Chemistry Commons^™

Fluorogenic Protein Labeling Using A Genetically Encoded Unstrained Alkene, X. Shang, X. Song, C. Faller, R. Lai, H. Li, Ronald Cerny, Wei Niu, Jiantao Guo

Department of Chemistry: Faculty Publications

We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.

Exploring Water Radiolysis In Proton Cancer Therapy: Time-Dependent, Non-Adiabatic Simulations Of H+ + (H2o)1-6, Austin J. Privett, Erico S. Teixeira, Christopher Stopera, Jorge A. Morales

Chemistry and Occupational Health Science

To elucidate microscopic details of proton cancer therapy (PCT), we apply the simplest-level electron nuclear dynamics (SLEND) method to H+ + (H2O)1-6 at ELab = 100 keV. These systems are computationally tractable prototypes to simulate water radiolysis reactionsÐi.e. the PCT processes that generate the DNA-damaging species against cancerous cells. To capture incipient bulk-water effects, ten (H2O)1-6 isomers are considered, ranging from quasi-planar/ multiplanar (H2O)1-6 to ªsmallest-dropº prism and cage (H2O)6 structures. SLEND is a time-dependent, variational, non-adiabatic and direct method that adopts a nuclear classicalmechanics description and an electronic single-determinantal wavefunction in the Thouless representation. Short-time SLEND/6-31G* (n = 1±6) …

Closing The Science And Achievement Gap: Overlap Of The Next Generation Science Standards And Culturally Relevant Pedagogy, Brenna G. Bloome

Departmental Honors Projects

The United States is experiencing both a science gap and an achievement gap within science education. To shrink the science gap and prepare American students for the innovative and rigorous STEM career fields ahead, the Next Generation Science Standards (NGSS) were implemented in science education. Additionally, culturally relevant pedagogy was implemented in general education to alleviate the achievement gap. To ensure that all students are prepared to succeed in the competitive global world they are going to be a part of, science education needs to incorporate both NGSS and culturally relevant pedagogy. To examine the overlap of both pedagogies working …

Assessment Of Surface Water Contamination From Coalbed Methane Fracturing-Derived Volatile Contaminants In Sullivan County, Indiana, Usa, Nicholas Meszaros, Bikram Subedi, Tristan Stamets, Naima Shifa

Faculty & Staff Research and Creative Activity

There is a growing concern over the contamination of surface water and the associated environmental and public health consequences from the recent proliferation in hydraulic fracturing in the USA. Petroleum hydrocarbon-derived contaminants of concern [benzene, toluene, ethylbenzene, and xylene (BTEX)] and various dissolved cations and anions were spatially determined in surface waters around 14 coalbed methane fracking wells in Sullivan County, IN, USA. At least one BTEX was detected in 69% of sampling sites (n=13) and 23% of sampling sites were found to be contaminated with all of the BTEX. Toluene was the most common BTEX compound detected across all …

A Review Of The Occurrence Of Pharmaceuticals And Personal Care Products In Indian Water Bodies, Keshava Balakrishna, Amlan Rath, Yerabham Praveenkumarreddy, Keerthi Siri Guruge, Bikram Subedi

Faculty & Staff Research and Creative Activity

Little information exists on the occurrence and the ultimate fate of pharmaceuticals in the water bodies in India despite being one of the world leaders in pharmaceutical production and consumption. This paper has reviewed 19 published reports of pharmaceutical occurrence in the aquatic environment in India [conventional activated sludge wastewater treatment plants (WTPs), hospital WTPs, rivers, and groundwater]. Carbamazepine (antipsychoactive), atenolol (antihypertensive), triclocarban and triclosan (antimicrobials), trimethoprim and sulfamethoxazole (antibacterials), ibuprofen and acetaminophen (analgesics), and caffeine (stimulant) are the most commonly detected at higher concentrations in Indian WTPs that treat predominantly the domestic sewage. The concentration of ciprofloxacin, sulfamethoxazole, amoxicillin, …

Investigating Medicinally Important Portein-Protein And Protein-Ligand Interactions : A Computational Approach, Cooper Ashley Taylor

Honors Theses

Molecular dynamics (MD) simulations and computational chemistry allow for an atomistic understanding of protein-protein and protein-ligand binding motifs. Through the use of MD, medicinally relevant complexes can be examined in detail unattainable by experimental methods. Within this work, systems pertinent to both Alzheimer’s Disease and HIV-1 are probed and thoroughly sampled to help elucidate potential therapeutic pathways. We used molecular dynamics and free energy estimations to gauge the affinity for the binary and ternary complexes of KLC1, APP and JIP1, three proteins all believed to be involved in the propagation of Alzheimer’s Disease. Two areas of thought exist suggesting that …

Ln(Ii)-Containing Cryptates: Synthesis And Properties, Akhila Nuwan Wijerathne Kuda-Wedagedara

Wayne State University Dissertations

LNII-CONTAINING CRYPTATES: SYNTHESIS AND PROPERTIES

by

AKHILA N. W. KUDA-WEDAGEDARA

May 2016

Advisor: Dr. Matthew J. Allen

Major: Chemistry

Degree: Doctor of Philosophy

Research projects described in this dissertation are focused on studying the physicochemical properties, including the photochemical, redox, and magnetic properties, of LnII-containing cryptates and how ligand structure influences metal–ligand interactions that in turn influence physicochemical properties. The results of these studies enable tailoring of the coordination properties of metal complexes that are important in applications including luminescent materials, chemical reductions, catalysis, and imaging.

A EuII-containing cryptate 2.1-EuII synthesized with an amine-rich ligand displayed bright yellow luminescence in …

Myeloperoxidase-Mediated Protein Lysine Oxidation Generates 2- Aminoadipic Acid And Lysine Nitrile In Vivo, Hongqiao Lin, Bruce S. Levison, Jennifer A. Buffa, Ying Huang, Xiaoming Fu, Zeneng Wang, Valentin Gogonea, Joseph A. Didonato, Stanley L. Hazen

Chemistry Faculty Publications

Recent studies reveal 2-aminoadipic acid (2-AAA) is both elevated in subjects at risk for diabetes and mechanistically linked to glucose homeostasis. Prior studies also suggest enrichment of protein-bound 2-AAA as an oxidative post-translational modification of lysyl residues in tissues associated with degenerative diseases of aging. While in vitro studies suggest redox active transition metals or myeloperoxidase (MPO) generated hypochlorous acid (HOCl) may produce protein-bound 2-AAA, the mechanism(s) responsible for generation of 2- AAA during inflammatory diseases are unknown. In initial studies we observed that traditional acid- or basecatalyzed protein hydrolysis methods previously employed to measure tissue 2-AAA can artificially generate …

Probing The Structural Evolution Of Gold−Aluminum Bimetallic Clusters (Au2AlN−, N = 3−11) Using Photoelectron Spectroscopy And Theoretical Calculations, Navneet S. Khetrapal, Tian Jian, Gary V. Lopez, Seema Pande, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We report a combined photoelectron spectroscopy and theoretical study of the structural evolution of aluminum cluster anions doped with two gold atoms, Au₂Al_n^– (n = 3−11). Well-resolved photoelectron spectra have been obtained at several photon energies and are used to compare with theoretical calculations to elucidate the structures of the bimetallic clusters. Global minima of the Au₂Al_n^– clusters were searched using the basin-hopping method combined with density functional theory calculations. Vertical detachment energies were computed for the low-lying isomers with the inclusion of spin−orbit effects and were used to generate simulated …

Evaluation Of Earth-Abundant Monometallic And Bimetallic Complexes For Catalytic Water Splitting, Kenneth Kwame Kpogo

Wayne State University Dissertations

The development of affordable water splitting catalysts from Earth-abundant transition metal ions such as Co and Mn is of immense scientific interest. Aiming to develop an efficient water splitting catalyst, a Co(II) complex featuring an asymmetric, pentadentate quinolyl-bispyridine ligand with a phenylenediamine backbone was synthesized and characterized by spectroscopic, spectrometric, and X-ray analysis. The Co ion was selected because of its ability to undergo redox conversions from 3d5 CoIV through 3d8 CoI thereby making it a suitable catalyst that can withstand harsh structural and electronic changes during catalysis. The electrocatalytic water reduction activity of the catalyst at neutral pH gave …

Real-Time Investigation Of Bulky Lesion Bypass By Y-Family Dna Polymerase, Dpo4, Using Single Molecule Fret, Pramodha Liyanage

Wayne State University Dissertations

DNA is constantly exposed to various DNA damaging agents that are generated by various internal and external sources. Some of this damage may not be able to be repaired by cellular machineries causing DNA replication to be blocked. Once the replication fork is blocked by a DNA adduct, damage tolerance DNA polymerases, mainly Y-family, are able to restore the DNA replication by synthesizing past the DNA adduct. Benzo[a]pyrene (B[a]P) is one of the most studied environmental carcinogens. It is known to make covalent DNA adducts after metabolic activation and the bulkiness of the B[a]P adducts impose a strong barrier to …

Attosecond Spectroscopy Probing Electron Correlation Dynamics, Alexander Heinecke Winney

Wayne State University Dissertations

Electrons are the driving force behind every chemical reaction. The exchange, ionization, or even relaxation of electrons is behind every bond broken or formed. According to the Bohr model of the atom, it takes an electron 150 as to orbit a proton[6]. With this as a unit time scale for an electron, it is clear that a pulse duration of several femtoseconds will not be sufficient to understanding electron dynamics. Our work demonstrates both technical and scientific achievements that push the boundaries of attosecond dynamics. TDSE studies show that amplification the yield of high harmonic generation (HHG) may be possible …

Investigation Of Atg11 And Its Interaction With Ypt1 In Autophagy, Hayley Cawthon

Senior Honors Theses and Projects

Autophagy is a cellular process conserved in eukaryotes that involves the trafficking of intracellular material from the cytosol to the vacuole/lysosome. This material is wrapped in a double membraned vesicle called an autophagosome, which ls constructed at the pre-autophagosomal structure. Many proteins are Involved In autophagy, one of them being Atgll. This protein is crucial in the selective autophagy pathway, and is responsible for proper formation of the pre-autophagosomal structure as well as recruiting the material intended for degradation to the autophagosome. Atgl 1 interacts with many other autophagy proteins, but it Is unknown whether it interacts with these binding …

Understanding The Interface That Enables The Interaction Between Two Dopamine Receptor Subtypes Known As D1 And D2 Implicated In Depression, Adam Baraka

Senior Honors Theses and Projects

The dopamine receptor subtypes known as DI and D2 have been shown to form a heteromer complex, which is thought to lead to the disruption of a multitude of signaling pathways within the brain. As a result, this has been proposed to lead to diseased states such as Alzheimer's and depression. In previous studies, it has been shown that the use of synthetic peptides corresponding to the surface interface of the interactions (specifically in the third intracellular loop of D2 interface) within the complex have served to compete against the formation of the heteromer. Through in vitro biochemical techniques such …

Expression And Purification Of Atg11: A Protein Involved In The Organization Of Autophagy, Carson Zois

Senior Honors Theses and Projects

Autophagy is a physiological process for the degradation of internal cell components to promote cell survival. This process allows the cell to maintain homeostasis, recycle damaged cellular components and helps protect against disease. Autophagy can be selective or non-selective. Non-selective, or bulk, autophagy occurs during times of cellular starvation and results in non-specific degradation of cytoplasmic materials. Selective autophagy targets specific components within the cytoplasm for degradation, and is always active. In both forms of autophagy, components are degraded when a double-membraned structure, called the autophagosome, encapsulates the target cargo and is then recruited to the lysosome in mammalian cells, …

Heterocycles Via The Pd-Catalyzed Heterofunctionalization Of Alkylidenecyclopropanes, Phillip Roman Lazzara

Dissertations

Natural compounds are often used as inspiration for novel chemical structures that provide medicinal benefits to human health. The unique 3-dimentional structures of these molecules make the majority of them synthetic challenges for organic chemists. While there is great diversity among these molecules, many of these carbon-based compounds exhibit similar key structural features. One of the most common features amongst biologically active molecules is a rigid carbon ring bearing nitrogen or oxygen atoms, which are known as heterocycles. The structural rigidity of heterocycles helps properly align key interactions of the molecule with those of a specific protein, which causes the …

Latent Fingerprint Enhancement On A Brass Metal Surface Using Paint Electrodeposition, Reika D. Haskell

Online Theses and Dissertations

Fingerprint evidence recovered at a crime scene plays a key role in apprehending a suspect. Cyanoacrylate fuming is one the most successful methods of enhancing fingerprints from metallic surfaces. Despite the success of cyanoacrylate fuming, fingerprint recovery on fired cartridge casings is rarely successful. Therefore, a new fingerprint development method is needed to enhance fingerprint evidence that may still be present on fired cartridge casings. The aim of this research project is to study the use of metal and paint electrodeposition to enhance fingerprints on a brass metal surface.

High throw power paint was used in the initial study; high …

Harnessing Solar Energy: Vapor Phase Polymerized Poly(3,4-Ethylenedioxythiophene) For Solid State Dye-Sensitized Solar Cells And The Photodegradation Of Organic Toxicants, Steven M. Boyer

Graduate Dissertations and Theses

Solar energy is the most abundant energy resource available and can be utilized for a variety of applications such as photovoltaics and promote chemical reactions. Dye-sensitized solar cells (DSSCs) are a class of photovoltaic cells that have been well studied for their low cost and environmentally friendly materials. Previous research focused on developing more efficient liquid phase solar cells, but little work has gone into solid state DSSCs. Moving towards the solid state would improve the lifetime of the cells, preventing leaking of electrolyte and corrosion of the electrode while potentially being a more scalable process for mass production, improving …

A Thermally Stabilized Fluorescent Organic Chromophore, Brendan P. Hughes

Graduate Dissertations and Theses

A fluorescent chromophore, hereby designated as cyanine dye, has been bound to generated zinc oxide nanoparticles. It has been shown that the material not only retains the characteristic absorption peak of the native chromophore, but it also continues to fluoresce with comparable intensity. The binding occurs through a Zn – O₂C bridge, which allows for vibrational relaxation as the dye heats up, yet also preserves the optical properties of the dye. This bond linkage can be observed from the comparison of FT-IR spectra of the nanoparticles and the native dye, designated by a shift in one of the …

Isolation And Spectroscopic Characterization Of Zn(Ii), Cu(Ii), And Pd(Ii) Complexes Of 1,3,4-Thiadiazole-Derived Ligand, Dariusz Karcz, Arkadiusz Matwijczuk, Bozena Boron, Bernadette Creaven, Leszek Fiedor, Andrzej Niewiadomy, Mariusz Gagos

Articles

A series of complexes incorporating Zn(II), Cu(II), and Pd(II) ions, and 4-(5-heptyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (L1) as model ligand, was synthesized in order to examine the nature of potential interactions between biologically active ligands, 1,3,4-thiadiazoles and metal ions with proven biological relevance. The structures of the compounds isolated were characterized using a number of spectroscopic methods including IR, Uv–vis, AAS, steady state and time-resolved fluorescence (TRF). The results obtained suggest that the L1-Zn(II) and L1-Pd(II) complexes consist of one molecule of L1 and one acetate ion acting as ligands, while the L1-Cu(II) complex adapts a 2:1 (L1: metal) stoichiometry. The coordination of L1 …

Digital Fabrication Of An Atmospheric Aerosol Impactor, Stefan J. Vincent, Shawn Daley, Matthew E. Wise

CUP Undergraduate Research

Atmospheric aerosol (AA) particles are defined as solid or liquid particles suspended in the air. AA particles smaller than 10 μm (1x10^-5 meters) in diameter are small enough to bypass the upper respiratory system which functions as a filter for harmful substances entering the lungs. AA particles can be collected using a device called an aerosol impactor. After collection, the particles can be analyzed offline for chemical composition using a variety of analytical techniques. The weight of a commercially manufactured AA particle impactor poses an issue if it is attached to a mobile AA particle sampling platform such as …

The Anticancer Effects Of The Different Analogs Of Cysteine Deleted Tachyplesin On A549 Lung Cancer Cells, Nathan Riley Hendrickson

Master's Theses and Doctoral Dissertations

It has been previously shown that cysteine-deleted tachyplesin (CDT) and its many analogs display antibacterial effects. However, little has been said about its possible anticancer effects and which analogs serve as the best inhibitors of the growing cancer cells. This research focused on CDT and four of its analogs: All D-CDT, Reverse DCDT, Reverse CDT, and Serine-Control CDT. MTT assays against the A549 adenocarcinoma lung cancer cell line showed All D-CDT to be the most effective analog in preventing cancer cell growth. Hyaluronidase and apoptosis assays were performed to better understand the mechanism by which the All D-CDT is preventing …

Application Of Quantum Monte Carlo Methods To Molecular Potential Energy Surfaces, Andrew Douglas Powell

Doctoral Dissertations

"Various computational methods have been used to generate potential energy surfaces, which can help us simulate and interpret how atoms or molecules behave during a chemical reaction. For accurate work, ab initio wavefunction methods have traditionally been used, which have some disadvantages. For example, highly accurate methods scale poorly with system size (n⁷ or higher) and are mostly not well parallelized for calculations with multiple processors. One alternative method that has more favorable scaling with system size and is well parallelized is a computational technique called quantum Monte Carlo (QMC). QMC methods scale with the number of electrons as …

Optimization Of Solvent Suppression Sequences For Nmr Analysis Of Aqueous Solutions, Annalise Rose Pfaff

Doctoral Dissertations

"When the use of deuterated solvents is precluded in the NMR analysis of biomolecules in their natural environment, pre-saturation solvent suppression pulse sequences are frequently employed to avoid interference from the overbearing solvent signal. However, these sequences generally require extensive re-adjustment of NMR parameters between samples. For this reason, the EXCEPT (EXponentially Converging Eradication Pulse Train) solvent suppression sequence was developed, which exhibits a tolerance of over an order of magnitude in sample T₁ variation. EXCEPT uses an innovative version of "inversion-recovery nulling" with frequency-selective, low-power adiabatic pulses and exponentially decreasing interpulse delays that effectively reduce solvent net magnetization by …

Synthesis, Characterization, And Activity Of Co/Fe Alumina/Silica Supported Ft Catalysts And The Study Of Promoter Effect Of Ruthenium, Sunday Azubike Esumike

Doctoral Dissertations

The alumina and hybrid alumina-silica FT catalyst were prepared by one-step solgel/oil-drop methods using metal-nitrate-solutions (method-I), and nanoparticle-metaloxides (method-2). The nanoparticle-metal-oxides did not participate in solubility equilibria in contrast to metal nitrate in method-1 causing no metal ion seepage; therefore, method-2 yields higher XRF metal loading efficiency than method-1. The thermal analysis confirmed that the metal loading by method-1 and method-2 involved two different pathways. Method-1 involves solubility equilibria in the conversion of metal-nitrate to metal- hydroxide and finally to metal-oxide, while in method-2 nanoparticle-metal-oxide remained intact during sol-gel-oil-drop and calcination steps.

The alumina supported catalysts were dominated by γ-alumina …

Bis(N-Amidinohydrazones) And N-(Amidino)-N'-Aryl-Bishydrazones: New Classes Of Antibacterial/Antifungal Agents, Sanjib K. Shrestha, Liliia M. Kril, Keith D. Green, Stefan Kwiatkowski, Vitaliy M. Sviripa, Justin Robert Nickell, Linda Phyliss Dwoskin, David S. Watt, Sylvie Garneau-Tsodikova

Pharmaceutical Sciences Faculty Publications

The emergence of multidrug-resistant bacterial and fungal strains poses a threat to human health that requires the design and synthesis of new classes of antimicr obial agents. We evaluated bis(N-amidinohydrazones) and N-(amidino)-N'-aryl-bishydrazones for their antibacterial and antifungal activities against panels of Gram-positive/Gram-negative bacteria as well as fungi. We investigated their potential to develop resistance against both bacteria and fungi by a multi-step, resistance-selection method, explored their potential to induce the production of reactive oxygen species, and assessed their toxicity. In summary, we found that these compounds exhibited broad-spectrum antibacterial and antifungal activities against most of …

Synthesis Of Vorinostat And Cholesterol Conjugate To Enhance The Cancer Cell Uptake Selectivity, Nethrie D. Idippily, Chunfang Gan, Paul Orefice, Jane Peterson, Bin Su Ph.D.

Chemistry Faculty Publications

Histone deacetylase (HDAC) inhibitors modulate various cellular functions including proliferation, differentiation, and apoptosis. Vorinostat (SuberAniloHydroxamic Acid, SAHA) is the first HDAC inhibitor approved by FDA for cancer treatment. However, SAHA distributes in cancer tissue and normal tissue in similar levels. It will be ideal to selectively deliver SAHA into cancer cells. Rapidly growing cancer cells have a great need of cholesterol. Low-density lipoprotein (LDL) is the major cholesterol carrier in plasma and its uptake is mediated by LDL-receptor (LDL-R), a glycoprotein overexpressed on the surface of cancer cells. Herein, we designed and synthesized a SAHA cholesterol conjugate, and further formed …

Synthesis And Analysis Of Folate Histidine, Alexander Kampner

All Capstone Projects

A compound was specifically designed to further aid research on the detection and treatment of folate receptor positive cancer cells. A small but complex peptide chain was commercially produced to have a flexible glycine spacer and a six-histidine tag. Histidine tagging was chosen for its ability to bind to nickel. The compound in this report was purified and analyzed by HPLC and confirmed via mass spectrometry. This binding capacity and the ability of folate conjugates to bind to cancer cell receptors have both been explored for the past quarter of a century [1-3]. Folate conjugates have been successfully used as …

Bond Length And Bond Valence Relationships For Chromium Oxides, Chromium Sulfides, Molybdenum Oxides, And Molybdenum Sulfides, J. Labrecque, F. D. Hardcastle

Journal of the Arkansas Academy of Science

Pauling determined an empirical logarithmic dependence of bond order (bond valence), s, to bond length, R, s = exp(R₀ – R/ b), where R₀ is unit bond length and b is a fitting parameter. Recently, an expression was derived for relating the b fitting parameter to theoretically derived atomic orbital exponents. With a method to calculate b, both R₀ and atomic orbital exponents can be experimentally determined through optimized fitting for Cr-O, Cr-S, Mo-O, and Mo-S. In the present study, bond length – valence relationships are found for Cr-O, Cr-S, Mo-O, and Mo-S chemical …

Bond Length And Bond Valence For Tungsten-Oxygen And Tungsten-Sulfur Bonds, F. D. Hardcastle, R. Lykins

Journal of the Arkansas Academy of Science

In 1947, Linus Pauling presented an “empirical” dependence of bond valence (s, also referred to as bond order) and bond length R: s = exp[(R₀-R)/b], where R₀ is bond length of unit valence and “b” is a fitting parameter. Recently, an expression was derived for relating the b fitting parameter to theoretically derived atomic orbital exponents. With a method to calculate b, both R₀ and atomic orbital exponents can be experimentally determined through optimized fitting for W-O and W-S bonds. In the present study, bond …