Theses and Dissertations - Department of Chemistry & Biochemistry

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Computational Thermodynamics of Gas and Solution Phase Anions
(University of Alabama Libraries, 2020) McNeill, Ashley Shari; Dixon, David A.; University of Alabama Tuscaloosa
The work in this dissertation focuses on the computational analysis of the thermodynamics of anions in the gas phase and in aqueous solution to provide unique insights into the chemistry of a range of biologically and geochemically relevant chemical species. This often involves calculating properties for these species such as electron affinities and hydration free energies of the anions, which can be difficult or impossible to obtain experimentally. Systems of interest in this work include small peptides, enzyme-catalyzed biological reactions, and the gas phase and solvation energetics of a variety of anionic species including CO2-, H-, X- (halides), OX- (hypohalites), and YH- (chalcogen hydrides). The peptide work, performed largely with the composite correlated molecular orbital theory G3(MP2) method, is compared directly to experiments conducted with low-energy collision-induced dissociation negative ion mode mass spectrometry. Isotope fractionation studies, of significant use in many geochemical applications, are conducted on the overall reaction by the alanine transaminase enzyme (+H3NCH(CH3)COO? + ?OOCCH2CH2C(O)COO? ? CH3C(O)COO? + +H3NCH(CH2CH2COO?)COO?) in order to predict that 13C preferentially collects in the C2 site of pyruvate over alanine by 9‰ at equilibrium. This prediction, calculated from gas phase- and aqueous-optimized clusters with explicit H2O molecules at the MP2/aug-cc-pVDZ with and without the COSMO self-consistent reaction field for implicit solvation, is reflected in simpler models: without explicit solvation, with simpler analogues formaldehyde and methylamine, and from canonical functional group frequencies and reduced masses for R2C=O and R2CH-NH2. Solvation studies of the CO2-, H-, X-, OX-, and YH- anions and corresponding neutrals gave adiabatic electron affinities, reduction potentials, and gas phase and aqueous acidities that are generally in excellent agreement with experiment. These studies used a variety of computational methods, including heavy application of coupled cluster calculations with the Feller-Peterson-Dixon method to obtain high accuracy thermodynamic values. Absolute hydration free energies are determined for neutral and anionic species clustered with 4 to 8 explicit H2O molecules using a supermolecule-continuum approach.
Controlled Synthesis and Characterization of Magnetic Chalcospinels Nanocrystals
(University of Alabama Libraries, 2020) Akbari Afkhami, Farhad; Gupta, Arunava; University of Alabama Tuscaloosa
Binary and ternary metal chalcogenides have become well-known materials among chemists, physicists, material scientists, and other researchers of the field, and they have attracted significant attention because of their novel chemical, magnetic, electronic, mechanical and optical properties. Among the metal chalcogenides, chromium-based chalcospinels ACr2X4 (A = Cu, Co, Fe, Cd, and Hg; X = S, Se, and Te) have gained significant attention because they are a notable class of magnetic materials such as semiconductors, magnetic metals, and insulators. In this work, a general overview of binary and ternary metal chalcogenides and their nanocrystals has been provided. We have also provided an overview of the wet-chemical colloidal methods as an important approach to size and shape-controlled synthesize of nanocrystals. We have also discussed the importance of metal doping reactions as a pathway to create previously unavailable multielemental materials for high-performance applications. In this set of studies, colloidal nanocrystals of chromium-based chalcospinels of CuCr2S4 and CuCr2Se4 have been synthesized via hot-injection and heat-up methods and were characterized using experimental methodology comprised of different microstructural and structural tests. The magnetic properties of these nanocrystals have also been studied. The next studied system was Cr-doped pyrite CuSe2 nanocrystals, eventually leading to the observation of significant enhancement of ferromagnetic moment by Cr-doping in octahedral sites of the pyrite structure. We performed a unique reaction in which nanocrystals of CrxCu1-xSe2 (x = 0.1-0.5) formed in the pyrite phase, which is not stable in bulk form. The host p-CuSe2 nanocubes did also undergo a degradation influenced by the reaction temperature and the doping of Cr3+ ions in the pyrite crystal structure. The Cr-doped nanocrystals of the pyrite phase were formed during the heat-up procedure and by increasing the reaction temperature transformed to CuCr2Se4 spinel nanocrystals. To the best of our knowledge, no cationic substitution of chromium for copper has been reported on pyrite CuSe2 systems so far, likely due to the significant size difference between chromium and copper. Therefore, the results of this work are a powerful approach for the design and fabrication of new multielemental materials that may not be stable in the bulk form.
Investigations Involving Proton/Hydrogen Transfer in Peptides Using Mass Spectrometry
(University of Alabama Libraries, 2020) Jing, Xinyao; Cassady, Carolyn J.; University of Alabama Tuscaloosa
Mass spectrometry (MS) has been an important technique to ionize and sequence peptides, which makes MS indispensable in the field of proteomics. This dissertation contains studies of peptide ionization and dissociation using different methods. Various types of peptides were ionized with electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI) and dissociated by collision-induced dissociation (CID) or electron transfer dissociation (ETD). Mass spectra presented in this dissertation provide abundant information about peptide ionization and peptide sequencing. The addition of trivalent chromium, Cr(III), complexes to peptide solutions can increase the intensity of doubly protonated peptides, [M + 2H]2+, by ESI. [Cr(H2O)6](NO3)3Â·3H2O and [Cr(THF)3]Cl3 work as reagents that provide the most abundant [M + 2H]2+, the greatest [M + 2H]2+ to [M + H]+ ratio, and the cleanest mass spectra. The requirement of the aqueous solution indicates that water is involved in the mechanism, and the effect of the ESI design suggests that this Cr(III)-induced effect occurs during the ESI desolvation process. Cr(III) complexes and iron oxide nanoparticles can not be used as MALDI matrices to analyze acidic peptides. Cr(III) complexes produce intense background ions, and no peptide ions were observed with any iron oxide nanoparticles due to adsorption interactions. In both positive and negative ion modes, high-energy CID produces greater sequence coverage and less abundant product ions containing neutral losses compared with low-energy and medium-energy CID. The formation of immonium ions and the side-chain fragmentation can indicate the presence of specific amino acid residues. High-energy CID from [M ? H]? provides complementary sequence information to results from [M + H]+. In addition, the absence of selective cleavage adjacent to proline from [M ? H]? is beneficial because y-ions from [M + H]+ commonly dominate the mass spectra. Selective cleavage adjacent to acidic residues and C-terminal residue exclusion occur in both ion modes. In ETD of doubly protonated ions, [M + 2H]2+, carboxylic acid groups from either the C-terminus or the side chains of acidic residues do not have a significant effect on sequence coverage of c- and z-ions. With permethylation (conversion of -COOH to -COOCH3), the zn//+ to zn/+ ratios increase only for peptides with basic residues at the C-terminus. Therefore, hydrogen bonding between a carboxylic acid group and a basic residue may interfere with zn//+ formation. The generation of y-ions may involve a CID-like mechanism and could be affected by deprotonation of either -COOH and -SH through zwitterion formation.
Investigation of the RNA-Protein Structure-Function Relationships in the CRISPR-Cas10 Complex and Erythromycin-Resistance RNA Methyltransferases
(University of Alabama Libraries, 2021) Nasef, Mohamed; Dunkle, Jack A.; University of Alabama Tuscaloosa
CRISPR-Cas systems are a class of adaptive immune systems in prokaryotes that use small CRISPR RNAs (crRNAs) in conjunction with CRISPR-associated (Cas) nucleases to recognize and degrade foreign nucleic acids. Recent studies have revealed that type III CRISPR-Cas systems synthesize second messenger molecules, previously unknown to exist in prokaryotes, known as cyclic oligoadenylates (cOA). These molecules activate the Csm6 nuclease to promote RNA degradation and may also coordinate additional cellular responses to foreign nucleic acids. Although cOA production has been reconstituted and characterized for a few bacterial and archaeal type III systems, cOA generation and its regulation have not been explored for the Gram-positive bacterium, Staphylococcus epidermidis, as well as the specific target RNA sequence requirements. In chapter 2, we demonstrate that this system performs Mg2+ dependent synthesis of 3-6 nt cOA. We show that activation of cOA synthesis is perturbed by single nucleotide mismatches between the crRNA and target RNA at discrete positions and synthesis is antagonized by Csm3-mediated target RNA cleavage. In chapter 3, we mechanistically investigated the effect of single and multiple mismatches on the activation of cOA synthesis of type III-A Cas10-Csm complex from S. epidermidis. We show that mismatches at specific positions in target RNA significantly reduced the amount of cOAs produced in a sequence context-dependent manner. We also show that the defects are not due to perturbations in binding efficiencies or in RNA cleavage.In chapter 4, we focus on an erythromycin resistance methyltransferases (Erm) found in many Gram-positive pathogens. Erm proteins are S-adenosyl methionine-dependent Rossmann-fold methyltransferases which convert A2058 of 23S rRNA to m62A2058. This modificationsterically blocks binding of several classes of antibiotics to 23S rRNA, resulting in a multi-drug resistant phenotype in bacteria expressing the enzyme. ErmC is an erythromycin resistance methyltransferase found in many Gram-positive pathogens, while ErmE is found in the soil bacterium that biosynthesizes erythromycin. Whether ErmC and ErmE, which possess only 24 % sequence identity, use similar structural elements for rRNA substrate recognition and positioning is not known. To investigate this question, we used structural data from related proteins to guide site-saturation mutagenesis of key residues and characterized selected variants by antibiotic susceptibility testing, single turnover kinetics, and RNA affinity binding assays. We demonstrate that residues in α4, α5 and the α5-α6 linker are essential for methyltransferase function including: an aromatic residue on α4 that likely forms stacking interactions with the substrate adenosine, and basic residues in α5 and the α5-α6 linker which likely mediate conformational rearrangements in the protein and cognate rRNA upon interaction. The functional studies led us to a new structural model for the ErmC or ErmE-rRNA complex.
Electronic Effects in Multidentate Pyridinol and N-Heterocyclic Carbene Based Ligands for Transition Metal Catalyzed Carbon Dioxide Reduction
(University of Alabama Libraries, 2021) Boudreaux, Chance M; Papish, Elizabeth T.; University of Alabama Tuscaloosa
The design of new catalysts with high catalytic efficiency and robustness towards carbon dioxide (CO2) reduction is of paramount importance. A full understanding of the requirements for creating a catalyst of this type is a missing gap in the knowledge base which prevents progress in synthesizing solar fuels. Our research hypothesis is that through the control of steric and electronic factors we can design better catalysts using various transition metals. Multidentate ligands composed of pyridyl bound to N-heterocyclic carbene rings are a synthetically flexible scaffold capable of testing our hypotheses. The systematic tuning of this scaffold will elucidate the factors necessary to improve active catalysts and extend our results to more complex systems. These ligand motifs are also commonly seen in many active catalysts for CO2 reduction. Therefore, the systemic investigation of the properties that lead to higher activity in scaffolds containing these motifs can concurrently suggest improvements for many systems already available.Reduction catalysts, supported by a CNC-pincer moiety, are some of the most robust catalysts in the literature while maintaining good catalytic activity. The CNC-pincer scaffold have shown tremendous results with electronic tunability of the pyridyl N atom through para substitution of the pyridinol ring. A ruthenium(II) catalyst utilizing the CNC pincer has shown 250 turn-over numbers of carbon monoxide (CO) over 40 h with a catalyst loading of 100 ÂµM. The cobalt(I) systems are slower; however, they are even more robust than the ruthenium analog producing 203 TON of CO2 over 72 h with a catalyst loading of 1 ÂµM. Notably, the cobalt catalyst utilizes an inexpensive, less toxic, and earth abundant metal center compared to ruthenium. Another scaffold, with NCCN donors binding in a tetradentate fashion, is currently being investigated with nickel(II) and cobalt(II) metal centers. These studies are producing a better understanding of the catalyst structure needs for a solar to chemical fuel catalyst to enable a carbon-neutral fuel cycle within our current fuel infrastructure. This catalytic system will constitute an artificial photosynthesis scheme by producing fuels and other useful chemicals from carbon dioxide, mimicking how plants store solar energy in glucose.
Photo-Electroswitchable Arylaminoazobenzenes
(University of Alabama Libraries, 2021) Keane, Katie Strickland; Blackstock, Silas C.; University of Alabama Tuscaloosa
Azobenzenes consist of two phenyl rings linked by an azo unit (N=N), existing in E or Z isomeric forms. Their ability to reversibly transform between 'extended' thermodynamically favored E and higher energy 'contracted' Z isomeric forms upon photo-stimulation make them useful molecular 'flexors.' E→Z switching is rapidly achieved using light, which has popularized the use of azobenzenes in a variety of chemical systems to gain nano mechanical photoswitchable characteristics. In most cases, Z→E isomerization occurs slowly thermally or, when possible by photoisomerization, though slower than photo E→Z conversion and typically incomplete.To address the Z→E isomerization limits (slow or incomplete), we have developed using electron removal as a new azobenzene switching mechanism for amino-substituted azobenzenes and investigated the prospect of switching multiple azo linkages with a single electron loss event. Blackstock and coworkers have covalently attached a redox aryl amine to the azobenzene moiety allowing for rapid, catalytic, and compete Z→E isomerization upon oxidation. The oxidized redox auxiliary dramatically reduces the Z→E isomerization energy barrier by factors of at least 105. Once initiated, the aryl amine radical cation is chemically stable and persistent enough to exchange electrons with a neutral Z isomer amine, generating an efficient electron-transfer chain reaction for Z→E isomerization. The synthesis, photo- and thermoisomerization, and lifetime effects of linking multiple azobenzenes to a single arylamine redox center are investigated for four tertiary amine derivatives: 4-methoxy-4'-(N,N-dianisyl)-aminoazobenzene (11), N,N-bis(azobenzene)-p-anisidine (20), N,N-bis(2,2',6,6'-tetrafluoroazobenzene)-p-anisidine (21), and N,N,N-tris(azobenzene)amine (29). Blue light irradiation of these azobenzene systems yields an equilibrium of Z-enriched isomers as a photostationary state (PSS). Dynamic UV-vis and NMR spectroscopy are used to measure PSS compositions and thermal dynamics of these mixtures. Ortho-fluorination is employed to increase Z isomer lifetime from hours (20) to weeks (21), resulting in an extended switching time domain for the dual-flexor system. Electron loss from a single arylamine efficiently catalyzes the Z→E isomerization of up to three connected azobenzene units, resulting in rapid, large geometry changes for these conglomerate structures. Stimulated, reversible flexing is thus demonstrated using electronic excitation and electron transfer. Incorporating a photosensitizer (methylene blue) allows for a dual photo, photo-electron transfer Z,E switching mechanism, which can be easily cycled with light. Red light excites methylene blue, which in turn oxidizes the redox amine to achieve rapid, complete Z→E conversion. Thus, blue and red light irradiation in tandem is shown to generate an E→Z→E switching cycle for three of the systems (11, 20, and 29).
The role of outer-sphere residues and substrate-binding at the 3-mercaptopropionic acid dioxygenase (3mdo) active site: a combined spectroscopic and computational investigation
(University of Alabama Libraries, 2021) York, Nicholas James; Pierce, Brad S.; University of Alabama Tuscaloosa
Thiol Dioxygenases (TDOs) are non-heme iron enzymes that catalyze the O2-dependent oxidation of thiol-bearing amino acid derivatives to their corresponding sulfinic acid. Recently, considerable work has been focused on this class of enzymes, as sulfur metabolite imbalances have been correlated with neurodegenerative disorders such as Alzheimer’s, Parkinson’s, and motor neuron disease. The active site of this enzyme class is comprised of a mononuclear Fe(II) bound by three protein derived histidine residues. A conserved feature among structurally characterized TDOs is a sequence of serine, histidine, and tyrosine residues adjacent to the iron active site, deemed the SHY motif. By far, the most well studied TDO is mammalian cysteine dioxygenase (CDO) which oxidizes L-cysteine to cysteine sulfinic acid with high substrate-specificity. Unlike CDO, bacterial 3-mercaptopropionate dioxygenase from Azotobacter vinelandii (Av3MDO) is a promiscuous TDO that oxidizes a variety of thiol substrates. Given both enzymes show similar active site geometries, the drastic difference in substrate specificity is not well understood. This dissertation aims to address two unresolved topics among Av3MDO and TDOs in general. The first is the mode in which native substrate, 3MPA, binds to Av3MDO. Arguments have been made for both bidentate coordination through the substrate thiolate and carboxylate and monodentate through the thiolate only. Herein, crystallographic, spectroscopic, and computational studies are used to determine the mode of 3MPA coordination to the iron active site. Bidentate coordination was observed for a crystal structure of bound inhibitor, 3- hydroxypropionic acid, which was used as a basis for computational models of bidentate 3MPA coordination. These models showed agreement with spectroscopic data using either nitric oxide or cyanide as spectroscopic probes. The second aspect investigated is the role of the SHY motif in the active site. For Av3MDO, alterations to the SHY motif have been shown to drastically attenuate activity (kcat), catalytic efficiency (kcat/KM), and formation of NO-bound ES complex. However, the interactions between the SHY motif and iron active site are not fully understood. Spectroscopic studies presented herein reveal the flexible hydrogen bonding capabilities of Tyr159 in the SHY motif and its direct influence on the electronic structure of the iron active site.
Light-activated protic ruthenium anticancer compounds: structure function relationships and determining which factors influence toxicity
(University of Alabama Libraries, 2020-12) Gray, Jessica Lee; Papish, Elizabeth T.; University of Alabama Tuscaloosa
While research in the field of metallo-based chemotherapy drugs is extensive, understanding the effects of pH responsive ligands within these systems is limited. In 2017, the Papish group reported a new class of pH sensitive light-activated metallo drugs that are activated by light-triggered ligand dissociation also known as PACT or photoactivated chemotherapy. Three ruthenium complexes of the type [(N,N’)2Ru(6,6’-dhbp)]Cl2 (the photolabile ligand 6,6’-dhbp = 6,6’-dihydrohybipyridine; 1A: N,N’ = 2,2′-bipyridine (bpy) ; 2A: N,N = 1,10-phenanthroline (phen); 3A: N,N = 2,3-dihydro-[1,4]dioxino[2,3-f ][1,10]phenanthroline (dop)) were synthesized and found to be toxic against various breast cancer cell lines upon irradiation (λ = 450 nm) with compound 3 eliciting EC50 values as low as 4 µM. Phototoxicity indices with 3 were as high as 120, which shows that dark toxicity is limited. The complexes exhibited low overall photodissociation (ΦPD) despite good toxicity suggesting the mode of toxicity is not through a PACT driven pathway. Discussed herin, are the efforts to study the mode of action, physical properties, and which characteristics have the largest impact on light driven toxicity for compounds 1-3 and further investigation into newly developed compounds. The hydrophobicity (Log(Do/w)) and uptake properties of 1-3 are reported. Due to the presence of the protic ligand, 6,6’-dhbp, all of the complexes studied increase in hydrophobicity with pH with 3 being the most hydrophobic (3>2>1). Cellular studies have demonstrated that passive diffusion is the dominant pathway for cellular uptake and compound 3 accumulates in the nuclei of cancer cells (MCF7, MDA-MB-231, and HeLa); however it competes with active transport out of the cell (efflux). Subsequent research has shown that an increase in photodissociation does not result in an increase in toxicity and the primary mode of toxicity is likely via the production of singlet oxygen (1O2); a process known as photodynamic therapy (PDT). Singlet oxygen quantum yields (ΦΔ) were higher for 1-3 upon deprotenation with values as high as 0.87(9) for complex 2. New complexes are also reported which demonstrate improved ΦΔ’s, toxicity, and light selectivity against breast cancer cells demonstrating the importance of studying protic anticancer mettalo drugs.
Spectroelectrochemistry studies of perovskite electrode materials
(University of Alabama Libraries, 2021) Yadav, Jeetika; Pan, Shanlin; University of Alabama Tuscaloosa
Perovskite materials have interesting optoelectronic properties such as tunable bandgap, high photoluminescence, broad spectral range, and emission tunability in the entire visible region. These materials have been extensively used as an absorber layer in the solar cells however their applications in terms of electrochemiluminescence (ECL) in the lighting industry has not been explored. This dissertation presents a study of the electrochemiluminescence, stability, size-dependent, and luminescent properties of these materials. Chapter 1 of this dissertation provides extensive background and a broad review of current research progress made in the field of perovskite materials and their applications. Chapter 2 illustrates the operation principles of several selected electrochemistry and characterization techniques extensively applied in this doctoral research. The doctoral research work starts with the synthesis and photophysical studies of perovskite films in Chapter 3 to show their fluorescence emission and stability. Confocal fluorescence microscopy is used to study the red and green fluorescence from the perovskite films and the origin and relationship between both colors are described. The synthesized perovskite films are used as a device for light-emitting electrochemical cells (LECs) applications. Since the optoelectronics properties of perovskite materials are greatly dependent on their size and structure, a perovskite size and density gradient are developed on a conductive substrate upon a single potential application as shown in Chapter 4. Dark field scattering (DFS), fluorescence imaging, X-ray crystallography (XRD), and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry techniques demonstrate that the large-sized and low-density perovskite crystals are more stable than the smaller sized high-density perovskite crystals. Finally, spectroelectrochemistry and photophysics, stability of perovskite quantum dots are described in Chapter 5. The generated ECL of perovskite quantum dots studied by was stabilized by incorporated the perovskite quantum dots in polystyrene (PS) polymer matrix increasing the efficiency of ECL generation 2.5 folds. Challenges of this doctoral work and future perspectives are described in Chapter 6.
Synthesis of non-nucleoside methyltransferase inhibitors & investigation of pinacol phosphonate ester as a phosphonomethoxy source in antiviral drugs
(University of Alabama Libraries, 2021) Chakraborty, Amarraj; Snowden, Timothy S.; University of Alabama Tuscaloosa
Mixed lineage leukemia (MLL) is an incurable form of pediatric cancer. Disruptor of telomeric silencing 1-like (DOT1L), a lysine methyltransferase, is a critical enzyme associated with the initiation and progression of MLL-rearranged acute leukemias. Here we report a synthesis of 14 potential DOT1L inhibitors in a collaborative, early drug discovery investigation. Preparation of these inhibitors involved multiple reaction steps and challenging isolation procedures. However, overall yields for these inhibitors were improved from 3-11% up to 36-42% through optimization of reaction conditions and purification processes. Each target compound and >30 new polyaza heterocycles were characterized with 1H-, 13C-, and 2D-NMR spectroscopy and HRMS spectrometry. Four of the prepared compounds demonstrated confirmed inhibitory activity against DOT1L both in nucleosome and whole cell assays conducted at the University of Michigan Medical School. The most potent DOT1L inhibitor exhibited inhibitory activity with IC50 = 1.0 ± 0.1 μM, which was a 40-fold improvement in potency versus the initial hit. Screening against nine other methyltransferases established target selectivity of the most potent inhibitor and revealed another DOT1L inhibitor with modest inhibitory activity against the protein arginine methyltransferase PRMT3, which is associated with unrelated diseases.Phosphonomethyl ether is a functionality widely present in nucleoside phosphonate-containing antiviral therapeutics including the anti-HIV/ anti-HBV drugs Tenofovir Disoproxil Fumarate (TDF), Tenofovir Alafinamide (TAF), and Adefovir. Industrial-scale syntheses of these prodrugs require diethyl p-toluene sulfonyloxymethyl phosphonate (DESMP) to install a phosphonomethyl ether fragment via O-alkylation of a nucleobase segment under basic conditions. This step significantly diminishes overall yield due to complications arising from high water solubility of the corresponding phosphonate diester and partial hydrolysis to the monoester during workup. In collaboration with Professor Anthony J. Arduengo, III and the Medicines for All Institute at VCU, we designed and prepared an innovative phosphonate ester, which may prove advantageous over DESMP in the O-alkylation step. Pinacol sulfonyloxymethyl phosphonate esters were synthesized in three steps using inexpensive reagents and solvents. The optimized conditions facilitate reproducible isolation on moderate scale and limit chemical waste. Products from each step were successfully prepared as solids and were characterized with 1H-, 13C-, and 31P-NMR spectroscopy and HRMS spectrometry. Crystal structures of each product were obtained by X-ray crystallography.
Investigations of conserved structure-function relationships and enzymatic evolution
(University of Alabama Libraries, 2021) Conte, Juliana Victoria; Frantom, Patrick A.; University of Alabama Tuscaloosa
The E.coli SUF pathway is the iron-sulfur cluster biogenesis pathway responsible for assembling iron-sulfur clusters during times of oxidative stress and iron starvation. SufS is the cysteine desulfurase enzyme responsible for the acquisition of sulfur and subsequent transfer to transpersulfurase SufE. Recent studies have provided several crystal structures of SufS including two variants displaying stalled intermediates of the desulfurase reaction. Combining the structural data with biochemical investigations has uncovered several key elements in SufS activity. SufS is a homodimer proposed to use a half-sites mechanism involving conformational changes and communication through dimer interface interactions. Despite the significant contributions made to understanding SufS function, questions still remain about the specific roles of several structural elements involved in activity and regulation. Investigations discussed herein are aimed at probing structural components of SufS, including the beta hairpin structure. The beta hairpin makes up one wall of the active site of the opposite monomer. The proposed regulatory mechanism of SufS uses the beta hairpin dynamics to control access to the active site. In chapter 2 beta hairpin variants are shown to significantly disrupt SufS structure. Variants were unable to bind the PLP cofactor essential to catalysis and instability of the variants resulted in protein aggregation as demonstrated with size exclusion chromatography analysis. Chapter 3 focuses on single substitutions of residues located in and around the active site including Asn99, Arg56, and Arg359. Kinetic assays were conducted to determine defects in desulfurase activity by measuring the rate of alanine production, the product released by the desulfurase reaction. Asn99 variants exhibited a ten-fold decrease in turnover number, confirming Asn99 does play a role in generating an optimal environment for activity. This is likely due to the hydrogen bonds Asn99 forms with the glycine residues in the loop at the base of the beta hairpin, potentially contributing to the regulation of dynamics. Arg56 is located in a dynamic loop above the active site and was previously proposed to contribute to catalysis by hydrogen bonding with the sulfhydryl of the substrate cysteine. Kinetic analysis of both R56A and R56K variants is consistent with Arg56 having a significant role in SufS activity. It is possible that this residue is responsible for the deprotonation of SufE C51 and facilitating persulfide transfer. Kinetic analysis of the Arg359 variants suggest a role in cysteine binding and positioning the substrate for bond cleavage. The work presented here contributes to the current understanding of the SufS mechanism and may be more broadly applicable to other cysteine desulfurases.
Metal organic frameworks as sorbents for volatile organic compounds
(University of Alabama Libraries, 2021) Shankwitz, Jennifer Elizabeth; Szulczewski, Gregory J.; University of Alabama Tuscaloosa
Metal organic frameworks (MOFs) are a class of highly porous materials with large surface areas, large pore volumes, and chemical tunability. These features make MOFs desirable as sorbents for applications such as gas storage, gas separation, and gas sensing. In this work, MOF thin films of UiO-66-R, where R = -H, -NH2, and-NO2, were fabricated onto Au-coated Si wafers and Au-coated quartz crystal microbalance surfaces using a vapor-assisted conversion method. The films were then characterized by scanning electron microscopy, powder x-ray diffraction, x-ray photoelectron spectroscopy, reflection absorbance infrared spectroscopy, and Raman spectroscopy. The spectroscopy reveals that the films of UiO-66-H, UiO-66-NH2, and UiO-66-NO2 are polycrystalline and 1 – 3 µm thick. The diffraction patterns reveal that the UiO-66-NO2 film potentially has the most missing linker defects. The UiO-66-R films grown on quartz microbalance crystals were activated by heating under high vacuum and exposed to a known pressure of benzene, toluene, ethyl benzene, and the xylene isomers (BTEX). The Henry’s constant, which describes the adsorption capacity for each MOF, was calculated from the mass change during the adsorption isotherm at 30°C, 25°C, and 20°C. The enthalpy of adsorption and entropy change was determined by plotting the logarithm of Henry’s constants versus the reciprocal of temperature. The results reveal the Henry’s constant for BTEX increased in the following order: UiO-66-H < UiO-66-NH2 < UiO-66-NO2. The results suggest that the functional groups on the organic linker and missing linkers influence adsorption behavior. The Henry’s constant of the films UiO-66-H were an order of magnitude smaller than those obtained for UiO-66-NH2 and UiO-66-NO2 films, largely due to the large pore size and lack of any functional group. The results suggest that UiO-66-NO2 films contain more missing linker defects than UiO-66-NH2 films. As a result, the heat of adsorption and entropy change for BTEX molecules in UiO-66-NH2 films is more negative than UiO-66-NO2. In contrast, due to a large pore size caused by the missing linkers, the adsorption capacity of UiO-66-NO2 films is larger than UiO-66-NH2 films.
Supramolecular interactions as a basis for differential sensing applications
(University of Alabama Libraries, 2021) Ihde, Michael Henry; Bonizzoni, Marco; University of Alabama Tuscaloosa
In this work, we used supramolecular interactions to construct systems that respond to analytical stimuli and report on specific chemical species in solution using optical spectroscopic techniques (e.g. absorbance and fluorescence spectroscopy), affording low cost and high sensitivity. To obtain selectivity, we used cross reactive sensors (organic dyes, conjugated polymers) to generate differential response patterns when exposed to families of subtly different analytes of interest. The differential responses produced large data sets that were interpreted using well established pattern recognition algorithms, such as linear discriminant analysis (LDA) and principal component analysis (PCA). We first report on conditions and methods based on linear discriminant analysis to predict the identity and composition of samples containing metal ion mixtures without prior physical separation, a common shortcoming of these systems. We also report on a higher sensitivity metal ion sensing array composed of novel fluorene based conjugated polymers with high affinity groups to detect nine divalent metal cations down to 500 pM in freshwater, and to 100 nM in seawater samples collected from the Gulf of Mexico. This robust system was sufficiently sensitive for detection below the maximum mandated concentrations set by the US Environmental Protection Agency (EPA) for toxic metals in drinking water and aquatic ecosystems. Similar highly sensitive, fluorene based conjugated polymers were used again to detect pollutants with intrinsic characteristic light absorption such as polycyclic aromatic hydrocarbons (PAHs) and azo textile dyes. Instead of chemical interaction with these analytes, the polymers displayed good spectral overlap with the absorbance spectra of the targets, leading to changes in their optical spectrum caused by the inner filter effect, where the analytes themselves acted as “chemical filters”. Finally, we investigated the nature of the binding interactions between PAH probes and amine terminated poly(amidoamine) (PAMAM) dendrimers. Using time resolved fluorescence, fluorescence anisotropy, and selective quenching experiments, we used two probes, anthracene and pyrene, to highlight distinct binding modes and locations to the polycationic, macromolecular PAMAM hosts, paving the way for future applications of such charged polymers with interesting affinity towards hydrophobic guests.
Nitrosoarenes: magnetic anisotropy, donor-acceptor bonding and host-guest chemistry
(University of Alabama Libraries, 2021) Kelley, Sarah Ariel; Blackstock, Silas C.; University of Alabama Tuscaloosa
Nitrosoarenes (Ar-N=O) were first reported by Baeyer in 1874 after successful synthesis of nitrosobenzene via a diphenyl mercury reaction with nitrosyl bromide. C-nitroso compounds (R-N=O), like nitrosobenzene, fall between hydroxylamines (R-NH-OH) and nitro compounds (R-NO2) on the amine oxidation scale making them common intermediates for many synthetic amine oxidation reactions. Nitrosobenzenes exhibit a number of unique properties, which stem from their structure. A small energy gap between the HOMO (n*) and LUMO (?*) orbitals of the N=O function allows for several unique chemical and spectroscopic properties of nitrosoarenes. Nitrosobenzene and its derivatives have a blue-green color in monomeric form and reversibly dimerize to a colorless form in the solid state, thus yielding a dynamic covalent bonding reaction for this class of compounds. One area of our studies focuses on the very large (2-3 ppm) magnetic anisotropy of the nitroso group, which is evaluated for a series of ortho-substituted nitrosoarenes. The nitroso (-N=O) functions of these molecules are sterically forced into a primary (majority) orientation in the molecule by the ortho substituent, thereby allowing the NMR analysis of the magnetic environment around an oriented -N=O group at room temperature. Multiple substrates have been synthesized, including oriented 1,3-(bis)nitroso compounds, which have double the amount of shielding of the “syn” proton. A series of NMR techniques is employed to prove the NMR signal assignments for these compounds including: 1H, 13C, NOE, COSY, HSQC, and HMBC NMR spectroscopy. Also studied is the electron donor-acceptor (DA) bonding ability of the N=O group of N,N-dimethyl-4-nitrosobenzene (DMANB) and N,N-diethyl-4-nitrosobenzene (DEANB), in the monomeric state, as they complex and co-crystallize with electron-poor alkenes such as 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and tetracyanoethylene (TCNE). Finally, encapsulation of N,N-dimethyl-4-nitrosobenzene (DMANB) and p-nitrosocumene (p-NC) by organic host molecules such as octa-acid (OA), cucurbit[7]uril (CB7), and cyclodextrins (?,?,?-cd) in aqueous solution is studied.
Methodological studies of α-halogenated carbonyls and the synthetic investigation of dihydroresorcylide
(University of Alabama Libraries, 2020-12) Probasco, Kristina Claire; Jennings, Michael P.; University of Alabama Tuscaloosa
The research presented herein consisted of projects with focuses on metal enolates and silane chemistry, and their uses in methodology and total synthesis. The projects were divided into three distinct chapters. The first chapter covers the development of highly functionalized pyran motifs that are commonly found in classes of natural products such as Bryostatins via an intramolecular Heck reaction with a novel palladium enolate transfer. A bromoethoxy pentanoate compound was synthesized through several steps and was then subjected to catalytic reactions with conditions found in literature where many variations were changed in attempts to obtain the desired six-membered ring. The second chapter consists of the total synthesis of Dihydroresorcylide via a novel palladium enolate ring closure. This structure has been synthesized twice before, however both syntheses undergo a ring closing metathesis to create the macrocycle. The macrocyclization attempts were based on literature published by Buchwald and Hartwig. The third project studies the halogenation of a trialkylsilyl bond through what is believed to be a bromonium ion intermediate followed by an SN2 like elimination according to work published by Tamao and company. Majority of the halogenations proceeded in good yields and with complete inversion of stereochemistry.
Enhancing thermal isomerization rates of redox auxiliary-appended azobenzenes via redox auxiliary catalysis
(University of Alabama Libraries, 2020-08) Warner, David James; Blackstock, Silas C.; University of Alabama Tuscaloosa
Azobenzene exists in E or Z isomeric forms having different three-dimensional structures, chemical properties, optical properties and electronic properties. Azobenzene can switch between E and Z conformations using light and has been incorporated in chemical systems to impart photoswitchable characteristics. Thermal conversion from the Z to E often occurs slowly and is unideal when fast dynamics is desired. ZE photoswitching is typically incomplete, leaving a significant percentage of molecules in the Z conformation. The Blackstock group has covalently attached an easily oxidized aryl amine “redox auxiliary” (RA) to the azobenzene scaffold to facilitate rapid and complete ZE conversion by adding a catalytic amount of oxidant. We hypothesize that the oxidized Z isomer of a RA-appended azobenzene (RA-azo) will rapidly isomerize to the E conformation because oxidizing the RA greatly reduces the energetic barrier to ZE isomerization. The newly formed (E) RA•+ azo molecule will oxidize a neutral (Z) RA azo, generating a (Z) RA•+ azo radical cation. This (Z) RA•+ azo will undergo rapid ZE isomerization to yield another (E) RA•+ azo molecule, which will oxidize another neutral (Z) RA azo. To increase the electron catalysis turnover number, we incorporated a new RA. This new RA-azo underwent complete and rapid ZE switching using a lower electrocatalytic loading than other RA-azos previously studied. Rapid ZE conversion was also achieved in a photo-electrical cell device (PED), and several EZE switching cycles were achieved using light and voltage in tandem. Attaching two azobenzene moieties to the new RA allowed for electrocatalytic ZE switching of both moieties. The azobenzene ZE thermal isomerization half-life is ~2 days, but adding the RA (or most other substituents) reduces this half-life to hours or minutes. By developing an RA-azo with ortho fluorines, we produced an RA-azo exhbiting an exceptionally long half-life (t1/2 = 40 days) and the capability to undergo rapid and complete ZE switching upon addition of 0.11 mol% oxidant. This results in a 6,900,000 fold ZE rate acceleration. Extrapolating to the case of 100 mol% oxidant gives a 6,300,000,000 fold ZE rate acceleration, which is by far the greatest RA-facilitated ZE rate acceleration observed for any RA-azo studied by the Blackstock group to date.
Investigation of structural changes in vanadium containing transition metal oxides
(University of Alabama Libraries, 2020-12) Davenport, Matthew Austin; Allred, Jared M.; University of Alabama Tuscaloosa
We have completed an experiment to obtain diffuse scattering data for use in a comprehensive study of the local-structure changes as a function of molybdenum composition and have made large strides in interpreting some of the major changes found in this study. For these experiments, single crystals of molybdenum substituted VO2 with the formula V1-xMoxO2 were synthesized, with molybdenum compositions up to x = 0.60, using a novel, two-step chemical vapor transport synthesis. Using these large single crystals for total scattering experiments, we report the discovery of the sudden collapse of three-dimensional order in the low-temperature phase of V1-xMoxO2 at x = 0.17 and the emergence of a novel frustrated two-dimensional order at x = 0.19, with only a slight change in electronic properties. Single crystal diffuse x-ray scattering reveals that this transition from the 3D M1 phase to a 2D variant of the M2 phase results in long-range structural correlations along symmetry-equivalent (11L) planes of the tetragonal rutile structure, yet extremely short-range correlations transverse to these planes. Additionally, we report a combined study using single crystal X-ray diffraction, powder X-ray diffraction, and representational analysis to examine both the local and crystallographically averaged atomic structures simultaneously near x = 0.50. Between about x = 0.50 and 0.60, the average structure of V1-xMoxO2 is the parent rutile phase, but the local symmetry is broken by atomic displacements that are best described by an orthorhombic cell in the spacegroup Fmmm. This model is locally identical to the two-dimensionally ordered 2D-M2 phase except the correlation length is much shorter in the 2D plane, and longer in the frustrated one, making it more isotropic.
Using ketones as catalyst activators in palladium-catalyzed cross- coupling reactions
(University of Alabama Libraries, 2020) Gilliam, Ashley; Shaughnessy, Kevin; University of Alabama Tuscaloosa
PEPPSI-IPr (1) has become a very useful catalyst over the past decade. It has shown to be successful with almost every type of cross-coupling reaction that currently exists. These transformations have been used in catalytic studies and the pharmaceutical industry. This study used PEPPSI-IPr and 3-pentanone to greatly improve the yield of the Buchwald-Hartwig amination of various aryl bromides and aniline. This suggests that the ketone acted as the activator where aniline cannot. The importance of using the ketone as an activator for catalysis will be shown in various ways. This transformation has been successful with both sterically hindered and electronically modified substrates. However, the electron-rich substrates proved to produce higher yields than their electron-deficient counterparts. The transformation showed slight favor of sterically hindered substrates over non-hindered ones. The reaction mechanism for ketone activation remains unknown. The goal of this study was to gain further knowledge of how the ketone affects the reaction to better understand how this mechanism occurs. Other conditions of these reactions include low catalyst loading (PEPPSI-IPr, 1), the use of NaO-t-Bu as the base and dry toluene as the solvent over a range of temperatures, 20-80 °C. This study also demonstrated the importance of reagent addition order, and how it affected the transformation. The culmination of this study showed that without the ketone, the reaction was not very successful, producing 3-12% yields; however, with the ketone, most conditions afford yields between 60-100%. In order to convey the importance of the ketone in this reaction, we studied the affect of increasing ketone concentrations and temperatures on the 4-bromoanisole and 2-bromotoluene substrates in addition to a reaction rate profile for 4-bromoanisole.
Electron transfer dissociation and collision-induced dissociation mass spectrometry of metallated oligosaccharides
(University of Alabama Libraries, 2019) Duke, Ranelle Marie; Cassady, Carolyn J.; University of Alabama Tuscaloosa
Investigations of metallated glycans through tandem mass spectrometry (MS/MS) can further the field of glycomics, the sequencing of the human glycome. The field is hindered by the lack of an analytical technique that can determine all the stereo-diverse features of carbohydrates. In this dissertation, electron transfer dissociation (ETD) and collision-induced dissociation (CID) are utilized with metal-adducted oligosaccharides to explore the potential of these techniques to sequence glycans. The resulting mass spectra provide significant insight and information about the structure of oligosaccharides and how to distinguish between these complicated isomeric species. Using univalent, divalent, and trivalent transition metal adducts is valuable to glycan analysis. The ETD process requires multiply charged ions, which do not form via protonation for neutral glycans, and CID of protonated glycans produces uninformative glycosidic bond cleavage. The univalent and trivalent metals investigated did not produce ions sufficient for ETD studies, but CID of the trivalent metal adducts showed significant fragmentation. Dissociation of [M + Met]²⁺ from the divalent metals formed various fragment ions with ETD producing more cross-ring and internal cleavages, which are necessary for structural analysis. The two dissociation techniques are complementary. For both ETD and CID of all glycans studied, [M + Co]²⁺ provided the most uniform structurally informative dissociation. Permethylation is a common derivatization technique used in the study of glycans. Permethylation reduces the hydrophilicity of oligosaccharides by replacing all hydrogen atoms on oxygen and nitrogen atoms with methyl groups. Permethylation increases ion intensity in electrospray ionization (ESI) and prevents rearrangements of certain monosaccharides. In this study, permethylation reduced the fragmentation by both ETD and CID for the metallated glycans. The spectra for non-derivatized metallated oligosaccharides was more structurally informative, especially with ETD. For some exact mass ions, permethylation reduced the ambiguity in the spectra. The trivalent lanthanide metal series was investigated as metal adducts. ESI on mixtures of trivalent metals and tetrasaccharides produced [M + Met-H]²⁺, [M + Met + NO3]²⁺, and [M + Met-2H]⁺. For the larger heptasaccharide, both [M + Met-H]²⁺ and [M + Met]³⁺ formed. Dissociation of these ions by both ETD and CID yields extensive sequence information. All trivalent lanthanide cations are suitable for sequencing glycans, and the fragmentation did not vary by metal identity.
Mechanistic studies of water oxidation and carbon dioxide reduction using transition metal catalysts with protic ligands
(University of Alabama Libraries, 2019) Burks, Dalton Bodine; Papish, Elizabeth T.; University of Alabama Tuscaloosa
The majority of energy produced in the world is derived from fossil fuels which are finite and have deleterious environmental effects. For a sustainable and environmentally-friendly energy future, alternative, renewable energy sources are desired. Two reactions that could have applications towards developing renewable energy sources are water oxidation to produce hydrogen and carbon dioxide reduction to form various products (e.g. formic acid or carbon monoxide); however, these reactions require catalysts to efficiently produce the desired products. Efforts to synthesize, characterize, and study catalysts for these reactions are discussed in this dissertation. The first chapter serves as an introduction to energy-related catalytic reactions. In Chapter 2, 6,6ʹ-dihydroxybipyridine (6,6ʹ-dhbp)—a protic ligand used with several metals to produce catalysts for energy-related reactions—is studied to determine its thermodynamic acidity. In the following chapter, 6,6ʹ-dhbp is used as a ligand with copper to form complexes that are water oxidation catalysts. Chapters 4 and 5 focus on iridium and ruthenium complexes containing new bidentate ligands composed of pyridinol and N-heterocyclic carbenes (NHCs). These complexes, along with an iridium complex of 6,6ʹ-dhbp, were used as catalysts for the hydrogenation of carbon dioxide to formate and the reverse dehydrogenation of formic acid to carbon dioxide and hydrogen. However, the complexes containing the new bidentate pyridinol-NHC ligands were found to be precatalysts as they undergo transformations and decomposition during the course of the reaction. A nickel-pincer complex with a protic CNC-pincer derived of pyridinol and NHCs was used as a photocatalyst for carbon dioxide reduction in Chapter 6. The protic state of the hydroxy group in the 4-position of the pyridine ring was determined to be important for catalysis, as the deprotonated hydroxy group results in 10 times the catalytic ability as the protonated form. In the penultimate chapter, ruthenium-pincer complexes that are active carbon dioxide photoreduction catalysts are studied mechanistically by UV/vis and IR spectroscopies. The most active catalyst was studied in greater detail with real-time IR spectroscopy to help elucidate potential reaction pathways. The final chapter serves as a conclusion to summarize the results discussed in the dissertation.

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