Chemistry Commons^™

Modeled Affinity Constants For Phosphorus Adsorption And Desorption Due To Saltwater Intrusion, Yasemin Taşcı

USF Tampa Graduate Theses and Dissertations

It is important to understand the processes that regulate phosphorus (P) fluxes to coastal environments, because P is an important nutrient in coastal ecosystems. Phosphorus adsorbs to the surface of minerals in sediment and bedrock, and an influx of seawater can cause some of that P to desorb, raising the P concentration of ambient water. Although seawater-induced P desorption is thought to be an important source of P to coastal environments, the chemical reactions that underlie it have not been established. Previous work provides some relevant surface reactions and associated affinity constants between various aqueous P species and the surface …

Cationic Cobalt (Ii) Hydroformylation, Drew Michael Hood

LSU Doctoral Dissertations

While investigating a bimetallic cobalt hydroformylation catalyst a new class of monometallic cationic cobalt (II) hydroformylation catalyst were discovered. These newly discovered catalyst proved to be very unique with high hydroformylation activity under mild conditions. The pre-catalyst were characterized using various methods including NMR, EPR, MS, and X-ray crystallography. Similarly the active catalyst was also investigated using NMR, EPR, FTIR, and X-ray crystallography. Various catalyst modifications were investigated for their effects on hydroformylation activity. Likewise various reaction parameters were probed to determine their effect on hydroformylation activity. Finally the best cationic cobalt (II) catalyst were directly compared to industry standards …

Improving Coupled Enzyme Assays With Capillary Electrophoresis, Thu Hoai Nguyen

LSU Doctoral Dissertations

The goal of this project is to address limitations of coupled enzyme assays using capillary electrophoresis (CE). In some enzyme assays, it is ineffective to directly detect products and substrates spectroscopically (absorption or fluorescence). Coupling the enzyme-catalyzed reaction of interest with another enzyme-catalyzed reaction allows for indirect detection of product formation or substrate depletion for the target enzyme. While conventional coupled enzyme assays are facile for kinetic measurements, they can be problematic for inhibition screening due to spectral and inhibitor interferences. To address these limitations of coupled assays, CE has been used to develop enzyme assays for acetyl-coenzyme A carboxylase …

Infrared Laser Ablation For Biomolecule Sampling, Kelin Wang

LSU Doctoral Dissertations

In this research, an infrared laser at a wavelength of 3 µm was used to ablate material from tissue sections for biomolecule analysis. Pulsed infrared (IR) irradiation of tissue with a focused laser beam efficiently removed biomolecules, such as proteins, enzymes, DNA, and RNA from tissue sections for further analysis. In a proteomics project, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was used to determine regions of interest (ROI) for laser ablation. The matrix was then washed off. By overlaying the MSI generated heat-map, the section was sampled using IR laser ablation and custom stage-control software. Two ROI were selected …

Development Of Novel Free Radical Initiated Peptide Sequencing Reagent: Application To Identification And Characterization Of Peptides By Mass Spectrometry, Kaylee Gaspar, Kimberly Fabijanczuk, Tara Otegui, Jose Acosta, Jinshan Gao

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

By incorporating a high proton affinity moiety to the charge localized free radical-initiated peptide sequencing (CL-FRIPS) reagent, FRIPS-MS technique has extended the applicability to hydrophobic peptides and peptides without basic amino acid residues (lysine, arginine, and histidine). Herein, the CL-FRIPS reagent has three moieties: (1) pyridine acting as the basic site to locate the proton, (2) 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO, a stable free radical) acting as the free radical precursor to generate the nascent free radical in the gas phase, and (3) N-hydroxysuccinimide (NHS) activated carboxylic acid acting as the coupling site to derivatize the N-terminus of peptides. The CL-FRIPS reagent allows …

The Application Of The Gibbs Phase Rule And Critical Point University To Predict Critical Effects In Solid Liquid Phase Equilibria, Xingjian Wang

Research Horizons Day Posters

No abstract provided.

Lew.1wr1 Rats Have Altered Inflammation Responses During Type 1 Diabetes Induction, Madushika Wimalarathne, Kayleigh Cantrell, Joshua Derbort

Research Horizons Day Posters

No abstract provided.

Tracking Decitabine Incorporation Into Malignant Myeloid Cell Dna In Vitro And In Vivo By Lc-Ms/Ms With Enzymatic Digestion, Sujatha Chilakala, Ye Feng, Lan Li, Reda Mahfouz, Ebrahem Quteba, Yogen Saunthararajah, Yan Xu

Chemistry Faculty Publications

The DNA hypomethylating agents decitabine and 5-azacytidine are the only two drugs approved for treatment of all subtypes of the myeloid malignancy myelodysplastic syndromes (MDS). The key to drug activity is incorporation into target cell DNA, however, a practical method to measure this incorporation is un-available. Here, we report a sensitive and specific LC-MS/MS method to simultaneously measure decitabine incorporation and DNA hypomethylation. A stable heavy isotope of 2'-deoxycytidine was used as an internal standard and one-step multi-enzyme digestion was used to release the DNA bound drug. Enzyme-released decitabine along with other mononucleosides were separated by a reverse-phase C-18 column …

Lemon: A Framework For Rapidly Mining Structural Information From The Protein Data Bank, Jonathan Fine, Gaurav Chopra

Purdue University Libraries Open Access Publishing Fund

Motivation

The Protein Data Bank (PDB) currently holds over 140 000 biomolecular structures and continues to release new structures on a weekly basis. The PDB is an essential resource to the structural bioinformatics community to develop software that mine, use, categorize and analyze such data. New computational biology methods are evaluated using custom benchmarking sets derived as subsets of 3D experimentally determined structures and structural features from the PDB. Currently, such benchmarking features are manually curated with custom scripts in a non-standardized manner that results in slow distribution and updates with new experimental structures. Finally, there is a scarcity of …

The Ratio Of The Number Of States In Asymmetric And Symmetric Ozone Molecules Deviates From The Statistical Value Of 2, Igor Gayday, Alexander Teplukhin, Dmitri Babikov

Chemistry Faculty Research and Publications

Accurate calculations of vibrational states in singly and doubly substituted ozone molecules are carried out, up to dissociation threshold. Analysis of these spectra reveals noticeable deviations from the statistical factor of 2 for the ratio between the number of states in asymmetric and symmetric ozone molecules. It is found that, for the lower energy parts of spectra, the ratio is less than 2 in the singly substituted ozone molecules, but it is more than 2 in the doubly substituted ozone molecules. However, the upper parts of spectra, just below dissociation thresholds, exhibit a different behavior. In this energy range, the …

Binding Of Braco19 To A Telomeric G-Quadruplex Dna Probed By All-Atom Molecular Dynamics Simulations With Explicit Solvent., Babitha Machireddy, Holli-Joi Sullivan, Chun Wu

College of Science & Mathematics Departmental Research

Although BRACO19 is a potent G-quadruplex binder, its potential for clinical usage is hindered by its low selectivity towards DNA G-quadruplex over duplex. High-resolution structures of BRACO19 in complex with neither single-stranded telomeric DNA G-quadruplexes nor B-DNA duplex are available. In this study, the binding pathway of BRACO19 was probed by 27.5 µs molecular dynamics binding simulations with a free ligand (BRACO19) to a DNA duplex and three different topological folds of the human telomeric DNA G-quadruplex (parallel, anti-parallel and hybrid). The most stable binding modes were identified as end stacking and groove binding for the DNA G-quadruplexes and duplex, …

Optimization Of Remazol Brilliant Blue R Adsorption Onto Xanthium Italicum Using The Response Surface Method, Mohammed Saleh, Mutlu Yalvaç, Hüdaverdi Arslan

Karbala International Journal of Modern Science

In this study, the adsorption capacity of toxic and recalcitrant organic pollutant(s) Remazol Brilliant Blue R (RBBR) onto the invader Xanthium İtalicum (XI) plant was assessed using the Response Surface Method (RSM). The adsorp-tion behavior of RBBR was determined by the spectrophotometric method, FTIR and SEM analysis were used to characterize XI, Brunauer, the Emmett and Teller (BET) analysis was accomplished to find the surface area of the ad-sorbent. The experiment procedures were planned by the Central Composite Design (CCD) whereby a model was built to examine the effects of the different parameters and the possible interaction between them. The …

Wet Lay-Up Technique For Manufacturing Of Advanced Laminated Composites, Abdel-Hamid Mourad, Nizar Zaaroura, Nizamudeen Cherupurakal

Karbala International Journal of Modern Science

Incorporation of nanofillers into laminated composites is expected to produce a material with improved performance for many potential industrial applications. The focus of this work is to produce advanced composites by simple wet lay-up technique. The impact of adding three different nanofillers (multi-wall carbon nanotubes (MWCNT), silicon carbide (SiC) and aluminum oxide (Al2O3),) on the thermal and mechanical stability of woven Kevlar KM2Plus/epoxy composites was investigated. Silicon carbide and aluminum oxide were added at different weight percentages up to 3wt%, whereas the addition of multi-wall carbon nanotubes was limited to 1wt%. The mechanical behavior was evaluated through three-point bending tests. …

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

Investigating Cationic Metal Centers For Hydroformylation, Ryan Alexander Johnson

LSU Doctoral Dissertations

Bimetallic cooperativity can potentially increase activity of reactions. This concept is another way to increase reactivity besides simply focusing on the steric and electronic effects of a ligand. A binucleating tetrasphosphine ligand has been developed to showcase bimetallic cooperativity between two rhodium metal centers. Hydroformylation is a widely used industrial process to produce aldehydes from alkenes, H₂, and CO. The dirhodium catalyst, [Rh₂(μ-CO)(CO)₃(rac-et,ph-P4-Ph)](BF₄)₂,is highly active leading to favorable results when using a DMF/water solvent system, 1-hexene, 90 psi 1:1 H₂/CO, and 90° C: initial turnover frequency …

Quantitative Capabilities Of Stxm To Measure Spatially Resolved Organic Volume Fractions Of Mixed Organic ∕ Inorganic Particles, Matthew Fraund, Tim Park, Daniel Bonanno, Don Q. Pham, Ryan C. Moffet

Department of Chemistry Student Articles

Scanning transmission X-ray microscopy coupled with near-edge X-ray absorption and fine structure (STXM-NEXAFS) spectroscopy can be used to characterize the morphology and composition of aerosol particles. Here, two inorganic ∕ organic systems are used to validate the calculation of organic volume fraction (OVF) and determine the level of associated error by using carbon K-edge STXM data at 278, 285.4, 288.6, and 320 eV. Using the mixture of sodium chloride and sucrose as one system and ammonium sulfate and sucrose as another, three solutions were made with 10:1, 1:1, and 1:10 mass ratios (inorganic to organic). The OVFs of the organic-rich …

C–H/Π And C–H–O Interactions In Concert: A Study Of The Anisole–Methane Complex Using Resonant Ionization And Velocity Mapped Ion Imaging, James Makuvaza, Damian Kokkin, John Loman, Scott A. Reid

Chemistry Faculty Research and Publications

Noncovalent forces such as hydrogen bonding, halogen bonding, π–π stacking, and C–H/π and C–H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug–substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole–methane complex, where both C–H/π and C–H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and …

Purification And Characterization Of A Nonspecific Lipid Transfer Protein 1 (Nsltp1) From Ajwain (Trachyspermum Ammi) Seeds, Meshal Nazeer, Humera Waheed, Maria Saeed, Saman Yousuf Ali, M. Iqbal Choudhary, Zaheer Ul-Haq, Aftab Ahmed

Pharmacy Faculty Articles and Research

Ajwain (Trachyspermum ammi) belongs to the family Umbelliferae, is commonly used in traditional, and folk medicine due to its carminative, stimulant, antiseptic, diuretic, antihypertensive, and hepatoprotective activities. Non-specific lipid transfer proteins (nsLTPs) reported from various plants are known to be involved in transferring lipids between membranes and in plants defense response. Here, we describe the complete primary structure of a monomeric non-specific lipid transfer protein 1 (nsLTP1), with molecular weight of 9.66 kDa, from ajwain seeds. The nsLTP1 has been purified by combination of chromatographic techniques, and further characterized by mass spectrometry, and Edman degradation. The ajwain nsLTP1 …

Restoration Of Aberrant Mtor Signaling By Intranasal Rapamycin Reduces Oxidative Damage: Focus On Hne-Modified Proteins In A Mouse Model Of Down Syndrome, Fabio Di Domenico, Antonella Tramutola, Eugenio Barone, Chiara Lanzillotta, Olivia Defever, Andrea Arena, Ilaria Zuliani, Cesira Foppoli, Federica Iavarone, Federica Vincenzoni, Massimo Castagnola, D. Allan Butterfield, Marzia Perluigi

Chemistry Faculty Publications

Increasing evidences support the notion that the impairment of intracellular degradative machinery is responsible for the accumulation of oxidized/misfolded proteins that ultimately results in the deposition of protein aggregates. These events are key pathological aspects of “protein misfolding diseases”, including Alzheimer disease (AD). Interestingly, Down syndrome (DS) neuropathology shares many features with AD, such as the deposition of both amyloid plaques and neurofibrillary tangles. Studies from our group and others demonstrated, in DS brain, the dysfunction of both proteasome and autophagy degradative systems, coupled with increased oxidative damage. Further, we observed the aberrant increase of mTOR signaling and of its …

Hexacoordinated Tetrel-Bonded Complexes Between Tf4 (T = Si, Ge, Sn, Pb) And Nch. Competition Between Σ- And Π-Holes, Mariusz Michalczyk, Wiktor Zierkiewicz, Rafal Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

In order to accommodate the approach of two NCH bases, a tetrahedral TF4 molecule (T=Si,Ge,Sn,Pb) distorts into an octahedral structure in which the two bases can be situated either cis or trans to one another. The square planar geometry of TF4, associated with the trans arrangement of the bases, is higher in energy than its see-saw structure which corresponds to the cis trimer. On the other hand, the square geometry offers an unobstructed path of the bases to the π-holes above and below the tetrel atom so enjoys a higher interaction energy than is the case for the σ-holes approached …

Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation, Yi Rao, Yuqin Qian, Gang-Hua Deng, Ashlie Kinross, Nicholas J. Turro, Kenneth B. Eisenthal

Chemistry and Biochemistry Faculty Publications

This paper presents the first study of the rotations of rigid molecules in 3 dimensions at the air/water interface, using the femtosecond time resolved sum frequency generation (SFG) technique. For the purpose of this research, the aromatic dye molecule C153 was chosen as an example of a molecule having two functional groups that are SFG active, one being the hydrophilic −−C==O group and the other the hydrophobic −−CF₃ group. From polarized SFG measurements, the orientations of the two chromophores with respect to the surface normal were obtained. On combining these results with the known relative orientation of the two …

Annihilator Dimers Enhance Triplet Fusion Upconversion, Andrew B. Pun, Samuel N. Sanders, Matthew Y. Sfeir, Luis M. Campos, Daniel N. Congreve

Publications and Research

Optical upconversion is a net process by which two low energy photons are converted into one higher energy photon. There is vast potential to exploit upconversion in applications ranging from solar energy and biological imaging to data storage and photocatalysis. Here, we link two upconverting chromophores together to synthesize a series of novel tetracene dimers for use as annihilators. When compared with the monomer annihilator, TIPS–tetracene, the dimers yield a strong enhancement in the triplet fusion process, also known as triplet–triplet annihilation, as demonstrated via a large increase in upconversion efficiency and an order of magnitude reduction of the threshold …

Α-Actinin Anchors Psd-95 At Postsynaptic Sites, Lucas Matt, Karam Kim, Anne E. Hergarden, Tommaso Patriarchi, Zulfiqar A. Malik, Deborah K. Park, Dhrubajyoti Chowdhury, Olivia R. Buonarati, Peter B. Henderson, Yonghong Zhang

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Despite the central role PSD-95 plays in anchoring postsynaptic AMPARs, how PSD-95 itself is tethered to postsynaptic sites is not well understood. Here we show that the F-actin binding protein α-actinin binds to the very N-terminus of PSD-95. Knock-down (kd) of α-actinin phenocopies kd of PSD-95. Mutating lysine at position 10 or lysine at position 11 of PSD-95 to glutamate, or glutamate at position 53 or glutamate and aspartate at positions 213 and 217 of α-actinin, respectively, to lysine impairs in parallel PSD-95 binding to α-actinin and postsynaptic localization of PSD-95 and AMPARs. These experiments identify α-actinin as a critical …

National Chemistry Week In The Greater Lafayette Area: Chemistry Is Out Of This World!, Daniela Mesa Sanchez, Jessica Callus, Daisy Unsihuay

Engagement & Service-Learning Summit

National Chemistry Week (NCW), an outreach program initiated by the American Chemical Society (ACS), encourages scientists to bring their love of chemistry to the community. The Plutonium Chapter (Purdue University) of Iota Sigma Pi (ISP) organizes an annual celebration of this event in which over 1600 elementary school students are exposed to hands-on experiments related to the annual theme. In 2018, the theme was “Chemistry is Out of This World,” which allowed nearly a 100 volunteers to explore several space-themed experiments with children from three different school districts all over the Greater Lafayette area. Our poster outlines the preparation of …

Extraction Of Acids And Bases From Aqueous Phase To A Pseudoprotic Ionic Liquid, Nikolas Patsos, Karin Lewis, Francesco Picchioni, Mark N. Kobrak

Publications and Research

We report experiments on the extraction of acids and bases from an aqueous phase to a pseudoprotic ionic liquid phase consisting of an equimolar mixture of trihexylamine and octanoic acid. We observed the extraction of a wide range of acids and bases, and investigated the mechanism of extraction in detail. Our results confirmed the observation of the Hofmeister effect in these systems reported in our previous work, where the extent of the extraction of copper salts was significantly influenced by the interactions between extracted inorganic anions and the organic phase. Our results further demonstrated that the organic layer served as …

Self-Assembled Bismuth Selenide (Bi2se3) Quantum Dots Grown By Molecular Beam Epitaxy, Marcel S. Claro, Ido Levy, Abhinandan Gangopadhyay, David J. Smith, Maria C. Tamargo

Publications and Research

We report the growth of self-assembled Bi2se3 quantum dots (QDs) by molecular beam epitaxy on GaAs substrates using the droplet epitaxy technique. The QD formation occurs after anneal of Bismuth droplets under Selenium flux. Characterization by atomic force microscopy, scanning electron microscopy, X-ray diffraction, high-resolution transmission electron microscopy and X-ray reflectance spectroscopy is presented. Raman spectra confirm the QD quality. The quantum dots are crystalline, with hexagonal shape, and have average dimensions of 12-nm height (12 quintuple layers) and 46-nm width, and a density of 8.5 × 109 cm−2. this droplet growth technique provides a means to produce topological insulator …

Evaluating Seasonal Nutrient Fluxes In Emerging And Eroding Wetlands Of The Louisiana Delta Plain, Kiran Upreti

LSU Doctoral Dissertations

Deltaic wetlands can ameliorate high NO₃^- loads via denitrification, a dominant NO₃^- reduction pathway in inland and coastal habitats. Dissimilatory Nitrate Reduction to Ammonia (DNRA), in contrast to denitrification, conserves N within the system and has been found to be favored over denitrification with increase in salinity and temperature. There are no studies in the Louisiana Deltaic plain with simultaneous estimation of denitrification and DNRA. Increased P availability has been shown to increase denitrification so it is essential to understand P biogeochemistry when studying N cycle. Here, we evaluated net denitrification using N₂:Ar and …

Development Of Technology Of Potassium Percarbonate Production, N Erkaeva

Karakalpak Scientific Journal

In this paper, the results of a study on the production of potassium percarbonate are obtained. It has been established that the interaction of potassium carbonate and hydrogen peroxide produces potassium percarb onate in the form of К2СОЗ • 3H202, which exhibits individual properties. A flow chart for the production of potassium percarbonate has been developed.

Volume Diagram System Na+, K+, 1/2 Mg2+//1/2 S042-, Cl--H20 At 0°C, A Erkaev

Karakalpak Scientific Journal

Based on the findings of theoretical and experimental studies of first constructed volume diagram of phase equilibria 2Na+, 2K+, Mg2+ \\ SO42-' 2Сl- H20 at 0°C. The boundaries of the contact areas of the crystallization of salts. Established nine crystallization fields and lines of intersection, five of invariant (Pn), foteen monovariant (snx) and foteen divariant (Enx) nodal points

Total Reflection X-Ray Fluorescence, Martina Schmeling

Chemistry: Faculty Publications and Other Works

Total reflection X-ray fluorescence (TXRF) spectrometry is a non-destructive and surface sensitive multi-element analytical method based on energy dispersive X-ray fluorescence spectrometry with detection limits in the lower picogram range. It utilizes the total reflection of the primary X-ray beam at or below the critical angle of incidence. At this angle, the fluorescence intensity is substantially enhanced for samples present as small granular residue or as thin homogenous layer deposited at the surface of a thick substrate. Generally, two types of application exist: micro- and trace-analysis as well as surface and thin-layer analysis. For micro- and traceanalysis, a small amount …