Cancer is responsible for one fourth of the total deaths and is the second leading cause of death, behind heart disease, in the United States. However, there are as many approaches to curing cancer as there are types of cancer. One important issue in solid tumors is hypoxia, a lack of oxygen, which promotes angiogenesis and anaerobic metabolism, which can increase cancer progression and metastasis. The HIF transcription factor is responsible for the mediation of many processes involved during hypoxia and is linked to poor patient prognosis, increased cancer progression, and invasiveness of tumors. With this in mind, the HIF pathway has become an attractive target for small molecule inhibition. Herein, we describe the design and synthesis of small molecules that inhibit the HIF pathway. These compounds are based off an initial “hit” compound, KCN-1, from screening of a 10,000 compound library. KCN1 is both highly effective and has a low toxicity profile. Over 200 compounds have been synthesized by the Wang lab, with the best compound IVSR64b having an IC50 of 0.28 μM. Of special interest is that these compounds do not appear to have any inherent toxicity toward healthy tissues, but only affect cancer cells. Moreover, x-ray crystal structures for both KCN-1 and IVSR64b were obtained and used as the basis for computational modeling, which is still in progress.

Metalloporphyrin aggregation is critical for triplet-triplet annihilation (TTA) to occur. In order to maximize the efficiency of TTA, to use as a mechanism of photon upconversion in dye-sensitized solar cells, it is important to understand the phenomenon of absorber aggregation. The aggregation of ZnTPP in polymer films was investigated by fluorescence anisotropy and total internal reflection fluorescence microscopy (TIRFM). Single molecule spectroscopy (SMS) and spectromicroscopy were the techniques used to study single molecules and multimolecular aggregates of ZnTPP/ZnTPPS in polymer films/adsorbed on glass substrates.<p> Fluorescence anisotropy measurements consistently showed depolarized emission from films most concentrated with ZnTPP. This observation was likely a result of energy transfer in and among porphyrin aggregates. Fluorescence intensity decays were also obtained and they illustrated a pattern of decreased fluorescence lifetime (i.e. faster decays) as the concentration of porphyrin in the film increased. These results are consistent with the formation of aggregates, and their increased presence in more concentrated films. The formation of these aggregates quenches the fluorophores fluorescence, resulting in the observed shorter fluorescence lifetimes. <p> TIRFM was performed to study the structure of these polymer films doped with ZnTPP. It was determined that these films consisted of discrete domains and thus lacked homogeneity, and the presence of aggregates was clearly visible. Time-resolved TIRFM measurements were also performed but no interesting results were collected.<p> SMS and spectromicroscopy were the final techniques employed to study porphyrin aggregation. Preliminary measurements were performed with polymer films doped with ZnTPP, and the single step decay time trajectories collected indicated that single molecules were being studied. Furthermore, emission spectra of these molecules were collected and they were similar to those obtained for a bulk measurement, but the bands were slightly shifted in comparison. These measurements were repeated with ZnTPPS adsorbed to glass substrates. Two different patterns of decay trajectories were measured: (i) single step decays corresponding to single ZnTPPS molecules and (ii) multi step/complex decays representative of multimolecular aggregates. Emission spectra were also collected for the multimolecular aggregates, and they were consistent with those of an ensemble measurement but slightly blue-shifted. Such a shift is common when studying aggregates on such a highly polar surface. Thus, these results demonstrate that ZnTPPS aggregates form even at concentrations as low as 10-8 M, and can be studied using SMS despite their weak fluorescence emission.

Water-soluble fluorescent metallic clusters at sizes comparable to the Fermi wavelength of an electron (~0.5 nm for gold and silver) were created and their photophysical properties were investigated at the bulk and single molecule levels. We employed biocompatible dendrimer and peptide to prepare a series of strong fluorescent gold and silver clusters with chemical or photo reduction methods. Facilitated by the well-defined dendrimer size, electrospray ionization mass spectrometry indicates that the fluorescent silver nanocluster size ranges from 2 to 8 Ag atoms. The correlation of emission energy with the number of atoms, N, in each gold nanocluster is quantitatively fit for the smallest nanoclusters with no adjustable parameters by the simple scaling relation of EFermi/N1/3, in which EFermi is the Fermi energy of bulk gold. The transition energy scaling inversely with cluster radius indicates that electronic structure can be well described with the spherical jellium model and further demonstrates that these nanomaterials are multi-electron artificial atoms. Fluorescence from these small metal clusters can be considered protoplasmonic, molecular transitions of the free conduction electrons before the onset of collective dipole oscillations occurring when a continuous density of states is reached. In addition, very strong single molecular Stokes and Antistokes Raman enhancement by fluorescent silver clusters was observed. Pushing to larger sizes, we also created ~ 2nm diameter glutathione encapsulated luminescent gold nanoparticles. Distinct from similarly sized but nonluminescent gold nanoparticles, these 2 nm gold nanoparticles show bright, long lifetime emission but no plasmon absorption. The emission might arise from charge transfer between gold atoms and the thiol ligand. Providing the missing link between atomic and nanoparticle behavior in noble metals, these highly fluorescent, water-soluble gold and silver nanoclusters offer complementary transition energy size scalings at smaller dimensions than do semiconductor quantum dots. The unique discrete excitation and emission and strong Stokes and antistokes Raman enhancement coupled with facile creation in aqueous solution open new opportunities for noble metal nanoclusters as biological labels, energy transfer pairs, and other light emitters in nanoscale electronics.

Kawasaki disease (KD) is the most common cause of paediatric acquired heart disease, which may be attributed to the combined effects of infection, immunological response, and genetic susceptibility. The most severe complication in KD is acute coronary artery lesions (CALs), including myocardial infarction and coronary artery aneurysms. Mounting evidence indicates that adhesion molecules and chemokines play an important role in inflammation and cardiovascular disease on basis of pathogenesis. Thus, this study aimed to investigate the association of seven single nucleotide polymorphisms (SNPs) of adhesion molecules and chemokines (P-selectin 290G>A, PSGL-1 62G>A, MCP-1 -2518A>G, SDF-1 -801G>A, PECAM-1 L125V, PECAM-1 S563N and PECAM-1 R670G) with the risk of KD, sequelae of CALs and initial intravenous immunoglobulin (IVIG) treatment failure. A total of 301 KD children (185 without acute and chronic CALs, 81 with acute but without chronic CALs, and 33 with acute and chronic CALs) and 246 sex-matched healthy controls were recruited in the case-control study. In addition, 166 cases from the above KD children and 332 parents were recruited to carry out case-parent trio study. We found that PECAM-1 3 SNPs polymorphisms were not associated with above several risks, except for CALs in chronic stage. As compared with non-Leu-Ser-Arg haplotype, Leu-Ser-Arg haplotype was associated with a significant increased risk for CALs in the chronic stage (AOR 2.50, 95% CI 1.05-6.00, P=0.039). Analyses based on the diplotypes of PECAM-1 also showed that Leu-Ser-Arg allele had a significant increased risk of CALs in chronic stage in dominant manner (AOR 2.98, 95% CI 1.15-7.72, P=0.024). In addition, carriers of Leu-Ser-Arg allele had significant increased counts of platelet (¡Ñ1000/Cumm) (672.6¡Ó207.6 versus 563.1¡Ó196.8; P=0.027) within 10 days of diagnosis of KD. Moreover, we also found a significant correlation between each SNP and polymorphonuclear neutrophil counts by genotype analysis. As for other genes, there were no markedly different outcomes regardless of the risk of KD, sequelae of CALs or initial IVIG treatment failure. In conclusion, the haplotype Leu-Ser-Arg of PECAM-1 is a genetic marker of susceptibility to sequelae of chronic CALs for KD patients. However, the role of PECAM-1 SNPs in CALs formation in the chronic stage in KD patients still needs further evaluation.

This dissertation employs the density functional theory (DFT) to investigate the oxidation of carbon monoxide (CO) on the W(111) surface and on the surface of Wn (n=10¡V15) nanoparticles. Since the properties of materials are significantly dependent on material size, we look into the influence of both the size and surface structure of tungsten catalysts on the CO oxidation process. The work contains two parts. Part 1: The adsorption and dissociation of O2 and CO on W(111) surface and Wn (n=10¡V15) nanoparticles. The chemical adsorption of O2 and CO on solid catalysts plays a very important role in heterogeneous catalysis for the CO oxidation reaction. The configurations, adsorption energies, vibration frequencies and electronic structures of adsorbates on W(111) and Wn (n=10¡V15) nanoparticles have been calculated to investigate their surface activity. The results indicate that adsorption of O2 and CO on Wn (n=10¡V15) nanoparticles are more stable compared to on the W(111) surface. The minimum energy pathways and transition states of chemical reaction processes on metal surfaces were also studied by the nudged elastic band (NEB) method. The dissociation barriers of O2 chemisorbed on Wn (n=10¡V15) nanoparticles are smaller those for the W(111) surface. Our results demonstrate that both the surface structure and size of metal significantly influence the adsorption and dissociation properties of adsorbates. Density functional theory-molecular dynamics (DFT-MD) simulation was also adapted to clarify the mechanism of O2 deposition on the W(111) surface. Observations of the variations of energy and bond lengths as a function of time show that the interaction between O2 and W atoms weakens the O¡VO bond, giving rise to the dissociation process. We conclude that the dissociation probability of an O2 molecule is affected by chemisorbed O2 coverage in the vicinity. Part 2: The mechanism of CO oxidation on W(111) and Wn nanoparticles. The oxidation of the CO molecule on transition metals usually follows two reaction pathways, either the Eley-Rideal (ER) mechanism or the Langmuir-Hinshelwood (LH) mechanism. In the ER mechanism, the CO molecule in the gas phase reacts directly with activated O2. The LH mechanism generally involves a few elementary steps, namely the co-adsorption of the O2 and CO molecules, O2 dissociation to form atomic oxygen, diffusion of atomic oxygen, and desorption of CO2. The oxidation of CO on a W10 nanoparticle surface and the W(111) surface are investigated by DFT calculations. Three pathways were studied in this dissertation: (i) CO + O2¡÷CO2 + O, (ii) CO + O2¡÷CO + O + O¡÷CO2 + O and (iii) CO + O¡÷CO2 via both LH and ER mechanisms. The calculated results show that CO oxidation on both the W10 nanoparticle and W(111) surfaces follow the ER rather than the LH mechanism. The CO oxidation on the W10 nanoparticle and W(111) surfaces occurs most easily via pathway (i) as compared to other two.

The work presented herein focuses on the synthesis and characterization of new cyanide bridged molecular magnetic materials that form discrete molecules as well as three dimensional networks. This research is inspired by the recognition that the Prussian blue (PB) family exhibits a wide range of interesting magnetic properties such as photomagnetism, spin crossover, and high TC magnets owing to the presence of the cyanide bridge that promotes magnetic communication between adjacent metal spins. An underexplored facet of this research is the systematic development of the topic with anisotropic metal ions research that was undertaken as part of this dissertation. The resulting discoveries are materials that exhibit a wide range of bistable magnetic properties, including photomagnetism, long range magnetic ordering, SMM, and exchange-biased SMM behavior. New Prussian Blue analogs are presented in Chapter II of this thesis that are based on the nearly unexplored hexacyanoosmate(III) ion. A family of CoII PB derivatives of OsIII were found to exhibit photomagnetic and charge transfer induced spin transition (CTIST) behavior and a study of alkali metal cation dependence revealed marked differences in both the photomagnetic and CTIST properties, with the highest ordering temperature being observed for the K+ analog which exhibits a TC of 28.5 K. The phenomenon of linkage isomerism reported for PB analogs and other molecular materials that incorporate the [Cr(CN)6]3- ion wherein the CN ligand reverses its binding mode between the two metal centers was studied in detail as described in Chapter III. Small molecule models that incorporate [Cr(CN)6]3- and CoII ions were investigated by single crystal X-ray crystallography, magnetism, and solution IR studies and the data led to useful mechanistic information about the nature of the cyanide reversal process. The use of the anisotropic hexacyanoosmate(III) anion to form a trinuclear species with MnIII was undertaken in the study described in Chapter IV. The first SMM based on the hexacyanoosmate(III) ion was discovered and found to exhibit a very rare exchange biased SMM phenomena in one of its crystal forms. In Chapter V new building blocks with the pentadentate MPPA ligand are described which are ideally suited for the preparation of a range of model compounds of the dinuclear and trinuclear variety.

We have constructed a single molecule detection system with the capability to simultaneously measure many parameters, including transient fluorescence intensity, fluorescence lifetime, and photon anti-bunching behavior via the Hanbury Brown-Twiss photon-correlation technique. In addition, we apply the system to study the single DiI (1, 1 '- dioctadecyl- 3, 3 , 3 ', 3 ' - tetramethylindocarbocyanine perchlorate) molecule, to characterize the photo-physical behaviors. Cyanine dyes are the molecules that constitute of two nitrogen centers, one of which is positive charged, and is linked by a conjugated chain with odd number of carbon atoms to the other nitrogen center. Cyanine dyes are interested in the photo sensitization, optical recording media, nonlinear optics, laser dyes, and many interesting photophysical and photochemical behaviors. Among them, DiI plays an important role in single molecule fluorescence investigations. The high photo-stability, good QE, and low inter-system crossing rates, make it a pioneer for the widely investigations in single molecule studies. Our experimental goal is to understand the characteristic of the monitored single molecule by the measuring photo-physical parameters. Our results include the typical behaviors in DiI molecules: clear on-off blinking, fluorescence anti-bunching, one-step photo-bleaching, and consistent fluorescence polarization orientation. In addition, we also observed some change during measurement, which indicates the corresponding change of structure. Few molecules also exhibit non-zero probability around the zero delay time, which indicates the simultaneous existence of more than one quantum emitters in the detected region. These results demonstrate that the parameters are essential for understanding and characterizing the observed molecules in single molecule level.

Clusters of metal ions that possess large numbers of magnetically coupled unpaired electrons have attracted much interest in recent years due to their fascinating magnetic behavior. With an appreciable component of magnetic anisotropy, these large-spin paramagnetic molecules can exhibit an energy barrier to inversion of their magnetic dipole, leading to spontaneous magnetization and magnetic hysteresis below a critical temperature. Since this behavior is a property of an individual clusters rather than a collection of molecules, this phenomenon has been dubbed ??Single Molecule Magnetism??. Our approach to the study of new high-spin systems has been to exert a measure of synthetic control in the preparation of clusters. Specifically we are employing highly anisotropic metal ions with the anticipation that these ions would engender large overall magnetic anisotropy in the resulting clusters. The first step in this process was the development of the chemistry of two new d5 ReII (S = ??) complexes, namely [ReII(triphos)(CH3CN)3][PF6]2 and [Et4N][ReII(triphos)(CN)3]. The magnetic, optical and electrochemical properties were studied and theoretical models were developed to describe the origin of the large temperature independent paramagnetism that was observed. Next, we successfully employed transition metal cyanide chemistry using the ReII building blocks to prepare a family of isostructural, cubic clusters of the general formula {[MCl]4[Re(triphos)(CN)3]4} M = Mn, Fe, Co, Ni, Cu, Zn whose 3d ions adopt local tetrahedral geometries. Within the clusters, magnetic exchange is observed between the paramagnetic ions, which has been modeled using an Ising exchange model to account for the dominating anisotropy of the ReII ion. Despite the high pseudo-symmetry of the clusters (Td), this work has yielded a rare example of a metal-cyanide single molecule magnet, {[MCl]4[Re(triphos)(CN)3]4} with an S = 8 ground state, D = -0.39 cm-1 and an effective energy barrier for magnetization reversal of Ueff = 8.8 cm-1. The elucidation of this family of isostructural clusters has also allowed us to pursue fundamental work on the structure/property relationships of the exotic, paramagnetic ReII ion. As the clusters are soluble, stable compounds, the future of this chemistry lies in the development of a true building-block approach to ??super-clusters?? that exhibit very high ground state spin values.

In this study, an electrokinetics-induced elongation flow was created inside a gradual converging-diverging microchannel with different temperature (25, 35, 45, 55¢XC). The conformation of DNA molecules, local strain rate, and the relaxation time play important roles in determining the extent of DNA stretching. By using £gPIV/£gLIF measurements, the velocity/temperature distributions in microchannels can be secured. The local strain rate was estimated by £gPIV measurements. We observe the hydrodynamic stretching DNA molecules in elongation flow by confocal laser scanning microscope (CLSM). Through CLSM images analysis, relaxation time of DNA molecules was estimated. Finally, dynamic properties and stretching ratio of DNA molecules stretched by EOF driven at various electric field and temperature ware measured. The thermal effect and the electric field on the conformation were also studied and discussed.

We have engineered a mutant of HIV Reverse Transcriptase that can be fluorescently labeled by covalent attachment of the environmentally sensitive fluorophore 7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)coumarin (MDCC). The result is a polymerase that is kinetically indistinguishable from the wild-type enzyme, but provides a signal to monitor changes in enzyme structure that result from conformational changes induced by substrate binding. Using this system, we have expanded the kinetic model governing nucleotide binding to include an enzymatic isomerization following initial nucleotide binding. In doing so, we define the role of induced-fit in nucleotide specificity and mismatch discrimination. Additionally, we have characterized the kinetics governing the specificity and discrimination of several widely administered Nucleotide Reverse Transcriptase Inhibitors (NRTI’s) used to combat HIV infection including 3TC (Lamivudine), FTC (Emtricitabine), and AZT (Zidovudine) for the wild-type polymerase and mutants with clinical resistance to these compounds. Our findings resolve the apparent tighter binding of these inhibitor compounds compared to the correct nucleotide by showing that the affinity for the correct nucleotide is stronger than the inhibitors. The apparent weaker binding of the correct nucleotide is a result of a incomplete interpretation of binding data that fails to account for the importance of the reverse rate of the conformational change. The apparent Kd (Kd,app) measurements for correct nucleotide estimates Km rather than Kd because nucleotide binding does not reach equilibrium. The conformationally sensitive enzyme has also been used to characterize the kinetics governing DNA association. We show that DNA binding is governed by a two-step process where a fast initial association is followed by a second, slow isomerization that is off the pathway for nucleotide binding and incorporation. Finally, we have implemented single molecule techniques using fluorophore labeled nucleotides to study the effects of AZT incorporation on the DNA translocation dynamics of the polymerase. We find that primer termination with AZT results in DNA that fails to translocate, therefore occluding the next nucleotide from binding. This shift in translocation equilibrium exposes the newly formed phosphodiester bond to ATP- or pyrophosphate-mediated AZT excision; thereby rescuing productive polymerization. This finding represents the first kinetic measurement of DNA translocation by a polymerase. / text