Chemistry Commons^™

Exploring The Geometric And Electronic Properties Of Palladium Doped Silicon Clusters, Madison Winkeler, Ciara N. Richardson

Scholars Week

Transition metal-doped silicon clusters have unique properties and have been studied as building blocks for nanomaterials and microelectronics. Here, the structure and properties of candidate palladium doped silicon clusters (SinPd2: n=1-17) were determined using global optimization techniques on a high performance computing cluster at the San Diego Supercomputing Center. Then geometric structures were further optimized utilizing the B3LYP method with 6-311+G(d) basis sets for silicon and lanl2dz pseudopotential for palladium, followed by the larger DSDPBEP86 method with 6-311+G(2d) basis sets for silicon and SDD pseudopotential for palladium, as implemented in the Gaussian 16 program package. The energetics for each cluster …

New Methods For The Synthesis, Activation, And Application Of Thioglycosides, Samira Escopy

Dissertations

From their ubiquitous presence in Nature to their vital roles in biology and medicine, carbohydrates (sugars or glycans) are essential molecules of life, which are made and/or utilized by every living organism. Our cells are coated with sugars that are involved in almost every biological process and defensive mechanism in our body. To mention some of their crucial biological functions, carbohydrates are essential source of energy, they participate in blood coagulation, immune defense, cell growth, cell-cell interaction, and anti-inflammatory processes. Understanding of glycan functions and structure is crucial for the development of vaccines and therapeutics. Producing complex carbohydrates in sufficient …

Single-Molecule Localization Microscopy Of 3d Orientation And Anisotropic Wobble Using A Polarized Vortex Point Spread Function, Tianben Ding, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Within condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecule’s wobble, simultaneously from a single image. Even when imaging dim emitters (∼500 photons detected), the polarized vortex PSF can obtain 12 nm localization precision, 4°–8° orientation precision, and 26° wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics …

Non-Adiabatic Excited State Molecular Dynamics Using Ehrenfest And Modulated X-Ray Absorption In Titania, Alexander Matthew Meyer

LSU Doctoral Dissertations

This dissertation contains two separate sections aside from an introduction (Chapter 1): theory and methods (Chapter 2), time dependent density functional theory with Ehrenfest for excited state lifetimes in materials (Chapter 3), and simulated field modulated X-ray absorption in titania (Chapter 4).

Excited state lifetime in insulators and semiconductors can be difficult to compute using quantum chemistry due to their dense excited states. Non-radiative decay in these materials requires the use of non-adiabatic effects to dissipate energy through the means of electron-nuclear coupling such as coherent phonon generation. One method of approaching this challenge in these materials is using Ehrenfest …

Biotinylation As A Tool To Enhance The Uptake Of Small Molecules In Gram-Negative Bacteria, Ankit Pandeya, Ling Yang, Olaniyi Alegun, Chamikara Karunasena, Chad Risko, Zhenyu Li, Yinan Wei

Chemistry Faculty Publications

Antibiotic resistance is a major public health concern. The shrinking selection of effective antibiotics and lack of new development is making the situation worse. Gram-negative bacteria more specifically pose serious threat because of their double layered cell envelope and effective efflux systems, which is a challenge for drugs to penetrate. One promising approach to breach this barrier is the “Trojan horse strategy”. In this technique, an antibiotic molecule is conjugated with a nutrient molecule that helps the antibiotic to enter the cell through dedicated transporters for the nutrient. Here, we explored the approach using biotin conjugation with a florescent molecule …

The Photophysical Studies Of Transition Metal Polyimines Encapsulated In Metal Organic Frameworks (Mof’S), Jacob M. Mayers

USF Tampa Graduate Theses and Dissertations

Light harvesting systems provide a platform that converts solar energy into other forms of energy. One of the most common examples of photon capturing and conversion into chemical energy is observed in photosynthetic organisms in both Eurkaroyic and Prokaryotic domains. Nature provides a model for successful light harvesting platforms which includes the compartmentalization of antenna complexes that contain separated donor and acceptor pairs that participate in efficient electron transfer processes. In order to mimic such systems, crystalline porous materials that exhibits regular cavities and pore dimensions provides an excellent starting place. Metal organic frameworks (MOFs) are a class of porous …

Cu-Catalyzed Phenol O-Methylation With Methylboronic Acid, Mairead E. Bartlett, Yingchuan Zhu, Uma Bhagwat Gaffney, Joyce Lee, Miranda Wu, Betemariam Sharew, Angela K. Chavez, David J. Gorin

Chemistry: Faculty Publications

A Cu-catalyzed oxidative cross-coupling of phenols with methylboronic acid to form aryl methyl ethers has been developed, expanding the scope of Chan-Evans-Lam alkylation. Electron-deficient phenol derivatives with a broad array of functional groups are methylated in high yields. Increased reaction temperature and catalyst loading enables the methylation of substrates incorporating pyridine and dihydroquinolone motifs. Electron-rich phenol derivatives are poor substrates for the methylation; the characterization of C−H homodimerization products formed from these substrates illuminates a competing mechanistic pathway.

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Polyglyoxylamides With A Ph-Mediated Solubility And Depolymerization Switch, Quinton E. A. Sirianni, Xiaoli Liang, Georgina K. Such, Elizabeth Gillies

Chemistry Publications

Self-immolative polymers (SIPs) are characterized by their ability to depolymerize in response to the cleavage of a single end-cap or backbone moiety, making them attractive for numerous applications including sensors, transient plastics, and delivery vehicles. For many applications, it would be desirable to have an SIP capable of depolymerizing selectively under mildly acidic aqueous conditions. However, the poor solubility of most SIPs in water, accompanied by the competing effects of end-cap cleavage and depolymerization mechanisms, has made this a challenge. Here, we describe the development of polyglyoxylamides (PGAms) with pendent amino groups to achieve solubility switching at mildly acidic pH, …

Issue Of False Amphetamine Field Test Positives Caused By Sugar: Use Of Baeyer Test As A Secondary Test Solution, Reed A. Knutson, Jennah Duncan, Kara Peightal, Samuel Thomas

Department of Chemistry: Dissertations, Theses, and Student Research

The Marquis reagent is a well-established and widely used chemical presumptive test for 3,4-Methylenedioxymethamphetamine (MDMA) and methamphetamine. It is composed of concentrated sulfuric acid and 40% formaldehyde, which act upon alkaloids causing them to complex into larger molecules. This complexation causes a color change that can be visually interpreted as a positive or negative result. Almost any sugar molecule can be complexed in this way as well, due to their many OH groups. Experimentally it was found that the sugar molecules did complex with one another when the Marquis test was administered. The color produced by this reaction was brownish-red. …

Investigation Of Immobilized Enzymes In Confined Environment Of Mesoporous Host Matrices, Xiaoliang Wang

USF Tampa Graduate Theses and Dissertations

Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy, is attracting the interest of scientists from different disciplines with the expansion of MOF’s development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, …

Investigating Thermodynamics And Kinetics Of Methylene Blue And Eriochrome Black-T Adsorption On Activated Carbon Prepared From Coconut Husk, Abdul Rahman Wahoud, Lotfi Abdul Samed Bawazer

Hadhramout University Journal of Natural & Applied Sciences

In this research, the adsorption process was studied for methylene blue eriochrome black-T from aqueous solutions on the surface of activated carbon prepared from coconut husk by chemical activation with potassium hydroxide. The results show that the adsorption isotherm for methylene blue follows the Langmuir model while it follows the Freundlich model and the maximum adsorption capacity was 909 mg/g for methylene blue and 262 mg/g for eriochrome black-T. The equilibrium contact time reached in about 90 minutes at lower concentrations and 120 minutes at higher concentrations. Two simplified kinetic models including pseudo-first-order and pseudo-second-order equations were selected to follow …

Kinetic, Equilibrium And Application Studies For Removal Of Methylene Blue From Aqueous Solution Using Sesbenia Dates Activated Carbon, Mohammed Saleh Bashanaini, Gameel Ahmed Baghaffar, Waheeb Abdellah Bin Frejan

Hadhramout University Journal of Natural & Applied Sciences

In the present work, sesbenia dates as local agricultural waste has been successfully used for the preparation of activated carbon (AC) by sulphuric acid. This sulphuric acid based activated carbon (SD) and (MSACS) were used for the removal of one cationic dye viz., methylene blue (MB) from aqueous solutions. The structure and physical and chemical properties of (SD) and (MSACS) are investigated using (FTIR) and (SEM) analysis and pH surface and Boehm titration. The effect of the differential experimental parameters controlling the adsorption of dye onto (SD) and (MSACS), were thoroughly investigated, such as the effect of pH, initial dye …

Electro-Organic Synthesis Of Schiff-Bases And Azo-Schiff Bases By Electrochemical Reduction Of The Nitro Group Group In Different Media, Siba Naseef, Deep Bakair, Rushdi Mador

Hadhramout University Journal of Natural & Applied Sciences

In this research synthesized amino is derivative of Schiff-bases by using electrolysis cell. Electrochemical reduction of para-nitroaniline and electrocatalysed condensation have been carried out at zinc electrode and anode from coal in the presence of potassium chloride as supporting electrolyte in water/methanol solution, and in the application of 20V voltage, where interaction is in two stages: the first stage involves the electrochemical reduction of nitro group and get the amino and the second phase also, azo Schiff was synthesized between para-nitroaniline and metoxybenzealdehyde by electrolysis method, which was supplied with a zinc electrode as cathode to perform electrochemical reduction in …

The Primarily Undergraduate Nanomaterials Cooperative: A New Model For Supporting Collaborative Research At Small Institutions On A National Scale, Steven M. Huges, Mark P. Hendricks, Katherine M. Mullaugh, Mary E. Anderson, Anne K. Bently, Justin G. Clar, Clyde A. Daly Jr., Mark D. Ellison, Z. Vivian Feng, Natalia I. Gonzalex-Pech, Leslie S. Hamachi, Christine L. Heinecke, Joseph D. Keene, Adam M. Maley, Andrea M. Munro, Peter N. Njoki, Jacob H. Olshansky, Katherine E. Plass, Kathryn R. Riley, Matthew D. Sonntag, Sarah K. St. Angelo, Lucas B. Thompson, Emily J. Tollefson, Lauren E. Toote, Korin E. Wheeler

Chemistry Faculty Publications

The Primarily Undergraduate Nanomaterials Cooperative (PUNC) is an organization for research-active faculty studying nanomaterials at Primarily Undergraduate Institutions (PUIs), where undergraduate teaching and research go hand-in-hand. In this perspective, we outline the differences in maintaining an active research group at a PUI compared to an R1 institution. We also discuss the work of PUNC, which focuses on community building, instrument sharing, and facilitating new collaborations. Currently consisting of 37 members from across the United States, PUNC has created an online community consisting of its Web site (nanocooperative.org), a weekly online summer group meeting program for faculty and students, …

Using Covalent Modifications To Distinguish Protein Electrospray Mechanisms: Charged Residue Model (Crm) Vs. Chain Ejection Model (Cem), Lars Konermann, Douglas J. D. Pimlott

Chemistry Publications

Different mechanisms have been proposed for the formation of gaseous protein ions during electrospray ionization (ESI). In the charged residue model (CRM) ions are produced upon nanodroplet evaporation to dryness. This mechanism is thought to dominate in native ESI, where proteins retain compact conformations, with charge states close to the Rayleigh charge of protein-sized aqueous droplets. Much higher charge states are generated from proteins that are unfolded in solution. The chain ejection model (CEM) has been proposed for ESI under such denaturing conditions. In the CEM proteins are gradually expelled, while mobile H⁺ equilibrate between the droplet and its …

Fragment-Based Drug Discovery Of Sars-Cov-2 Therapeutics, Hannah Johnson '22

Student Publications & Research

During the COVID-19 pandemic, the usual drug development timeline has been substantially condensed. This shortened timeline aims to allow for a safe and effective therapy to be discovered as soon as possible as the number of global COVID cases rise. Moreover, the COVID Moonshot open-sourced initiative has allowed the development of a COVID antiviral to accelerate. After the published fragment screening on the main protease (MPro) of SARS-CoV2 yielded 66 fragment hits, a fragment (x0434) was selected to build novel compounds. SeeSAR was used to gather preliminary knowledge of the three-dimensional structure of the biomolecular targeted protein and selected fragment …

Pollution In Rainwater Harvesting: A Challenge For Sustainability And Resilience Of Urban Agriculture, Yang Deng

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Water plays a pivotal role in urban agriculture. Although rainwater harvesting (RWH) is viewed as a sustainable route for crop irrigation at an urban setting, rainwater contaminants challenge the RWH practices due to potential threats to the health of crops, soil, and human (i.e., farm workers and food consumers). This frontier review article first recognized principal pollutants of irrigation concern in harvested rainwater based on literature data and crop irrigation demands. Major traditional pollutants, likely exceeding irrigation quality criteria, include particles, some toxic metals (e.g., Cd, Cu, and Zn), certain synthetic organic chemicals (e.g., agrochemicals and polycyclic aromatic hydrocarbons), and …

College Of Natural Sciences Scholarship Brunch Program, November 6th 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the program for the first annual College of Natural Sciences Scholarship Brunch, held on November 6th, 2021 at McCrory Gardens.

College Of Natural Sciences Newsletter, November 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 11

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Media Coverage of CNS
Page 4 2021 Day of Scholars
Page 5 Astronomy Outreach
Page 6 SDSU Faculty & Students Host American Society for Microbiology Annual Conference
Page 7 Scholarship Brunch
Page 8 Open PRAIRIE Data, SI Final Exam Review Sessions
Page 9 Aamlid Family Anatomy Lab Photos

Facile Synthesis Of Tertiary Amine Pendant Polymers By Cu0-Mediated Atrp Under Aqueous Conditions, Collin M. Britten, Kristen Lason, Keisha Walters

Chemical Engineering Faculty Publications and Presentations

Cu⁰-mediated atom transfer radical polymerization (ATRP) in aqueous media is extended to tertiary amine-pendant methacrylate polymers with poly([2-dimethylamino]ethyl methacrylate) (PDMAEMA) serving as a model polymer. By increasing the concentration of deactivating Cu^II species, reducing the reaction temperature, and increasing the supporting halide concentration to 1 M, polymers with well-defined molecular weight distributions (MWDs) are achieved in under 4 h. MWDs show good agreement with theoretical values, with polydispersity indices (Đ) as low as 1.14. Furthermore, this reaction system shows a remarkable tolerance to dissolved oxygen, with little to no deleterious effects observed for polymerizations run …

Bisindolylmaleimide Ix: A Novel Anti-Sars-Cov2 Agent Targeting Viral Main Protease 3clpro Demonstrated By Virtual Screening Pipeline And In-Vitro Validation Assays, Yash Gupta, Dawid Maciorowski, Samantha E. Zak, Krysten A. Jones, Rahul S. Kathayat, Saara-Anne Azizi, Raman Mathur, Catherine M. Pearce, David J. Ilc, Hamza Husein, Andrew S. Herbert, Ajay Bharti, Brijesh Rathi, Ravi Durvasula, Daniel P. Becker, Bryan C. Dickinson, John M. Dye, Prakasha Kempaiah

Chemistry: Faculty Publications and Other Works

SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2′-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = …

Molecular Mechanisms Underlying Enhanced Hemichannel Function Of A Cataract-Associated Cx50 Mutant, Jun-Jie Tong, Umair Khan, Bassam George Haddad, Peter J. Minogue, Eric C. Beyer, Vivian M. Berthoud, Steve L. Reichow, Lisa Ebihra

Chemistry Faculty Publications and Presentations

Connexin-50 (Cx50) is among the most frequently mutated genes associated with congenital cataracts. Although most of these disease-linked variants cause loss of function because of misfolding or aberrant trafficking, others directly alter channel properties. The mechanistic bases for such functional defects are mostly unknown. We investigated the functional and structural properties of a cataract-linked mutant, Cx50T39R (T39R), in the Xenopus oocyte system. T39R exhibited greatly enhanced hemichannel currents with altered voltage-gating properties compared to Cx50 and induced cell death. Coexpression of mutant T39R with wild-type Cx50 (to mimic the heterozygous state) resulted in hemichannel currents whose properties were indistinguishable from …

Aqueous Wastewater Treatment With Aluminium Oxide, Silicon Dioxide And Alginite, Anifat Adenike Bankole

Theses

Wastewater, regardless of the source, has always found its way into the environment. If not treated it can pose a threat to the life of humans as well as aquatic organisms. In regard to the treatment of wastewater containing remnant organic dyes, the adsorption of these on recyclable sorbent materials such as alginite, alumina, and silica gel was evaluated. The main objective of this thesis is to evaluate the sorption process for dye tainted water specifically stemming from educational and research laboratories. Adsorption studies of the wastewater with sorbent materials were carried out under different experimental conditions. The study investigates …

Preparation And Evaluation Of Crocetin-Coated Biodegradable Polymer On Top Of Magnetite Nanoparticles For Their Anticancer Effects, Sulafa Saeed Abdelhalim

Theses

Liver cancer is still one of the leading causes of cancer-related deaths worldwide. This is due to many reasons including lack of effective drugs, late diagnosis of this type of cancer due to the overlapping of symptoms with many other liver diseases, and lack of effective screening tests. Targeted drug delivery systems offer many promising advantages compared to conventional chemotherapy. Targeted delivery will mitigate the bad side effects of chemotherapy such as drug resistance, low therapeutic value since the drug mostly will be administered through an IV affecting healthy and cancer cells alike, and that leads us to an important …

Synthesis Of Alkylthio Benzene Derivatives Via Simultaneous Diazotization And Nucleophilic Displacement, Abraham Alvarado, Juan D. Deleija, Jose J. Gutierrez

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

Alkylthio benzene derivatives were effectively synthesized by simultaneous diazotization of aromatic amines and nucleophilic displacement. The method is fairly general and proceeds in moderate yields. Product yields were comparable regardless of steric hindrance of the thiol or of the functional group present in the starting material. The newly developed procedure allowed for the incorporation of a tertiary alkylthio group, which cannot be easily introduced otherwise. The products were characterized by 1H NMR and 13C NMR.

Colloidal Nanomaterial Surface Chemistry And Characterization Studied By Linear And Nonlinear Spectroscopy, Asela Sampath Dikkumbura

LSU Doctoral Dissertations

Recent studies have demonstrated the use of nanomaterials such as metallic nanoparticles, liposomes, and polymer microparticles for biomedical applications, encompassing the field of nanomedicine. For developing novel core-shell metallic nanoparticles with controlled surface morphology, the in situ growth dynamics of colloidal silver-gold core-shell (Ag@Au CS) nanoparticles (NPs) in water are monitored in a stepwise synthesis approach using time-dependent second harmonic generation (SHG) and extinction spectroscopy. Transmission electron microscopy images show that the CS NP surface morphology becomes more smooth and uniform as the reaction proceeds, corresponding to lower, stable SHG signals and narrower plasmonic spectra that are compared to finite-difference …

Understanding Hyperporphyrin Spectra: Tddft Calculations On Diprotonated Tetrakis(-Aminophenyl)Porphyrin., Jeanet Conradie, Carl C. Wamser, Abhik Ghosh

Chemistry Faculty Publications and Presentations

A detailed TDDFT study (with all-electron STO-TZ2P basis sets and the COSMO solvation model) has been carried out on the effect of diprotonation on the UV-vis-NIR spectra of free-base tetraphenylporphyrin and tetrakis(-aminophenyl)porphyrin. The diprotonated forms have been modeled as their bis-formate complexes, i.e., as so-called porphyrin diacids. The dramatic redshift of the Q-band of the TAPP diacid has been explained in terms of an elevated "a" HOMO and lowered LUMOs, both reflecting infusion of aminophenyl character into the otherwise classic Gouterman-type frontier MOs. The exercise has also yielded valuable information on the performance of different exchange-correlation functionals. Thus, the hybrid …

Janus-Tinbco2 For Hydrogen Evolution Reaction With High Conductivity And Catalytic Activity, Li-Li Xu, Dong-Yan Ren, Xiao-Feng Zhao, Yong Yi

Journal of Electrochemistry

Exploring the potential hydrogen evolution reaction (HER) catalysts with the high activity and high conductivity has always been a hot spot in the research of renewable energy development. Ti₂C, as one of the 2D-MXene, has excellent properties relating to many active sites, mechanical stability, conductivity, etc., and has become a potential HER catalyst. However, the modification of the surface of Ti₂C by terminal O will reduce the conductivity, thereby limiting the transport of electrons between the valence band and the conduction band. In this study, an electric double layer Janus-TiNbCO₂ was constructed by Nb doping. …

Effect Of Alkyl Chain Length Of Symmetrical Quaternary Ammonium Hydroxide On Oxalic Acid Electroreduction Reaction, Bo Huang, Xin-Sheng Zhang, Dong-Fang Niu, Shuo-Zhen Hu

Journal of Electrochemistry

Glyoxylic acid with the dual characteristics of acid and aldehyde is an important chemical raw material and organic synthesis intermediate, which is extensively used in the perfumery, pharmaceutical and fine chemical industries. A family of symmetric quaternary ammonium hydroxides (QAHs) with different alkyl chain lengths was used as the additives in generating glyoxylic acid from oxalic acid electroreduction reaction (OAER). The effects of alkyl chain length on OAER and the corresponding side reaction, i.e., hydrogen evolution reaction (HER), were investigated. Linear sweep voltammetric (LSV) results showed that the adsorption of the additives suppressed more on the HER than that on …