Chemistry Commons^™

Fluorescence Microscopy Of Biophysical Protein Dynamics In Nanoporous Hydrogels, Anuj Saini, Lydia Kisley

Faculty Scholarship

Proteins within nanoporous hydrogels have important biotechnological applications in pharmaceutical purification, tissue engineering, water treatment, biosensors, and medical implants. Yet, oftentimes proteins that are functional in solution lose activity when in contact with soft, nanostructured, condensed phase materials due to perturbations in the folded state, conformation, diffusion, and adsorption dynamics of the protein by the material. Fluorescence microscopy experimentally measures the biophysical dynamics of proteins within hydrogels at the nanoscale and can overcome the limitations of conventional ensemble techniques. An explanation of the benefits of fluorescence is provided, and principles of fluorescence microscope instrumentation and analysis are discussed. Then several …

An Exploration Of Protein And Dna Components In Fingerprint Residue, Ashley Borrego

Student Theses

The main focus of this project was to investigate the protein and DNA components in both sebaceous and eccrine fingerprints. This study investigated the relative content of DNA and proteins in eccrine fingerprints to sebaceous fingerprints. All volunteers were instructed to wash and dry their hands prior to depositing parallel thumbprints. Twenty volunteers were instructed to touch their face to produce sebaceous prints, and 5 volunteers were instructed to wear gloves over a heat source to produce sweaty or eccrine prints. Microscopy was used to score the cellular debris of the right fingerprint on a scale of 1-4 based on …

Modeling Chemical Reactivity In Aqueous And Organic Systems: From Electronic Structure Methods To Force Field Development, Caitlin Gibson Bresnahan

LSU Doctoral Dissertations

Modeling reactivity in chemical systems has evolved dramatically in line with the capabilities of modern computing. Despite the advances in computational ability, the level in which one can model a system depends on a number of factors including the region of reactivity, size of the system, level of sophistication required in the molecular description, and so on. Electronic structure methods allow for a detailed description of the potential energy surface and inherently include all essential physics required for reactivity to occur, however these methods are limited by their computational expense. On the other hand, force fields allow for an atomistic …

Our Envirome, Spring/Summer 2019, Issue 40

Sustain Magazine

No abstract provided.

Plastic Pollution, Fall/Winter 2019, Issue 39.3

Sustain Magazine

No abstract provided.

Plastic Pollution, Fall/Winter 2019, Issue 39.2

Sustain Magazine

No abstract provided.

Plastic Pollution, Fall/Winter 2019, Issue 39

Sustain Magazine

No abstract provided.

Synthesis Of Unsymmetrical Bis(Phosphine) Oxides And Their Phosphines Via Secondary Phosphine Oxide Precursors, James R. Pedroarena, Bryan P. Nell, Lev N. Zakharov, David R. Tyler

Chemistry Publications

The unsymmetrical bidentate phosphine ligands (Me)₂PCH₂CH₂CH₂P(Et)₂ (14), (Me)₂PCH₂CH₂CH₂P(iPr)₂ (15), (Me)₂PCH₂CH₂CH₂P(Cy)₂ (16), and (Me)₂PCH₂CH₂CH₂P(Ph)₂ (17) were synthesized using air–stable phosphine oxide intermediates. In the first step, sodium phosphinites formed by deprotonation of (Me)₂P(O)H, (Et)₂P(O)H, and (iPr)₂P(O)H were alkylated by 1-bromo-3-chloropropane. The different substitution rates of the chloride and bromide groups allowed the isolation of the intermediates (Me)₂P(O)CH …

A Panel Of Protein Kinase Chemosensors Distinguishes Different Types Of Fatty Liver Disease, Jon R. Beck, Fatima Cabral, Karuna Rasineni, Carol A. Casey, Edward N. Harris, Cliff I. Stains

Department of Chemistry: Faculty Publications

The worldwide incidence of fatty liver disease continues to rise, which may account for concurrent increases in the frequencies of more aggressive liver ailments. Given the existence of histologically identical fatty liver disease subtypes, there is a critical need for the identification of methods that can classify disease and potentially predict progression. Herein, we show that a panel of protein kinase chemosensors can distinguish fatty liver disease subtypes. These direct activity measurements highlight distinct differences between histologically identical fatty liver diseases arising from diets rich in fat versus alcohol and identify a previously unreported decrease in p38α activity associated with …

Global Sinusoidal Seasonality In Precipitation Isotopes, Scott T. Allen, Scott Jasechko, Wouter R. Berghuijs, Jeffrey M. Welker, Gregory R. Goldsmith, James W. Kirchner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantifying seasonal variations in precipitation δ²H and δ¹⁸O is important for many stable isotope applications, including inferring plant water sources and streamflow ages. Our objective is to develop a data product that concisely quantifies the seasonality of stable isotope ratios in precipitation. We fit sine curves defined by amplitude, phase, and offset parameters to quantify annual precipitation isotope cycles at 653 meteorological stations on all seven continents. At most of these stations, including in tropical and subtropical regions, sine curves can represent the seasonal cycles in precipitation isotopes. Additionally, the amplitude, phase, and offset parameters of …

Untangling The Formation Of Methoxymethanol (Ch3Och2Oh) And Dimethyl Peroxide (Ch3Ooch3) In Star-Forming Regions, Cheng Zhu, Robert Frigge, Alexandre Bergantini, Ryan C. Fortenberry, Ralf I. Kaiser

Faculty and Student Publications

© 2019. The American Astronomical Society. All rights reserved.. Methoxymethanol (CH3OCH2OH) was recently detected toward the MM1 core in the high-mass star-forming region NGC 6334I. However, the underlying formation mechanisms of this complex organic molecule (COM) as well as its structural isomers ethylene glycol (HOCH2CH2OH) and the hitherto unobserved dimethyl peroxide (CH3OOCH3) are still elusive. Here, we report the very first confirmed synthesis of dimethyl peroxide - at various deuteration levels within interstellar analogous ices of D3-methanol (CD3OH) exposed to ionizing radiation at ultralow temperatures of 5 K. The discrimination of specific isomers is achieved by exploiting reflectron time-of-flight mass …

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 …

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 …

Chemistry And Biochemistry News, Georgia Southern University

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

• Professor wins Jean Dreyfus Lectureship Grant
• Dr. Wu wins the University Excellence in Research Award 2019-20

Visualizing The Fate And Distribution Of Pahs In Spartina And Avicennia Tissues From Barataria Basin, La, Kristina Jeannette Sebastian

LSU Master's Theses

During crude oil spill events, vegetation in marsh environments sequester polycyclic aromatic hydrocarbons (PAHs) from the crude oil by partitioning from the air phase through the waxy cuticle on the leaf surface. Recent studies from Macondo oil-impacted marshes have demonstrated that cycling of low molecular weight petrogenic PAHs occurs through the cuticle and other leaf tissue. At present, our understanding of how PAHs travel through the cuticle is coarse and limited by grab samples across the entire leaf, which preventing a full understanding the dynamics of PAH cycling in this environment. Multiphoton (MP) confocal microscopy visualizes the distribution of PAHs …

The Analysis Of Trifluoromethylbenzimidazole (Tfmbi) Crystals Using Physical Chemistry Techniques To Explain Ferroelectric And Anti-Ferroelectric Properties Of The Compound, Kanwar Bhullar

Honors College Theses

Ferroelectrics are a group of materials possessing the unique chemical property of being able to switch their electrical polarity when exposed to an electric field. This property makes ferroelectrics a promising field of study with the potential to impact various future technologies in information and energy storage, as well as quantum mechanics. Understanding molecular structures of ferroelectric (and opposite anti-ferroelectric) materials, and how they relate to the compound’s properties is essential to harnessing the potential these materials carry. The report discusses analysis of anti-ferroelectric material trifluoromethylbenzimidazole (TFMBI), by subjecting the compound to various physical and computational chemistry techniques at varying …

Assessing Affective Differences Between A Virtual General Chemistry Experiment And A Similar Hands-On Experiment, Cory Hensen, Jack Barbera

Chemistry Faculty Publications and Presentations

To date, few general chemistry laboratory studies have included affective measures despite calls for more research on aspects of this domain. This shortage of studies may be partially due to the scarcity of affective measures that have been designed for, or tested in, the college laboratory setting. To provide measures for use in this environment, several existing affective scales were adapted for this new context. Before data from the scales were utilized to study the environment, evidence was provided for the validity and reliability of the data generated from them. Once sufficient evidence was provided, it was possible to determine …

Self-Assembly Of Conducting Polymer Nano- And Microstructures For Energy Storage, Luciano Matteo Santino

Arts & Sciences Graduate Student Theses and Dissertations

Plastics are materials composed of many long chains of molecules with repeating subunits; strong interactions between neighboring molecules lead to the material used throughout the world. Plastics are commonly thought to be insulating, in stark contrast to the conductivity of metals. However, certain polymer structures were discovered to exhibit semiconducting properties, the subject of the Nobel Prize in Chemistry in 2000. Conducting polymers have a unique molecular structure with an electronically conjugated backbone, allowing electrons to freely travel both across the chain and in between chains. This work focuses on controlling the kinetics of the reaction between the vapors of …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Graduate Student Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and for …

Novel Self-Assembly Of Fullerene-Based Dyads, Ashley D. Anderson

Theses and Dissertations

Eventual depletion and environmental toxicity of natural non-renewable energy resources are two issues pushing research toward alternative energy resources. Nature’s process of renewable, unlimited, clean energy production is photosynthesis and porphyrins are a critical component due to their ability to undergo photoinduced electron transfer. This property also makes porphyrins excellent candidates for applications such as solar cells, water splitting, and optical sensing. Researchers have previously tethered porphyrins to fullerene (C60), an excellent electron acceptor, to mimic the reaction centers in photosynthesis. Photoinduced electron transfer in these donor-acceptor dyads has been investigated with particular focus on factors such as the donor, …

Solid-State Nmr Of Co2 Mineralization And Nmr Crystallography, Jinlei Cui

Arts & Sciences Graduate Student Theses and Dissertations

The work described in this dissertation has been accomplished by using solid-state nuclear magnetic resonance (SSNMR) spectroscopy to investigate CO2 mineralization and to refine the positions of protons in the crystalline system. The reaction of forsterite (Mg2SiO4) and 13CO2 is presented here, which is measured using in-situ 13C NMR spectroscopy without removing the sample from the reactor. 29Si SSNMR is used to investigate the reaction of forsterite with 13CO2 in the presence of water or NaCl brine as a function of depth in the sample. Additionally, we also show that NMR crystallography can significantly improve structure refinement of hydrogens’ positions …

Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott

Arts & Sciences Graduate Student Theses and Dissertations

This work is focused on iron trafficking through ABC transporters in Staphylococcus aureus and combatting the growing antimicrobial resistance crisis by exploiting virulence factors as therapeutic targets. Specifically, the goal was to understand the role of a siderophore-binding lipoprotein FhuD2 in S. aureus iron trafficking. While S. aureus endogenously produces three metallophores for metal sequestration from the host, FhuD2 is thought to scavenge metals from hydroxamate-based xenosiderophores encountered in the host environment. FhuD2 is a critical virulence factor and vaccine candidate (Novartis) for MRSA. Since xenosiderophore scavenging systems are often dispensable, it was hypothesized that FhuD2 must be playing another …

Solid-State Nmr Of Co2 Mineralization And Nmr Crystallography, Jinlei Cui

Arts & Sciences Graduate Student Theses and Dissertations

The work described in this dissertation has been accomplished by using solid-state nuclear magnetic resonance (SSNMR) spectroscopy to investigate CO2 mineralization and to refine the positions of protons in the crystalline system. The reaction of forsterite (Mg2SiO4) and 13CO2 is presented here, which is measured using in-situ 13C NMR spectroscopy without removing the sample from the reactor. 29Si SSNMR is used to investigate the reaction of forsterite with 13CO2 in the presence of water or NaCl brine as a function of depth in the sample. Additionally, we also show that NMR crystallography can significantly improve structure refinement of hydrogens’ positions …

Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott

Arts & Sciences Graduate Student Theses and Dissertations

This work is focused on iron trafficking through ABC transporters in Staphylococcus aureus and combatting the growing antimicrobial resistance crisis by exploiting virulence factors as therapeutic targets. Specifically, the goal was to understand the role of a siderophore-binding lipoprotein FhuD2 in S. aureus iron trafficking. While S. aureus endogenously produces three metallophores for metal sequestration from the host, FhuD2 is thought to scavenge metals from hydroxamate-based xenosiderophores encountered in the host environment. FhuD2 is a critical virulence factor and vaccine candidate (Novartis) for MRSA. Since xenosiderophore scavenging systems are often dispensable, it was hypothesized that FhuD2 must be playing another …

Electron Decoupling With Chirped Microwave Pulses For Magic Angle Spinning Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy, Edward Paul Saliba

Arts & Sciences Graduate Student Theses and Dissertations

Dynamic nuclear polarization (DNP) is a method of generating hyperpolarization of nuclear spins for nuclear magnetic resonance (NMR) spectroscopy. Coherent, time domain techniques make the possibility of DNP directly to spins of interest at room temperature and higher feasible in magic angle spinning (MAS) NMR, allowing for optimal experimental repetition times to be limited by the T_1 of the electron, rather than a much longer T_1DNP, with excellent resolution. The strong hyperfine couplings that make such direct DNP transfers possible, however, can lead to short nuclear relaxation times that result in broadening of nuclear resonances and reduce sensitivity. This dissertation …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Graduate Student Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and for …

A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers

Arts & Sciences Graduate Student Theses and Dissertations

The grand challenge of biophysics is to use the fundamental laws of physics to predict howbiological molecules will move and interact. The atomistic HIPPO (Hydrogen-likeIntermolecular Polarizable Potential) force field is meant to address this challenge. It does so bybreaking down the intermolecular potential energy function of biomolecular interactions intophysically meaningful components (electrostatics, polarization, dispersion, and exchangerepulsion)and using this function to drive molecular dynamics simulations. This force field isable to achieve accuracy within 1 kcal/mol for each component when compared with ab initioSymmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy becauseit introduces a model electron density on every …

Wave Function Engineering In Cdse/Pbs Core/Shell Nanocrystal Heterostructures, Brian Matthew Wieliczka

Arts & Sciences Graduate Student Theses and Dissertations

Colloidal semiconducting nanocrystals hold significant potential for third generation photovoltaics as solution processable materials that can surpass the Shockley-Queisser limit through multiexciton generation. In pursuit of this goal, the synthesis and optical characterization of CdSe/PbS core/shell quantum dots is reported. The spectroscopic behavior of these particles demonstrates their potential for use in optoelectronic devices, taking advantage of wave function engineering of the electron and hole. The rock salt PbS shell grows on all sides of the underlying zinc blende CdSe quantum dot, creating a core/shell structure. With increasing shell thickness, the band edge absorption and photoluminescence transitions decrease in energy …

Extensive Soot Compaction By Cloud Processing From Laboratory And Field Observations, Janarjan Bhandari, Swarup China, Kamal Kant Chandrakar, Greg Kinney, Will Cantrell, Raymond Shaw, Lynn Mazzoleni, Giulia Girotto, Noopur Sharma, Kyle Gorkowski, Stefania Gilardoni, Stefano Decesari, Maria Cristina Facchini, Nicola Zanca, Giulia Pavese, Francesco Esposito, Manvendra K Dubey, Allison C Aiken, Rajan K Chakrabarty, Hans Moosmüller, Timothy B Onasch, Rahul A Zaveri, Barbara V Scarnato, Paulo Fialho, Claudio Mazzoleni

Michigan Tech Publications, Part 1

Soot particles form during combustion of carbonaceous materials and impact climate and air quality. When freshly emitted, they are typically fractal-like aggregates. After atmospheric aging, they can act as cloud condensation nuclei, and water condensation or evaporation restructure them to more compact aggregates, affecting their optical, aerodynamic, and surface properties. Here we survey the morphology of ambient soot particles from various locations and different environmental and aging conditions. We used electron microscopy and show extensive soot compaction after cloud processing. We further performed laboratory experiments to simulate atmospheric cloud processing under controlled conditions. We find that soot particles sampled after …

Chemistry And Biochemistry News, Georgia Southern University

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

• Chemistry students shine Georgia Southern's name abroad