Chemistry Commons^™

Interplay Between Oxo And Fluoro In Vanadium Oxyfluorides For Centrosymmetric And Non-Centrosymmetric Structure Formation, Prashanth Sandineni, Amitava Choudhury, Hooman Yaghoobnejad Asl, Weiguo Zhang, P. Shiv Halasyamani, Kartik Ghosh

Chemistry Faculty Research & Creative Works

Herein, we report the syntheses of two lithium-vanadium oxide-fluoride compounds crystallized from the same reaction mixture through a time variation experiment. A low temperature hydrothermal route employing a viscous paste of V₂O₅, oxalic acid, LiF, and HF allowed the crystallization of one metastable phase initially, Li₂VO_0.55 (H₂O)_0.45F₅·2H₂O (I), which on prolonged heating transforms to a chemically similar yet structurally different phase, Li₃VOF₅ (II). Compound I crystallizes in centrosymmetric space group, I2/a with a = 6.052(3), b = 7.928(4), …

Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

The following sections are included:

• Present State of Computational Modelling in Fluorescence Nanoscopy

• Recent Contributions to Computational Modelling in Fluorescence Nanoscopy

• Outlook on Computational Modelling in Fluorescence Nanoscopy

• Acknowledgments

• References

Chapter 1.3: 3-D Topo Surface Visualization Of Acid-Base Species Distributions: Corner Buttes, Corner Pits, Curving Ridge Crests And Dilution Plains, Garon C. Smith, Md Mainul Hossain

Water Topos: A 3-D Trend Surface Approach to Viewing and Teaching Aqueous Equilibrium Chemistry

This chapter adds 3-D species distribution topos to earlier surfaces that showed pH (Chapter 1.1) and buffer capacity behavior (Chapter 1.2) during titration and dilution procedures. It constructs trend surfaces by plotting computed alpha distribution coefficients above a composition grid with “mL of NaOH” as the x-axis and overall system dilution (log C) as the y-axis. The systematic shift from protonated to deprotonated forms is clearly visualized on a linear z-axis. Because pH and buffer capacity surfaces accompany the species topos, it is easy to see their interrelationships. On the basis of their graphical appearance, features …

Development And Validation Of A Dft-Based Force Field For A Hydrated Homoalanine Polypeptide, Ying Yuan, Zhonghua Ma, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

A new force field has been created for simulating hydrated alanine polypeptides using the adaptive force matching (AFM) method. Only density functional theory calculations using the Perdew–Burke–Ernzerhof exchange–correlation functional and the D3 dispersion correction were used to fit the force field. The new force field, AFM2020, predicts NMR scalar coupling constants for hydrated homopolymeric alanine in better agreements with experimental data than several other models including those fitted directly to such data. For Ala₇, the new force field shows about 15% helical conformations, 20% conformation in the β basin, and 65% polyproline II. The predicted helical population of …

Physicochemical Properties And Formulation Development Of A Novel Compound Inhibiting Staphylococcus Aureus Biofilm Formation, Nan Wang, Feng Qi, Haqing Yu, Bryan D. Yestrepsky, Scott D. Larsen, Honglan Shi, Juan Ji, David W. Anderson, Hao Li, Hongmin Sun

Chemistry Faculty Research & Creative Works

The emergence of antibiotic resistance over the past several decades has given urgency to new antibacterial strategies that apply less selective pressure. A new class of anti-virulence compounds were developed that are active against methicillin-resistant Staphylococcus aureus (MRSA), by inhibiting bacterial virulence without hindering their growth to reduce the selective pressure for resistance development. One of the compounds CCG-211790 has demonstrated potent anti-biofilm activity against MRSA. This new class of anti-virulence compounds inhibited the gene expression of virulence factors involved in biofilm formation and disrupted the biofilm structures. In this study, the physicochemical properties of CCG- 211790, including morphology, solubility …

Mechanism Of Action Of Dihydropteridine Reductase, Gabriela Arias De La Rosa

Dissertations, Theses, and Capstone Projects

Human dihydropteridine reductase is an enzyme that transfers a hydride from NADH to reduce quinonoid 7,8-dihydropterin (qBH₂) to 5,6,7,8-tetrahydropterin (BH₄), which is a cofactor important in the production of neurotransmitters.DHPR deficiency causes a drastic form of the neurological genetic disease phenylketonuria (PKU) that does not benefit from a phenylalanine-free diet.From site-directed mutagenesis studies, mostly on Rat DHPR, we know that certain residues are important for cofactor binding, substrate binding, and hydride transfer; however, there are still some questions about how DHPR works, particularly, because there is not a crystal structure of the tertiary complex: What is …

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …

Interactions Of Organic Fluorophores With Plasmonic Surface Lattice Resonances, Robert J. Collison

Dissertations, Theses, and Capstone Projects

It is common knowledge that metals, alloys and pure elements alike, are lustrous and reflective, the more so when a metal surface is flat, polished, and free from oxidation and surface fouling. However, some metals reflect visible light, in the 380 nm to 740 nm range of wavelengths, much more strongly than others. In particular, some metals reflect wavelengths in certain portions of the ultraviolet (UV), visible, and near-infrared (NIR) regime, let us say 200 nm to 2000 nm, while absorbing light strongly in other segments of this range. There are several factors that account for this difference between various …

Role Of Protonation State Changes And Hydrogen Bonding Around The Oxygen Evolving Complex Of Photosystem Ii, Divya Matta

Dissertations, Theses, and Capstone Projects

The mechanism of natural photosynthesis involves the use of solar energy to produce O₂ we breathe and food and fuel we intake. This process results in the biological oxidation of water that takes place at room temperature, neutral pH using earth abundant elements Ca and Mn. Understanding how this challenging chemical reaction occurs in photosynthesis can be useful for designing better artificial photosynthetic complexes that can be used as biofuels. My doctoral work is to study the deprotonation and oxidation events elucidating the mechanistic details of proton coupled electron transfer reaction in a photosynthetic protein.

The O₂ evolution …

Using The Marcus Inverted Region And Artificial Cofactors To Create A Charge Separated State In De Novo Designed Proteins, Eskil Me Andersen

Dissertations, Theses, and Capstone Projects

To create an efficient de novo photosynthetic protein it is important to create long lived charge separated states. Achieving stable charge separation leads to an increase in the efficiency of the photosynthetic reaction which in turn leads to higher yields of end products, such as biofuels, electrical charge, or synthetic chemicals. In an attempt to create charge separated states in de novo proteins we hypothesized that we could engineer the free energy gaps in the proteins from excited primary donor (PD) to acceptor (A), and A back to ground state PD such that the forward electron transfer (ET) would be …

Experimental And Computational Design Of Nanostructured Materials For High Performance Supercapacitor Devices, Basant A. Ali

Theses and Dissertations

Both energy conversion and storage technologies need to be developed hand-to-hand simultaneously to overcome the energy crises. To this end, supercapacitors (SCs) have the potential to be the energy storage platform due to their fast charging capability and long cycling stability. However, their low energy is the bottleneck towards their wide implementation compared to batteries. Also, current research is based on guess and check methods to modify electrode materials with limited properties prediction. In this thesis, density functional theory (DFT) has been employed as a tool to identify potential SC electrode materials. Then, the gained knowledge was used to develop …

Substituent Effects On The Solubility And Electronic Properties Of The Cyanine Dye Cy5: Density Functional And Time-Dependent Density Functional Theory Calculations, Austin Biaggne, William B. Knowlton, Bernard Yurke, Jeunghoon Lee, Lan Li

Materials Science and Engineering Faculty Publications and Presentations

The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of …

Heterocycles In The Treatment Of Neglected Tropical Diseases, Kush K. Maheshwari, Debasish Bandyopadhyay

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

Background: Neglected Tropical Diseases (NTDs) affect a huge population of the world and the majority of the victims belong to the poor community of the developing countries. Until now, the World Health Organization (WHO) has identified 20 tropical diseases as NTDs that must be addressed with high priority. However, many heterocyclic scaffolds have demonstrated potent therapeutic activity against several NTDs.

Objective: There are three major objectives: (1) To discuss the causes, symptoms, and current status of all the 20 NTDs; (2) To explore the available heterocyclic drugs, as well as their mechanisms of action (if known), that are being used …

Pressure-Induced Site Swapping, Luminescence Quenching, And Color Tunability Of Gd2hf2o7:Eu3+ Nanoparticles, Santosh K. Gupta, Hisham Abdou, Yuanbing Mao

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

High-pressure (HP) studies have been an active research area in fundamental physics and to meet demand of several technological applications. In this paper, we have explored the HP effect on optical properties of pyrochlore Gd2Hf2O7:5%Eu3+ (GHOE) nanoparticles (NPs). We have investigated several aspects of their optical properties under HP such as charge transfer transitions, emission dynamics, asymmetry ratio, excited state lifetime, and color coordinates. HP photoluminescence (PL) spectra indicate the irreversible and complete disappearance of charge transfer beyond ~5.4 GPa (up to 53 GPa) owing to the reduced charge density around O2− ion in the GHOE NPs. Elevated pressure induces …

Four Isotope-Labeled Recombination Pathways Of Ozone Formation, Dmitri Babikov, Elizaveta Grushnikova, Igor Gayday, Alexander Teplukhin

Chemistry Faculty Research and Publications

A theoretical approach is developed for the description of all possible recombination pathways in the ozone forming reaction, without neglecting any process a priori, and without decoupling the individual pathways one from another. These pathways become physically distinct when a rare isotope of oxygen is introduced, such as ¹⁸O, which represents a sensitive probe of the ozone forming reaction. Each isotopologue of O₃ contains two types of physically distinct entrance channels and two types of physically distinct product wells, creating four recombination pathways. Calculations are done for singly and doubly substituted isotopologues of ozone, eight rate coefficients …

The Mechanism Of Β-N-Methylamino-L-Alanine Inhibition Of Trna Aminoacylation And Its Impact On Misincorporation, Nien-Ching Han, Tammy J. Bullwinkle, Kaeli F. Loeb, Kym F. Faull, Kyle Mohler, Jesse Rinehart, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

β-N-methylamino-l-alanine (BMAA) is a nonproteinogenic amino acid that has been associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD). BMAA has been found in human protein extracts; however, the mechanism by which it enters the proteome is still unclear. It has been suggested that BMAA is misincorporated at serine codons during protein synthesis, but direct evidence of its cotranslational incorporation is currently lacking. Here, using LC-MS–purified BMAA and several biochemical assays, we sought to determine whether any aminoacyl-tRNA synthetase (aaRS) utilizes BMAA as a substrate for aminoacylation. Despite BMAA's previously predicted misincorporation at serine …

Coastal Watershed Monitoring And Management: Geomorphology, Geochemistry, And Hydrologic Modeling Of Los Peñasquitos Creek, Ca, Ravleen Khalsa-Basra

Theses

Rivers in semi-arid climates are directly influenced by local geographic and hydrologic conditions and impacted by modifications to hydrology via urbanization. Changes can influence erosion, morphology, habitat sustainability, and watershed health. In highly urbanized southern California coastal regions, these rare open spaces provide vital ecosystem services. Los Peñasquitos Creek in San Diego County is one such watershed. Using stream surveying and laboratory methods we quantified channel characteristics, grain size distribution, total metal concentration [M], organic carbon (%OC), and phosphate to longitudinally characterize the creek for improved management. Results identified three distinct reaches in the watershed (upper, middle, lower). Downstream, depth …

Nanoengineered Materials For Energy Conversion & Storage Applications: A Density Functional Theory Study, Ahmed Biby

Theses and Dissertations

The conventional approach for the development of novel materials has become long relative to the desired product development cycle. Thus, the sluggish pace of the development of materials within the conventional approach hinders the rapid transformation of the scientific outcomes into useful technological products. To this end, the field of hierarchical materials informatics evolved to bridge this gap. In this field, the multiscale material internal structure is considered the starting point and the core of this approach. This being said, the density functional theory (DFT) was used to generate useful materials data for the advancement of the hierarchical materials data-bases …

Otolith Microchemistry Reveals Low Habitat Connectivity Of California Killifish (Fundulus Parvipinnis) Across A Range Of Spatial Scales, Lisa Robison

Theses

As wetlands face continued fragmentation worldwide, an understanding of habitat connectivity and how fishes that rely on these environments is imperative to conduct effective marine management. Site fidelity and habitat connectivity are vital measures of the interdependence of fish populations living in neighboring marshes (or in regions of a single marsh).

Here, we examine the habitat connectivity, site fidelity, and movement of California killifish (Fundulus parvipinnis) within and among three estuaries in Southern California through otolith microelemental analysis. Assessing the site fidelity of estuarine fishes is important to determine the level of connectivity between spatially distinct populations within …

Data From: Realization Of Lewis Basic Sodium Anion In The Nabh3- Cluster, Alexander I. Boldyrev, Nikita Fedik

Browse all Datasets

Project reports the first example of dative bond formed by Na- (anion) in a cluster NaBH3-.

Copper-Ligand Clusters Dictate Size Of Cyclized Peptide Formed During Alkyne-Azide Cycloaddition On Solid Support, Rene Kandler, Samir Das, Arundhati Nag

Chemistry

Peptide and peptidomimetic cyclization by copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction have been used to mimic disulfide bonds, alpha helices, amide bonds, and for one-bead-one-compound (OBOC) library development. A limited number of solid-supported CuAAC cyclization methods resulting in monomeric cyclic peptide formation have been reported for specific peptide sequences, but there exists no general study on monocyclic peptide formation using CuAAC cyclization. Since several cyclic peptides identified from an OBOC CuAAC cyclized library has been shown to have important biological applications, we discuss here an efficient method of alkyne-azide 'click' catalyzed monomeric cyclic peptide formation on a solid support. The reason …

Eager Sentinels: The Pcr-Free Biosensor For A Fast, Simple, And Sensitive Detection Of Rna, Artavazd Badalyan

Funded Research Records

No abstract provided.

Using Quantitative Methods To Investigate Student Attitudes Toward Chemistry: Women Of Color Deserve The Spotlight, Guizella A. Rocabado Delgadillo

USF Tampa Graduate Theses and Dissertations

The field of Chemistry Education Research (CER) has been interested in understanding the reasons why students struggle in organic chemistry courses. Reports show that students perceive the material as difficult and have trouble keeping pace with the volume of content taught within the course. Beyond these and other explanations of why students struggle in organic chemistry are affective factors, such as attitude toward chemistry, that influence students’ success and retention in this course. Studies have shown that in many instances, underrepresented groups of students report less positive attitudes than their peers. Of greater concern are the students representing multiple marginalized …

Improving Conceptual Understanding Of Gas Behavior Through The Use Of Screencasts And Simulations, Brianna L. Martinez, Ryan D. Sweeder, Jessica Vandenplas, Deborah Herrington

Peer Reviewed Articles

Engagement with particle-level simulations can help students visualize the motion and interactions of gas particles, thus helping them develop a more scientifically accurate mental model. Such engagement outside of class prior to formal instruction can help meet the needs of students from diverse backgrounds and provide instructors with a common experience upon which to build with further instruction. Yet, even with well-designed scaffolds, students may not attend to the most salient aspects of the simulation. In this case, a screencast where an instructor provides narrated use of the simulation and points students towards the important observations may provide additional benefits. …

Role Of Antizyme Inhibitor Proteins In Cancers And Beyond, Venella Tulluri, Venkatesh V. Nemmara

College of Science & Mathematics Departmental Research

Polyamines are multivalent organic cations essential for many cellular functions, including cell growth, differentiation, and proliferation. However, elevated polyamine levels are associated with a slew of pathological conditions, including multiple cancers. Intracellular polyamine levels are primarily controlled by the autoregulatory circuit comprising two different protein types, Antizymes (OAZ) and Antizyme Inhibitors (AZIN), which regulate the activity of the polyamine biosynthetic enzyme ornithine decarboxylase (ODC). While OAZ functions to decrease the intracellular polyamine levels by inhibiting ODC activity and exerting a negative control of polyamine uptake, AZIN operates to increase intracellular polyamine levels by binding and sequestering OAZ to relieve ODC …

Synthesis And Cytotoxicity Of Trisubstituted Imidazoles, Venkata Agasthya Kasibotla

Theses and Dissertations

Aza heterocyclic compounds are an important class of organic compounds that play a major role in medicinal chemistry. Majority of the heterocyclic motifs such as imidazoles, triazoles, piperazines etc. act as building blocks for synthesizing active pharmaceutical ingredients. Several pharmaceutical drugs include these motifs due to their varying physicochemical properties, which enable them to exhibit wide range of pharmacological activities ranging from anti-fungal, anti-neoplastic, anti-helmintic, anti-microbial etc. Owing to their electron rich ring system, imidazole and piperazine based motifs have become an attractive target for design and development of novel chemical structures as new drugs. In the current study, we …

Development Of Engineered Soil Surrogates For Modeling Natural Soil Sorption Behavior, Ghada Yehia Abdalla

LSU Doctoral Dissertations

The land produces more than 95% of the global food supply, and with a continuously growing population, we need to optimize the use of the available agricultural land. Soil organic matter (SOM) is an essential component of soils, especially concerning their fertility and sorption behavior. The chemical composition of the SOM consists of lipids, lignin, and cellulose. However, the heterogeneous and complex nature of SOM, and real soils, makes their study challenging and introduces uncontrollable factors.

Therefore, structural mimics of natural soils with increasing complexity representing the real soil functionality were synthesized and evaluated for bulk properties related to their …

The Fireproofing Abilities Of Sodium Polyacrylate In The Form Of A Gel, Water Based Paint, And Spray, Sydni Moore

Journal of the South Carolina Academy of Science

No abstract provided.

The Effect Of Alcalase Concentration On The Proteins From The Shells Of Litopenaeus Setiferus (White Shrimp), Liam T. Quan

Journal of the South Carolina Academy of Science

Chitin is a naturally abundant polymer that also happens to be biodegradable. Chitin can be used in a variety of different products such as biodegradable plastics, papers, medical products, foods, and medical treatments. To extract chitin, shells must be demineralized and deproteinized. The goal of this experiment was to examine the effect of the protease Alcalase in the deproteinization of litopenaeus setiferus shells. The hypothesis was that if the concentration of Alcalase increased, then the absorbance of proteins in the spectrophotometer reading would increase. The null hypothesis was that if the concentration increased there would be no change in absorption. …

Investigating Alternative Synthesis And Impregnation Methods For Silver Nanoparticles, Yash Patel

Journal of the South Carolina Academy of Science

No abstract provided.