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Full-Text Articles in Chemistry

Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey Feb 2019

Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey

All Dissertations, Theses, and Capstone Projects

The displacement of water from surfaces upon biomolecular recognition and association makes a significant contribution to the free energy changes of these processes. We therefore posit that accurate characterization of local structural and thermodynamic molecular water properties can improve computational model accuracy and predictivity of recognition and association processes. In this thesis, we discuss Solvation Thermodynamic Mapping (STM) methods that we have developed using inhomogeneous fluid solvation theory (IST) to better characterize active site water structural and thermodynamic properties on protein surfaces and the open source tools that we have developed, GIST-CPPTRAJ and SSTMap, which implement these methods which we ...


Palladium Complexes Bearing Κ²-N,N And Κ³-N,N,O Pendant Amine Bis(Phenolate) Ligands, Brendan J. Graziano, Eric M. Collins, Nathaniel C. Mccutcheon, Claire L. Griffith, Nicole M. Braunscheidel, Trilisa M. Perrine, Bradley M. Wile Jan 2019

Palladium Complexes Bearing Κ²-N,N And Κ³-N,N,O Pendant Amine Bis(Phenolate) Ligands, Brendan J. Graziano, Eric M. Collins, Nathaniel C. Mccutcheon, Claire L. Griffith, Nicole M. Braunscheidel, Trilisa M. Perrine, Bradley M. Wile

Chemistry Faculty Scholarship

The synthesis and characterization of ten new palladium(II) amine bis(phenolate) complexes is reported. Solution and single-crystal X-ray diffraction studies reveal the presence of both κ2-N,N and κ3-N,N,O binding modes in these square planar complexes. For complexes with sterically less demanding phenolate donors, addition of external acidic or basic reagents allows for the selective masking of a coordination site at Pd. Complexes bearing bulky cumyl substituents on phenolate donors exhibited unusual 1H NMR spectroscopic features that are consistent with an anagostic interaction with the palladium center. Computational analysis at the ωB97X-D ...


Inhibition Of Hsv-1 Binding By Egcg-Stearate, Valerie Paschalis Jan 2019

Inhibition Of Hsv-1 Binding By Egcg-Stearate, Valerie Paschalis

Theses, Dissertations and Culminating Projects

Herpes simplex virus type 1 (HSV-1) is the causative agent of oral herpes, and is able to establish lifelong latent infection along with painful, recurring symptoms. Epigallocatechin-3- gallate (EGCG) is the most abundant polyphenol derived from green tea (Camellia sinensis), whose anti-inflammatory, antioxidant, anti-cancer, and antiviral properties have been widely studied. Although EGCG is not chemically stable and has poor hydrophobicity, lipophilic derivatives of EGCG have shown increased stability as well as increased antiviral efficacy against HSV. Previous studies have demonstrated that EGCG stearate (EGCG-S), a derivative of EGCG esterified at the 4’ position with stearic acid, is able to ...


Call For Abstracts - Resrb 2019, July 8-9, Wrocław, Poland, Wojciech M. Budzianowski Dec 2018

Call For Abstracts - Resrb 2019, July 8-9, Wrocław, Poland, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.


Side Chain Modifications To Improve Peptide Structure–Activity Relations, Neelam Lahankar Dec 2018

Side Chain Modifications To Improve Peptide Structure–Activity Relations, Neelam Lahankar

Seton Hall University Dissertations and Theses (ETDs)

While natural peptides, are ideal starting points for peptide-based drug design and development, they suffer from high conformational instability, which results in susceptibility to proteolytic degradation and poor bioavailability. Peptidomimetics in recent years has helped circumvent these shortcomings by improving the pharmacological properties of polypeptides. Peptidomimetics contain essential elements (pharmacophores) that mimic a natural peptide or protein in 3D space and retain the ability to interact with the biological target producing the same biological effect. In contrast, they offer conformationally restricted structures, potentially minimizing cross-target interactions, which leads to better transport properties through biologic membranes and resistance to immune responses ...


Inequality, Rubber, And Thermodynamics In Indonesia, Ernest M. Oleksy Dec 2018

Inequality, Rubber, And Thermodynamics In Indonesia, Ernest M. Oleksy

The Downtown Review

Intersectionality has led the charge in ensuring that workplace justice is assured to all people, irrespective of their identities. While intersectionality is a useful theory for explaining inequality, what must not be understated is the contributions that postcolonialism and the blue-collar working identity can have on harsh working conditions. Particularly, miners in Indonesia have had to work in very hostile environments where they are at-risk for sulfur poisoning as they mine for materials to vulcanize rubber. This article serves two purposes. The first is to call attention to how place can help explain the differential experiences of miners in the ...


The Chemical Causes And Social Effects Of Acid Rain, Ernest M. Oleksy Dec 2018

The Chemical Causes And Social Effects Of Acid Rain, Ernest M. Oleksy

The Downtown Review

While global warming tends to dominate the collective conscious for environmentalism of academics and the public alike, many other physical phenomena bear serious implications for humanity's future. One such phenomenon, acid rain, has been under-reported considering how damaging it is to the ecosystem and how much politicking is involved when determining how to address it. This article serves two purposes. The first is to inform readers of the basic chemical processes underlying acid rain and why it is damaging to organisms. The second is to inform readers of how acid rain has been portrayed by other publications, like the ...


Heat And Work, The First Law Of Thermodynamics From The Boltzmann Pov, Carl W. David Dec 2018

Heat And Work, The First Law Of Thermodynamics From The Boltzmann Pov, Carl W. David

Chemistry Education Materials

The First Law of Thermodynamics is discussed in terms of the Boltzmann distribution.


My Experience Teaching General Chemistry To A Student Who Is Visually Impaired, Katherine M E Stewart Dec 2018

My Experience Teaching General Chemistry To A Student Who Is Visually Impaired, Katherine M E Stewart

Journal of Science Education for Students with Disabilities

This paper summarizes my experience with teaching a first-year, General Chemistry course to a visually impaired student. This includes accommodations and modifications for both the lecture material and the laboratory. Included are also examples of formats and syntax for txt-based quizzes, tests, and laboratory reports, as well as other general accommodations for both the student and the service dog.


Novel Dna Origami Based Lateral Flow Assay Development, Adrienne Walker Dec 2018

Novel Dna Origami Based Lateral Flow Assay Development, Adrienne Walker

Adrienne Walker

Lateral flow assays (LFA) are used for point-of-care qualitative diagnostics of an analyte of interest, often in non-laboratory environments. Traditionally, the format of a lateral flow assay utilizes immobilized antibodies on a membrane as the capture probe in conjunction with a reporting immunological recognition system for an analyte captured between them in a sandwich format. However, there are several shortcomings of antibodies which recommend their replacement with other recognition elements if possible. Among the reasons for seeking alternatives are the long time required to raise and identify a selective and strongly binding antibody, the cost of antibodies, their poor shelf ...


Novel Dna Origami Based Lateral Flow Assay Development, Adrienne Walker Dec 2018

Novel Dna Origami Based Lateral Flow Assay Development, Adrienne Walker

Adrienne Walker

Lateral flow assays (LFA) are used for point-of-care qualitative diagnostics of an analyte of interest, often in non-laboratory environments. Traditionally, the format of a lateral flow assay utilizes immobilized antibodies on a membrane as the capture probe in conjunction with a reporting immunological recognition system for an analyte captured between them in a sandwich format. However, there are several shortcomings of antibodies which recommend their replacement with other recognition elements if possible. Among the reasons for seeking alternatives are the long time required to raise and identify a selective and strongly binding antibody, the cost of antibodies, their poor shelf ...


Nonlinear Optical Characterization Of Solids, Alex Farnsworth Dec 2018

Nonlinear Optical Characterization Of Solids, Alex Farnsworth

Undergraduate Honors Theses

Vibrational Sum Frequency Generation (VSFG) and the similar Second Harmonic Generation (SHG) are both classified as nonlinear optical phenomena, with the hallmark trait being that the input and output frequencies are different. Both of these systems are remarkable tools due to their surface specific nature. Still, there is much that is not known about the response from these systems, especially the nonresonant SFG response. We have worked to better understand SFG signal, specifically the nonresonant temporal profile. We have also collected results that call into question some underlying assumptions about time-based suppression methods when working with single crystal substrates.

As ...


Polyhedral Oligomeric Silsesquioxane-Phosphate Glass Matrix Nanocomposites With Additional Chapter On Phosphate Glass-Poly(Ethylene Terephthalate) Matrix Composites, Kyoungtae Kim Dec 2018

Polyhedral Oligomeric Silsesquioxane-Phosphate Glass Matrix Nanocomposites With Additional Chapter On Phosphate Glass-Poly(Ethylene Terephthalate) Matrix Composites, Kyoungtae Kim

Dissertations

Preparation and characterization of tin fluorophosphate glass (Pglass) matrix nanocomposites incorporating polyhedral oligomeric silsesquioxane (POSS) were investigated on the structural, thermal, morphological, mechanical, and rheological properties. Various processes including synthesis, extrusion and sintering processes were applied to prepare the nanocomposite samples. Another application of POSS with hydrophobic functional groups on the well-structured nanoscale silicate cage with three silanol groups was investigated to present the feasibility to use POSS molecule as a coating material on the surface of the hydrophilic inorganic glass. In addition, Poly(ethylene terephthalate) polymer matrix composites incorporating Pglass was studied to present the benefits of the Pglass ...


Chemistry Student Attitudes And Utilization Of Office Hours, Dieng Barbacar, Edgar Gomez, Andre Rodriguez Dec 2018

Chemistry Student Attitudes And Utilization Of Office Hours, Dieng Barbacar, Edgar Gomez, Andre Rodriguez

Publications and Research

While research has demonstrated that faculty-student interactions increase retention and graduation rates, faculty often report that their office hours are underutilized. To better understand students’ attitudes, usage and plans towards faculty hours a survey was administered in the second to third week of the fall 2018 semester to students in 5 sections of general chemistry courses. The goal was to better understand how students perceive the benefits and hindrances of office hours, along with current or planned attendance. Prior to survey administration, it was speculated that not attending office hours could be because they were not scheduled at a convenient ...


Blue Carbon: Methane Emissions From Managed Saline Ponds In The South Bay Salt Pond Restoration Project, San Francisco Bay, Haley J. Miller, Glenn E. Woerndle, Steve Crooks, Jason K. Keller Dec 2018

Blue Carbon: Methane Emissions From Managed Saline Ponds In The South Bay Salt Pond Restoration Project, San Francisco Bay, Haley J. Miller, Glenn E. Woerndle, Steve Crooks, Jason K. Keller

Biology, Chemistry, and Environmental Sciences Faculty Data Sets

This data set reports net methane (CH4) emissions from managed saline ponds and a restored salt marsh associated with the South Bay Salt Ponds Restoration Project, San Francisco Bay, CA, USA. Associated biogeochemical and physical data are also reported. Data were collected on five sampling dates over the course of the study: November 2016, January 2017, March 2017, June 2017 and August 2017. Logistics (e.g., weather and road conditions) and nesting birds did not allow us to sample all locations during all sampling events.

Methane emissions were measured using static chambers and biogeochemical data were measured on porewater ...


Computational Quantum Chemistry Studies Of The Interactions Of Amino Acids Side Chains With The Guanine Radical Cation., Edward Acheampong Dec 2018

Computational Quantum Chemistry Studies Of The Interactions Of Amino Acids Side Chains With The Guanine Radical Cation., Edward Acheampong

Electronic Theses and Dissertations

Guanine is generally accepted as the most easily oxidized DNA base when cells are subjected to ionizing radiation, photoionization or photosensitization. At pH 7, the midpoint reduction potential is on the order of 0.2 – 0.3 V higher than those of the radicals of e.g. tyrosine, tryptophan cysteine and histidine, so that the radical “repair” (or at least, a thermodynamically favorable reaction) involving these amino acids is feasible. Computational quantum studies have been done on tyrosine, tryptophan, cysteine and histidine side chains as they appear in histones. Density functional theory was employed using B3LYP/6-31G+ (d, p) basis ...


Ray Et Al.: Pheromone Of The Velvet Longhorned Beetle Trichoferus Campestris, Ann M. Ray, Joseph A. Francese, Yunfan Zou, Kristopher Watson, Damon J. Crook, Jocelyn G. Millar Dec 2018

Ray Et Al.: Pheromone Of The Velvet Longhorned Beetle Trichoferus Campestris, Ann M. Ray, Joseph A. Francese, Yunfan Zou, Kristopher Watson, Damon J. Crook, Jocelyn G. Millar

Faculty Scholarship

No abstract provided.


Relative Permittivity As A Function Of Co-Solvent And Impedance Spectroscopy For Quantifying Anions In Solution, Yahya Sami Alseiha Dec 2018

Relative Permittivity As A Function Of Co-Solvent And Impedance Spectroscopy For Quantifying Anions In Solution, Yahya Sami Alseiha

Electronic Theses and Dissertations

This work measured relative permittivity from 15.0 to 55.0 °C of aqueous solutions containing acetone or tetrahydrofuran using a BI 870 dielectric meter. A cubic polynomial fit resulted in coefficients for calculating permittivity as a function of temperature and mole fraction. Literature values for other co-solvent system resulted in similar polynomial coefficients. Using BI 870, permittivity measurements of ionic solutions were not possible because of high conductivity. A simple method using impedance spectroscopy measured these solutions. Impedance decreases with increasing temperature and decreases with increasing ionic strength. Due to the temperature dependence of impedance, all measurements were at ...


Extraction And Purification Of Biologically Active Metabolites From Rhodococcus Sp. Mtm3w5.2, Mohrah Alenazi Dec 2018

Extraction And Purification Of Biologically Active Metabolites From Rhodococcus Sp. Mtm3w5.2, Mohrah Alenazi

Electronic Theses and Dissertations

Rhodococcushas been recognized as a potential antibiotic producer. Recently, a strain of Rhodococcussp. MTM3W5.2 was isolated from a soil sample collected in Morristown, Tennessee and was found to produce an inhibitory compound which is active against other related species. The purpose of this research is to extract, purify and analyze the active metabolite. The compound was extracted from RM broth cultures and purified by preliminary fractionation of crude extract through a Sephadex LH-20 column. Further purification was completed using semi-preparative reversed phase column chromatography. Final purification was obtained using multiple rounds of an analytical C18 HPLC column ...


Molecular Dynamics Investigation Of The Thermodynamics Of Nanoscale Droplets And Kinetics Of Weakly Correlated Systems, Kai Yang Leong Dec 2018

Molecular Dynamics Investigation Of The Thermodynamics Of Nanoscale Droplets And Kinetics Of Weakly Correlated Systems, Kai Yang Leong

Theses and Dissertations

The surface tension of nanoscale droplets of water was studied with molecular dynamics simulations using the BLYPSP-4F water potential. The internal pressure of the droplet was measured using a correlation between the pressure and density, established through a series of bulk simulations performed at pressures from 1 to 1000 bar. Such a procedure allows for reliable determination of internal pressure without the need to calculate the local Virial. The surface tension, estimated with the Young-Laplace relation, shows a good agreement with the Tolman equation with a Tolman length of -0.48 Å. The interface of a liquid water droplet is ...


Synthesis, Characterization, And Catalytic Activity Of Copper Palladium Oxide Solid Solutions., Gregory L. Christensen Dec 2018

Synthesis, Characterization, And Catalytic Activity Of Copper Palladium Oxide Solid Solutions., Gregory L. Christensen

Student Research Projects, Dissertations, and Theses - Chemistry Department

CuxPd1-xO forms a homogeneous solid solution over the wide range of 0 ≤ x ≤ 0.725 in which compositional variation can be correlated with structural and chemical environmental changes. After a small lag at low Cu2+ concentrations, where the lattice cell parameters are pinned to that of the pure PdO structure, CuxPd1-xO lattice parameters follow Vegard’s law in which the cell volume decreases linearly with x, indicating a homogenous solution in which Cu2+ randomly replaces the larger Pd2+ cation. The crystal structure also undergoes an increase in the c ...


Synthesis Of Dicamba Glucosides For The Study Of Environmental Dicamba Drift Effects On Soybeans, Holly Wallace Dec 2018

Synthesis Of Dicamba Glucosides For The Study Of Environmental Dicamba Drift Effects On Soybeans, Holly Wallace

Theses and Dissertations

The most popular herbicide used for weed control has been glyphosate for many years in the Midwestern United States. Plants have begun to develop a resistance to glyphosate due to over use of the herbicide. This herbicide resistance has pushed farmers to turn to alternative herbicides such as dicamba and 2,4-D. Recently agrochemical companies have developed genetically modified crops that are resistant to herbicides such as dicamba. These modified crops allow farmers to spray their fields with dicamba without fear of crop damage. Farmers of non-genetically modified crops, however, suffer damage and loss of yield from herbicide drift effects ...


Inorganic Electrocatalysts For Innovative Water Splitting And Organic Upgrading, Nan Jiang Dec 2018

Inorganic Electrocatalysts For Innovative Water Splitting And Organic Upgrading, Nan Jiang

All Graduate Theses and Dissertations

The booming worldwide demand for energy and the increasing concerns about global warming due to fossil fuel consumption have urged the development of techniques for storing and converting renewable and clean energy resources. Electrocatlytic or photoelectrocatalytic water splitting to generate green energy carrier H2 with sustainable energy input, like solar, has been regarded as an attractive strategy for carbon-neutral energy needs. However, the sluggish kinetics for both half reactions (HER and OER), high overpotentials and thermodynamic requirements, and H2 and O2 gas crossover have been regarded as the major challenges, which limit its widespread application.

On account ...


Carbon Monoxide On Demand: Light-Induced Co Release Of Flavonols, Stacey N. Anderson Dec 2018

Carbon Monoxide On Demand: Light-Induced Co Release Of Flavonols, Stacey N. Anderson

All Graduate Theses and Dissertations

Carbon monoxide (CO) is an extremely useful molecule with applications in industrial manufacturing, synthetic procedures as a C1 building block, and as a potential pharmaceutical to produce anti-inflammatory effects and vasodilation. However, the toxicity associated with CO has prevented its full utilization. In order to safely handle CO, compounds and molecules have been developed that act as storage materials for the gas. Ideal storage platforms only release CO upon stimulation via a trigger. Light activation is the most desirable trigger as it can be regulated in terms of the intensity and the wavelength of light used. The majority of light-induced ...


Quantum Mechanical Studies Of N-H···N Hydrogen Bonding In Acetamide Derivatives And Amino Acids, Sandra J. Lundell Dec 2018

Quantum Mechanical Studies Of N-H···N Hydrogen Bonding In Acetamide Derivatives And Amino Acids, Sandra J. Lundell

All Graduate Theses and Dissertations

Proteins are made of vast chains of amino acids that twist and fold into intricate designs. These structures are held in place by networks of noncovalent interactions. One of these, the hydrogen bond, forms bridges between adjacent pieces of the protein chain and is one of the most important contributors to the shape and stability of proteins. Hydrogen bonds come in all shapes and sizes and a full understanding of these not only aids in our understanding of proteins in general but can bridge the gap to finding cures to many protein-related diseases, such as sickle-cell anemia. The primary aim ...


Cigarette Litter Leachates: A Statistical Study Of Elements In Freshwater And Saltwater, Cintly Guzman Hernandez Dec 2018

Cigarette Litter Leachates: A Statistical Study Of Elements In Freshwater And Saltwater, Cintly Guzman Hernandez

Honors Theses

Cigarette butts are the most common item found in coastal litter cleanups as approximately 4.5 trillion smoked cigarette butts are discarded into the environment every year. Cigarette butts can leach toxic heavy metals and nicotine along with other compounds from tobacco combustion. Past research in our lab has analyzed elements leached from cigarette butts into freshwater. The cigarette butts consisted of smoked and unsmoked butts that were soaked varying periods of time, and at different pH levels to identify the relationship of these variables to the amount of metal leached. The elements analyzed were Al, Ba, Cd, Cr, Cu ...


Nano To Global: Small Structures And Their Impact On Energy Markets, Kurt W. Kolasinski Nov 2018

Nano To Global: Small Structures And Their Impact On Energy Markets, Kurt W. Kolasinski

Sustainability Research & Creative Activities Seminar Presentations

No abstract provided.


Molecular Fossils From Phytoplankton Reveal Secular Pco2 Trend Over The Phanerozoic, Caitlyn R. Witkowski, Johan W. H. Weijers, Brian S. Blais, Stefan Schouten, Jaap S. Sinninghe Damsté Nov 2018

Molecular Fossils From Phytoplankton Reveal Secular Pco2 Trend Over The Phanerozoic, Caitlyn R. Witkowski, Johan W. H. Weijers, Brian S. Blais, Stefan Schouten, Jaap S. Sinninghe Damsté

Science and Technology Faculty Journal Articles

Past changes in the atmospheric concentration of carbon dioxide (PCO2) have had a major impact on earth system dynamics; yet, reconstructing secular trends of past PCO2 remains a prevalent challenge in paleoclimate studies. The current long-term PCO2reconstructions rely largely on the compilation of many different proxies, often with discrepancies among proxies, particularly for periods older than 100 million years (Ma). Here, we reconstructed Phanerozoic PCO2 from a single proxy: the stable carbon isotopic fractionation associated with photosynthesis (Ɛp) that increases as PCO2 increases. This concept has been widely applied to alkenones, but here, we expand ...


Spontaneity, Carl W. David Nov 2018

Spontaneity, Carl W. David

Chemistry Education Materials

An attempt is made to better understand thermodynamic spontaneity.


Arsenoplatins Vs. Combination Of Platinum Drugs And Arsenic Trioxide, Denana Miodragovic Nov 2018

Arsenoplatins Vs. Combination Of Platinum Drugs And Arsenic Trioxide, Denana Miodragovic

Faculty Research and Creative Activities Symposium

No abstract provided.