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A Proposed Mechanism To Induce Multi-Layer Polydiacetylene-Coated Filter Color Response To Bacteria , Timothy Hanks

Chemistry Publications

The purpose of this study was to develop a multi-layer diacetylene (PDA)-coated filter and to verify the proposed color response mechanism of PDA-coated filters to bacteria. Unlike other reports which immobilize PDA lipo- somes on solid support or create monolayer Langmuir films, multi-layer PDA-coated filters were generated by directly evaporating organic solvents. Different from incorporating functional headgroups or inserting phospho- lipids into PDA, we reported that bacterial growth can trigger the color change of PDA sensors without any mod- ification or phospholipid insertion. The mechanism that pH change from bacteria metabolites lead to color change of PDA filter was proposed …

Twenty Years Of Exceptional Success: The MOlecular EDucation And REsearch COnsortium In UNdergraduate Computational ChemistRy (Mercury)” , George C. Shields

Chemistry Publications

The molecular education and research consortium in undergraduate computational chemistry (MERCURY) consortium, established in 2000, has contributed greatly to the scientific development of faculty and undergraduates. The MERCURY faculty peer-reviewed publication rate from 2001 to 2019 of 1.7 papers/faculty/year is 3.4 times the rate of the physical science faculty at primarily undergraduate institutions. We have worked with over 1000 students on research projects since 2001, and 75% of our undergraduate research students have been under-represented in chemistry, either female or students of color. Approximately half of our alumni attend graduate school for the purpose of obtaining advanced degrees in STEM …

Maintaining A High Degree Of Research Productivity At A Pui As Your Career Advances, George C. Shields, Scott E. Feller

Chemistry Publications

In this perspective, two experienced academic administrators who are computational chemists discuss strategies for how to maintain an active research program at a pre- dominately undergraduate institution as your career progresses. More responsibility equates to less time for research, so planning for research to remain a priority is essential. We all have the same amount of time, so figuring out how to use yours bet- ter is the key to remaining active. Professional organizations such as Council on Undergraduate Research, consortia of computational chemists such as Molecular Education and Research Consortium in computational chemistRY and Midwest Undergraduate Computational Chemistry Consortium, …

A Critical Analysis Of Electrospray Techniques For The Determination Of Accelerated Rates And Mechanisms Of Chemical Reactions In Droplets, G. Rovelli, M. I. Jacobs, M. D. Willis, Rebecca J. Rapf, A. M. Prophet, K. R. Wilson

Chemistry Faculty Research

Electrospray and Electrosonic Spray Ionization Mass Spectrometry (ESI-MS and ESSI-MS) have been widely used to report evidence that many chemical reactions in micro- and nano-droplets are dramatically accelerated by factors of ∼102 to 106 relative to macroscale bulk solutions. Despite electrospray's relative simplicity to both generate and detect reaction products in charged droplets using mass spectrometry, substantial complexity exists in how the electrospray process itself impacts the interpretation of the mechanism of these observed accelerated rates. ESI and ESSI are both coupled multi-phase processes, in which analytes in small charged droplets are transferred and detected as gas-phase ions with a …

Controlling Transition Metal-Catalyzed Alkyne Annulations Utilizing Polarized Ynol Ethers, Brandon L. Coles-Taylor

Electronic Theses and Dissertations

Transition metal-catalyzed alkyne annulations have developed into incredibly powerful synthetic tools over there the past quarter century. These reactions provide rapid access to important organic scaffolds such as indole, quinoline, isoquinoline, indene, and isocoumarin scaffolds. Transition metal mediated alkyne annulations have proven invaluable in synthetic fields, such as natural product total synthesis, by offering efficient pathways to otherwise synthetically difficult to access substrates.

Foundational works performed by chemist such as Larock, Ackermann, Satoh, and Miura have been established through relying upon the usage of symmetrical alkynes. When unsymmetrical alkynes are used in annulation processes mixtures of regioisomers are often isolated. …

Development Towards An Ethylene Sensing Artificial Metalloenzyme, Mitchell Lee Ellinwood

Electronic Theses and Dissertations

Ethylene (ethene) is the essential ripening hormone for climacteric plants, and consequently its detection and quantification is of considerable interest to the horticulture industry. Its detection however is a non-trivial pursuit, traditionally requiring expensive and inaccessible instrumentation that fail to provide in vivo information about ethylene. A ruthenium based fluorescent probe for the selective detection of ethylene has recently been developed, and it was envisioned that this probe could be made biocompatible by encasing it within a protein scaffold making it an artificial metalloenzyme. To this end biotinylated N-heterocyclic carbenes (NHCs) were synthesized, which can be appended onto the ruthenium …

A Diverse View Of Science To Catalyse Change: Valuing Diversity Leads To Scientific Excellence, The Progress Of Science And, Most Importantly, It Is Simply The Right Thing To Do. We Must Value Diversity Not Only In Words, But Also In Actions, César A. Urbina-Blanco, Safia Z. Jilani, Isaiah R. Speight, Michael J. Bojdys, Tomislav Friščić, J. Fraser Stoddart, Toby L. Nelson, James Mack, Renã A. S. Robinson, Emanuel A. Waddell, Jodie L. Lutkenhaus, Murrell Godfrey, Martine I. Abboud, Stephen O. Aderinto, Damilola Aderohunmu, Lučka Bibič, João Borges, Vy M. Dong, Lori Ferrins

Faculty and Student Publications

No abstract provided.

Organic Blue Tadf Chromophore Tag For Monitoring Transfection Studies, Brandon G. Bresler

Browse all Theses and Dissertations

A novel organic TADF chromophore was synthesized via a 3-step process to emit a blue fluorescent light upon excitation. The chromophore was covalently attached to a 61% isobutyryl amidated poly(ethyleneimine) (PEI-IBAm0.61) non-viral gene vector utilized in gene transfection experiments. The gene vectors are loaded with a green fluorescent protein (GFP) and are monitored via fluorescence microscopy. The addition of the blue chromophore therefore allows for the monitoring of the movements of the PEI-IBAm0.61 through the full delivery mechanism of the GFP inside the cells. This can give vital information about the overall toxicity of these non-viral gene vectors to biological …

Development And Application Of Chemical Tools To Identify Kinase-Substrate Interactions, Aparni Kithulgoda Gamage

Wayne State University Dissertations

Post translational modifications regulate a variety of biological processes inside the cell.Protein phosphorylation is one such PTM modification catalyzed by protein kinases, which aid to transfer a signal from one place to another inside the cell. However, irregularities in kinase-mediated signaling are often implicated in many diseases, making kinases effective drug targets. To understand kinase-related disease formation and to discover drugs to treat these diseases, it is crucial to have a clear understanding on kinase-mediated cell signaling networks. A current gap in the kinase biology field is a lack of tools to identify which kinase phosphorylates which protein substrate inside …

Spectroscopic Study On Pseudomonas Aeruginosa Biofilm In The Presence Of The Aptamer-Dna Scaffolded Silver Nanoclusters, Bidisha Sengupta, Prakash Adhikari, Esther Mallet, Ronald Havner, Prabhakar Pradhan

Faculty Publications

We report the effectiveness of silver nanocluster (Ag-NC) against the biofilm of Pseudomonas aeruginosa (PA). Two DNA aptamers specific for PA and part of their sequences were chosen as templates for growing the Ag-NC. While circular dichroism (CD) studies determined the presence of secondary structures, UV/Vis absorption, and fluorescence spectroscopic studies confirmed the formation of the fluorescent Ag-NC on the DNA templates. Furthermore, mesoscopic physics-based partial wave spectroscopy (PWS) was used to analyze the backscattered light signal that can detect the degree of nanoscale mass density/refractive index fluctuations to identify the biofilm formation, comparatively among the different aptamers with respect …

Chemistry In Medicine, Olivia Visaggio, Alyssa Bondi, Matthew Gillingham, Hailey Loughlin

Student Research Poster Presentations 2020

The chemistry behind medicine is important and necessary to study many different drugs and their effects. In this project, we focused on the chemical composition and mechanisms of various drugs. The drugs we focused on include Opioids, NSAIDs, and other medications, such as Benzodiazepines and antibiotics. For each drug, we provided its structure as well as the functional groups, which include a part of a molecule that is recognized based on its arrangement of atoms. Organic Chemistry provides individuals with an understanding of various organic compounds, and this field of study is important as it explains the ways in which …

Advancement Of Predictive Modeling Of Zeta Potentials (Ζ) In Metal Oxide Nanoparticles With Correlation Intensity Index (Cii), Andrey A. Toropov, Natalia Sizochenko, Alla P. Toropova, Danuta Leszczynska, Jerzy Leszczynski

Articles

It was expected that index of the ideality of correlation (IIC) and correlation intensity index (CII) could be used as possible tools to improve the predictive power of the quantitative model for zeta potential of nanoparticles. In this paper, we test how the statistical quality of quantitative structure-activity models for zeta potentials (ζ, a common measurement that reflects surface charge and stability of nanomaterial) could be improved with the use of these two indexes. Our hypothesis was tested using the benchmark data set that consists of 87 measurements of zeta potentials in water. We used quasi-SMILES molecular representation to take …

Chemical Synthesis And Biological Evaluation Of Benzimidazoles As Chemotherapeutics, Leonard Barasa

Theses and Dissertations

Nitrogen-containing heterocycles are among the most important structural motifs of chemical substances, which are well represented among natural products, and pharmaceuticals. The presence of nitrogen in heterocycles help to modulates physicochemical properties and the pKa profile of therapeutic leads.

Benzimidazole is a heterocyclic structure and a privileged scaffold that is routinely used during drug discovery efforts. The benzimidazole scaffold has structural similarity to purine which makes it a useful structural motif for the development of pharmaceutical or biological interesting molecules. Benzimidazole derivatives possess a wide variety of biological activities, including anti-bacterial, anti-cancer, and anti-inflammatory activities. Development of synthetic methods to …

Nanotoxicity Of Zrs3 Probed In A Bioluminescence Test On E. Coli Bacteria: The Effect Of Evolving H2s, Olga Zakharova, Alexander Gusev, Jehad Abourahma, Nataliia S. Vorobeva, Dmitry V. Sokolov, Dmitry S. Muratov, Denis V. Kuznetsov, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Materials from a large family of transition metal trichalcogenides (TMTCs) attract considerable attention because of their potential applications in electronics, optoelectronics and energy storage, but information on their toxicity is lacking. In this study, we investigated the toxicity of ZrS3, a prominent TMTC material, toward photoluminescent E. coli bacteria in a bioluminescence test. We found that freshly prepared ZrS3 suspensions in physiological saline solution with concentrations as high as 1 g/L did not exhibit any toxic effects on the bacteria. However, ZrS3 suspensions that were stored for 24 h prior to the bioluminescence tests were very toxic to the bacteria …

Influence Of Conformational Restriction On The Antibacterial Activity And Ribosomal Selectivity Of Aminoglycoside Antibiotics, Michael Gabriel Pirrone

Wayne State University Dissertations

The ever-increasing threat posed by multidrug-resistant infectious bacteria necessitates

the development of novel antibiotics. Aminoglycoside antibiotics are growing in interest due to

their broad spectrum of activity, lack of known drug related allergies, low manufacturing cost,

and their well-studied mechanism of action. The simplification of rational drug design due to the

well-studied mechanism of action is the key to overcoming the issues presented by these drugs,

namely ototoxicity and nephrotoxicity.

A study of the effect of the conformation of the aminoglycoside ring I side chain is

described wherein it was discovered that an increase in a particular conformation augments the …

Quantitative Nmr-Based Biomedical Metabolomics: Current Status And Applications, Alexandra A. Crook, Robert Powers

Department of Chemistry: Faculty Publications

Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, …

Methods Ofmaking And Using Lignin Derivatives, Mark Alan Helle, Chin Li Cheung

Department of Chemistry: Faculty Publications

Materials and methods for preparing reactive lignin and for preparing a bio-based adhesive are described herein.

Electron Density Reconstruction Of Lipids In The 𝐇𝐈𝐈 Phase, Plinio Rosales Lopez, David A. Ruiter, Paul Harper

Summer Research

Lipids are molecules that contain hydrocarbons and are the building blocks of the structure of biological cells. The lipids we study have a polar head (hydrophilic), a nonpolar tail (lipophilic) and are oil soluble. From a biophysical perspective, it is of great interest to study the electron density of these lipids in order to observe different characteristics like the phase change of the lipid structure. The electron density of the hexagonal phase (HII) was modeled this summer. This research has implications in finding a synthetic substitute for lung proteins. In addition, this research has implications in the biological field in …

Expression And Cell Surface Re-Engineering Of Thrombomodulin On Macrophages, Mallorie L. Boron

ETD Archive

Thrombomodulin (TM) is a transmembrane glycoprotein that is primarily expressed on the surface of endothelial cells, where it serves as a receptor of thrombin for protein C activation, which regulates coagulation and inflammation. Research has revealed that TM is also expressed in immune cells, including monocytes and macrophages, however, its function is unclear. In this dissertation study, the TM expression in THP-1 monocytes upon their differentiation to macrophages was profiled. Due to the beneficial roles of TM, the protein has caught the attention to be used as a therapeutic. A recombinant form of TM can be expressed that contains EGF-like …

Determination Of Dynorphins And Tnf- A By Lc-Ms/Ms In Biological Samples: Applicable To Studying Inflammatory Mechanisms, Karthik Chandu

ETD Archive

Dynorphins are endogenous opioid peptides that have been implicated as initiators ofimmune and inflammatory response through upregulation ofinflammatory cytokine and chemokine production, as well having a role in glutamate-induced neuro-inflammation and neurotoxicity. Being extremely potent peptides, the physiologic concentrations of dynorphins are very low ranging from 0.16 pg/mL during the absence of a stimulus to 23.5 pg/mL when stimulated in disease condition. Previously published HPLC-mass spectrometry techniques have insufficient detection capabilities for quantification and detection ofdynorphins. As a result, immunoassay quantification has been the most utilized technique for analysis of dynorphins in physiologic samples. Although being sensitive, immunoassays have some …

Computational Modeling Of Coumarin Acidity, George Du Laney, Leah Knoor, Mark Muyskens

Summer Research

This summer’s research focused on the photoacidic behavior of hydroxylated coumarins.

A photoacid has two primary pKa values : ground state (pKa ) and excited state (pKa *). Computational modeling was used to predict these values.

Exploring The Scope And Limitations Of The Oxidative Deamination Of N-Acetyl Neuraminic Acid, Mohammed Bakr Hawsawi

Wayne State University Dissertations

Sialic acids are molecules of importance in the fields of carbohydrate chemistry and glycoscience, and their diversity make them even more attractive to scientific research. Modifications of sialic acid derivatives may lead to several biological and chemical features that can be utilized for medicinal purposes. The modern drug therapy is dependent on the chemical discoveries of potent and effective molecules. N-Acetyl neuraminic acid is the parent and most common molecule in sialic acid family that received considerable attention in glycochemical research. This dissertation explores the scope as well as the limitations of the Zbiral oxidative deamination of N-acetyl neuraminic acid …

In Situ Cultivation Of Potential Pah Degrading Bacteria From Coastal Sediment, Kyle Benkel

Honors Undergraduate Theses

Oil spills can introduce potentially carcinogenic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), into coastal environments. Bioremediation uses the natural microorganisms in the environment to remove these pollutants. Traditional studies of these organisms are limited in the types of bacteria isolated due to the limitations of traditional culturing methods. In this study, diffusion chambers were used to culture and isolate potential PAH degrading bacteria from the coastal sediment obtained from the Chandeleur Islands. The diffusion chambers trapped bacteria in agar that contained 1 ppm benzo[a]pyrene. The bacteria were isolated from the diffusion chambers, and the 16S rRNA gene was sequenced …

Detection Of A Peptide Hormone - Somatostatin - Label-Free Split-Aptameric Probes, Charles A. Dowis

Honors Undergraduate Theses

Peptide hormones are important biomolecules that transduce downstream effects such as cell proliferation, regulation, and gene expression. Their levels have been upregulated in various disorders such as cancer, yet detection methods are lacking. We designed two split aptamer-based assays for the detection of a peptide hormone – Somatostatin (SST) – with different signal readouts: fluorescent readout based on light-up aptamers and the colorimetric readout of ABTS peroxidation from a G-quadruplex. We used an already selected split-aptamer –SSTA5–for SST for our designs and we had expected the developed detection systems to exhibit detection and quantification capabilities that would hopefully allow their …

Development Of A Computer Algorithm For Generation Of Primers For Nucleic Acid Sequence Based Amplification (Nasba), Rohit Karnati

Honors Undergraduate Theses

Nucleic acid sequence based amplification (NASBA) is a primer based isothermal method of RNA/DNA amplification. Currently, primer design for NASBA has been restricted to hand creating sequences of oligonucleotides that must follow a set of rules to be compatible for the amplification process. This process of hand-creating primers is prone to error and time intensive. The detection of mutants, post amplification, also offers a benefit in point of care scenarios and the design of hybridization probes for sequences in the region of amplification is also an erroneous and time intensive process. By creating a program to design primers and hybridization …

Synthesis Of Polyacrylic Acid - Dopamine Nanoparticles As Radical Scavengers For Antioxidant Applications, Russell D. Cox

Honors Undergraduate Theses

The antioxidant activity of novel drugs has been of increasing interest in recent years. Free radicals are linked as a cause to many diseases such as atherosclerosis and cancer,1 so development of drugs that can scavenge and break down free radicals is needed. One such potential solution is using dopamine, which is water-soluble and an antioxidant. However, the tendency of antioxidant drugs reacting undesirably with proteins and other biochemical compounds is a big issue for the drugs' antioxidant potential. One solution is by encapsulating the antioxidant compound in biocompatible polymer nanoparticles. In this project, dopamine is bound to the polymer …

Thermal Atomic Layer Deposition Of Silver Metal Films: Synthesis And Characterization Of Thermally Stable Silver Metal Precursors, Harshani Jayabahu Arachchilage

Wayne State University Dissertations

ABSTRACT

THERMAL ATOMIC LAYER DEPOSITION OF SILVER METAL FILMS: SYNTHESIS AND CHARACTERIZATION OF THERMALLY STABLE SILVER METAL PRECURSORS

by

HARSHANI JAYABAHU ARACHCHILAGE

August 2020

Advisor: Professor Charles H. Winter

Major: Chemistry (Inorganic)

Degree: Doctor of Philosophy

Traditional film deposition techniques such as PVD and CVD are widely used in the microelectronics industry. However, the lack of thickness control and conformality requirements limit these techniques for current and future applications. By contrast, ALD offers the deposition of ultra-thin conformal films with accurate thickness control due to the self-limiting growth behavior. Ag metal has the lowest resistivity (1.59 µΩ cm) of all …

Preliminary Isolation And Characterization Of Root Extract Components Of Dalea Jamesii, Hyojin Ahn

Undergraduate Honors Theses

The plant genus Dalea (Fabaceae) has been found to be prolific in its production of phenolic secondary metabolites including flavonoids, isoflavonoids, chalcones, pterocarpans, stilbenes, and other biosynthetically related compounds. Biological testing has revealed wide-ranging activities for these metabolites in many prior reports. Dalea jamesii has not yet been investigated for its chemical content. This study will be conducted with the hypothesis that unique phenolic secondary metabolites will be produced in the roots of D. jamesii. It will be of interest to determine if the isolated metabolites exhibit biomedically related activities. It will also be of interest to investigate whether the …

Environmental Forensics Of Complexly Contaminated Sites: A Complimentary Fingerprinting Approach, Michael A. Kruge, Azucena Lara-Gonzalo, José Luis Gallego

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The environmental forensics approach is most often applied in petroleum and fuel spill incidents, for which sophisticated chemical fingerprinting procedures have evolved. In cases in which pollutant discharges occur in settings with prior contamination, more care must be taken in source discrimination, requiring further advances in methodology. Additional obstacles can arise if the spill is an atypical industrial discharge. This would necessitate painstaking characterization of unfamiliar substances lying outside of existing regulatory regimes and thus overlooked by mandated analytical protocols (i.e., contaminants of emerging concern). Towards these ends, this paper presents a systematic, multi-faceted GC-MS approach using the saturated, aromatic, …

Characterization Of Coal Particles In The Soil Of A Former Rail Yard And Urban Brownfield: Liberty State Park, Jersey City (Nj), Usa, Diane F. Hagmann, Michael A. Kruge, Nina M. Goodey, Jennifer Adams Krumins

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

From the 1850's until the 1960's, the Central Railroad of New Jersey was among several major railways shipping anthracite and bituminous coal to the New York City area, transferring coal from railcar to barge at its extensive rail yard and port facility in Jersey City. The 490 ha Liberty State Park was developed on the site after the rail yard closed, but a ca. 100 ha brownfield zone within the park remains off limits to visitors pending future remediation. As part of an environmental forensic and industrial archeological investigation of this zone, the present study characterizes anthracite and bituminous coal …