Self-assembled monolayers (SAMs) derived from long chain alkanethiols are known to exhibit generalized trends as a function of chain length where n denotes the number of methylene units (CH2). For n 3, these trends are no longer manifest. It can be shown that SAMs of short chain lengths are much more affected by the presence and type of functional group. The reduction of electrochemically induced SAMs derived from cysteine (cys), cystine ((cys)2), mercaptopropionic acid (MPA) and mercaptoethylamine (MEA) from Au(111) highlight the effect of the two functional groups evaluated (R-CO2 - and R-NH2). The reductive desorption of these species was monitored by cyclic voltammetry and electrochemical impedance spectroscopy (EIS) in 0.1 M KClO4 and 0.1 M NaOH. The work presented herein demonstrates that under short time frames of immobilization, the presence of NH2 provides a stabilizing effect to the SAM. Cys and (cys)2 SAMs that maintain both functional groups are generally found to provide the lowest surface coverage under the short term conditions of assembly. The thiol derived monolayers (cys) are consistently higher packed than the disulfide SAMs iv from (cys)2 in both media evaluated. In 0.1 M NaOH however, cys coverage is consistent with coverages obtained from very long incubation times. In the presence of the strong base the disulfide species, (cys)2, desorbs at potentials that are always more positive than those of the thiol species (cys), further supporting poor monolayer formation. Additionally, these monolayers also exhibit the presence of two separate processes in 0.1 M KClO4, whereas only desorption is noted in 0.1 M NaOH. It is likely that a deprotonation of the amine group occurs prior to the desorption of the SAM. The SAM desorption occurs near -0.65 V vs. SCE, and the de-protonation at about -0.50 V vs. SCE. Since the monolayers formed from cys are better formed than those from (cys)2, this deprotonation is much more pronounced in the cys SAMs. The presence of only the CO2 - group (MPA) on the SAM, yields surface coverage that is intermediate compared to the bi-functionalized SAMs formed from cys and (cys)2 and the NH2 containing SAMs of MEA. In the potential region up to and prior to desorption, only one process is noted in both media. SAMs derived from MEA provide the highest surface coverage of the four species, approximating theoretical values. The presence of two surface species is observed in both media, as a result of trans and gauche binding. Of the four species evaluated, MEA appears to be most suitable for rapid SAM formation. The disulfide species, (cys)2, is found to be unsuitable for short-term preparation of SAMs.

A series of cyclophanedienes (CPDs) with different internal functional groups were synthesized. Dicyano CPD 85, cyano methyl CPD 127 and phenylethynyl/methyl CPD 138 were synthesized from bis-bromomethyl aromatics via a thiacyclophane- thiomethylcyclophane route. Diformyl cyclophanediene 152 and bis(hydroxymethyl) CPD 159 were obtained by the functional group transformation of CPDs 85 and 152 respectively. Cyclophanedienes with internal olefinic groups were obtained by three different routes: the best was the functional group transformations of the dicyano mercaptomethylcyclophane 99 followed by a Hoffmann elimination. Using the best synthetic route, CPDs with substituted vinyl groups such as alkylvinyl (162, 163, 178 and 198), butadienyl (184, 185 and 186), styryl (202, 203 and 204), nitro-substituted styryl (210, 211 and 212), methoxy-substituted styryl (218, 219 and 220) and methyl-substituted styryl (226, 227 and 228) were synthesized. Cyclophanediene 235 with an internal ethynyl (alkynyl) group was also synthesized by a similar synthetic route; however, it gave two major interesting side products; vinyl-ethynyl CPD 237 and vinyl-styryl CPD 240. The cyclophanedienes except dicyano 85, cyano-methyl 127 and diformyl 152 were converted to their corresponding dihydropyrenes both thermally and photochemically. Dicyano CPD 85 and cyano-methyl CPD 127 were converted photochemically to the DHPs 86 and 128, respectively. Diformyl CPD 152 underwent decomposition in any attempt to transform it into the DHP 154 either thermally or photochemically. Diphenylethynyl DHPs 141 and 247 were obtained by the Sonogashira coupling of diethynyl DHP 236. The Eglinton coupling reaction was used to achieve butadiynyl DHPs 257 and 254. Naphthoyl DHPs 248 and 250 were synthesized by the Friedel-Crafts acylation reaction of DHPs 179 and 167, respectively. All compounds were characterized by NMR, IR, and UV spectroscopy and mass spectrometry. Dicyano CPD 85 was quite stable towards thermal isomerization to the dihydropyrene 86 and showed a calculated half life of ~ 36 years (three orders of magnitude higher than that of benzo CPD 53 i.e., 7.3 days) at room temperature, whereas CPDs 127 (cyano methyl), 138 (phenylethynyl/methyl) and 152 (diformyl) showed half lives less than a month at 20 oC. Cyclophanedienes with internal ethynyl and substituted vinyl groups were quite stable thermally and showed half lives of several years (1-16 years) at room temperature. CPDs with cis substituted internal vinyl groups were thermally more stable than their trans counterparts. Electron withdrawing substituent (NO2) at the para positions of the internal styryl groups accelerate, whereas electron donating groups (MeO, Me) decelerate the thermal return reaction. Naphthoyl CPDs 249 and 251 isomerized at rates about 6-12 times faster than their non naphthoylated analogues 178 and 166 respectively. DHPs with internal ethenyl (167, 238 and 241), substituted ethynyl (139, 141 and 247) and trans substituted vinyl (199, 207, 215, 223 and 231) groups failed to open under visible light irradiation. Dicyano DHP 86, diethynyl DHP 236 and the unsymmetrical isomers of internal olefinic CPDs (206, 214, 222 and 230) formed photostationary states (pss). Disubstituted vinyl (179) and cis substituted vinyl DHPs (164, 205, 213, 221 and 229) opened completely; however their opening rates although faster than the parent 43, were 4-6 times slower than the benzo DHP 47. Introduction of an electron withdrawing substituent on the internal styryl group decelerated the visible opening reaction whereas electron donating groups accelerated it. 2-Naphthoyl divinyl DHP 250 opened at rates quite comparable to those of benzo DHP 47 whereas 2-naphthoyl diisobutenyl 248 opened about 25 times faster than the benzo DHP. The [1,5]-sigmatropic rearrangement of the internal nitrile (DHPs 86 and 128) and formyl (DHP 153) groups was observed. The sigmatropic rearrangement of the nitrile group in 86 was quite favorable in CDCl3 (Eact = 23.4 + 0.7 kcal/mol) compared to benzene (Eact = 28.6 + 1.2 kcal/mol). Formyl groups showed a much higher migration aptitude and Eact is estimated to be < 20 kcal/mol in any solvent. In this study, the best switch pair obtained was naphthoyl diisobutyl 248/249 which in comparison with previously the best switch pair 47/53 (benzo) showed much higher stability of the cyclophanediene (two orders of magnitude); moreover, the dihydropyrene opened about 25 times faster as well and is one of the best new photochromes yet.

A variety of highly hydrated ions were generated and studied using electrospray ionization mass spectrometry (ESI-MS) including proton, a series of triply charged lanthanide ions, the doubly charged lead ion and various methylated guanidinium ions. In each case large hydrated water clusters were mass selected and fragmented through collision induced dissociation (CID) to investigate their properties. The fragmentation of protonated water clusters highlighted the stability of the “magic” water cluster [H(H2O)21]+. Typically unstable triply charge lanthanide water clusters and the previously unobserved doubly charged lead water clusters were generated. Fragmentation studies indicated that both the charge density and the geometry of the clusters affect their stability. The charge reduction of triply charged lanthanide clusters led to the direct observation of ion evaporation. Finally, the dehydration of various methylated guanidinium ions indicated a structural basis for differences in their ability to hydrogen bond.

The synthesis, characterization and self-assembly behavior of semiconductor quantum dots (QDs) with mixed polystyrene (PS) / poly (methyl methacrylate) (PMMA) polymer brush layers (PS/PMMA-CdS) are described. The environmentally-responsive PS/PMMA-CdS nanoparticles are investigated in various solvents with different polarities. Static and dynamic light scattering results suggest conformational changes in the mixed brush structure in response to different solvent polarities. UV-vis and photoluminescence spectra show that QD sizes and optical properties are independent of the solvent medium due to protection by the block copolymer. Long-term stability of QD size distributions in the studied solvents is demonstrated for period of up to six months. 2D 1H NOESY experiments indicate that PS and PMMA coronal chains are statistically distributed around the QDs within the mixed brush layer. PS/PMMA-CdS nanoparticles are also shown to self-assemble at the polymer/polymer interface of a phase-separating blend of the corresponding homopolymers, forming an encapsulating shell surrounding PMMA islands in a PS matrix. The segregated QDs regulate phase separation during spin-coating and dramatically stabilize the spin-coated blend morphologies during subsequent annealing. Free-standing arrays of QD/polymer rings are developed by selective solvent washing and removal of homopolymers from the spin-coated films. After converting the PMMA coronal chains to poly (methacrylic acid) (PMAA) via a hydrolysis reaction, the resulting amphiphilic PS/PMAA-CdS nanoparticles are found to show rich and tunable self-assembly behavior in mixtures of organic solvents and water. The block copolymer-like self-assembly behavior of PS/PMAA-CdS suggests phase separation of randomly-distributed PS and PMAA chains within the mixed brush structure, leading to anisotropic interactions between nanoparticles mediated by energetic contributions from interfacial tension and chain stretching. As a result, PS/PMAA-CdS forms a wide range of interesting colloidal superstructures, including spherical supermicelles, worms, and vesicles, all with well-defined internal organization of QDs. Based on annealing experiments at a relative low water content above cwc, a mechanism of the formation of worm-like and continent aggregates is proposed. Thermodynamic and kinetic aspects of formation of the various QD/polymer colloids are also described.

The study of interfacial processes has long been of interest to scientists. The properties of a material are generally governed by the characteristics of its surface, thus the development of surface specific experimental methods are always of great importance to the scientific community. This thesis presents the results of the spectroelectrochemical characterization of a cysteine-Ag adsorbate-substrate system. The system was probed using two spectroelectrochemical methods. The chiral effect which cysteine has on the electronic structure of the Ag substrate was studied by performing in situ second harmonic generation optical rotatory dispersion (SHG-ORD) experiments. Rotation angles (phi) obtained indicated that the overlayers of adsorbed cysteine molecules imprinted the electronic structure of the Ag with their inherent optical activity. Results also indicate that there are one or more other processes which are contributing to the observed phi values. The second half of this thesis discusses the effect that pH and applied potential have on the adsorption geometry of L-cysteine on polycrystalline Ag as studied by surface enhanced Raman scattering (SERS). Results obtained under neutral and acidic conditions showed that the coadsorption of Cl- plays an important role in the adsorption geometry. At more positive potentials Cl- will be coadsorbed on the Ag surface with cysteine. The Cl- helps to stabilize the adsorbed cysteine via interactions with the protonated amino group. Consequently, as the potential is changed in the cathodic direction the Cl- becomes desorbed from the surface, resulting in changing intensities observed in the SERS spectra. Tracking of which peaks, and consequently vibrational modes, are changing and in which way allowed for a qualitative determination of the adsorption geometry as a function of both pH and potential.

The self-assembled complex (Pden)4(bipy)4+8 is potentially suited as a portal for synthetic ion channels (Pden = (1, 2-ethylenediamine) Pd(II), bipy = 4, 4'-bipyridine). This thesis examines the solution speciation of mixtures of Pden and bipy and the ion channel activity of the proposed channel. A model which describes the concentration of the species in solution as a function of pH and Pden:bipy ratio was developed. The method determines the solution speciation by solving the mass balance equation for each species using the total concentration of Pden, bipy and H+ and the cumulative formations constants for species in solution. This model is general and can be applied to other systems provided that the cumulative macroscopic formation constants (logßpbh) of the species are either known or can be estimated. The cumulative macroscopic formation constant for a species is determined by an additive free energy process as the sum of the logarithms of a microscopic formation constant (logß'pbh) and a statistical factor (logY). Values for logß'pbh were estimated using stepwise formation constants (logK) for model systems which were determined by potentiometric titration. Values for logY were calculated from the symmetries of the species. The model calculates the concentration of each species as a function of pH and Pden:bipy ratio to give a map of the species and their relative concentrations. The model shows that (Pden)4(bipy)4 is the single most abundant species between pH = 4 and 7 and a Pden:bipy ratio of 1:0.4 to 1:6. Under optimum conditions, (Pden)4(bipy)4 holds a maximum of -80 % of the total Pd in solution when the total [Pd] = 1 x 10-5 M. The apparent equilibrium constants for 2.(Pden)(bipy)2 = (Pden)2(bipy)3+bipy and 4.(Pden)(bipy) = (Pden)4(bipy)4 were -0.6 and --106, respectively, at Pden:bipy = 1:1 and pH = 7. The model also permits analysis of the relative rates of formation of (Pden)4(bipy)4 from a number of different precursors. The dominant stepwise processes for the formation of (Pden)4(bipy)4 are dimerization of (Pden)2(bipy)2, addition of Pden to (Pden)3(bipy)4 and addition of (Pden)2(bipy) to (Pden)2(bipy)3. Other possible pathways to (Pden)4(bipy)4 involve less abundant species so are disfavored. Lipophilic derivatives of Pden (PdenR) were synthesized from 1-bromodecane or 1-bromohexadecane and solketal in 30 % and 23 % overall yield, respectively. The complex PdenR was reacted with bipy in acetonitrile and the resultant solution was then tested for ion channel activity using the bilayer clamp experiment. The decyl derivative (R = C10H21) was inactive but a range of activity which include erratic behaviors, short openings and Iong openings were observed for the hexadecyl derivative (R = C16H33) using the bilayer clamp technique. Erratic openings were observed before all short and long openings, but were also observed independently. Hille pore radii, calculated from the observed conductances, were between ˜ 1 and 6.5 Å for the rare short openings. The Hille radii for long opening pores were between ˜1 and 14 Å and these pores did not show any ion selectivity. Channels that exhibit long opening activity were also observed in the absence of Pden:bipy. The large Hille radii and activity in the absence of bipy indicate that the proposed (PdenR)4(bipy)4 channel did not form possibly because the local concentration of bipy was not high enough to compete with the lipid for coordination sites on PdenR. The implications of these findings for self-assembly of ion channels in lipid bilayer membranes are discussed.

The ING (INhibitor of Growth) tumor suppressor genes are conserved from yeast to humans and are implicated in several processes important to cell proliferation and apoptosis. ING proteins contain a plant homeodomain (PHD) finger that suggests these proteins may modulate transcription factor-mediated pathways. Little is known about the mechanism of action of INGs, especially in the context of normal development. The ING family of proteins includes at least five different genes, ING1-ING5, with evidence for alternate promoter usage and splicing that generate multiple isoforms. To elucidate the role of ING in different tissues to modulate function, I used amphibian metamorphosis as a model system in which a single stimulus, thyroid hormone (TH), initiates apoptosis, proliferation, and remodeling in the tail, hindlimb, and brain, respectively. I discovered seven ING1 and three ING2 transcript variants in Xenopus laevis and investigated their expression patterns. High expression levels of most variants were found in adult brain, testis, and eye. During natural metamorphosis or precocious metamorphosis induced by treating tadpoles with exogenous TH, ING1 and ING2 transcript variant levels were differentially regulated in a tissue-specific manner. Some variant levels increased with the induction of apoptosis of the tail, while levels of the same variants decreased upon induction of proliferation and differentiation in the hindlimb. Although levels of all INC variants were relatively high in whole brain, they did not change during metamorphosis or TH treatment. Given that ING has previously been shown to modulate apoptosis, it is likely that upregulation of specific isoforms may contribute to the tissue-specific TH-mediated response in the tail, and that downregulation facilitates proliferation of the hindlimb. To further investigate the hypothesis that ING is regulated by TH, an analysis of 1NG1 and ING2 genomic sequences was carried out. Promoter sequences for each variant were determined and putative thyroid hormone response elements (TREs) located. To test whether thyroid hormone receptors associate with these elements, chromatin immunoprecipitations (ChIP) assays were done on tail homogenates from premetamorphic tadpoles treated with TH or vehicle control. Both thyroid hormone receptor α (TRα) and thyroid hormone receptor β (TRβ) differentially associate with ING1 and ING2 promoter regions. TR association increased significantly on promoters for ING variant transcripts that increase upon TH treatment, and decreased significantly on promoters for ING variant transcripts that decrease upon TH treatment. ChIPs also showed that ING associates with TH-regulated promoters including TRβ, TH-Responsive Basic Leucine Zipper Transcription Factor (TH/bZIP), ING1 and ING2. Furthermore, TR and ING were shown to co-immunoprecipitate with both purified proteins and using total tail homogenates from metamorphic tadpoles. The antibodies used for these experiments were made against Xenopus TRβ and ING2 and were characterized as part of this thesis. Bioinformatics revealed that TREs are present in promoters of ING genes for other species including human, mouse, and a related frog species, Xenopus tropicalis; therefore, it is likely that modulation by TH is a conserved mechanism of ING regulation. These data suggest that there may be antagonistic regulation of ING transcript variants by TH that correlates with tissue fate. TRs associate with ING promoters, and ING is associated with TR-regulated promoters. Moreover, TR and ING proteins co-immunoprecipitate. It is therefore likely that TR and ING are co-regulators of gene expression during TH-dependent tadpole metamorphosis. This thesis contributes to the understanding of ING which is relevant to elucidating many disease states, as well as being critical in understanding the role of this tumor suppressor in the context of TH regulation and normal development.

Several photochromic dihydropyrenes were designed to test whether the DHP molecule retains its response to light when it is bound to the first row transition metals. DAP 26, NDAP 22 and BDAP 21 were composed of the parent DHP 11, naphthoyl-DHP 38 and the BDHP 12 fragments respectively that were bound via a Sonogashira coupling to the phenanthroline unit through an acetylene linker. A condensation reaction between DHP-imid 29 and BDHP-imid 50 with phenanthroline diketone 28 in the presence of an excess of NH4+OAc- yielded the imidazole functionalized dihydropyrenes DHP-imid 23 and BDHP-imid 24 respectively. PDD 25 which is a [e]pyrazino annelated DHP 11 was obtained from condensation of the DHP-diamine, generated in situ from its dinitro precursor 45, with phenanthroline diketone 28. Compounds 21, 24 and 25 responded reversibly to UV and visible irradiation while also undergoing thermal return. NDAP 22 decomposed upon exposure to UV while being converted from its open to the closed state. Acac and hfac complexes of BDAP 52-55 and of PDD 60-61 were synthesized by reacting Co(acac)2(H2O)2 51 and M(hfac)2 59 (where M = Co2+, Mn2+, Ni2+) with one equivalent of either BDAP 21 or PDD 25 photochrome respectively. Co(acac)2(BDAP) 52 and Co(acac)2(PDD) 60 complexes showed reversible opening and closing under alternative UV and visible irradiation for at least 10 cycles. Mn(hfac)2(BDAP) 53, Ni(hfac)2(BDAP) 54 and Co(hfac)2(BDAP) 55 complexes opened upon exposure to visible light and then closed with heating in the dark. Thermodynamic parameters ΔEact, ΔH‡ and ΔS‡ were determined after fitting the closing rate constant data for each species at 54, 64 and 74 °C (unless stated otherwise) to Arrhenius and Eyring equations.

Variable temperature ESR studies of radicals generated photolytically from simple aliphatic alcohols and ethers in cyclopropane solution reveal complex linewidth effects. Isotropic modulation of the proton hyperfine splittings (hfs) through restricted rotation about C-0 and C-C single bonds is observable in the region 230>T>150K. Such effects can be distinguished from anisotropic viscosity-dependent line broadening. In spectra from alcohol radicals resolved 2nd order structure causes no ambiguity in the interpretation. Restricted rotation about Ca-0H modulates aaH and aBH out-of-phase with a0H in the series RCHOH [R= CH3, C2H5, C2H5CH2, (CH3)2CHCH2, (CH3)3CCH2]. A general model for the process is discussed. In cases three and four restricted Co-C rotation allows the diastereotopic inequivalence of the 6-protons to be manifested as a broadening of MB = 0 components. Preferred conformations consistent with all the foregoing modulation effects and with observed HB and HY splittings are presented. The analysis is supported by results for radicals RCHOR' from related ethers and by spectral simulation. The spectrum of the 1-hydroxycyclohexyl radical demonstrates previously unobserved fine structure and a low-temperature linewidth effect tentatively attributed to radical site inversion. A second series of alcohol-derived radicals R1R2R3CCHOH with an increasingly bulky Ca substituent has been studied. The Ha hfs provide evidence of a steric flattening not hitherto observed. This effect correlates well with literature values of steric parameters for the R1R2R3C substituent. In the case R1,R2 = CH3, R3 = C2H5 an observed specific y-H interaction is assigned to a locked conformation of the crowded system. A series of highly alkylated cyclic ethers has been examined. The dramatic temperature-dependent changes in the spectrum of the 5,5-dimethyl-l,3-dioxan-2-yl radical are attributed to restricted ring flipping. A fast exchange limit spectrum has been obtained for the first time in such systems, allowing evaluation of thermodynamic parameters. the 2,4,8,10-tetraoxyspiro[5,5]undecan-3-yl radical exhibits similar behaviour. The 2,2,5,5-tetramethyl and 5,5-diethyl-2,2-dimethyl-l,3--dioxan-4-yl radicals have fixed conformations which give rise to enhanced values of ayH in agreement with theoretical calculations. In the latter case a splitting of 4.27 G is assigned to a single y-methylene proton in behaviour analogous to R1R2R3CCHOH.

The renin-angiotensin-aldosterone system (RAAS) plays an essential role in maintaining plasma volume and arterial blood pressure by regulating angiotensin II levels. Dysregulation of the RAAS can result from an underlying disorder that results in a severe and untreatable form of hypertension, known as secondary hypertension. Measurement of plasma renin activity is a commonly employed method of diagnosing secondary hypertension. Plasma renin activity is quantified by determining the amount of angiotensin I generated through the enzymatic cleavage of angiotensinogen by renin. Radioimmunoassay is routinely used to measure plasma renin activity, however there are limitations to the method. With the prevalence of hypertension on the rise, there is need for a more accurate and rapid method of assessing the RAAS for diagnostic purposes and therapeutic monitoring. Multiplexed measurement of angiotensin I and angiotensin II would provide comprehensive understanding of the RAAS by determining dysregulation in the production of either molecule. In this thesis, the relationship between endogenous angiotensin I concentrations and plasma renin activity are studied in order to examine the research hypothesis that measurement of angiotensin I concentration correlates with plasma renin activity and whether this may provide a more accurate and rapid method of screening for hypertension when multiplexed with angiotensin II. To overcome the current limitations of radioimmunoassay for measuring plasma renin activity, a mass spectrometric-based method was developed to measure angiotensin I and plasma renin activity. Evaluation of the assay against radioimmunoassay demonstrates that the assay is reproducible and provides a linear response over a diagnostically relevant concentration range. Comparison of endogenous levels of angiotensin I with normal plasma renin activity levels show a correlation in this study (R=0.74). Comparison of plasma renin activity values by radioimmunoassay and iMALDI also show correlation (R=0.98), indicating that the iMALDI assay may provide an improved method for diagnosing secondary hypertension.