Chemistry Commons^™

A Nosy Neighbor: Purification And Functional Characterization Of Lpg2149, Ashley M. Holahan

The Journal of Purdue Undergraduate Research

Ubiquitination is a process that marks proteins for various cell-signaling pathways, namely protein degradation and other processes. Th ese pathways are essential in a wide array of cellular processes, including defense mechanisms against invading pathogens. Th e ubiquitination process is universally found in all eukaryotic organisms, including plants and animals, and thus plays a vital role in cellular homeostasis. Recently, more discoveries have been made on prokaryotic effector proteins that hijack the ubiquitination system even when they do not possess a ubiquitin system of their own. MavC, also known as lpg2147 (Gan, Nakayasu, Hollenbeck, & Luo, 2019; Puvar et al., …

Effects Of Nitrate On Arsenic Mobilization During Aquifer Storage And Recovery, Hania Hawasli

USF Tampa Graduate Theses and Dissertations

Aquifer storage and recovery technology is used to sustain water resources and to prevent saltwater intrusion. The injected water can come from various resources, including treated wastewater. In pilot ASR studies in the Tampa Bay region, researchers found high As concentrations in the recovered water from the oxidation of the arsenopyrite that is embedded in the aquifers. The presence of dissolved O2 in the injected water is a major factor in the arsenopyrite oxidation during ASR, however the effects of NO3- on the arsenopyrite has not been studied yet. This is an important knowledge gap because injected water may contain …

Hydrogen/Deuterium Exchange Measurements May Provide An Incomplete View Of Protein Dynamics: A Case Study On Cytochrome, Pablo M Scrosati, Victor Yin, Lars Konermann

Chemistry Publications

Many aspects of protein function rely on conformational fluctuations. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) provides a window into these dynamics. Despite the widespread use of HDX-MS, it remains unclear whether this technique provides a truly comprehensive view of protein dynamics. HDX is mediated by H-bond-opening/closing events, implying that HDX methods provide an H-bond-centric view. This raises the question if there could be fluctuations that leave the H-bond network unaffected, thereby rendering them undetectable by HDX-MS. We explore this issue in experiments on cytochrome

Post-Polymerization ‘Click’ End-Capping Of Polyglyoxylate Self-Immolative Polymers, Peter G. Maschmeyer, Xiaoli Liang, Allison Hung, Oksana Ahmadzai, Annmaree L. Kenny, Yuan C. Luong, Timothy N. Forder, Haoxiang Zeng, Elizabeth R. Gillies, Derrick A. Roberts

Chemistry Publications

No abstract provided.

Bioadhesives, 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.

Organic Synthesis, Kevin M. Shea, Libretext

Open Educational Resources: Textbooks

My goal in writing this text is to help advanced undergraduates and beginning graduate students learn key topics in organic chemistry that often don't come up in your Organic I and II classes. So, you can think about this as an Organic III text. My focus is on key reaction types that enable the construction of complex organic molecules: pericyclic reactions, transition metal catalyzed reactions, rearrangements, fragmentations, radical reactions, and carbene reactions. I hope that this text is a resource that helps you understand the mechanisms of these reactions and enables you to use these reactions in your own syntheses. …

Lateral Growth Of Xenon Hydrate Films On Mica, Avinash Kumar Both, Chin Li Cheung

Department of Chemistry: Faculty Publications

In this paper, we report an in situ optical microscopy study of lateral growth of xenon (Xe) hydrate thin films on mica at sub-zero temperatures. The interactions between a solid surface and water molecules can strongly affect the alignment of water molecules and induce ice-like ordered structures within the water layer at the water-surface interface. Mica was chosen as a model surface to study the surface effect of hydrophilic sheet silicates on the lateral growth of Xe hydrate films. Under the experimental conditions, the lateral growth of Xe hydrate films was measured to be at an average rapid rate of …

National Chemistry Week: From Irl To The Web, Ilayda Kelley, Daniela Mesa Sanchez

Purdue Journal of Service-Learning and International Engagement

National Chemistry Week, an outreach program initiated by the American Chemical Society (ACS), encourages scientists to bring their love of chemistry to their community. Celebrated nationwide, ACS invites businesses, schools, and individuals to organize and participate in community events to promote the value of chemistry in everyday life. The Purdue graduate student chapter of Iota Sigma Pi, a national honor society for women in chemistry, annually organizes one such celebration. On a normal year, this event is a large logistical undertaking in which 100+ volunteers go directly to over 70 local elementary school classrooms and perform a series of activities …

Synergistic Anticancer Response Of Curcumin And Piperine Loaded Lignin-G-P (Nipam-Co-Dmaema) Gold Nanogels Against Glioblastoma Multiforme, Xinyi Zhao, Bilal Javad, Daxing Cui, James Curtin, Furong Tian

Articles

Glioblastoma multiforme (GBM) is the most aggressive and commonly diag- 11 nosed brain cancer and presents a strong resistance to routine chemotherapeutic drugs. 12 The present study involves the synthesis of Lignin-g- p (NIPAM-co-DMAEMA) gold 13 nanogel, loaded with curcumin and piperine to treat GBM. The application has three 14 functions: (1) overcome the limitations of biodistribution, (2) enhance the toxicity of an- 15 ticancer drugs against GBM, (3) identify the uptake pathway. Atom transfer radical 16 polymerization was used to synthesize the Lignin-g-PNIPAM network, crosslinked with 17 the gold nanoparticles (GNPs) to self-assemble into nanogels. The size distribution and …

Self-Immolative Dendron Hydrogels, Karanpreet Gill, Xueli Mei, Elizabeth Gillies

Chemistry Publications

Smart hydrogels are of great interest in areas such as drug delivery and sensing. Dendrimer-based hydrogels can exhibit tunable properties due to their structural precision. We prepared hydrogels from self-immolative dendrons. Controlled hydrogel degradation in response to light was demonstrated and the hydrogel properties as a function of dendron generation were compared.

Systematic Evaluation Of A Novel Self-Healing Poly(Acrylamide-Co-Vinyl Acetate)/Alginate Polymer Gel For Fluid Flow Control In High Temperature And High Salinity Reservoirs, Jingyang Pu, Baojun Bai, Thomas P. Schuman

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Preferential fluid flow often occurs when water and CO₂ is injected into mature oilfields, sig-nificantly reducing their injection efficiency. Particle gels have been evaluated and applied to control the short circulation problems. This study systematically investigated a novel poly(acrylamide-co-vinyl acetate)/alginate-based interpenetrated gel system (Alg-IPNG) which is designed to control the preferential fluid flow problems in high-temperature reservoirs. Chromium acetate was incorporated into the gel system to provide the delayed crosslinking feature of the particle gels. The alginate polymer system can also take advantage of the Ca²⁺ ions in the formation water, which exist in most reservoirs, to reinforce …

Cyclic Peptide-Gadolinium Nanocomplexes As Sirna Delivery Tools, Amir Nasrolahi Shirazi, Muhammad Imran Sajid, Dindyal Mandal, David Stickley, Stephanie Nagasawa, Joshua Long, Sandeep Lohan, Keykavous Parang, Rakesh Kumar Tiwari

Pharmacy Faculty Articles and Research

We have recently reported that a cyclic peptide containing five tryptophan, five arginine, and one cysteine amino acids [(WR)₅C], was able to produce peptide-capped gadolinium nanoparticles, [(WR)₅C]-GdNPs, in the range of 240 to 260 nm upon mixing with an aqueous solution of GdCl₃. Herein, we report [(WR)₅C]-GdNPs as an efficient siRNA delivery system. The peptide-based gadolinium nanoparticles (50 µM) did not exhibit significant cytotoxicity (~93% cell viability at 50 µM) in human leukemia T lymphoblast cells (CCRF-CEM) and triple-negative breast cancer cells (MDA-MB-231) after 48 h. Fluorescence-activated cell sorting (FACS) analysis indicated …

The Ion Pair Thermal Model Of Maldi Ms, Shiyue Fang

Michigan Tech Publications, Part 1

The ion pair thermal model for MALDI MS is described. Key elements of the model include thermal desorption and ionization, strong tendency to neutralization via ion pair formation and proton transfer in the gas phase, thermal equilibrium, overall charge neutral plume, and thermal energy assisted free ion generation via ion pair separation by ion extraction potential. The quantities of ions in the solid sample and in the gaseous plume are estimated. Ion yields of different classes of molecules including peptides, nucleic acids, permanent salts and neutral molecules are estimated at the macroscale and single ion pair levels. The estimated ion …

Evaluating Halogen-Bond Strength As A Function Of Molecular Structure Using Nuclear Magnetic Resonance Spectroscopy And Computational Analysis, Quang Minh Dang, Jeffrey H. Simpson, Carol A. Parish, Michael C. Leopold

Chemistry Faculty Publications

Halogen bonding (XB) is a highly directional, non-covalent intermolecular interaction between a molecule (XB donor) presenting a halogen with an electron-deficient region or sigma hole (σ-hole) and an electron-rich or Lewis-base molecule (XB acceptor). A systematic, experimental, and theoretical study of solution-phase XB strength as a function of the molecular structure for both XB donor and acceptor molecules is presented. The impact of specific structural features is assessed using ¹⁹F and ¹H nuclear magnetic resonance (NMR) titrations to determine association constants, density functional theory calculations for interaction energies and bond lengths, as well as ¹⁹F–¹H …

Designed, Highly Expressing, Thermostable Dengue Virus 2 Envelope Protein Dimers Elicit Quaternary Epitope Antibodies, Stephen T. Kudlacek, Stefan Metz, Devina Thiono, Alexander M. Payne, Thanh T.N. Phan, Shaomin Tian, Lawrence J. Forsberg, Jack Mcguire, Ian Selm, Shu Zhang, Ashutosh Tripathy, Joseph S. Harrison, Nathan I. Niceley, Sandrine Soman, Michael K. Mccracken, Gregory D. Gromowski, Richard G. Jarman, Lakshmanane Premkumar, Aravinda M. De Silva, Brian Kuhlman

College of the Pacific Faculty Articles

Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.

Rapid Analysis Of Adp-Ribosylation Dynamics And Site-Specificity Using Tlc-Maldi, Sean R. Wallace, Leila Y. Chihab, Miles Yamasaki, Braden T. Yoshinaga

Chemistry and Biochemistry

Poly(ADP-ribose) polymerases, PARPs, transfer ADP-ribose onto target proteins from nicotinamide adenine dinucleotide (NAD+). Current mass spectrometric analytical methods require proteolysis of target proteins, limiting the study of dynamic ADP-ribosylation on contiguous proteins. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates multisite analysis of ADP-ribosylation. We observe divergent ADP-ribosylation dynamics for the catalytic domains of PARPs 14 and 15, with PARP15 modifying more sites on itself (+3–4 ADP-ribose) than the closely related PARP14 protein (+1–2 ADP-ribose)─despite similar numbers of potential modification sites. We identify, for the first time, a minimal peptide fragment (18 amino-acids) that is preferentially …

Scaffold-Based [Fe]-Hydrogenase Model: H2 Activation Initiates Fe(0)-Hydride Extrusion And Non-Biomimetic Hydride Transfer, S. A. Kerns, J. Seo, V. M. Lynch, Jason M. Shearer, S. T. Goralski, E. R. Sullivan, M. J. Rose

Chemistry Faculty Research

We report the synthesis and reactivity of a model of [Fe]-hydrogenase derived from an anthracene-based scaffold that includes the endogenous, organometallic acyl(methylene) donor. In comparison to other non-scaffolded acyl-containing complexes, the complex described herein retains molecularly well-defined chemistry upon addition of multiple equivalents of exogenous base. Clean deprotonation of the acyl(methylene) C-H bond with a phenolate base results in the formation of a dimeric motif that contains a new Fe-C(methine) bond resulting from coordination of the deprotonated methylene unit to an adjacent iron center. This effective second carbanion in the ligand framework was demonstrated to drive heterolytic H₂ activation …

Chitosan Graphene Composite Fabrication And Characterization For Treatment Of Harmful Algal Blooms And Toxins, Sarah Zetterholm

Master's Theses

Chitosan graphene composites were fabricated and characterized as a management strategy for harmful algal blooms (HABs) caused by various species of cyanobacteria. These chitosan graphene materials were compared to previously studied chitosan graphene-oxide composites in both material properties and HAB treatment. In previous studies, adsorption of the cyanobacteria onto the surface of the composite materials has been observed. Investigations of the pure materials for these composites are also included in this study to determine whether removal is a result of charge interactions with the composite, or as an inherent property of the graphene or graphene oxide. Initial results suggest that …

Comparison Of Design Approaches For Low-Cost Sampling Mechanisms In Open-Source Chemical Instrumentation, Greggory Murray, Samuel Bednarski, Michael Hall, Samuel W. Foster, Sijun Jin, Joshua J. Davis, Wei Xue, Eric Constans, James P. Grinias

College of Science & Mathematics Departmental Research

Robotic positioning systems are used in a variety of chemical instruments, primarily for liquid handling purposes, such as autosamplers from vials or well plates. Here, two approaches to the design of open-source autosampler positioning systems for use with 96-well plates are described and compared. The first system, a 3-axis design similar to many low-cost 3D printers that are available on the market, is constructed using an aluminum frame and stepper motors. The other system relies upon a series of 3D printed parts to achieve movement with a series of linker arms based on Selective Compliance Assembly Robot Arm (SCARA) design …

New Approach For Assigning Mean Oxidation Number Of Carbons To Organonitrogen And Organosulfur Compounds, Pong Kau Yuen, Cheng Man Diana Lau

Faculty Publications

Organonitrogen and organosulfur compounds are abundant in the natural environment. To understand the biological redox pathways properly, it is important for learners to be able to count the oxidation number of organic carbons. However, the process of counting is not always easy. In addition, organonitrogen and organosulfur molecules are seldom studied. To compensate these problems, this paper explores the bonddividing method, which can effectively determine the mean oxidation number of carbons of organonitrogen and organosulfur molecules. This method uses the cleavage of carbon-sulfur and carbon-nitrogen bonds to obtain the organic and inorganic fragments. The mean oxidation numbers of carbon atoms, …

Inductively Coupled Plasma Optical Emission Spectroscopy (Icp-Oes) Analysis Of Trace Metals In Cigarette Litter Collected At Mcneese State University In Lake Charles, La, United States, Liliya Snaychuk, Trey Vaughan, Zachary Ullery, Chris Douvris, Derek Bussan

EKU Faculty and Staff Scholarship

Cigarette smoking is the most commonly used form of tobacco in the world. It is practiced by a large portion of the population, especially young people. These people often ignore or disregard the harmful toxic impacts that cigarettes have on both themselves and the environment. The United States Center for Disease Control estimates that nearly 40 million U.S. adults still smoke cigarettes, with nearly 1600 U.S. youth starting cigarette smoking every day. Although it is well-known that smoking cigarettes is addictive and leads to a numerous health conditions including cancer, chronic pulmonary and heart disease, the effect of disposing the …

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

Editorial: Discovery And Development Of Drugs For Neglected Diseases: Chagas Disease, Human African Trypanosomiasis, And Leishmaniasis, Gildardo Rivera, Navin B. Patel, Debasish Bandyopadhyay

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Twenty tropical diseases have been listed by the World Health Organization (WHO) as Neglected Tropical Diseases (NTDs). These tropical diseases are called “neglected” for three primary reasons: 1) These diseases are widespread worldwide among the economically weaker (neglected?) section of the society; 2) Although the total number of mortality, morbidity, disability, and health disparity caused annually by the NTDs is more than that attributed by the so-called elite diseases like cancer, diabetes, human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), cardio- or neurological diseases but NTD patients do not receive comparable attention or treatment opportunities either from the governments or healthcare professionals …

Effects Of Redwood Bark And Leaf Leachate On Different Lichen Populations Found Within The Redwood Forest Of Arcata, Ca, Courtney Michelle Harris, Phoebe Hughes

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

3d-Printable And Open-Source Modular Smartphone Visible Spectrophotometer, Brandon Winters, Nick Banfield, Cassandra Dixon, Anna Swensen, Dakota Holman, Braxton Fillbrown

Chemistry Faculty Publications

The past four decades have brought significant and increasingly rapid changes to the world of instrument design, fabrication, and availability due to the emergence of 3D printing, open-source code and equipment, and low-cost electronics. These, along with other technological advances represent a nexus in time ripe for the wide-spread production and availability of low-cost sophisticated scientific equipment. To that end, the design of a 3D printable and open-source, modular spectrometer is described. This specific instrument is distinctly different from others that have been reported in recent years in that it was designed outside of the “black box” paradigm of …

Are Rural And Small Community Aerated Wastewater Stabilization Ponds A Neglected Source Of Microplastic Pollution?, Zhiqiang Gao, James V. Cizdziel, Kendall Wontor, Haitao Lu

Faculty and Student Publications

Wastewater treatment systems collect and treat sewage that includes microplastics (MPs). However, we are not aware of any studies on the occurrence and distribution of MPs in wastewater stabilization ponds (WSPs), which serve small communities worldwide. Here, we characterized MPs (~45 µm–5 mm) in an aerated WSP serving ~500 houses and an adjacent lake. Putative MPs were most abundant in duckweed (Lemna minor) and sludge (75 ± 22 and 12.8 ± 3.1 particles/g, respectively: ±1 standard deviation (SD), n = 6, dry weight). In the water, average concentrations (particles/L ± 1 SD, n = 6) were highest in the pond …

Thin Safety Margin: The Sefor Super-Prompt-Critical Transient Experiments, Ozark Mountains, Arkansas 1970–1971, Jerry Havens, Collis Geren

Arkansas Scholarly Editions

Thin Safety Margin charts the history of SEFOR, a twenty-megawatt reactor that operated for three years in the rural Ozark Mountains of Arkansas as part of an internationally sponsored program designed to demonstrate the Doppler effect in plutonium-oxide-fueled fast reactors. Authors Jerry Havens and Collis Geren draw upon this history to assess the accidental explosion risk inherent in using fast reactors to reduce the energy industry’s carbon dioxide emissions.

If a sufficiently powerful fast-neutron explosion were to cause the containment of a reactor such as SEFOR’s to fail, the reactor’s radiotoxic plutonium fuel could vaporize and escape into the surrounding …

The Coastal Monitor: Vol. 7 No. 3, John Tanacredi Ph.D.

The Coastal Monitor

Where has all the pollution gone? No hazardous toxic algal blooms? Incredible summer estuarine water quality! No fish kills. Banner years in recreational fisheries for Stripers and Blues and incredible numbers of Humpback whales! No going to restaurants, so greater at home use of water and septic systems! Since March 2020, drier years than most, thus reducing runoff with fertilizers and organic pesticides, resulting in reduced water contamination. So maybe, just maybe, this COVID- 19 period which has altered our collective lives forever, has also resulted in a grand experiment on what has been hiding in plain sight? That is, …

Analysis Of Oxycontin Addiction And Recovery From Both A Physical And Psychological Lens, Meagan Munley, Carrie Flickinger

Fall Showcase for Research and Creative Inquiry

We will investigate the physical impacts both short and long term effects of of substance use. In doing so we will frame an argument for the substance's addictive properties as it relates to both its physically addictive and sociological addictive properties. In doing, so a stronger understanding of how an individual can move through the stages of substance use, to abuse, and finally addiction will be reviewed. We will then address current treatment strategies for the substance and how they address or fail to address both the physical and sociological impacts of its use.

Analysis Of Fluoxetine (Prozac) Addiction And Recovery From Both A Physical And Psychological Lens, Kristen Dobek, Hannah Couch

Fall Showcase for Research and Creative Inquiry

We will investigate the physical impacts both short and long term effects of of substance use. In doing so we will frame an argument for the substance's addictive properties as it relates to both its physically addictive and sociological addictive properties. In doing, so a stronger understanding of how an individual can move through the stages of substance use, to abuse, and finally addiction will be reviewed. We will then address current treatment strategies for the substance and how they address or fail to address both the physical and sociological impacts of its use.