Chemistry Commons^™

A Dna-Conjugated Small Molecule Catalyst Enzyme Mimic For Site-Selective Ester Hydrolysis, Moira L. Flanagan, A. Emilia Arguello, Drew E. Colman, Jiyeon Kim, Jesse N. Krejci, Shimu Liu, Yueyu Yao, Yu Zhang, David J. Gorin

Chemistry: Faculty Publications

The challenge of site-selectivity must be overcome in many chemical research contexts, including selective functionalization in complex natural products and labeling of one biomolecule in a living system. Synthetic catalysts incorporating molecular recognition domains can mimic naturally-occurring enzymes to direct a chemical reaction to a particular instance of a functional group. We propose that DNA-conjugated small molecule catalysts (DCats), prepared by tethering a small molecule catalyst to a DNA aptamer, are a promising class of reagents for site-selective transformations. Specifically, a DNA-imidazole conjugate able to increase the rate of ester hydrolysis in a target ester by >100-fold compared with equimolar …

Detection And Characterization Of The Tin Dihydride (Snh2 And Snd2) Molecule In The Gas Phase, Tony C. Smith, Dennis J. Clouthier

Chemistry Faculty Publications

The SnH₂ and SnD₂ molecules have been detected for the first time in the gas phase by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the ùB₁–X̃¹A₁ electronic transition. These reactive species were prepared in a pulsed electric discharge jet using (CH₃)₄Sn or SnH₄/SnD₄ precursors diluted in high pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state energy levels were measured from single rovibronic level emission spectra. The LIF spectrum of SnD_{2 …}

Zb716, A Steroidal Selective Estrogen Receptor Degrader (Serd), Is Orally Efficacious In Blocking Tumor Growth In Mouse Xenograft Models., S. Guo, Changde Zhang, M. Bratton, M Mottamal, Jiawang Liu, Peng Ma, P. Ma, Shilong Zheng

Faculty and Staff Publications

Advances in oral SERDs development so far have been confined to nonsteroidal molecules such as those containing a cinnamic acid moiety, which are in earlystage clinical evaluation. ZB716 was previously reported as an orally bioavailable SERD structurally analogous to fulvestrant. In this study, we examined the binding details of ZB716 to the estrogen receptor alpha (ERα) by computer modeling to reveal its interactions with the ligand binding domain as a steroidal molecule. We also found that ZB716 modulates ERα-coregulator interactions in nearly identical manner to fulvestrant. The ability of ZB716 to inhibit cell growth and downregulate ER expression in endocrine …

Structural Tuning Of Boron Difluoride Formazanate Electrochemiluminescence Mediated By Tri-N-Propylamine, Mahdi Hesari, Stephanie M. Barbon, Rayner B. Mendes, Viktor N. Staroverov, Zhifeng Ding, Joe Gilroy

Chemistry Publications

Electrochemistry and electrogenerated chemiluminescence (ECL) of boron difluoride formazanate complexes bearing p-methoxyphenyl N-substituents were studied experimentally and computationally. It was shown that the substituents at the 3-position (R³) of the formazanate backbone play a critical role in the electrochemistry and ECL of the complexes in the presence of tri-n-propylamine (TPrA). The ECL emission of 1a (R³ = cyano), 1b (R³ = phenyl), and 1c (R³ = p-C₆H₄OMe) occurred at peak wavelengths of 724 nm (1.71 eV), 704 nm (1.76 eV), and 723 nm (1.71 eV), consistent …

Flavin-N5 Covalent Intermediate In A Nonredox Dehalogenation Reaction Catalyzed By An Atypical Flavoenzyme, Yumin Dai, Karina Kizjakina, Ashley C. Campbell, David A. Korasick, John J. Tanner, Pablo Sobrado

Chemistry Faculty Research & Creative Works

The flavin-dependent enzyme 2-haloacrylate hydratase (2-HAH) catalyzes the conversion of 2-chloroacrylate, a major component in the manufacture of acrylic polymers, to pyruvate. The enzyme was expressed in Escherichia coli, purified, and characterized. 2-HAH was shown to be monomeric in solution and contained a non-covalent, yet tightly bound, flavin adenine dinucleotide (FAD). Although the catalyzed reaction was redox-neutral, 2-HAH was active only in the reduced state. A covalent flavin-substrate intermediate, consistent with the flavin-acrylate iminium ion, was trapped with cyanoborohydride and characterized by mass spectrometry. Small-angle X-ray scattering was consistent with 2-HAH belonging to the succinate dehydrogenase/fumarate reductase family of flavoproteins. …

The Van Der Waals Fluid's Liquid Vapor Coexistence Locus, Carl W. David

Chemistry Education Materials

The liquid vapor coexistence locus is plotted from the analytical solution to the Maxwell construction for the van der Waals fluid.

Ruthenium Complexes Of The General Formula [Rucl 2 (Phox) 2 ] As Precatalysts In Propargylic Substitution Reactions, Negar Jourabchian, Kellsie Jurkowski, Eike Bauer

Chemistry & Biochemistry Faculty Works

After activation by chloride abstraction utilizing NaBArF as an activator (BArF = tetrakis(3,5-bis(trifluoromethyl)phenyl)borate), a complex of the general formula [RuCl2 (PHOX)2 ] was utilized as a catalyst in propargylic substitution reactions, where PHOX is a phosphinooxazoline ligand. Oxygen and nitrogen-centered nucleophiles could be employed in the substitution of a propargylic acetate to obtain the corresponding propargylic substitution products in 87% to 9% isolated yields (45 °C, 16 h reaction time, toluene solvent, 1-2 mol% catalyst loading, 1-2 mol% activator).

Analysis Of Veterinary Drug Residues In Imported And Domestic Crawfish Using Liquid Chromatography—Mass Spectrometry, Emily Kate Wall

LSU Master's Theses

Aquaculture production has greatly increased over the past few decades, and will continue to grow as the world fisheries become overfished and demand for seafood increases. With increased production comes more intense cultivation methods and heavy use of formulated feeds that may contain veterinary drug residues. Currently no antibiotics are allowed in the U.S. for crawfish aquaculture; yet, detectable levels of various antibiotics have been found in imported seafood samples.The FDA is responsible for testing aquaculture products entering the United States, but only has the capabilities to test a minimal amount of those imports. Additionally, for crawfish there is only …

E‑Cigarette Airflow Rate Modulates Toxicant Profiles And Can Lead To Concerning Levels Of Solvent Consumption, Tetiana Korzun, Maryana Lazurko, Tetiana Korzun, Ian Munhenzva, Kelley Barsanti, Yilin Huang, R. Paul Jensen, Jorge O. Escobedo, Wentai Luo, David H. Peyton, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Electronic cigarettes enabling enhanced airflow have grown in popularity in recent years. The objective of this study is to show that flow rates modulate the levels of specific aerosol toxicants produced in electronic cigarettes. Flow rates used in various laboratory investigations involving e-cigarettes have varied widely to date, and can thus promote interlaboratory variability in aerosol product profiles. The thermal decomposition of hydroxyacetone and glycolaldehyde is less favorable at lower temperatures, supporting the observations of these products at higher flow rates/lower heating coil temperatures. Higher temperatures promote the formation of acetaldehyde from hydroxyacetone and formaldehyde from both hydroxyacetone and glycolaldehyde. …

Spermidine-Regulated Biosynthesis Of Heat-Stable Antifungal Factor (Hsaf) In Lysobacter Enzymogenes Oh11, Yuan Chen, Fengquan Liu, Liangcheng Du

Liangcheng Du Publications

Heat-Stable Antifungal Factor (HSAF) and its analogs are antifungal natural products produced by the biocontrol agent Lysobacter enzymogenes. The production of HSAF is greatly influenced by environmental stimuli and nutrients, but the underlying molecular mechanism is mostly unclear. Here, we found that HSAF production in L. enzymogenes OH11 is strictly controlled by spermidine, which is the most prevalent triamine in bacteria. When added into OH11 cultures, spermidine regulated the production of HSAF and analogs in a concentration-dependent manner. To verify the role of spermidine, we deleted LeSDC and LeADC genes, encoding S-adenosylmethionine decarboxylase and arginine decarboxylase, respectively, that are the …

Structural Evolution Of Gold-Doped Bismuth Clusters AubiN– (N = 4−8), Seema Pande, Tian Jian, Navneet S. Khetrapal, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The structures of gold-doped bismuth clusters, AuBi_n⁻ (n = 4−8), are investigated through a joint photoelectron spectroscopy and density functional theory (DFT) study. Well-resolved photoelectron spectra are obtained at several photon energies. Global minimum searches coupled with DFT calculations yield low-lying structures, whose relative energies are further evaluated by single-point energy calculations at the CCSD(T) level of theory. Vertical detachment energies are calculated with the inclusion of spin−orbit effects to compare with the experimental data. Three-dimensional structures are found to be dominant in this size range, while a planar low-lying isomer is observed only for AuBi_{4 …}

Electrokinetic Flow Of Aqueous Electrolyte In Amorphous Silica Nanotubes, Chris D. Daub, Natalie Cann, D. Bratko, Alenka Luzar

Chemistry Publications

We study the pressure-driven flow of aqueous NaCl in amorphous silica nanotubes using nonequilibrium molecular dynamics simulations featuring both polarizable and non-polarizable molecular models. Different pressures, electrolyte concentrations and pore sizes are examined. Our results indicate a flow that deviates considerably from the predictions of Poiseuille fluid mechanics. Due to preferential adsorption of the different ionic species by surface SiO! or SiOH groups, we find that a significant electric current is generated, but with opposite polarities using polarizable vs. fixed charge models for water and ions, emphasizing the need for careful parameterization in such complex systems. We also examine the …

Curvature Dependence Of The Effect Of Ionic Functionalization On The Attraction Among Nanoparticles In Dispersion, B. Shadrack Jabes, D. Bratko, Alenka Luzar

Chemistry Publications

Solubilization of nanoparticles facilitates nanomaterial processing and enables new applications. An effective method to improve dispersibility in water is provided by ionic functionalization.We explore how the necessary extent of functionalization depends on the particle geometry. Using molecular dynamics/umbrella sampling simulations, we determine the effect of the solute curvature on solventaveraged interactions among ionizing graphitic nanoparticles in aqueous dispersion. We tune the hydrophilicity of molecular-brush coated fullerenes, carbon nanotubes, and graphane platelets by gradually replacing a fraction of the methyl end groups of the alkyl coating by the ionizing –COOK or –NH3Cl groups. To assess the change in nanoparticles’ dispersibility in …

High-Resolution Infrared Spectroscopy Of The V18 And V26 Bands Of Trans-1,3-Pentadiene, Minh Tran

Chemistry Honors Papers

A high-resolution absorbance spectrum of trans-1,3-pentadiene was obtained using a quantum cascade laser-based spectrometer. All spectra were calibrated using a methanol reference spectrum generated by SpectraPlot using the HITRAN Database. The frequency uncertainty is estimated as 0.002 cm^-1. Two peaks at 976.69 and 1003.50 cm^-1 were assigned to ν₁₈ and ν₂₆ bands respectively. Supporting calculations of the anharmonic vibrational frequencies and rotational constants were performed at the MP2/cc-pVTZ level of theory. Two specific motions were assigned to the vibrational modes ν₁₈ and ν₂₆. A spectrum of the ν₂₆ band was …

High-Resolution Infrared Spectroscopy Of The V23 And V22 Vibrational Bands Of Methyl Vinyl Ketone, Michael Iranpour

Chemistry Honors Papers

The high-resolution Infrared spectrum of methyl vinyl ketone (C4H6O) has been acquired in the region containing the v₂₂ and v₂₃ bands near 987 cm^-1 and 1001cm^-1, respectively, using a quantum cascade laser-based spectrometer. All acquired spectra underwent frequency calibrations that will prove useful during future atmospheric measurements of methyl vinyl ketone. Anharmonic calculations were performed at the MP2/ccp-pVTZ level of theory to obtain the vibrational frequencies and the excited state rotational constants of cis-methyl vinyl ketone. These calculations supported the assignment of the Q-branch features at 1001.031 and 987.592 cm^-1 to the v …

Synthesis, Structure And Reactivity Of Heterobimetallic Complexes For Small Molecule Activation And Catalysis, Amelie Nicolay

Link Foundation Energy Fellowship Reports

Society remains tied to fossil fuels while increasing pressure on the climate suggests a transition to renewable energy resources. However, the efficiency of processes enabling such a transition has considerable room for improvement. Relevantly, natural systems have evolved enzymes that enable a very efficient conversion of small molecules such as H2, CO and CO2,1 and perform these conversions more selectively and under milder conditions than current industrial processes. Many of these enzymes rely on multimetallic, and often heterometallic, active sites of abundant transition metals, for example in [NiFe] or [CuMo] carbon monoxide dehydrogenases.2 In addition, close proximity between metal centers …

Biomimetic Macromolecules For Macrophage Targeting And Modulation, Joshua Whited

ETD Archive

Carbohydrate recognition has come to the forefront of biological aiming to uncover the mechanisms of physiological and pathological processes. Cell surface glycans are involved in processes including cellular adhesion, cell signaling, and immune response. A new approach for profiling cell surface glycans has great potential for a wide range of biomedical applications. Lectins have been conventionally used to determine the structure and function of glycoproteins, however, their numbers are still restricted compared to the number of glycan structures. Boronic acid has proven a remarkable small molecule capable of binding diols in aqueous solution. This interaction indicates boronic acid derived molecules …

Oxidation Of Ferrocene Derivatives With Dibenzoyl Peroxide And Meta-Chloroperoxybenzoic Acid, Jos M. Halstead

ETD Archive

The chemical oxidation of ferrocene and related derivatives (RFc) via organic peroxides solvated in acetonitrile was studied spectrophotometrically by varying concentration and temperature to determine kinetics and activation parameters. The reaction rate of ferrocene with dibenzoyl peroxide depends strongly on whether electron withdrawing or donating substituents are present. Products were analyzed and the effect of different solvents on reactivity were studied. The rate law was first order in both oxidant and reductant, and steric and solvent effects are consistent with outer sphere electron transfer (ET) as the rate-controlling step. B3YLP calculations were conducted to determine reorganization energies using Marcus theory …

Digital Design And Fabrication Of An Atmospheric Aerosol Impactor Using A Formlabs Form 2 Sla 3d Printer, Stefan Vincent

CUP Undergraduate Research

Atmospheric aerosol (AA) particles are defined as solid or liquid particles suspended in the air. AA particles smaller than 10 μm in diameter are small enough to bypass the upper respiratory system which functions as a filter for harmful substances entering the lungs. AA particles can be collected using a device called an aerosol impactor. After collection, the particles can be analyzed offline for chemical composition using a variety of analytical techniques. The weight of a commercially manufactured AA particle impactor poses an issue if attached to a mobile AA particle sampling platform such as an unmanned aerial vehicle (UAV). …

Audiobook Of A World From Dust, Ben Mcfarland

Faculty Open Access Books

A World From Dust is a popular science book about the chemical sequence behind the evolution of creation.

It’s about how geology, biology, and chemistry worked together over billions of years, providing a hidden order under the random flow of genes and lava and water.

It’s about the chemical job that each element takes up in life, and how that job is predictable from its place on the periodic table.

It can be told as the story of many elements: how iron and sulfur gave a spark of life; how manganese was a key for oxygen; and how copper and …

X-Ray Spectroscopy Of Nio And Nanodiamond At Ssrl, Jackson Earl

STAR Program Research Presentations

The first aspect of this research project focuses on investigating the surface chemistry of high pressure high temperature (HPHT) nanodiamond by using X-ray spectroscopy techniques at the Stanford Synchrotron Radiation Lightsource (SSRL). HPHT nanodiamond is being examined as a biosensing tool for electric field detection based on the fluorescent nitrogen vacancy center hosted within diamond. With use of the transition edge spectrometer (TES), a state-of-the-art X-ray fluorescence detector, we are able to probe the surface and bulk properties of diamond. Preliminary work using density functional theory (DFT) has been done, offering insight into ground state energies and electronic structure. DFT …

Probing The Surface Of Nanodiamonds At Stanford Synchrotron Radiation Lightsource And San Jose State University, Jocelyn Valenzuela, Jackson Earl, Cynthia Melendrez, Grace Jeanpierre, Dennis Nordlund, Abraham Wolcott

STAR Program Research Presentations

The nitrogen-vacancy center in diamond is a promising tool in oncology, electric field sensing, and quantum cryptography. High-pressure high-temperature (HPHT) nanodiamonds (NDs) are prime contenders for these fields because they host nitrogen-vacancy centers (NVCs) which are applicable towards cancer detection and electric and magnetic field sensing. However, to apply HPHT NDs to these fields, the surface must first be functionalized—a difficult process because of the inert nature of the surface. The project at hand focuses on surface modification of HPHT NDs with amines to allow for further bioconjugation of small molecules and plasmonic shells. This is done via liquid-phase chemistry …

Large Effect Quantitative Trait Loci For Salicinoid Phenolic Glycosides In Populus: Implications For Gene Discovery, Scott A. Woolbright, Brian J. Rehill, Richard L. Lindroth, Stephen P. Difazio, Gregory D. Martinsen, Matthew S. Zinkgraf, Gerard J. Allan, Paul Keim, Thomas G. Whitham

Faculty & Staff Scholarship

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full-sib population of hybrid cottonwoods (Populus spp.) to search for quanti- tative trait loci (QTL) for the SPGs salicortin and HCH-salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH-salicortin (R2 = .52) that colocated with a …

Sulfur Resistance Of Ce-Mn/Tio2 Catalysts For Low-Temperature Nh3–Scr, Quan Xu, Wenjing Yang, Jason Street, Yan Lou

Faculty & Staff Scholarship

Ce-Mn/TiO2 catalyst prepared using a simple impregnation method demonstrated a better low-temperature selective catalytic reduction of NO with NH3 (NH3–SCR) activity in comparison with the sol-gel method. The Ce-Mn/TiO2 catalyst loading with 20% Ce had the best low-temperature activity and achieved a NO conversion rate higher than 90% at 140–260°C with a 99.7% NO conversion rate at 180°C. The Ce-Mn/TiO2 catalyst only had a 6% NO conversion rate decrease after 100ppm of SO2 was added to the stream. When SO2 was removed from the stream, the catalyst was able to recover completely. The crystal structure, morphology, textural properties and valence …

Combining Semi-Synthesis With Plant And Microbial Biocatalysis: New Frontiers In Producing A Chemical Arsenal Against Cancer†, Samuel Gary, Janet Adegboye, Brian Popp, Jean-Christophe Cocuron, Brooklyn Woodrum, Nik Kovinich

Faculty & Staff Scholarship

Natural products (NPs) that exhibit anticancer activities are frequently not potent enough to be used clinically as therapeutics. Semi-synthesis and metabolic engineering are promising approaches for producing more efficacious derivatives of anticancer NPs (ACNPs), but each technique alone can be inefficient at obtaining specific ACNP derivatives that may be suspected to have enhanced anticancer activity. Here, we demonstrate that the methods of semi-synthesis and biocatalysis can be used as modules in succession and in different combinations to produce 6,8-dibromogenkwanin, a derivative of the ACNP apigenin. Further, we demonstrated that soybean seed coats can be used as a biocatalyst to convert …

Chemical Applications Of Transition Metal Nanomaterials: Nanoscale Toughening Mechanism Of Molybdenum Disulfide-Epoxy Nanocomposites And Mammalian Toxicity Of Silver Nanoparticles, John David Ryan

Browse all Theses and Dissertations

The emerging world of nanotechnology has been of great interest within the last few decades. In this regard, nanomaterials have since been implemented in a number of commercial applications including: aerospace technology, coatings, sensors, and biomedical technology. This work aimed to elucidate upon the applications of transition metal nanomaterials in two separate experimental studies. The first of these studies involved the investigation of two-dimensional molybdenum disulfide (MoS2) nanoparticles, and their role in the toughening mechanism of epoxy composites. Two separate exfoliation techniques were implanted to target the influence surface chemistry of the nanomaterial and solvent quality had on the bulk …

Metabolic And Transcriptional Modules Independently Diversify Plasma Cell Lifespan And Function, Wing Y. Lam, Arijita Jash, Cong-Hui Yao, Lucas D'Souza, Rachel Wong, Ryan M. Nunley, Gordon P. Meares, Gary J. Patti, Deepta Bhattacharya

Faculty & Staff Scholarship

Plasma cell survival and the consequent duration of immunity vary widely with infection or vaccination. Using fluorescent glucose analog uptake, we defined multiple developmentally independent mouse plasma cell populations with varying life- spans. Long-lived plasma cells imported more fluo- rescent glucose analog, expressed higher surface levels of the amino acid transporter CD98, and had more autophagosome mass than did short-lived cells. Low amino acid concentrations triggered re- ductions in both antibody secretion and mitochon- drial respiration, especially by short-lived plasma cells. To explain these observations, we found that glutamine was used for both mitochondrial respira- tion and anaplerotic reactions, yielding …

Lesson Plan: How Sweet It Is… The Effects Of Sucrose (Table Sugar) On The Body, Sheryl Hemkin

1. Sucrose

No abstract provided.

Structure Of The Ambrosia Beetle (Coleoptera: Curculionidae) Mycangia Revealed Through Micro-Computed Tomography, You Li, Yongying Ruan, Matthew T. Kasson, Edward L. Stanley, Conrad P.D.T Gillett, Andrew J. Johnson, Mengna Zhang, Jiri Hulcr

Faculty & Staff Scholarship

Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) rely on a symbiosis with fungi for their nutrition. Symbiotic fungi are preserved and transported in specialized storage structures called mycangia. Although pivotal in the symbiosis, mycangia have been notoriously difficult to study, given their minute size and membranous structure. We compared the application of novel visualization methods for the study of mycangia, namely micro-computed tomography (micro-CT) and laser ablation tomography (LATscan) with traditional paraffin sectioning. Micro-CT scanning has shown the greatest promise in new organ discovery, while sectioning remains the only method with sufficient resolution for cellular visualization. All three common types …

Quantitative Line Assignment In Optical Emission Spectroscopy, Jessica Chappell

Electronic Theses and Dissertations

Quantitative elemental analysis using Optical Emission Spectroscopy (OES) starts with a high level of confidence in spectral line assignment from reference databases. Spectral interferences caused by instrumental and line broadening decrease the resolution of OES spectra creating uncertainty in the elemental profile of a sample for the first time. An approach has been developed to quantify spectral interferences for individual line assignment in OES. The algorithm calculates a statistical interference factor (SIF) that combines a physical understanding of plasma emission with a Bayesian analysis of the OES spectrum. It can be used on a single optical spectrum and still address …