Other Chemistry Commons^™

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 …

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 …

Bis(2-Quinolylmethyl)Ethylenediaminediacetic Acids (Bqendas), Tqen–Edta Hybrid Molecules As Fluorescent Zinc Sensors, Shawn Burdette, Yju Mikata, Saaya Takeuchi, Hideo Konno, Satoshi Iwatsuki, Sakiko Akaji, Ikuko Hamagami, Masato Aoyama, Keiko Yasuda, Satoshi Tamotsu

Shawn C. Burdette

Molecular hybrids of TQEN (N,N,N′,N′-tetrakis(2-quinolylmethyl)ethylenediamine) and EDTA (ethylenediamine-N,N,N′,N′-tetraacetic acid) were examined as fluorescent Zn2+ sensors. Upon the addition of Zn2+, N,N-BQENDA (N,N-bis(2-quinolylmethyl)ethylenediamine-N′,N′-diacetic acid, 1a) exhibits a 30-fold emission enhancement at 456 nm (λex = 315 nm, ϕZn = 0.018) in buffer (HEPES, pH = 7.5, 100 mM KCl). The fluorescence enhancement is Zn2+-specific as Cd2+ induces much smaller increases (ICd/I0 = 5 and ICd/IZn = 16%). These spectroscopic properties, as well as the excellent water-solubility, represent a significant improvement compared to the parent TQEN sensor (ϕZn = 0.007, ICd/IZn = 64%). The isoquinoline analog N,N-1-isoBQENDA (N,N-bis(1-isoquinolylmethyl)ethylenediamine-N′,N′-diacetic acid, 1b) possesses a …

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.

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 …

Three-Dimensional Periodic Graphene Nanostructures, Peter M. Wilson, Gilbert N. Mbah, Thomas G. Smith, Daniel Schmidt, Rebecca Y. Lai, Tino Hofmann, Alexander Sinitskii

Chemistry Department: Faculty Publications

Graphene is a basic building block for many known and emerging carbon-based materials whose properties largely depend on the way how graphene is structured at the nanoscale. Synthesis of novel threedimensional (3D) nanostructures of graphene would be an important advance for fundamental research and various applications. In this paper, we discuss the possibility of fabricating complex 3D graphene nanostructures by growing graphene on pre-synthesized nanostructured metal templates by chemical vapor deposition (CVD) and then etching away the metal. In the proof-of-concept experiments, we study this idea using two types of metal nanostructures, inverse opals and slanted nanopillar arrays grown by …

Metallurgical And Corrosion Assessment Of Submerged Tanker S.S. Montebello, Dana Medlin, James D. Carr, Donald L. Johnson, David L. Conlin

Chemistry Department: Faculty Publications

The Union Oil Tanker S.S. Montebello was torpedoed and sunk six miles (9.7 km) off the coast of Cambria, California by a Japanese submarine on December 23, 1941, two weeks after the attack on Pearl Harbor. With close proximity to the National Monterey Bay Marine Sanctuary, concern about possible crude oil contamination led to the most recent expedition to the site in October 2011. Assessment of the shell plate found that the average corrosion rate was very low and the structure will remain stable for many decades.

Advances In Chemical And Structural Characterization Of Concretion With Implications For Modeling Marine Corrosion, Donald L. Johnson, Robert J. Deangelis, Dana J. Medlin, James D. Carr, David L. Conlin

Chemistry Department: Faculty Publications

The Weinsnumber model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selectedarea EDS …

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 …

Highly Selective Gas Sensor Arrays Based On Thermally Reduced Graphene Oxide, Alexey Lipatov, Alexey Varezhnikov, Peter Wilson, Victor Sysoev, Andrei Kolmakov, Alexander Sinitskii

Chemistry Department: Faculty Publications

The electrical properties of reduced graphene oxide (rGO) have been previously shown to be very sensitive to surface adsorbates, thus making rGO a very promising platform for highly sensitive gas sensors. However, poor selectivity of rGO-based gas sensors remains a major problem for their practical use. In this paper, we address the selectivity problem by employing an array of rGO-based integrated sensors instead of focusing on the performance of a single sensing element. Each rGO-based device in such an array has a unique sensor response due to the irregular structure of rGO films at different levels of organization, ranging from …

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 …

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.

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.

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.

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.