Current global population growth has led to higher demands for food production, increasing our reliance on synthetic fertilizers. These are formed via the Haber Process, where nitrogen from air and hydrogen (currently obtained from natural gas combustion) is used to produce the needed ammonia. More sustainable ways of generating hydrogen gas that don’t involve burning fossil fuels are necessary. One possible replacement is nanoscale cobalt phosphide, a known, effective electrocatalyst for the hydrogen evolution reaction (HER), defined as transforming two protons and two electrons into hydrogen gas. However, this electrocatalytic system requires energy input to achieve the transformation. This project investigates the design of a synthesis to produce an indium phosphide/cobalt phosphide (InP/CoP) core/shell structure that can generate H₂ photocatalytically. The InP quantum dot will be used to generate a photoexcited electron using visible light, and then this photoexcited electron will be transferred to the CoP catalyst to perform the desired proton reduction step. Regeneration of the quantum dot ground state will be mediated through the use of a sacrificial electron donor. Here we present our findings evaluating several approaches to the colloidal synthesis of the desired core-shell heterostructure using an aminophosphine precursor and the corresponding metal halides. Success of the various syntheses was determined by examining data from multiple characterization techniques including UV-Vis spectroscopy, X-ray diffraction, electron microscopy, and elemental analysis. We expect these methods to be generalizable to a suite of electrocatalytically active transition metal phosphide shell materials. This work will ultimately contribute new methods to the sustainable production of hydrogen for industrial scale applications.

The three essential structures of life are RNA, protein and a lipid bilayer membrane. We hypothesize that these three structures formed co-dependently in an aqueous environment, as opposed to forming independently in diverse environments. In our scheme, a vesicle (membrane) formed and bound nucleobases and amino acids, the building blocks of RNA and proteins, respectively. Then, the resulting confinement and conformational constraints imposed by the membrane on the nucleobases and amino acids facilitated the formation of RNA and proteins, leading to the origin of life. The work presented here addresses one part of the hypothesis: “Do amino acids increase vesicle formation?” An increase in vesicle formation due to the addition of amino acids would support the hypothesis that membranes and proteins evolved co-dependently. It would suggest that amino acids stabilize vesicles, increasing the likelihood that fatty acid membranes and amino acids co-localized. Our experiments used decanoic acid, a prebiotic fatty acid that spontaneously forms membranes when dissolved in water. In the first part of the research, we added aqueous solutions of amino acids to a solution of decanoic acid at pH 6.83 and determined the extent of vesicle formation by measuring light scattering with a spectrophotometer. In the second part, we added amino acids to a decanoic acid solution above the pH at which vesicles form, and then slowly acidified the solution until vesicle formation began; again, we used light scattering as a measure of the extent of vesicle formation. We found that specific amino acids do in fact increase vesicle formation and also have an effect on the pH at which vesicles form. The next step in this research will be the addition of multiple types of amino acids and peptides additions in order to search for combinations that increase vesicle formation the most. The results contribute to the the possible driving mechanism behind the emergence of protocells.

This project seeks to relate chemical composition of hop oil extracts to their measured sensory qualities. Sensory properties of beer are the result of their unique chemical makeup fingerprint. Feature selection implemented in this analysis allows subtle differences in composition to be related to sensory profiles. Separation and content identification of the extracts was achieved with gas chromatography – mass spectrometry (GC-MS) instrumentation. Data pre-processing and analysis were completed using MATLAB software and peak finding algorithms developed exclusively by in-lab personnel. Feature selection strategies facilitated the comparison of individual analyte peak heights to sensory data. Several selection methodologies were tested to compare their utility in finding correlations. These approaches included data tiling and peak table-based strategies. The mathematical nature of data correlation, linear or otherwise, was then investigated. Preliminary results suggest that there may be a complex relationship between the sensory profiles and chemical composition. Exploration in this research path will enable the use of data analysis methods developed herein to better determine which compounds present in food and drink contribute to unique sensory attributes.

Increasing world energy consumption is accompanied by rising concerns over non-renewable fossil fuel usage and its detrimental environmental impacts. Even if we were to try to meet future energy demands exclusively with fossil fuels, we would fall woefully short of our projected global needs. Consequently, there are compelling economic and environmental reasons that support a dramatic shift in future energy utilization to renewable technologies. The development of solar-driven technologies to generate renewable, transportable, and storable fuel sources is desirable since these energy-dense fuels can be used in the future regardless of the time of day, season, or geographic location. My research explores the utilization of nanomaterials for solar energy-catalyzed biomass decomposition into fuels and valuable, small molecules with diverse industrial applications. Specifically, this work shows the potential of using nanomaterials of a variety of structures to convert lignin (which composes 20-30% of biomass) into more useful small molecule components. To do this, we strive to understand how to make a nanomaterial that both efficiently absorbs light and subsequently uses that absorbed energy to power lignin degradation. The ability of a nanomaterial to absorb light and catalyze this reaction depends on its electronic properties, which is dependent on both its elemental composition and morphology. Our work explores the various catalytic efficiencies of nanomaterial systems of different shapes and sizes.

Energy efficiency of important industrial chemical reactions is a motivation behind scientific research across a wide range of disciplines as a response to the growing energy crisis. Electrocatalysts play a crucial role in improving energy efficiency in the interconversion of electrical and chemical energy, and are essential components in any sustainable solar fuels conversion scheme. An issue in the widespread use of renewable energy sources is the fluctuation between energy demand and energy supply. This issue can be solved by using the renewable energy source to generate chemical fuels, storing the energy from the sun or wind in energy-dense chemical bonds to be released on-demand. One such fuel is molecular hydrogen, H2. Molecular [Ni(PNP)2]2+ catalysts are highly active catalysts for the hydrogen evolution reaction (HER) that employ pendant amines—an end group that assists with hydrogen production by allowing for efficient proton transfer. However, as molecular species, these catalysts suffer from low stability and low potential for scalability. The primary focus of this research is to develop an efficient nano-scale Ni2P synthesis based off prior syntheses in the literature, that incorporates cooperative ligands for HER on the surface. Our end goal is to determine the best method to synthesize Ni2P nanoparticles with enhanced activity due to the cooperative effects of pendant amine functionalities to create a nanomaterial catalyst with properties that meet and surpass the molecular [Ni(PNP)2]2+ catalysts for HER.

Many biochemical processes rely on the conversion of electrical energy into chemical energy. Tryptophan is one aromatic amino acid that facilitates electron transport through proteins by means of reduction and oxidation reactions, allowing for the energy conversion to occur. The ability for a protein to tune the reduction potential of tryptophan is critical to its function in reactions within enzymes such as cryptochromes, which are involved in regulation of circadian rhythm, and photolyases, which are involved in DNA repair. This tuning of the reduction potential is achieved by modulation of the microenvironment surrounding tryptophan residues within a protein. In order to study the relationship between protein environment and tryptophan oxidation, we have designed and synthesized a series of model peptides to engineer specific environments which have the same geometry but differing charge states and levels of solvent exposure. The reduction potential of each peptide was determined via differential pulse voltammetry over a pH range from 1-7.5 in order to determine how the pH dependence of tryptophan's reduction potential responds to changes in its microenvironment. The results indicate that the reduction potential of tryptophan at the physiologically relevant pH=7.5 increases with increasing positive charge in the surrounding microenvironment. The results across the entire pH range indicate that the pKa of oxidized tryptophan increases with decreased solvent exposure. Finally, our entire series of peptides indicates that the tryptophan oxidation reaction does not directly follow the expected Nernstian behavior for pH dependence of a single proton-coupled electron transfer reaction and thus indicates that the oxidation process may have differing degrees of reversibility in difference environments.

The catalytic activity of many metals can be increased when the catalyst exists as tiny nanoclusters as opposed to large bulk-like metal particles. Thus materials, or supports, that facilitate the growth of nanoparticle catalysts are highly desired. Of these supports, the most widely used are metal-oxides. The growth of catalysts on these supports can be better understood by studying the chemical bonding at the metal-oxide interface. The Mallouk group has found a calcium niobate nanosheet, HCa₂Nb₃O₁₀, that when used as a support both resists and reverses the coalescence of metal-oxide or hydroxide nanoparticles on the surface. These nanosheets are of additional interest because they are smooth on the atomic scale, similar to single crystal surfaces, with a large ratio of terrace sites to edge sites. Here, calorimetric measurements of the adsorption energies of silver and copper vapor on oxide thin films composed of four layers of these nanosheets are directly measured using adsorption calorimetry in ultrahigh vacuum. The initial heat of adsorption of silver atoms was found to be ~112 kJ/mol which closely resembles the predicted density functional theory (DFT) values for silver monomers. The growth mode of silver was determined using a surface sensitive spectroscopy technique, low-energy He+ ion scattering spectroscopy (LEIS). The number density of silver particles, as estimated from the LEIS data, was found to be ~2.2x10¹⁰ particles/cm² at 1.7 monolayer silver coverage. This is much lower than the particle densities on other metal-oxide supports and is attributed to the lower density of step/nanosheet edges on this support. The evolution of the LEIS signal indicates that silver grew as 3D nanoparticles. This data encourages further investigations of the adsorption calorimetry of different metals on this interesting support.

Many membranes spontaneously demix into coexisting liquid phases. These include membranes that are as simple as three-component lipid vesicles and as complex as protein-rich vacuole membranes within living yeast cells. The resulting membrane phases are enriched in particular lipids and proteins. Membrane phase separation is one of several mechanisms proposed to explain the observation of heterogenous distributions of lipids and proteins in cell membranes ("rafts"), which are thought to be important in cell signaling, apoptosis, and protein regulation. The overwhelming majority of experiments that probe phase separation in membranes uses only one type of lipid (namely phosphatidylcholine). However, it is known that biological membranes also contain significant fractions of other kinds of lipids (e.g. phosphatidylethanolamine, or PE-lipids). An experimental challenge is that membranes composed of high fractions of PE-lipids are unstable – the lipids assemble in tubes instead of lying in sheets. In my project, I am [1] determining the maximum amount of saturated and unsaturated PE-lipids that can be incorporated into stable membranes, [2] measuring the temperature at which the membranes demix into coexisting phases, and [3] imaging the vesicles by fluorescence microscopy. Results from Aim 1 inform future researchers which lipid ratios they can use to produce stable membranes. Results from Aim 2 provide data against which the scientific community can calibrate molecular dynamics simulations. Results from Aim 3 provide a direct test of a recent prediction that PE-lipids should be anti-registered across fluctuating membranes.

New techniques in mapping genome structure have revealed a high level of spatial organization in the nucleus. The 3D location of a gene within this high order structure is thought to impact its transcriptional state. Long-range DNA loops could link distal regulatory elements to their gene targets. To test this hypothesis we plan to develop a programmable system that allows us to loop DNA loci together, bringing them in spatial proximity. We hope to explore whether we can create or disrupt interactions between genes and regulatory elements by engineering new DNA loops. We will use programmable CRISPR-Cas DNA binding domains to target specific sites in the genome. The CRISPR-Cas complex will be tethered to an interaction domain (ID) that can dimerize with another ID at a distant DNA locus. A main challenge faced when building DNA loops is free IDs are likely to outcompete looping interactions between complexes bound to DNA. To favor interactions between complexes bound to DNA, we will use protein switches designed in the Baker lab to sense whether the CRISPR-Cas complex has engaged its DNA target. I am currently testing prototype protein switch designs and measuring their ability to activate when assembled on DNA. Initial results have shown that our switch designs can activate upon DNA binding, but that our system still needs optimization. After our switch design is optimized, we can move on to the full-fledged looping system and begin to assess the regulatory consequences that spatial repositioning has on gene regulation.

Osteocalcin is a protein implicated in bone growth and bone reconstruction in several vertebrates, including humans. In this project, we analyzed the decarboxylated form of osteocalcin’s first alpha helix (hOC-a1) using circular dichroism and isotherms. Circular dichroism spectroscopy uses polarized light to determine whether the peptide fragment forms alpha helices or beta sheets. Using adsorption isotherm experiments will determine the protein’s ability to bind onto hydroxyapatite, silica, and titania mineral surfaces. Osteocalcin is known to change conformation and form a helical structure in the presence of calcium ions and adsorb onto HAP. Previous studies attributed these characteristics to the gamma-carboxyglutamic acid (Gla) residues at positions 17, 21, and 24, which lie within its first of three alpha helices. However, a mutant form of osteocalcin which has its Gla residues reduced to glutamic acid has also been shown to adsorb onto HAP. It is unknown why the protein containing glutamic acid in place of Gla can adsorb onto the mineral surface. Using circular dichroism, the experiment showed that the decarboxylated hOC-a1 peptide fragment was a random coil and unable to form a helical structure with or without the presence of calcium ions. Isotherms determined the peptide fragment’s ability to non-cooperatively bind onto HAP, as well as silica and titania. This project determined that the decarboxylated peptide fragment could adsorb onto the mineral surfaces as a random coil, suggesting there are alternative mechanisms of adsorption in comparison to the native protein. The Drobny Group intends to continue studies of the peptide fragment by labeling residues and performing experiments using solid-state nuclear magnetic resonance spectroscopy (ssNMR).

Poly-ADP-ribose polymerases (PARPs) are enzymes that catalyze the post-translational transfer of adenosine diphosphate (ADP) from NAD+ to target proteins. Of the 17 PARPs, some have been studied extensively and are known to have important cellular functions while little is currenty understood about others. A cellular imbalance of one of these PARP enzymes, PARP4, has been correlated with several disease states, including cancers, though its cellular roles are largely unknown. Inhibitors of PARP4 are useful as tools to investigate the enzyme's functions and evaluate the inhibitors' therapuetic potential. In this research, several compounds were tested as inhibitors of PARP4 using a PARP inhibition screening assay. Initial results identified a potent, somewhat selective compound, and revealed which parts of the compound were important for PARP4 inhibition. This was used to direct the synthesis and testing of potentially more selective inhibitors of PARP4. This presentation discusses the inhibition results and their significance towards learning more about PARP4 biology, which can help inform researchers of this enzyme's role in disease states and give insight into developing treatments for such diseases. 

Probiotics are an area of significant clinical research, as they have been shown to aid digestion, fight infections, and even mitigate irritable bowel syndrome; however, probiotic colonies must grow and thrive in the extreme pH environment present in the human digestive tract. Previous experiments focused on the production of the surface protein Elongation Factor Thermally Unstable (EF-Tu), which attaches to glycoproteins lining the intestines and has been used as a biomarker for probiotic health. The growth of several strains of probiotics (Lactobacillus bulgaricus, Lactobacillus acidophilus, and Bifidobacterium longum) in both lysogeny broth (LB) and De Man, Rogosa, and Sharpe broth (MRS) was evaluated. The fractions of secreted, cytosolic, and membrane proteins were quantified using a Bradford assay. Finally, the relative amount of EF-Tu was determined by tryptic digestion and liquid chromatography-mass spectrometry (LC-MS). LB was found to be a more effective growth medium for the range of bacteria tested, with 24 hours at 37°C the ideal incubation period. To isolate the secreted proteins, the supernatant was drawn off the broth culture after centrifugation. Freeze-thaw lysis was used to extract cytosolic proteins, with three cycles determined as optimal for protein recover. Sodium deoxycholate was used to separate proteins from the membrane. All three protein samples were separated and run through a sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the EF-Tu bands (roughly 43 kDa) were excised and sent for analysis by LC-MS. Using the information obtained from this research study, pharmaceutical companies can create more suitably tailored probiotic products, and make them more accessible and understandable to the general population. 

Imidacloprid is the most widely used agricultural pesticide in the world. As a neonicotinoid, it is highly potent against insects while having low toxicity to mammals. One area of concern is its effect on honeybees, possibly playing a role in colony collapse disorder (CCD), a sudden disappearance of worker bees from an otherwise healthy population. Bees are known to be sensitive to imidacloprid at high concentrations, but what is unclear is whether chronic exposure to the low doses used to protect crops can also be harmful. The E.U. and Canada have taken steps to ban the use of imidacloprid as a precaution, and the U.S. EPA has warned users of its potential for leaching into groundwater. It may also persist for years in soil, pollen, and nectar. Due to its low volatility, high boiling point, and high solubility in polar solvents, imidacloprid can be difficult to reliably detect in environmental samples using current gas chromatography (GC) methods. To address this, we evaluated GC-MS detection of imidacloprid in methanol standards, spiked water, and spiked honey. Samples were evaluated after clean-up with both C18 solid-phase extraction (SPE) and dispersive solid-phase extraction (DSPE) methods, using two different GC columns (Restek Rxi-5MS and Rtx-1701). Samples were also subjected to a range of pH conditions, and ionized by both electron ionization (EI) and chemical ionization (CI). As GC is typically faster, cheaper, and easier than liquid chromatography, currently the method of choice for detection of neonicotinoids, our research could benefit the study of imidacloprid toxicity by reducing the attendant time, cost, and training requirements. Preliminary results have shown reliable detection of imidacloprid-urea, the main hydrolysis compound of imidacloprid, at pH 5-7.

My presentation reviews existing literature on the use of boron clusters in liquid crystals. Liquid crystalline substances are usually composed of long, thin carbon-based (organic) molecules and have applications in electronic display technology and chromatography. Many compounds with liquid crystalline phases contain rigid substituent groups. The rigidity of inorganic boron clusters and their ability to form linear compounds by attaching groups to atoms on opposite ends of the cluster make them an intriguing starting point for the synthesis of new liquid crystalline materials. Work conducted on the synthesis and properties of boron cluster-based liquid crystals in comparison with organic cyclohexane- or benzene-based analogues is discussed. In addition, new derivatives of a specific boron cluster, CB11­H12­-, synthesized in our lab using microwave and stardard Schlenk line techniques, are presented, along with an evaluation of their potential as precursors for new liquid crystals. We present a relaible pathway to a new difunctionalized carboxylic acid derivative.

In recent years, researchers have dedicated much effort to overcoming the ~250nm spatial resolution limit of light in order to reveal biological details that have been obscured by diffraction. A new form of super-resolution microscopy called expansion microscopy (ExM) has enabled ~65nm image resolution or better by physically expanding fixed specimens in a swellable hydrogel polymer. While ExM allows researchers to achieve high resolution with standard microscopes, the technique requires the use of water-immersion lenses, rather than higher-resolution oil-immersion objective lenses, when imaging more ~5 µm deep due to spherical aberrations caused by refractive index mismatch with oil lenses and water-based hydrogels (n=1.5 vs n=1.3). Oil-immersion lenses also collect more signal than water-immersion lenses, enabling higher signal to noise with oil-immersion lenses under the same excitation conditions. I have developed an index-matching technique that significantly reduces spherical aberrations when imaging with oil lenses and expanded specimens, facilitating improved resolution (~1.12x lateral improvement and 1.5x axial improvement) for depths of up to 25 μm. Expanded specimens are index-matched by simply incubating the specimen in a high-index iohexol solution which equilibrates with the specimen in approximately 18 hours. A modest ~17.5% shrinkage of the hydrogel is produced as a result in the current implementation, which I can in principle compensate for by tuning the hydrogel recipe to achieve a slightly higher expansion factor. I found that the iohexol solution on its own accelerated the rate of fluorophore bleaching and led to some fluorophore quenching. However, the addition of the triplet-state quencher n-propyl-gallate effectively mitigated this chemical bleaching. Ultimately, this iohexol-facilitated index-matching procedure not only combines the utility of ExM and the high collection efficiency of oil immersion objectives but allows researchers to use common chemicals and readily available instruments to obtain images that reveal a previously inaccessible wealth of information.

Hybrid organic-inorganic perovskite films have exhibited power conversion efficiencies (PCEs) over 22% in photovoltaic devices. Despite high PCE, non-radiative recombination at surface defects remains a major material challenge in achieving theoretical efficiency limits. We have recently shown that surface passivation using Lewis bases on model CH3NH3PbI3 perovskite films can increase the external photoluminescence quantum efficiency (PLQE) to 30% and internal PLQE to near unity. This puts CH3NH3PbI3 alongside Gallium Arsenide, currently the highest performance solar cell material, as the only other semiconductor with such high radiative efficiency. Recently, several other alloyed perovskite compositions such as (HC(NH2)2¬)xCs1-xPb(I1-yBry)3 have been investigated for photovoltaic applications due to their increased stability. Preliminary studies have shown that the surface chemistry and effect of Lewis bases on these alloyed perovskites depends on their composition. In order to understand these differences, we investigate the nature of defects, surface chemistry and the effect of Lewis bases on these alloyed compositions. We test a library of Lewis-bases as ligands on alloyed perovskite compositions and use time-correlated single-photon counting and photoluminescence quantum yield measurements to quantify changes in charge carrier lifetimes. We also use glow discharge optical emission spectroscopy to show that the ligands are primarily confined at the surface and thus, act as surface treatments. Furthermore, we use solid-state nuclear magnetic resonance along with X-ray photoelectron spectroscopy to show that the behavior of ligands is consistent with that of a typical Lewis-bases. This study demonstrates the importance of surface defects in alloyed perovskite compositions and the importance of surface passivation in achieving higher optoelectronic quality materials. The information gained in this study will be critical in optimizing the design of alloyed perovskite composition devices.

Perovskites are a class of material with the formula ABX₃ with lead-halide perovskites having promising photovoltaic properties. Over the past few years syntheses of colloidal inorganic lead-halide perovskites have been reported. Recently concerns over the toxicity and instability of lead-halide perovskites have driven research toward lead-free alternatives, including double perovskites with the elpasolite structure. Elpasolites are double perovskites where the divalent cation is replaced with a trivalent and a monovalent cation to get the formula A₂BCX₆. Despite this motivation towards less toxic alternatives, synthetic approaches remain limited with no examples of heterometallic elpasolite nanocrystals being reported. We report colloidal synthesis and characterization of nanocrystals of Cs₂AgBiX₆ (X = Cl, Br) elpasolites via hot-injection of TMS-halide under inert atmosphere and rapid quenching with an ice bath. We further show that through postsynthetic anion exchange or cation extraction the nanocrystals can be converted to new materials, such as the previously experimentally unknown Cs₂AgBiI₆. Nanocrystals of Cs₂AgBiI₆ were made via anion-exchange using trimethylsilyl iodide and have strong absorption throughout the visible region which confirms predictions that this material could be a good photovoltaic absorber. The synthetic methodologies presented are expected to be generalizable, with work already under way to optimize this for more well-known nanocrystals. This work also shows how ion-exchange reactivity of nanocrystals can lead to the discovery and development of lead-free halide perovskite materials which would be difficult, if not impossible, to make via direct synthesis.

Over 70 million people are infected by HIV and 79 million of Americans by HPV every year. Even in developed countries, these particular sexually transmitted diseases (STDs) grow at an unyieldingly steady rate. In the Chiu Group, we address this increase in infection by working on the development of a fully automated microfluidic instrument to help improve early diagnosis of HIV and HPV. While many diagnostic techniques already exist, our goal is to advance state-of-the art approaches in novel microfluidic technologies, primarily concerning the reduction of cost to run clinical samples, shortening the time required to analyze samples, and enhancing the reliability of results. We are developing our automated microfluidic instrument in two phases. The first is a preparative step in which we create high-quality microfluidic chips that help digitize thousands of nanoliter droplets in a static array of wells. In the following experimental step, we amplify target HIV/HPV sequences in these nanodroplets from patient samples through polymerase chain reaction (dPCR) and the static array format provides a direct readout through changes in fluorescence of the sample droplets.The successful implementation of the instrument together with the microfluidic chip will maintain a high level of accuracy and sensitivity as well as observe a large decrease in cost and time for diagnostics. Among the conventional diagnostic instruments available today, our development will offer a faster, cheaper, and more accessible way to diagnose HIV and HPV, and ultimately slow the rate of STD cases throughout the world.

Utilizing protein-based systems, specifically nuclease-dead Cas9 variants, to alter mammalian gene expression is an emergent subfield in synthetic biology. Such methodologies offer means to study a vast diversity of genetic networks including but not limited to cell fate decisions, stem cell differentiation, cell signaling networks, and key genetic players in tumorigenesis. Here, we offer a novel chemical tool for which drug concentration can control gene expression within target cells, by using new chemically induced dimerization systems that can respond to multiple chemical agonists and antagonists. Within our system, we use a protease dead NS3a complex, which functions as a scaffolding complex, and an entirely synthetic protein complex, either a danoprevir-NS3a complex reader (DNCR) or a grazoprevir-NS3a complex reader (GNCR), which specifically bind NS3a only when danoprevir or grazoprevir, respectively, are introduced. Furthermore, nuclease-dead Cas9 offers a means for target sequence specific tethering of nuclear effectors, and may be directed using sgRNAs. The sgRNA sequence may be elongated to allow for a protein specific tethering complex. Here we use an orthogonal scaffold RNA/RNA-binding protein pair (MS2/MCP and PP7/PCP) to localize DNCR (bound to PCP) or GNCR (bound to MCP) to select DNA sequences. The corresponding NS3a complex is fused to enhancer protein VPR, which serves to upregulate gene expression when in sufficiently close proximity. Hence upon drug induction, NS3a-VPR will bind the DNCR-PCP (or GNCR-PCP) complex tethered to dCas9 localized ideally upstream of a target gene, and induce gene expression upon introduction of danoprevir (or grazoprevir). As a direct function of this research, we have demonstrated CID capacity for linearized fold increase of several endogenous and non-endogenous genes in correlation to drug concentration, and now seek to demonstrate the capacity of our tool by studying the concentration-dependence of scaffold function in the JNK pathway.

Protons take part in many important reactions such as redox, acid-base chemistry and biochemistry; however, the mechanisms for proton transfer and hydronium’s stabilization are less understood. Hydronium sequestered in 18-crown-6 ether (CE) has an unusually broad and intense vibrational absorbance (OH-feature) compared to bare hydronium. One environmental factor affecting this OH-feature is the range of hydrogen bonded geometries between the hydrogen atoms in hydronium and the oxygen atoms in the CE, which is sampled by the complex even in its ground vibrational state. The breadth of the OH-feature is attributed to changes of the OH stretch frequency of hydronium as it rattles within the CE, and to the CE distorting to accommodate the hydronium. Hydronium will donate a proton to diethyl ether in the binary complex, because the diethyl ether is a stronger base than water. However, when hydronium hydrogen bonds to three diethyl ether molecules in a ternary complex, all three hydrogen atoms in hydronium are pulled by the ether molecules preventing any one of the protons from transferring. The hydrogen bonded geometries we analyze involve complexes of hydronium with both simple ethers and cyclic CE molecules. The CE hydrogen bonds to all three of the hydrogen atoms in hydronium similarly to the ternary complex, thus the CE complex prevents proton transfer. We explore several other environmental factors, including increasing the rigidity of the CE by replacing carbon-carbon single bonds with carbon-carbon double bonds. This increase in CE rigidity reduces the rattling of the hydronium. We also explore the effects of reducing electron density on the oxygen atoms in the CE by replacing hydrogen atoms in the CE with fluorine atoms. Optimizations, frequencies and potential energy scans are made at the B3LYP level of theory using a 6-311G(2d,p) basis.

Colloidal semiconductor quantum dots (QDs) have recently garnered attention for applications in nanoscale technologies including photovoltaics, displays, sensing, and energy storage. Radiative luminescence originating from recombination between one electron and one hole in the excited state is vital to the performance of these materials for these applications. One prominent relaxation pathway that competes with radiative luminescence in QDs is non-radiative Auger recombination, a process that can either be detrimental to device performance or in some cases harnessed to enhance various technologies. For this project, we use redox chemistry to controllably engineer negative trions (two electrons and one hole) in colloidal QDs, purposely introducing a negative-trion Auger recombination pathway. Previous results have demonstrated a size dependence of negative-trion Auger recombination rates in various QDs. This work uses time-resolved photoluminescence spectroscopy to explore the difference in size dependence for QDs with and without trap states. Preliminary findings indicate that negative-trion Auger recombination generally occurs more efficiently and exhibits a shallower size dependence when one of the carriers is trapped than when all carriers are delocalized. This work will allow for future scientists and engineers to design QDs that either suppress or make use of Auger recombination to optimize device performance.