Other Chemistry Commons^™

Molecular Probes For The Detection Of Zn2+ And Fe3+ Ions, Erendra Manandhar

Dissertations

A number of molecular probes have been designed and synthesized for the detection of Zn²⁺ and Fe³⁺ ions. Two types of functional groups have been incorporated into the molecular scaffolds to utilize different fluorescent mechanisms. The first class of receptors contains a pyrene moiety. These molecular probes use the excimer mechanism for the detection of Zn²⁺ ion. The probes work well in an organic solvent with a detection limit of 20 nM (one ppb). Alternatives are made to make them water soluble, but this proved to be difficult. An interesting ion-induced self-assembly system will also be discussed. …

Ranking Methods For Global Optimization Of Molecular Structures, John Norman Mcmeen Jr

Electronic Theses and Dissertations

This work presents heuristics for searching large sets of molecular structures for low-energy, stable systems. The goal is to find the globally optimal structures in less time or by consuming less computational resources. The strategies intermittently evaluate and rank structures during molecular dynamics optimizations, culling possible weaker solutions from evaluations earlier, leaving better solutions to receive more simulation time. Although some imprecision was introduced from not allowing all structures to fully optimize before ranking, the strategies identify metrics that can be used to make these searches more efficient when computational resources are limited.

Selective Indicators For Optical Determination Of Disease Biomarkers, Lovemore Hakuna

Dissertations and Theses

The most abundant biological thiols, homocysteine (Hcy), cysteine (Cys) and glutathione (GSH) have been the subject of intense research due to their association with a wide range of diseases. They play a key role in maintaining the redox status of biological systems. Selective detection methods for these thiols are challenging due to their similar structures and properties. Current commercially available detection methods use separations, fragile and expensive enzymatic or immunogenic materials and complex instrumentation. This has led to a global effort towards developing simple and inexpensive optical probes and indicators selective for specific biological thiols.

Highly selective chemical probes and …

Peptide Arrays For Detecting Naphthenic Acids In Oil Sands Process Affected Water, Kamaljit Kaur, Subir Bhattacharjee, Rajesh G. Pillai, Sahar Ahmed, Sarfuddin Azmi

Pharmacy Faculty Articles and Research

Naphthenic acids (NAs) are water-soluble components of petroleum. The characterization and quantification of NAs by analytical methods have proved quite challenging, whilst the toxic effects of these water-soluble compounds on a variety of organisms adversely affecting reproduction and steroid production is becoming apparent. In this study, we report a fluorescence-based competitive binding method for rapid sensing of the presence of NAs using cellulosic peptide array strips as sensors. The peptide array was designed from sequences derived from the estrogen receptor (ER). Several of these peptides were able to detect the presence of NAs at low micromolar (∼5 mg L^{−1 …}

Polyol Induced Extraction (Pie) Of Water From Organic Solvents, Mithilesh Deshpande

Seton Hall University Dissertations and Theses (ETDs)

Acetonitrile (ACN) is used in huge quantities for Reversed Phase High Performance Liquid Chromatography (RP-HPLC) experiments. For most of the part, these results in waste that is only contaminated with large amounts of water, buffer and trace organic impurities. It would seem worthwhile to purify the ACN from water using a mass separating agent (MSA). In a quest for an MSA, our investigation reveals polyols as a new class of MSAs. It is observed that when a polyol such as glycerol, sorbitol, erythritol, xylitol, Isomalt® or maltitol is added to a mixture of ACN-water, the ACN separates out of the …

Water In The Computer Lab! (A Computational Project For Undergraduate Inorganic Chemistry), Bradley M. Wile, Trilisa M. Perrine

Chemistry and Biochemistry Faculty Scholarship

No abstract provided.

Heat Release Of Polyurethanes Containing Potential Flame Retardants Based On Boron And Phosphorus Chemistries, Vladimir Benin, Bastien Gardelle, Alexander Morgan

Chemistry Faculty Publications

Using a polyurethane of methylene diphenyl isocyanate and 1,3-propane diol, several new non-halogenated aromatic boron and phosphorus flame retardants were evaluated for heat release reduction potential using the pyrolysis combustion flow calorimeter (PCFC). The polyurethanes were prepared in the presence of the potential flame retardants via solvent mixing and copolymerization methods, and were then analyzed via spectroscopic methods to determine if the flame retardant was still present in the final product. PCFC testing on the resulting products showed that the flame retardant molecule can have different effects on heat release depending upon how it is mixed into the polyurethane. Some …

Light Switchable Optical Materials From Azobenzene Crosslinked Poly (N-Isopropylacrylamide)-Based Microgels, Qiang Matthew Zhang, Xue Li, Molla R. Islam, Menglian Wei, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

4,4′-Di(acrylamido)-azobenzene was used as a crosslinker in poly(N-isopropylacrylamide)-based microgels. The microgels were subsequently used to fabricate microgel-based optical materials (etalons), which exhibited optical properties that were switchable upon exposure to UV irradiation. We also show that the extent of the response depended on the UV exposure time. These materials could find applications for controlled/triggered drug delivery, as well as in various optical applications.

Poly (N-Isopropylacrylamide) Microgel-Based Thin Film Actuators For Humidity Sensing, Molla R. Islam, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this submission we fabricated a humidity-responsive polymer-based actuator by layering negatively charged poly(N-isopropylacrylamide)-co-acrylic acid microgels and positively charged poly(diallyldimethyl ammonium chloride) on top of a flexible plastic substrate. We show that the extent of the actuation (bending) was dependent on the atmospheric humidity. This property was used to detect atmospheric humidity by hanging weights from the actuator, which were rested on the pan of a top loading balance. This was done in such a way that the amount of the mass resting on the balance depended on the extent of actuator bending, which could then be related to humidity. …

Determination Of Corrosion Inhibitor Lubricity Improver In Jet Fuel By Liquid Chromatography-Electrospray Ionization Mass Spectrometry, David W. Johnson, Milissa Flake, Ryan Adams

Chemistry Faculty Publications

Military jet fuel (JP-8) is very similar to commercial jet fuel (Jet A) except for the presence of three additives, fuel system icing inhibitor, corrosion inhibitor–lubricity improver (CI-LI), and antistatic additive, which are added to improve characteristics of JP-8. Of particular interest is the CI-LI additive; the most common active ingredient is a dimer of linoleic acid. This article focuses on quantification of the active ingredient in the CI-LI additive by liquid chromatography–mass spectrometry (LC–MS). This method will allow the determination of CI-LI content in military jet fuel samples.

A Novel Label-Free Colorimetric Assay For Dna Concentration In Solution, Molla R. Islam, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Optical devices were fabricated by sandwiching a “monolithic” poly(N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) (pNIPAm-co-APMAH) microgel layer between two semitransparent Au layers. These devices, referred to as etalons, exhibit characteristic multipeak reflectance spectra, and the position of the peaks in the spectra primarily depends on the distance between the Au surfaces mediated by the microgel layer thickness. Here, we show that the positively charged microgel layer can collapse in the presence of negatively charged single stranded DNA (ssDNA) due to ssDNA induced microgel crosslinking. The collapse results in a change in the etalon's optical properties, which can be used to detect target DNA …

Heavy Metal Analysis In Lens And Aqueous Humor Of Cataract Patients By Total Reflection X-Ray Fluorescence Spectrometry, Martina Schmeling, Bruce I. Gaines, Susanne Tidow-Kebritchi

Chemistry: Faculty Publications and Other Works

The human eye is continuously exposed to the environment yet little is known about how much of toxins, specifically heavy metals are present in its different parts and how they influence vision and acuity. To shed light into this subject, aqueous humor and lens samples were collected from 14 cataract patients to study the presence and concentration of selected metals in the eye. Subjects undergoing routine cataract surgery were consecutively enrolled for study by simple random sampling. Prior to surgery, subject demographic were compiled. The surgical procedure involved small incision cataract removal using phacoemulsification. During the procedure, a small aliquot …

Poly (N-Isopropylacrylamide) Microgel-Based Optical Devices For Sensing And Biosensing, Molla R. Islam, Andrews Ahiabu, Xue Li, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Responsive polymer-based materials have found numerous applications due to their ease of synthesis and the variety of stimuli that they can be made responsive to. In this review, we highlight the group’s efforts utilizing thermoresponsive poly (N-isopropylacrylamide) (pNIPAm) microgel-based optical devices for various sensing and biosensing applications.

Computational Study Of The Nitric Oxide Autoxidation Mechanism Using Quantum Chemistry Methods, Yazen Abusad

Collection of Engaged Learning

Nitric oxide (NO) is a critical cell-signaling messenger in the immune, cardiovascular, and nervous systems. It is linked to several diseases, and due to its high reactivity, and toxicity as a free radical, NO possesses a controversial effect on cell viability. The S-nitrosylation of protein thiol groups is a key mechanism in NO redox signal transduction, and lends a mechanistic basis for NO as a cell regulator. Numerous experiments have shown that the rate-limiting step of S-nitrosylation is NO autoxidation, independent of thiol concentration. Due to the transient nature, and structural variety of reactive nitrogen species, very little is known …

A Small Molecule That Binds And Inhibits The Etv1 Transcription Factor Oncoprotein, Marius C. Pop, Nicolas Stransky, Colin W. Garvie, Jean-Philippe Theurillat, Emily C. Hartman, Timothy A. Lewis, Cheng Zhong, Elizabeth K. Culyba, Fallon Lin, Douglas S. Daniels, Raymond Pagliarini, Lucienne Ronco, Angela N. Koehler, Levi A. Garraway

Chemistry Faculty Publications

Members of the ETS transcription factor family have been implicated in several cancers, where they are often dysregulated by genomic derangement. ETS variant 1 (ETV1) is an ETS factor gene that undergoes chromosomal translocation in prostate cancers and Ewing's sarcomas, amplification in melanomas, and lineage dysregulation in gastrointestinal stromal tumors. Pharmacologic perturbation of ETV1 would be appealing in these cancers; however, oncogenic transcription factors are often deemed “undruggable” by conventional methods. Here, we used small-molecule microarray (SMM) screens to identify and characterize drug-like compounds that modulate the biological function of ETV1. We identified the 1,3,5-triazine small molecule BRD32048 as a …

Hydration Of The Sulfuric Acid−Methylamine Complex And Implications For Aerosol Formation, Danielle J. Bustos, Berhane Temelso, George C. Shields

Faculty Journal Articles

The binary H₂SO₄−H₂O nucleation is one of the most important pathways by which aerosols form in the atmosphere, and the presence of ternary species like amines increases aerosol formation rates. In this study, we focus on the hydration of a ternary system of sulfuric acid (H₂SO₄), methylamine (NH₂CH₃), and up to six waters to evaluate its implications for aerosol formation. By combining molecular dynamics (MD) sampling with high-level ab initio calculations, we determine the thermodynamics of forming H₂SO₄(NH₂CH₃)(H …

Dipole Bound Excited States Of Polycyclic Aromatic Hydrocarbons Containing Nitrogen And Their Relation To The Interstellar Medium, Mallory L. Theis

Honors College Theses

Polycyclic aromatic hydrocarbons (PAHs) are the most abundant type of molecule present in the interstellar medium (ISM). It has been hypothesized that nitrogen replacement within a ring is likely for PAHs present in the ISM. Additionally, electrons, protons, and hydrogen atoms are readily added to or removed from PAHs creating a truly diverse set of chemistries in various interstellar regions. The presence of a nitrogen within a PAH (called a PANH herein) that is additionally dehydrogenated leads to a neutral radical with a large dipole moment. It has recently been shown through the use of high-level quantum chemical computations for …

Serial Transfer Can Aid The Evolution Of Autocatalytic Sets, Wim Hordijk, Nilesh Vaidya, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: The concept of an autocatalytic set of molecules has been posited theoretically and demonstrated empirically with catalytic RNA molecules. For this concept to have significance in a realistic origins-of-life scenario, it will be important to demonstrate the evolvability of such sets. Here, we employ a Gillespie algorithm to improve and expand on previous simulations of an empirical system of self-assembling RNA fragments that has the ability to spontaneously form autocatalytic networks. We specifically examine the role of serial transfer as a plausible means to allow time-dependent changes in set composition, and compare the results to equilibrium, or "batch" scenarios. …

Functional Variants Of Metal-Binding Domains 5 And 6 Of The Human Wilson Protein, Sandra Weitzner

Honors Theses

Wilson's disease is caused by mutations in atp7b, a gene that encodes a copper-transporting P_1B-type ATPase, otherwise known as the Wilson protein. Over 300 different mutations cause Wilson's disease, and we focused on missense mutations occurring in the 650 amino acid N-terminus of the Wilson protein. This portion of the protein includes six metal-binding domains that function to azquire Cu(I) from the cytosol, prior to passing it through the ATP-driven membrane-spanning pump. Of particular interest are metal-binding domains 5 and 6 (WLN5-6) since we know that they are absolutely required for function of the enzyme. Several missense mutations …

Parkinson Disease-Associated Mutation R1441h In Lrrk2 Prolongs The “Active State” Of Its Gtpase Domain, Jingling Liao, Chun-Xiang Wu, Christopher Burlak, Sheng Zhang, Dali Liu

Chemistry: Faculty Publications and Other Works

Mutation in leucine-rich-repeat kinase 2 (LRRK2) is a common cause of Parkinson disease (PD). A disease-causing point mutation R1441H/G/C in the GTPase domain of LRRK2 leads to overactivation of its kinase domain. However, the mechanism by which this mutation alters the normal function of its GTPase domain [Ras of complex proteins (Roc)] remains unclear. Here, we report the effects of R1441H mutation (Roc_R1441H) on the structure and activity of Roc. We show that Roc forms a stable monomeric conformation in solution that is catalytically active, thus demonstrating that LRRK2 is a bona fide self-contained GTPase. We further show …

Responsive Polymers For Biosensing And Protein Delivery, Molla R. Islam, Yongfeng Gao, Xue Li, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this feature article, we review some of the most recent advances in the field of materials chemistry for biosensing, disease diagnostics, and drug delivery. Our recent work on the development of responsive polymer-based platforms for biosensing and drug delivery will also be highlighted. This feature article is meant to outline the breadth of the utility of polymer-based materials for select applications, as well as their enormous potential impact on future technologies.

Structural Dynamics Of A Single-Stranded Rna–Helix Junction Using Nmr, Catherine D. Eichhorn, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, ¹³C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A₆-tract and forms an acute pivot point for …

Evolution Of Selected Isoprene Oxidation Products In Dark Aqueous Ammonium Sulfate, D.M. Ashraf Ul Habib

Dissertations, Master's Theses and Master's Reports - Open

The aqueous phase processing of glyoxylic acid, pyruvic acid, oxalic acid and methylglyoxal was studied simulating dark and radical free atmospheric aqueous aerosol. A novel observation of the cleavage of a carbon-carbon bond in pyruvic acid and glyoxylic acid leading to their decarboxylation was made in the presence of ammonium salts but no decarboxylation was observed from oxalic acid. The empirical rate constants for decarboxylation were determined. The structure of the acid, ionic environment of solution and concentration of species found to affect the decarboxylation process. A tentative set of reaction mechanisms was proposed involving nucleophilic attack by ammonia on …

Jupiter's Great Red Spot Is Composed Of Ammonia And Phosphine, Erika Rosenberger

Natural Sciences Student Research Presentations

In Jupiter's Great Red Spot, ammonia, phosphine, and para-Hydrogen were found. The Great Red Spot is the local maximum of ammonia, the most abundant compound of the atmosphere. The abundance of ammonia in the Spot is regulated by a complex interaction between photochemistry, condensation, precipitation, and atmospheric dynamics. Ammonia is found most abundant in the regions at around 400-500 mbar when phosphine is the most abundant at 600 mbar. The photo-dissociation reaction of phosphine that occurs in the Spot helps explain why the planet Jupiter and the Great Red Spot is red. The reaction sequence proposed by scientists Prinn and …

Spatial And Seasonal Variability Of Cloud Condensation Nuclei Number Concentrations Over The Extended North African Continent And The Mediterranean, Hesham Abdel-Monem Afify Hassan

Legacy Theses & Dissertations (2009 - 2024)

The spatiotemporal variability of cloud condensation nuclei (CCN) number concentration is investigated over the extended domain of the North African continent and Mediterranean which is an essential step for better understanding of aerosol-cloud interactions and associated climate impacts over the region. The study is performed by analyzing the output for the period from 2004 to 2011 from the well-validated global chemistry and aerosol transport model GEOS-Chem-APM. The analysis shows that the dominant aerosol type for CCN number concentration is secondary particles all over the domain. Spatial analysis reveals the existence of four characteristic subdomains of variability: over the Mediterranean and …

Thin Layer Chromatography For Forensic Science, Kseniya Chumachenko

A with Honors Projects

For this Parkland A with Honors project, the author works to identify a good or better recipe for the solution for chromatography projects in a forensic science lab class.

Science Classics, Mark Masthay

Chemistry Faculty Publications

An essay on the impact of the works in the Imprints and Impressions: Milestones in Human Progress, an exhibition of rare books from the collection of Stuart Rose. Exhibition was held Sept. 29-Nov. 9, 2014, at the University of Dayton.

Stop Rotating! One Substitution Halts The B19- Motor, Francisco Cervantes-Navarro, Gerarso Martínez-Guajardo, Edison Osorio, Diego Moreno, William Tiznado, Rafael Islas, Kelling J. Donald, Gabriel Merino

Chemistry Faculty Publications

The B₁₉^- anion and other boron species have been dubbed ‘Wankel motors’ for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B₁₉^- is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB₁₈ species is shown computationally to enforce bond localization.

Critical Phenoneme In A Ternary System Of Water, Isobutyric Acid, And Octanol, Kerry Rice

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Iterative Assembly Of Two Separate Polyketide Chains By The Same Single-Module Bacterial Polyketide Synthase In The Biosynthesis Of Hsaf, Yaoyao Li, Haotong Chen, Yanjiao Ding, Yunxuan Xie, Haoxin Wang, Ronald Cerny, Yuemao Shen, Liangcheng Du

Ronald Cerny Publications

HSAF (1) was isolated from the biocontrol agent Lysobacter enzymogenes (Figure 1).^[1-4]

This bacterial metabolite belongs to polycyclic tetramate macrolactams (PTM) that are

emerging as a new class of natural products with distinct structural features. ^{[5, 6]} HSAF

exhibits a potent antifungal activity and shows a novel mode of action.^[1-4] The HSAF

biosynthetic gene cluster contains only a single-module hybrid polyketide synthasenonribosomal

peptide synthetase (PKS-NRPS), although the PTM scaffold is apparently

derived from two separate hexaketide chains and an ornithine residue.^[1-4] This suggests that

the same PKS module would act not only iteratively, but also …