Two new, highly base-labile urethane-based $\alpha$-amino protecting groups were examined for their utility in peptide synthesis. The first such system examined, 3H-benz(e)indene)-1-methoxycarbonyl (eBimoc) 59, was synthesized from 1H-benz(e)indene 60 for which a practical large-scale synthesis was developed. Treatment of an eBimoc protected model amine shows that both deblocking and by-product scavenging are much faster than for the corresponding 9-fluorenemethoxycarbonyl derivative (Fmoc) 3. Unfortunately eBimoc protection proved to be too sensitive for general use in peptide synthesis as significant decomposition was noted even in the absence of base in the commonly used solvent DMF. The system was stable in the non-polar solvent CH$\sb2$Cl$\sb2$ but this limitation suggested a search for a more appropriate group of this type. The desired properties were found in the case of the benzo(b)thiophenesulfone-2-methoxycarbonyl (Bsmoc) group 47 which has previously been used for peptide synthesis but only under standard Fmoc conditions in spite of the fact that the Bsmoc residue is far more sensitive to base than the Fmoc group. It has now been found that with Bsmoc protection very short deblocking times and very dilute solutions of organic amines are of practical utility for solid phase syntheses. Methods were developed for the loading of a range of Bsmoc amino acids onto normal resins for the assembly of peptide acids or peptide amides. Monitoring techniques were developed in anticipation of executing automated syntheses. Several model peptides including leucine enkephalin, acyl carrier protein (65-74), and the 1-6 fragment of toxin #2 of the scorpion Androctonus Australis Hector (Val-Lys-Asp-Gly-Tyr-Ile) were assembled. The last-named sequence is known to suffer formation of aminosuccinimide side products upon application of Fmoc chemistry. Such side reactions could be reduced by application of the Bsmoc group. A general protocol for the use of Bsmoc protection involved deblocking via 2% piperidine for 5 minutes, a method which gave good results for all three model sequences. In addition to switching to lower concentrations of piperidine for deblocking, one could shift to weaker bases such as morpholine to avoid problems arising from the presence Asp-Gly and related sequences.

Flavoenzymes mediate a large number of oxidation and reduction reactions throughout nature. This wide variety of catalytic transformations is accomplished by virtue of a versatile flavin cofactor (usually FAD or FMN). The variety and nature of each individual non-covalent interaction has a specific effect on cofactor binding and reactivity. These non-covalent interactions are studied in the oxidized and one electron reduced states using model compounds to replicate enzymatic interactions. The effects of hydrogen bonding and aromatic stacking were examined in the oxidized and reduced states. The flavin undergoes hydrogen bonding to the oxidized state and is governed mainly by hydrogen bond donor ability and sterics of the model receptor. Hydrogen bonding is significantly enhanced in the one electron reduced state indicating selective recognition by hydrogen bonding of the reduced state with respect to the oxidized flavin. Aromatic stacking recognizes (binds) strongly the oxidized flavin and increases with increased aromatic overlap of flavin and aromatic stacking group. Reduction of the flavin is disfavored by aromatic stacking and thus reduces the association of the model receptor with the reduced flavin (as compared to association with the oxidized flavin.) A model for electrostatic interactions with the pyrimidine of flavin is examined. When linked to a primary recognition unit, electrostatic moieties (heteroatoms) are found to interact favorably with the electron deficient flavin. These interactions are a model for the positioning of main chain carbonyl groups in close proximity to the flavin aromatic face. Size and polarizability of the heteroatom governs the strength of interaction while reduction of the flavin has a mitigating effect. The electrostatic surface of the flavin is not uniform and distinct areas of this surface are found to interact differentially with dipoles. Positioning of the dipole with respect to the quadrupole of the flavin is found to modulate recognition of the flavin by approximately 0.5 Kcal/mol. Many of the reactions that flavoenzymes catalyze are the conversion between thiols and disulfides. A model for the interaction of thiols and disulfides with the flavin is developed. Preliminary results of these studies are discussed.

Organic photovoltaics (OPVs) that have been studied to date have poor power conversion efficiencies. This dissertation focuses on various molecular designs that could lead to both a fundamental understanding of photoinduced charge separation at a molecular level and also provide a solution to improve bulk properties of organic materials to overcome the poor efficiencies of OPV devices. The effect of molecular architectures on the efficiency of electron transfer, a primary step in OPVs functioning, is evaluated in this work. We have shown that even though dendrimer provides an interesting architecture for efficient electron transfer due to the presence of multiple peripheries around a single core, this architecture leads to trapping of charge at the dendritic core. This results in a decrease in the electron transfer efficiency in solution and also limits the possibility of charge transport to the electron in a photovoltaic device. Non-conjugated polymers containing conductive EDOT units at side chains were also designed and synthesized. The frontier energy levels of these polymers can be easily tuned by changing the conjugation lengths of side chain EDOT oligomers. Moreover, by incorporating crosslinkable units as co-side chains, the absorption bandwidth of these polymers can be manipulated as well.

This work involves syntheses, characterization and electronic spectroscopic study of PPE-related segmented oligomers with and without pendant hydroxyl groups (“sticky” groups). The crystal organization of the molecules was studied and, as much as possible, correlated with their optoelectronic properties. Multi-step syntheses using Sonogashira coupling methodology was used to make all the final molecules. Synthesis, characterization and electronic spectroscopic studies were carried out for the following systems having hydroxyl-pendant sticky groups: 1,4-bis(phenylethynyl)-2,5-bis(2-hydroxyethoxy)benzene, BHE-PE2.5; 2,5-bis(2-hydroxyethoxy)-1,4-bis(3,4,5-trimethoxyphenylethynyl)benzene (B6OMe-PE2.5); 2,5-bis-(2-hydroxyethoxy)-1,4-bis-(4′ -biphenylethynyl)-benzene (BHE-PEBP2.5). A number of model or synthetic intermediate systems were made having the same chromophores as the sticky group systems, but with hydroxyl being protected or replaced with a non-hydrogen-bonding group: 1,4-dimethoxy-2,5-bis(2-phenylethynyl)benzene, BOMe-PE2.5; 2,5-bis(2-acetoxyethoxy)-1,4-bis(phenylethynyl)benzene BAc-PE2.5 (a diacetate analogue of BHE-PE2.5); 2,5-bis-(2-acetoxyethoxy)-1,4-bis-(4 ′-biphenylethynyl)-benzene (BAc-BPE2.5). All the PE oligomers have two UV-vis absorbance bands, one in 304-320 nm and other in the 350–370 nm region. Fluorescence emission is found in the 390–400 nm region upon excitation at various wavelengths. Fluorescence quantum yields in acetonitrile at room temperature range between 0.50-0.92. B6OMe-PE2.5 has the highest quantum efficiency, which may be attributed to the methoxy end groups. BHE-PE2.5 crystallographically packs with its central phenyl rings criss-cross stacked along the π stack axis, potentially yielding crossed-dipole interactions. This type of packing motif is unusual and potentially interesting for electronic purposes. The addition of an extra phenyl ring in BHE-PEBP2.5 disrupts the criss-cross π-stacking motif. The addition of methoxy groups in B6OMe-PE2.5 provided additional hydrogen bonding receptor sites, which also disrupts criss-cross π-stacking. LED devices with configuration ITO/PEDOT-PSS/emitter/Ca(Al) were fabricated by Dr. Ali Cirpan of Karasz group in Polymer Science and Engineering Department using all the oligomers as emissive layers. All except B6OMe-PE2.5 showed electroluminescence. The most promising results by far among these were obtained for BOMe-PE2.5 in terms of luminescence efficiency (0.55 cd/A) and strength, probably because its crystallography does not include π-stacking. Alternating block copolymer analogues of model compound BHE-PE2.5 were synthesized by step growth polymerization with bis acid chlorides. Poly-Terphthaloyl PE, Poly-Isophthaloyl PE, Poly-Oxaloyl PE and Poly-Adipoyl PE degrees of polymerization ranging from 2-10 based on GPC analysis. These systems exhibited electronic spectra similar to their molecular analogues, but were not effective as emissive layers in our typical LED configuration. 2,5-Bis[2-{2-(4-pyrenebutyryloxy)-ethoxy}-ethoxy]-1,4-bis[2-phenylethynyl]benzene PE-Py8 was synthesized from BHE-PE2.5 as an energy transfer multichromophore. This study aimed to provide insights for possible efficient energy harvesting using phenyleneethynylene as an energy acceptor core unit. Its solution photophysical properties showed dominant energy transfer from pyrene antennae to central chromophore on direct excitation of pyrene with an efficiency of ηET=42% in chloroform. 2,7-Bis(3,4,5-trimethoxyphenylethynyl)fluorene OFPE was synthesized and characterized with the objective to achieve blue fluorescence emission and provide extra photostability compared to its 1,4-phenylenevinylene analogue (OFPV) having same end groups but olefin linkers instead of alkynes. OFPE exhibited good photoluminescence quantum yield in solution (0.72 in acetonitrile) with strong blue emission having CIE color coordinates of (0.166, 0.108). Its LEDs with the above-stated configuration had good solid state luminescence at 430 nm with a maximum efficiency of 0.42 at 10 V using an emitter layer made of a 50% (w/w) blend with PMMA.

Self-assembly of nanoparticles present an excellent tool to bridge the gap between the synthetic "bottom up" and lithographic "top down" approaches. Nanoparticles provide versatile tools for materials applications as they feature unique electronic, magnetic and optical properties associated with their core material. The present study utilizes the 'bricks and mortar' method, where dendrimers and proteins were used as mortar' and nanoparticles as 'bricks'. Non-covalent assembly mechanisms were used in exploring nanocomposite structures such as morphology, spacing, and achieving materials with tunable properties. The nanoparticles were synthesized and assembled with a series of dendrimer generations and various proteins providing a systematic increase in interparticle spacing. The modulation of optical and magnetic properties based upon the type of spacer was studied. In addition, we sought to incorporate inherent protein function into the nanoparticle ensembles, thereby greatly expanding the scope for development of new functional materials. The collective optical or magnetic response of the nanocomposite with tunable properties paves the way for the creation of new novel functional materials.

Directed assembly provides a method to generate nanoscale materials with intrinsic electronic, optical, and magnetic properties. The approach combines self-assembly (bottom-up approaches) with current top down techniques to create nanoscale materials. Noncovalent interactions, such as hydrogen bonding, electrostatics, and π-stacking, can be used spatially to guide molecules into supramolecular or nanoscale complexes. This thesis demonstrates new nanofabrication methods, starting with relatively simple interactions, such as host-guest chemistry, and proceeding to more complex nanoscale materials. Chapter 1 provides a general overview of the motivation behind nanofabrication techniques. Chapter 2 provides a fundamental understanding of noncovalent interactions and their use within bottom-up approaches. Chapter 3 cites specific host-guest chemistry of an azobenzene flavin moiety that tunes the optical properties of the push-pull system. Chapter 4 provides a method to assemble organic nanowires through cooperative dipolar and hydrogen bonding interactions. And finally, Chapter 5 facilitates the combination of bottom-up and top down approaches by introducing nanoimprinted polymer patterns as self-assembly templates.

We have developed copper-catalyzed cross-coupling reactions for the formation of carbon-carbon and carbon-sulfur bonds. These newly developed methods demonstrate that the conditions of the traditional Ullmann reaction can be improved. We describe the synthesis of diarylacetylenes through the cross-coupling of aryl iodides and phenylacetylene using [Cu(phen)PPh 3Br] as the catalyst. This method is then utilized for the synthesis of 2-aryl-benzo[b]furans via a copper-catalyzed cross-coupling reaction between aryl acetylenes and 2-iodophenols and a subsequent 5-endo-dig cyclization. The formation of carbon-acetylene bonds is also extended to include vinyl iodides for the purpose of synthesizing 1,3-enynes. Due the lack of a general metal-mediated synthesis of aryl sulfides, we developed a copper-catalyzed cross-coupling reaction between aryl iodides and thiols using a catalytic amount of CuI and 2,9-dimethyl-1,10-phenanthroline as an additive. This method was also extended to include vinyl iodides for the synthesis of vinyl sulfides using [Cu(phen)(PPh3)2]NO3 as the catalyst. All of these methods afford the desired product in good to excellent yields without the use of palladium or expensive/air sensitive additives.

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