Hybrid organic-inorganic materials represent a new class of materials having scientific and technological potential. In this thesis, Polyhedral Oligomeric Silsesquioxanes (POSS) are used as an inorganic building block which has been tethered to an organic polymer. POSS are silica precusors, having a well defined silsesquioxane cental core surrounded by an organic periphery which makes them compatible with monomers and possibly polymers. The objectives of this study are to (1) study the basic structures of POSS homopolymers, (2) to incorporate POSS building blocks by a bottomup approach into polymer chains and study the resulting morphologies, and (3) to study the thin film behavior of POSS block copolymers. PMA and styryl POSS homopolymers of different peripheries were synthesized by ATRP and mass spectrometry studies were carried out by MALDI-TOF and ESI. PMA POSS chains undergo a number of fragmentations while styrly POSS chains have a relatively robust backbone. Poly(ethylene-butylene-b-MAPOSS), AB type copolymers and poly(MAPOSS-b-styrene-b-MAPOSS), ABA type copolymers were synthesized by a combination of anionic and ATRP polymerization. Spheres, inverse cylinders, lamellar and crystalline lamellar morphologies were observed for the poly(ethylene-butylene-b- MAPOSS) copolymers. In the poly(MAPOSS-b-styrene-b-MAPOSS) copolymers, cylindrical, lamellar and perforated lamellar morphologies were obtained. Beyond the interaction parameter (χ), total degree of polymerization (N) and volume fraction (f), the conformational asymmetry (ε) also plays an important role in determining the morphology of these block copolymer. Crystallization of the POSS phase and better thermal properties were observed in the both block copolymers. Thin film studies of poly(MAPOSS-b-styrene-b-MAPOSS) copolymers showed that the microdomains can be oriented either parallel or perpendicular to the substrate depending upon the film thickness, morphology and relative volume fractions of the connecting blocks. By removal of the organic phase, ordered mesoporous low dielectric constant silica films were obtained. These hybrid block copolymers are a potential candidate for nanopatterning applications.

No description available.

No description available.

No description available.

No description available.

No description available.

No description available.

Ca2+ and calmodulin play important roles in many physiologically crucial pathways. The conformational landscape of calmodulin is intriguing. Conformational changes allow for binding target-proteins, while binding Ca2+ yields population shifts within the landscape. Thus, target-proteins become Ca2+-sensitive upon calmodulin binding. Calmodulin regulates more than 300 target-proteins, and mutations are linked to lethal disorders. The mechanisms underlying Ca2+ and target-protein binding are complex and pose interesting questions. Such questions are typically addressed with experiments which fail to provide simultaneous molecular and dynamics insights. In this thesis, questions on binding mechanisms are probed with molecular dynamics simulations together with tailored unsupervised learning and data analysis. In Paper 1, a free energy landscape estimator based on Gaussian mixture models with cross-validation was developed and used to evaluate the efficiency of regular molecular dynamics compared to temperature-enhanced molecular dynamics. This comparison revealed interesting properties of the free energy landscapes, highlighting different behaviors of the Ca2+-bound and unbound calmodulin conformational ensembles. In Paper 2, spectral clustering was used to shed light on Ca2+ and target protein binding. With these tools, it was possible to characterize differences in target-protein binding depending on Ca2+-state as well as N-terminal or C-terminal lobe binding. This work invites data-driven analysis into the field of biomolecule molecular dynamics, provides further insight into calmodulin’s Ca2+ and targetprotein binding, and serves as a stepping-stone towards a complete understanding of calmodulin’s Ca2+-dependent conformational ensembles. / <p>QC 20180912</p>

<p> Affinity capillary electrophoresis (ACE) is a versatile technique for assessing non-covalent molecular interactions in free solution provided that there are significant changes in apparent analyte mobility as a result of specific complexation. The thermodynamics of receptor binding are vital for controlling the selectivity in molecular recognition, which are dependent on the electrolyte composition of solution. In addition, the conformational properties of the complex (e.g., size, shape) can also contribute a secondary influence on receptor selectivity that has been relatively unexplored in ACE to date. In this study, dynamic 1:1 host-guest inclusion complexation involving a anionic resorcin[4]arene with a group of neutral corticosteroids was examined by ACE, where the macrocycle serves as both an intrinsic buffer and electrokinetic host. The tetraethylsulphonate derivative of 2-methylresorcin[4]arene (TESMR) was first synthesized via an acid-catalyzed condensation reaction, which was then fully characterized in terms of its weak acidity (pKa), mobility, UV spectral and buffer capacity properties. TESMR solutions were demonstrated to have stable intrinsic buffer and ion transport properties at pH 7.5 even at low ionic strength. It was determined that over a 200 % enhancement in the apparent binding constant (KB) was realized by ACE when using TESMR as an intrinsic buffer at pH 7.5 relative to an extrinsic sodium phosphate buffer system, which was also confirmed by 1H-NMR. The coupling of thermodynamic (KB) and electrokinetic (μep, AC) factors associated with complex formation in buffered aqueous solutions that minimize the effects of extrinsic electrolytes serves to enhance enthalpy-driven molecular recognition processes by ACE.</p> / Thesis / Master of Science (MSc)

No / The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein folding and improve structure prediction efforts, especially with respect to difficult to characterize states, such as disordered or unfolded states. Host-guest peptide series are a useful tool in examining the propensities of the amino acids free from the surrounding protein structure. Here, we compare the distributions of the backbone dihedral angles (φ/ψ) of the 20 proteogenic amino acids in two different sequence contexts using the AAXAA and GGXGG host-guest pentapeptide series. We further examine their intrinsic behaviors across three environmental contexts: water at 298 K, water at 498 K, and 8 M urea at 298 K. The GGXGG systems provide the intrinsic amino acid propensities devoid of any conformational context. The alanine residues in the AAXAA series enforce backbone chirality, thereby providing a model of the intrinsic behavior of amino acids in a protein chain. Our results show modest differences in φ/ψ distributions due to the steric constraints of the Ala side chains, the magnitudes of which are dependent on the denaturing conditions. One of the strongest factors modulating φ/ψ distributions was the protonation of titratable side chains, and the largest differences observed were in the amino acid propensities for the rarely sampled αL region. / NIH