Chemistry Commons^™

Effect Of Carbon Hybridization In C—F Bond As An Electron Donor In Triel Bonds, Qingqing Yang, Zongqing Chi, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The ability of the F atom of HC≡CF, H₂C=CHF and H₃CCH₂F to serve as an electron donor to the triel (Tr) atom of TrR₃ in the context of a triel bond is assessed by ab initio calculations. The triel bond formed by C_sp3—F is strongest, as high as 30 kcal/mol, followed by C_sp2—F, and then by C_sp—F whose triel bonds can be as small as 1 kcal/mol. The noncovalent bond strength diminishes in the order Tr = Al > Ga > B, consistent with the intensity of the π-hole …

Thermoresponsive Self-Immolative Polyglyoxylamides., Amir Rabiee Kenaree, Quinton E. A. Sirianni, Kyle Classen, Elizabeth R. Gillies

Chemistry Publications

Thermoresponsive polymers with lower critical solution temperatures (LCSTs) are of significant interest for a wide range of applications from sensors to drug delivery vehicles. However, the most widely investigated LCST polymers have nondegradable backbones, limiting their applications

The Bio3d Packages For Structural Bioinformatics, Barry J. Grant, Lars Skjærven, Xin-Qiu Joe Yao

Chemistry Faculty Publications

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise …

Stay Calm And Focus On The Learning Outcomes: Tools For Taking Biophysical Chemistry Online, Maria Ballester, Brian L. Van Hoozen Jr., Arthur Sikora

Chemistry and Physics Faculty Articles

Course specific learning outcomes are an important tool to define the scope of a course and can be very helpful when designing experiments and assessments. With slight modification, these learning outcomes can serve as a guide when transitioning to the distance learning format especially in courses with a traditional lab. Here we present such an example for the biophysical chemistry course.

Structural Organization And Chemical Activity Revealed By New Developments In Single-Molecule Fluorescence And Orientation Imaging, Tianben Ding

McKelvey School of Engineering Graduate Student Theses & Dissertations

Single-molecule (SM) fluorescence and its localization are important and versatile tools for understanding and quantifying dynamical nanoscale behavior of nanoparticles and biological systems. By actively controlling the concentration of fluorescent molecules and precisely localizing individual single molecules, it is possible to overcome the classical diffraction limit and achieve 'super-resolution' with image resolution on the order of 10 nanometers.

Single molecules also can be considered as nanoscale sensors since their fluorescence changes in response to their local nanoenvironment. This dissertation discusses extending this SM approach to resolve heterogeneity and dynamics of nanoscale materials and biophysical structures by using positions and orientations …

Production Of Medical Radioisotopes Using Titanium Accelerator Targets, Christopher Shaun Loveless

Arts & Sciences Graduate Student Theses and Dissertations

Theranostic radiopharmaceuticals enable diagnostic imaging and radionuclide therapy in patients using a single molecular agent labeled with a diagnostic-therapeutic pair (e.g., 68Ga/177Lu) or a theranostic radionuclide (e.g., 131I). This theranostic approach can help inform patient-specific treatment plans and improve clinical outcomes. Radionuclide pairs used in theranostic agents fall into two categories: pseudo matched-pairs (e.g., 68Ga/177Lu) and matched-pairs (e.g., 124I/131I). Pseudo matched-pair radionuclides have similar chemistries and pharmacokinetics when bound to the same bioconjugate molecule. In contrast, identical chemistries and pharmacokinetics can be obtained by using the matched-pair radionuclides.The isotopes of Sc include two diagnostic radioisotopes, 43Sc & 44Sc, and one …

Development And Application Of Mass Spectrometry-Based Approaches For Protein Higher Order Structure Analysis And Protein-Protein Interaction Characterization, Mengru Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Proteins, one of the most fundamental biomolecules, adopt unique higher order structures (HOS) to enable diverse biological functions. Deciphering protein HOS is crucial to gain deeper insights of their working mechanisms and to develop biotherapeutics. Mass spectrometry (MS)-based approaches evolved rapidly in the past 30 years and are now playing critical roles in protein HOS characterization. One of those approaches is MS-based footprinting whose principle is to map the solvent accessible surface area (SASA) to deliver structural information. Protein footprinting can be achieved by reversible labeling, e.g., hydrogen-deuterium exchange (HDX), and by irreversible labeling using radical-based reagents or other targeted …

Transition Metal Complexes Of Pyridyltriazole And Bipyridine Ligands, Sen Gao

LSU Doctoral Dissertations

Four Ni(II) complexes have been obtained with the pyridyltriazole ligand, bpt, or the bis(pyridyltriazole) ligand, m-xpt, in chapter 2. This work was carried out as a comparison with the previously established coordination chemistry of copper(II) with bpt and m-xpt. Initially, the reaction between Ni(II) and bpt only produced one mononuclear compound, [Ni(bpt)₂(H₂O)₂](NO₃)₂ (1). In order to study the formation of Ni-bpt and Ni-m-xpt complexes in solution, mixtures of Ni(NO₃)₂ and ligand (m-xpt or bpt) were prepared in different ratios and …

Highly Swelling Ph-Responsive Microgels For Dual Mode Near Infra-Red Fluorescence Reporting And Imaging, Mingning Zhu, Dongdong Lu, Qing Lian, Shanglin Wu, Wenkai Wang, L. Andrew Lyon, Weiguang Wan, Paulo Bártolo, Mark Dickinson, Brian R. Saunders

Engineering Faculty Articles and Research

Near infra-red (NIR) fluorescence is a desirable property for probe particles because such deeply penetrating light enables remote reporting of the local environment in complex surroundings and imaging. Here, two NIR non-radiative energy transfer (NRET) fluorophores (Cy5 and Cy5.5) are coupled to preformed pH-responsive poly(ethylacrylate-methacrylic acid-divinylbenzene) microgel particles (PEA-MAA-5/5.5 MGs) to obtain new NIR fluorescent probes that are cytocompatible and swell strongly. NIR ratiometric photoluminescence (PL) intensity analysis enables reporting of pH-triggered PEA-MAA-5/5.5 MG particle swelling ratios over a very wide range (from 1–90). The dispersions have greatly improved colloidal stability compared to a reference temperature-responsive NIR MG based on …

Multicourse Comparative Study Of The Core Aspects For Flipped Learning: Investigating In-Class Structure And Student Use Of Video Resources, Nicole Naibert, Emryse Geye, Michael M. Phillips, Jack Barbera

Chemistry Faculty Publications and Presentations

Since 2013, the number of publications on flipped learning within chemistry have steadily increased. However, most of these studies focus on flipped course reforms within individual institutions, while the outcomes of any learning environment are dependent on how the environment is structured and the degree to which students interact with its elements. In this study, we apply a coordinated set of assessment practices to investigate similarities among flipped chemistry courses at five institutions in the United States. All courses in the study followed the two basic tenets of flipped learning: (1) foundational information was delivered through preclass materials (PCMs), and …

Erratum: Basis Set Dependence Of Higher-Order Correlation Effects In Π -Type Interactions (J. Chem. Phys. (2012) 136 (014103) Doi: 10.1155/2019/4057848), Emily J. Carrell, Cara M. Thorne, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

For a sequence of three correlation consistent basis sets,1 an algebraic expression can be obtained from Feller's three-parameter exponential function for the complete basis set (CBS) limit of the Hartree–Fock (HF) energy.2 During the derivation of a general three-point algebraic expression for the HF CBS limit,3 it was recognized that Eq. (2) in our original paper4 had the wrong sign in the last term in the denominator. The correct equation is as follows: (Formula Presented). (Table Presented).

Second Harmonic Generation Spectroscopy And Microscopy Of Liposomes, Nanoparticles, And Cells, Prakash Hamal

LSU Doctoral Dissertations

Second harmonic generation (SHG) is used to investigate the factors that impact nanoparticle-based drug-delivery applications. In the first study, molecular adsorption and transport kinetics of a positively-charged dye, malachite green isothiocyanate (MGITC), is characterized at the surface of different colloidal liposomes in water using SHG spectroscopy. The molecular interactions of MGITC is compared to our previous investigations with malachite green (MG). In comparison to MG, MGITC demonstrates stronger adsorption and faster transport through lipid membranes. Correspondingly, the SHG experimental results are in excellent agreement with the molecular dynamics (MD) simulations results. A key finding illustrates the importance of functional groups, …

Near Simultaneous Laser Scanning Confocal And Atomic Force Microscopy (Conpokal) On Live Cells, Joree N. Sandin, Surya P. Aryal, Thomas E. Wilkop, Christopher I. Richards, Martha E. Grady

Physiology Faculty Publications

Techniques available for micro- and nano-scale mechanical characterization have exploded in the last few decades. From further development of the scanning and transmission electron microscope, to the invention of atomic force microscopy, and advances in fluorescent imaging, there have been substantial gains in technologies that enable the study of small materials. Conpokal is a portmanteau that combines confocal microscopy with atomic force microscopy (AFM), where a probe "pokes" the surface. Although each technique is extremely effective for the qualitative and/or quantitative image collection on their own, Conpokal provides the capability to test with blended fluorescence imaging and mechanical characterization. Designed …

H-Atom Ladder Operator Revisited, Carl W. David

Chemistry Education Materials

An error laden note (Am. J. Phys., 34, 984,(1966)) concerning the ladder operator solution to the hydrogen atom electronic energy levels is corrected.

Isolation, Structure Elucidation, And Synthesis Of Natural Products From Marine Cyanobacteria, Keren Solomon

Electronic Theses and Dissertations

This thesis describes the isolation, structure elucidation, and synthesis of natural products from marine cyanobacteria. A crude extract from a cyanobacterium collected in Curacao showed selective affinity for the dopamine D₅ receptor in a screen against a panel of CNS receptors. Due to the high similarity of the D₅ and D₁ receptor, to date there are no known ligands that differentiate them. Attempts to purify the compound responsible for this affinity led to the isolation of the known compound caylobolide A. A second extract from a cyanobacterium collected in Panama underwent bioassay-guided fractionation and yielded the novel …

Advanced Solid-State Lithium Batteries For Electric Vehicles, Yelsin Mendez Camacho

International Programs

Solid-state lithium batteries (SSLBs) may have the potential to safe and long-distance driving in electric-vehicles (EV). […] However, manufacturing processes and new materials need to be developed to make these batteries commercially available.

Electrostatic Denaturation Of Dna-Cisplatin Adducts, Eddie Madrigal

Master's Theses

In this thesis, electrochemical approaches are used to determine the properties of deoxyribonucleic acid (DNA) by electrostatic denaturation. The electrochemical routine involves an application of a destabilization potential, an equilibration potential, and a square wave voltammogram (SWV) to monitor the extent of melting. Our method uses a monolayer consisting of thiol modified DNA and mercaptohexanol on a gold electrode. These electrodes are then incubated in a complementary sequence tagged with methylene blue. By using our electrostatic denaturation technique, different parameters are explored, such as surface densities, surface coverages, and ionic strengths. As proof of concept, these techniques were applied toward …

Electroactive Anion Receptor With High Affinity For Arsenate, Samuel I. Etkind, Douglas A. Vander Griend, Timothy M. Swager

University Faculty Publications and Creative Works

Herein, we present the synthesis and characterization of a macrocyclic polyamide cage that incorporates redox-active 1,4-dithiin units. UV/vis titration experiments with eight anions in acetonitrile revealed high affinity for H2AsO4− (log β2 = 10.4−+0.40.4) and HCO3− (log β2 = 8.3−+0.30.4) over other common anionic guests, such as Cl− (log K1:1 = 3.20−+0.030.02), HSO4− (log K1:1 = 3.57−+0.020.03), and H2PO4− (log K1:1 = 4.24−+0.050.04), by the selective formation of HG2 complexes. The recognition of arsenate over phosphate is rare among both proteins and synthetic receptors, and though the origin of selectivity is not known, exploiting the difference in the binding stoichiometry …

Structure And Function Of A Flavin-Dependent S-Monooxygenase From Garlic (Allium Sativum), Hannah Valentino, Ashley C. Campbell, Jonathan P. Schuermann, Nazneen Sultana, Han G. Nam, Sophie Leblanc, John J. Tanner, Pablo Sobrado

Chemistry Faculty Research & Creative Works

Allicin is a component of the characteristic smell and flavor of garlic (Allium sativum). A flavin-containing monooxygenase (FMO) produced by A. sativum (AsFMO) was previously proposed to oxidize S-allyl-L-cysteine (SAC) to alliin, an allicin precursor. Here, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC; however, the enzyme was highly active with L-cysteine, N-acetyl-L-cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly (KD of …

University Of Kentucky Measurements Of Wind, Temperature, Pressure And Humidity In Support Of Lapse-Rate Using Multisite Fixed-Wing And Rotorcraft Unmanned Aerial Systems, Sean C. C. Bailey, Michael P. Sama, Caleb A. Canter, Luis Felipe Pampolini, Zachary S. Lippay, Travis J. Schuyler, Jonathan D. Hamilton, Sean B. Macphee, Isaac S. Rowe, Christopher D. Sanders, Virginia G. Smith, Christina N. Vezzi, Harrison M. Wight, Jesse B. Hoagg, Marcelo I. Guzman, Suzanne Weaver Smith

Mechanical Engineering Faculty Publications

In July 2018, unmanned aerial systems (UASs) were deployed to measure the properties of the lower atmosphere within the San Luis Valley, an elevated valley in Colorado, USA, as part of the Lower Atmospheric Profiling Studies at Elevation – a Remotely-piloted Aircraft Team Experiment (LAPSE-RATE). Measurement objectives included detailing boundary layer transition, canyon cold-air drainage and convection initiation within the valley. Details of the contribution to LAPSE-RATE made by the University of Kentucky are provided here, which include measurements by seven different fixed-wing and rotorcraft UASs totaling over 178 flights with validated data. The data from these coordinated UAS flights …

Formation Of Gaseous Proteins Via The Ion Evaporation Model (Iem) In Electrospray Mass Spectrometry., Elnaz Aliyari, Lars Konermann

Chemistry Publications

The mechanisms whereby protein ions are released into the gas phase from charged droplets during electrospray ionization (ESI) continue to be controversial. Several pathways have been proposed. For native ESI the charged residue model (CRM) is favored; it entails the liberation of proteins via solvent evaporation to dryness. Unfolded proteins likely follow the chain ejection model (CEM), which involves the gradual expulsion of stretched-out chains from the droplet. According to the ion evaporation model (IEM) ions undergo electrostatically driven desorption from the droplet surface. The IEM is well supported for small precharged species such as Na⁺. However, it …

Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity, oxidative stress and apoptosis. In type 2 diabetes, these stressful conditions contribute to the malfunction and loss of functional insulin-producing β-cells. Current treatment methods for diabetes include insulin therapy, islet transplant and anti-diabetes medication. These treatments are not curative and ignore other factors that contribute to the pathogenesis of diabetes beyond insulin resistance and islet β-cell failure. Previous research on β-cells has focused on ways to replace functional β-cell mass, trigger β-cell proliferation, …

Structure And Unprecedented Reactivity Of A Mononuclear Nonheme Cobalt(Iii) Iodosylbenzene Complex, J. Yang, M. S. Seo, K. H. Kim, Y. M. Lee, S. Fukuzumi, Jason M. Shearer, W. Nam

Chemistry Faculty Research

A mononuclear nonheme cobalt(III) iodosylbenzene complex, [Co^III(TQA)(OIPh)(OH)]²⁺ (1), is synthesized and characterized structurally and spectroscopically. While 1 is a sluggish oxidant in oxidation reactions, it becomes a competent oxidant in oxygen atom transfer reactions, such as olefin epoxidation, in the presence of a small amount of proton. More interestingly, 1 shows a nucleophilic reactivity in aldehyde deformylation reaction, demonstrating that 1 has an amphoteric reactivity. Another interesting observation is that 1 can be used as an oxygen atom donor in the generation of high-valent metal-oxo complexes. To our knowledge, we present the first crystal structure …

Nowotny Chimney Ladder Phases With Group 5 Metals: Crystal And Electronic Structure And Relations To The Crsi2 Structure Type, Evgney V. Dikarev, Zheng Wei, Maxim S. Likhanov, Nikita V. Sytov, Andrei V. Shevelkov

Chemistry Department Faculty Scholarship

Nowotny chimney ladder (NCL) phases are intermetallic compounds formed by transition metals and metals of groups 13 and 14. This family can be expanded by combining two p-elements from different groups with those transition metals, for which the corresponding binary NCL phases are unknown. In this paper, we present three new compounds in the V-Al-Ge, Nb-Al-Ge, and Nb-Ga-Ge systems related to the TiSi₂ structure type (Sp. Gr. Fddd) obtained with the standard ampule technique. The crystal structures of the new compounds were determined using synchrotron powder X-ray diffraction data. A transition to the CrSi₂ structure type was detected …

Response Of Photoluminescence Of H-Terminated And Hydrosilylated Porous Si Powders To Rinsing And Temperature, Kurt W. Kolasinski, Joseph D. Swanson, Benjamin Roe, Teresa Lee

Chemistry Faculty Publications

The photoluminescence (PL) response of porous Si has potential applications in a number of sensor and bioimaging techniques. However, many questions still remain regarding how to stabilize and enhance the PL signal, as well as how PL responds to environmental factors. Regenerative electroless etching (ReEtching) was used to produce photoluminescent porous Si directly from Si powder. As etched, the material was H-terminated. The intensity and peak wavelength were greatly aected by the rinsing protocol employed. The highest intensity and bluest PL were obtained when dilute HCl(aq) rinsing was followed by pentane wetting and vacuum oven drying. Roughly half of the …

Synthesis And Assessment Of Radiotherapy-Enhancing Nanoparticles, Hayden Winter

Dissertations and Theses

Radiation Therapy (RT) is a common treatment for cancerous lesions that acts by ionizing matter in the affected tissue, causing cell death. The disadvantage of RT is that it is most often delivered via an external beam of radiation which must pass through healthy tissues to reach the target site, ionizing matter within healthy tissues as well. To address this drawback, techniques are being developed for increasing RT-induced cell death in a target tissue while minimizing cell death in surrounding tissues. This effect is known as radiation dose enhancement or RT enhancement.

The approach to RT enhancement studied in this …

Synthesis Of Alpha-Methylselenocysteine, Its Relevant Analogues, And An Unnatural Glutathione Disulfide Core, Robert J. Wehrle

Dissertations

Selenoproteins, such as glutathione peroxidase, have gained interest for their ability to act as antioxidants, and their potential to act as anti-cancer agents. Synthesizing and studying selenoproteins can be problematic, however, due to their propensity to degrade from over-oxidation. The degradation from over-oxidation can be avoided by the incorporation of the unnatural amino acid, alpha-methylselenocysteine. A synthesis utilizing methyl malonic esters was used to synthesize protected (R)-alpha-methylselenocysteine efficiently (46% over four steps) and in high enantio-purity (88% enantiomeric excess). Using similar procedures, the (S)-enantiomer was also synthesized as well as a beta-analogue.

The use of enzymes …

Machine Learning Approaches For Improving Prediction Performance Of Structure-Activity Relationship Models, Gabriel Idakwo

Dissertations

In silico bioactivity prediction studies are designed to complement in vivo and in vitro efforts to assess the activity and properties of small molecules. In silico methods such as Quantitative Structure-Activity/Property Relationship (QSAR) are used to correlate the structure of a molecule to its biological property in drug design and toxicological studies. In this body of work, I started with two in-depth reviews into the application of machine learning based approaches and feature reduction methods to QSAR, and then investigated solutions to three common challenges faced in machine learning based QSAR studies.

First, to improve the prediction accuracy of learning …

Structures Of Disodium Hydrogen Citrate Monohydrate, Na2hc6h5o7(H2o), And Diammonium Sodium Citrate, (Nh4)2nac6h5o7, From Powder Diffraction Data, Jerry Hong '20, Shivang Bhaskar, Joseph T. Golab, James A. Kaduk

Student Publications & Research

No abstract provided.

California - Peralta Weigh Station, University Of Denver

FEAT Heavy-Duty Vehicle Measurements

Relevant Publications

Environmental Science & Technology Publication (2001)

Environmental Science & Technology Publication (2012)

Environmental Science & Technology Publication (2013)

Environmental Science & Technology Publication (2018)

Air & Waste Management Journal (2021)

2008 Final Report

2009 Final Report

2010 Final Report

2012 Final Report

2017 Final Report