Chemistry Commons^™

Algal Biomarkers As A Proxy For Pco2: Constraints From Late Quaternary Sapropels In The Eastern Mediterranean, Caitlyn R. Witkowski, Marcel T.J. Van Der Meer, Brian Blais, Jaap S. Sinninghe Damsté, Stefan Schouten

Science and Technology Department Faculty Journal Articles

Records of carbon dioxide concentrations (partial pressure expressed as pCO2) over Earth’s history provide trends that are critical to understand our changing world. To better constrain pCO2 estimations, here we test organic pCO2 proxies against the direct measurements of pCO2 recorded in ice cores. Based on the concept of stable carbon isotopic fractionation due to photosynthetic CO2 fixation (Ɛp), we use the stable carbon isotopic composition (δ13C) of the recently proposed biomarker phytol (from all photoautotrophs), as well as the conventionally used alkenone biomarkers (from specific species) for comparison, to reconstruct pCO2 over several Quaternary …

Synthesis And Characterization Of Water-Soluble Polyaniline For Hydrazine Detection / Hazira Hussin, Hazira Hussin

Student Works (2020-2029)

In this study, polyaniline (PAni) was synthesized through the chemical oxidation method using aniline (Ani) as a monomer, hydrochloric acid (HCl) as a dopant, and ammonium persulphate (APS) as an initiator. PAni was rendered water soluble through treating with cellulose derivatives. Cellulose derivatives such as methylcellulose (MC), hydroxypropyl cellulose (HPC), and hydroxypropyl methylcellulose (HPMC) were used as a stabilizer to improve the solubility of PAni in an aqueous medium. The water-soluble PAni-cellulose derivative was applied as a chemical sensor for hydrazine detection. The chemical structures and electrical conducting behaviours of PAni-cellulose derivatives were investigated using Fourier transform infrared (FTIR) and …

Ru(Ii)-Diimine Complexes And Cytochrome P450 Working Hand-In-Hand, Celine Eidenschenk, Lionel Cheruzel

Faculty Publications, Chemistry

With a growing interest in utilizing visible light to drive biocatalytic processes, several light-harvesting units and approaches have been employed to harness the synthetic potential of heme monooxygenases and carry out selective oxyfunctionalization of a wide range of substrates. While the fields of cytochrome P450 and Ru(II) photochemistry have separately been prolific, it is not until the turn of the 21st century that they converged. Non-covalent and subsequently covalently attached Ru(II) complexes were used to promote rapid intramolecular electron transfer in bacterial P450 enzymes. Photocatalytic activity with Ru(II)-modified P450 enzymes was achieved under reductive conditions with a judicious choice of …

Nucleic Acid Delivery With Α-Tocopherol-Polyethyleneimine-Polyethylene Glycol Nanocarrier System., A K M Nawshad Hossian, Seetharama D Jois, Subash C. Jonnalagadda, George Mattheolabakis

College of Science & Mathematics Departmental Research

Purpose: Nucleic acid-based therapies are a promising therapeutic tool. The major obstacle in their clinical translation is their efficient delivery to the desired tissue. We developed a novel nanosized delivery system composed of conjugates of α-tocopherol, polyethyleneimine, and polyethylene glycol (TPP) to deliver nucleic acids.

Methods: We synthesized a panel of TPP molecules using different molecular weights of PEG and PEI and analyzed with various analytical approaches. The optimized version of TPP (TPP

Results: Through a panel of synthesized molecules, TPP

Conclusion: These results indicate that we successfully synthesized the TPP

Feasibility Of Modifying Existing Chemistry Demonstrations By Using Substitute Materials, Dane Mykel M. Quiambao, Armando M. Guidote Jr, Rhodora F. Nicdao

Chemistry Faculty Publications

This study aimed to reiterate the use of Chemistry demonstrations as effective teaching tools to students while addressing some of its drawbacks, which discourages teachers from doing them such as cost and safety. Four chosen existing Chemistry demonstrations (Blue Bottle Experiment, Copper Sulfate Experiment, Blown Away, Dancing Flames) were modified by using substitute reagents, which are more accessible, relatively safer, and at lower cost. These demonstrations were chosen based on how easily the substitute reagents will be obtained. Afterwards, with the permission of a private junior high school, they were presented to a group of Grade 9 students of their …

Mechanism And Chemoselectivity For Hocl-Mediated Oxidation Of Zinc-Bound Thiolates, Lindsay Zumwalt, Arden Perkins, O. Maduka Ogba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantum mechanical calculations reveal the preferred mechanism and origins of chemoselectivity for HOCl‐mediated oxidation of zinc‐bound thiolates implicated in bacterial redox sensing. Distortion/interaction models show that minimizing geometric distortion at the zinc complex during the rate‐limiting nucleophilic substitution step controls the mechanistic preference for OH over Cl transfer with HOCl and the chemoselectivity for HOCl over H2O2.

Mechanism And Chemoselectivity For Hocl-Mediated Oxidation Of Zinc-Bound Thiolates, Lindsay Zumwalt, Arden Perkins, O. Maduka Ogba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantum mechanical calculations reveal the preferred mechanism and origins of chemoselectivity for HOCl‐mediated oxidation of zinc‐bound thiolates implicated in bacterial redox sensing. Distortion/interaction models show that minimizing geometric distortion at the zinc complex during the rate‐limiting nucleophilic substitution step controls the mechanistic preference for OH over Cl transfer with HOCl and the chemoselectivity for HOCl over H₂O₂.

Indoline‐6‐Sulfonamide Inhibitors Of The Bacterial Enzyme Dape, Cory T. Reidl, Tahirah K. Heath, Iman Darwish, Rachel M. Torrez, Maxwell Moore, Elliot Gild, Boguslaw P. Nocek, Anna Starus, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Inhibitors of the bacterial enzyme dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18) hold promise as antibiotics with a new mechanism of action. Herein we describe the discovery of a new series of indoline sulfonamide DapE inhibitors from a high-throughput screen and the synthesis of a series of analogs. Inhibitory potency was measured by a ninhydrin-based DapE assay recently developed by our group. Molecular docking experiments suggest active site binding with the sulfonamide acting as a zinc-binding group (ZBG).

Indoline-6-Sulfonamide Inhibitors Of The Bacterial Enzyme Dape, Cory T. Reidl, Tahirah K. Heath, Iman Darwish, Rachel M. Torrez, Maxwell Moore, Elliot Gild, Boguslaw P. Nocek, Anna Starus, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Inhibitors of the bacterial enzyme dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18) hold promise as antibiotics with a new mechanism of action. Herein we describe the discovery of a new series of indoline sulfonamide DapE inhibitors from a high-throughput screen and the synthesis of a series of analogs. Inhibitory potency was measured by a ninhydrin-based DapE assay recently developed by our group. Molecular docking experiments suggest active site binding with the sulfonamide acting as a zinc-binding group (ZBG).

Synthesis And Characterization Of Silver Nanoparticles In Lamellar Lyotropic Liquid Crystal, Siti Mariah Mohd Yasin

Student Works (2020-2029)

Lamellar lyotropic liquid crystal-silver nanoparticles (LLLC-AgNPs) are synthesized using the in-situ method. The polarizer microscope showed a mosaic-like pattern with fan shape textures. The high resolution transmission electron microscope (HRTEM) confirmed that the AgNPs are spherical in shape with 4 – 12 nm size. Differential scanning calorimetry (DSC) determined the LLLC-AgNPs transition anisotropic phase to the highly ordered isotropic phase at 300 °C, and crystallinity was completed at 350 °C. Thermogravimetric analysis (TGA) verified that the LLLC-AgNPs were completely decomposed at 700 °C. Ultra-violet visible spectroscopy (UV-vis) found the absorption peaks at around 400 nm and proved that the AgNPs …

Design And Synthesis Of Core–Shell Microgels With One‐Step Clickable Crosslinked Cores And Ultralow Crosslinked Shells, Molla R. Islam, Chelsea Nguy, Sanika Pandit, L. Andrew Lyon

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The present study is conducted to explore the engineering of core–shell microgels such that the core can be rapidly labeled with a variety of fluorophores, while the shell retains the softness needed in specific biomedical applications. Azide containing crosslinked core particles based on a crosslinked poly(N‐isopropylacrylamide) particle, using a one‐pot, multistep polymerization is synthesized. A core–shell microgel is then synthesized by growing a crosslinker‐free poly(N‐isopropylacrylamide)‐co‐acrylic acid (ULC10AAc) shell through a two‐step seed and feed polymerization. A simple “click” reaction between the azide present on the core and dibenzocyclooctyne containing fluorophores to make dyed core–shell …

Synthesis Of New Pyrazole & Thiazole Derivatives As Antimicrobial And Anticancer Agents, Ibrahim Saleh Alkhaibari

Student Theses and Dissertations

This thesis contains two chapters. In chapter one, we are reporting an efficient synthesis of eighty new pyrazole derivatives: sixty 4-trifluoromethyl and 3,5 bis(trifluoromethyl)phenyl substituted pyrazole-derived anilines, and twenty 4-trifluoromethyl-phenyl substituted pyrazole-derived hydrazones. Some of the pyrazole derivatives have been tested against several bacterial strains and have shown promising results. In Chapter two, we are reporting a synthesis of novel fused-thiazole- nootkatone derivatives. These compounds have been tested as well against a broad spectrum of Gram-positive and Gram-negative bacteria. However, they have just shown activity against some of the Gram-positive bacteria. Further anti-cancer and toxicity studies of these compounds are …

Misconceptions On Chemical Bonding Among Form Four Pupils, Quah Mei Ling

Student Works (2020-2029)

The learning of chemical bonding in chemistry is an abstract concept for all students. The process of learning chemistry can be classified into three levels which are macroscopic, sub-microscopic, and symbolic levels. Students have problems correlating all three levels in learning chemical bonding. During the transition of these three levels, students face difficulties in relating the macroscopic and sub-microscopic levels which lead to misconceptions. Therefore, the purpose of conducting this study was to explore the misconceptions of chemical bonding which includes ionic bonding and covalent bonding among Form Four students. This study aimed to answer two research questions; 1) what …

Determining The Structure And Function Of Newly Discovered Immune Systems, Ryan N. Jackson

Funded Research Records

No abstract provided.

Synthesis Of Biologically Active Phosphorus Heterocycles, Giri Gnawali

Dissertations

This dissertation work is divided into two parts. The first part is focused in the development of methodology for the synthesis of phostones and phosphonosugars and advancement thereof. The second part is focused in the development of affinity probes based on analogs of natural products cyclophostin and the cyclipostins.

Phostone (3) and phosphonosugars are cyclic phosphonates. The anomeric carbon of sugar is replaced by a phosphorus atom. The synthesis of phostones has been achieved starting form the key intermediate, γ,δ-epoxy vinyl phosphonate (1). The palladium catalyzed ring opening of γ,δ-epoxy vinyl phosphonates by a nucleophile results …

Novel Antibacterial Compounds And Methods Of Making And Using Same, Amit Basu, Christopher W. Reid, Michael Saladino

Science and Technology Department Faculty Journal Articles

The invention provides novel antibacterial diamide compounds, pharmaceutical compositions comprising the compounds and methods for treating or preventing an infection in a subject using the compounds.

All-Carbon Conductors For Electronic And Electrical Wiring Applications, Federico Cesano, M. Jasim Uddin, Karen Lozano, Marco Zanetti, Domenica Scarano

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

Electrical conductors based on carbons have recently attracted a growing interest due to the prospect of replacing metals. Electrical conductors without metals could represent not only an alternative for traditional wiring, but also a step forward in the progress and advancing of technology. This result can be achieved by combining high electrical conductivity with other properties, that are dexterity, light weight, environmental stability, high strength and flexibility. As the best mechanical properties, high electrical/thermal conductivity of the assembled fibers are all generally associated with low concentration of defects in the fiber backbone and in the individual carbon “building blocks”, a …

Mitochondrial Oxidative And Nitrosative Stress And Alzheimer Disease, D. Allan Butterfield, Debra Boyd-Kimball

Chemistry Faculty Publications

Oxidative and nitrosative stress are widely recognized as critical factors in the pathogenesis and progression of Alzheimer disease (AD) and its earlier stage, amnestic mild cognitive impairment (MCI). A major source of free radicals that lead to oxidative and nitrosative damage is mitochondria. This review paper discusses oxidative and nitrosative stress and markers thereof in the brain, along with redox proteomics, which are techniques that have been pioneered in the Butterfield laboratory. Selected biological alterations in—and oxidative and nitrosative modifications of—mitochondria in AD and MCI and systems of relevance thereof also are presented. The review article concludes with a section …

Annual Concentration And Flux Of Non-Sea-Salt Sulfate In The Wais Divide Ice Core (Wdc) For The Last 11,000 Years, Jihong Cole-Dai

Ice Core and Environmental Chemistry Lab Datasets and Publications

Annual concentration and flux of non-sea-slat sulfate in the WAIS Divide ice core (WDC) for the last 11,000 years.

The Statue Of Liberty Laboratory Activity: The Chemistry Of Copper, Jihyun Kim, Marcus D. Allen

Open Educational Resources

In this lab activity we observe chemical changes of copper in acidic conditions, salt water, and a mixture of lemon juice and vinegar and salt, and we discuss whether the Statue of Liberty would hold as much cultural icon today had the Lady Statue remain the original shiny brown color.

Yellowstone National Park - Pems Snowcoach Measurements, University Of Denver

Non-Road Vehicle Data

Relevant Publications

Environmental Science & Technology Publication (2006)

Air & Waste Management Publication (2009)

Environmental Science & Technology Publication (2014)

2005 Final Report

2006 Final Report

2012 Final Report

Yellowstone National Park - Feat Snowmobile Measurements, University Of Denver

Non-Road Vehicle Data

Relevant Publications

Environmental Science & Technology Publication (1999)

Environmental Science & Technology Publication (2001)

Environmental Science & Technology Publication (2005)

1998 Final Report

1999 Final Report

2005 Final Report

Small Molecule Synthetic Carbohydrate Receptors, Marcelo F. Bravo Carranco

Dissertations, Theses, and Capstone Projects

Carbohydrate – receptor interactions are often involved in the attachment of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered “undruggable”, meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs) – small molecules that bind carbohydrates – could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of …

Asymmetric Alpha-Stannylation Of Heterocycles And Their Subsequent Use In Cross-Coupling Reactions, Haoran Zhao

Dissertations, Theses, and Capstone Projects

α-Substituted oxygen-containing heterocycles are commonly present in biologically active molecules. Statistics shows that at least one α-substituted ether moiety appears in over 20% of the top 200 small-molecule pharmaceuticals. This project illustrates a reliable regioselective method to introduce simple cyclic ethers towards the diversification of small molecules. Aryl halides bearing various functional groups were well tolerated independent of their electronic properties. It was found that cyclohexyl spectator ligands on tin selectively slows transmetallation of undesired units, circumventing the competitive transfer of n-butyl group from ⁿBu₃SnR reagents. Compared to the normally used ⁿBu₃SnR reagents, Cy …

Excitons In Self-Assembled Hybrid Systems Of Molecular Aggregate Light-Harvesting Nanotubes: Charge-Transfer Substrates And Solution-Stabilized Nanocomposites, Kara Ng

Dissertations, Theses, and Capstone Projects

Delocalized Frenkel excitons-coherently-shared excitations among chromophores-are responsible for the remarkable effciency of supramolecular light-harvesting aggregates within photosynthetic organisms. Despite tremendous progress towards a deeper understanding of these photosynthetic complexes, as well as progress in the development of organic solar cells, the possibility of using bio-inspired molecular nanostructures for large-scale solar energy conversion has not been realized yet. The persistent limitations in translating natures design principles for applications in optoelectronic devices have been the supramolecular structures fragility, and the Frenkel excitons delicate nature. The structural instability, both dis-assembly and spontaneous re-assembly of aggregates. Analysis of the absorption spectrum of a model …

Pointing The Zinc Finger On Protein Folding: Energetic Investigation Into The Role Of The Metal-Ion In The Metal-Induced Protein Folding Of Zinc Finger Motifs, Inna Bakman-Sanchez

Dissertations, Theses, and Capstone Projects

Interactions between inorganic metal-ion cofactors and organic protein scaffolds are important for the proper structure and function of metalloproteins. Zinc finger proteins (ZFPs) are an example of proteins with such crucial metal-protein interactions. Incorporation of the Zn(II)-ion into ZFPs allows for their correct folding into structures that can carry out vital biological functions which include gene expression and tumor suppression. In addition, engineered ZFPs have shown to be promising genetic therapeutics in the clinic. And yet, there is still a gap in a quantitative understanding of the energetic contribution of the metal-protein interactions towards the structure and function of these …

Peo-Ppo-Peo Surfactant Mixtures As Templates For Silicas With Very Large Cylindrical Mesopores At Ambient Temperature And With Helical Mesopores At Sub-Ambient Temperature, Laurance Beaton

Dissertations, Theses, and Capstone Projects

The original research described herein concerns the synthesis of mesoporous silicas through a surfactant-templating method. The approach taken involved the use of a mixed surfactant system of two poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) surfactants, with one of the copolymers containing a much larger percentage of hydrophobic (PPO) blocks than the employed co-surfactant. Systematic adjustments of experimental parameters initially enabled the preparation of 2-D hexagonally ordered mesoporous silicas (SBA-15) of uncommonly large pore diameter at ambient temperature. Comparable silica was synthesized with and without temperature control. Additional adjustments to experimental parameters, including reduction of the relative amount of framework precursor used in …

Inversion Modeling Of Japonica Rice Canopy Chlorophyll Content With Uav Hyperspectral Remote Sensing, Yingli Cao, Kailun Jiang, Jingxian Wu, Fenghua Yu, Wen Du, Tongyu Xu

Electrical Engineering Faculty Publications and Presentations

Chlorophyll content is an important indicator of the growth status of japonica rice. The objective of this paper is to develop an inversion model that can predict japonica rice chlorophyll content by using hyperspectral image of rice canopy collected with unmanned aerial vehicle (UAV). UAV-based hyperspectral remote sensing can provide timely and cost-effective monitoring of chlorophyll content over a large region. The study was based on hyperspectral data collected at the Shenyang Agricultural College Academician Japonica Rice Experimental Base in 2018 and 2019. In order to extract the salient information embedded in the high-dimensional hyperspectral data, we first perform dimension …

Structural Investigation Of Bacilliredoxins: Enzymes Involved In Bacillithiol Redox Metabolism, Colin Mchugh, Paul Cook

Student Summer Scholars Manuscripts

Bacillithiol is an important compound involved in intracellular redox homeostasis and fosfomycin resistance mechanisms of some Gram-positive bacterial pathogens. Cellular regeneration of active bacillithiol (BSH) from a disulfide (BSSB) or mixed disulfide state (BSS-Protein) involves the bacilliredoxin enzymes BrxA/B. An X-ray crystallographic structure of apo BrxA from Bacillus subtilis has been previously characterized, but no BrxB or BSSB-bound Brx structure currently exists. Here we present an X-ray crystallographic structure of BrxA from the pathogen Staphylococcus aureus with a bacillithiol disulfide (BSSB) bound in the active site. Elucidation of this structure will help researchers to understand how BSSB binds in bacilliredoxins, …

Meteorological Conditions And Transport Of Air Pollutants At Bachok Marine Research Station (Bmrs) In Peninsular Malaysia, Mohyeddin Noraini

Student Works (2020-2029)

This study is focused at relatively new regional Global Atmospheric Watch (GAW) station at Peninsular Malaysia – Bachok Marine Research Station (BMRS) using the observational and remote sensing data. The study consists of three main objectives. Firstly, to investigate the meteorological conditions during two major Southeast Asia monsoon – NE and SW monsoon. Secondly, to determine the potential sources of air pollution at BMRS during the monsoon periods. Thirdly, to examine the relations of carbon dioxide (CO2), methane (CH4) and particulate matters (PM10, and PM2.5) with the meteorological conditions during intensive case study periods. The first case study (CS1) was …