Chemistry Commons^™

Light-Harvesting, Redox Control, And Biomimicry Of The Photosynthetic Antennas Of Green Sulfur Bacteria, Gregory Scott Orf

Arts & Sciences Graduate Student Theses and Dissertations

The green sulfur bacteria (class Chlorobea) are obligately anaerobic photoautotrophic prokaryotes. Members of this bacterial class are found in anoxic, sulfur- or iron-rich environments such as hydrothermal vents and hot springs. These bacteria are champions of lowlight adaptation, with some species being able to thrive photosynthetically on less than eight photons hr-1 per pigment. We have studied the two photosynthetic antenna complexes from these organisms that are responsible for light capture: the chlorosome and the Fenna-Matthews-Olson (FMO) protein.In regards to the chlorosome, we studied, using steady-state and time-resolved spectroscopic methods, the effect of incorporation of an expected, but as-yet-undiscovered-in-nature, light-harvesting …

Biological Degredation Of Acetaldehyde In Southern California Wetlands, Anthony Castagnola, Brandon Lamb, Mary Senstad, Sovandara Hok

Student Scholar Symposium Abstracts and Posters

Oxygenated hydrocarbons are ubiquitous in the atmosphere with levels ranging from low ppt (acetaldehyde) to low ppb(methanol). As an OH sink and an atmospheric HOx source, oxygenated hydrocarbons have a direct impact on the oxidative capacity of the atmosphere. A better understanding of the processes that produce and destroy these species in natural water would improve our understanding of the role that these systems play in cycling these species into or out of the atmosphere. These species can be lost to chemical, photochemical, and partical mediated (abiotic and biotic) processes in natural waters. Chemical loss and photochemical loss are believed …

Effects Of Ecologically Realistic Heating Profiles On Feeding In The Intertidal Hermit Crab, Pagurus Sameulis, Paige Davis

Student Scholar Symposium Abstracts and Posters

The intertidal zone is an ideal habitat to investigate effects of global warming because species living in it are very close to their physiological limits. Initial studies of invertebrate physiological responses to heat stress have employed relatively abrupt increases in temperature. My research investigates effects of ecologically more realistic temperature profiles on feeding in the intertidal hermit crab, Pagurus sameulis. Recent work in the Wright lab showed that feeding in this species is inhibited by an abrupt increase in temperature. Because temperature change in the natural environment of Pagurus is much more gradual, I hypothesize that such a gradual temperature …

Biological Degradation Of Acetaldehyde In Southern California Coastal Waters, Mary Senstad, Sovanndara Hok, Ori Barashy, Catherine D. Clark, Warren J. De Bruyn

Student Scholar Symposium Abstracts and Posters

Oxygenated hydrocarbons are ubiquitous in the atmosphere with levels ranging from low ppt (acetaldehyde) to low ppb (methanol). As an OH sink and an atmospheric HOx and ozone source, oxygenated hydrocarbons have a direct impact on the oxidative capacity of the atmosphere. The oceans are one of the largest sources of uncertainty in current atmospheric budget estimates of these species. A better understanding of the processes that produce and destroy these species in seawater would improve our understanding of the role of the oceans in cycling these species into or out of the atmosphere. We have measured the degradation rate …

Removal Of Pb And H2s From Acs Test Procedure For Meta-Phosphoric Acid, Christopher Atlas, Ron Lacock

Student Scholar Symposium Abstracts and Posters

In the pursuit of green chemistry, adequate substitutes for lead acetate and hydrogen sulfide were investigated for use in the ACS test procedure for stabilizer in meta-phosphoric acid. In the current ACS procedure lead acetate is used to form insoluble lead phosphate. In order to remove lead from the solution lanthanum chloride was investigated with positive results. Hydrogen Sulfide is currently used to precipitate lead by forming insoluble lead sulfide. Several substitutes including oxalic acid and sulfuric acid were investigated. Preliminary testing showed that lanthanum chloride and oxalic acid are sufficient in precipitating phosphate and lead out of the sample …

Analysis Of Secondary Wastewater Treatment, Jennifer Magana

Student Scholar Symposium Abstracts and Posters

At the Irvine Ranch Water District, two types of secondary treatment are utilized: a sludge and Dual Media Filters (DMF) process and Membrane Bioreactor (MBR) process. This study was proposed to analyze the electrical conductivity (EC) of each secondary effluent and possible reasons for differences. After testing the two effluents using an electrical conductivity probe and ion chromatography, it was discovered that there is no significant difference between the two, though secondary treatment raises the nitrate levels in general.

Revealing Important Nocturnal And Day-To-Day Variations In Fire Smoke Emissions Through A Multiplatform Inversion, Pablo E. Saide, David A. Peterson, Arlindo Da Silva, Bruce Anderson, Luke D. Ziemba, Glenn Diskin, Glen Sachse, Johnathan Hair, Carolyn Butler, Marta Fenn, Jose L. Jimenez, Pedro Campuzano-Jost, Anne E. Perring, Joshua P. Schwarz, Milos Z. Markovic, Phil Russell, Jens Redemann, Yohei Shinozuka, David G. Streets, Fang Yan, Jack Dibb, Robert Yokelson, O. Brian Toon, Edward Hyer, Gregory R. Carmichael

Chemistry and Biochemistry Faculty Publications

We couple airborne, ground-based, and satellite observations; conduct regional simulations; and develop and apply an inversion technique to constrain hourly smoke emissions from the Rim Fire, the third largest observed in California, USA. Emissions constrainedwithmultiplatform data show notable nocturnal enhancements (sometimes over a factor of 20), correlate better with daily burned area data, and are a factor of 2–4 higher than a priori estimates, highlighting the need for improved characterization of diurnal profiles and day-to-day variability when modeling extreme fires. Constraining only with satellite data results in smaller enhancements mainly due to missing retrievals near the emissions source, suggesting that …

First Steps Of Putting Research Into Practice: Utilizing Concept Inventories To Identify Biochemistry Misconceptions And The Development Of A Guided Inquiry Activity To Correct The Identified Misconceptions, Ellen Humphreys

Master of Science in Chemical Sciences Theses

It is known that students leave science classes with an incomplete or incorrect understanding of some of the concepts covered in the courses. Identification of these misconceptions is difficult, as it usually involves conducting an hour long one-on-one interview with a student. Concept inventories were developed as a way for professors to identify misconceptions in their classroom in an efficient manner. However, there is no collection of biology, chemistry and biochemistry concept inventories and there has been no analysis of the quality of these inventories. One goal of the research was to collect these inventories and do the much needed …

Synthesis And Application Of Pdib Nanostructures In Solar Cells, John T. Ferguson

Mahurin Honors College Capstone Experience/Thesis Projects

Perylenediimide bridged silsesquioxane (PDIB) nanoparticles were synthesized by sol-gel processes as described by the Stöber method. These particles were synthesized homogeneously from solution and with the use of silica nanoparticles and bipyridine iodide bridged silsesquioxane (BPIB) nanoparticles as nucleation sites. The morphology of the resulting particles was confirmed by TEM and the presence of PDI confirmed by UV spectroscopy. Although further research will test all of the particles across a range of concentrations and sizes, the silica nucleated PDIB nanoparticles were analyzed in the active layer of bulk heterojunction organic photovoltaic devices in conjunction with P3HT polymer. Devices with the …

Benchmark Structures And Harmonic Vibrational Frequencies Near The Ccsd(T) Complete Basis Set Limit For Small Water Clusters: (H2o)N = 2, 3, 4, 5, 6, J. Coleman Howard, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

A series of (H₂O)_n clusters ranging from the dimer to the hexamer have been characterized with the CCSD(T) and the 2-body: Many-body CCSD(T):MP2 methods near the complete basis set (CBS) limit to generate benchmark-quality optimized structures and harmonic vibrational frequencies for these important systems. Quadruple-ζ correlation-consistent basis sets that augment the O atoms with diffuse functions have been employed in the analytic computation of harmonic vibrational frequencies for the global minima of the dimer, trimer, tetramer, and pentamer as well as the ring, book, cage, and prism isomers of the hexamer. Prior calibration [J. Chem. Phys. 2013, …

The Interaction Of Glutathione With Platinum, And The Role Of Ph In Altering Ligand Formation Between Platinum And N-Acetylcysteine, Kyle B. Mann

Mahurin Honors College Capstone Experience/Thesis Projects

Cisplatin is an important anti-cancer drug. Structurally, cisplatin is a coordination complex, which means that it has a central metallic atom: platinum. Side interactions prevent cisplatin from effectively treating cancerous cells by reaction with DNA. Cisplatin has a high rate of forming protein adducts, primarily with sulfur containing amino acids. To better understand how cisplatin interacts with sulfur containing amino acids in the body, a platinum compound with an ethylenediamine ligand attached was reacted with N-acetylcysteine and glutathione. The reactions of cysteine with platinum were performed at three pH values: 7.0, 8.5, and 10. NMR spectroscopy was used to examine …

Relative Reaction Rates Of The Amino Acids Cysteine, Methionine, And Histidine With Analogs Of The Anti-Cancer Drug Cisplatin, Cynthia A. Tope

Mahurin Honors College Capstone Experience/Thesis Projects

We are studying the reaction of analogs of the anticancer drug cisplatin with amino acids that differ in size and shape. The reaction of cisplatin with proteins likely precedes reaction with DNA in the body, forming a variety of products that may be toxic to the human body. The size and shape of the platinum(II) complexes often affects the rate of reaction with proteins, more so than with DNA. In this study, triamine cisplatin analogs are reacted with the amino acids cysteine, methionine, and histidine simultaneously. These reactions are monitored by NMR spectroscopy. The effect of the bulk of the …

Thermoelectric Properties Of Nano-Meso-Micro Β-Mno2 Powders As A Function Of Electrical Resistance: Experiment And Theory, Morgan Hedden

Senior Honors Projects, 2010-2019

In this work, the thermoelectric properties of Beta-MnO² powders as a function of electrical resistance are measured and compared to theoretical models. The discovery of a giant Seebeck coefficient by Song et al. in these powders rejuvenated interest in understanding the physical mechanism behind it. A simple pestle and mortar method was used to modify the MnO² powder sizes. We and the largest S coefficient, power factor, and thermal conductivity values were found to be S=-316 uV/K, (sigma)S² =5.8x10^-7 W/mK² and k=0.2096 W/(mK), all observed at a particle electrical resistance of R=9.8 Ohms. From these …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Graduation Weekend

Effects Of Anions And Amino Acids On Surface Tension Of Water, Diana Al Husseini

Senior Honors Projects, 2010-2019

Hofmeister series is a set of ions in order of their abilities to affect physical properties in aqueous solutions. Franz Hofmeister was the first to discover the specific ion effects on protein solubility in aqueous solutions. Although the Hofmeister phenomena are general, their mechanisms are still not fully understood. Herein, we use optical tensiometry by a pendant drop method to study the Hofmeister anion effects on the surface tension of water. It has been observed that the surface tension of water increases linearly as the salt concentrations increase. The effects of salts follow a specific trend with respect to the …

The Synthesis And Study Of The Biological And Colloidal Properties Of Bolaamphiphiles, Louis M. Damiano

Senior Honors Projects, 2010-2019

Over the past decade, antibiotic resistant bacteria have caused infections in patients throughout the world.^[1] The rise in antibiotic resistance is primarily due to the misuse and overuse of antibiotics. ^[1] To counter the increase in antibiotic resistance, infection control mechanisms have been aggressively researched in recent years. In particular, drug delivery has become a focal point to fight antibiotic resistant infections.^[2] Amphiphiles have a wide range of applications in the clinical setting, including the ability to inhibit bacterial transference because of their bactericidal activity. ^[3] Bolaamphiphiles are a subclass of amphiphiles that possess two or more hydrophilic …

Analysis Of Nitrogen And Phosphorus Nutrients In Lake Sediment, Kelsey L. Berrier

Senior Honors Projects, 2010-2019

Analytical methods for the determination of nitrogen and phosphorus nutrients (NO₃-N, NH₄-N and PO₄-P) in sediment were studied with the goal of developing extraction steps compatible with analysis by ion chromatography (IC). Research focused on extractant solution composition, Dionex OnGuard^® sample pretreatment cartridges for salt removal, and chromatographic resolution. Aqueous test samples, lake sediment samples and spiked lake sediment samples were analyzed. Dionex Ag, Ag/H, and H cartridges were studied for the pretreatment step. Silver (Ag) cartridges were found effective in removing >99% of interfering chloride ion to allow NO₃-N determination …

Examination Of The Structure, Force Resistance, And Elasticity Of Muscle Proteins, Tracy A. Caldwell

Senior Honors Projects, 2010-2019

Obscurin and titin are made up of independently folded domains that can be studied individually. Both are comprised of mostly Ig (immunoglobulin) or FnIII (Fibronectin type III)- like domains, which are made of two beta sheets held together by a hydrophobic core. High resolution structures of a limited number of both titin and obscurin domains have been determined using both nuclear magnetic resonance (NMR) and X-ray crystallography. These structures have been complemented by low resolution methods such as small angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM). Here, other high and low resolution structures not previously published will be presented …

Aqueous Foam Stabilized By Tricephalic Amphiphilic Surfactants, Seth A. Heerschap

Senior Honors Projects, 2010-2019

Aqueous foams can be described as a close packing of gas bubbles stabilized by surface active molecules. Their complex and diverse properties make them attractive for many chemical and physical applications where foaming, emulsifying or coating processes are needed. The recent synthesis of multi-cephalic and multi-tailed amphiphilic molecules have reportedly enhanced their antibacterial activity in connection with tail length and nature of the head group.

This report covers the foamability of two triple head, double tail cationic surfactants (M-1,14,14, M-P,14,14) and a triple head single tail cationic surfactant (M-1,1,14) and compares them with commercially available single headed, single tailed anionic …

Applications Of Organic Probes For Imaging And Analysis Of Different Cancer Cell Models, Hong Guan

Theses and Dissertations

Novel techniques for better studying cancer cell behavior and progression are extremely important. Our lab is interested in synthesizing specifically designed organic reagents and applying them in the studies of cancers. In this dissertation, we used organic probes to investigate cancer cells in the following topics: determination of amino acid concentration in different types of cancers, tumor toxicity of organic probes towards HER2 positive breast cancer cells, glycoproteins identification in breast cancer cells and development of enzyme activity assay for colon cancer cells.

The first chapter was focused on the determination of cysteine/homocysteine concentrations using turn-on sensors in cancer cells. …

Impact Of Ocean Acidification On Aphotic Biogeochemical Production Of Reactive Oxygen Species, Sarah Ann Murphy

Theses and Dissertations

Reactive oxygen species (ROS) are critical to global maintenance of the global organic carbon cycle, sulfur cycle, oxygen cycle, and transition metal cycles. The primary source of ROS is commonly considered to be photolysis or photochemically driven reactions, however ROS also exist in aphotic zones. A geochemical mechanism for the same in dark environments based on the tidally driven, episodic movement of anoxic groundwaters through oxidized, Fe(III) rich sediments is shown. Predictive models were developed based on in vitro experiments and tested using sediment samples collected from a saline tidal creek in the estuary at Murrell’s Inlet, South Carolina. These …

Investigation Of Spontaneous Combustion Inhibition Of Coal Fires Utilizing Differential Scanning Calorimetry And Thermogravimetric Analysis, Christopher J. Raymond

Master of Science in Chemical Sciences Theses

Self-oxidation of coals can result in spontaneous combustion events at any time during mining, transporting, or processing, causing environmental, economical, and safety concerns. The total global primary coal production as of 2012 was 8.7 billion tons. Of that, 1.1 billion tons of coal was mined in the US, which accounts for 41% of the domestic electricity production. Spontaneous coal combustion, although dependent on coal rank, is a naturally occurring phenomenon that often causes damage to industrial and commercial facilities and freight, reduces the caloric value of coal, can release noxious gases and particulate matter, and increases CO₂ pollution levels …

Metals On Titania/Hopg As Models For Heterogeneous Catalysts, Randima Piyumalie Galhenage

Theses and Dissertations

The work done in this thesis is mainly focused on understanding the nanoscale morphology and activity of model heterogeneous catalysts. In order to do this we design and prepare model catalytic surfaces in ultrahigh vacuum (UHV) and study these surfaces using electron and ion based microscopies and spectroscopies. The nucleation, growth and chemical activity of mono and bimetallic clusters on TiO₂(110) were investigated in order to understand how activity is influenced by cluster sizes, interactions with the oxide support and surface compositions of the bimetallic clusters. For example, Au-based and Pt-based bimetallic clusters such as Co-Au, Co-Pt, and …

Facile Method For Large Scale Alignment Of One Dimensional Nanoparticles And Its Biomedical Application, Sheng Feng

Theses and Dissertations

Topographical cues can profoundly affect cellular behaviors. This thesis investigate how to utilize the topographical cues generated by two techniques, flow assembly and electrospinning, to regulate cellular behaviors.

First of all, a facile and robust method to align one-dimensional (1D) nanoparticles (NPs) in large scale has been developed. Using flow assembly, representative rod-like nanoparticles, including tobacco mosaic virus (TMV), gold nanorods and bacteriophage M13, have been aligned inside capillaries by controlling flow rate and substrate surface properties. The properties of 1D NPs, such as stiffness and aspect ratio, play a critical role in the alignment. Furthermore, these hierarchically organized structures …

Tempo-Containing Romp Polymers As A Component For Treatment Of Traumatic Brain Injuries, Cameron H. Feriante

Honors College Theses

During a traumatic brain injury (TBI) sustained in combination with hemorrhagic shock the brain undergoes anoxic conditions resulting from swelling and blood loss. Traditional intravenous solutions are used to replace blood volume, but are unable to replace the blood’s oxygen carrying capacity. A proposed treatment based on isotonic solutions containing hemoglobin-based oxygen carriers (HBOC’s) which were intended to provide readily available oxygen was developed. However, cell-free hemoglobin was shown to have excessive oxidative potential. Polynitroxylated Pegylated Hemoglobin (PNPH) was developed to address this shortcoming. During PNPH synthesis a combination of polyethylene glycol (PEG) and (2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl (TEMPO), is bound to the …

A Review On The Bulk And Surface Chemistry Of Iron In Atmospherically-Relevant Systems Containing Humic Like Substances (Hulis), Hind A. Al-Abadleh

Chemistry Faculty Publications

As the fourth most abundant element by mass in the Earth’s crust, iron is ubiquitous and its chemistry is rich and interdisciplinary in nature. This review synthesizes the current state of knowledge of iron chemistry in multicomponent atmospheric aerosols, which is also applicable to other atmospherically-relevant systems that include iron-containing anthropogenic nanodust, ocean surfaces and buildings. Because of the abundance of humic-like substances (HULIS) in these systems, studies on their chemistry with iron and those used as models for HULIS are the focus of this review. Findings from field measurements and laboratory studies are summarized to highlight major themes in …

The Effect Of Extended Π-Conjugation On The Spectroscopic And Electrochemical Properties Of Boron Difluoride Formazanate Complexes, Stephanie M. Barbon, Viktor N. Staroverov, Joe Gilroy

Chemistry Publications

The effect of extended π-conjugation on the spectroscopic and electrochemical properties of boron difluoride (BF₂) formazanate complexes was studied by the systematic comparison of phenyl- and naphthyl-substituted derivatives. Each of the BF₂ complexes described was characterized by ¹H, ¹³C, ¹¹B and ¹⁹F NMR spectroscopy, cyclic voltammetry, infrared spectroscopy, UV-vis absorption and emission spectroscopy and mass spectrometry. X-ray crystallography and electronic structure calculations were used to rationalize the trends observed, including direct comparison of 3-cyano-, 3-nitro- and 3-phenyl-substituted BF₂ formazanate complexes. In all cases, the wavelength of maximum absorption and emission were red-shifted …

Molecular Characterization Of Free Tropospheric Aerosol Collected At The Pico Mountain Observatory: A Case Study With A Long-Range Transported Biomass Burning Plume, K. Dzepina, C. Mazzoleni, Paulo Fialho, Swarup China, B. Zhang, R. C. Owen, D. Helmig, D. Helmig, S. Kumar, Judith Perlinger, L. Kramer, M. P. Dziobak, M. T. Ampadu, S. Olsen, D. J. Wuebbles, Lynn Mazzoleni

Department of Chemistry Publications

Free tropospheric aerosol was sampled at the Pico Mountain Observatory located at 2225 m above mean sea level on Pico Island of the Azores archipelago in the North Atlantic. The observatory is located ~ 3900 km east and downwind of North America, which enables studies of free tropospheric air transported over long distances. Aerosol samples collected on filters from June to October 2012 were analyzed to characterize organic carbon, elemental carbon, and inorganic ions. The average ambient concentration of aerosol was 0.9 ± 0.7 μg m−3. On average, organic aerosol components represent the largest mass fraction of the total measured …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 93rd Annual Meeting of the Virginia Academy of Science, May 21-23, 2015, James Madison University, Richmond, Virginia

A Rapid Lc-Ms/Ms Method For Quantification Of Csuoh0901, A Novel Antitumor Agent, In Rat Plasma, Ramakrishna R. Voggu, Ravali Alagandula, Xiang Zhou, Bin Su Ph.D., Bo Zhong, Baochuan Guo

Chemistry Faculty Publications

CSUOH0901, a novel anticancer derivative of nimesulide, exhibits very promising anticancer activities in various cancer cell lines. In order to support further pharmacological and toxicological studies of this promising anticancer drug candidate, an LC-MS/MS method was developed and validated in accordance with the US Food and Drug Administration guidelines. The drug molecules were extracted from plasma samples by protein precipitation and then analyzed with LC-ESI-MS/MS. An excellent analyte separation was achieved using a phenomenex C18 column with a mobile phase of 90% methanol and 5 m m of ammonium formate. The validated linear dynamic range was between 0.5 and 100 …