Chemistry Commons^™

Optimization Of Cation Exchange Chromatography Purification Of A Small Peptide: An Industrial And Practical Approach, Jamin Willoughby

Honors Theses

Ion exchange chromatography (IEX) is a common chemical separation technique that is used to separate ionizable target molecules from a liquid mixture mobile phase by adsorption of the molecule to a stationary phase. In chromatography, the stationary phase is a porous solid that the target molecule and mobile phase flows through, and is commonly referred to as the resin. Resins are commonly packed into hollow cylindrical columns. The mobile phase is the liquid solvent which flows through the column containing the stationary phase. The target molecule will have an affinity for the resin and adsorb to it, while impurities in …

The Efficient Synthesis Of D-Xylulose And Formal Synthesis Of Syringolide 1, Sudhakar Kalagara, Gabriel Orozco, Shizue Mito

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

Wittig reaction and asymmetric dihydroxylation were used as the key steps in the synthesis of D-xylulose, a commercially available but costly carbohydrate. The effects of protecting groups and reactions conditions on asymmetric dihydroxylation are demonstrated. Optically pure D-xylulose was obtained after 4-6 steps from readily available hydroxyacetone and ethylene glycol. The method also involves some other valuable intermediates along the synthesis. Those intermediates were applied in the formal synthesis of Syringolides. A key precursor butenolide to Syringolide 1, the first non-proteinaceous specific elicitors of plant hypersensitive response, was obtained after 3 steps from the intermediate (8–10 steps from hydroxyacetone and …

Modular Synthesis And Transition Metal-Free Alkynylation/Alkenylation Of Castagnoli–Cushmanderived N,O- And N,S-Heterocyclic Vinyl Chlorides, Timothy K. Beng, Abdikani Omar Farah, Victoria Shearer

All Faculty Scholarship for the College of the Sciences

A modular and functional group-tolerant protocol for the transition metal-free coupling of novel N,O- and N,S-heterocyclic vinyl chlorides with terminal acetylenes and styrenes has been developed, leading to the epimerization-free synthesis of fully carbofunctionalized dihydro-1,4-oxazines/thiazines. Bicyclic morpholines have also been prepared through the interrogation of newly synthesized cross-conjugated dienes in Diels–Alder reactions. The use of environmentally benign reaction media endows the current strategy with a practical advantage.

Cosore: A Community Database For Continuous Soil Respiration And Other Soil-Atmosphere Greenhouse Gas Flux Data, Ben Bond-Lamberty, Danielle S. Christianson, Avni Malhotra, Stephanie C. Pennington, Debjani Sihi, Amir Aghakouchak, Hassan Anjileli, M. Altaf Arain, Juan J. Armesto, Samaneh Ashraf, Mioko Ataka, Dennis Baldocchi, Thomas Andrew Black, Nina Buchmann, Mariah S. Carbone, Shih-Chieh Chang, Patrick Crill, Peter S. Curtis, Eric A. Davidson, Ankur R. Desai, John E. Drake, Tarek S. El-Madany, Michael Gavazzi, Carolyn-Monika Görres, Christopher M. Gough, Michael Goulden, Jillian Gregg, Omar Gutiérrez Del Arroyo, Jin-Sheng He, Takashi Hirano, Anya Hopple, Holly Hughes, Järvi Järveoja, Rachhpal Jassal, Jinshi Jian, Haiming Kan, Jason Kaye, Yuji Kominami, Naishen Liang, David Lipson, Catriona A. Macdonald, Kadmiel Maseyk, Kayla Mathes, Marguerite Mauritz, Melanie A. Mayes, Steve Mcnulty, Guofang Miao, Mirco Migliavacca, Scott Miller, Chelcy F. Miniat, Jennifer G. Nietz, Mats B. Nilsson, Asko Noormets, Hamidreza Norouzi, Christine S. O'Connell, Bruce Osborne, Cecilio Oyonarte, Zhuo Pang, Matthias Peichl, Elise Pendall, Jorge F. Perez-Quezada, Claire L. Phillips, Richard P. Phillips, James W. Raich, Alexandre A. Renchon, Nadine K. Ruehr, Enrique P. Sánchez-Cañete, Matthew Saunders, Kathleen E. Savage, Marion Schrumpf, Russell L. Scott, Ulli Seibt, Whendee L. Silver, Wu Sun, Daphne Szutu, Kentaro Takagi, Masahiro Takagi, Munemasa Teramoto, Mark G. Tjoelker, Susan Trumbore, Masahito Ueyama, Rodrigo Vargas, Ruth K. Varner, Joseph Verfaillie, Christoph Vogel, Jinsong Wang, Greg Winston, Tana E. Wood, Juying Wu, Thomas Wutzler, Jiye Zeng, Tianshan Zha, Quan Zhang, Junliang Zou

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-to-atmosphere CO₂ flux, commonly though imprecisely termed soil respiration (R_S), is one of the largest carbon fluxes in the Earth system. An increasing number of high-frequency R_S measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems …

A Fuzzy Assessment Model For Hospitals Services Quality Based On Patient Experience, Mohamed Khodyer Alkafaji, Eman Salih Al-Shamery

Karbala International Journal of Modern Science

The patient's experience is a lens for services assessment that provide from healthcare institutions because the patient is the first and the last recipient for the service. The patient's experience carries a lot of uncertainty and an ultimate decision cannot be taken from the patient about the services, but it carries the partial truth. Many artificial intelligence technologies deal with the concept of partial truth, such as genetic algorithms and neural networks, but the fuzzy logic remains pioneering to deal with uncertainty. This paper aims to develop an assessment model by using fuzzy inference that is able to assess the …

A Laser Induced Fluorescence Design For Renewable Energy Application, Shaimaa S. Mahdi, Intisar A. Hamad

Karbala International Journal of Modern Science

Biomass is considered to be one of the highest potential renewable energy sources to meet the requirements of energy in the world, where it can be used as an effective alternative for renewable energy sources, including electricity and heating, as well as fuel used in transport. One of the most common problems accompanying the usage of biomass through gasification processes to produce gases is the amounts of undesirable formed Tars. In this paper, a Laser Induced Fluorescence spectroscopy (LIF) method was incorporated to identify the produced Tar compounds at high temperature in the gasification technology. The effect of tars deposition …

Treatment Of A Worn Mineral Oil Effluent By Electrocoagulation Using Aluminium Electrodes, Serge Raoul Tchamango Dr, God Promess Lactio, Inès Estelle Nkenmogne Kamdem, Martin Benoît Ngassoum

Karbala International Journal of Modern Science

Water pollution by oils is more and more a preoccupation because of its increasing occurrence and the hazard to human life and environment. Depollution of oily effluents can sometimes generate a secondary pollution (with chemical coagulation / flocculation processes) or be very costly (ultracentrifugation). In this work, electrocoagulation with aluminium electrodes was applied to the treatment of a worn mineral oil effluent. For this to be achieved, the influence of the pH and the current density on the turbidity and organic matter was first investigated. A liquid-liquid extraction was then carried out on the oil samples in order to isolate …

A Systematic Mapping Study On The Risk Factors Leading To Type Ii Diabetes Mellitus, Karar N. J Musafer, Fahrul Zaman Huyop, Mufeed J Ewadh, Eko Supriyanto, Mohammad Rava

Karbala International Journal of Modern Science

Diabetes is one of the most common diseases that has had devastating effects on the general population. It is also among the most popular research trends in modern medicine. Thus, due to the complexity and desirability of this particular affliction, there is a lot of demand towards understanding this disease better, so that it can pave the way towards better solutions in combating diabetes. The aim of this review is to provide a categorization of the risk factors leading to Type II Diabetes. In order to provide a justification for the type of diabetes, an explanation is provided which covers …

Chemical Composition And Antibacterial Activity Of The Essential Oil Of Myrtus Communis Leaves, Hajar El Hartiti, Amine El Mostaphi, Mariam Barrahi, Aouatif Ben Ali, Nabila Chahboun, Rajaa Amiyare, Abdelkader Zarrouk, Brahim Bourkhiss, Mohammed Ouhssine

Karbala International Journal of Modern Science

The aim of this work is to determine the yield of the essential oil of the Myrtus communis leaves, to identify its chemical composition and to evaluate its antibacterial properties. The plant is harvested from Sidi Ahmed Chrif, a region in Ouazzane, Morocco. The extraction of the essential oil was carried out by hydrodistillation in a Clevenger apparatus type. The average yield was 0.7%. The analysis of this oil by Gas Chromatography coupled with Mass Spectrum (GC/MS) allows the identification of 32 compounds. Eucalyptol was the main compound with 42.43%, followed by myrtenyl acetate (21.25%) and α-pinene (19.39%). Myrtle essential …

Hormones Of Maize Crop As Affected By Potassium Fertilization , Water Quality And Ascobin Foliar Application ., Qais Hussain Al-Samak Prof., Fatima Karim Khudair Alasadi

Karbala International Journal of Modern Science

A pot assay on the plastic container of the wire sunshade in the University of Kerbala's Agricultural Division was conducted to research the impact of potassium treatment, the salinity of irrigation water and ascobin sprinkling, just as their connections, on the some plant hormones activities (auxin, gibberellin and abscisic acid) in developing Zea mays crops in a soil with sandy texture during the farming fall period of 2017–2018. The trial was planned as a factorial one with three factors, Potassium adding are 0, 100 and 200 Kg K.ha^–1 . the irrigation water salinity are 1, 3 and 6 ds.m …

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

Mutating Lpar4 In The Visual System Using Crispr, Thomas A. Gonzalez

S.U.R.E Posters

The visual system is developed throughout the embryonic stage and is dictated by axon guidance molecules that tell the growing fibers of nerve cells, axons, where to grow. The ends of axons, called growth cones, continuously sprout out or collapse based on the axon guidance molecules. Research has shown that lysophosphatidic acid (LPA) causes growth cone collapse, so it is hypothesized that it is an axon guidance molecule. LPA binds to specific receptors, known as Lpars of which there are at least five known. Previous research indicates that Lpar 1,2, and 3 are not required in mice for growth cone …

Discovery Research For New Optical Materials, Kameron Johnson

S.U.R.E Posters

This project utilizes the MGI approach in order to discover new compounds at an accelerated rate. Novel materials for optical applications, such as luminescent scintillators, are desired for improvement of properties. Using density functional theory (DFT) calculations, new single-crystal scintillating materials can be optimized leading to more efficient scintillation. (5) Two existing compounds in the quaternary system Na-O-Si-Y were chosen and further modified using substitutions into proposed structures that can be investigated. The two original compounds, NaO4SiY and NaO26Si6Y9, were chosen and modified because of their already high density by substituting yttrium for lanthanum, sodium for potassium and yttrium for …

Elucidating The Effect Of The Antibiotic Tetracycline On The Regulatory Function Of The Guanidine Sensing Riboswitch Ykkcd, Thomas K. Sullivan

S.U.R.E Posters

The primary objective of this research is to develop an assay – one more feasible for undergraduate institutions than currently available methods – that will enable evaluation of the concomitant binding of, guanidine and tetracycline to the ykkCD bacterial guanidine sensor riboswitch. This noncoding regulatory RNA, in addition to guanidine, also recognizes tetracycline, a translation-inhibiting antibiotic, via a high-affinity aptamer domain. The resulting conformational change by the riboswitch upregulates the expression of genes that are downstream of this regulator, most of which are membrane transporter that expel toxins from bacteria. This phenomenon exemplifies the increasing issue of bacterial antibiotic resistance, …

Photoredox Mediated Alkylation Of Imines With Potassium Organotrifluoroborates In The Presence Of An Organic Photocatalyst, Jackson W. Barrett, Evan H. Thibodeaux, Molly A. Quetel, Eric J. Walters

S.U.R.E Posters

Our group is investigating the application of an organic photocatalyst, 9-mesityl-10-methyl acridinium tetrafluoroborate (Mes-Acr-Me), to the alkylation of aryl imines with potassium organotrifluoroborates. In the past, our group has employed an potassium isopropyltrifluoroborate for model reactions, but we desired to expand our BF₃K scope to see the effects of variation in the alkyl group of the organotetrafluoroborate. In addition, we also wanted to study the substituent electronic effects in the imine, which was done using a series of competition experiments.

Using Nucleic Acid-Gold Nanoparticle Conjugate In The Fight Against Bacteria That Are Resistant To Tetracycline Antibiotics, Allen T. Livingston

S.U.R.E Posters

Antibiotic resistance is major problem in modern medicine. Seventy percent of bacterial strains are resistant to at least one antibiotic, making treatment of bacterial infections ever more expensive and difficult. Currently, we are investigating the therapeutic potency of nucleic acid-gold nanoparticle conjugates as treatments against bacteria that are resistant to the antibiotic tetracycline. We hypothesize that by attaching RNA that binds to tetracycline to silver or gold nanoparticles the resulting conjugates will work as a “Trojan-horse” tetracycline-delivery vehicle that smuggles the antibiotic into the cell without being detected by cellular defense systems. Moreover, we reason that silver or gold ions …

Water-Soluble Graphene In Agar Gel As Electrolyte For Magnesium-Air Battery, Liew Siaw Ying

Student Works (2020-2029)

Presently, ever-increasing demands on energy and the global environmental issues have given the impetus to investigate the new battery systems which are inexpensive, efficient, having high performance, and also green to the environment. Among all the battery technologies, magnesium-air (Mg-air) battery is an attractive battery to be developed owing to the interesting properties of the Mg anode. Mg has high specific energy (6.46 kWh kg-1) and reactivity, apart from its high abundance, lower cost, low toxicity, and comparatively safe to handle in the atmosphere. Nevertheless, Mg-air battery is still not being widely investigated as compared to the other batteries. Electrolyte …

Covalent Organic Frameworks As An Organic Scaffold For Heterogeneous Catalysis Including C-H Activation, Harsh Vardhan

USF Tampa Graduate Theses and Dissertations

Linking small organic molecules into an extended solid usually afford disordered amorphous polymers. The instigation of order into such a material is of profound interest to induce inherent fine control of the overall structure. Covalent organic frameworks (COFs) are new class of porous crystalline material prepared by connecting organic building blocks via strong covalent bonds. The judicious choice of organic monomers can give rise to highly ordered and predictable frameworks with high crystallinity, surface area, and thermal/chemical stability. The role of connecting linkages such as B─O, C─C, C─N extends the principle of fundamental molecular covalent chemistry to the formation of …

Solving Complex Eigenvalue Problems On A Quantum Annealer With Applications To Quantum Scattering Resonances, Alexander Teplukhin, Brian K. Kendrick, Dmitri Babikov

Chemistry Faculty Research and Publications

Quantum computing is a new and rapidly evolving paradigm for solving chemistry problems. In previous work, we developed the Quantum Annealer Eigensolver (QAE) and applied it to the calculation of the vibrational spectrum of a molecule on the D-Wave quantum annealer. However, the original QAE methodology was applicable to real symmetric matrices only. For many physics and chemistry problems, the diagonalization of complex matrices is required. For example, the calculation of quantum scattering resonances can be formulated as a complex eigenvalue problem where the real part of the eigenvalue is the resonance energy and the imaginary part is proportional to …

Clean & Fast Amide Couplings In Water, Nicklas Buckbinder, Sudripet Sharma, Sachin Handa

Undergraduate Research Events

EDC

(1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide) is a carbodiimide that is well known reagent for the amide coupling reactions between an amine and carboxylic acid in the presence of a base. It is the commonly used coupling agent in industries because it produces a water-soluble urea byproduct, which can be easily removed by an aqueous work-up. However, our methodology, the desired amide product precipitates out of the reaction mixture, and no additional work-up is required.3 Using aqueous micelles of PS-750-M as a solvent dramatically increases the rate of reaction.2 The filtrate recovered can be recycled to perform several coupling runs after post-reaction manipulation.

Modification Of Chm20 Lab: Synthesis Of Aspirin, Nicole Diaz, Amy Musselman Prof.

KU Inspires! Undergraduate Research Day

No abstract provided.

Developing Novel Tale-Based Rapid Detection Of Pathogenic Dna Utilizing 2d Graphene Oxide Nanosheets And Quantum Dots, Narayan Neupane

Masters Theses & Specialist Projects

A faster method of quantitative detection of specific dsDNA of pathogenic bacteria such as the Shiga toxin 2 gene (stx2) present in E. coli O157:H7 is of great importance. There is a need for a simple and facile method for sensitive detection of pathogenic gene which is crucial for the prevention and earlier treatment of any infectious diseases. A Transcriptional Activator-Like Effector (TALE) is a novel class of DNA-binding proteins with the unique modularity, flexibility and easy programmability compared to previously discovered DNA- binding proteins. TALEs can bind to any DNA sequences through its unique variable di- residues …

Bentonite Reinforced Chitosan Scaffold: Effect Of Bentonite Exfoliation On Scaffold Properties, Soma Chakraborty, Cristine Joy M. Pimentel

Chemistry Faculty Publications

Chitosan is under investigation as biodegradable scaffolding material for tissue engineering. Crosslinked chitosan alone cannot form a self-supporting scaffold hence it needs reinforcement. The group reported fabrication of chitosan scaffolds reinforced by exfoliated and non-exfoliated bentonite and compared their properties. Scaffolds were fabricated by freeze-drying technique. Bentonite was exfoliated by allowing it to swell in water for a certain time interval. XRD profile showed that swelling reduced the crystallinity of bentonite. Both types of bentonite dispersed well in the chitosan matrix and imparted structural stability to the scaffolds. Scaffolds had interconnected pores, apparent porosity of scaffold with exfoliated bentonite was …

Adaptation Of Pt-Dna Binding Experiments Into A Multiweek Upperlevel Biochemistry Laboratory Activity, Keira Naff

Fall Showcase for Research and Creative Inquiry

Platinum-based drugs are commonly used as anti-cancer therapeutics due to their abilities to bind to DNA and prohibit proliferation in cells. Although the concept of drug interactions within biomolecules is often introduced in undergraduate courses such as biochemistry and toxicology, there are very few laboratory activities that exist that provide undergraduate students with the opportunity to investigate this topic in the lab. During the Summer 2020 PRISM program, we worked to create a multi-week laboratory activity for upper-level biochemistry students focused on the investigation of the DNA binding abilities of common Pt anticancer therapeutics through biochemical modeling and wet laboratory …

Seasonal Ely Copper Mine Superfund Site Shotgun Metagenomic And Metatranscriptomic Data Analysis, Lesley Ann Giddings, George Chlipala, Heather Driscoll, Kieran Bhave, Kevin Kunstman, Stefan Green, Katherine Morillo, Holly Peterson, Mark Maienschein-Cline

Chemistry: Faculty Publications

High throughput sequencing data collected from acid rock drainage (ARD) communities can reveal the active taxonomic and functional diversity of these extreme environments, which can be exploited for bioremediation, pharmaceutical, and industrial applications. Here, we report a seasonal comparison of a microbiome and transcriptome in Ely Brook (EB-90M), a confluence of clean water and upstream tributaries that drains the Ely Copper Mine Superfund site in Vershire, VT, USA. Nucleic acids were extracted from EB-90M water and sediment followed by shotgun sequencing using the Illumina NextSeq platform. Approximately 575,933 contigs with a total length of 1.54 Gbp were generated. Contigs of …

All-Atomic Molecular Dynamic Studies Of Human And Drosophila Cdk8: Insights Into Their Kinase Domains, The Lxxll Motifs, And Drug Binding Site, Wu Xu, Xiao-Jun Xie, Ali K. Faust, Mengmeng Liu, Xiao Li, Feng Chen, Ashlin A. Naquin, Avery C. Walton, Peter W. Kishbaugh, Jun-Yuan Ji

Faculty Publications

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 …

Ultra-High Vibrational And Rotational Motion Of The Hf Molecule Via Infrared (Ir) Laser Excitation, Toria Tucker, Jingwei (Mike) Ling, Bridget Gourley

Annual Student Research Poster Session

Our goals this summer were to build on previous work in our group modeling ultra-high vibrational and rotational excitation in small molecules via unique pulse sequencing of an infrared (IR) laser. The system was modeled both using Fortran and Mathematica as programming languages. We were able to demonstrate that different numerical techniques for propagating coupled differential equations forward in time led to equivalent levels of vibrational excitation and allowed for identical visualization of molecular state probabilities as a function of time. Work including the rotational motion progressed to the point of being able to see both significant excitation when rotations …

Visualizing And Analyzing Structures Of Coordination Polymers Synthesized In Ionic Liquids, Natalie Husby, Akane Inoue, Hilary Eppley

Annual Student Research Poster Session

Synthesis of metal organic frameworks can result in different products based on the solvent that is used. One option is to use ionic liquids (ILs, or room temperature molten salts) to create novel metal organic coordination polymers. Our group analyzed metal organic polymers synthesized in ILs with the goal of cataloging the topology of the structures, the connectivity of the organic ligands, and the roles of the ILs in the syntheses. We used Sci-Finder Scholar to find papers where compounds were synthesized using ILs, and determined whether the IL played the role as the cation, anion, or neither in the …

De Novo Molecular Design Using 3d Molecular Structure Information, Gillian Hughes

Annual Student Research Poster Session

Predicting small molecule potency against a target receptor is critically important in the drug discovery process. By evaluating literature and associated GitHub repositories, we developed a deep learning model based on 3-D molecule and protein structure information to generate new small molecules and predict their binding affinity with protein receptors.

Supervisor: Hongzhou Zhang, PhD

A Brief Overview Of Analyzing Testing Procedures In The Quality Control Lab At Elanco Animal Health, Gina Fedrighi

Annual Student Research Poster Session

The study of testing procedures within the quality control lab was conducted at Elanco Animal Health through the summer internship program. The internship program focuses on the development of young professionals as research and manufacturing leaders in the pharmaceutical industry. The purpose of this project was to determine ways in which to save both time and money in the quality control lab through the study of various quality testing procedures. Quality Control plays a vital role in the manufacturing process in order to ensure quality of products and consistency between batches. It is important to improve upon the current testing …