<p>Chlamydia trachomatis, an obligate intracellular bacterium, is the most common sexually transmitted pathogen in the developed world as well as the leading cause of infectious blindness worldwide. The development of comprehensive therapeutics for infections is impeded by the fact that relatively little is known about the molecular underpinnings of C. trachomatis pathogenesis, as this microorganism has been historically refractory to genetic manipulation. Recent studies strongly suggest that the survival of C. trachomatis is dependent upon the secretion of a number of effector proteins and enzymes that interfere with host signaling. However, the exact role of many of these effector molecules in chlamydial pathogenesis remains elusive. Thus, there is a need for the discovery and development of chemical biology tools that can be used to probe the function of chlamydial effectors, and in turn possibly reveal therapeutic targets for antibiotic development. Here we report efforts toward the design, synthesis, and evaluation of small molecules as probes for chlamydial effectors. Combined with the utilization of bioinformatics and proteomics techniques, we have made progress towards investigating the role of chlamydial effector enzymes in pathogenesis.</p> / Dissertation

<p>Biological electron transfer (ET) reactions are typically described in the framework of coherent two-state electron tunneling or multi-step hopping. Yet, these ET reactions may involve multiple redox cofactors in van der Waals contact with each other and with vibronic broadenings on the same scale as the energy gaps among the species. In this regime, fluctuations of the molecule and its medium can produce transient energy level matching among multiple electronic states. This transient degeneracy, or flickering electronic resonance among states, is found to support coherent (ballistic) charge transfer. Importantly, ET rates arising from a flickering resonance (FR) mechanism will decay exponentially with distance because the probability of energy matching multiple states is multiplicative. The distance dependence of FR transport thus mimics the exponential decay that is usually associated with electron tunneling, although FR transport involves real carrier population on the bridge and is not a tunneling phenomenon. Likely candidates for FR transport are macromolecules with ET groups in van der Waals contact: DNA, bacterial nanowires, multi-heme proteins, strongly coupled porphyrin arrays, and proteins with closely packed redox-active residues. The theory developed here is used to analyze DNA charge-transfer kinetics, and we find that charge transfer distances up to 3-4 bases may be accounted for with this mechanism. Thus, the observed rapid (exponential) distance dependence of DNA ET rates over distances of ≲10 Å does not necessarily prove a tunneling mechanism.</p><p>Molecular structures that direct charge transport in two or three dimensions could help to enable the development of molecule-based electrical switches and gates. As a step toward this goal, we use theory, modeling and simulation to explore DNA three-way junctions (TWJs). Molecular dynamics (MD) simulations and quantum calculations, indicate that DNA TWJs undergo dynamic interconversion among “well stacked” conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol (PEG) linking groups (“extenders”) lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared to double-stranded DNA. Furthermore, we redesigned DNA TWJs that have equally coupled output pathways for charge. The TWJ was also designed to switch between the two conductive states in responsive to an applied electric field.</p><p>Computationally aided drug discovery confronts the problem to balance performance and computation cost. Earlier study reveals that a less-expensive docking approach is not reliable to estimate the protein-ligand affinity in exploring drug candidates targeting CARM1 (coactivator-associated arginine methyltransferase 1). However, more accurate binding free energy calculation based on molecular dynamics sampling is not affordable in a high throughput screening. A truncated MD method was developed and can be used to estimate the binding free energy with similar accuracy with the full-system MD methods, while reducing the computation cost ten fold. Thus, this truncated MD method is feasible in a high throughput screening towards drug discovery.</p> / Dissertation

Triazabutadienes are nitrogen containing compounds with interesting acid-responsive behavior. These compounds are relatively stable, but once activated by an electrophile, for example through protonation, fall apart to yield diazonium and imine compounds. In general, diazonium compounds are unstable and require harsh methods of synthesis. Therefore, the use of triazabutadiene compounds as precursors to diazonium compounds, allows for a mild and more controlled access to this reactive moiety. This opens up diazonium chemistry to more complex chemical biology applications, as well as in the development of applications in organic synthesis. In an effort to design triazabutadiene systems that release diazonium compounds in physiological conditions, water-soluble imidazolium-based triazabutadienes were synthesized by coupling N-heterocycle imidazolium carbenes to aryl azides. These compounds were shown to have pH-dependent reactivity, generating aryl diazonium salts in buffered solutions ranging from pH 4-7. This reactivity made these compounds one of the mildest ways of generating aryl diazonium salts in aqueous solutions. Initial stability and reactivity studies were performed by NMR, and by altering the sterics of the imidazolium core and the electronics of the phenyl group. It was determined that the rate and stability were influenced by the sterics and electronics of the scaffold. Electron withdrawing substituents on the phenyl and steric bulk on the imidazole core resulted in stable triazabutadienes, with the opposite being observed for the electron donating substituents on the phenyl and small substituents on the imidazole. Water-soluble triazabutadienes were synthesized to be further utilized as chemical biology probes. In organic solvents, the triazabutadienes reacted with resorcinol, an electron-rich phenyl group to form stable azo compounds. In more physiologically relevant conditions, the triazabutadiene compound was stirred in a pH 6 phosphate/citric buffer solution with a tyrosine analogue and an azo adduct was isolated. This indicated it was possible to target tyrosine residues with a triazabutadiene delivered aryl diazonium through the formation of azo bonds that could be cleaved under mild reducing conditions using sodium dithionite. In addition, the triazabutadiene compounds were found to undergo light-induced isomerism generating the Z isomer in solution upon irradiation. The Z isomer was observed to be more reactive, and would degrade even in basic solutions when irradiated with 350 nm light. This light responsiveness was utilized to enhance the reactivity of triazabutadiene attached onto protein and viral surfaces, allowing the generation and capture of aryl diazonium salts by electron rich aryl-fluorophore conjugates as well as antibody proteins in the case of the virus. Alkyl triazabutadiene compounds were synthesized by coupling N-heterocycle carbenes onto alkyl azides. These compounds were then shown to be capable of delivering alkyl diazonium compounds to carboxylic acids for esterification. This method diversifies esterification from only methyl substituents, as is the case with diazomethane and TMS-diazomethane, to larger more diverse alkyl groups. In conclusion, this work shows that the triazabutadiene compounds have interesting activity that will be vital in the development of novel probes for the study of biological process, as well as the development of reagents for chemical synthesis.

The process of nucleation is an essential part of understanding and controlling phase changes in a wide array of systems. In the past theories such as Classical Nucleation Theory have been used as a tool to aid experimentalist in the study of phase mechanisms. However, recent studies have shown in detail that theories such as this are not reliable, given that it can mispredict nucleation rates by several orders of magnitude. As a result newer methodologies must be developed into order to improve upon these deficiencies. In this study we use atomistic simulations to examine the non-ideal deviations from classical theory observed in both simple and complex systems. In addition to this we present new algorithms that can be used to improve the rate at which the nucleation properties of these simulations can be sampled. Lastly we apply these new methods to study an atmospherically relevant system that involves the nucleation of water in the presence of multiple charged ionic species. From these studies it was found that the deviation of more realistic systems from the classical theory can be attributed to both the creation of loosely bound clusters as well as the formation of highly ordered stacking in surface induced systems. The algorithms presented in this work have been shown to quickly and accurately replicate previously published data with very little increase to the computational overhead. Finally the application to the atmospherically relevant system showed an interesting trend where the nucleation rate was more heavily correlated to the number of water molecules that could be successfully bound to the ion pair instead of the quality of the bond.

<p> Optical activity is typically first introduced to a prospective chemist in her sophomore year organic chemistry course. Here, she is taught that optical activity is a consequence of chirality, for example, <i> L-</i>tartaric acid has a specific rotation of +12&deg; at the sodium <i> D-</i>line. However, this leaves said chemist with a wildly skewed and rather vague understanding of the concept of optical activity. There are two major problems with the current understanding of optical activity. The first is that both theory and experiment have shown that optical activity is, in fact, not a consequence of chirality. Molecules belonging to one of four achiral point groups (<i>C_s</i>, <i>C</i>₂<i>_v</i>, <i>S</i>₄, and <i>D</i>₂<i>_d</i>) can display optical activity in particular directions. However, measurement requires an anisotropic medium which presents major challenges. The second problem is that we lack structure-property relationships; specific rotations generally speaking are impossible to connect to molecular structure. Herein, we emphasize optical activity in achiral molecules whose high symmetry and simplified electronic structure are used to establish structure&ndash;property relationships. First, achiral optical activity is emphasized by showing that achiral polyaromatic hydrocarbons (PAH) are actually significantly more optically active than their helicene isomers. Next, small, planar, conjugated hydrocarbons are used to interpret optical activity by analysis of their &pi; wave functions that can be intuited from structure. Finally, it is shown that aromaticity is generally deleterious for optical activity. A simple explanation is offered based on Kekule structures.</p>

Organic photovoltaics (OPVs) are used to convert sunlight into electricity by using thin films of organic semiconductors. OPVs have the potential to produce low cost, lightweight, flexible devices with an eased manufacturing process. This technology contains the potential to increase the use of clean, sustainable solar energy, helping manage the global energy and environmental crisis that results majorly from the constant use of fossil fuels as an energy source. The ability to modulate the physical properties of organic molecules by tuning their chemical structure is an advantage for OPVs. Phthalocyanines (Pcs) are highly π-conjugated synthetic porphyrin analogs that have been explored as active layer components in OPVs due to their high extinction coefficients and hole mobilities. The Pc structure can be modified by the introduction of metals in the core and the incorporation of substituents into the periphery. These modifications tend to tune the solubility, photophysical properties and condensed phase organization of Pcs. The research work in this dissertation describes improved methods towards substituted Pc derivatives addressing: (1) the use of mass spectrometry techniques for Pcs characterization, (2) efforts to achieve materials with near-infrared (NIR) absorption, and (3) the potential of Pc as electron-acceptor materials. Herein, the synthesis of a series of asymmetric and symmetric metallated Pcs has been established, which resulted in interesting chemical, photophysical and electrochemical properties. The materials investigated in this thesis increase the potential of Pcs as organic semiconductors for OPVs.

Semiconductor nanocrystals are a desirable class of nanomaterials for electronic, energy conversion, and biomedical applications. The work presented in this thesis aids in the understanding of the fundamental chemistry that governs the way organic ligands coordinate to the surfaces of these nanocrystals. Using NMR, XPS, and TGA-MS a new binding mode of thiol ligands was identified on the surface of metal sulfide nanocrystals. This binding mode, crystal-bound ligands, has increased stability to removal compared to traditional surface-bound ligands. Taking advantage of the crystal-bound ligand coordination allows for the development of more active and potentially more stable photocatalysts. Overall, stabilizing the surface of a nanocrystal using crystal-bound ligands resulted in an enhancement in photocatalytic efficiency compared to a surface-bound ligand sample. Additionally, computational models of ligand coordination to surfaces were developed, providing new insights on the structural implications of ligand coordination.

Ligand-based computational drug discovery (LB-CADD) methods have been used widely over the last several decades to aid medicinal chemistry campaigns via virtual high-throughput screening (vHTS) and de-novo molecular design. A new de-novo drug design algorithm, BCL::EvoGen, based on a stochastic search algorithm was implemented within the BioChemical Library developed at Vanderbilt University. The EvoGen algorithm leverages reaction-based structure modification methods to iteratively build chemical structures, and ligand-based molecule scoring functions to guide molecular design. Results indicate that the EvoGen algorithm is capable of designing high-scoring molecules with novel and chemically reasonable structures. In a second study, LB-CADD models were used to prioritize a subset of a compound library the discovery of muscarinic acetylcholine receptor M5 negative allosteric modulators. An orthosteric antagonist VU0549108 (VU108) was discovered which exhibited an M5 IC50 of 5.23 uM and moderate selectivity across other muscarinic receptors. In addition, VU108 contains a novel chemical scaffold not previously associated with muscarinic receptor ligands.

<p> Lysozyme, known as N-acetylmuramide glycanhydrolase, is a powerful enzyme of bi-ological significance found in abundance in tears, saliva, and human milk. Lysozyme damages bacterial cell walls by catalyzing hydrolysis of 1,4-beta-linkages between N-acytylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. Lysozyme misfolding is involved in amyloidosis, along with other proteins, and contributes to neuronal cell death as associated with neurodegenerative diseases such as Alzheimer&rsquo;s, Parkinson&rsquo;s, and Huntington&rsquo;s diseases. </p><p> In this research, lysozyme protein from hen egg-white was stored in buffer solution at pH 2 and pH 2.7 at a temperature of 60&deg;C, to see how the acidic buffer solution and the ele-vated temperature affect the lysozyme fibril formation. The highest concentration of the solu-tion had a tendency to form fibrils fastest; the lowest concentration of lysozyme needed longer time to form fibrils. Lysozyme structures before and after forming the fibrils were imaged on a mica substrate using tapping mode atomic force microscopy (AMF). Also the fi-bril formation of lysozyme was analyzed using fluorescence spectroscopy to see the change of the primary and secondary structure of hen egg white lysozyme. In this technique, the amino acid tryptophan (Trp) was observed, which has a maximum absorbance near 350 nm, before growing the fibrils. The maximum emission changed after the fibril formation occurred as detected near 340 nm.</p>

The old bimetallic nickel complexes, meso- and rac-Ni2Cl4(et,ph-P4) were investigated as possible catalysts for the oxidative cleavage of alkenes using an unsaturated fatty acid, oleic acid, as the substrate. The new bimetallic nickel complexes with a stronger chelating tetraphosphine ligand, meso- and rac-Ni2Cl4(et,ph-P4-Ph), were also synthesized and tested for the oxidative cleavage of oleic acid. All four dinickel complexes were found to be active for the oxidative cleavage of oleic acid, producing extremely small amounts of aldehyde product. The Stanley research group also discovered the oxidative cleavage of alkenes using only the old et,ph-P4 tetraphosphine ligands with no metal centers. As a result of this discovery, the oxidative cleavage of oleic acid was attempted with both old and new tetraphosphine ligands (without metal centers) and found to be active, producing extremely small amounts of aldehyde as well. In attempt to make the system catalytic, some simple phosphine ligands (PPh3, P(C6H11)3, and dppm) and some mono- and bimetallic cobalt complexes were tested for the oxidative cleavage of oleic acid. The phosphine ligands and monometallic cobalt complex, [Co(H2O)6][BF4]4, found to be active, but still only producing an extremely small amount of aldehyde. The reactivity of the bimetallic nickel complexes with H2O was investigated through 31P NMR studies and the bridged-hydroxide complexes, rac-[Ni2(ì-OH)Cl2(et,ph-P4)]+ and meso- and rac-[Ni2(ì-OH)Cl2(et,ph-P4-Ph)]+ was proposed to be the most stable intermediate during the reaction. Further studies, such as COSY-NMR, are needed to prove this proposal, however. Numerous synthetic methods were explored to synthesize a bimetallic cobalt carbonyl complex for hydroformylation and aldehyde-water shift catalysis. The first method was the reduction of the dicobalt tetrachloride complexes, meso- and rac-Co2Cl4(et,ph-P4)/(et,ph-P4-Ph), in the presence of CO using 1:1 H2/CO, NaBH4, LAH, LiEt3BH, Mg, and Zn. Of these reducing agents, Zn resulted in the cleanest reduction by FT-IR analyses, yielding a proposed mixture of the dicationic penta- and hexacarbonyl dicobalt complexes, meso- and rac-[Co2(CO)5-6(et,ph-P4)/(et,ph-P4-Ph)]2+. The H2/CO reduction results indicated that perhaps, a 1:6 H2/CO, not the 1:1 mixture originally used, would be a more suitable autoclave gas mixture. Future experiments will be performed to test this hypothesis. Experiments using Co2(CO)8 resulted in a mixture of cobalt carbonyl complexes, including the formation of [Co(CO)4]-. Preliminary experiments to reduce the non-halide containing dicobalt complexes, [Co2(H2O)x(et,ph-P4)/(et,ph-P4-Ph)][BF4]2, using 1:1 H2/CO and Zn resulted in incomplete reductions. Future experiments using a stronger one-electron reducing agent in the presence of CO with an easily isolable by product should be a better synthetic route for the formation of a bimetallic cobalt carbonyl complex.