In this dissertation, the mechanisms of nanosuspension stabilization via polymer adsorption on nanoparticle surface were investigated. As the electrokinetic behavior and colloidal stability depend on the surface characteristics, altering the surface adsorbed polymers affords the different surface properties of nanoparticles and leads to the insight on the mechanism of nanoparticle stabilization. Drug nanosuspensions were prepared by wet milling of drug with water as medium and polymers as stabilizers. Block copolymers were evaluated based on varying the hydrophobic and hydrophilic amounts, polymer concentration, and polymer affinity differences onto the nanoparticle surface. Specifically, block copolymers of ethylene oxide (EO) and propylene oxide (PO) with different EO chain lengths were used to modify the nanoparticle surface and investigate the mechanisms of stabilization by varying the ratio of hydrophobic (PO) and hydrophilic (EO) units. It was hypothesized that the PO chain of block copolymers adsorb at the solid-solution interface and the EO chain provides steric hindrance preventing aggregation. Block copolymer adsorption layer thicknesses were experimentally determined with adsorption layer thicknesses increasing from 4.7 to 9.5 nm as the number of EO increase from 26 to 133 monomer units. Nanoparticle aggregation occurred with insufficient polymer monolayer coverage and electrokinetic zeta potential greater than -20 mV. The amount of block copolymers on the surface of nanoparticles was quantified and the affinity of polymer adsorption increased as the copolymer hydrophobic units increased. The amount adsorbed and affinity provides a qualitative ranking of the affinities between a specific polymer and nanoparticle substrate to provide a method in determining the mechanism of stabilization, where specific functional groups for adsorption could be selected for maximum nanoparticle stability. A molecular modeling was conducted to visualize and support the mathematical model and the proposed mechanism of block copolymer adsorption onto a nanoparticle surface. The time lapse molecular modeling of a block copolymer in an aqueous media showed the hydrophobic units adsorbing onto the nanoparticle surface with the hydrophilic units projecting into the aqueous media. For the first time in pharmaceutical research, a systematic series of studies were conducted to elucidate the mechanisms of adsorption with both surface charge and polymer affinity analyses. A series of studies evaluating the adsorption properties polymer stabilizers provided useful information on how a block copolymer comprised of both hydrophilic and hydrophobic domains adsorbs onto an active pharmaceutical ingredient. A systematic set of experimental techniques were presented with novel analysis tools and predictors to construct stable nanoparticle formulations.

Photoelectron Photoion Coincidence (PEPICO) Spectroscopy studies on two small oxygenated species are presented here. Diethyl Ether (Et2O) and Acetic Anhydride (AcOAc) were chosen because of their and their fragments' relevance to combustion chemistry. The Imaging PEPICO (iPEPICO) experiment at the VUV beamline of the Swiss Light Source (SLS) was utilized to provide dissociative ionization data of the two molecules of interest. In this experiment, the unimolecular fragmentation pathways of energy selected ions can be studied with high energy resolution. The iPEPICO experimental setup also allows the measurement of the dissociation rates, which is indispensable to derive accurate thermochemical information on large ions. The experimental data on the fragmentation of ions of interest are then examined through modeling the experimental ion fractional abundances (breakdown curves, BDCs) and reaction rates, in a modeling framework based on the RRKM statistical theory. In our first project, diethyl ether was studied to provide the appearance energies of its daughter ions along with the dissociation pathways of the molecular ion, leading to thermochemical data (such as heats of formation) pertinent to combustion chemistry. A revised ionization energy (IE) differing from the reviewed National Institute of Standards and Technology (NIST) was also proposed. In the second project presented, AcOAc was also measured on the iPEPICO apparatus to understand its dissociative photoionization processes. The appearance of trace amounts of acetone in the ionization spectra, discrepancies in the statistical models of the branching ratios, and the quantum chemical calculations all point to the existence of a post-transition-state bifurcation, when a single TS separates multiple products, namely a methyl-loss fragment and acetone, as well. The acetyl cation, as well as the methyl cation at higher energies, appear to be formed by both parallel and sequential dissociation processes.

Poly-N-isopropylacrylamide (PNIPAM) gels grafted to redox-active metal monomers undergo sudden expansion-contraction activity in response to change in environmental conditions, such as temperature, pH, ion concentration, and oxidation states of the metal. The relevance of these conditions to biological systems has garnered attention for PNIPAM-based polymer as potential biomedical materials. Candidate transition metal monomers containing ruthenium and nickel cores were designed and synthesized for copolymerization with NIPAM and cross-linker methylene-bis-acrylamide in order to attain metallopolymer microspheres with a high percentage of metal incorporation. Synthesis of 4-vinyl-4'-methyl-2,2'-bipyridine (vmbpy) was optimized from literature procedures for usage in the metal-containing monomers. Metal-containing monomers were then synthesized, purified, and characterized using electrospray ionization mass spectrometry (ESI-MS), proton nuclear magnetic resonance ( 1 H-NMR), X-ray diffraction, Ultraviolet-Visible light (UV-Vis) spectroscopy, and spectrofluorometry. While the Ru complex was pure and exhibited interesting photochemical properties, lability of the ligands on the Ni monomers resulted in complication of their synthesis. Polymer microspheres of poly(NIPAM-co-vmbpy), the cross-linked copolymer constructed from NIPAM and vmbpy monomers, were synthesized from modified emulsion polymerization procedures. Experimental setup parameters and conditions—such as the methods of injection of initiator and stirring, the time duration for incubating the emulsion, and the initiation temperature—were varied to assess their influences on the material properties of the final product. The polymers were tested for size and morphological uniformity by dynamic light scattering (DLS) and scanning electron microscopy (SEM). While varying the method of initiator injection had no measurable effect on the product, strong mechanical stirring and incubation of the polymer emulsion for 15-25 minutes at 71 °C procured similar polymer products. Consistent properties ensured the polymers' suitability for further material development. Preliminary morphological and spectroscopic characterization was conducted of metallopolymers made from Ru and Ni grafted to PNIPAM. Metallopolymers containing polypyridyl Ru cores exhibited desirable spectroscopic properties and spherical morphology.

Dirhodium complexes have been known for their catalytic reactivities toward C-H bond activation for nearly two decades. However, both experimental and theoretical studies have not given a clear explanation on the roles of each metal in the reactivities, largely due to the limited number of available bimetallic species. To study the system systematically, we set our goal to synthesize bimetallic complexes from two independent approaches. In the first approach, five N, N’ -diarylformamidines with symmetric or asymmetric substituents on the phenyl groups were synthesized and fully characterized. Formamidines without bulky substituents exhibited fluxionality in solution, which was proved by a single set of signal in 1 H NMR. In contrast, two sets of signals were observed for formamidines with bulky substituents in the ortho positions, indicating two major stereoisomers ( E and Z conformers) co-existing in solution. In solid state, strong stability for E conformers was gained from a pair of H bonds between two ligands facing each other. The phenomenon was observed for all ligands but N, N’ -bis(2,6-dimethylphenyl)formamidine ( L2 ), in which ligands in Z conformation were connected through H bonds from both sides of a ligand and an infinite chain structure formed in solid state. Metallation of the formamidines with diethylzinc and mesitylmagnesium bromide produced ten complexes in a variety of geometries, indicating a rich diversity in geometry for the formamidine family as coordination ligands. Among these complexes, three bimetallic complexes, with metal atoms close in distance, are potential candidates for the formation of complexes with metal-metal bonds. In each dizinc complex, two formamidinates (deprotonated formamidines) spanned over the two Zn atoms and brought them together, while in the dimagnesium complex, the two Mg atoms were bridged by two bromides, resulting in a Mg 2 Br 2 cubic core. In the other approach, two newly designed tripodal ligands were obtained at relatively high yields. Each of the ligands contains three branches built up from a central atom C or N. Lone pairs on the three branches of a deprotonated ligand working together could behave like a three-prong clamp and secure two metal centers closely in the pocket. A dichromium complex with a geometry matching our initial design was successfully synthesized. Meanwhile, two monometallic complexes, potential candidates as precursors to heterobimetallic complexes, were obtained.

Exposure of DNA to reactive oxygen species (ROS) results in the modified nucleobases (lesions) as well as strand scissions under physiological conditions. Due to its lowest oxidation potential (1.29 eV), guanine is the most easily oxidisable nucleobase. Furthermore, it has been observed that the 5'-guanine in G-tracts (e.g. GGG) has even lower oxidation potential (1.00 V vs. NHE). One of the representative G-rich examples is telomeres that consist of repeating units of 5'-d [TTAGGG]-3' found at the ends of chromosomes. Telomeres play an important role in biological functions, serving as guardians of genome stability; however, their G-rich nature implies that they can be readily oxidized. So how does nature protect these biologically important regions from oxidation? We believe the formation of a secondary structure known as G-Quadruplex in telomeric regions can partly serve as a protective role. In the first part of this work, we investigated DNA G-Quadruplex damage under various oxidation conditions and compare the damage results with single-stranded telomeric sequences. Damage to G-Quadruplex is generally less than single strands and is condition dependent. Guanines are the primary damage sites, but damage of adenine and thymine is also possible. Based on our studies, telomeric DNA can be readily oxidized to produce DNA lesions. How do DNA lesions affect the conformation and the stability of telomeric G-Quadruplex DNA? In the second part, we sought to address this question using various biophysical methods. Several native (OxodG, OxodA, and abasic site) and non-native (8-NH 2 -dA and 8-Br-dA) lesions were tested. UV thermal denaturation and circular dichroism revealed that the conformation and the stability of G-Quadruplex DNA are dependent on the location and the type of lesion in the sequence. G-Quadruplex DNA containing OxodG maintains its conformation with a decreased stability. Abasic site in the TTA loop affects the conformation of G-Quadruplex DNA but shows little effect on its stability. An unexpected stabilization of telomeric G-Quadruplex DNA was observed when deoxyadenosine (dA) in the loops was replaced with its native oxidized form OxodA. This is the first example of native DNA lesion that increases the stability of G-Quadruplex DNA. Like OxodA lesion, 8-NH 2 -dA (a non native DNA lesion) increases the stability of G-Quadruplex DNA while 8-Br-dA only affects the stability in KCl but has no significant effect in NaCl. In addition, studies of the effect of OxodA lesion on the human telomerase activity using TRAP assay will be discussed.

The DART ion source was introduced in 2005 at the ASMS Sanibel Conference and immediately afterward Professor Sparkman was contemplating of a way to get our lab this revolutionary mass spectrometry ionization technique. It did not take long because it was delivered to the Pacific Mass Spectrometry Facility in August 2006 and I was able to being using and learning the technique. The ion source creates excited state helium metastables (2 3 S) with an ionization potential of 19.8 eV are created by a glow discharge at atmospheric pressure. The metastables are sent through an optional heater, to aid in desorption, enter the open-air to directly ionize your sample or ionize reagent species to react with the analyte molecules. The most observed ionization mechanism is the formation of protonated molecules from a proton-transfer reaction between the analyte and protonated water clusters. The limited to no sample preparation with the "soft" ionization provide very quick identification of intact organic ions in or on various types of matrices. When the DART is coupled to a high resolving power instrument, such as the JEOL AccuTOF, accurate masses and accurate isotope ratios are assigned to aid in the determination of unknown elemental compositions. This research discusses the formation of the metastable species and how they are used to produce analyte and reagent ions within the open-air sample gap of the DART-mass spectrometer interface. A description of the fundamentals on the operation including real time visualization of the fluid dynamics and confirmation of the formation of a hydroxyl radical in the proposed formation of the protonated water clusters, along with applications developed in the Pacific Mass Spectrometry Facility will also be discussed. These include cleavage, desorption, and ionization of solid-phase peptides, desorption of aqueous metal ions using a heated wire filament and the increased ion transmission with the Vapur interface using metal coated glass tube for the transfer tube.

It has long been known that the efficiency of anticancer drugs is limited by the emergence of resistance due to the evolving repair of such DNA lesions in malignant cells. Therefore, development of pharmaceutical agents, which can interfere with the DNA repair pathways, may represent a novel approach to enhance the cytotoxic effects of chemotherapy by reducing drug resistance. Abasic sites (AP sites) are the key intermediates in the BER pathway and promising targets for BER inhibition. In chapter 2, we report the synthesis of two small molecules specifically targeting at AP sites and the evaluation of their activity in terms of interstrand crosslinking formation. Our results show no covalent adduct is induced, which is due to the weak DNA binding affinity. In chapter 3, we try to use TFOs to deliver the interstrand crosslinking moiety to the AP site in a sequence specific manner. Two modified phosphoramidites were synthesized and incorporated into the 5' end of TFOs. The activity was evaluated by using various biophysical and biochemical experiments. The work reported in chapter 4 is focused on the G-quadruplex structure formed in the guanine rich telomeric sequence. Many studies have shown G4 ligands can induce and stabilize G-quadruplex within telomere region and inhibit the activity of telomerase that is overexpressed in 80-90% of cancer cells. Our results indicate that phenanthroline based metal complexes, Ni(Phen) 2 , have strong binding affinity and selectivity towards G-quadruplex over duplex DNA. The effect of Ni(Phen) 2 on telomerase activity and cytotoxicity towards cancer cells was also investigated. Calixarenes containing DNA building units such as nucleotides, nucleosides, and nucleobases have recently aroused much interest because of their versatile applications. In chapter 5, we report the synthesis of calix[4]arenes ( 5.11-5.14 ) functionalized with a single nucleobase (thymine, adenine, guanine, or cytosine) at the upper rim via click chemistry. Their complexation with alkali metal ions was examined using MALDI-TOF mass spectrometry and their molecular interactions were determined using 1 H NMR. All calix[4]arene derivatives show good complexation with alkali metal ions with apparent selectivity. The results also reveal that nucleobase-calix[4]arenes are capable of self-association in CDC1 3 and calix[4]arenes bearing complementary nucleobases can bind to each other via base pairing.

Trans-2-Aminocyclohexanol (TACH) is a promising model for pH-triggerable molecular switches with a variety of potential applications. In particular, such a switch, when incorporated into cationic liposomes, provides a novel design of the pH-sensitive helper lipids for gene delivery. Protonation of TACH molecules results in a strong intramolecular hydrogen bond between the amino and its neighboring hydroxyl groups, which triggers a conformational flip, and forces changes of the relative position of other substituents on the ring. In this work, a library of TACH-lipids has been designed and built based on structural modifications of both hydrophilic headgroups and hydrophobic tails, and their conformational behavior has been studied by 1 H NMR. NMR-titration has been done to quantitatively monitor the conformational switch for TACH derivatives. It was discovered that conformational behavior of TACH-lipids is independent from the length or shape of their hydrophobic tails. Therefore, a simplified model was suggested based on TACH with diethyl groups instead of hydrocarbon tails. Conformational study of these models has demonstrated that the position of equilibrium shift A [special characters omitted] BH + can be effectively changed by altering structure of NR 2 R 3 group. Furthermore, the pH-induced conformational flip occurs in a certain pH range that mostly depends on the basicity of group NR 2 R 3 , allowing a broad tuning of the pH-sensitivity of TACH-based conformational switches in a wide range of acidity. The hydrophilic OH group was also modified to influence the conformational equilibrium. External stimuli including addition of acid, change of solvent and of the solution ionic strength also showed impact on conformation equilibrium to different extents. To explore the potential to serve as pH-sensitive helper lipids in gene delivery, a variety of TACH-lipids were incorporated into lipoplexes together with the cationic lipid DOTAP to mediate DNA transfection in Bl6F1 and HeLa cancer cell lines. The lipoplex comprising TACH-lipid 3o (R 1 = C 19 H 37 ; R 2 R 3 = CF 3 CH 2 NH) exhibited one to two orders of magnitude better transfection efficiency than the one with the conventional helper lipid DOPE while only inducing slight higher cytotoxicity. Thus, the lipid can be suggested as a novel helper lipid for efficient gene transfection with low cytotoxicity.

Our research involved two projects: Crown Aza and Crown ether. Crown Aza are compounds that have nitrogens as the hetero-atoms in the macrocycle. In the first aim, the 1 H NMR spectrum of strongly-coupled di-iron complexes shows 5 different conformations, but is unable to identify these conformers. Calculation using Density Functional Theory (DFT) were performed to attempt to quantify these conformers to correlate with the experimental NMR data. The second aim of this study was to utilize the carbonyl functional group of the macrocycles to couple the iron complexes to obtain tetramers or higher oligomers. Visible spectra of the selective reduction of iron mono-keto-macrocycles with boron trifluoride and triethylsilane showed a coupling reaction to form a di-iron complex. A mixture of iron mono-keto-macrocycic with iron diketo-dimacrocycle showed a new species with an intense NIR absorption at 1010 nm. This intense band at 1010 nm is extremely rare in transition metal compounds and is of potential interest in photodynamic therapy. This indicates a new species is formed with a very low energy gap between the ground and excited states. Our second interest is in ionizable crown ethers that have many potential applications from environmental to medical. These macrocyclic poly-ethers contain phosphorous and oxygen atoms which produce a charged moiety in the ring to form a neutral complex with our targeted ions. They are significantly different from all ionizable cyclic poly-ethers in the literature. They vary in ring size from 16-crown-6 to 22-crown-8 using ethylene or propylene linkages between the oxygen atoms. Theoretical calculations revealed these ionizable crown ethers can accommodate ions from 2.6 angstroms to 4.2 angstroms in diameter. Strontium 90 ( 90 Sr 2+ ) is a radioactive product ion from nuclear fission reactions. The Phosphorous containing macrocyclic poly-ether with 2 charges could form complexes with Strontium and are possible candidates for clean-up agents of radioactive materials. The synthesis of ionizable crown ethers is discussed.

The current dissertation describes a multidisciplinary research project centered on the discovery and investigation of the anticancer activities exhibited by novel piperazinylpyrimidine derivatives designed to target kinases protein family. Primary screening of the antiproliferative effects implemented by these successfully synthesized new agents has resulted in the candidacy of 4 , 15 , and 16 as not only prototype representatives of the class, but surprisingly also as optimized agents for either globally cytotoxic, 16 , or selectively cytostatic, 4 and 15 , agents. Subjecting 4 , 15 , and 16 to screening tests aiming at measuring their binding to or their functional inhibition of selected sets of kinases has revealed the tendency of 4 to target PDGFR subfamily and the ability of 4 , 15 , and 16 to recognize CSNK1D. Docking as well as binding profiles comparative studies hypothesize 4 , 15 , and 16 as type-I kinase inhibitors. Further preclinical investigation of 15 against MDA-MB-468 triple negative breast cancer cell line revealed that 15 exhibits a time as well as dose-dependent antiproliferative activity mediated by the induction of both time and dose independent G2/M arrest and dose dependent apoptosis. Globally studying the molecular events accompanied with the 15 /MDA-MB-468 incidence has revealed the phosphorylation of TP53 and the consequent activation of its transcriptional activity as a hallmark molecular event relevant to the above observed effects on the cellular, cell cycle, and programmed cell death levels. Apart from the above experimentally oriented investigation, another theoretically driven inquiry was pursued aiming at studying the inherent ability of certain kinases to be more promiscuous towards binding to small molecules than others. Throughout the analysis of a reported dataset, dephosphorylated members of PDGFR subfamily were found to more potently bind to structurally diverse kinase inhibitors compared to INSR subfamily. A molecular dynamics study was performed to compare between the topological, energetic, and dynamic properties of the binding area usually targeted by kinase inhibitors in both KIT, as a representative of the more promiscuous PDGFR subfamily, and INSR, as a representative of the less promiscuous INSR subfamily. Interestingly enough, the binding area in both kinases showed significantly different properties which, to a large extent, can explain their different overall attitudes towards binding small molecules. As a representative example, the binding area of INSR tends to be more energetically self-stabilizing than that in KIT. Additionally, the topological analysis revealed that the binding are in KIT tends to be more rigid and to have bigger size than that of INSR. The current work has successfully cross-implemented experimental, theoretical, and computational studies aiming at the development of novel kinase inhibitors and/or promising anticancer preclinical candidates.