Chemistry Commons^™

The Electronic Structure Of The Pyranopterin Dithiolene Cofactor And Radical Reporters Of Excited State Interactions, Benjamin William Stein

Chemistry and Chemical Biology ETDs

Crystal structures of multiple molybdenum enzymes clearly demonstrate interesting structural distortions involving the pyranopterin dithiolene. These distortions can be correlated with pyranopterin oxidation state through the use of DFT geometry optimized structures of the possible oxidation states, and these are correlated with enzyme family. The potential role of the pyranopterin dithiolene in electron transfer in the varied enzyme familes has been explored through the use of non-equilibrium Green's function (NEGF) electron transport calculations. These calculations demonstrate clear differences in electron transport behavior as a function of pyranopterin oxidation state. The Jahn-Teller effect can strongly impact the geometric and electronic structures …

Electrochemical Investigation Of Homogenous Species At An Electrode Interface, Christopher Alan Larsen Iii

Chemistry and Chemical Biology ETDs

CO₂ reduction is a pressing problem worldwide, and one obstacle in the electrochemical conversion of CO₂ to more useful C₁ products such as methanol and formic acid is the kinetic barrier known as overpotential. The overpotential of rearranging the nuclei in CO₂ to accommodate electron transfer can be lowered by pre-bending the CO₂ molecule in an adduct-mediated complex. The work presented in Part I utilizes a combination of hard and soft donors on pincer-like ligands to effect the bending of CO₂ prior to electrochemical reduction. A large majority of the work consists of using …

Theory, Multiscale Simulations, And Experiments On Mesoscale Multifunctional Systems, Lance Edward Edens

Chemistry and Chemical Biology ETDs

Computational simulations use theoretical models to reproduce, as accurately as possible, the observed real-world behavior of complex structures. Guided by experimental observations, many multiscale/coarse-grained simulations seek to explore increasingly complicated systems. Here, a multiscale/coarse-grained simulation program (called TM2) is developed with applications to 1) properties and mechanisms of DNA and DNA polymerases, and 2) adhesion between whole bacterial cells and patterned surfaces. Results from the bacterial adhesion application form a part of a larger collaborative effort aimed at creating multifunctional, controllable surfaces to capture and kill pathogenic bacteria. The application of TM2 is first demonstrated by a coarse-grained model for …

Spectroscopic And Computational Studies Of Molybdenum Enzymes And Models, Chao Dong

Chemistry and Chemical Biology ETDs

In this dissertation spectroscopic methods such as electronic absorption (EAS), resonance Raman (rRaman), electron paramagnetic resonance (EPR), and MCD spectroscopies have been used in combination with DFT calculations for the interpretation of experimental results. These methods have been used to investigate the molybdenum coordination environment in enzymes and model complexes. Xanthine oxidase (XO), one of the canonical molybdenum enzyme families, hydroxylizes heterocyclic substrates by inserting an oxygen atom from molybdenum-activated water into a substrate C-H bond. This generates reducing equivalents that pass through two iron sulfur clusters and then to FAD, where oxidation of the FAD takes place. In this …

Study Of Novel Synthetic Methodologies For Indolyl Derivatives And Beta-Fluoroenals, Xiaobei Chen

Chemistry and Chemical Biology ETDs

One of the central goals in modern organic synthesis is to develop efficient synthetic strategies for the preparation and study of complex molecules possessing interesting structural, biological, and physical properties. Toward this end, my Ph. D. work focuses on the development of novel synthetic methodologies for the facile construction of synthetically and biologically significant molecular architectures. The tert-prenylated indoles and indolines are widely present in a large collection of natural products and biologically active compounds. Although significant efforts have been made on the development of efficient methods to prepare these intriguing molecular architectures, few methods have been explored to introduce …

Development Of Novel Efficient Organocatalytic Reactions For The Construction Of Complex Molecular Architectures, Aiguo Song

Chemistry and Chemical Biology ETDs

Facile construction of synthetically and medicinally significant optically active molecular architectures from simple and readily available materials via catalytic enantioselective cascade processes is the cental goal in organic synthesis. Toward this end, my Ph.D. work focuses on the development of novel organocatalytic asymmetric cascade reactions and their application in the synthesis of versatile molecular structures. A novel amine catalyzed decarboxylative enantioselective Diels—Alder reaction between aldehydes and readily available coumarin-3-carboxylic acids as dienophiles via dienamine catalysis has been realized. Notably, the decarboxylation facilitates the release of the catalyst in the Diels—Alder reaction adducts and achieves high reaction efficiency in terms of …

Criteria For Evolution Of Successful Proteins: Fold Fitness And Domain Dynamics Explored, Tyrel Bryan

Chemistry and Chemical Biology ETDs

The Haloacid Dehalogenase Superfamily (HADSF) is a ubiquitous family of enzyme with more than 32,000 members. A variety of reactions are catalyzed by HAD members, but a majority of HAD members are phosphatases. Dephosphorlyation of organophosphate metabolites are carried out in the conserved Rossmann-like core domain. The Rossman-like core domain houses the conserved active site residues necessary for catalysis and also supports domain inserts associated with substrate binding. This dissertation will focus primarily on investigating fold fitness and domain dynamics of HAD proteins more specifically three C2 capped proteins. The first part will focus on whether or not the prevailing …

Development Of Novel Small Molecules For Imaging And Drug Release, Yanting Cao

Chemistry and Chemical Biology ETDs

Small organic molecules, including small molecule based fluorescent probes, small molecule based drugs or prodrugs, and smart multifunctional fluorescent drug delivery systems play important roles in biological research, drug discovery, and clinical practices. Despite the significant progress made in these fields, the development of novel and diverse small molecules is needed to meet various demands for research and clinical applications. My Ph.D study focuses on the development of novel functional molecules for recognition, imaging and drug release. In the first part, a turn-on fluorescent probe is developed for the detection of intracellular adenosine-5'-triphosphate (ATP) levels based on multiplexing recognitions. Considering …

Spectroscopic Studies Of Conjugated Polymer Nanostructures And Polymer/Acceptor Blends, Jian Gao

Chemistry and Chemical Biology ETDs

This dissertation presents the results of investigations into organic semiconducting systems at the nano- to mesoscales through spectroscopic and electrical imaging techniques. Particular emphasis was put on capturing the role of conformation and morphology on electronic properties and processes. The combination of experimental methods and data analysis techniques used in this work reveals useful insights into the correlations between polymer structures and their photovoltaic device performance, and provide clues to developing better performing organic solar cells. The main approach of this work is using prototypical conjugated polymer systems, either ensemble or in their nanostructures, to study the solar cell active …

Stable Solar Cells Through Controlled Block Copolymer Self-Assembly And Cooperative Hydrogen Bonding Interactions, Fei Li

Chemistry and Chemical Biology ETDs

Current state-of-the-art polymer solar cells adopt the bulk-heterojunction (BHJ) morphologies where the electron donors (i.e. conjugated polymer) and electron acceptors (i.e. fullerenes) as active layers are mixed in an intimate way. The phase separation that modulates the exciton diffusion and charge transport in the current BHJ morphology is an uncontrolled process and thus results in random domain sizes of the polymer/fullerene blend. In addition, the polymer and fullerenes in the blend are intrinsically two immiscible materials and they tend to undergo macrophase separation eventually, which leads to deteriorated device performance. One way to address the abovementioned issues is to attach …

Theoretical Studies Of Transition Metal Catalysis, Ryan S. Johnson

Chemistry and Chemical Biology ETDs

Transition metal catalysis, being critical to nearly all aspects of the modern industrial world, is the focus of a series of theoretical studies which seek to elucidate the fundamental and electronic origins of enhanced chemical activity and selectivity. The application of density functional theory on extended single metal and alloyed surfaces, supported single metal atoms, and gas phase cationic species illuminate various aspects of transition metal catalysis in a wide range of enviornments. Adsorption, reactivity, and other mechanistic details developed here suggest possible mechanisms used to aid interpretation of experimental results and guide developement of future catalysts.

Simulations Of Chemical Catalysis, Gregory K. Smith

Chemistry and Chemical Biology ETDs

This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows.

Project 1 — Bacterial Enzyme SpvC

The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a β-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC …

Synthesis, Characterization, And Electrochemical Evaluation Of Novel, Highly Active Catalysts For The Oxygen Reduction Reaction In Alkaline Media, Danae Jacquelyne Davis

Chemistry and Chemical Biology ETDs

Efficient electrocatalysts for the oxygen reduction reaction (ORR) are needed for fuel cells and next generation metal-air batteries, as the overall efficiency of these systems is currently limited by cathode kinetics. While Pt and Pt-based alloys demonstrate excellent electrocatalytic activities, their prohibitive cost and rarity ultimately prevents their widespread utilization. Catalyst materials that are highly active, stable, and cost effective are needed. Manganese oxide (α-MnO₂) catalysts doped with varying amounts of Cu or Ni were synthesized, characterized, and evaluated for their performance as catalysts for the oxygen reduction reaction in alkaline electrolyte. Cu-α-MnO₂ nanowire catalysts consistently attained …

Spectroscopic Studies Of Conformation And Packing In Polythiophenes, Edwards T. Niles

Chemistry and Chemical Biology ETDs

This thesis employs variants of spectroscopic techniques to evaluate intermolecular interactions between P3HT chains in solution and in the solid state. Emphasis was put on understanding not only how intermolecular interactions within P3HT chains affect electronic properties, but also to assess changes due to the addition of weak and strong electron acceptors. To this end, optical and magnetic spectroscopies were focused on to correlate observed changes in electronic properties to physical changes in the polymer structure. To assess changes in intermolecular interactions, self-assembly was used to form P3HT nanofibers and were studied using resonance Raman, and transient absorption, and temperature- …

Determining The Function Of Hotdog-Fold Thioesterases, Yajun Wu

Chemistry and Chemical Biology ETDs

The enzymes that hydrolyze thioesters to the free acids and free thiols are called thioesterases. Based on the different folding strategy, most thioesterases are classified into two superfamiles: the hotdog-fold enzyme superfamily or alpha/beta-fold hydrolase enzyme superfamily. Hotdog-fold thioesterases share high degree similarity in structure which resembles a hotdog'. YigI is one of the last two uncharacterized hotdog-fold thioesterases from E.coli. To study the function of YigI, substrate specificity profile was determined by thioesterase activity assay. YigI possesses a preference for long chain acyl-CoA over shorter chain acyl-CoA. The highest activity was found in catalysis of myristoyl-CoA. By alignment with …

Development Of Novel Reaction-Based Fluorescent Probes, Weimin Xuan

Chemistry and Chemical Biology ETDs

Fluorescent probes have been proved to be very valuable tools in chemical and biological applications, and extensive exploration has been made. Recently, reaction-based fluorescent probes became a new design trend and displayed great potential with remarkable implementation to the conventional design method. However, this field is still underdeveloped, and a lot of problems remain to be solved. As part of our groups research interest, my Ph.D. study centered on the development of new reaction-based fluorescent probes. Firstly, our previous research on Hg²⁺ was continued. In this work, we developed a novel ratiometric fluorescent probe for Hg²⁺ with impressive …

Antimicrobial Activity And Mechanistic Study For The Poly(Phenylene Ethynylene) (Ppe)-Based Cationic Conjugated Polyelectrolytes And Oligo-Phenylene Ethynylenes, Ying Wang

Chemistry and Chemical Biology ETDs

My dissertation work focuses on recent progress made in elucidating the intermolecular interactions between a novel class of synthetic phenylene ethynylene (PPE)-based conjugated polyelectrolyte polymers (CPEs) and oligomers (OPEs) and multiscale cellular targets that give rise to their remarkable broad spectrum biocidal activity. We studied the interactions and self-assembly behaviors of the CPEs and OPEs with a set of vital biomolecules, including lipids, proteins and nucleic acids, that reveal the potential pathways by which the synthetic biocidal agents could exert toxicity. Then, we explored the antimicrobial effects and mechanisms of the CPEs and OPEs on multiple clinically relevant pathogens, with …

Spectroscopic And Computational Electronic Structure Studies Of Donor-Acceptor Systems, Diana Habel-Rodriguez

Chemistry and Chemical Biology ETDs

Three molecular systems have been studied, which exhibit strong intramolecular electronic communication between constituent moieties. Experimental results for electronic absorption, resonance Raman, electron paramagnetic resonance (EPR), and magnetic circular dichroism (MCD) spectroscopies are presented. Density functional theory (DFT) electronic structure calculations were employed to augment the interpretation of experimental results. Using a valence bond configuration interaction (VBCI) model we show that the ground state properties of the molecules are influenced by excited state configurations. Donor ( = semiquinone)-bridge-acceptor ( = nitronylnitroxide) biradicals show strong ferromagnetic donor-acceptor coupling, and contributions to the ferromagnetic coupling from spin delocalization and spin polarization mechanisms …

Catalytic Mechanism And Function Evolvement Studies Of Phosphatases Within Haloacid Dehalogenase Superfamily (Hadsf), Li Zheng

Chemistry and Chemical Biology ETDs

The haloacid dehalogenase superfamily (HADSF) is one of the largest known enzyme superfamilies, having more than 32,000 nonredundant members. Enzymes in this superfamily catalyze a number of different chemical reactions including dehalogenation, phosphoryl transfer, and hydrolysis of phosphate esters and phosphates. The vast majority of HADSF members are phosphatases, which contain a highly conserved core domain that is constructed to catalyze hydrolysis reactions of phosphorylated sugars or nucleotides by using an active site Asp nucleophile and a Mg²⁺ cofactor. Most phosphatases possess a cap domain, which in association with the core domain assists active site desolvation and binds the …

Structure To Function: Case Studies Of Hotdog-Fold Superfamily Thioesterases From Escherichia Coli, John A. Latham

Chemistry and Chemical Biology ETDs

My doctoral research primarily focuses on the Escherichia coli hotdog-fold thioesterases ydiI and ybgC. The ydiI gene is colocalized in the operon ydiHIJ. A substrate screen provided evidence that YdiI prefers aryl-CoA substrates and discriminated against the analogous aryl-ACP, unlike the paralog YbdB which works on 2,4-DHB-EntB in the enterobactin synthesis pathway. A bioinformatic approach showed that in some bacteria, ydiI is colocalized with genes from the menaquinone pathway. YdiI was shown to catalyze the hydrolysis of DHNA-CoA with physiological relevance (k_cat/K_M ~ 10⁵). Furthermore, the E. coli YdiI- strain was shown to …

Alkynal Involved Organocatalytic Reactions, Xinshuai Zhang

Chemistry and Chemical Biology ETDs

During the past twenty years, vast progress has been achieved in the field of organocatalysis. One of the fruitful areas is iminium catalysis using α, β-unsaturated aldehydes as essential reactants. Enals involved enantioselective reactions (including single-step reactions and cascade/tandem reactions) represent an enormous and fruitful research branch. In contrast, the protocols for the corresponding alkynals, even in single-step conjugate addition reactions, are extremely rare. Toward this end, my Ph. D. research work mainly focuses on the development of alkynal involved organocatalytic reactions and expands the scope of organocatalysis by uncovering new activation modes. Unlike enals, ynals with sp hybridized C≡C …

Development Of Novel Organocatalytic Cascade Reactions And Application In Organic Systheses, Xixi Song

Chemistry and Chemical Biology ETDs

The development of new catalytic reactions, particularly synthetically efficient cascade processes for the facile preparation of important molecular architectures, which otherwise are difficult to access via traditional methods, is of considerable significance. Toward this end, my Ph.D. work focuses on developing new organocatalytic reactions and their applications in organic syntheses. A novel direct organocatalytic stereoselective α-arylation methodology has been discovered. The cross-coupling-like products are assembled using simple enals and various brominated aromatic systems, such as p-bromophenols, bromonaphthols and 3-bromoindoles. The products have been applied in the concise photo-syntheses of [α]-annulated carbazoles. Moreover, an unexpected reaction has been identified with aliphatic …

A Proposed Palladium-Catalyzed Cycle For The Epoxidation Of Alkenes, Marie Vernell Parkes

Chemistry and Chemical Biology ETDs

Epoxides are an important chemical functional group, used in a wide variety of processes, from the small-scale production of pharmaceuticals to the large-scale production of propylene oxide. Current methods for production of epoxides require costly multi-step syntheses that use toxic or explosive reagents, result in low yields, and produce co-products that must be removed and often disposed. The development of an atom-efficient general method, preferably catalytic, for converting alkenes to epoxides using safe, cheap, and readily available molecular oxygen as the stoichiometric oxidant would be a great advance in both industrial and academic chemistry. Presented here is a proposed catalytic …

Function Assignment Within The Haloacid Dehalogenase Superfamily, Hua Huang

Chemistry and Chemical Biology ETDs

The HaloacidDehalogenase Enzyme Superfamily (HADSF) is a ubiquitous family of enzymes. Presently, more than 45,000 deposited gene sequences encode proteins of the HADSF, and only a fraction of these have defined structure and/or function. The work described in this thesis focuses on function determination in several members of the HADSF. An integrated bioinformatic-protein structure-enzyme mechanism approach was used to differentiate and track D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GHMB) and histidinol phosphatephosphatase (HisB)orthologues; 2-keto-3-deoxynononic acid 9-phosphatephosphatase (KDN9PP) and 2-keto-3-deoxy-D-manno-octulosonic acid 8-phosphatephosphatase (KDO8PP)orthologues; inorganic pyrophosphatase and β-phosphoglucomutase(β-PGM) orthologues. In addition, a structure-function/bioinformatic analysis was carried-out on the bifunctional 1,3-diposphoglycerate acyltransferase/Cys-S-glyceryl-3-phosphate phosphatase (FKBH). Each study began …

Evolution Of Structure And Function Among Hotdog-Fold Thioesterases And Had Family Phosphatases, Wang Min

Chemistry and Chemical Biology ETDs

My doctoral research began with the function assignment to two domains of fusion protein BT4699, from Bacteriodes thetaiotaomicron, BF1314 from Bacteriodes fragilis and PG1653 from Porphyromonas gingivalis. BT4699, however, is insoluble, so its orthologue BF1314 and PG1653 were prepared and studied. The fusion proteins consist of a domain that belong to a large family of phosphatases known as Haloacid Dehalogenase (HAD) superfamily, and a domain belong to the hotdog-fold thioesterase superfamily. The genes encoding the fusion proteins located at an operon that encoding enzymes involved in the menaquinone biosynthetic pathway. So we assumed that the thioesterase domain is connected to …

I. The Synthesis And Coordination Chemistry Of Novel 6Π-Electron Ligands. Ii. Improvement Of Student Writing Skills In Chemistry Lab Reports Through The Use Of Calibrated Peer Review, Wilson Ngambeki William

Chemistry and Chemical Biology ETDs

ABSTRACT I

The goal of this study was to synthesize and characterize a set of coordination complexes containing 6π-cationic ligands. These compounds could be extremely useful as catalysts for the polymerization of olefins that are widely used in the synthetic polymer industry. The original strategy was to synthesize the 6π-cationic ligands using (Ph₂P)₃CH (1) and (Me₂P)₃CH (10) as precursors; however, both precursors 1 and 10 were found to be highly reactive leading to the fragmentation products (Ph₂P)₂CH₂ and (Me₂P)₂CH₂ respectively. In trying …

Structural Characterization Of Metal Binding In Metallo-Β-Lactamases Using X-Ray Absorption Spectroscopy, Robert M. Breece

Chemistry and Chemical Biology ETDs

In an effort to probe the structure and mechanism of metallo-β-lactamases, the metal-binding behaviors of several enzymes were studied using EXAFS (Extended X-ray Absorption Fine Structure). Three members of the metallo-β-lactamase subclass B1, BcII from Bacillus cereus, Bla2 from Bacillus anthracis and CcrA from Bacillus fragilis, were compared to examine metal-binding behavior within a subclass. Each system exhibits different metal-binding behavior including cooperative binding (BcII), sequential binding (CcrA), and differential binding between zinc(II) and cobalt(II) forms (Bla2). The metal-binding behavior of subclass B3 of L1 from Stenotrophomonas maltophilia was explored with RFQ (rapid-freeze quenched) EXAFS and site selective metal …

Mechanistic Studies On Xanthine Oxidoreductase Enzymes, Abebe Berhane

Chemistry and Chemical Biology ETDs

In humans, the xanthine oxidoreductase enzymes are known to catalyze the final two steps of purine metabolism by converting hypoxanthine successively to xanthine and uric acid. Xanthine oxidoreductase also metabolizes a wide variety of drugs in vivo, and activates a number of antiviral prodrugs of clinical importance. Therefore, understanding the reaction mechanism of this enzyme is of prime importance in furthering our understanding of enzyme-drug interactions. In order to provide a greater understanding on the reaction mechanism, theoretical and enzymatic spectroscopic experimental approaches have been utilized. The theoretical approaches were used to elucidate the electronic structure and geometry of the …

Probing Morphology-Dependent Aggregation And Photocurrent Generation In Polymer/Fullerene Photovoltaic Devices, Yongqian Gao

Chemistry and Chemical Biology ETDs

In this dissertation, new spectroscopic and electrical imaging approaches were developed to map morphology-dependent aggregation properties of polymer chains in model solar cell devices. These techniques reveal new correlations between local structure and material performance on sub-micron size scales which are not accessible by other techniques. Resonance Raman spectroscopic imaging was developed as a physical probe to identify and spatially map morphology-dependent variations of intra- and interchain interactions and order in poly-3-hexylthiophene (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) photovoltaic blend thin films. The C=C band of P3HT backbone was decomposed into aggregated and unaggregated component contribution at ~1450 cm …

Quantitative Structure-Property Relationships For Predicting Chlorine Demand And Disinfection Byproducts Formation In Drinking Water, Gebhard Balthazar Luilo

Chemistry and Chemical Biology ETDs

Models are important tools for designing or redesigning water treatment processes and technologies to minimize disinfection byproducts (DBPs) formation without compromising disinfection efficiency. Empirical models, which are the most common, are based on bulk water quality parameters that vary with time and space. These parameters may not always have linear relationships with chlorine demand and DBPs formation which make structure-based models more attractive to study. In this dissertation, Quantitative Structure-Property Relationship (QSPR) models which make use of structural properties of individual molecules were developed using experimental data obtained from the literature. The amounts are reported in moles of chlorine (HOCl) …