DNA sequences containing contiguous AA or TT mismatches, as well as sequences containing a 3-deazacytidine analogue were synthesized. Irradiation of anthraquinone abstracts an electron from the DNA. The loss of an electron from double-stranded DNA results in the formation of a radical cation that migrates through the DNA where it reacts irreversibly with H2O or O2 at GG steps. Subsequent treatment with piperidine or Fpg enzyme cleaves the backbone of the DNA at the site of reaction. DNA oligomers were designed to contain contiguous AA, TT, or G3-deazacytidine mismatches. It was revealed that the mismatches destabilize the duplex DNA; however, there is no measurable effect on the overall secondary structure of the DNA. The contiguous (AA)n mismatch, where n lt 7, was shown to have no effect on charge migration efficiency. In contrast, the contiguous (TT)n mismatch, where n gt 2, was shown to have near complete inhibition of charge migration through the mismatch region. Charge migration through the G3-deazacytidine mismatch was shown to have no effect on charge migration efficiency as well. Interestingly, reaction at the (G3-deazacytidine)2 base pairs revealed a change in the ratio of oxidative damage at the Gs. In (GC)2 base pairs, the ratio of damage at the two Gs is 10:1 with the majority of damage occurring at the 5-G. However, the (G3-deazacytidine)2 base pairs had an equal distribution of damage at the 5 and 3-Gs, with the amount of total reactivity equaling the (GC)2 base pairs. These findings indicate that the base composition in mismatched DNA determines the effect on charge migration efficiency and trapping reactivity.

Thermoresponsive polymers such as poly(N-isopropylacrylamide) (PNIPAM) have lower critical solution temperature (LCST) in aqueous solutions. Below the LCST, these polymers are hydrophilic with an extended coil conformation. Above the LCST, they undergo a sharp phase transition to form a collapsed hydrophobic conformation. The LCSTs are also affected by cosolutes and the effects of anions on LCSTs follow the Hofmeister series. We successfully used a simple digital melting point apparatus to study the effects of heating rates, solvent compositions, cosolutes, and redox state, on the LCSTs of thermoresponsive polymers. Moreover, the temperature range of the apparatus allowed for analyses at much higher temperatures and provides a simple way to examine irregular clouding behavior in more complex systems. Meanwhile, stimuli-responsive surfaces grafted with thermoresponsive polymers can switch from hydrophilic to hydrophobic thermally. As the LCST can be subsequently changed with the addition of salts, the salt effects on the wettability of these thermoresponsive surfaces will dramatically impact the surface performance. In this dissertation, I prepared PNIPAM/SiO2 nanocomposite surfaces by a covalent layer-by- layer assembly procedure and such surfaces were then used in studies of salts effects on surface wettability. Both the effects of anions and cations on the changes of advancing angles (Delta Theta a) of the PNIPAM/SiO2 nanocomposite surfaces were significant (Delta Theta a up to 90 degrees). The anion effects on the surface wettability followed the Hofmeister effect as expected. Parallel studies on solution showed that variation of cations had a large effect on the LCST of PNIPAM too. Moreover, analyses of the Theta a and LCST data using activity instead of using concentration showed different orders for the cation effects which were readily grouped by the cation charge numbers. No difference was seen for the anion effects in similar studies. AFM studies showed that surface morphology changes were correlated with the Delta Theta a.

Caffeine is a commercially important member of a group of purine alkaloids found in coffee, tea and cacao particularly. It is an important ingredient in beverages and most important chemical element of stimulating pharmaceuticals. Caffeine is either manufactured by total synthesis or as a by-product from the decaffeinated coffee manufacturing. To investigate the equilibrium relationship of caffeine in ion exchange systems, which are widely used for recovery and purification processes, was the aim of this study. The effects of initial caffeine concentration and pH of the solution on equilibrium were also investigated. Stock solutions of caffeine were prepared for screening of available adsorbents and cation exchange resins. A batch type operation was carried out in a shaker bath at 40 oC with 200 rpm agitation rate. After preliminary experiments, only Lewatit S100, which is a strongly acidic cation exchange resin with s-dvb copolymer matrix, was studied. For the analysis of samples, HPLC equipment with Shimadzu PDA Detector at 254 nm and Nucleosil 100 C18 column was used. As mobile phase, a mixture of 8% acetonitrile, 8% 2-Propanol, and 1% acetic acid was introduced at 1.5 mL/min flow rate. Results showed that, the caffeine uptake capacity of cation exchange resin was poor. A set of experiments were performed at three initial concentrations (0.005 M, 0.0075 M, and 0.01 M) and four different pH regions (acidic, slightly acidic, neutral, and basic). It was found that, at extreme pH conditions, the caffeine loading capacity of the resin was slightly increased. A significant effect of initial caffeine concentration, however, couldn&rsquo / t be observed. Due to the poor performance of gel type cation exchange resin and large molecular structure of caffeine molecule, Lewatit&rsquo / s SPC 112 macroporous resin was studied briefly for caffeine uptake performance. It was observed that SPC 112 has also poor but better loading capacity than S100 cation exchange resin.

The aim of the present study is to identify the di®erentially expressed genes be- tween two di®erent conditions and apply it in predicting the class of new samples using the microarray data. Microarray data analysis poses many challenges to the statis- ticians because of its high dimensionality and small sample size, dubbed as "small n large p problem". Microarray data has been extensively studied by many statisticians and geneticists. Generally, it is said to follow a normal distribution with equal vari- ances in two conditions, but it is not true in general. Since the number of replications is very small, the sample estimates of variances are not appropriate for the testing. Therefore, we have to consider the Bayesian approach to approximate the variances in two conditions. Because the number of genes to be tested is usually large and the test is to be repeated thousands of times, there is a multiplicity problem. To remove the defect arising from multiple comparison, we use the False Discovery Rate (FDR) correction. Applying the hypothesis test repeatedly gene by gene for several thousands of genes, there is a great chance of selecting false genes as di®erentially expressed, even though the signi¯cance level is set very small. For the test to be reliable, the probability of selecting true positive should be high. To control the false positive rate, we have applied the FDR correction, in which the p -values for each of the gene is compared with its corresponding threshold. A gene is, then, said to be di®erentially expressed if the p-value is less than the threshold. We have developed a new method of selecting informative genes based on the Bayesian Version of Behrens-Fisher distribution which assumes the unequal variances in two conditions. Since the assumption of equal variances fail in most of the situation and the equal variance is a special case of unequal variance, we have tried to solve the problem of ¯nding di®erentially expressed genes in the unequal variance cases. We have found that the developed method selects the actual expressed genes in the simulated data and compared this method with the recent methods such as Fox and Dimmic’s t-test method, Tusher and Tibshirani’s SAM method among others. The next step of this research is to check whether the genes selected by the pro- posed Behrens -Fisher method is useful for the classi¯cation of samples. Using the genes selected by the proposed method that combines the Behrens Fisher gene se- lection method with some other statistical learning methods, we have found better classi¯cation result. The reason behind it is the capability of selecting the genes based on the knowledge of prior and data. In the case of microarray data due to the small sample size and the large number of variables, the variances obtained by the sample is not reliable in the sense that it is not positive de¯nite and not invertible. So, we have derived the Bayesian version of the Behrens Fisher distribution to remove that insu±ciency. The e±ciency of this established method has been demonstrated by ap- plying them in three real microarray data and calculating the misclassi¯cation error rates on the corresponding test sets. Moreover, we have compared our result with some of the other popular methods, such as Nearest Shrunken Centroid and Support Vector Machines method, found in the literature. We have studied the classi¯cation performance of di®erent classi¯ers before and after taking the correlation between the genes. The classi¯cation performance of the classi¯er has been signi¯cantly improved once the correlation was accounted. The classi¯cation performance of di®erent classi¯ers have been measured by the misclas- si¯cation rates and the confusion matrix. The another problem in the multiple testing of large number of hypothesis is the correlation among the test statistics. we have taken the correlation between the test statistics into account. If there were no correlation, then it will not a®ect the shape of the normalized histogram of the test statistics. As shown by Efron, the degree of the correlation among the test statistics either widens or shrinks the tail of the histogram of the test statistics. Thus the usual rejection region as obtained by the signi¯cance level is not su±cient. The rejection region should be rede¯ned accordingly and depends on the degree of correlation. The e®ect of the correlation in selecting the appropriate rejection region have also been studied.

A redox flow battery (RFB) is an electrochemical energy storage device in which the storage medium is in the form of liquid electrolyte, which is stored in external reservoirs separate from the cell stack. The storage capacity of such systems is limited by the size of the external tanks, making the RFB an ideal technology for grid level energy storage. The vanadium redox flow battery (VRB) is a particularly attractive variant of the RFB, due to its use of a single transition-metal element in both the positive and negative electrolytes. However, the performance of the VRB is affected by the cross-over of electrolytes through the ion-exchange membrane which separates the positive and negative electrolytes. Cross-over causes degradation of energy storage efficiency and long term capacity loss. Previous studies of ion cross-over have focused primarily on the measurement of ion diffusion across ion exchange membranes in the absence of electrical current. In this work a novel VRB cell is described in which ion cross-over can be measured directly in the presence and absence of electrical current. Measurements are made of cross-over using this cell with three different types of ion exchange membrane in both charge and discharge modes. The results reported in this work show that the rate of ion cross-over can be greatly enhanced or suppressed depending upon the magnitude of the current flow and its direction relative to the ion concentration gradient. / text

The cation&ndash;&pi; interaction has been long-established to play an important role in molecular recognition, supramolecular chemistry, and molecular biology. In contrast, its potential application in small-molecule catalysis, especially as a selectivity-determining factor in asymmetric synthesis has been overlooked until very recently. This dissertation begins with an extensive literature review on the state-of-the-art research on the application of cation&ndash;&pi; interactions in non-enzymatic catalysis of organic and organometallic transformations. The research in this field has been largely inspired and guided by the related biosynthetic systems incorporating the same type of interactions.</p> / Chemistry and Chemical Biology

Bulky 1,4-diamines 1,2-[2,4,6-(CH3)3-C6H3NH-CH2]2-C6H4 and 1,2-(2,6-iPr2C6H3NHCH2)2-C6H4 were utilized as pro-ligands for the formation of novel three-coordinate aluminum alkyl compounds with the general formula [(1,4-diamido)AlR], where R = Me or Et. The synthesis of analogous aluminum hydrides was also explored resulting in the formation of four-coordinate complexes incorporating bridging hydrides. The three-coordinate aluminum complexes were developed as single-component catalysts in the ring opening polymerization of cyclic esters. The main focus was on caprolactone polymerization, but other monomers were explored, including lactide, butyrolactone, cis-cyclooctene, and diphenylacetylene. The mechanism of polymerization with caprolactone was also studied. The coordination chemistry of other metals and non-metals with the 1,4-diamido ligands were also investigated. Phosphorus, boron, zinc, and zirconium were the main focus. [(1,4-diamido)PCl] complexes were successfully synthesised as precursors to the formation of cationic phosphenium species, [(1,4-diamido)P]+.

The overall efficiency of photovoltaics is dictated by processes occurring within it. These processes include exciton formation, diffusion, dissociation and charge collection. This dissertation will focus around the fundamental issue of charge collection. In organic photovoltaics (OPVs) the rate of charge injection is dominated by the interaction between dissimilar materials, usually organic compound interacting with inorganic ones. In order to improve this rate of injection and, by direct consequence the efficiency of this process, fundamental knowledge of this organic-inorganic interface must be gained. In this work the focus will reside solely on creating molecules capable of probing the interface between the indium tin oxide (ITO) and the donor layer. At this interface, the usual charge transfer being transferred is the hole. Chapters 2 and 3 detail the synthesis and photophysical characterization of porphyrin-perylene diimide (Por-PDI) and porphyrin-fullerene (Por-C₆₀) molecular dyads. The idea behind these moieties is that covalent attachment of these species to ITO should lead to a robust ohmic contact. Since these molecular dyads are capable of producing charge-separated states after photoexcitation, they should have the capacity to produce a radical-cation in close proximity to the ITO. This will translate to a capacity for probing the dynamics of the hole injection at this interface. Studies performed demonstrate that in fact these dyads are capable of producing a charge-separated state upon photo-excitation. The lifetimes of these states were determine to be 35 ps and 3 ns for the Por-PDI and Por-C₆₀ respectively. Chapter 4 takes a different turn. It is focused on the application and extension of a solvent-free synthesis of metallated phthalocyanines (Pcs). Shown in chapter 4 is the synthesis of a series of metallated Pcs using various transition metals and group 3 elements. Photophysical and electrochemical investigation of these materials shows that they have near-infrared absorption and relative high HOMO levels making them potential candidates for OPV applications. In addition, they displayed non-linear optical behavior due to their highly polarizable pi-systems and the presence of axial susbtituents. Finally Chapter 5 describes the synthesis and characterization of porphyrin possessing rigid linkers. This chapter also shows the further directions in which the various ideas presented in this work could be driven.

Studies in this dissertation were conducted to explore the roles of organic cation transporters (OCTs) in the disposition of N-butylpyridinium Chloride (NBuPy-Cl) and structurally related ILs. Following a single i.v. dose to rats, the blood concentration of NBuPy-Cl and 1-butyl-1-methylpyrrolidinium chloride (BmPy-Cl) decreased in a biphasic manner with a clearance of 3.3 and 7 ml/min, respectively. More than 84% of dosed compounds were excreted in the urine. Depending on the vehicle, the dermal absorption of BmPy-Cl and NBuPy-Cl (5 mg/kg, 125 μg/cm²) was 10-35% at 96 h. Following a single oral (50 mg/kg) administration to rats, the maximum blood concentrations of both ILs were reached in less than 90 min in rats. Most of the orally dosed NBuPy-Cl (62-68 %) was excreted in the urine in 72 h. However, more of the dosed BmPy-Cl was eliminated in the feces Its oral bioavailability was only 47%. The elimination differences between BmPy-Cl and NBuPy-Cl were not altered by the size (0.5, 5, or 50 mg/kg) or frequency (1 or 5 administrations) of oral doses. In all urine and blood samples, only parent compounds were detected. Co-administration of NBuPy-Cl and inulin intravenously to rats revealed that the clearance of NBuPy-Cl exceeded the rat glomerular filtration rate, suggesting a renal secretion processing. The in vitro transport studies demonstrated that NBuPy-Cl, BmPy-Cl and 1-butyl-3-methylimidazolium chloride are substrates (Kt, 9~277 μM), as well as inhibitors (IC₅₀: 0.2~7.5 μM), of rOCT1/2 and hOCT2. Their inhibitory effects increased dramatically with increasing the alkyl chain length. The IC₅₀ values were 0.1, 3.8, 14 and 671 μM (hexyl-, butyl-, ethyl-pyridinium and pyridinium chloride) for rOCT2 mediated metformin transport. Similar structurally related inhibitory kinetics were observed for rOCT1 and hOCT2. In vivo co-administration of NBuPy-Cl prolonged the plasma half-life and reduced renal clearance of the diabetic drug, metformin. In summary, BmPy-Cl and NBuPy-Cl are partially absorbed from gastrointestinal tract. The present in blood is eliminated rapidly in the urine as parent, by renal filtration and OCT-mediated secretion. ILs also compete with other substrates of OCTs and have the potential to alter their pharmacokinetic profiles.

The effect of calcium uptake by hydration and diffusion from an adjacent calcium-rich soil on the performance of a geosynthetic clay liner (GCL) is examined for three cases. In Case 1 the GCL rested directly on a soil with a high calcium (1800 mg/l) concentration in the pore water (called “calcium rich soil” herein). Case 2 involved a GCL resting on 300 mm of soil with a low (200 - 300 mg/l) calcium concentration in the pore water (“foundation soil”) overlying the calcium rich soil. In the third (“control case”), the GCL only rested on the foundation soil. The overburden pressure was 15 kPa. The moisture content of GCL increased to 96%, 86% and 108% in the first 279 days for Cases 1, 2 and 3 respectively. Under isothermal conditions, the GCL moisture content decreased to 80% and 67% for Cases 1 and 2 respectively and increased to 113% for Case 3. After 1100 days, the hydraulic conductivity (k) of the GCL was 4×10-11 m/s for Case 3 but had increased up to about 7×10-11 m/s and 2×10-10 m/s for cases with and without the foundation layer respectively. The results are used to calibrate finite element models. A good correlation was found between k the bulk void ratio (eB) of GCL. Leakage and contaminant transport through 10 mm diameter hole in a geomembrane in a composite liner involving a GCL is examined at a stress of 100 kPa for hydraulic heads of 0.3 or 1 m. When permeated with distilled water, the interface transmissivity (θ) was about 2.3 × 10 11 m2/s. After 800 days of permeation with 0.14M NaCl there was only about 3% increase in the flow despite an order of magnitude increase in GCL permeability near the hole because θ decreased from 2.3×10-11 m2/s to 1.1×10-11 m2/s and controlled the leakage despite the increase in GCL permeability. Numerical modeling demonstrated reasonable agreement with the observed transport. / Thesis (Ph.D, Civil Engineering) -- Queen's University, 2010-09-09 12:20:42.298