Physical Sciences and Mathematics Commons^™

Ppld Is A De-N-Acetylase Of The Cell Wall Linkage Unit Of Streptococcal Rhamnopolysaccharides, Jeffrey S. Rush, Prakash Parajuli, Alessandro Ruda, Jian Li, Amol Arunrao Pohane, Svetlana Zamakhaeva, Mohammad M. Rahman, Jennifer C. Chang, Artemis Gogos, Cameron W. Kenner, Gérard Lambeau, Michael J. Federle, Konstantin V. Korotkov, Göran Widmalm, Natalia Korotkova

Molecular and Cellular Biochemistry Faculty Publications

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates …

Special Issue: Microbiota-Gut-Brain Axis, Mark Obrenovich, Prakash Reddy

Chemistry Faculty Research & Creative Works

No abstract provided.

Collisional Excitation And Non-Lte Modeling Of Interstellar Chiral Propylene Oxide, Karlis Dzenis, Alexandre Faure, B. A. Mcguire, A. J. Remijan, P. J. Dagdigian, C. Rist, Richard Dawes, Ernesto Quintas-Sánchez, F. Lique, M. Hochlaf

Chemistry Faculty Research & Creative Works

The first set of theoretical rotational cross sections for propylene oxide (CH₃CHCH₂O) colliding with cold He atoms has been obtained at the full quantum level using a high-accuracy potential energy surface. By scaling the collision reduced mass, rotational rate coefficients for collisions with para-H₂ are deduced in the temperature range 5-30 K. These collisional coefficients are combined with radiative data in a non-LTE radiative transfer model in order to reproduce observations of propylene oxide made toward the Sagittarius B2(N) molecular cloud with the Green Bank and Parkes radio telescopes. The three detected absorption lines are …

A Novel Branched Polymer Gel System With Delayed Gelation Property For Conformance Control, Tao Song, Qi Feng, Thomas P. Schuman, Jie Cao, Baojun Bai

Chemistry Faculty Research & Creative Works

Excessive water production from oil reservoirs not only affects the economical production of oil, but it also results in serious environmental concerns. Polymer gels have been widely applied to decrease water production and thus improve oil production. However, traditional polymer gels such as partially hydrolyzed polyacrylamide (HPAM)/chromium (III) gel systems usually have a short gelation time and cannot meet the requirement of some conformance control projects. This paper introduces a novel polymer gel system of which crosslinking time can be significantly delayed. A branched polymer grafted from arginine by the surface initiation method is synthesized as the backbone, chromium acetate …

Collisional Excitation And Non-Lte Modeling Of Interstellar Chiral Propylene Oxide, Karlis Dzenis, Alexandre Faure, B. A. Mcguire, A. J. Remijan, P. J. Dagdigian, C. Rist, Richard Dawes, Ernesto Quintas-Sánchez, F. Lique, M. Hochlaf

Chemistry Faculty Research & Creative Works

The first set of theoretical rotational cross sections for propylene oxide (CH₃CHCH₂O) colliding with cold He atoms has been obtained at the full quantum level using a high-accuracy potential energy surface. By scaling the collision reduced mass, rotational rate coefficients for collisions with para-H2 are deduced in the temperature range 5-30 K. These collisional coefficients are combined with radiative data in a non-LTE radiative transfer model in order to reproduce observations of propylene oxide made toward the Sagittarius B2(N) molecular cloud with the Green Bank and Parkes radio telescopes. The three detected absorption lines are found …

Noninvasive Detection, Tracking, And Characterization Of Aerogel Implants Using Diagnostic Ultrasound, Sagar Ghimire, Martina Rodriguez Sala, Swetha Chandrasekaran, Grigorios Raptopoulos, Marcus Worsley, Patrina Paraskevopoulou, Nicholas Leventis, Firouzeh Sabri

Chemistry Faculty Research & Creative Works

Medical implants are routinely tracked and monitored using different techniques, such as MRI, X‐ray, and ultrasound. Due to the need for ionizing radiation, the two former methods pose a significant risk to tissue. Ultrasound imaging, however, is non‐invasive and presents no known risk to human tissue. Aerogels are an emerging material with great potential in biomedical implants. While qualitative observation of ultrasound images by experts can already provide a lot of infor-mation about the implants and the surrounding structures, this paper describes the development and study of two simple B‐Mode image analysis techniques based on attenuation measurements and echogenicity comparisons, …

Chemistry Matters February 2022, Otterbein University Chemistry Department

Chemistry Matters Department Newsletter

In this Issue:

Letter from the Chair, Faculty Scholarship, Chemistry in Action, Structural Methods in Chemistry, Summer Student Work, New Instrumentation Supports Student Learning, Post-COVID Adjustments in 2020 and Beyond, Otterbein University Students Benefit from Faculty Involvement in National Organizations, and Otterbein Student Chapter of ACS Nationally Recognized for the Second Year in a Row

Dynamic Interactions In Semiconducting Polymers; New Materials For Soft Electronics With Biomimetic Properties, Michael Udunyi Ocheje

Electronic Theses and Dissertations

The development of materials that can stretch while remaining conductive has generated significant research interest. The push for the development of these materials is due to their potential for cheaper, more durable electronics with the new functions (stretchability and healability) and form factors required for the next generation of wearable and skin-inspired electronics. Polymeric semiconductors have emerged as prime candidates for the development of these materials, due to their π-delocalized network which makes them conductive, their synthetic versatility, and their intrinsic mechanical properties. Furthermore, their ability to be solution processed provides an avenue for printing, roll-to-roll, and large area solution …

Comprehensive Evaluation Of A High-Temperature Resistant Re-Crosslinkable Preformed Particle Gel For Water Management, Bowen Yu, Shuda Zhao, Yifu Long, Baojun Bai, Thomas P. Schuman

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Gel treatment has been widely applied to control conformance for improving oil recovery and control water production in mature oil fields. However, most of the hydrogel systems are limited when being applied in the harsh environments of high temperatures. A systematic evaluation was conducted in this study to evaluate a modified PPG product, the high temperature resistant re-crosslinkable preformed particle gel (HT-RPPG) which can re-crosslink to form a bulky material and keep thermostable in the large-opening features after placement. This material was developed to overcome the limitations of conventional PPGs in the reservoirs with large- opening features such as open …

Special Issue: Microbiota–Gut–Brain Axis, Mark Obrenovich, V. (Prakash) Reddy

Chemistry Faculty Research & Creative Works

No abstract provided.

All-Atom Simulations Uncover Structural And Dynamical Properties Of Sting Proteins In The Membrane System, Rachel Payne, Silvia Crivelli, Masakatsu Watanabe Ph.D.

Chemistry Faculty Publications

Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of Type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiates a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study these biological pathways’ structural and dynamical responses. Here, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed …

Phosphorylation Of The Aggregate-Forming Protein Alpha-Synuclein On Serine-129 Inhibits Its Dna-Bending Properties, Sydney E. Dent, Dennisha P. King, Valerie R. Osterberg, Eleanor K. Adams, Marilyn R. Mackiewicz, Tamily A. Weissman, Vivek K. Unni

Chemistry Faculty Publications and Presentations

Alpha-synuclein (aSyn) is a vertebrate protein, normally found within the presynaptic nerve terminal and nucleus, which is known to form somatic and neuritic aggregates in certain neurodegenerative diseases. Disease-associated aggregates of aSyn are heavily phosphorylated at serine-129 (pSyn), while normal aSyn protein is not. Within the nucleus, aSyn can directly bind DNA, but the mechanism of binding and the potential modulatory roles of phosphorylation are poorly understood. Here we demonstrate using a combination of electrophoretic mobility shift assay and atomic force microscopy approaches that both aSyn and pSyn can bind DNA within the major groove, in a DNA length-dependent manner …

Adverse Reactions In A Phase 1 Trial Of The Anti-Malarial Dm1157: An Example Of Pharmacokinetic Modeling And Simulation Guiding Clinical Trial Decisions, Stephen J. Balevic, Shruti M. Raja, Rachel Randall, Gregory A. Deye, Thomas Conrad, Aya Nakamura, David H. Peyton, Sandra Shotwell, Katherine May Liebman, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

Introduction: There is an urgent need to develop new drugs to treat malaria due to increasing resistance to first-line therapeutics targeting the causative organism, Plasmodium falciparum (P. falciparum). One drug candidate is DM1157, a small molecule that inhibits the formation of hemozoin, which protects P. falciparum from heme toxicity. We describe a first-in-human, phase 1 trial of DM1157 in healthy adult volunteers that was halted early because of significant toxicity.

Methods: Adverse events were summarized using descriptive statistics. We used pharmacokinetic modeling to quantitatively assess whether the DM1157 exposure needed for P. falciparum inhibition was achievable at safe doses.

Results: …

Diketopyrrolopyrrole Derivatives For Single Material Solar Cells, Adam M. Cassar

Electronic Theses and Dissertations

Although diketopyrrolopyrroles (DPPs) have been extensively studied as organic pigments and dyes and as building blocks for molecular and polymeric organic electronic materials, their propensity for self-organization has been given surprisingly little attention. Self-organization provides control over the morphology and supramolecular structure of materials and, consequently, the performance of a material. The dependence of performance on supramolecular structure is particularly delicate in bulk heterojunction organic solar cells and the emerging low-cost single material organic solar cells (SMOSC). Most donor-acceptor dyads and triads presently developed for SMOSCs consist of dyes as electron donors and fullerene derivatives as electron acceptors, but their …

A Biomimetic Model For Oxidative Metabolism Of Thiopurine Drugs, Oluyemi Oludare Alo

Dissertations and Theses

Type B hepatotoxicity has been reported for thiopurines, and this has limited their clinical uses. Although a lot of research has been done on thiopurines, the precise mechanism of their hepatotoxicity is still unclear. The results of the in vitro and in vivo experiments aimed at assessing the products of their CYP450-mediated bioactivation have been contradictory. Although it has been theorized that the hepatic toxicity of this class of drug is caused by their bioactivation to electrophilic reactive metabolite (RM) and concomitant protein binding to form immunogenic adducts, resulting in direct cellular dysfunction or an immune response via the formation …

Surface Modified Hybrid Znsno3 Nanocubes For Enhanced Piezoelectric Power Generation And Wireless Sensory Application, Sk Md Ali Zaker Shawon, Zaida D. Carballo, Valeria Suarez Vega, Chen Lin, Muhammad Sufian Rafaqut, Andrew Xu Sun, James Li, Mohammed Jasim Uddin

Chemistry Faculty Publications and Presentations

Piezoelectric Nanogenerators (PENGs), which can convert ambient mechanical stimuli into electrical energy, are held in high regard due to their cost-effectiveness, energy harvesting applications, and potential as self-powered sensors. We report an aluminum-doped zinc stannate (ZnSnO3) PENG that can achieve high electrical outputs with respect to the external force. In order to enrich the piezoelectric mechanics, a low-temperature solution method was adopted in our work to synthesize ZnSnO3 nanocubes with an average side length of only 30 – 55 nm. Furthermore, ZnSnO3 was doped with 1 wt% to 5 wt% of aluminum nanoparticles. We report that 2 wt% of aluminum …

Understanding The Proton Transport In Non-Aqueous Histidine-Based Nanostructures, Jiang Bian

Dissertations, Theses, and Capstone Projects

Over the past two decades, proton transport has been extensively studied because of the many applications to the development of new technological devices. In particular, understanding proton transport permits the design of new materials with desired properties for constructing effective proton exchange membranes (PEM) in fuel cells. Current PEM technology involves biocummulative perfluorinated membranes that operate under hydrated conditions, for which the proton conductivity is limited by the usually high temperature that fuel cells operate. Therefore, it is of great interest to study the alternative systems that have the potential to conduct protons, in particular, those that are able to …

Water-Based Lead Generation, Brian Olson

Dissertations, Theses, and Capstone Projects

Water-based Lead Generation. The opioid epidemic and the SARS-CoV-2 pandemic are current serious challenges whose devastating effects could be assuaged through the development of new drugs. Opioids that are functional painkillers, that are less likely to cause overdose, and small molecule drugs that could inhibit the life cycle of SARS-CoV-2 would be useful. The work herein investigated the use of water molecules for lead generation in drug development against opioid receptors and SARS-CoV-2 viral proteins. In opioid receptor binding sites, purported bridging waters were obtained from crystal waters or from molecular dynamics simulations, as Hydration Site Analysis was used to …

Whole-Genome Sequencing And Rna-Seq Reveal Differences In Genetic Mechanism For Flowering Response Between Weedy Rice And Cultivated Rice, Richard S. Garcia, Sapphire Coronejo, Jonathan Concepcion, Prasanta K. Subudhi

Faculty Publications

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified …

Imidazole Derivative Improves Antioxidant Status And Causes Differential Alteration Of Redox-Status In Drosophila Melanogaster, Elizabeth Temidayo Oluwayemi, Oluwakemi Josephine Awakan, Abiodun Omokehinde Eseola, Winfried Plass, Oluyomi Stephen Adeyemi

Karbala International Journal of Modern Science

This study investigated the toxicity of a new imidazole compound, 1-(1,4,5-triphenyl-1H-imidazol-2-yl)-naphthalen-2-ol, through the evaluation of selected oxidative stress markers and antioxidants. Both male and female D. melanogaster (3–5 days old) were fed a diet containing the imidazole derivative (20, 50, and 100 mg IMZ/kg diet) for five days. After cessation of imidazole treatment, half the population of the imidazole-exposed flies was homogenized for biochemical assays, while the other half of the flies was allowed to have a normal diet for an additional five days to see if any induced effect would be resolved. Imidazole derivatives did not significantly …

Glcms Based Multi-Inputs 1d Cnn Deep Learning Neural Network For Covid-19 Texture Feature Extraction And Classification, Elaf Ali Abbood, Tawfiq A. Al-Assadi

Karbala International Journal of Modern Science

Coronavirus disease 2019 epidemic (COVID-19) is an infectious disease that appeared because of the newest version of discovered coronavirus. The advent and rapid spread of this disease over the world necessitated a concerted effort to contain and eradicate it. Computer Tomography (CT) imaging and X-Ray images are considered as one of the important medical examinations used for disease diagnosis. To speed up and confirm the correctness of the medical diagnosis, many artificial intelligence techniques and machine learning methods are proposed. In this paper, a new and efficient proposed system is introduced to extract appropriate and meaningful features for CT scans …

A Convenient Green Method To Synthesize Β-Carotene From Edible Carrot And Nanoparticle Formation, Baker A. Joda, Zena M. Abed Al-Kadhim, Hussian J. Ahmed, Alaa K. H. Al-Khalaf

Karbala International Journal of Modern Science

A simple green chemistry approach was used to synthesize β-carotene from edible carrot without using solvent and heat. In this study, beta-carotene was extracted from edible carrots through a natural extraction method with several physical technical steps. The extracted sample was isolated using high-performance liquid chromatography (HPLC). A β-carotene peak was detected from HPLC with an absorbance maximum (2.135 mAU). The absorption of UV-Visible spectrum indicated that beta-carotene absorbs most strongly between 230-300 and 400-500 nm. The functional groups, namely, C=C (1649 cm^-1), =C-H (900-900 cm^-1) vibrations of antisymmetric deformation of CH₃ groups and CH …

Machine Learning-Based Soft Computing Regression Analysis Approach For Crime Data Prediction, Rabia Musheer Aziz, Aftab Hussain, Prajwal Sharma, Pavan Kumar

Karbala International Journal of Modern Science

The crime rate in India is considerably increasing day by day. Consequently, the data associated with crime is also increasing, opening doors for data-driven approaches to these data to extract insightful knowledge, which can help police and other law enforcement organizations of the country in crime control and prevention. Crime prediction using machine learning algorithms on crime data can predict region-wise crime counts. In this paper, a machine learning-based soft computing regression analysis approach for Indian Crime Data Analysis (ICDA) is proposed. Different regression algorithms, namely, Simple Linear Regression (SLR), Multiple Linear Regression (MLR), Decision Tree Regression (DTR), Support Vector …

Atomistic Simulation Of Na+ And Cl- Ions Binding Mechanisms To Tobermorite 14Å As A Model For Alkali Activated Cements, Ahmed Abdelkawy

Theses and Dissertations

The production of ordinary Portland cement (OPC) is responsible for ~8% of all man-made CO2 emissions. Unfortunately, due to the continuous increase in the number of construction projects, and since virtually all projects depend on hardened cement from the hydration of OPC as the main binding material, the production of OPC is not expected to decrease. Alkali-activated cement produced from the alkaline activation of byproducts of industries, such as iron and coal industries, or processed clays represents a potential substitute for OPC. However, the interaction of the reaction products of AAC with corrosive ions from the environment, such as Cl-, …

Transition Metal Phosphides For High Performance Electrochemical Energy Storage Devices, Amina Saleh

Theses and Dissertations

Electrochemical energy storage technologies are nowadays playing a leading role in the global effort to address the energy challenges. A lot of attention has been devoted to designing hybrid devices known as supercapatteries which combine the merits of supercapacitors (high power density) and rechargeable batteries (high energy density). Transition metal phosphides (TMP) are a rising star for supercapattery anode materials thanks to their high conductivity, metalloid characteristics, and kinetic favorability for fast electron transport. Herein, new TMP-based materials were synthesized for use as supercapattery positive electrodes, via a multifaceted approach to yield devices enjoying concurrently high power and energy densities. …

Design And Fabrication Of Nanostructured Electrodes For Complementary Electrochemical And Photoelectrochemical Water Splitting, Kholoud El Sayed Abousalem

Theses and Dissertations

Designing highly active, durable, and nonprecious electrodes for overall water splitting is of urgent scientific importance to realize sustainable hydrogen production. Accordingly, the need to search efficient energy production systems is of crucial necessity. In this thesis, two various systems for sustainable hydrogen production have been reported using electrochemical and photoelectrochemical pathways. In the first part of the thesis, electrochemical water splitting involving both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) has been established. To this end, an innovative approach is demonstrated to synthesize flower-like 3D homogenous trimetallic Mn, Ni, Co phosphide catalysts directly on nickel foam via …

Metabolic Features Of Brain Function With Relevance To Clinical Features Of Alzheimer And Parkinson Diseases, David Allan Butterfield, Maria Favia, Iolanda Spera, Annalisa Campanella, Martina Lanza, Alessandra Castegna

Chemistry Faculty Publications

Brain metabolism is comprised in Alzheimer’s disease (AD) and Parkinson’s disease (PD). Since the brain primarily relies on metabolism of glucose, ketone bodies, and amino acids, aspects of these metabolic processes in these disorders—and particularly how these altered metabolic processes are related to oxidative and/or nitrosative stress and the resulting damaged targets—are reviewed in this paper. Greater understanding of the decreased functions in brain metabolism in AD and PD is posited to lead to potentially important therapeutic strategies to address both of these disorders, which cause relatively long-lasting decreased quality of life in patients.

Determination Of Dissociation Constants Of Protein Ligands By Thermal Shift Assay, Jaina A. Bhayani, Miguel Ballicora

Chemistry: Faculty Publications and Other Works

The thermal shift assay (TSA) is a powerful tool used to detect molecular interactions between proteins and ligands. Using temperature as a physical denaturant and an extrinsic fluorescent dye, the TSA tracks protein unfolding. This method precisely determines the midpoint of the unfolding transition (Tm" role="presentation">), which can shift upon the addition of a ligand. Though experimental protocols have been well developed, the thermal shift assay data traditionally yielded qualitative results. Quantitative methods for Kd" role="presentation"> determination relied either on empirical and inaccurate usage of Tm" role="presentation"> or on isothermal approaches, which do not take full advantage of the …

The Molecular Structure And Curious Motions In 1,1-Difluorosilacyclopent-3-Ene And Silacyclopent-3-Ene As Determined By Microwave Spectroscopy And Quantum Chemical Calculations, Thomas M.C. Mcfadden, Nicole Moon, Frank E. Marshall, Amanda J. Duerden, Esther J. Ocola, Jaan Laane, Gamil A. Guirgis, Garry S. Grubbs

Chemistry Faculty Research & Creative Works

The molecules 1,1-difluorosilacyclopent-3-ene (3SiCPF2) and silacyclopent-3-ene (3SiCP) have been synthesized and studied using chirped pulse, Fourier transform microwave (CP-FTMW) spectroscopy. For 3SiCP this is the first ever microwave study of the molecule and, for 3SiCPF2, the spectra reported in this work have been combined with that of previous work in a global fit. The spectra of each contain splitting which has been fit using a Hamiltonian consisting of semirigid and Coriolis coupling parameters. A refit of the original 3SiCPF2 work was also carried out. All fits and approaches are reported. Analyses of the spectra provide evidence that the molecule is …

Acetate Solutions With 3.9 V Electrochemical Stability Window As An Electrolyte For Low-Cost And High-Performance Aqueous Sodium-Ion Batteries, Dao-Yun Lan, Xiao-Feng Qu, Yu-Ting Tang, Li-Ying Liu, Jun Liu

Journal of Electrochemistry

Low-cost and high-safety aqueous sodium-ion batteries have received widespread attention in the field of large-scale energy storage, but the narrow electrochemical stability window (1.23 V) of water limits the energy density of aqueous sodium-ion batteries. The “water-in-salt” strategy which uses the interaction between cations and water molecules in the solution can inhibit water decomposition and broaden the electrochemical stability window of water. In this work, two types of low-cost salts, namely, ammonium acetate (NH₄CH₃COOH) and sodium acetate (NaCH₃COOH), were used to configure a mixed aqueous electrolyte for aqueous sodium-ion batteries. The solution consisted of …