Other Chemistry Commons^™

Nanoscale Imaging Of Electrocatalytic Nanomaterials By High-Resolution Scanning Electrochemical Microscopy, Xiang Wang

Dissertations, Theses, and Capstone Projects

Numerous insights of the structure–electrochemical activity relationship of nanocatalysts have been obtained by using macroscopic electrochemical measurements over the last several decades. However, signals measured by large electrodes are inevitably averaged out of many nanocatalysts, non-uniformed sizes, uneven morphologies, and multiple crystallographic facets. Over the last ten years, Scanning Electrochemical Microscopy (SECM) has advanced electrochemical measurements toward micro- to nanoscale level at a high spatial resolution. The advantages of using nanoelectrode in SECM include fast mass transfer of reactive species, dominated radial diffusion pattern, small double layer capacitance and small RC constant. In this thesis, high-resolution SECM is applied to …

Analysis Of Blue Fountain Pen Ink By Uv-Vis Spectroscopy, Atr-Ftir Spectroscopy, And Thin Layer Chromatography Enhanced With Rgb Spot Evaluation To Construct A Database For Comparison And Identification., Elliot D. Quinteros

Dissertations and Theses

Pen ink can be a crucial piece of physical evidence in the area of Forensic Science. For example, evidence such as notes, letters, printed documents, checks, currency, ransom notes, and books may contain ink. Analysis of ink is typically done for identification or differentiation purposes. To improve existing methods, it was proposed to create a database with many samples and experimental information. The methods used and evaluated were thin-layer chromatography (TLC) enhanced with RGB spot evaluation, UV-Vis spectroscopy, and ATR-FTIR spectroscopy. All three methods were used to analyze 89 fountain pen ink samples. All three methods were able to discriminate …

Enhanced Platinum (Ii) Drug Delivery For Anti-Cancer Therapy, Marek T. Wlodarczyk

Dissertations, Theses, and Capstone Projects

Over the years, anti-cancer therapies have improved the overall survival rate of patients. Nevertheless, the traditional free drug therapies still suffer from side effects and systemic toxicity, resulting in low drug dosages in the clinic. This often leads to suboptimal drug concentrations reaching cancer cells, contributing to treatment failure and drug resistance. Among available anti-cancer therapies, metallodrugs are of great interest. Platinum (II)-based agents are highly potent and are used to treat many cancers, including ovarian cancer (OC). Cisplatin (cis-diaminedichloroplatinum (II)) is the first Food and Drug Administration (FDA)-approved metallodrug for treatment of solid tumors, and its mechanism …

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

Mapping Gadolinium Contrast In A Complex Ionic And Photosynthesis Environment Of Pineapple By Near-Infrared And X-Ray Imaging, Subhendra Sarkar, Zoya Vinokur, Chen Xu, Tetiana Soloviova, Amina Shahbaz, Aldona Gjoni

Publications and Research

This work explores the diffusivity of a lanthanide complex, Eovist (Gadolinium-Ethoxy Benzyl Diethylenetriamine pentaacetate) that is stable in neutral media but is not in acidic environment. In the current work an acidic fruit model like pineapple that is rich in transition metals was used and a possible transmetallation reaction among Eovist and transition metal complexes was tested using X-ray imaging. Another goal of this work was to perturb the usual and the unusual photosynthesis systems that pineapple has maintained for millions of years during the evolution of circadian genes for efficient water conservation by dark photosynthesis. To detect such photosynthesis …

Chemistry 104 Laboratory Manual, Boris Kalmatsky

Open Educational Resources

No abstract provided.

The Use Of A Modified Hess’ Cognitive Rigor Matrix To Assess Students’ Depth Of Knowledge In Key Concepts Of Gas Stoichiometry And Chemical Equilibrium, Maria Greene

Dissertations, Theses, and Capstone Projects

The research presented as part of this dissertation is a combination of two separate studies conducted to assess and evaluate undergraduate general chemistry students’ understanding and depth of knowledge (DOK) of concepts in gas stoichiometry and chemical equilibrium. The two separate studies were conducted using a modified Hess Cognitive Rigor Matrix (CRM) to analyze students’ responses to multiple-choice questions (MCQ) and their written rationales to their answer choices. The Hess Cognitive Rigor Matrix, which is an incorporation and coordination of both Bloom’s and Webb’s DOK taxonomies, allowed the facilitation of the opportunity to code students’ written responses across the four …

Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman

Publications and Research

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …

Development Of A Screening Method For Drugs Of Abuse By Direct Analysis Of Dried Urine Spots Coupled To Mass Spectrometry, Melanie Goldstein

Student Theses

Fast and easy screening procedures are essential in any forensic toxicology laboratory to differentiate negative samples from presumptive positive cases. Immunoassay techniques, such as enzyme multiplied immunoassay technique (EMIT), are routinely employed as screening procedures. However, these techniques lack specificity (only differentiate group of drugs and not individual compounds) and it is difficult to add new compounds to the panel. Direct analysis of dried urine spots (DUS) by mass spectrometry (MS) offers a novel strategy to overcome these issues. DUS offer an improved storage alternative for biological samples, reducing costs and space requirements. In this work, an original method to …

The Forensic Analysis Of Skin-Safe Stamp Pad Inks, Swetha Rajagopal

Student Theses

Skin-safe stamp pad inks are currently being used at locations such as clubs, zoos and other events with the purpose of stamping individuals that visit the location. This is done in an attempt to monitor the number and activity of visitors. Ink manufacturing companies generally tend to experiment with a number of different combinations of the different components of ink, in order to obtain desirable properties. The combinations are usually proprietary and that very nature of the inks ends up making them, possibly unique and individual. The analysis, identification and possible individualization of the chemical composition of these inks could …

Preparation Of Enantioenriched Alkyltin Species And Their Application In Stereospecific Transformations, Glenn O. Ralph

Dissertations, Theses, and Capstone Projects

Organometallic reagents containing the tin-carbon bond are used extensively in modern synthetic chemistry for the formation of new bonds to carbon. Over recent decades, transition metal catalyzed cross coupling reactions between two C(sp²) centers have been widely developed. However, the introduction of a C(sp³) center complicates the catalytic cycle, and opens unproductive chemical pathways which lead to isomerization, elimination, and racemization. Our lab has developed a modified-Stille reaction to combat the deleterious effects of β-hydride elimination. Our protocol enables unactivated 2° alkyl organotin nucleophiles to undergo efficient cross coupling reactions with C(sp²) electrophiles, avoiding …

Valence Electrons And Charge On Ions. (Worksheet), Katarzyna Dorota Chung

Open Educational Resources

No abstract provided.

Organic Photochemistry: Remote Delivery Of Reactive Oxygen Intermediates Via A Heterogeneous Approach, Niluksha Walalawela Abeykoon

Dissertations, Theses, and Capstone Projects

Photosensitized oxidation reactions produce a number of intermediates species, which are generated in varying amounts over time. This complexity presents major challenges in the study of oxidation processes. Mechanistic efforts to separate and deliver reactive oxygen intermediates enable their controlled use in processes such as bacterial inactivation. This thesis describes a heterogeneous reaction approach taken to control the generation and delivery of reactive oxygen intermediates. The mechanistic details of photosensitized reactions were elucidated via synthetic, materials, and physical organic techniques to optimize the delivery of reactive oxygen intermediates. This thesis contains six chapters as described below.

Chapter 1 gives a …

Experiential Learning Activity: Biodiesel Inquiry Project, Ji Kim

Open Educational Resources

The activity described herein can be implemented in introductory chemistry and high school chemistry courses. The main goal of the project is to integrate a ubiquitous biodiesel production with experiential learning by providing a community-based project. The students work in groups, research the benefits of using biodiesel over petroleum-based diesel, collect waste cooking oil from home or restaurants, develop simple and cost-effective methods to produce biodiesel.

The Quantification Of Cocaine From The Erythroxylum Coca Plant And The Comparison On High Performance Liquid Chromatography And Gas Chromatography Mass Spectroscopy As An Analytical Method., Tuesday James

Student Theses

Cocaine is derived from the Erythroxylum coca plant, is a highly addictive stimulant abused all over the world. There are two types of Erythroxylum coca plants that produce cocaine; the E. Coca and E. Novogranatense. Cocaine exists as the salt, and the freebase which is typically referred to as “crack” due to the crackling sound it makes when heated. It is popular because it is inexpensive and easily available on the streets, mainly in poor urban areas. The purpose of this project was to determine the amount of cocaine that can be extracted from E.coca and to assess which analytical …

The Advanced Spectroscopic Analysis Of Organic Gunshot Residue And Explosives, Jennifer M. Leonard

Dissertations, Theses, and Capstone Projects

With the prevalence of shooting cases and terrorist attacks/or threats that plague the current state of the criminal justice system, it is of paramount importance to be able to detect, identify and interpret the presence of gunshot residue or explosives material. This concern is seen in law enforcement agencies and the media throughout the United States and abroad.

Currently, the typical method of analyzing gunshot residue in most crime laboratories serves to identify the inorganic constituents of the primer residue, namely lead, barium and antimony. However, it is possible that the organic matter from the propellant could provide different information …

From The Making To The Tuning To The Use Of Chlorins For Biomedical Applications, Junior Gonzales

Dissertations, Theses, and Capstone Projects

Chlorins are porphyrins missing a double bond. These pigments are optimal platforms for the development of novel dyes that display drug-like attributes such as photodynamic therapy (PDT) agents. More recently, it was demonstrated that chlorins can serve both as a PDT agent and as a modality for fluorescence or PET imaging. Thus, multifunctional chlorins eliminate the differences that may occur in specificity, uptake, and distribution between separate compounds or constructs for imaging and therapy. The overall goal of this dissertation is to take advantage of the reputed intrinsic attributes of chlorins as a viable tool in biomedical applications. In this …

Chelating Ligands And Nanomaterials Based On Graphene Oxide For The Reduction And Sequestration Of Radiometals And Protein Purification, Sam Groveman

Dissertations, Theses, and Capstone Projects

Nuclear waste remediation and protein purification using immobilized metals can benefit enormously from the design and implementation of novel chelating nanomaterials. Available commercial resins capable of sequestering metals are based on bulk materials such as organic polymers, ceramics, and their composites. The use of two-dimensional nanoplatforms with large surface areas expands the horizon for the research and development of new systems with higher efficiency and lower cost. Fundamental science challenges remain in the synthesis and characterization of these nanomaterials and their integration with known or novel coordinating ligands.

Chemical exfoliation of graphite under strong oxidizing conditions yields graphene oxide (GO) …

Design Of Collagen-Mimetic Peptides, Parminder Jeet Kaur

Dissertations, Theses, and Capstone Projects

Collagen is the major component of the extracellular matrix and is involved in a wide range of cellular functions during tissue development and action. At the core of the diverse functions of this versatile protein is its remarkable ability to form supramolecular structures through self-assembly and/or through interactions with other biomolecules. One typical example of such supramolecular structure is the fibrils of collagen types I, II and III of the connective tissues. These fibrils have staggered arrangement of the laterally associated collagen triple helices – the structural unit of collagen – to form long, smooth fibrils with a characteristic 67 …

Probing The Structure And Photophysics Of Porphyrinoid Systems For Functional Materials, Christopher D. Farley

Dissertations, Theses, and Capstone Projects

Porphyrins (Pors) and their many cousins, including phthalocyanines (Pcs), corroles (Cors), subphthalocyanines (SubPcs), porphyrazines (Pzs), and naphthalocyanines (NPcs), play amazingly diverse roles in biological and non-biological systems because of their unique and tunable physical and chemical properties. These compounds, collectively known as porphyrinoids, can be employed in any number of functional devices that have the potential to address the challenges of modern society. Their incorporation into such devices, however, depends on many structural factors that must be well understood and carefully controlled in order to achieve the desired behavior. Self-assembly and self-organization are key processes for developing these new technologies, …

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and …

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is …