 635 n

MRI is a powerful imaging method that offers several advantages including non-ionizing radiation, significant depth of penetration, and great spatial resolution. Current demand for precision medicine and the movement toward personalized medicine have encouraged researchers in the field of medical imaging to develop MRI-based techniques. Various techniques are now available for molecular imaging by MRI. MRI started by utilizing T1 relaxation properties of molecules but soon after other relaxation mechanisms such as T2 and recently Chemical Exchange Saturation Transfer (CEST) were developed. Each of those MRI techniques offers advantages and disadvantages such as differences in experimental procedures, complexity of the method, selectivity and specificity of signals, and translation into clinical applications. We have been developing MRI techniques and responsive contrast agents for CEST MRI in the Pagel laboratory (Contrast Agent and Molecular Imaging Laboratory, also called CAMEL) for the past decade. We have mainly utilized MRI techniques and responsive contrast agents to detect and measure cancer biomarkers. Detection of the activity of enzymes and measurement of pH have been our main focus, and we have developed catalyCEST MRI probes and techniques for the detection of the activity of enzymes and acidoCEST for the measurement of pH. My research started with investigation on paramagnetic agents as potential CEST MRI probes (paraCEST) and continued with an investigation on diamagnetic agents (diaCEST). I completed several projects in which I prepared and evaluated paraCEST and diaCEST contrast agents for the detection of DT-diaphorase, and alkaline phosphatase enzymes, respectively. Although CEST MRI was my main activity in CAMEL, I started a new direction in CAMEL after encountering a series of observations that were unexplainable with CEST MRI. Through my research, I introduced a new class of responsive contrast agents based on the T2-Exchange (T2-Ex) relaxation

The main goals of this research were to synthesize nitrogen oxide releasing diazeniumdiolates and their prodrugs and to evaluate their pharmacological effects. The different projects and their results are described below. i. Comparison of HNO and NO donating properties of cyclic amine diazeniumdiolates Diazeniumdiolates are an attractive class of donor compounds as they can be tuned to release NO or both NO and HNO depending upon the amine backbone. Isopropylamine (IPA/NO) and cyclohexylamine (CHA/NO) diazeniumdiolates are currently the only examples of primary amine based diazeniumdiolates. A series of structurally related cyclic amine based diazeniumdiolates were synthesized and characterized. An acetoxymethyl derivative was also synthesized to facilitate cellular uptake and to achieve higher HNO levels in cells. ii. Nitrogen oxide releasing diazeiumdiolate based adducts of N-des-methyl-tamoxifen Nitrogen oxide (NO/HNO) donating diazeniumdiolate adducts of N-desmethyltamoxifen (a key metabolite of the breast cancer drug tamoxifen) were synthesized. DEA/NO-AcOM, an NO donor was also synthesized to monitor the effect of NO on breast cancer cell survival. Derivatives of N-desmethyltamoxifen were found to be effective towards estrogen receptor positive (ER+) cells only. DEA/NO-AcOM was found to be cytotoxic towards estrogen-dependent and independent cell lines, in combination with tamoxifen, or by itself. iii. Synthesis and characterization of nitrogen oxide adducts with non-steroidal anti-inflammatory drugs (NSAIDs) Our group has shown HNO releasing diazeniumdiolate derivatized aspirin to be comparably effective in preventing gastric ulceration to NO-releasing diazeniumdiolate based aspirin analogues. Series of such NSAID adducts were further extended by synthesizing such derivatives of indomethacin and niflumic acid. NO/HNO releasing analogues of aspirin and indomethacin were cytotoxic towards two different breast cancer cell lines, irrespective of estrogen dependen

In organic photovoltaic (OPV) devices, the outer interface structures are crucial in establishing the environment to which charge collection efficiency is keenly sensitive. These outer structures consist of both the physical electrodes and the subsequent electrode contacts formed by integrating electrodes with photoactive materials. Currently, fundamental understanding and strict control of contact effects within OPVs is insufficient. This dissertation is a compilation of this author's research devoted to understanding, modifying, characterizing, and controlling contact effects in OPVs. An overview of the role of electrodes and electrode contacts in OPVs is presented in the Introduction (Chapter 1). The following three chapters each embody a fulfilled research project focusing on a specific aspect of the roles and impacts of electrodes and contacts in OPVs. Chapter 2 presents the work of a modeling study on the impacts of electrical surface heterogeneity on OPV performance and establishes guidelines for acceptable degrees of surface electrical heterogeneity. Chapter 3 explores the use of electrochemically deposited and doped conductive polymers as interlayers for OPVs. Chapter 4 utilizes metal-insulator-semiconductor capacitor (MIS-C) structures as a unique platform for isolating the role of electrodes and contacts in facilitating deleterious non-ideal injection and transport pathways in OPVs. The Conclusion (Chapter 5) presents the author's suggestions for future studies involving electrodes and electrode contacts in OPVs.

Nitric oxide (NO) has been shown to both suppress and promote tumor growth, depending in part on concentration. Exogenous delivery of NO may lead to tumor suppression. Recent studies have proposed ruthenium nitrosyl complexes as catalytic donors of NO in reductive environments. Catalytic donation can provide a long-term, elevated NO flux compared to single use donors. Site-specific delivery is desirable to reduce systemic side effects, such as lowering of blood pressure. Three new ruthenium nitrosyl complexes were synthesized to impart site-specificity through amide coupling to polymers, silica nanoparticles, iron oxide nanoparticles and antibodies. The catalytic activity of new and existing compounds was then assessed. However, upon one-electron reduction of ruthenium nitrosyl complexes, insignificant amounts of NO were detected, suggesting an alternative mechanism than that proposed in prior reports. The mechanism of [Ru(EDTA)NO]²⁻ decay was more thoroughly analyzed. Spectrophotometric decay of [Ru(EDTA)NO]²⁻ indicates that one or multiple nitrogen oxide species are released. Previous studies have suggested a disproportionation mechanism leading to the generation of more highly reduced species such as N₂ and NH₄⁺. Experiments were designed to analyze possible decomposition products such as [Ru(EDTA)NO]⁻ and [Ru(EDTA)H₂O]²⁻. A disproportionation mechanism was determined likely. Decomposition of [Ru(EDTA)NO]²⁻ was also observable following reductive nitrosylation of [Ru(EDTA)H₂O]⁻ in the presence of HNO. The decomposition product, [Ru(EDTA)H₂O]²⁻, was observed through the binding of pyrazine (pz) or dipyridine (bipy) and formation of [Ru(EDTA)pz]²⁻ or [Ru(EDTA)bipy]³⁻. Formation of [Ru(EDTA)bipy]³⁻ or [Ru(EDTA)pz]²⁻ via reductive nitrosylation of [Ru(EDTA)H₂O]⁻ also provides an indirect method of HNO detection that is selective from NO.

Nitric oxide plays a major role in physiology and disease pathology. There are many available methods for the detection of NO; however, these techniques typically detect products of nitric oxide decomposition. Herein, I present a novel method of direct nitric oxide detection using a nitrophorin mutant to capture NO on an optical waveguide platform. Nitrophorins are unique among ferric proteins for their ability to bind NO strongly. The spectral shift of the Soret band of the Nitrophorin was used to monitor NO concentration. The limit of detection was found to be 18 nM, and a linear response to 225 nM. The sensor is highly specific, non-destructive and reusable. Detection of NO was demonstrated in a solution of BSA at serum level concentration, and cell culture solution containing 10% FBS. This method allows for direct NO with high specificity, low detection limit and good temporal resolution. Also described herein are the investigations of the structure of the NO receptor, soluble guanylate cyclase (sGC). sGC is a 150 kDa heterodimeric protein that catalyzes the production of cyclic guanosine monophosphate from guanosine triphosphate, which leads to many downstream affects such as vasodilation. The structural analysis was performed with transmission electron microscopy (TEM). Data presented indicate that the protein is too heterogeneous to be reconstructed with TEM. This is either the result of the sample preparations examined, the purity of the sample, the inherent flexibility or conformational heterogeneity of the protein after applying the sample to the TEM grid.The final project presented describes the use of silica colloidal crystals for the enhancement of the sensitivity of protein microarrays as a function of silica particle size. Protein microarrays are a tool used to discover biomarkers of diseases, and increasing the sensitivity lowers the limit of detection of the method. This is accomplished by an increase of the surface area available for proteins to bi

Nanoparticles (nPs) demonstrate significant advantages over other sensor and marker technologies. The most useful optical nanosensor and label platform for biological samples would be non-toxic, hydrophilic, resistant to non-specific protein interactions and degradation over time or under harsh conditions, highly retentive of entrapped components, and easily functionalized for target specificity. The work described here is part of an investigation into the fabrication and application of polyacrylamide, polyacrylamide/silica hybrid, and polystyrene-core silica-shell nPs. Polyacrylamide (PA) nP nitric oxide (NO) sensors were made by co-entrapping 4, 5-diaminofluorescein (DAF-2) and Texas Red dextran in 60 nm PAnPs. Sensors were used to measure NO produced by a diazeniumdiolate NO donor in solution, and have a response time of 30 seconds or less. Entrapped DAF-2 was protected from non-specific interactions with bovine serum albumin (BSA). Sensor response to NO in FBS solutions was reduced compared to buffer, although improvement over free dyes was observed. The sensors were applied to J477A.1 macrophages as well as a HT1080 cell line (HTRiNOS) in preliminary studies for measuring intracellular NO production. Polyacrylamide/silica hybrid nPs were fabricated and nP architecture was evaluated by transmission electron microscopy. Isopycnic centrifugation of nP samples indicates that the hybrid nPs have a density between 1.70 and 1.76 g/cm³. Silica in the hybrid nPs was covalently labeled with Texas Red, suggesting that the hybrid nPs may be used as ratiometric or possibly multiplexed sensors. Hybrid nPs coated with 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) exhibit reduced adsorption of TRITC-BSA compared to uncoated hybrid nPs. Hybrid nP pH sensors were prepared and responded reproducibly and reversibly to changes in pH, nominally from pH 6.0 to 8.0. Core-shell nPs for scintillation proximity assay (SPA) were fabricated by entrapping the scintillants p-terphenyl and

This dissertation describes the preparation and characterization of magneto and electro-active hybrid nanocomposite materials. In this research, two hybrid nanocomposite materials, gold-cobalt oxide nanowires and ferrocene functional polymer brushes on electrode surface, were investigated. Polymerizations of magnetic colloidal monomers to form electro-active nanowires and ferrocene functional monomers on electrode to form electro-active polymer brushes were demonstrated. The central focus of this research is utilizing colloidal polymerization and surface-initiated polymerization to prepare electro-active hybrid nanocomposite materials for potential applications in energy storage and conversion.Colloidal polymerization has been developed as a novel synthetic methodology to prepare 1-D mesostructures via dipolar assembly and chemical reaction. This method was exploited to synthesize multicomponent 1-D nanowires by using polymer-coated ferromagnetic gold-cobalt core-shell nanoparticles as colloidal monomers. Prepared semiconductor cobalt oxide nanowires with gold inclusions exhibited enhanced optical and electrochemical properties compared to cobalt oxide nanowires. This research provided a platform in fabricating a wide range multicomponent semiconductor nanowires as new nanostructured electrodes for potential applications in energy storage and conversion. Further, self-assembled gold-cobalt core-shell nanoparticles were utilized to align novel gold nanoparticles on a substrate. This facile and template free approach enabled the linear and ring assembly of noble gold metal on a substrate.Indium tin oxide (ITO) thin films are key components as transparent electrodes in a number of optoelectronic devices. The modification of ITO surfaces with polymers via electropolymerization has been widely investigated to improve surface compatibility and charge injection from the interface. However, there remain challenges to prepare polymers possessing, well-defined interfacial che

Phthalocyanines (Pcs) are highly conjugated synthetic porphyrin analogs that exhibit high extinction coefficients and hole mobilities, and strong pi-pi interactions. We have developed a general method for the synthesis of peripherally functionalized Pc chromophores using `click' chemistry, wherein an alkynyl substituted Pc is reacted with an azide, providing an elegant route to the creation of a library of numerous Pcs. We have also developed a simple route to the synthesis of tri- and tetravalent metal Pc derivatives such as titanyl phthalocyanine (TiOPc) involving solvent-free conditions. Solvent-free conditions are environmentally friendly and industrially economical, and in the present context effectively eliminate the formation of non-metallated phthalocyanine (H2Pc), a side product often seen in other routes that interferes with their purification. We have also prepared and characterized thin-films of some of these Pcs, TiOPcs in particular, wherein we have developed an easy route to various TiOPc polymorphs exhibiting different near-IR sensitivities via spin-coating whose optical properties are reminiscent of Phase-I and Phase-II polymorphs of the unmodified TiOPc. Phase-II is particularly interesting as it is photoelectrically active in the near-IR region with a Q-band maximum at ca. 890 nm. We have also fabricated and characterized organic solar cells in both planar heterojunction (PHJ) and bulk heterojunction (BHJ) architectures based on one of these materials, which exhibited good near-IR photoactivity with the absorption spectrum extending up to 1 micrometer in the near-IR. The incident and absorbed photon to current efficiency (IPCE and APCE) spectra showed contributions from the TiOPc in the near-IR region with local maxima around 680 nm and 920 nm, corresponding to the Frenkel and the charge-transfer (CT) bands of the TiOPc, respectively.

The ability to directly monitor the presence of specific proteins or nucleic acids in a variety of in vitro and in vivo contexts has great utility for understanding biology as well as for the development of diagnostic agents. Herein I describe several methodologies, utilizing split-protein reassembly, which provides potentially general strategies for sequence-specific detection of DNA and RNA sequences as well as poly(ADP-ribose). I also provide a new split-protein approach for the direct detection of native proteins, such as the cancer marker HER2.The green fluorescent protein (GFP) provides a convenient sensor for reporting on a variety of cellular events. A series of spectroscopically distinct GFP variants was developed for sequence-specifically reporting on DNA. Each of these variants was demonstrated to provide a sensitive readout for the presence of a particular DNA sequence. Furthermore, utilizing a method of mixed split-protein complementation, I was able to simultaneously report on the presence of two distinct DNA sequences in the same solution.To provide a general solution for reporting on the presence of particular RNA sequences, a method was developed that utilized elements from a hybridization-based detection strategy coupled with split-protein reassembly. Specifically, DNA guide sequences complementary to an intended target were attached to hairpin sites that served as binding sites for high-affinity zinc fingers. Localization of the zinc fingers allowed for reassembly of the attached split enzyme, providing a sensitive readout for the presence of potentially any RNA sequence of interest. This methodology was applied to the detection of mRNA encoding VEGF, hDM2, and HER2, each of which may be overexpressed in cancer.A method was established for reporting on the presence of modifications to DNA and proteins that are elicited in response to DNA damage. Specifically, sensors were designed, which incorporated endogenous damage-recognition domains, to repor

The process of forcibly dewetting a solid substrate from a bulk liquid so as to leave a thin residual layer on the surface is referred to as forced dewetting. This novel experimental approach helps to investigate interfacial species by minimizing the interference of the bulk liquid when coupled with spectroscopy. In this work, the scope of liquids investigating using this approach has been expanded from simple fluids to one type of complex fluid, a nematic liquid crystal, 4-n-pentyl-4'-cyanobiphenyl (5CB).In order to better understand the interfacial behavior of the simple fluids, water, chloroform, and n-pentane vapors were adsorbed onto omega-terminated SAM-modifed Ag (11-mercaptoundecanoic acid, 11-mercaptoundenanol, and undecanethiol) surfaces under vapor-saturated conditions. The kinetics of solvent adsorption on each of these surfaces were investigated and the thicknesses of the adsorbed layer were compared to predictions from Lifshitz theory of long-range van der Waals interactions. Although the predicted thicknesses do not match the experimental values for adsorbed films, the predicted thicknesses do match those observed experimentally using forced dewetting. The correlation between these predicted and observed thicknesses implies that residual film formation under the conditions of forced dewetting used in this laboratory is dictated by interfacial forces alone.The surface adsorption behavior of 5CB was investigated using surface-enhanced Raman spectroscopy with the aid of localized surface plasmon resonances-surface plasmon polaritron coupling. The results clearly indicate that 5CB is adsorbed to smooth Ag surface in a facial orientation with pi-d orbital interaction suggested.Finally, forced dewetting studies of bare, -NH2-temintaed SAM, and -CH3-temintaed SAM modified-SiO2 substrates from 5CB were undertaken. Residual layer thicknesses were monitored as a function of substrate velocity. The transition from the regime in which interfacial forces dictate r

CueO is a multicopper oxidase and catalyses the four-electron reduction of dioxygen to water and functions to protect Escherichia coli against copper-induced toxicity. The mechanism of oxygen reduction in multicopper oxidases has been well studied, but the key structures of the reaction intermediates are not known. A combination of kinetic measurements, mutagenesis and X-ray crystallographic studies were conducted to entrap and structurally characterize the reaction states in CueO. CueO has a methionine-rich insert and a labile copper binding site, two features found only in multicopper oxidases involved in copper detoxification. The role of these features in CueO activity has been investigated. In a separate study, a simple mathematical model based on infectivity amongst clustered receptors was developed to explain the chemotactic sensitivity, response range and other key features of chemotaxis.This study describes the successful entrapment of three out of four functional states in CueO. The crystal structures of these reaction states are presented. Using single-turnover oxygen reduction kinetics that were measured using a stopped-flow device, the optical absorption features of three different fully oxidized forms of CueO were captured: the native intermediate, the resting oxidized state and another intermediate lying between them. Stopped-flow studies combined with electron transfer kinetic measurements revealed a role of the conserved residue, E506, in either the protonation of the native intermediate or the release of water molecules formed as a product of the reaction.Cu(I) and Ag(I) bound crystal structures of CueO were determined revealing three binding sites along the methionine-rich helix used by both metal ions. The labile, regulatory copper site in CueO was shown to be a Cu(I) susbtrate oxidation site. Ag(I) was shown to be a potent inhibitor of all CueO activities in vitro and copper detoxification by the cue system in vivo. The cus system was discovered

Transition metal clusters are a unique class of chemical substances. Not only do they have well-defined molecular structures, they also exhibit interesting and potentially useful properties that are inherent to metal-metal bonded species. They may be viewed as atom-like building blocks with adjustable properties. Detailed in this dissertation are the efforts to develop synthetic methodologies necessary to bring a cluster system out of the limited sphere of fundamental cluster chemistry and into general synthetic applicability. Specifically, the design and synthesis, structural characterization, and synthetic applications of the cluster complexes of the [Re₆(μ₃-Se)₈]²⁺ core will be discussed. Chapter 1 provides necessary background information of the [Re₆(μ₃-Se)₈]²⁺ core-containing cluster system, the rationales of cluster-supported synthetic and structural chemistry, and the impetus for these endeavors. Chapter 2 details the synthetic applications of stereospecific complexes of the [Re₆(μ₃-Se)₈]²⁺ clusters for the assembly of nanoscopic multicluster arrays using molecular and supramolecular approaches. The synthesis and structural characterization of a triangle-shaped tricluster array and a tetracluster assembly composed of two hydrogen-bonded diclusters are described. Chapters 3 and 4 describe the synthesis of the [Re₆(μ₃-Se)₈]²⁺ core-containing cluster complexes with the water-soluble 1,3,5-triaza-7-phosphaadamantane (PTA) ligand and the chemistry of these cluster-complex ligands for the coordination of a variety of secondary metal ions. In Chapter 5, the supramolecular chemistry of the cluster-PTA complexes with Ag(I) is detailed. The coordination of Ag(I) to a cluster complex with two PTA ligands disposed trans- to each other produces a 2-dimensional, porous solid with nano-sized hydrophobic pores that are potentially useful for storage of hydrocarbons and for occlusion of certain substrates for activation and possible catalysis. Chapter 6 summarizes the efforts

Aberrant protein-protein interactions have been implicated in numerous human diseases. Hence it becomes important to understand the physicochemical basis of these interactions as well as to develop methods to selectively target these protein surfaces. However, it is difficult to target such protein surfaces by small molecules as these surfaces (≥ 600 Ų) are large and flat. We demonstrate the feasibility of utilizing a small beta-sheet scaffold for targeting thrombin as proof of principle. Thrombin is a trypsinlike serine protease generated in the penultimate step of the blood coagulation cascade. Thrombin has numerous potential interaction sites to test our methodology. This strategy was further extended to target the Vascular Endothelial Growth Factor (VEGF). VEGF is a disulfide-linked cytokine that exerts its activity by binding to two high affinity receptors. VEGF has been implicated in angiogenesis where the growth of new blood capillaries provides nourishment to tumor cells and damage delicate retinal tissues. This will help us to develop a new scaffold and provide essential chemical and structural information necessary for binding these discrete protein surfaces. Furthermore, this facilitates the subsequent transfer of minimal epitope information to a small molecule.

High-resolution pulsed beam Fourier Transform Microwave Spectroscopy (PBFTMS) technique has been used to investigate the rotational spectra, molecular structures and electronic charge distribution of organometallic and organic molecules. The thesis reports high-resolution rotational spectral findings for nine different asymmetric-top molecules in the singlet electronic ground state including: Cyclopentadienyltungstentricarbonylhydride, Bis-(cyclopentadienyl)tungstendihydride, Tetracarbonylethyleneosmium, two substituted Ferrocenes and an organic keto-enol tautomeric system, Z-2-Hydroxypyridine and 2-Pyridone. Moreover, gas-phase rotational constants and distortion constants have also been reported for an excited vibrational state of Cyclopentadienylnickelnitrosyl complex using a high-resolution Fourier Transform Spectrometer (FTS) system at Kitt Peak Arizona, (KPNO). Preliminary microwave results for a fluxional molecule, Cyclopentadienyliridiumdicarbonyl are also presented in this work. Extensive Density Functional Theory (DFT) calculations have been performed in conjunction with the experiments to provide additional insight toward further understanding the equilibrium structures, structural isomers and electric field distributions of these molecules. These calculations were not only helpful in predicting the preliminary structure and rotational constants of the molecules of interest, but also advantageous in analyzing the observed spectra.

The G-quadruplex secondary structure has evolved as a promising anti-tumor target in recent years. This distinctive structure has been proposed to form in the promoter regions of a variety of genes, including the c-MYC oncogene, which is over-expressed in 60% of cancers. The G-quadruplex structure in the c-MYC promoter acts as the repressor element, disruption of which leads to subsequent upregulation of the gene. Hence, stabilization of the G-quadruplex structure with small molecules has been an area of much interest. In this dissertation, the structural aspects of the c-MYC G-quadruplex, and development of unique ligands that stabilize this secondary DNA structure have been explored. The G-quadruplex structure adopts an intramolecular parallel-stranded conformation in solution, and various ligands have been shown to induce structural changes. Cationic porphyrins are such a class of compounds that selectively bind to and stabilize the c-MYC G-quadruplex and in some cases also induce a structural change. The extensively studied cationic porphyrin, TMPyP4, stabilizes the c-MYC G-quadruplex and represses the gene transcription. This detail has been the basis of the research presented herein. Structure-based drug design has been used to develop other novel ligands having bisintercatating properties for enhanced stabilization of the G-quadruplex. A hybrid molecule, having both intercalation and alkylation properties, has also been investigated that has shown to lower the gene expression. Thus, a prototype of ligands are presented that can serve as the base for development of compounds with promising therapeutic properties.