Physical Sciences and Mathematics Commons^™

Fluorescent Lifetimes Of Oils And Oil Distillates In Artificial Seawater, Warren J. De Bruyn, Aaron Harrison, Emma Kocik, Dhivya Manickam, Ethan Truong, Catherine D. Clark

Chemistry Faculty and Staff Publications

Supporting data associated with a study of the fluorescent lifetimes of eleven oil and oil distillates in artificial seawater are given. The table is a list of the oil and oil distillate names along with the associated sample numbers used in this study and their API densities.

The excel data file contains lifetimes as a function of emission wavelength for different oils and oil products shown by sample number. The lifetimes were measured with a Horiba DeltaFlex Lifetime System that uses pulsed diode light sources. There is a separate sheet for each excitation source: 268, 285 and 348 nm. Lifetimes …

Supporting Data For Impact Of The Macrophyte Nymphaea Odorata (Lily Pads) On Dissolved Organic Matter (Dom) In A Lake, Kyle Juetten, Warren J. De Bruyn, Zachary Landram, Aaron Harrison, Angela Strecker, Catherine D. Clark

Chemistry Faculty and Staff Publications

(Files are available for download below.)

This is supporting data for a publication on the role of lily pads in contributing to the dissolved organic matter pool in Lake Louise, a small lake in the Pacific Northwest region of the USA. Specifically, this data includes the absorbance and fluorescence spectra of the Lake Louise water samples (taken weekly over the course of 2018). These files include large spreadsheets with raw and corrected absorbance and fluorescence intensity data as a function of wavelength, as well as the raw and corrected absorbance and fluorescence 3D excitation-emission matrix spectra (EEMs). These files are …

Supporting Information For Chromophoric Dissolved Organic Matter (Cdom) Across An Elevational Gradient From Sea Level To Mountain Lakes In The Pacific Northwest, Kyle Juetten, Angela L. Strecker, Aaron Harrison, Zachary Landram, Warren J. De Bruyn, Catherine D. Clark

Chemistry Faculty and Staff Publications

This dataset is in support of Juetten et al., which has been submitted to the Journal of Geophysical Research Biogeosciences for consideration for publication. Chromophoric dissolved organic matter (CDOM) in lakes across elevation gradients is a complex function of topography, climate, vegetation coverage, land use, and lake properties. To examine sources and processing of CDOM from sea level to mountain lakes (3 to 1574 m), we measured CDOM optical properties, lake characteristics, and water quality parameters in 62 freshwater lakes in the Pacific Northwest, USA. Higher elevation lakes had lower dissolved organic carbon (DOC) and absorbance. These lakes had higher …

Stacked Antiaromatic Porphyrins, Ryo Nozawa, Hiroko Tanaka, Won-Young Cha, Yongseok Hong, Ichiro Hisaki, Soji Shimizu, Ji-Young Shin, Tim Kowalczyk, Stephan Irle, Dongho Kim, Hiroshi Shinokubo

Chemistry Faculty and Staff Publications

Aromaticity is a key concept in organic chemistry. Even though this concept has already been theoretically extrapolated to three dimensions, it usually still remains restricted to planar molecules in organic chemistry textbooks. Stacking of antiaromatic π-systems has been proposed to induce three-dimensional aromaticity as a result of strong frontier orbital interactions. However, experimental evidence to support this prediction still remains elusive so far. Here we report that close stacking of antiaromatic porphyrins diminishes their inherent antiaromaticity in the solid state as well as in solution. The antiaromatic stacking furthermore allows a delocalization of the π-electrons, which enhances the two-photon absorption …

Acene-Linked Covalent Organic Frameworks As Candidate Materials For Singlet Fission, Viktor Laszlo, Tim Kowalczyk

Chemistry Faculty and Staff Publications

Two-dimensional covalent organic frameworks (COFs) are a versatile class of porous materials that can be tailored for solar energy conversion applications through the incorporation of organic chromophores as linker units. In this work we examine whether such COFs can be engineered to support singlet fission (SF), the generation of two triplet excitons from a single photoexcitation. We simulate the structural and electronic properties of a series of COFs possessing embedded polyacene linkers from benzene through pentacene. Detailed electronic structure calculations suggest that necessary conditions on the energy and electronic coupling for SF can be met with COF architectures closely related …

Structure Of The Human Factor Viii C2 Domain In Complex With The 3e6 Inhibitory Antibody., P. Clint Spiegel, Michelle E. Wuerth, Rebecca K. Cragerud

Chemistry Faculty and Staff Publications

Blood coagulation factor VIII is a glycoprotein cofactor that is essential for the intrinsic pathway of the blood coagulation cascade. Inhibitory antibodies arise either spontaneously or in response to therapeutic infusion of functional factor VIII into hemophilia A patients, many of which are specific to the factor VIII C2 domain. The immune response is largely parsed into “classical” and “non-classical” inhibitory antibodies, which bind to opposing faces cooperatively. In this study, the 2.61Å resolution structure of the C2 domain in complex with the antigen-binding fragment of the 3E6 classical inhibitory antibody is reported. The binding interface is largely conserved when …

The 1.7 Å X-Ray Crystal Structure Of The Porcine Factor Viii C2 Domain And Binding Analysis To Anti-Human C2 Domain Antibodies And Phospholipid Surfaces, P. Clint Spiegel, Caileen M. Brison, Steven M. Mullen, Michelle E. Wuerth, Kira Podolsky, Matthew Cook, Jacob A. Herman, Justin D. Walter, Shannon L. Meeks

Chemistry Faculty and Staff Publications

The factor VIII C2 domain is essential for binding to activated platelet surfaces as well as the cofactor activity of factor VIII in blood coagulation. Inhibitory antibodies against the C2 domain commonly develop following factor VIII replacement therapy for hemophilia A patients, or they may spontaneously arise in cases of acquired hemophilia. Porcine factor VIII is an effective therapeutic for hemophilia patients with inhibitor due to its low cross-reactivity; however, the molecular basis for this behavior is poorly understood. In this study, the X-ray crystal structure of the porcine factor VIII C2 domain was determined, and superposition of the human …

Characterization And Solution Structure Of The Factor Viii C2 Domain In A Ternary Complex With Classical And Non-Classical Inhibitor Antibodies, P. Clint Spiegel, Justin D. Walter, Rachel Werther, Maria S. Polozova, Julie Pohlman, John F. Healey, Shannon L. Meeks, Pete Lollar

Chemistry Faculty and Staff Publications

The most significant complication for patients with severe cases of congenital or acquired hemophilia A is the development of inhibitor antibodies against coagulation factor VIII (fVIII). The C2 domain of fVIII is a significant antigenic target of anti-fVIII antibodies. Here, we have utilized small angle x-ray scattering (SAXS) and biochemical techniques to characterize interactions between two different classes of anti-C2 domain inhibitor antibodies and the isolated C2 domain. Multiple assays indicated that antibodies 3E6 and G99 bind independently to the fVIII C2 domain and can form a stable ternary complex. SAXS-derived numerical estimates of dimensional parameters for all studied complexes …

Organic-Vapor-Liquid-Solid Deposition With An Impinging Gas Jet, Daniel W. (Daniel Wainwright) Shaw, Kevin A. (Kevin Anthony) Bufkin, Alexandr A. Baronov, Brad L. Johnson, David L. Patrick

Chemistry Faculty and Staff Publications

A method for rapid, mass-efficient deposition of highly crystalline organic films under near ambient conditions of pressure and temperature is reported based on delivery of an organic precursor via an impinging gas jet to a substrate coated by a thin liquid solvent layer. Films of the organic semiconductor tetracene were deposited by sublimation into a flow of argon carrier gas directed at an indium-tin-oxide/glass substrate coated by a thin layer of bis(2-ethylhexyl)sebecate, and growth was followed in situ with optical microscopy. A fluid dynamics model is applied to account for the gas phase transport and aggregation, and the results compared …

Thiostrepton Inhibits Stable 70s Ribosome Binding And Ribosome-Dependent Gtpase Activation Of Elongation Factor G And Elongation Factor 4, P. Clint Spiegel, Justin D. Walter, Margaret Hunter, Melanie Cobb, Geoff Traeger

Chemistry Faculty and Staff Publications

Thiostrepton, a macrocyclic thiopeptide antibiotic, inhibits prokaryotic translation by interfering with the function of elongation factor G (EF-G). Here, we have used 70S ribosome binding and GTP hydrolysis assays to study the effects of thiostrepton on EF-G and a newly described translation factor, elongation factor 4 (EF4). In the presence of thiostrepton, ribosome-dependent GTP hydrolysis is inhibited for both EF-G and EF4, with IC(50) values equivalent tothe 70S ribosome concentration (0.15 μM). Further studies indicate the mode of thiostrepton inhibition is to abrogate the stable bind- ing of EF-G and EF4 to the 70S ribosome. In support of this model, …

Simulations Of Luminescent Solar Concentrators: Effects Of Polarization And Fluorophore Alignment, Stephen Mcdowall, Brad L. Johnson, David L. Patrick

Chemistry Faculty and Staff Publications

We model the effects of dye molecule alignment on the collection efficiency of luminescent solar concentrators (LSCs). A Monte Carlo model for photontransport in LSC’s is derived and utilized, which incorporates the effects of fluorescent-dye-molecular alignment and the subsequent control over absorption, emission, and propagation properties. We focus on the effects of molecular alignment statistics on photon absorption and subsequent emission, including polarization and propagation direction imparted by dipole direction, to model device light-capture efficiency, defined as the ratio of the amount of light reaching particular slab edges to that incident on a face. We find that modest control of …

Expression, Purification, And Analysis Of Unknown Translation Factors From Escherichia Coli: A Synthesis Approach, Justin D. Walter, Peter Littlefield, Scott P. Delbecq, Gerry Prody, P. Clint Spiegel

Chemistry Faculty and Staff Publications

New approaches are currently being developed to expose biochemistry and molecular biology undergraduates to a more interactive learning environment. Here, we propose a unique project-based laboratory module, which incorporates exposure to biophysical chemistry approaches to address problems in protein chemistry. Each of the experiments described herein contributes to the stepwise process of isolating, identifying, and analyzing a protein involved in a central biological process, prokaryotic translation. Students are provided with expression plasmids that harbor an unknown translation factor, and it is their charge to complete a series of experiments that will allow them to develop hypotheses for discovering the identity …

Elongation Factor G Stabilizes The Hybrid-State Conformation Of The 70s Ribosome, P. Clint Spiegel, Dmitri N. Ermolenko, Harry F. Noller

Chemistry Faculty and Staff Publications

Following peptide bond formation, transfer RNAs (tRNAs) and messenger RNA (mRNA) are translocated through the ribosome, a process catalyzed by elongation factor EF-G. Here, we have used a combination of chemical footprinting, peptidyl transferase activity assays, and mRNA toeprinting to monitor the effects of EF-G on the positions of tRNA and mRNA relative to the A, P, and E sites of the ribosome in the presence of GTP, GDP, GDPNP, and fusidic acid. Chemical footprinting experiments show that binding of EF-G in the presence of the non-hydrolyzable GTP analog GDPNP or GDP·fusidic acid induces movement of a deacylated tRNA from …

Getting Organized At The Nanoscale With Thermotropic Liquid Crystal Solvents, David L. Patrick, F. Scott Wilkinson, Tiffany L. Fegurgur

Chemistry Faculty and Staff Publications

This paper summarizes recent progress toward an emerging, unconventional application of thermotropic liquid crystals (LCs) - their use as solvents for controlling the assembly of non-LC nanoscale building blocks. LCs offer a number of potential advantages compared to conventional isotropic solvents, including the ability to influence building block orientation and other structural properties. Strategies are reviewed for the exploitation of LC media to engineer order in a range of systems, including oriented organic monolayers, chiral films, and nanometer-scale particles.

Structural And Biochemical Analyses Of Dna And Rna Binding By A Bifunctional Homing Endonuclease And Group I Intron Splicing Factor, Jill M. Bolduc, P. Clint Spiegel, Pivali Chatterjee, Kristina L. Brady, Maureen E. Downing, Mark G. Caprara, Richard B. Waring, Barry L. Stoddard

Chemistry Faculty and Staff Publications

We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 Å resolution. The structure demonstrates the remarkable structural conservation of the (3-sheet DNA-binding motif between highly divergent enzyme subfamilies. DNA recognition by I-AniI was further studied using nucleoside deletion and DMS modification interference analyses. Correlation of these results with the crystal structure provides information on the relative importance of individual nucleotide contacts for DNA recognition. Alignment and modeling of two homologous maturases reveals conserved basic surface residues, distant …

Formation Of Uniaxial Molecular Films By Liquid-Crystal Imprinting In A Magnetic Field, Joseph D. Mougous, Andrew J. Brackley, Katherine Foland, Robert T. Baker, David L. Patrick

Chemistry Faculty and Staff Publications

Scanning tunneling microscopy was used to study molecular order in monolayer organic films formed by solution-phase growth from thermotropic liquid crystal solvents. The films develop macroscopically uniaxial alignment, with adlayer orientation controlled by an external magnetic field through interactions mediated by the liquid crystal. Results are presented for two films deposited from nematic and smectic- A solvents, along with a discussion of the alignment mechanism.