Chemistry Commons^™

On The Conformational Dynamics Of Dna: A Perspective From Molecular Dynamics Simulations, Ning Ma

USF Tampa Graduate Theses and Dissertations

The main focus of my dissertation is on the conformational motion of DNA, studied by applying tools from the computational chemistry field. In addition, studies of relative α- and 310 helical stabilities in peptides/mini-proteins, and a molecular flooding study of the retinoid X-receptor as part of a continuing drug design effort are presented. In molecular biology, it has been well known that sequence determines structure, and structure controls function. For proteins or DNA to work properly, the correct configuration is required. Mutations may alter the structure, which can cause malfunction. Non-mutational effects, such as a change in environment may also …

Catalyzed Synthesis Of Zinc Clays By Prebiotic Central Metabolites, Marcelo I. Guzman, Ruixin Zhou, Kaustuv Basu, Hyman Hartman, Christopher J. Matocha, S. Kelly Sears, Hajatollah Vali

Chemistry Faculty Publications

How primordial metabolic networks such as the reverse tricarboxylic acid (rTCA) cycle and clay mineral catalysts coevolved remains a mystery in the puzzle to understand the origin of life. While prebiotic reactions from the rTCA cycle were accomplished via photochemistry on semiconductor minerals, the synthesis of clays was demonstrated at low temperature and ambient pressure catalyzed by oxalate. Herein, the crystallization of clay minerals is catalyzed by succinate, an example of a photoproduced intermediate from central metabolism. The experiments connect the synthesis of sauconite, a model for clay minerals, to prebiotic photochemistry. We report the temperature, pH, and concentration dependence …

Molecular Mass Of L-Arginine-Based Potentially Carcinogenic Heterocyclic Amines, Irene S. Hwang

Honors Theses

Investigation of cancer-inducing molecules in cooked foods has led to the discovery of mutagenic heterocyclic amines (HCAs) in meat. The amino acids creatin(in)e and L-phenylalanine form the precursors for these HCAs. Recent research here at Andrews University have found similar mutagenic HCAs produced from plant-based proteins when L-arginine, rather than creatin(in)e, is substituted in high temperature reactions (simulated cooking) with L-phenylalanine. Our research focused on developing HPLC methods to isolate individual candidates that are then screened for mutagenicity via the Ames test. Mass spectroscopy methods were also developed to identfy the molecular structure of these lead mutagenic L-arginine-based HCAs.

Fluorescence Analysis Of Pamam Dendrimers, Ansel Nam

Honors Theses

Despite their lack of conjugation, polyamidoamine (PAMAM) dendrimers are intrinsically fluorescent, and this fluorescent is somewhat manipulable through altering the dendrimer's solvent. This level of fluorescence is dependent on a number of the dendrimer's qualities: the pH of the solvent, the mass percent concentration of the dendrimer in solvent, and the generation size of the dendrimer. In past studies, fluorescent intensity increased as generation size increased and pH decreased. Thus, this research project will attempt to replicate those results as well as further analyze the efficiency of fluorescence of PAMAM dendrimer in comparison to fluorescein.

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …

Protein Engineering Of Cota Laccase By Using Bacillus Subtilis Spore Display, Silu Sheng

Dissertations

Spore display offers advantages over more commonly utilized microbe cell-surface display systems. For instance, protein-folding problems associated with the expressed recombinant polypeptide crossing membranes are avoided. Hence, a different region of protein space can be explored that previously was not accessible. In addition, spores tolerate many physical/chemical extremes. The aim is to improve pH stability using spore display. The maximum activity of CotA is between pH 4 and 5 for the substrate ABTS (ABTS = diammonium 2, 2’-azino-bis(3-ethylbenzothiazoline-6-sulfonate)). However, the activity dramatically decreases at pH 4. The activity is not significantly altered at pH 5. CotA is used as a …

Synthesis And Detection Of Dna Damage, Xun Gao

Dissertations

The biological effects of DNA alkyl adducts are difficult to evaluate at the cellular level due to their instability. Synthesis of oligonucleotides that contain a single N7-alkylguanine has become a vital tool to achieve the above goal. However, the instability of N7-alkyguanines is not compatible with the phosphoramidite chemistry used by solid-phase oligonucleotide synthesis either. Development of chemically stable analogues of unstable DNA lesions enables accurate study of polymerase bypass. The design and successful synthesis of N7-hydroxyethyl-9-deaza-2′-deoxyguanosine and N7-oxoethyl-9-deaza-2′-deoxyguanosine as the stable analogues of N7-hydroxyethyl- 2'-deoxyguanosine and N7-oxoethyl-2′-deoxyguanosine, respectively, are reported. The synthesis of these two nucleosides whose N7 side …

Alternative Process Photography: Beyond Digital And Film, Laura Michaud

Senior Honors Projects

The first permanent photograph was created in 1826 by Joseph Nicéphore Niépce. To do this, he coated light sensitive chemicals on a metal plate and exposed it in a camera obscura (a box with a small hole; a “pinhole camera”). Once the plate was properly exposed to light, he used more chemicals to stop the plate from being light sensitive and make the image permanent on the plate. Throughout the years, many photographers and chemists used many different chemicals, materials, and procedures to create permanent and beautiful images (i.e. Daguerreotypes, Calotypes, Heliographs, etc). With each new process, the previous processes …

Investigation Of Hkust-1 And Related Composites With Protein Adsorption, Ramitha Rupasinghe

Undergraduate Research Symposium 2017

Metal Organic Frameworks (MOFs) possess well-ordered porous structures that have been shown to adsorb proteins. MOFs can be enhanced by combining them with suitable materials to make composites. Enhancements include, but are not limited to, changing pore sizes, adding functional groups, improving selectivity of adsorption, and increasing stability. Previous research has shown high adsorption of proteins by the MOF, HKUST-1 but no research has been done to investigate the adsorption by its related composites, such as HKUST-1/GO, HKUST-1/ magnetite and HKUST-1/magnetite/GO. In this research, HKUST-1 and composites based on graphene oxide (GO) and magnetite were synthesized, characterized by FTIR, XRD …

High Performance Supercapacitor Device Based On Polymer Derived Carbon Nanofiber With Enhanced Capacity At Elevated Temperatures, Charith Ranaweera

Paper and Posters Presentations

Recently, supercapacitors are attracting considerable interest as a promising energy storage device. In this study, we report the high performing supercapacitor based on cobalt oxide embedded carbon nanofibers (CNF@CO) fabricated by electrospinning of cobalt acetate and polyacrylonitrile mixture in to carbon nanofibers (CNF) and subsequent pyrolyzed at 800 oC under nitrogen atmosphere. Morphology and electrochemical properties of the fabricated CNF@CO was studied in detailed. Embedding of cobalt oxide in to CNF showed a remarkable improvement in the charge storage capacitance, specific capacitance of 360 F/g and 1100 F/g were observed for CNF and CNF@CO, respectively. We studied the effect of …

Effect Of Chemical Treatment On The Electrochemical Properties Of Carbon Nanotubes, Tucker Morey

Paper and Posters Presentations

Supercapacitors are electrochemical energy storage devices primarily attractive for their fast charging and discharging capability, long lasting stability and safe handling. Because of these unique qualities, supercapacitors are ideal candidates for a number of applications including regenerative breaking in cars, static random access memory and motor starters. To date, three main material classes have been investigated for electrode applications. These include carbonaceous materials, metal oxides and polymers or their composites. Metal oxide based supercapacitors have high capacitance, but severely suffer in stability, making carbonaceous materials that store charges through double layer adsorption mechanism particularly attractive. In addition, carbonaceous materials are …

An Expedited, Regiospecific Para-Bromination Of Activated Aryls, Kathryn E. Dudley

Masters Theses & Specialist Projects

Electrophilic Aromatic Substitution (EAS) is one of the most frequently used aryl substitution methods. Aside from the fact that most EAS reactions require an acid and an oxidizer to proceed, the reactions involving activated aryls typically produce a mixture of ortho- and para- products as well as an ortho-/para- disubstituted product. Regiospecificity in aromatic substitution is key in the production of many compounds in a variety of disciplines. Since EAS is one of the most often used substitution methods, it is extremely important to develop an efficient method for regiospecific substitutions. Previous research developed a method of ortho-substitution by using …

The Effects Of Carrier Ligands On Cisplatin Binding To Cysteine And Methionine, Adam C.R Smith

Masters Theses & Specialist Projects

We have reacted several derivatives of the anticancer drug cisplatin with N-acetyl-Lcysteine (N-AcCys) and N-acetyl-L-methionine (N-AcMet), which are two of the primary amino acid targets of platinum. NMR spectroscopy was used to monitor the reactions and determine the effect the different ligands would have on the platinum reactivity. Several of the platinum compounds were tested at pH of 4 and 7, and with platinum:amino acid ratios of 1:1, 2:1 and 1:2. Competition reactions between cysteine and methionine were done to confirm which would react with the platinum compound first. [Pt(dien)(NO3)]+ reacts faster with methionine than with cysteine at both pH …

Synthesis, Characterization, And Properties Of Graphene-Based Hybrids With Cobalt Oxides For Electrochemical Energy Storage And Electrocatalytic Glucose Sensing, Sara C. Botero Carrizosa

Masters Theses & Specialist Projects

A library of graphene-based hybrid materials was synthesized as novel hybrid electrochemical electrodes for electrochemical energy conversion and storage devices and electrocatalytical sensing namely enzymeless glucose sensing. The materials used were supercapacitive graphene-family nanomaterials (multilayer graphene-MLG; graphene oxide-GO, chemically reduced GO-rGO and electrochemical reduced GOErGO) and pseudocapacitive nanostructured transition metal oxides including cobalt oxide polymorphs (CoO and Co3O4) and cobalt nanoparticles (CoNP). These were combined through physisorption, electrodeposition, and hydrothermal syntheses approaches. This project was carried out to enhance electrochemical performance and to develop electrocatalytic platforms by tailoring structural properties and desired interfaces. Particularly, electrodeposition and hydrothermal synthesis facilitate chemically-bridged …

Environmentally Friendly Synthesis Of Transition Metalorganic Hybrid Nanocomposites, Aubrey N. Penn

Masters Theses & Specialist Projects

Research on metal nanoparticles (MNPs) synthesis and their applications for optoelectronic devices has been a recent interest in the fields of nanoscience and nanotechnology Photovoltaics are one of such systems in which MNPs have shown to be quite useful, due to unique physical, optical, magnetic, and electronic properties, including the metal nanoparticles synthesized in this research.

Owing to the challenges with the most common physical and chemical methods of preparing MNPs, including the use of high temperatures, toxic reducing agents, and environmentally hazardous organic solvents, there is a critical need for a benign synthesis procedure for MNPs. In this work, …

Regiospecific P-Bromination Of Activated Aromatic Systems – Greener Approach, Elnaz Jalali

Masters Theses & Specialist Projects

The halogenated derivatives of heterocyclic compounds (haloarenes) are highly utilized in many fields of chemistry, including drug discovery, medicinal, and material chemistry. There are a variety of ways to functionalize an aromatic system and introduce halogen substituent into the ring. However, electrophilic aromatic substitution (EAS) has been the focus of growing attention, particularly for electronrich substrates.

Electrophilic aromatic bromination protocols are one of the most important electrophilic aromatic substitution reactions. However, preparation of bromoarenes classically recommends the use of highly oxidative agents along with utilizing various metal catalysts in a halogenated solvent. The corrosive and toxic nature of these reagents …

Detection And Quantitation Of Tetracycline Antibiotics In Agricultural Swine Wastes, Ali Jamal Abdulrheem

Masters Theses & Specialist Projects

The spread of tetracyclines through agricultural systems is causing the present bacteria to develop antibiotic resistance. The spread of this bacteria, as well as the tetracycline antibiotics in the environment is dangerous because these antibiotics pose health hazards for humans. The overuse of antibiotics, which are added to livestock feed, results in the antibiotics being released into the environment via animal feces. In this research, we have attempted to design an analytical method to isolate antibiotics from agricultural wastes with subsequent detection using liquid chromatography and mass spectrometry (LC-MS). The antibiotics investigated in this study were tetracycline, chlortetracycline, and oxytetracycline. …

Tio2/Pdms Buoyant Photocatalyst For Water Remediation And Cu‑Rbs Organic/Inorganic Hybrid For Thermoelectric Applications, John R. Bertram

Masters Theses & Specialist Projects

Two novel materials have been developed: TiO2/poly(dimethylsiloxane) (PDMS) beads as buoyant photocatalyst materials for water remediation, and copper rhodamine‑B silane (Cu‑RBS) as an n ‑type organic/inorganic hybrid for thermoelectric applications. The approach to incorporate TiO2 into low‑density PDMS beads addresses many of the challenges traditionally encountered when creating buoyant photocatalysts, an area which is crucial for wide‑spread remediation of water resources, including natural bodies of water. The performance and reusability of the buoyant photocatalyst materials, demonstrated by using methylene blue as a model degradation target, is strong enough for environmental application. The use of a kinetic model and the introduction …

Investigating The Effects Of Pre-Laboratory Videos With Associated Questions On The Performance And Overall Laboratory Experience Of Organic Chemistry Students, Shareef Gamal Mohamed Kotb

Health Sciences Student Work

Background: Teachers struggle communicating ideas to students (Moreno et al, 2001). One of the aspects of teaching that’s most concerning is when students experience cognitive overload: the total effort exerted by working memory to grasp new information (Mayer, et al, 2002). The educational community found that introducing multimedia in learning minimizes cognitive overload (Mayer, et al, 2002). Little research has related to undergraduate chemistry classes, specifically the relationship between organic chemistry pre-laboratory multimedia and student learning. Purpose: The purpose of this capstone is to investigate the subjective efficacy of integrating pre-laboratory videos for lab preparation in an undergraduate organic chemistry …

Special Elements Of Excellence: Spring 2017, Department Of Chemistry

Chemistry News

• Chair's Welcome
• The Science Behind Crafting Beer
• 10 Year Chemistry Building Celebration 8th Annual Research Chemistry Research Day & Spring 2017 Awards
• KALSEC Tour - An Insider's Look
• New Faculty Specialist!
• 2017 Million Dollar Club
• Frontiers in Chemistry Lectureship
• Recent Awards received by Students and Faculty of the WMU Department of Chemistry
• Examples of Published Research from the Faculty of WMU Department of Chemistry

Correlated Mutation In The Evolution Of Catalysis In Uracil Dna Glycosylase Superfamily, Bo Xia, Yinling Liu, Jose Guevara, Jing Li, Celeste Jilich, Ye Yang, Liangjiang Wang, Brian N. Dominy, Weiguo Cao

Publications

Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG …

Polychlorinated Biphenyls, Polybrominated Biphenyls, Polychlorinated Dibenzo-P-Dioxins And Polychlorinated Dibenzofurans, Prasada Rao S. Kodavanti, Joseph Valdez, Jae-Ho Yang, Margarita Curras Collazo, Bommanna G. Loganathan

Faculty & Staff Research and Creative Activity

Environmental contamination levels, human exposure, toxicokinetics, and health effects of PCBs, PBBs, PCDDs/PCDFs are discussed.

The Coastal Monitor: Vol 2. No 1., John Tanacredi Ph.D.

The Coastal Monitor

There is something enchanting and vibrant about viewing the coast. Every day at CERCOM we are welcomed by either a vivid sunrise, a view of the barrier island Fire Island and a blending of the sky across the horizon, ultimately flooding the Great South Bay with either clouds or sunshine that reveals the Bay’s surface as either shimmering with sunlight, or an integration of sky and water as an endless ocean. I don’t normally wax poetic but the varying sights along the near shore ocean and this embayment beckon our scientific inquisitiveness. What’s below the surface water? How do animals …

Theoretical Study Of Ozone Forming Recombination Reaction And Anomalous Isotope Effect Associated With It, Alexander Teplukhin

Dissertations (1934 -)

The ozone forming recombination reaction stands out among many chemical processes that take place in the atmosphere. This reaction is responsible for the reconstruction of ozone layer, which protects life on Earth from harmful ultra-violate radiation and is a source of so-called anomalous isotope effect in ozone. The reaction was intensively studied, but at a very basic level. There were only couple of papers where the recombination rate coefficient was computed and found to roughly agree with the experimental data. In this dissertation, the recombination process in ozone is approached using new and efficient method, which includes several modern techniques. …

Ruthenium-Catalyzed Dehydrogenative And Dehydrative C-H Coupling Reactions Of Arenes With Alcohols And Carbonyl Compounds, Hanbin Lee

Dissertations (1934 -)

Despite their outstanding achievements, the requirement of preformed functional groups and wasteful byproduct formation are inherent disadvantages associated with the transition metal catalyzed cross-coupling methods. Inspired by the needs for green and sustainable chemistry, transition metal catalyzed dehydrogenative and dehydrative coupling methods have been recognized as environmentally sustainable and atom economical synthetic routes for the new C-C bond formation. The catalytic activation of C-H and C-O bonds allows the formation of coupling products from ubiquitous hydrocarbon substrates by releasing hydrogen or water byproduct. However, these novel protocols require relatively harsh conditions due to their low reactivity of C-H and C-O …

Technical Feasibility Of Selectively Separating Rare Earth Elements By Vapor Phase Extraction And Condensation, Katie Lyons

Graduate Theses & Non-Theses

Experiments were performed to evaluate the technical feasibility of selectively separating selected rare earth halides (bromides and chlorides) using a volatilization and condensation technique. Initially, optimum chloridizing and bromidizing roast parameters were secured in studies performed on reagent grade rare earth oxide samples and subsequently confirmed in tests performed on mineral ore and concentrate samples. The volatilization and condensation experiments were performed by placing the subject rare earth halide samples in an argon-purged multiple-zone tube furnace wherein the temperature profile was controlled to establish separate vaporization and condensation regions. Following each experiment, condensate and solid residue samples were analyzed to …

Synthesis, Kinetic And Catalytic Studies Of Manganese Complexes With Corrole And Porphyrin Ligands, Haleh Jeddi

Masters Theses & Specialist Projects

High-valent transition metal-oxo intermediates play a significant role in the catalytic cycle of the ubiquitous cytochrome P450 enzymes and in biomimetic catalytic systems. In this work, manganese(III) porphyrin and corrole systems (2) were synthesized and characterized by UV-vis absorbance and 1H-NMR, matching literaturereported spectroscopic data. Manganese(V)-oxo corroles (3) and a manganese(IV)-oxo porphyrin (4) were successfully generated by chemical oxidation using mchloroperoxybenzoic acid (m-CPBA), and their oxidation reactions with organic reductants were comparatively investigated. Results from single-turnover kinetic studies indicate that in the tris(pentafluorophenyl)corrole system (3a), the active oxidizing intermediate differs in different solvents. The active oxidizing intermediate in acetonitrile is …

Effects Of Binding Affinity Between Bovine Serum Albumin And Platinum Drugs, Nathan Puckett

Masters Theses & Specialist Projects

Platinum complex drugs such as cisplatin have been used as highly successful chemotherapy drugs since the 1970s. We are interested in how the ligands attached to cisplatin analogs influences their reactivity with biologically relevant targets along with time and amount. For this study, reactions were conducted to determine the reactivity between different platinum compounds and the protein bovine serum albumin. Various platinum compounds with different ligands were reacted in varying amounts with albumin in ammonium acetate buffer for either 1 hour, 4 hours, or 24 hours. Each reaction was quenched after the designated reaction time by dialysis and the platinum …

Antimicrobial Activities Of Tea-Derived Flavonoids Against Skin Staphylococci, Ahyun Hong

CUP Undergraduate Research

This thesis investigates the antimicrobial activities of tea-derived flavonoids against skin Staphylococci. Four hypotheses were tested: (1) Teas that contain high polyphenolic contents possess higher antimicrobial activity against skin bacteria (e.g. S. aureus and S. epidermidis); (2) Different tea infusions and tea-derived individual catechins show differential inhibition of S. aureus and S. epidermidis; (3) Different tea infusions and tea-derived individual catechins show differential inhibition of S. aureus isolated from individuals with and without chronic atopic dermatitis; (4) EGCg, the most abundant polyphenols found in tea, possess the highest anti-staphylococcal activity. We employed multiple methods such as Folin-Ciocalteau colorimetric …

Inelastic Rate Coefficients For Collisions Of C₆Hˉ With H₂ And He, Kyle M. Walker, François Lique, Fabien Dumouchel, Richard Dawes

Chemistry Faculty Research & Creative Works

The recent detection of anions in the interstellar medium has shown that they exist in a variety of astrophysical environments -- circumstellar envelopes, cold dense molecular clouds and star-forming regions. Both radiative and collisional processes contribute to molecular excitation and de-excitation in these regions so that the ‘local thermodynamic equilibrium’ approximation, where collisions cause the gas to behave thermally, is not generally valid. Therefore, along with radiative coefficients, collisional excitation rate coefficients are needed to accurately model the anionic emission from these environments. We focus on the calculation of state-to-state rate coefficients of the C₆H^- molecule in …