For the past twenty years, scientists have attempted to learn more about the effects of pollution on coral species. However, identifying coral species in today's scientific community is more of an art than a science. For the last five years, researchers have been attempting to address this problem by comparing the skeletal structures of different coral species. Coral calcification is distinctive because it involves the formation of rapid aragonite super saturation. Aragonite is a very unusual form of calcium carbonate. It is much less thermodynamically stable than the primary form of calcium carbonate--calcite. There are two lines of thought as to why aragonite is preferentially precipitated in coral skeletons. One, the proteins secreted by the polyps within the coral create microenvironments that promote aragonite precipitation. Two, the magnesium from the surrounding ocean water interacts with the proteins in such a way that aragonite becomes the more energetically favorable precipitate. Our research examined the proteins and water involved in these calcification sites and compared them among species of coral collected from the Mo’orea Islands using Thermo Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), Energy Dispersive X-Ray Spectroscopy (EDS) and Fourier Transform Infrared Spectroscopy (FT-IR). In short, we wanted to compare the magnesium, water content, and protein content/functional groups between species in the hope of finding species or site-specific trends. Our results confirmed the correlation between magnesium and protein, and discovered that the way in which corals create their exoskeleton is highly evolutionarily conserved.

Long intergenic non-coding RNAs (lincRNAs) have been discovered to be widespread in mammalian genomes, with thousands existing in humans alone. lincRNAs exceed 200 nucleotides in length and are capped and polyadenylated. They do not overlap with protein-coding genes, and generally exhibit poor sequence conservation across divergent species. The lincRNA cyrano, discovered in zebrafish, possesses a very highly conserved 300 nucletotide region in at least 80 species. Cyrano has also been demonstrated to be essential in embryonic development in zebrafish. Given the sequence conservation of cyrano, we hypothesized that the secondary structure of the 300 nucleotide region was conserved across divergent species. Using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) we determined the RNA structure of this 300 nucleotide conserved region in vitro in mouse, human, and zebrafish. Four structural motifs were found to be common in all of the species. To validate the integrity of these secondary structural motifs, we aim to probe the structure of the 300 nucleotide conserved region as it exists in the cell by performing SHAPE in vivo. Currently, our findings represent some of the first steps towards understanding the roles of lincRNAs and non-coding RNAs in general. The miniscule amount of information we collectively know about this vast new enigma of the genome emphasizes the need for biochemists to tackle this issue and improve the methods at our disposal. 

Using the UC Irvine Whole Air Sampler, I measured volatile organic compounds (VOCs) onboard the NASA DC-8 during the Student Airborne Research Program. High levels of the harmful chemical ozone were observed near the surface over the Sierra Nevada mountains, which led to the focus of my independent research project on the study of VOC data in order to investigate factors that contributed to ozone production. This was done by calculating the hydroxyl radical reactivity, which can, in proper conditions, be used to predict ozone formation potential. I divided the region into three boxes from east to west, based on wind direction, and the reactivity was analyzed over each region with respect to methane, non-methane alkanes, alkenes, aromatics, and biogenic compounds. In the westernmost box the reactivity was 1.7 ± 0.5 s-1 (1σ), in the middle section it was 1.4 ± 1 s-1, and in the easternmost region it was 0.8 ± 0.3 s-1. I compared the data in the Sierra Nevada region with a region known to be heavily polluted, the Los Angeles (LA) basin, and it was observed that the reactivity was 1.1 ± 0.6 s-1, lower than in two of the mountainous regions. In the Sierra Nevada mountains a major percentage of the hydroxyl radical reactivity was the result of biogenic influence, at 24% for the western box, 39% for the middle box, and 31% for the easternmost box, in contrast to only 2% biogenic contribution in LA. My work indicates that biogenic factors greatly contributed to overall ozone formation in the Sierra Nevada mountains. These mountains are strategically protected, and high pollution levels of ozone and other VOCs could lead to health impacts for visitors, vegetation, and wildlife.

The diffusion of ions into a nano-scale ZnO lattice has gained attention in the past decade as a possible solution to the rapid fracturing of ZnO electrodes in bulk batteries and as an alternative to conventional LiCoO₂ and LiFePO₄ materials which are expensive to manufacture and environmentally hazardous. Experiments have shown that utilizing bulk (ie. not nano-structured) ZnO electrodes fracture in discrete segments (a leapfrog effect) after only a few charge/discharge cycles, diminishing the effective charging/discharging capacity. Current efforts are aimed at using nano-scale lattices which fall within the size range of the cracking separations and thus are not susceptible to leapfrog fracturing. Using an optimized quantum dot structure and conventional ab initio electron structure theory methods, the effects of lithium ion intercalation into a Zn₃₃O₃₃ quantum dot lattice were investigated. The main research questions were: (1) where are the potential energy valleys in which lithium ions can settle; (2) What effect does lattice expansion have on the energy of a lithium-ion charged quantum dot; and (3) how does doping the dot with iron affect the energy? Using a rigid and a relaxed scan of a lithium entering and exiting through the C3v axis of the quantum dot, the potential energy landscape was mapped, illustrating the presence of multiple potential valleys in which ions could settle. We used single point calculations to determine the optimal expansion factor after observing expansion in previous molecular dynamics simulations. Currently preliminary results indicate a possible trend regarding iron positioning within the lattice and we hope to improve our data by introducing a larger Zn₈₄O₈₄ dot. Hopefully our findings will demonstrate that nano-scale iron doped ZnO lattices are not subject to leapfrog fracturing and may therefore be cheap and viable options as battery electrodes.

Photosynthesis is how plants gather energy from the sun and store it as chemical energy. This pathway involves multiple energy gathering antennae that absorb light and move electrons through photosystems to store the energy in NADPH and ATP and in turn split water into O₂ and 2H₂. There are two mechanisms proposed for the O-O bond forming step catalyzed by the oxygen evolving complex (OEC), Mn^dang-CaMn₃O₅, of photosystem II, and the dangling Mn (Mn^dang) and Ca ions have both been shown to be involved. One mechanism is through nucleophilic attack by an OH^- that is coordinated to the Ca ion at an electrophilic Mn(V)≡O species, and the other is through radical coupling between two Mn(IV)-O• species. Recent data shows that the nucleophilic attack mechanism is the most likely mechanism. Because the O-O bond forming step occurs after the rate-determining step, these intermediates are not observable in photosystem II. This project involves the synthesis and isolation of species that are representative of the Mn^dang-O-Ca fragment, and intermediates involved in one of the proposed mechanisms for O-O bond formation by the OEC. We are using [Mn(II)(N₃S^Me2(tren))]⁺ as our Mn starting material, and [(dipp-DAD)Ca²⁺(OH)₂]^2- as Ca-(OH)₂ source. The reaction between these two compounds will be monitored by UV-Vis, in the presence of an oxidant, to detect changes in the Mn ion’s electronic environment. So far we have been able to isolate the previously reported [(dipp-DAD)Ca²⁺(THF)₃] precursor complex, and our next step will be to generate hydroxide derivative and monitor its reaction with [Mn(II)(N₃S^Me2(tren))]⁺ using the method described above.

Alkanes, or saturated hydrocarbons, are the major constituents of natural gas and petroleum. Conversion of the chemically inert bonds of alkanes to more useful functional groups (like alcohols, aldehydes, and carboxylic acids) requires a great deal of energy and is often expensive. For this reason, functionality is often added using olefin precursors, or unsaturated hydrocarbons. Thus, more efficient and cost-effective conversions of alkanes to olefins, or alkane dehydrogenation, are highly desirable. Prior work shows alkane dehydrogenation may be achieved with iridium and rhodium pincer complexes. While significant success in this type of alkane functionalization has been achieved with Ir^I systems, these C–H bond-activating systems are inhibited by nitrogen and water, and can be self-inhibited by olefins. In contrast, Ir^III complexes have been shown to be tolerant to these inhibitors and are able to activate the C–H bonds of alkanes. Our experimental and computational results show usage of Brønsted acids to generate new Ir^III systems, in particular (^dmPhebox)Ir(OAc)(X) complexes, leads to an increase in the rate of C-H activation over the previously reported (^dmPhebox)Ir(OAc)₂(OH₂) system. The product of this activation and dehydrogenation reaction is olefin and (^dmPhebox)Ir(OAc)(H). Optimized conditions for this alkane dehydrogenation system and mechanistic studies will be presented.

All biological systems are dependent on properly folded protein molecules to function correctly. To enable major developments in biotechnology and medicine, an understanding of the protein folding process is needed. Advances in this field have been made, however most of the knowledge gained has been concentrated on structured beta-sheets and alpha-helices. Experimental studies of beta-strand association and the effects of conformational dynamics in unstructured loop regions remain scarce, in part because the timescales of the dynamics leave few spectroscopic methods available for measuring kinetics. Using a model system consisting of two beta-strands connected by a loop of variable length and composition, measurements of beta-strand association dynamics on microsecond to millisecond timescales have been made by employing Relaxation Dispersion Nuclear Magnetic Resonance (NMR) techniques. In addition, using multidimensional NMR and Circular Dichroism spectroscopy, sequence-specific thermodynamic effects in the folding of these peptides have been examined. Loop closure was originally thought to be so fast that it would be negligible in the protein folding process, however our measurements show that loop closure rates can vary significantly depending on size and composition. Peptides containing all-glycine loops of length 3 – 16 have been shown to have folding rate constants (1/kf) of 12.3 – 109 microseconds with unfolding rate constants (1/ku) of 636 – 191 microseconds at 300 Kelvin. Insertion of structured beta-turns into the loop region were shown to increase the rate of folding, from 231 microseconds for an all glycine 10-loop to 25.0 microseconds for a length-10 loop containing an organized turn. These measurements have shown that the interplay of conformational entropy and residual segmental motion are crucial to understanding the stability and dynamics of beta-sheets. Current and future work on this project seeks to understand how tuning the dynamics of beta-sheets will affect thermodynamics and kinetics of ligand binding in biologically relevant systems.

Every year bee specialists report detection of larger numbers of bee colonies suffering from colony collapse disorder. One of the suggested causes of colony collapse disorder is the increasing use of neonicotinoid pesticides in farming agriculture. Neonicotinoids like clothianidin, thiacloprid and imidacloprid are effective insect neurotoxins created as a safer alternative to previous insecticides. Neonicotinoid pesticides have many distribution methods including dusting methods and application to soil and root systems; leading to their dispersion in a multitude of matrices. The quantity of these pesticides in water and soil samples needs to be measured to further asses the effect of these pesticides on bees and other species including fish and humans. However, differences in extraction methodology can lead to differences in analyte detection. Water and soil samples are complex matrices to be separated before being assessed through gas chromatography-mass spectrometry or liquid chromatography–mass spectrometry. Here I present my work in comparing methods for extracting imidacloprid, a specific pesticide in the neonicotinoid category. Results from determining a reliable and accurate method of imidacloprid will help to increase the ability for future research to be conducted on collected environmental samples.

Expansion Microscopy (ExM) is a revolutionary type of fluorescence microscopy that enables super-resolution on conventional microscopes of fixed specimens that have been chemically incorporated into a hydrogel polymer matrix, enzymatically digested, and physically expanded. The original ExM approach utilized special tri-functional antibodies containing a DNA-dye-linker complex to tether the fluorescent dyes to the expandable polymer and yielded an isotropic expansion of ~4x in all directions and a lateral spatial resolution of ~70nm. Recently, we have created a simplified ExM methodology, using conventional fluorescently labeled antibodies or fluorescent proteins, and a variety of commonly available reagents yielding increased fluorescence retention for cultured cells and tissue specimens. Additionally, we have extended this new approach of ExM to Drosophila larvae and brain tissue using an optimized solution of enzymes to digest the robust outer surface of larvae (cuticle) and allow for uniform expansion of the polymer. These simplified methods for expansion microscopy will enable super-resolution microscopy on a wide range of biological samples without the need for specialized reagents or equipment.

Copper-doped semiconductor nanocrystals (NCs) combine the large effective Stokes shifts and broad PL spectra of bulk copper-doped semiconductors with the solution-processability of colloidal semiconductor nanocrystals. These properties make copper-doped NCs attractive materials for applications such as luminescent solar concentrators and light-emitting diodes. Copper-doped CdSe NCs are particularly desirable materials because their tunable absorption spans the visible spectrum, and they provide a useful model system for studying the photophysics of copper-doped semiconductor NCs. However, both fundamental studies and applications of copper-doped CdSe NCs have been limited by the inability to simultaneously control the NC diameter, size dispersity and copper dopant concentration during synthesis, This poster reports a new one-pot synthesis of copper-doped CdSe NCs that enables precise control of NC size and copper concentration while maintaining a narrow size distribution. This level of synthetic control is achieved by separating the nanocrystal growth and copper-doping steps, and tuning the reactivity of the copper precursor. Post-synthetic treatments with various surface ligands are also used to tune copper dopant concentration. Fundamental photophysical studies enabled by access to the high-quality copper-doped CdSe NCs provided by this new synthetic method will also be discussed.

The oxygen evolving complex (OEC) is the enzyme in Photosystem II responsible for oxidizing water into oxygen gas. The OEC, a Mn₄O₅Ca cofactor, has one manganese “dangling” off a cubane, and it undergoes several conformational changes as photons provide energy for the splitting of water. The mechanisms and intermediates for the transitions between states are not fully understood, so research into manganese dioxygen chemistry will illuminate this important biological process. In order to characterize intermediates more successfully, we use synthetic, small molecule, ligand framed analogues that emulate the properties of the enzyme. Synthetic analogues have a distinct advantage in characterizing intermediates because the enzyme is limited to activity under conditions of a living organism such as temperature and solvent. By tuning the conditions and coordination sphere of our manganese complexes, we can stabilize metastable intermediates in order to spectroscopically characterize them. Our target is to synthesize a mononuclear manganese superoxo complex modeling the dangling manganese, which has been previously reported as an active site in oxygen evolution. A superoxo must be the last intermediate in oxygen evolution, so by characterizing our complex, we can determine viable mechanisms for the evolution of oxygen off the dangling manganese. We designed the ligand to be sterically bulky and have a low coordination number so there is a selective open coordination site for dioxygen binding. The lower coordination number raises the manganese’s Lewis acidity which allows for reversible oxygen binding. A trans thiolate is incorporated into the ligand framework as it has been previously shown that the sulfur to metal charge transfer band is in the visible region, giving the complex an easily identifiable spectroscopic property. By synthesizing our superoxo complex then characterizing its properties, we can better understand the complex mechanisms of oxygen evolution.

Electronic cigarettes use a heating coil to aerosolize a liquid made of ingredients which are only approved safe by oral consumption. However, there remains a question as to whether these components may react or decompose to form other, potentially harmful or toxic, substances when exposed to the high temperatures of the vaporizer. Gas chromatography and mass spectrometry (GC/MS) were used to identify chemicals in generic e-liquid and in the vapor produced from the e-cigarettes. A replica of an electronic cigarette was constructed in order to have better control over the temperature coil and produce vapor in a range of 200-700 ⁰C. Seven of the common and commercially available e-liquids were investigated in this study. The chemicals were quantified in a low parts per million (ppm).The nature and the toxicity of the identified chemicals were then discussed based on the available literature information.

The purpose of this experiment was to investigate the feasibility of the electrochemical synthesis of ferrate and bleach using a boron-doped diamond electrochemical cell. As ferrate's only byproduct in oxidation reactions is Fe(III), ferrate is a powerful alternative in the disinfection of waste water treatment to eliminate pathogenic bacteria such as E. coli. from water streams, where more traditional disinfectants give halogenated byproducts. However, ferrate degrades rapidly outside of basic solution and current synthetic methods are prohibitively expensive and require hazardous reagents. The two competing syntheses are direct electrochemical production and wet oxidation by concentrated bleach. In the first, difficulties present relating to stability of the electrode; continual oxidation wears the electrode, increasing management and production costs. In the chemical synthesis high concentrations of bleach are required, equilibrium lies to the left, and yield is low. This project attempted to remedy the first by using diamond, a highly chemically resistive carbon allotrope, as the electrode, and to see to what extent electrochemical processes are still hindered. To remedy the difficulty of chemical synthesis the electrochemical cell was also used to oxidize bleach and investigate yields therein. In each case electrochemical synthesis of bleach and ferrate was compared to other methods.

Upper-division quantum chemistry courses can be intimidating to students due to the complicated nature of quantum theory and the heavy math usage. Learning objectives are sometimes lost in formalism, and students thus have trouble understanding quantum mechanics and appreciating its importance, especially in the context of chemical and biological systems. We are working to change how quantum chemistry is taught and presented and thus improve student learning outcomes. To this end, we are creating a free, interactive quantum chemistry e-textbook. We have formulated a revised set of five learning objectives: to cultivate and apply the mathematical foundations of quantum theory; to explain the properties, simplifications, and assumptions of the core quantum models; to explain the various features of relevant visual representations; to apply quantum theory to spectroscopic analysis, atoms, molecules, and chemical bonding; and to describe macroscopic phenomena using quantum theory. These objectives are intended to make quantum chemistry approachable to students in all scientific fields. We developed an initial design of the e-textbook based on the principles of minimal navigational effort, minimal clutter, maximal sense of place, and easy discoverability to keep students focused and interested. Ultimately, revising the standard quantum chemistry curriculum to emphasize core learning objectives and conceptual understanding will help students better comprehend the material and develop a stronger appreciation for the many applications of quantum mechanics.

Microplastics are a marine pollutant estimated to be in the range of 4-8 million tons released annually in to the world’s oceans. Microplastics have been shown to bio-accumulate in marine life, specifically fish and bivalves. Due to the hydrophobic properties of plastics, non-polar organic pollutants will interact chemically and physically. Adsorption of pollutants allows plastics in the marine environment to act as a distribution vector. This project focuses on the microplastic content in food grade sea salts, specifically those made from solar evaporation. Due to the nature of how sea water is concentrated down to form sea salt, these salt crystals are at risk of harboring microplastics. We have investigated the potential for microplastic bound organic molecules in sea salts. To address this we analyzed four kinds of commercially available salt. These salts were dissolved in water and filtered through 2 micron filters, and analyzed by Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) to characterize the filtrate. Following this, we washed the filtrate with dichloromethane and analyzed this with Gas Chromatography Mass Spectrometry (GC-MS). SEM analysis showed particles of 5-500 m diameter present in teh filtered salt solutions. When microplastics were washed with dichloromethane, phthalic acid was identified in the eluted fraction by GC-MS. Thus, preliminary results indicate the presence of organic pollutant absorbed to the surface of microplastics in sea-salt. Future work will focus on improving extraction of persistent organic pollutants. With microplastics becoming an ever more present pollutant in the global marine environment, the continuation of our research should include the health hazards of ingestion of large quantities of microplastics that have been exposed to the marine environment.

During the height of the last glaciation, the Puget Lowlands were covered by a large lake, Glacial Lake Russell, which catastrophically emptied sometime between 13,000 and 15,000 years ago through the straights of Juan de Fuca. Three icebergs once suspended in Glacial Lake Russell, became stranded in water-logged sediments in North Seattle. These icebergs deformed the landscape, forming three basins of varying depths that became bogs. The creation of these basins in this manner is a relatively rare geological occurrence. A volcanic ash layer was recovered from one of these peat bogs in North Seattle, Washington. The purpose of this research was to determine the age, volcano of origin, and chemical composition of a volcanic ash sample recovered from a peat bog in North Seattle, as a means to gain a better understanding of significant geologic events in this region. Chemical fingerprinting by Ion Chromatography (IC) provided concentrations of specific ions of interest, and carbon dating analysis allowed for the determination of an approximate age for the ash layer. Inductive Coupled Plasma Mass Spectrometry (ICP-MS), was used to determine metal distribution in the ash layer leading us closer to gaining a clearer understanding of when eruptions occurred and when the region was ice free. The ash layer is not present in the upland sediments, and is theorized to have eroded off seasonal snow-pack and settled in the bog. Large, stranded ice takes a few hundred years to melt out, and the mass of the ice can be approximated from the mass of the sediments displaced from the basin. This could help narrow down when exactly Glacial Lake Russell emptied. Understanding the mechanisms of how this rare form of deformation occurred would advance the geological understanding of the Puget Sound Region.

Arsenic is a toxic heavy metal to humans that can cause serious health damages. Exposure to arsenic can cause various health conditions such as skin damage, lung, bladder, kidney and liver cancer, as well as nerve and circulatory problems. Arsenic contamination in water and soil can be naturally sourced from local geology or human sourced from pesticide and preservative uses. Studies have shown that rice will uptake arsenic from water and soil. Rice is a very easily digestible grain which makes it very suitable source of nutrition for children, whom are more susceptible to toxins. Therefore, it is important to develop and continue the study of methods that can help to quantitatively detect arsenic in rice. For this experiment, the objective was to look at a previously published method used to detect arsenic and validate its effectiveness on five store-bought rice samples. The broader implication of this experiment is to validate a method and modify it to gain quantitative data in order to assess whether harmful levels can be detected and to determine background levels of arsenic in rice. Rice was powdered and 1.0 g of rice sample was digested in 10mL of 0.28M nitric acid for 90 minutes at 95°C. The samples were analyzed with ICP-MS to detect arsenic based on its mass. A calibration plot with a correlation coefficient of 0.96278 and a slope of 1856.48 was created. The calibration plot was made from concentration of 1ppb, 5 ppb, 10 ppb, and 50ppb in which all had intensities that were detectable. The detection value of the samples falls in between the calibration intensities. The data that is obtained suggests mean concentration of arsenic range from 1ppb to 30 ppb in 10mL solution of HNO3. This indicates that there is a range of 10 ppb to 300ppb per grams of rice. These data are corroborated by other studies analyzing levels of arsenic in rice.

Chelating agents are widely used in plants and human industries to capture metal ions and control free metal ion concentrations. Constituent ions in soils (e.g. Ca²⁺, Mg²⁺) influence the exchange of a metal ion between two chelating agents. Predicting changes in reaction pathways and the magnitude of kinetic effects is fundamental to understanding dynamic metal speciation where strong chelating ligands control metal ion speciation. This research focuses on the influence of calcium ions on the exchange rate of Ni between nitrilotriacetic acid (NTA) and 1,2-cyclohexylenedinitrilotetraacetic acid (CDTA). Capillary electrophoresis was used to monitor the changes in free chelating agent and nickel-chelating agent complex concentration with time at different pHs and reactant concentrations. Reaction rates and order were compared to those in the absence of calcium ion. The presence of calcium ions reduces overall exchange rates and alters reaction order under the conditions studied. Kinetic modeling is used to support a proposed mechanism for the influence of calcium on this exchange reaction. Knowledge about dynamic metal speciation is fundamental to understanding the ideal soil compositions for plants’ uptake of essential metals and developing remediation methods for hazardous waste sites.