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A novel methodology has been developed for the formation of block copolymers that combines ring-opening metathesis polymerization (ROMP) with functional chain-transfer agents (CTAs), functional chain-terminators (CTs) and self-assembly. Telechelic homopolymers of cyclooctene derivatives that are end-functionalized with hydrogen-bonding or metal-coordination sites are formed via the combination of ROMP with a corresponding functional CTA. These telechelic homopolymers are fashioned with a high control over molecular weight and without the need for post-polymerization procedures. The homopolymers undergo fast and efficient self-assembly with their complement homopolymer or small molecule analogues to form block copolymer architectures. The block copolymers have similar association constants to small molecule analogues described in the literature, regardless of size or the nature of the complementary unit or the polymer side-chain. The ROMP of side-chain functionalized norbornene polymers is coupled with functional CTs to produce block copolymer with main- and side-chain self-assembly sites. Combinations of these norbornene polymers with their complement polymer via self-assembly produce non-covalent AB type block copolymers fast and efficiently. ABA type block copolymers are realized by combining the difunctional homopolymer formed via the CTA pathway with the CT synthesized mono-functional polymer. These polymers show similar association constants regardless of the sequence of polymer formation.

In this paper, we discuss the effect of the hydrogen-bonding on the photoluminescent(PL) properties of 1-pyrenecarboxylic acid (PCA)/ poly(methyl methacrylate) (PMMA). Isolated fluorophore can be obtained when PCA molecules were blended and septrated by PMMA, i. e. excimer emission can be more efficiently prevented. With the use of non-solvent, toluene, in the preparation step, excimer emission of PCA can be more effeiciently prevented as compared to the good solvent, tetrahydrofuran(THF). With a high PMMA/PCA ratio of 1000/1, emission spectra show no sign of excimer formation. Intermolecular hydrogen bonding between PMMA and PCA helps to prevent the excimer formation. Solvents used in the preparative state play important role on the final PL properties of the solid film. In the blend, partial carbonyl groups in PMMA band with carboxylic acid group in PCA, this causes the appearance of a stretching band at 1718 cm-1 in infrared spectroscopy. The hydrogen-bond interactions help to the prevention of excimer formation in the PMMA/PCA blending systems.

Properly folded proteins are necessary for all living organisms. Incorrectly folded proteins can lead to a variety of diseases such as Alzheimer’s Disease or Bovine Spongiform Encephalitis (Mad Cow Disease). Understanding the forces involved in protein folding is essential to the understanding and treatment of protein misfolding diseases. When proteins fold, a significant amount of surface area is buried in the protein interior. It has long been known that burial of hydrophobic surface area was important to the stability of the folded structure. However, the impact of burying polar surface area is not well understood. Theoretical results suggest that burying polar groups decreases the stability, but experimental evidence supports the belief that polar group burial increases the stability. Studies of tyrosine to phenylalanine mutations have shown the removal of the tyrosine OH group generally decreases stability. Through computational investigations into the effect of buried tyrosine on protein stability, favorable van der Waals interactions are shown to correlate with the change in stability caused by replacing the tyrosine with phenylalanine to remove the polar OH group. Two large-scale studies on nearly 1000 high-resolution x-ray structures are presented. The first investigates the electrostatic and van der Waals interactions, analyzing the energetics of burying various atom groups in the protein interior. The second large-scale study analyzes the packing differences in the interior of the protein and shows that hydrogen bonding increases packing, decreasing the volume of a hydrogen bonded backbone by about 1.5 Å3 per hydrogen bond. Finally, a structural comparison between RNase Sa and a variant in which five lysines replaced five acidic groups to reverse the net charge is presented. It is shown that these mutations have a marginal impact on the structure, with only small changes in some loop regions.

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, August 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (p. 96-115).

Ongoing efforts to improve the efficiency of organic photovoltaic cells emphasize the significance of the architecture of molecular assemblies in thin films, at nanometer and micron length scales, to enhance both exciton diffusion and charge transport, in donor and acceptor layers. Controlled growth of molecules via self-assembly techniques presents new opportunities to develop nano-structured organic thin films for electronic devices. This thesis is focused on controlling the orientation of phthalocyanine molecular assemblies in thin films in order to demonstrate the impact of microscopic control of molecular order on electrical properties and organic solar cell device performance.The studies performed here provide insights into the self-assembling behavior, film morphology, nanoscale electrical conductivity, and photovoltaic properties of a disk-shaped peripherally substituted phthalocyanine (Pc) molecule possessing amide functional groups in the side chains. Amide functionality was integrated in the side chains of this phthalocyanine molecule with the purpose of increasing the intra-columnar interaction through formation of a hydrogen bonding network between molecules, and to guide columnar orientation in a preferred direction via specific surface-molecule interactions. It is realized that molecule-substrate interactions must dominate over molecule-molecule interactions to achieve control over the deposition of molecules in a preferred direction for organic solar cell applications. Microscopic imaging and spectroscopic studies confirm the formation of flat-lying, well ordered, layered phthalocyanine films as anticipated.The remarkable electrical conductivity of the flat-lying phthalocyanine molecules, as studied by Conducting tip Atomic Force Microscopy (C-AFM) provide the impetus for the formation of organic solar cells based on layers of these hydrogen bonding phthalocyanine molecules. The photocurrent from devices that are made with the ordered Pc molecules and disordered Pc molecules as the primary photoactive donor layer, and vacuum deposited C60 as the acceptor material, were evaluated. The results presented here demonstrate the feasibility of increasing the photogenerated current by controlling the molecular organization in the photo active layer.

Self-assembly is an efficient method for generating large numbers of structurally diverse catalysts for screening. In this work, the method of self-assembly was explored in the construction of bifunctional catalysts, from a chiral aminophosphine, 2-formylphenylboronic acid, and a (thio)urea-containing diol. These catalysts were evaluated by their effect on the asymmetric aza-Morita-Baylis-Hillman reaction. In the second half of this thesis, the hydrogen bonding abilities of different dithiosquaramides were analyzed. As thioureas have been shown to be stronger hydrogen bond donors than ureas, it was hypothesized that dithiosquaramides may also follow a similar trend. Affinities of corresponding squaramides and dithiosquaramides to chloride, sulfate, and tosylate were compared, as well as their abilities to catalyze the Freidel-Crafts alkylation between indole and trans-β-nitrostyrene.

Self-assembly is an efficient method for generating large numbers of structurally diverse catalysts for screening. In this work, the method of self-assembly was explored in the construction of bifunctional catalysts, from a chiral aminophosphine, 2-formylphenylboronic acid, and a (thio)urea-containing diol. These catalysts were evaluated by their effect on the asymmetric aza-Morita-Baylis-Hillman reaction. In the second half of this thesis, the hydrogen bonding abilities of different dithiosquaramides were analyzed. As thioureas have been shown to be stronger hydrogen bond donors than ureas, it was hypothesized that dithiosquaramides may also follow a similar trend. Affinities of corresponding squaramides and dithiosquaramides to chloride, sulfate, and tosylate were compared, as well as their abilities to catalyze the Freidel-Crafts alkylation between indole and trans-β-nitrostyrene.

The molecular conformations, potential energy functions and vibrational spectra of several cyclic molecules have been investigated by ab initio and density functional theory calculations and by infrared and Raman spectroscopy. The ab initio computations of 3-cyclopenten-1-ol predict that its lowest energy conformer has a weak pi-type intramolecular hydrogen bonding. The three other conformers lie 301 to 411 cm^-1 higher in energy. The infrared and Raman spectra of this molecule confirm the presence of the four conformers. The energy difference between the two conformers of lowest energy was also determined from the experimental spectroscopic data and was found to be 435 plus/minus 160 cm^-1, in reasonable agreement with the ab initio computations results. Ab initio calculations for cyclopentane and d1, 1,1-d2, 1,1,2,2,3,3-d6, and d10 isotopomers confirm cyclopentane confirmed that has twist and bent structures and that these differ in energy by less than 10 cm^-1. The bending angle is 41.5 degrees and the twisting angle is 43.2 degrees. A complete vibrational assignment for each of the isotopomers was achieved. Ab initio calculations were also carried out for methylcyclopropane, cyclopropylsilane, cylopropylgermane, cyclopropylamine, cyclopropanethiol and cyclopropanol. The structure and the potential energy function for internal rotation was calculated for each and compared to available experimental results determined from infrared and Raman spectra. The calculated barriers to internal rotation agree very well with the experimental data. The structures, relative energies, and frequencies for the lowest energy vibrations of the twisted, bent, and planar forms of cyclohexene and four of its oxygen analogs were calculated and compared to experimental results. The calculated structural data agree very well with that from the microwave work, but the computed barriers are somewhat lower than those based on far-infrared data. 4-Silaspiro-(3,3)-heptane possesses two four-membered rings, each puckered with and angle of 34 degrees. The molecule possesses a two-dimensional ring-puckering potential energy surface with four equivalent minima. The ab initio calculations predict a barrier to planarity of each ring of 582 cm^-1 while the energy of the structure with both rings planar is 1220 cm^-1 higher. The calculated infrared and Raman spectra were compared to those previously published, and the agreement is excellent.