Other Chemistry Commons^™

Human Serine Racemase Structure/Activity Relationship Studies Provide Mechanistic Insight And Point To Position 84 As A Hot Spot For Β-Elimination Function, David L. Nelson, Greg A. Applegate, Matthew L. Beio, Danielle L. Graham, David B. Berkowitz

Department of Chemistry: Faculty Publications

There is currently great interest in human serine racemase, the enzyme responsible for producing the NMDA co-agonist D-serine. Reported correlation of D-serine levels with disorders including Alzheimer’s disease, ALS, and ischemic brain damage (elevated D-serine) and schizophrenia (reduced D-serine) has further piqued this interest. Reported here is a structure/activity relationship study of position Ser⁸⁴, the putative re-face base. In the most extreme case of functional reprogramming, the S84D mutant displays a dramatic reversal of β-elimination substrate specificity in favor of L-serine over the normally preferred L-serine-O-sulfate (~1200-fold change in k_cat/K_{m …}

Assessment Of Metabolic Changes In Mycobacterium Smegmatis Wild Type And Alr Mutant Strains: Evidence For A New Pathway Of D-Alanine Biosynthesis., Darrell D. Marshall, Steven Halouska, Denise K. Zinniel, Robert J. Fenton, Katie Kenealy, Harpreet K. Chahal, Govardhan Rathnaiah, Raul G. Barletta, Robert Powers

Department of Chemistry: Faculty Publications

In mycobacteria, D-alanine is an essential precursor for peptidoglycan biosynthesis. The only confirmed enzymatic pathway to form D-alanine is through the racemization of L-alanine by alanine racemase (Alr, EC 5.1.1.1). Nevertheless, the essentiality of Alr in Mycobacterium tuberculosis and Mycobacterium smegmatis for cell survivability in the absence of D-alanine has been a point of controversy with contradictory results reported in the literature. To address this issue, we examined the effects of alr inactivation on the cellular metabolism of M. smegmatis. The M. smegmatis alr insertion mutant TAM23 exhibited essentially identical growth to wild type mc²155 in the …

Transcriptional And Antagonistic Responses Of Biocontrol Strain Lysobacter Enzymogenes Oh11 To The Plant Pathogenic Oomycete Pythium Aphanidermatum, Yangyang Zhao, Guoliang Qian, Yuan Chen, Liangcheng Du, Fengquan Liu

Department of Chemistry: Faculty Publications

Lysobacter enzymogenes is a ubiquitous, beneficial, plant-associated bacterium emerging as a novel biological control agent. It has the potential to become a new source of antimicrobial secondary metabolites such as the Heat-Stable Antifungal Factor (HSAF), which is a broad-spectrum antimycotic with a novel mode of action. However, very little information about how L. enzymogenes detects and responds to fungi or oomycetes has been reported. An in vitro confrontation bioassay between the pathogenic oomycete Pythium aphanidermatum and the biocontrol bacterial strain L. enzymogenes OH11 was used to analyze the transcriptional changes in the bacteria that were induced by the oomycetes. Analysis …

Ion Mobility-Resolved Collision-Induced Dissociation And Electron Transfer Dissociation Of N-Glycopeptides: Gathering Orthogonal Connectivity Information From A Single Mass- Selected Precursor Ion Population, Venkata Kolli, Katherine N. Schumacher, Eric Dodds

Department of Chemistry: Faculty Publications

Glycopeptide-level mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses are commonly performed to establish site-specific protein glycosylation profiles that are of central importance to gaining structure-function insights on glycoproteins. Confoundingly, the complete characterization of glycopeptide connectivity usually requires the acquisition of multiple MS/MS fragmentation spectra. Complementary ion fragmentation techniques such as collision-induced dissociation (CID) and electron transfer dissociation (ETD) are often applied in concert to address this need. While structurally informative, the requirement for acquisition of two MS/MS spectra per analyte places considerable limitations upon the breadth and depth of large-scale glycoproteomic inquiry. Here, a previously developed method of …

A Computational Study Of Silver Doped Cdse Quantum Dots, Heather Gaebler

Theses and Dissertations (Comprehensive)

Due to quantum dot’s ability to emit photons when subjected to light of sufficient energy, they have become optimal candidates for biomedical research and for optoelectronic applications. Fascination towards quantum dots arises from the fact that their properties are easily fine-tuned through a variety of different techniques. Electronic doping is a popular technique used to control the properties of quantum dots through the addition of different elements.

Via density functional theory calculations, this work investigated how the structural energies and HOMO-LUMO gaps were altered by the addition of impurity atoms. First, interstitial and substitutional doping styles were investigated at 0 …

Assessment Of Short-Term Toxicity Of Titanium Dioxide Nano Fiber (Tdnf) In Sprague Dawley Rats, Daniel A. Hunter

College of Graduate Studies: Theses & Dissertations

Nanotechnology is easily becoming one of the fastest growing markets around the globe. Synthetic nanomaterials have many unique chemical and physical properties, mainly due to their huge specific surface area and chemical makeup. Specifically, titanium dioxide (TiO₂) nanomaterials have high stability, anticorrosive and photocatalytic properties. These nanomaterials have applications for semiconductor photocatalysis, treatment of water, as a photoactive material in nanocrystalline solar cells, and medicine. However, not much is known about the toxicity of TiO₂ in the nanofiber form. The objective of the present study is to investigate the adverse effects associated with acute ingestion of TiO …

Approaches Toward Novel 1,2,3-Triazole Sensors For The Detection Of Anions And Heavy Metal Cations, Richard D. Govan

College of Graduate Studies: Theses & Dissertations

Cations and anions play pivotal roles in biological and physiological processes, however an imbalance in concentration of any ion can be detrimental. Therefore, research into the selective recognition of anions and heavy metal cations has acquired much attention. One approach involves the use of chemosensors. Upon interaction with targeted analytes, chemosensors produce a distinct response, in some cases a fluorescent or colorimetric signal. The 1,2,3-triazole unit has much potential as a chemical sensor due to its unique photophysical properties. The specificity, selectivity, and signaling mechanism of triazole sensors can be tuned with conjugation in the motif and choice and placement …

Preventing Gene Expression Through The Interruption Of Dna Binding, Olivia Perdue

Honors College Theses

The interruption of DNA binding is a gateway to the inhibition of unregulated expression of genes which can possibly lead to illnesses such as cancer and epilepsy. The goal of this research is to produce high affinity DNA binding molecules which could act to displace the binding of natural transcription factor thus reducing the over- or under-expression of various proteins. Literature shows that the interruption of DNA binding can be completed using both organic and inorganic means, such as by means of natural transcription factors like the NF-κB protein or with metal-ligand complexes in order to bind DNA. NF-κB, a …

Investigating Stress Response Across Integrated Biological Systems, Alice A. Han

Graduate Theses, Dissertations, and Problem Reports (ETD)

The impact that a stressor has on a living system, whether it is on a cellular, organ, or even a whole organism level, can affect the overall health of the system. Monitoring the biochemical response resulting from a stressful experience offers insight into the numerous potential outcomes ranging on the spectrum of survival and death. Accessing this information not only provides a heightened understanding of the biochemical adaptions that occur, but also allows for the development of prediction models (to assess prospective influences of the stressor) or potential therapeutic treatments (to alleviate adverse effects) using measurable, quantifiable, and comparable metrics. …

Separation Of Transition And Heavy Metals Using Stationary Phase Gradients And Chelation Thin Layer Chromatography / Evaluation Of The Effectiveness Of Pogil-Pcl Workshops, Stacy L. Stegall

Theses and Dissertations

Gradient surfaces exhibit a variation in functionality along the length of the surface. One method for preparing gradients is controlled-rate infusion (CRI). In Part 1 of this work, CRI was used to prepare gradients for the purpose of separating transition and heavy metals. Initial work on this project was focused on controlling the retention of the metal ions by varying the number of amine groups, aminoalkoxysilane concentration, and the infusion time. The retention factors of four metal ions varied predictably with increasing number of amine groups, increasing aminoalkoxysilane concentration, and increasing infusion time, producing small but useful changes in the …

Polyol Induced Partitioning Of Essential Oils In Aqueous Organic Solvent Mixtures, Thomas Delmastro

Seton Hall University Dissertations and Theses (ETDs)

Polyol Induced Extraction (PIE) was developed and patented at Seton Hall University by Drs. John R. Sowa Jr., Wyatt R. Murphy, and Mithilesh Deshpande. It was originally discovered and implemented as a method to recycle and reuse waste acetonitrile during the production shortage in 2008. Through the use of PIE, a solvent mixture containing acetonitrile and water can be separated by employing a polyol mass separating agent, which induces a phase separation. The system is separated into its corresponding aqueous and organic phases, with the organic phase being a highly purified organic liquid. Based on the successful experimental results that …

The Tribology And Chemistry Of Phosphorus Containing Lubricant Additives, David W. Johnson

Chemistry Faculty Publications

Phosphate esters, thiophosphate esters and metal thiophosphates have been used as lubricant additives for over 50 years. Recently, phosphorus‐containing ionic liquids have emerged as a new class of lubricant additives. While the use of phosphorus compounds has been extensive, a detailed knowledge of how they work has been a much more recent development. In this chapter, the use of phosphate esters, thiophosphate esters, metal thiophosphates and phosphorus‐containing ionic liquids as antiwear or extreme pressure additives is discussed. The primary emphasis will be on how they form a protective film, which is both durable and reduces friction. The first part of …

The Investigation Of The Electrical Control Of Hemimicelles And Admicelles On Gold For Analyte Preconcentration, Dheyaa Hussein Al-Karawi

Masters Theses & Specialist Projects

Hemimicelles and admicelles are well-investigated wonders in modern science; they are surfactant monolayers and surface adsorbed micelles, respectively. Capacitance measurements for monitoring the formation of dodecyl sulfate (DS) surfactant monolayer on positively charged gold substrates (planar gold) and the adsorbance of 2-naphthol onto DS surfactant monolayer were performed. The investigation of the electrical control of DS at various concentrations (4, 6, 16, and 32 mM) below and above the critical micelle concentration (CMC= 8 mM) on gold surfaces for analyte preconcentration, prior to chromatographic analysis, is presented. Charged ionic surfactants, such as DS, drawn to a surface of opposite charge …

Probing The Structure And Photophysics Of Porphyrinoid Systems For Functional Materials, Christopher D. Farley

Dissertations, Theses, and Capstone Projects

Porphyrins (Pors) and their many cousins, including phthalocyanines (Pcs), corroles (Cors), subphthalocyanines (SubPcs), porphyrazines (Pzs), and naphthalocyanines (NPcs), play amazingly diverse roles in biological and non-biological systems because of their unique and tunable physical and chemical properties. These compounds, collectively known as porphyrinoids, can be employed in any number of functional devices that have the potential to address the challenges of modern society. Their incorporation into such devices, however, depends on many structural factors that must be well understood and carefully controlled in order to achieve the desired behavior. Self-assembly and self-organization are key processes for developing these new technologies, …

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and …

Electrophilic Activation Of Silicon–Hydrogen Bonds In Catalytic Hydrosilations, Mark C. Lipke, Allegra L. Liberman-Martin, T. Don Tilley

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Hydrosilation reactions represent an important class of chemical transformations and there has been considerable recent interest in expanding the scope of these reactions by developing new catalysts. A major theme to emerge from these investigations is the development of catalysts with electrophilic character that transfer electrophilicity to silicon by Si-H activation. This type of mechanism has been proposed for catalysts ranging from Group 4 transition metals to Group 15 main group species. Additionally, other electrophilic silicon species, such as silylene complexes and η3-H2SiRR′ complexes, have been identified as intermediates in hydrosilation reactions. In this Review, different types of catalysts are …

Lubricants For Turbine Engines, David W. Johnson

Chemistry Faculty Publications

The lubricant systems used in turbine engine applications are discussed with respect to the particular problems associated with aircraft applications. After initially describing the relevant specifications, the typical basestocks are described along with some common degradation schemes. The additive systems, including antioxidants, anti-foaming agents, and anti-wear additives needed to achieve the typical specifications, are described along with their mechanism of action and degradation mechanisms. The methods used for the monitoring of lubricant health, including in-line and offline methods, are also discussed. Finally, future changes in specifications, basestocks, and additives are discussed with respect to new, high-performance bearing materials.

Gc Verification Of The Spacecraft Atmosphere Monitor, Jessica S. Castro, Richard D. Kidd, Jeffrey D. Hein

STAR Program Research Presentations

International Space Station crew members face the unique challenge of maintaining air quality due to the volatile organic compounds (VOCs) that have the potential to accumulate at unsafe levels. The Spacecraft Atmosphere Monitor (SAM) is a miniature gas chromatograph/mass spectrometer (GCMS) designed to measure major constituents (such as N₂, O₂ and CO₂) and trace VOCs within the cabin of the spacecraft. The gas chromatograph is responsible for separating the sample into its components in order to be characterized. The oven of the gas chromatograph must reach a temperature of 150°C in order to heat constituents …

Peroxiredoxin Catalysis At Atomic Resolution, Arden Perkins, Derek Parsonage, Kimberly J. Nelson, O. Maduka Ogba, Paul Ha-Yeon Cheong, Leslie B. Poole, P. Andrew Karplus

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ-subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and show novel conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to …

The Synthesis Of Chemosensors For Toxic Analytes, Johnathan Hugh Broome

Dissertations

A number of chemosensors have been designed and synthesized to target cations (Zn²⁺ions), neutral molecules (cathinones), charged molecules (aminoindanes), and anions. The Zn²⁺ ion sensor featured bistriazole designed binding unit and ferrocene signaling units. Characterization of Zn²⁺ ion binding was carried out with electrochemical techniques (CV and DPV), ¹H-NMR, mass spectrometry, and molecular modelling. It exhibited a 1:1 binding stoichiometry with Zn²⁺ and had an affinity for ZnCl₂ (Log K_1:1 = 4.1 ± 0.02) over other Zn²⁺ salts.

The cathinone probe was designed to selectively bind mephedrone over common street drugs …