Digital Commons Network^™

The Importance Of Properly Modeling The Hydrogen Bond In Histidine, Falonne M. Tchodimo, Guoquan Zhou, Hua-Jun Fan

Pursue: Undergraduate Research Journal

The hydrogen bond plays a vital role in many reactions. This study is to investigate the effect of different hydrogen bonding modes, such as single and double hydrogen bonds, via the quantum mechanic (QM) methods. Four histidine models (A, B, C, and D) with different numbers of intra-molecular hydrogen bonds were studied. The QM model results indicate that the double hydrogen bond is plausible and has a more stable geometry. However, this study suggests that the data from QM methods require further evaluation with solvation models to produce an even better energy profile.

Pursue Undergraduate Research Journal Volume 2 (Issue 1) 2019

Pursue: Undergraduate Research Journal

The scholarly journal, “PURSUE: Undergraduate Research Journal” (ISSN 2473-6201), provides undergraduates an avenue to publish their original research abstracts and articles in the following areas: psychology, sociology, biology, chemistry, physics, engineering, computer science, mathematics, humanities, agriculture, architecture, health, business, and education (this list is not exclusive).

The original research articles included in this journal are peer reviewed and selected by the journal’s Editorial Board. The review process allows undergraduate researchers to receive feedback from notable scientists in their field of study and teach them about the publication process. Publication of their work will not only inform the scientific community; it …

First Generation Amperometric Biosensing Of Galactose With Xerogel-Carbon Nanotube Layer-By-Layer Assemblies, Najwa Labban, Mulugeta B. Wayu, Ciara M. Steele, Tess S. Munoz, Julie A. Pollock, William S. Case, Michael C. Leopold

Chemistry Faculty Publications

A first-generation amperometric galactose biosensor has been systematically developed utilizing layer-by-layer (LbL) construction of xerogels, polymers, and carbon nanotubes toward a greater fundamental understanding of sensor design with these materials and the potential development of a more efficient galactosemia diagnostic tool for clinical application. The effect of several parameters (xerogel silane precursor, buffer pH, enzyme concentration, drying time and the inclusion of a polyurethane (PU) outer layer) on galactose sensitivity were investigated with the critical nature of xerogel selection being demonstrated. Xerogels formed from silanes with medium, aliphatic side chains were shown to exhibit significant enhancements in sensitivity with the …

Halogen Bonding Interactions For Aromatic And Non-Aromatic Explosive Detection, Arjun K. A. Jaini, Lillian B. Hughes, Michael K. Kitimet, Kevin John Ulep, Michael C. Leopold, Carol A. Parish

Chemistry Faculty Publications

Improved sensing strategies are needed for facile, accurate and rapid detection of aromatic and nonaromatic explosives. Density functional theory was used to evaluate the relative binding interaction energies between halogen-containing sensor model molecules and nitro-containing explosives. Interaction energies ranged from –18 to –14 kJ/mol and highly directional halogen bonding interactions were observed with bond distances ranging between 3.0 and 3.4 Å. In all geometry optimized structures, the sigma-hole of electropositive potential on the halogen aligned with a lone pair of electrons on the nitro-moiety of the explosive. The computational results predict that the strongest interactions will occur with iodine-based sensors …

Effect Of Carbonaceous Nanoparticles On Naturally Occurring Iron Reduction By Carboxylates, Ashleen Reddy

All Master's Theses

The emission of ambient particulate matter (PM) is regulated by many institutions due to the detrimental effects on health, environment and climate; yet many underlying mechanisms of PM reactivity are still not well understood. In the current study, the effect of carbonaceous nanoparticles (CNPs), contained within ultrafine PM (particle diameter ≤ 100 nm), is investigated on naturally occurring processes that increase the abundance of bioavailable iron. Enhancing iron bioavailability (i) increases primary productivity of iron-limited microorganisms, affecting the carbon cycle and global climate, and (ii) increase toxicity of inhaled particles through the associated production of reactive oxygen species (ROS). Specifically, …

The Chemical Analysis And Biological Activities Of The Secondary Metabolites From Dalea Mollis And Dalea Albiflora, Nicholas Peter Hansen

All Master's Theses

Multidrug resistance has increased since the introduction of drugs used to prevent growth and kill microorganisms in a host. This has caused a worldwide search to discover new drugs effective against microorganisms. Mechanisms of drug resistance include, but are not limited to, the production of biofilms and efflux pumps. Efflux pumps prevent antimicrobial drugs from reaching their biological target, so the coordinated use of efflux pump inhibitors and antimicrobial drugs has been identified as a potential treatment for multidrug-resistant microorganisms. The secondary metabolites of Dalea mollis and Dalea albiflora were tested against multidrug-resistant (MDR) and engineered strains of the fungi …

Modular Synthesis And Hydroalkylation Of Vicinally Functionalized Ketopiperazines: A Solution To The Piperazine Problem, Antonio Moreno

All Master's Theses

The stereocontrolled synthesis of functionalized piperazines is of great interest to pharmaceutical companies owing to their multiple biological activities such as antidepressant, antiparasitic, anticancer and antiretroviral. Current methods towards functionalized piperazines include intramolecular cyclization of appropriately tethered on acyclic precursors as well as α-C–H functionalization of intact piperazine rings. Although effective for the most part, these methods suffer from drawbacks such as the use of expensive catalysts, potentially toxic reagents, limited scope and functional group compatibility. Seeking to side-step some of the aforementioned limitations, we herein describe a step-economical-, cost-effective-, transition metal-free-, and mild approach to highly functionalized piperazines, including …

Seasonal Soil Carbon Fluxes In Transitioning Agricultural Soils In Central Washington State: Relations To Land-Use, Environmental Factors And Soil Carbon-Nitrogen Characteristics, Brandon Kautzman

All Master's Theses

Changing agricultural land-use practices to increase soil carbon sequestration contributes to climate change mitigation and improved food security by moving CO₂ from the atmosphere into soil as soil organic carbon (SOC). In 2016, a farm in Thorp, Washington, Spoon Full Farm, began converting land historically farmed using conventional methods of tillage and synthetic fertilizers to conservation farming methods with direct seeding and organic soil amendments with a goal of sequestering carbon in the soil. This project evaluates relationships of soil CO₂ respiration and net ecological exchange (NEE) with land-use types, seasonal environmental factors (air temperature, relative humidity, soil …

Effect Of Iron On The Oxidative Capacity Of Carbonaceous Nanoparticles, Daniel Chavez

All Master's Theses

Inhalation of ambient particulate matter (PM_2.5) emitted during combustion of fuels has negative impacts on human health. Triggered in part by the generation of reactive oxygen species (ROS) that lead to oxidative stress, significant gaps exist in the understanding of the detailed chemistry of these detrimental effects. Trace metals and carbonaceous material of the nanometer-sized particles contained in PM_2.5 have been implicated as key players in causing these effects. Here, the role of Fe is investigated with carbonaceous nanoparticles (CNP) while mimicking simple cellular conditions. By adding environmentally representative and controlled concentrations of Fe(II) or Fe(III) to …

Esterification Of Lignin As Carbon Fiber Production Precursor​, Jarudech Rakphong

Chulalongkorn University Theses and Dissertations (Chula ETD)

This research investigated the optimized condition (i.e., esterifying agent, reaction time, reaction temperature) to modify lignin for utilization as a precursor in carbon fiber production. The lignin was successfully modified by esterification reaction in dimethylformamide solvent under different reaction temperatures and times using different types of fatty acid chloride including butyryl chloride, octanoyl chloride, and lauroyl chloride as an esterifying agent. The effects of fatty acid chloride chain length and degree of substitution on the chemical structure, functional groups, morphology, crystallinity, thermal properties, and solubility of esterified-lignin were studied. The chemical structure of the obtained product was characterized by FTIR …

Chemical Constituents From The Twigs And Branches Of Garcinia Schomburgkiana, Nindyashinta Darnasmara

Chulalongkorn University Theses and Dissertations (Chula ETD)

The phytochemical investigation from the dichloromethane extract of the twigs and branches of Garcinia schomburgkiana led to the isolation of fourteen known compounds, including 2'-hydroxydihydrochalcone (1), 1-(2'-6'-dihydroxyphenyl)-3-phenyl-1-propanone (2), cudratricusxanthone K (3), pancixanthone A (4), euxanthone (5), 1,4,5-trihydroxyxanthone (6), osajaxanthone (7), 1,2,7-trihydroxyxanthone (8), 1,3,7-trihydroxy-2,4-diprenylxanthone (9), 1,5-dihydroxyxanthone (10), 7-epiclusianone (11), oblongifolin C (12), clusiacitran B (13), and aucuparin (14). Among all isolated compounds, 2'-hydroxydihydrochalcone, 1-(2'-6'-dihydroxyphenyl)-3-phenyl-1-propanone, and cudratricusxanthone K were isolated from genus Garcinia for the first time. Moreover, 7-epiclusianone, pancixanthone A, 1,4,5-trihydroxyxanthone, osajaxanthone, 1,2,7-trihydroxyxanthone, and 1,3,7-trihydroxy-2,4-diprenylxanthone discovered in G. schomburgkiana for the first time. The structures of all isolated compounds were characterized …

Florida Science: The Science That Makes Florida Different, Terence W. Cavanaugh

Secondary Level Resources

This book was created to assist students with their understanding of how science occurs in Florida. When teaching science or any subject it’s important to remember to begin with the concrete and then move to the abstract. I have found that it has helped my students when I begin by teaching science concepts in a concrete manner and expand from there. For example, when I taught about topographic maps, the students were much more successful in their learning when I started with local topographic maps that included the school and the surrounding area than with places that had mountains or …

Environmental Forensic Characterization Of Former Rail Yard Soils Located Adjacent To The Statue Of Liberty In The New York/New Jersey Harbor, Diane Hagmann, Michael A. Kruge, Matthew Chi-Hymn Cheung, Maria Mastalerz, José Luis Gallego, Jay Prakash Singh, Jennifer Krumins, Xiaona N. Li, Nina M. Goodey

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Identifying inorganic and organic soil contaminants in urban brownfields can give insights into the adverse effects of industrial activities on soil function, ecological health, and environmental quality. Liberty State Park in Jersey City (N.J., USA) once supported a major rail yard that had dock facilities for both cargo and passenger service; a portion remains closed to the public, and a forest developed and spread in this area. The objectives of this study were to: 1) characterize the organic and inorganic compounds in Liberty State Park soils and compare the findings to an uncontaminated reference site (Hutcheson Memorial Forest); and 2) …

Design And Development Of Chemically And Biologically Stable Salvinorin-Based Ligands For Opioid Receptors, Tanner Neilson

Honors Theses

The number of opioid prescriptions as a method in pain management increased dramatically in the mid 1990’s following Dr. James Campbell’s 1995 Presidential address to the American Pain Society, where he called for patient pain to be included as a vital sign. The rapid increase in prescriptions in the early 2000’s coupled with a massive effort by pharmaceutical companies to downplay the addictiveness of these drugs has led to a consistent increase in opioid-related drug overdoses, with 47,600 of 70,237 drug related deaths involving opioids in 2017. Opioid analgesics most commonly act upon the mu-opioid receptor (MOR), which is one …

The Impact Of Post Translational Modification On The Aggregation Of The Ss-Amyloid Peptide In The Presence Or Absence Of Lipids, Albert Walton Pilkington Iv

Graduate Theses, Dissertations, and Problem Reports (ETD)

Alzheimer’s disease (AD) is a neurodegenerative condition afflicting 5.7 million Americans with no effective treatments. The pathology of AD is described by the formation of neurotoxic oligomers formed by the self-assembly of amyloid-β (Aβ). The affinity of oligomers for cellular membranes disrupts calcium homeostasis and is believed to be the underlying cause of neurotoxicity; however, due to the metastability of oligomers, it has been difficult to understand their role in membrane interactions and self-assembly. Here we utilize post translational modifications (PTM) to understand the role of specific amino acids on Aβ₄₀-membrane interactions and self-assembly. We employ ThT, AFM, …

Biogeochemical Response To Vegetation And Hydrologic Change In An Alaskan Boreal Fen Ecosystem, Danielle L. Rupp

Dissertations, Master's Theses and Master's Reports

Boreal peatlands store approximately one third of the earth’s terrestrial carbon, locked away in currently waterlogged and frozen conditions. Peatlands of boreal and arctic ecosystems are affected increasingly by shifting hydrology caused by climate change. The consequences of these relatively rapid ecosystem changes on carbon cycling between the landscape and the atmosphere could provide an amplifying feedback to climate warming. Alternatively, the advancement of terrestrial vegetation into once waterlogged soils could uptake carbon as a sink. Previous work suggests that fens will become an increasingly dominant landscape feature in the boreal. However, studies investigating fens, their response to hydrologic and …

Development Of Cooperative Photocatalysts, Tossapong Phuangburee

Chulalongkorn University Theses and Dissertations (Chula ETD)

Photosynthesis involves electron/energy transfer between photocatalyst and catalyst. This concept called “cooperative photocatalyst” is of interest for researchers to develop sustainable photocatalytic systems. In this dissertation, two catalytic systems including graphene oxide (GO) and copper complexes as catalysts were combined with photocatalysts to achieve alcohol oxidation and atom-transfer radical addition (ATRA), respectively. In the first system, GO was modified with porphyrin derivatives (TPP or ZnTPP) using sonication method. The prepared composites were characterized by spectroscopic techniques such as UV-Vis, FTIR, Raman spectroscopy. The photocatalytic activity of the GO-ZnTPP was significantly lower than that of GO-TPP due to the interactions between …

Spatial Patterns Of Particulate Organic Carbon Concentrations And Isotopic Signatures Across A Salinity Gradient In A River Dominated Estuary, Lauren E. Alvaro, John C. Lehrter, Mai Fung

Gulf and Caribbean Research

No abstract provided.

The Synthesis Of Ferrocene-Based Ionic Liquids, Stephen Petrochko

Williams Honors College, Honors Research Projects

Ionic liquids are compounds which are held together through ionic interactions, and can be classified as salts. However, while most salts have very high melting temperatures, ionic liquids are a class of compounds that can melt at very low temperatures, often at room temperatures. Ionic liquids can have optimal electronic properties for electrochemical applications, particularly for the easy transport of charges. Some new materials are being explored for the development of ionic liquids; one of these materials is ferrocene. Varying the substituents which are attached to ferrocene may produce a material that can be used as an electrolyte in energy …

Xflow: An Algorithm For Extracting Ion Chromatograms, Mathew M. Gutierrez, Rob Smith

Graduate Student Theses, Dissertations, & Professional Papers

Abstract: Mass spectrometry is a fundamental tool for modern proteomics. The increasing availability of mass spectrometry data paired with the increasing sensitivity and fidelity of the instruments necessitates new and more potent analytical methods. To that end, we have created and present XFlow, a feature detection algorithm for extracting ion chromatograms from MS1 LC-MS data. XFlow is a parameter-free procedurally agnostic feature detection algorithm that utilizes the latent properties of ion chromatograms to resolve them from the surrounding noise present in MS1 data. XFlow is designed to function on either profile or centroided data across different resolutions and instruments. This …

Antitumor Properties Of Imidazolium Salts, Jenna Frantz

Williams Honors College, Honors Research Projects

This is the final write-up for an honors research project for the University of Akron Williams Honors College. Synthesis of novel imidazolium salts was conducted. Following synthesis of imidazolium salts, the stability of the compound was tested at 37°C over a 72-hour period to give preliminary information about drug stability in vivo. 2D NMR was also conducted to confirm the structure of TPP-1. The student wrote an experimental protocol for the use of C57BL/6 mice and performed the online CITI training by the IRB to prepare to work with animals in a study of the antitumor properties of imidazolium salts …

X-Ray Crystal Structure Of Au36(Sph-Pch3)24 Nanomolecules, Vigneshraja Ganeshraj

Electronic Theses and Dissertations

Au36(SR)24 is one of the most comNanomolecules (NM) in gold NM field and crystal structures of Au36(SR)24 with different thiolate protecting ligand such as tert-butylbenzene thiol, thiophenol and cyclopentane thiol have been reported. It has been predicted that aromatic thiol protected Au36(SR)24 NM have same core structures like the other reported Au36(SR)24 NMs. Due to the steric and electronic conjugation effects the staples on the gold core exhibit minor changes in the bond length without affecting the gold core. By varying the Gold:Thiol ratio the NM size can be controlled. Herein, we report the synthesis, isolation and characterization of two …

A Computational Approach To Predicting And Understanding New Psychoactive Substances (Nps) For Developing A Database For State And Federal Crime Laboratories, Caroline Amelia Spencer

Electronic Theses and Dissertations

The object of this dissertation was to use a computational approach to predict and understand new psychoactive substances (NPS) to develop a database for state and federal crime. The primary scope of the dissertation was to better understand the interactions that take place between new psychoactive substances and their corresponding receptors. Through analysis of the interactions between the amino acids within the receptors and the NPS an understanding into the pharmacology and toxicology of these drugs can be gained. NPS such as synthetic cannabinoids fentanyl and its analogs and kratom have become more problematic for both state and federal crime …

The Dynamic Nature And Biophysical Characterization Of Isu1, Fe-S Cluster Assembly Scaffold Protein In Saccharomyces Cerevisiae, And Its Significance To Human Disease, Brianne Elizabeth Lewis

Wayne State University Dissertations

Mitochondrial Fe-S cluster biosynthesis is accomplished within yeast utilizing the biophysical characteristics of the “Isu1” scaffold protein. As a member of a highly homologous protein family, Isu1 has sequence conservation with orthologs and a conserved ability to assemble [2Fe-2S] clusters. Regardless of species, scaffold orthologs can exist in both “disordered” and “structured” conformations and is directly related to conformations utilized during Fe-cofactor assembly. During assembly, the scaffold directs the delivery and the utilization of both Fe(II) and sulfide substrates in order to produce [2Fe-2S] clusters, however Zn(II) binding can alter the activity of the scaffold with stabilizing the protein in …

Neuroprotective Effects Of Melatonin And Celecoxib Against Ethanol-Induced Neurodegeneration: A Computational And Pharmacological Approach, Lina T. Al Kury, Alam Zeb, Zain Ul Abidin, Nadeem Irshad, Imran Malik, Arooj Mohsin Alvi, Atif Ali Khan Khalil, Sareer Ahmad, Muhammad Faheem, Arif Ullah Khan, Fawad Ali Shah, Shupeng Li

All Works

© 2019 Al Kury et al. This work is published and licensed by Dove Medical Press Limited. Purpose: Melatonin and celecoxib are antioxidants and anti-inflammatory agents that exert protective effects in different experimental models. In this study, the neuroprotective effects of melatonin and celecoxib were demonstrated against ethanol-induced neuronal injury by in silico, morphological, and biochemical approaches. Methods: For the in silico study, 3-D structures were constructed and docking analysis performed. For in vivo studies, rats were treated with ethanol, melatonin, and celecoxib. Brain samples were collected for biochemical and morphological analysis. Results: Homology modeling was performed to build 3-D …

Compound-Specific Isotope Analysis Of Amino Acids In Biological Tissues: Applications In Forensic Entomology, Food Authentication And Soft-Biometrics In Humans, Mayara Patricia Viana De Matos

Graduate Theses, Dissertations, and Problem Reports (ETD)

In this work we demonstrate the power of compound-specific isotope analysis (CSIA) to analyze proteinaceous biological materials in three distinct forensic applications, including: 1) linking necrophagous blow flies in different life stages to their primary carrion diet; 2) identifying the harvesting area of oysters for food authentication purposes; and 3) the ability to predict biometric traits about humans from their hair.

In the first application, we measured the amino-acid-level fractionation that occurs at each major life stage of Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) blow flies. Adult blow flies oviposited on raw pork muscle, beef muscle, or chicken liver. Larvae, pupae …

Nanomaterials Of Iron Oxide, Boron, And Boron Nitride: On The Path To Magnetic Guided Bioconjugates For Medical Applications, John Ryan Wozny

Graduate Research Theses & Dissertations

The functionalization of boron-based bioconjugates has long been studied for their potential use as a drug candidate for boron neutron capture therapy (BNCT). Also, magnetic nanoparticles have received greater attention due to their interesting magnetic properties and behaviors for selectively guiding them with an external magnetic field through the blood. A combination of the two ideas gives the framework for nanotechnology that has the potential to revolutionize drug delivery systems. This thesis will focus systematically on individual elements required for the many moving pieces required for magnetic drug targeting.

The research discussed in this thesis is divided into three parts. …

Thermostability And Excision Activity Of Polymorphic Forms Of Hogg1, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

Objectives: Reactive oxygen species (ROS) oxidize guanine residues in DNA to form 7,8-dihydro-oxo-2′-deoxyguanosine (8oxoG) lesions in the genome. Human 8-oxoguanine glycosylase-1 (hOGG1) recognizes and excises this highly mutagenic species when it is base-paired opposite a cytosine. We sought to characterize biochemically several hOGG1 variants that have been found in cancer tissues and cell lines, reasoning that if these variants have reduced repair capabilities, they could lead to an increased chance of mutagenesis and carcinogenesis. Results: We have over-expressed and purified the R46Q, A85S, R154H, and S232T hOGG1 variants and have investigated their repair efficiency and thermostability. The hOGG1 variants showed …

Green Chemistry In United States Science Policy, Emily Jarvis

Chemistry and Biochemistry Faculty Works

Although optimizing each of the Twelve Principles of Green Chemistry is necessary for achieving the greenest possible chemistry in the lab, there are additional creative ways to promote green chemistry not encompassed by these. Communicating to society the importance of green chemistry beyond the laboratory is essential. Of course, doing this effectively presents distinct challenges to those encountered when designing chemical syntheses. Here, I discuss several observations from my time working in federal science policy as an American Association for the Advancement of Science/American Chemical Society Congressional Science Fellow in the United States Senate. I suggest a practical science policy …

Multidimensional Mass Spectrometry Of Chemonic™ Ccg-6 Nonionic Surfactant With Separation By Polarity And Shape, Charles Johnson

Williams Honors College, Honors Research Projects

Chemonic™ CCG-6 surfactant is a water-soluble poly(ethylene glycol) (PEG) conjugated alkyl glyceride emollient. This surfactant exists as a complex mixture of a glycerol cores conjugated with poly(ethylene glycol) branches (PEGylation) that were partially esterified with caprylic (C8) and capric (C10) acids. These may be esterified on one, two, or all three arms of the glyceride. The architecture of the structures in this mixture was studied using multidimensional mass spectrometry (MS). Mass spectrometry was interfaced with ultra-performance liquid chromatography (UPLC) and ion mobility (IM) separation. The mixture was separated by reversed-phase LC, oligomers of the star-branched polymer were separated according to …