Chemistry Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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-.

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

Funded Research Records

No abstract provided.

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 …

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 …

Coating Compositions And Methods For Using The Same, Fateme Rezaei, Thomas P. Schuman, Glenn Morrison

Chemical and Biochemical Engineering Faculty Research & Creative Works

Coating compositions and methods for using the same are disclosed. The coating compositions can include an aminosilica adsorbent. The coating compositions can adsorb CO₂.

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.

Effects Of Ionic Liquids On Metalloproteins., Aashka Y Patel, Keertana S Jonnalagadda, Nicholas Paradis, Timothy Vaden, Chun Wu, Gregory A. Caputo

College of Science & Mathematics Departmental Research

In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein …

Collisional Excitation Of Interstellar Pn By H₂: New Interaction Potential And Scattering Calculations, Benjamin Desrousseaux, Ernesto Quintas-Sánchez, Richard Dawes, Sarantos Marinakis, François Lique

Chemistry Faculty Research & Creative Works

Rotational excitation of interstellar PN molecules induced by collisions with H₂ is investigated. We present the first ab initio four-dimensional potential energy surface (PES) for the PN-H₂ van der Waals system. The PES was obtained using an explicitly correlated coupled cluster approach with single, double, and perturbative triple excitations [CCSD(T)-F12b]. The method of interpolating moving least squares was used to construct an analytical PES from these data. The equilibrium structure of the complex was found to be linear, with H₂ aligned at the N end of the PN molecule, at an intermolecular separation of 4.2 Å. The …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Dr. Rafael Quirino awarded NSF-IRES grant

• Dr. Arpita Saha wins 2021 Felton Jenkins Jr. Hall of Fame Faculty Award

Regulation Of Kv11.1 Isoform Expression By Polyadenylate Binding Protein Nuclear 1, Matthew R. Stump, Rachel T. Nguyen, Rachel H. Drgastin, Delaney Search, Quiming Gong, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The Kv11.1 voltage-gated potassium channel, encoded by the KCNH2 gene, conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation to generate two C-terminal Kv11.1 isoforms in the heart. Utilization of a poly(A) signal in exon 15 produces the full-length, functional Kv11.1a isoform, while intron 9 polyadenylation generates the C-terminally truncated, nonfunctional Kv11.1a-USO isoform. The relative expression of Kv11.1a and Kv11.1a-USO isoforms plays an important role in the regulation of Kv11.1 channel function. In this study, we tested the hypothesis that the RNA polyadenylate binding protein nuclear 1 (PABPN1) interacts with a unique 22 nt …

Cardiac Inflammation, Oxidative Stress, Nrf2 Expression, And Coagulation Events In Mice With Experimental Chronic Kidney Disease, Abderrahim Nemmar, Suhail Al-Salam, Sumaya Beegam, Nur Elena Zaaba, Javed Yasin, Naserddine Hamadi, Badreldin H. Ali

All Works

Chronic kidney disease (CKD) is known to be associated with cardiovascular dysfunction. Dietary adenine intake in mice is also known to induce CKD. However, in this experimental model, the mechanisms underlying the cardiotoxicity and coagulation disturbances are not fully understood. Here, we evaluated cardiac inflammation, oxidative stress, DNA damage, and coagulation events in mice with adenine (0.2% w/w in feed for 4 weeks)-induced CKD. Control mice were fed with normal chow for the same duration. Adenine increased water intake, urine output, relative kidney weight, the plasma concentrations of urea and creatinine, and the urinary concentrations of kidney injury molecule-1 and …

Synthesis And Evaluation Of Cellulose-Based, 1,2,3-Triazolium-Functionalized Polymerized Ionic Liquids: Thermal Transitions, Ionic Conductivities, And Morphological Properties, Rose J. Miller, Vanessa M. Smith, Stacey A. Love, Sarah M. Byron, David Salas-De La Cruz, Kevin M. Miller

Faculty & Staff Research and Creative Activity

A series of 1,2,3-triazolium-functionalized cellulose derivatives were prepared using an azide–alkyne “click” cyclization strategy, followed by quaternization. As cellulose represents an inexpensive and sustainable biomacromolecule, the ability to functionalize the backbone with an ionic liquid and generate conductive materials is of great interest. Here, three different counteranions ([Br], [OTf], and [NTf2]) were employed to explore the interplay between thermal, conductive, and morphological properties using a diverse set of techniques including nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray scattering, and dielectric relaxation spectroscopy (DRS). Functionalization of native cellulose resulted in …

Anharmonic Vibrational Frequencies And Spectroscopic Constants For The Detection Of Ethynol In Space, Jax D. Dallas, Brent R. Westbrook, Ryan C. Fortenberry

Faculty and Student Publications

The ethynol (HCCOH) molecule has recently been shown to be present in simulated astrochemical ices possibly linking it to molecular building blocks for interstellar complex organic molecules like amino acids. The proposed reaction mechanism suggests the simultaneous formation of both ketene and ethynol from mixed carbon monoxide/water ice in simulated interstellar conditions. Rigorous anharmonic spectral data within both the IR and microwave regions are needed for possible detection of ethynol in the interstellar medium. This study provides the first such data for this molecule from high-level quantum chemical computations where experiment is currently lacking. Ethynol has a (Formula presented.) comparable …

Molecular Strategies To Overcome Antibiotic Resistance, Luting Fang

Arts & Sciences Graduate Student Theses and Dissertations

Antibiotics have greatly reduced the number of deaths caused by infectious diseases for the last 70 years, but as a result of overuse, antimicrobial resistance emerged. Resistance is the major reason why most traditional antibiotics currently have reduced clinical efficacy. However, there is still a drive to overcome this resistance in a variety of ways. There are two main avenues of research to overcome resistance; to discover and develop new drug candidates acting on new targets and pathways, and to determine the mechanisms of antibiotic resistance in order to combat it through multi-drug therapies, bringing back the effectiveness of antibiotics …

Structural And Functional Examination Of A Nonribosomal Peptide Synthetase Producing Β-Lactone Antibiotics, Erin Marie Gemmell

Arts & Sciences Graduate Student Theses and Dissertations

With the amount of antibiotic resistant infections increasing and the number of new antibiotics entering the pharmaceutical pipeline decreasing, the need to develop new antibiotic is imperative. Utilizing bacteria’s biosynthetic pathways for antimicrobial secondary metabolite production, would allow for unique, complex, and stereoselective compounds to be tested for novel mechanisms of action. The work described herein utilizes a β-lactone forming nonribosomal peptide synthetase (NRPS) to form a library of analogs of the nonribosomal peptide (NRP) natural product, obafluorin. β-lactones are very reactive electrophiles that can form covalent bonds with a wide range of biological targets that may provide alternative mechanisms …