The Brome Mosaic Virus (BMV) is an RNA virus that infects granary plants. It consists of three distinct viral particles which consists of each of three distinct BMV RNA molecules wrapped by many copies of the Coat Protein (CP). CP's regulatory roles in the replication processes of BMV are conducted through controlling the efficiency of both RNA replication and protein translation. Previous studies have shown that a 22-residue peptide (CPNT) derived from the N terminal region of CP can penetrate the host cell membrane and deliver the BMV genomic RNA into the host cell. The long-term goal of this project is to investigate the conformational characteristics of CPNT and to explore its binding characteristics on the different parts of BMV genomic RNA. As a first step, a 29 residue-long peptide mimicking the N-terminal region of CP (CPNT-1) was chemically synthesized and its overall conformation was investigated using Circular Dichroism (CD) and nuclear magnetic resonance (NMR). The CD spectra showed that it has only 12% of a-helix structure and 50% of random coil, implicating high conformational flexibility. Given that these Cys residues are not a part of the functionally crucial region of CPNT, we designed a new CPNT construct without any Cys residues (CPNT-2). Our preliminary results showed that the 1 dimensional NMR spectra showed that CPNT forms appreciable amount of secondary and/or tertiary structures in native sequence (27 amino acid residues on N’ end: CPNT-2). When the end of CPNT was replaced by multiple Cys residues (CPNT-1), it is either aggregated or becomes a random, flexible conformation. CD as well as nuclear magnetic resonance analyses have been performed on CPNT-2 and the preliminary data showed that the peptide forms secondary structure. Currently we are investigating the detailed structural characteristics of CPNT-2 using CD and nuclear magnetic resonance analysis.

When a photon is absorbed by materials called semiconductor nanocrystals or quantum dots (QDs), the energy from the photon is also absorbed and can be used to excite the semiconductor nanocrystals. If the energy of the photon is at least twice the energy of the bandgap, or the energy between two specific states, at least two charge carriers can be created. Charge carriers are inherent in any material which can absorb energy and undergo a process of excitation to a higher energy state by the photon followed by relaxation to its normal energy state accompanied by a release of energy. Conversely, when the energy of the light does not exceed twice the band gap, only one excitation is observed. If a material exhibits the property of creating multiple charge carriers, often called Multiple Exciton Generation (MEG), it can be stated that this material will likely enhance a solar cell since energy from the light absorbed by the cell will result in multiple charge carriers created followed by multiple relaxations and the releasing of energy. MEG has been shown to exist in a variety of QDs. Here, we attempt to confirm the presence of MEG in germanium QDs. This was done by pumping 400 nm and 800 nm light with a pump-probe laser and collecting the absorbance spectra at different power levels. The spectra can be analyzed to demonstrate if MEG occurs by comparing the absorbance at these different power levels. The results have provided no conclusive evidence of MEG in germanium nanoparticles. This result allows for further research to be performed on what may impact MEG and what materials are ideal for MEG.

There is high demand for clean, inexpensive, alternative fuel sources to supplement or replace fossil fuels.  The alga, Botryococcus braunii, is well-studied due to its high oil content (15-76%) and ability to store extracellular hydrocarbons which can be extracted and converted to a variety of fuels. Investigation of variable growing conditions for potential biodiesel sources can help researchers determine optimum conditions for maximizing hydrocarbon yields while lowering production costs.  Though oil from B. braunii is still too expensive to produce commercially, utilization of natural light outdoors can lower the overall cost of production. This work models the normal outdoor light levels found in the Pacific Northwest.  Growth rates of algae exposed to light intensities averaging 0.78 Klux for a daily cycle of 8 hours of light were compared with that of algae grown under standard conditions of 10 Klux for a daily cycle of 12 hours of light.  Studying these conditions allows for a more accurate estimate of the amount of supplemental light needed for optimal growth during the fall and winter for an outdoor photobioreactor.  This type of data is critical to evaluating the role algal-derived biodiesel might play in a suite of alternative energy sources for the Pacific Northwest.

The concept of dynamically causing physical distortion of molecular frameworks to influence reactivity offers an intriguing opportunity for synthetic polymer chemists and materials scientists. Strained rings have been shown to undergo chemical transformations under different stimuli but their mechanochemical behavior is a relatively newer field of study. We postulate that directing a reaction pathway mechanochemically may be a viable means to increasing the selectivity in the ring opening event. Before the mechanochemistry is investigated, the polymeric materials containing these ring systems must be designed and synthesized. The development of our strained ring system is multi-step synthesis starting from a commercially available small molecule. Once the strained ring small molecule is created, the final step of the synthesis is to incorporate it in the middle portion of a polymer. After the molecular framework has been built, its mechanochemical reactivity is studied via solution-based experiments using an ultrasound probe and processor (20 kHz) of variable power output (up to 750 watts). This approach will facilitate product characterization, mechanistic inquiries, and reactivity profiles. Collectively, the ambitious research objectives provide a fundamental basis of how mechanical forces may be used to guide and control reaction profiles.

Ultra-high vacuum (UHV) techniques make it possible to observe interactions on clean, ordered surfaces without the complexity of realistic systems.  Final construction and testing of an improved UHV adsorption microcalorimeter capable of measuring the heat of adsorption of metals on single crystalline surfaces have recently been completed.  This calorimeter is the first of its kind to employ an electron beam evaporator to create a high, stable flux of metal atoms with low source radiation, which is then pulsed onto the thin single crystalline sample. Due to the properties of the electron beam evaporator, metals with high heats of sublimation such as Pd, Pt, and Au can be evaporated while maintaining the base pressures necessary for maintaining ideal surface conditions.  The new chamber is also equipped with a sample preparation chamber in which metal oxide surfaces can be grown on single crystalline samples.  Absolute calibration of the microcalorimeter was achieved by measuring the heat of formation of Cu multilayers on a Pt(111) surface, indicating that the theory behind our electron beam evaporator is correct, and will allow for the first direct measurements of the heats of adsorption of catalytically important metals such as Pt, Pd, and Au on any surface.

The reduction of CO₂ has become a global priority as the concerns of climate change and the adverse effects of atmospheric carbon dioxide on the environment continue to rise. One method of reducing CO₂ emissions is through conversion and utilization as a chemical feedstock. CO₂ is cheap, nontoxic, and can be recycled to produce valuable new products, making it an attractive feedstock. The increasing importance of CO₂ utilization processes requires a better understanding of the underlying mechanisms of its conversion. The industrial conversion of CO₂ is typically achieved using a heterogeneous catalyst, usually consisting of small transition metal particles supported on a high surface area metal oxide. Our project focuses on elucidating the mechanism of the reverse water-gas shift (RWGS) reaction on platinum, an extensively studied catalyst with a highly active surface. Our goals are (1) to quantitatively measure the RWGS rate under conditions of low H coverage and (2) to compare the measured rate to the rate of CO₂ dissociation (the rate-limiting step according to the surface redox mechanism) and to the theoretical rate calculated using a micro-kinetic model based on the associative mechanism. The information we gather from the investigation will clarify whether the RWGS reaction proceeds on platinum via the surface redox mechanism or the associative mechanism.

This project demonstrates a new synthetic approach to tetrapod-shaped colloidal nano structures using a combination of Mn doped CdSe quantum dot cores and CdS rods. These structures are achieved using a variation in quantum dot hot injection synthesis in which Mn is added before the injection of the anionic precursors. Once the initial synthesis is complete the products are characterized by UV/VIS absorption, photo-luminescence, EPR, and TEM imaging. Once characterized the doped quantum dots are re-immersed for arm growth to achieve the tetrapod shape. Mn doping provides a magnetic probe in the nano particle that would allow us to probe the carriers during temperature dependent luminescence. Semiconductor quantum dots are believed to be useful materials in solar energy cell applications because their band-gap can be manipulated by changing the size of the particles. However, one of the limiting factors in the efficiency of these dots is the fast recombination of the carriers in the material. Tetrapod nano structure semiconductors have demonstrated the ability to extend the lifetime of exitonic emission which enables greater separation of the carriers and may potentially increase the efficiency of future solar applications. Preliminary results show that Mn doped tetrapods can be synthesized using this method; however yields need to be maximized in order for future applications to come to fruition.

Motivated by recent interest in developing compact, inexpensive, and reliable eye-safe lasers, the effect of quantum confinement on a saturable absorber material, cobalt-doped zinc selenide (Co²⁺:ZnSe), was explored in colloidal quantum dots. Co²⁺:ZnSe diluted magnetic semiconductor quantum dots (DMS-QDs) are semiconducting nanocrystals with structural lattices that include substitutional magnetic ions in addition to the primary metal cations. While previous work has been conducted on the saturability of optical absorption in bulk Co²⁺:ZnSe, the research presented here focuses entirely on quantum-confined colloidal DMS-QDs. The ability of these particular DMS-QDs to behave as saturable absorbers was explored in depth. This property is directly related to the long lived ⁴T₂(F) excited state of the Co²⁺ dopants, which gives rise to bleaching of the Co²⁺ ligand field transitions, leading to increased transmission of light upon irradiation at high powers. Specifically, absorbance features associated with excitation of ground-state electrons localized in the d-orbitals of the dopants are lost. To examine the saturable absorber behavior of Co²⁺:ZnSe, we looked at the optical transmittance of the quantum dots as a function of photoexcitation power. This was done by slowly increasing the power of a pump laser exciting the sample and observing changes in the absorbance spectrum at characteristic Co²⁺ ligand-field transition features. The bleaching of the ligand field Co²⁺:ZnSe in its nanocrystal form demonstrates that these colloidal materials are candidates for saturable absorbers in Q-switched eye-safe lasers. From this point, it should also be possible to explore excitation of the electrons from the first excited state (⁴T₂(F)) into higher energy states (excited-state absorption).

This research explores the function and dynamics of gold nanoparticles functionalized with azobenzene- modified DNA. When exposed to UV light, the azobenzene groups photoisomerize, melting the DNA and dissociating aggregated nanoparticles. This process is reversible with introduction to blue light, initiating the isomerization that allows the DNA to rehybridize and the particles to form aggregates once again. Our research focuses on the dynamics of this transition, determining the extent of trans-cis isomerization of the azobenzene DNA coupled to gold nanoparticles, a process which is monitored through pronounced changes in light absorption between the trans and cis conformations. This information creates a baseline for future photoswitching calculations, accounting for differences in behavior between free azobenzene DNA and such DNA in the presence of gold nanoparticles. We also use the kinetics of the light-induced dissociation and reassociation to provide information about the composition of the DNA, with respect to location of the azobenzene group embedded in the DNA strand. This information can assist with detection and location of base-pair mismatches within the coupled DNA.

The selective activation and functionalization of the C-H bonds of arenes and alkanes would directly yield products that are of importance to industry. Late transition metal complexes have shown great promise in the selective activation of C-H bonds. Coordinated acetate has also been shown to facilitate thermolytic C-H activation by electrophilic metal centers. The results of our studies concerning the reactivity of high valent tridentate rhodium and iridium bis-acetate complexes with unactivated arenes and alkanes will be presented. Specifically, the reactions of the complexes (NCN)Ir(OAc)₂(H₂O) (1) and (NOCON)M(OAc)₂(H₂O) (2; M= Rh, Ir) under a variety of conditions will be discussed. Novel complex 2 was synthesized in 65% yield and characterized using 1H and 13C NMR spectroscopy and X-ray crystallography.

In the past decade, there has been increasing interest in the potential of new thin-film solar technologies. Research in this field has focused largely on organic photovoltaics (OPVs) utilizing a bulk heterojunction (BHJ) design, consisting of blended films of conjugated polymer electron donors and fullerene electron acceptors.Use of semiconductor nanocrystals or “quantum dots” as a replacement acceptor material for the fullerene has been proposed as an alternative. In this research, charge transfer between lead sulfide nanocrystals and a conducting polymer, "poly(2,3-didecyl-quinoxaline-5,8-diyl-alt-N-octyldithieno[3,2-b:2′,3′-d]pyrrole) " or PDTPQx is investigated by time resolved spectroscopy. Previous work has found that incident light exciting the polymer results in transfer of an electron from the polymer to lead sulfide nanocrystals present in the blend. This electron transfer leaves a net positive charge on the polymer, which is accompanied by a characteristic spectroscopic signature. It is found in this research that selective excitation of the lead sulfide nanocrystals using an infrared laser also results in observable positive charge carriers on PDTPQx. This indicates that light absorption at the lead sulfide nanocrystals results in transfer of positive charges from the nanocrystals to the polymer. Confirmation of this additional charge transfer process has important implications for the potential this system in photovoltaics.

Colloidal semiconductor nanocrystals (NCs), often referred to as quantum dots, are a class of materials that exhibit size dependent photo physical properties. This class of materials has great potential for application in a variety of fields such as photovoltaics, light emitting diodes and spintronics. Doping NCs with transition metals provides additional tunability of the optical and physical properties has been synthesized. By tuning the energy gap of these NCs within thermal reach of the Mn2+ 4T1 excited state a highly temperature sensitive dual emission is acheived. The synthetic route to these dual emitting nanocrystals required the synthesis of a Mn2+:ZnSe core followed by the sequential growth of three shell layers. Doping Mn2+ into a Zn1-xCdxSe allow however, could prove to be a more efficient route to dual emitting nanocrystals with higher stability. Successful incorporation of Mn2+ into Zn1-xCdxSe alloys has resulted in dual emitting NCs.

Solar cells, through their ability to convert energy from light directly into electricity, pose a promising alternative for supplying our world’s growing demand for clean affordable energy. Many factors governing the efficiency of these photovoltaic devices are still being explored and improved upon through methods aimed at boosting photo-voltages, improving energy-conversion efficiency, and finding materials accessible for large-scale production and implementation. Here, I investigate the potential of a new type of solar cell that utilizes electron-impurity Auger de-excitation. I will discuss the effect of Auger de-excitation observed in Mn doped CdS quantum dots and explore the potential for boosting the photo-voltage via the harvesting of hot electrons. I will explain the processes involved in both synthesizing Mn:CdS quantum dots and fabricating quantum dot-based solid-state devices. I will show preliminary results from photoluminescence quenching measurements used to quantify Auger de-excitation in fabricated solid-state devices as well as device properties and characterization measurements. In the future, full-cell PV devices will be constructed and tested against the efficiencies of today’s leading solar cells.

Organic photovoltaics (OPVs) are a promising solar energy technology due to the possibility of cost-competitive large-scale manufacture. Polymer based devices typically have a bulk heterojunction (BHJ) architecture. However, BHJ materials degrade rapidly under typical operating conditions, contributing to limited device lifetimes. The degradation due to photooxidation of a model OPV system of poly[9,9’-dioctylfluorene-alt-(bis(N,N’-(4-butylphenyl))-bis(N, N’-phenyl-1,4-phenylenediamine)] (PFB) and poly[9,9’-dioctylfluorene-alt-1,4-benzothaidiazole] (F8BT) was studied by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Photooxidation products as a function of increasing photon dose at 405 nm were identified in PFB:F8BT, PFB-only, and F8BT-only films. Degradation kinetics on these films were determined by fitting Gaussian peaks to the IR spectra and measuring changes in peak area as a function of photon dose. Preliminary results suggest that multiple carbonyl species are formed in both polymers under ambient conditions. Analysis of the data collected in this experiment will be used to potentially evaluate the chemical kinetics of the degradation process and the formation of undesired chemical species in order to find a way to extend the lifetime of the device. Gaining insight into what limits the lifetime of current solar cell materials will help to improve the durability of plastic solar cells, and thereby solar energy as a widespread technology.

The acid-catalyzed dehydration of 4-methylcyclohexanol yields a mixture of several isomeric methylcyclohexene products. The major product of this elimination reaction, 4-methylcyclohexene, is produced through the E2 mechanism. However, mechanisms for the formation of the minor methylcyclohexene products are not predicted by the traditional textbook explanations of carbocation rearrangements. 1-methylcyclohexene is thought to be produced by means of an E1 mechanism in which rearrangement of a carbocation intermediate takes place. This experiment was designed to classify the hydride shifts by observing the products of this reaction using 1,2-²H-4-methylcyclohexanol. The deuterated starting materials for this reaction were prepared in our lab. Gas chromatography-mass spectroscopy and nuclear magnetic resonance analysis were used in the characterization of the products and for the classification of the pair of 1,2 hydryde shifts in tendem and of the single 1,3 di-axial hydride shift, leading to the formation of the 1-methylcyclohexene product. This is useful to know when trying to predict the products of reactions in which intermolecular rearrangements occur during carbocation intermediates.

It is well known that mammals contain several types of phospholipase A2. The cytosolic phospholipases A2 (cPLA₂s) are one type, and are composed of six enzymes: cPLA₂alpha, cPLA₂beta, cPLA₂gamma, cPLA₂delta, cPLA₂epsilon, and cPLA₂zeta. There has been significant interest in the cPLA₂alpha isoform because of the enzyme's 10 fold preference for the hydrolysis at the sn-2 position of the glycerol backbone in phospholipids, resulting in the liberation of arachidonic acid. Arachidonic acid serves as a precursor for several highly regulated inflammatory mediators that play an important role in asthma, atherosclerosis, and arthritis. To address these problems, inhibitors that target cPLA₂alpha have been developed to serve as anti-inflammatory therapeutics. Wyeth pharmaceuticals has released a class of indole inhibitors that inhibit cPLA₂zeta at <10 nM IC₅₀. However, a recent study has shown that in cPLA₂alpha^-/- stimulated lung fibroblasts arachidonic acid production is lessened but still pressent. cPLA₂zeta has been identified as the other enzyme involved in the release of arachidonic acid. Consequently, my research project is to develop a selective and potent inhibitor of the cPLA₂zeta isoform. Our synthetic strategy is to modify the scaffold of Wyeth's cPLA₂alpha inhibitor. Analysis of the structure-activity relationships and 3D molecular modeling has revealed 4 different places on the scaffold to introduce substitutions. To date, we have generated and assayed over 20 inhibitors, with many more in progress. These inhibitors display low nanomolar potency, but are not selective for cPLA₂zeta. Our main focus is to increase the selectivity of our inhibitors towards cPLA₂zeta in order to further regulate and understand cPLA₂zeta's role in arachidonic acid production. 

Single molecule microscopy techniques make it possible to observe the fluorescence of individual dye molecules. One observation previously obscured in ensemble measurements is fluorescence intermittency, where molecules undergo prolonged non-emissive periods, as well as other intermediate emissive states. We are trying to identify the photochemical processes that cause these fluctuations in intensity. The fluorescence of dye molecules can be affected by the environment in which they are immersed, specifically the substrate they are in. The polymer polyvinylidene fluoride (PVDF) is of special interest because of its ferroelectric properties, which allows polarization of domains in the polymer. I have been exploring procedures to make PVDF films with a high degree of domain polarization. Using infrared (IR) spectroscopy, I have characterized the percentage of domain polarization in these films. Future investigation is still needed though to understand how PVDF will act as a substrate and what influences it will have on fluorescent organic dyes. An expanded knowledge of organic materials is essential for the design of photochemically stable devices. Based on organic electronics, these new devices will be greener alternatives to semiconductor technologies.

Surface plasmons of metal nanoparticles have been the source of much scientific study over the last decade due to their immediate and significant applications in biosensing, surface-enhanced Raman Specroscopy (SERS), and light absorption engineering in semiconductor nanodevices. Surface plasmons can be generated by high-energy electrons coupling with natural plasmonic resonances of a nanometal’s electron cloud. An abundant source of such relativistic electrons can be found in common electron energy-loss spectroscopy (EELS) experiment, in which surface plasmons generated by the experiment can further couple with plasmons of other nearby nanoparticles, giving rise to “hot spots” with very strong electric fields. Often these hot spots can magnify an incident electric field over 100-fold, giving rise to many of the applications mentioned previously. This work aims to produce a computational model that computes plasmon excitation due to a fast electron by using an existing Discrete Dipole Approximation (DDA) framework, and to compare theoretical results from metal nano-rods and metal nano-cubes with experimental data. Unlike experimental data, computational models are not limited by detector resolution; meaning that such a model will give significant insight into details of the EEL experiment. In this work we explore results that are higher-resolution than what is currently obtainable by modern techniques. The existence of such a model will allow researchers to obtain preliminary data before running time-consuming and expensive experiments, will allow enormous insight into the deeper physics of surface plasmons, and will give experimental results a theoretical foothold while also improving on their accuracy.

In eukaryotic organisms, ubiquitin is a small protein modifier that is attached to proteins and targets them for proteasomal degradation. In an analogous fashion, in Mycobacterium tuberculosis (Mtb), the prokaryotic ubiquitin-like protein (Pup) is conjugated to lysine side-chains of substrate proteins and targets them for degradation by the Mtb 20S proteasome. This pathway has been shown to be essential for Mtb infection in mice, and is a potential target for theraputic reseach. The enzyme PafA is responsible for attaching Pup to its substrates and has previously been shown to be essential for lethal infections by Mtb in mice. We have developed a fluorescent activity-based probe to monitor PafA activity in vitro by conjugating Fluorescein isothiocyanate (FITC) to free lysine, a known substrate of PafA. FITC-Lys demonstrates a high degree of specificity for PafA, even in the presence of cell lysates. This probe was employed to visualize PafA activity by in-gel fluorescence. It has allowed us to identify a minimal sequence of Pup, the C-terminal 26 amino acids, that is recognized by PafA. Alanine mutants of the 25th and 26th C-terminal residues demonstrate that leucines at these positions are critical for PafA interaction.

Organic photovoltaics (OPVs) are a promising low-cost option in developing renewable energies. OPVs are solar cells made from organic semiconductors instead of the more traditionally used inorganic semiconductors such as silicon. OPVs have several advantages including: low cost, ease of processing, physical flexibility, and highly tunable properties. Therefore, if the efficiency of OPVs can be increased, they could become a major, inexpensive renewable energy source. Electron-accepting materials used in OPVs have traditionally been fullerene-based due to their high electron mobility. However, fullerenes contribute little to light harvesting in an OPV as they have negligible absorption in the solar spectrum. Thus, our goal was to develop new electron-accepting materials for OPVs that absorb significantly in the solar spectrum as a means to increase light harvesting and therefore OPV efficiency. A series of novel oligomers with an oligothiophene-naphthalene diimide (NDI) structure was synthesized. All oligomers exhibited absorption in the visible region with band gaps ranging from 1.39 eV to 2.06 eV, and could therefore contribute to light harvesting in an OPV. Solution-processed solar cells using the new oligomers as the electron-acceptors showed power conversion efficiencies up to 1.5%. Overall, these new materials exhibited that non-fullerenes can function as the electron-accepting material in OPVs while contributing to light harvesting. This approach therefore shows promise for increasing OPV efficiency to make OPVs a viable, cost-effective renewable energy source.

Diluted magnetic semiconductor (DMS) technology combines the properties of a semiconductor with ferromagnetism. Nanoparticles doped with magnetic elements such as Manganese offer a prime example of this type of material. Our specific task was to analyze the effects of p-type doping with nitrogen in ZnO quantum dots (QD) of 2.4 nm in diameter. p-type doping in this material involves the replacement of an O^2- ion with an N^2- ion, which has one less electron resulting in a hole due to an empty N^2- p-orbital. We hypothesize that when p-type doping is combined with paramagnetic Mn²⁺ doping, the unpaired 3d electrons of two Mn²⁺ ions separated by an N^2- ion will adopt a ferromagnetic orientation as opposed to their traditional antiferromagnetic state. Testing for this experiment was done with the development version of Gaussian. Energy calculations within this program and further data analysis reveal information such as the total energy of each state of the system, molecular orbital data, and energy diagrams concerning the semiconductor properties of these materials. Results show that the lowest energy state occurs when the Mn²⁺ ions adopt a ferromagnetic arrangement with the N^2- hole sharing this alignment. The potential for this QD and others with similar properties is extreme as many semiconductor applications could be revolutionized by DMS's. New applications such as solar cells made of DMS's are also under consideration.

The structure and assembly of a protein determines its function and role in a biological system.  By attaching a pair of spin labels to a protein, it is possible to measure the distance between the two spin labels using double electron-electron resonance spectroscopy (DEER).  A spin label is an organic molecule with an unpaired electron.  The spin label concentration is measured using an electron paramagnetic resonance (EPR) spectrometer.  There is a positive linear relationship between the amplitude of a spectra and the concentration of spin labels.  The goal of this experiment is to develop a protocol that will accurately and reproducibly measure spin label concentration in a sample.  This is achieved by obtaining spectra for 10, 20, 50, 100, and 200 uM of TEMPO spin labels so we can determine a standard calibration curve.  By obtaining more spectra, we will be able to minimize the discrepancies of the amplitude based on the calibration curve for a given concentration.  Using the calibration curve, the number of pairs of spin labels that are attached to a protein in a given protein sample can be determined using DEER.  Establishing this protocol is important because it will allow us to monitor the labeling efficiency which is crucial for the distance measurements.

Many important enzymatic reactions require the transport of electrons to function properly. This transport is commonly achieved by passing an electron to several different residues on the peptide chain which composes the enzyme. Tryptophan, a common amino acid, participates in this electron transfer by way of an oxidized radical tryptophan intermediate. We hypothesize that hydrogen bonding characteristics have significant influence on the electron transfer behavior of tryptophan. Understanding the effects and implications of hydrogen bonding would greatly affect how we engineer enzyme structure for reactions involving this type of mechanism. Using EPR (electron paramagnetic resonance) spectroscopy, we recently discovered that the strength and position of the hydrogen bond correlates directly to shifts in the g-tensor, a proportionality constant used to describe the resonance condition of the radical electron. Using computational chemistry software, we are gathering data to better understand how g-tensors change as the geometry of the hydrogen bond is altered. Our main goal is to determine trends which describe how changing specific structural features alters the corresponding g-tensor values of the radical tryptophan. We hope these trends will allow us to understand if and how hydrogen bonding is occurring at a radical tryptophan.

DEER (double electron electron resonance) is a pulsed EPR (electron paramagnetic resonance) spectroscopy technique that is used to measure distances between unpaired electrons. DEER can be applied in structural biology to accurately characterize the structure of spin-labeled proteins, at the scale of several nanometers. EPR is commonly conducted using microwave frequencies at around 10 GHz (X-band), but spectral resolution and sensitivity can be improved by increasing the microwave frequencies to around 35 GHz (Q-band). Microwaves are concentrated on the sample of interest through the use of a resonator. Resonators developed for use with traditional continuous wave (CW) EPR experiments are designed with a high quality factor (i.e. most efficient storage of microwave energy) at a single resonance frequency. However, DEER requires a wide resonance bandwidth, which means that the quality factor of the resonator must be lowered, often at the expense of sensitivity. The goal of this project is to develop a Q-band resonant cavity for use with DEER that combines a bandwidth of 60-70 MHz with high accuracy and sensitivity. The resonator is designed using CST Microwave Studio, an electromagnetics modeling software package, to maximize its bandwidth and power conversion efficiency. A cylindrical cavity geometry is chosen due its ease of construction and simple tuning procedure. We anticipate that, after further development and testing, this initial design will serve as a platform that can be easily modified to accomodate other advanced EPR techniques.

It is a common dilemma for undergraduate students to feel like their class material is inapplicable to the real world. This project aims to enhance traditional homework assignments with problems based on current scientific literature. The current class of interest is Physical Chemistry for Biochemists I at the University of Washington, taught by Dr. Munira Khalil. I developed homework questions using journal articles that focused on concepts of thermodynamics important in biochemistry. The questions test the students’ comprehension of the article and their ability to solve quantitative problems based on research presented in the article. These questions were integrated with traditional assignments already given in this course. Dr. Khalil’s class in Fall 2011 served as a test run for the literature focused homework assignments. At the end of this course, students evaluate the homework through an online survey. These evaluations were used to adjust the homework assignments for the same course in Winter 2012. Information from both quarters of surveys gave insight into how learning about research influenced a student’s interest and performance in the class.

Over the past ten years we have analyzed a variety of plants that produce volatile oils grown in our Chemical Garden on The Evergreen State College campus. These plants lend themselves well to extraction by steam or ethereal solvents and are easily analyzed through Gas-Chromatography Mass Spectrometry (GC/MS). The plants we have focused on are garlic, St. John's Wort, hops, mints, and lavender. This poster reports on our progress towards isolating and identifying individual constituents of Devil's Club (Oplopanax horridus), a local plant with a long history of use as a medicine. We have been curious as to the best time of year to harvest the plant, as there is some debate in the herbalism community on this point. The Devil's Club was distilled at different times of the year and analyzed using GC/MS. The non volatile constituents were extracted using a number of different solvents and analyzed using Thin Layer Chromatography (TLC). This research will provide information on the effects of harvest time on constituent levels, as well as providing knowledge of the chemical make up of this plant.

Model membranes are important tools for investigating physical properties of lipid bilayers. Unfortunately, current techniques for producing giant unilamellar vesicles (GUVs) with biologically and physically relevant properties (namely: inclusion of charged lipids, encapsulation of high salt buffer, and compositional asymmetry between the inner and outer leaflets) are difficult, unreliable, and/or low throughput. We examine a method called cDICE, developed by Abkarian et al., that has the potential to address all of these issues. Our results here for charged lipids in high salt buffers are promising, whereas asymmetry has proven difficult to measure.

Electron paramagnetic resonance (EPR) spectroscopy is a technique for analyzing chemical species with unpaired electrons (spin centers). An EPR spectrum provides information on the structure of the spin center as well as the total number of spin centers in a sample. The ability to use EPR to quantitatively determine the spin concentration of a sample is contingent on accurate comparison to a known concentration standard. For biological systems, a commonly used standard is a complex of copper(II) and EDTA (ethylenediaminetetraacetic acid); however, the presence of multiple species of copper-ligand complexes results in an EPR spectrum with overlapping signals that are not easily quantifiable. In an effort to develop a more accurate single-species standard, the coordination of EDTA to copper(II) as a function of acidity and its effect on the EPR spectrum is explored. Analysis of these spectra shows a single species of a copper(II) EDTA complex at pH three, with potential for use as a spin concentration standard.