Other Chemistry Commons^™

Assessment Of Metabolic Changes In Mycobacterium Smegmatis Wild Type And Alr Mutant Strains: Evidence For A New Pathway Of D-Alanine Biosynthesis., Darrell D. Marshall, Steven Halouska, Denise K. Zinniel, Robert J. Fenton, Katie Kenealy, Harpreet K. Chahal, Govardhan Rathnaiah, Raul G. Barletta, Robert Powers

Department of Chemistry: Faculty Publications

In mycobacteria, D-alanine is an essential precursor for peptidoglycan biosynthesis. The only confirmed enzymatic pathway to form D-alanine is through the racemization of L-alanine by alanine racemase (Alr, EC 5.1.1.1). Nevertheless, the essentiality of Alr in Mycobacterium tuberculosis and Mycobacterium smegmatis for cell survivability in the absence of D-alanine has been a point of controversy with contradictory results reported in the literature. To address this issue, we examined the effects of alr inactivation on the cellular metabolism of M. smegmatis. The M. smegmatis alr insertion mutant TAM23 exhibited essentially identical growth to wild type mc²155 in the …

Transcriptional And Antagonistic Responses Of Biocontrol Strain Lysobacter Enzymogenes Oh11 To The Plant Pathogenic Oomycete Pythium Aphanidermatum, Yangyang Zhao, Guoliang Qian, Yuan Chen, Liangcheng Du, Fengquan Liu

Department of Chemistry: Faculty Publications

Lysobacter enzymogenes is a ubiquitous, beneficial, plant-associated bacterium emerging as a novel biological control agent. It has the potential to become a new source of antimicrobial secondary metabolites such as the Heat-Stable Antifungal Factor (HSAF), which is a broad-spectrum antimycotic with a novel mode of action. However, very little information about how L. enzymogenes detects and responds to fungi or oomycetes has been reported. An in vitro confrontation bioassay between the pathogenic oomycete Pythium aphanidermatum and the biocontrol bacterial strain L. enzymogenes OH11 was used to analyze the transcriptional changes in the bacteria that were induced by the oomycetes. Analysis …

Ion Mobility-Resolved Collision-Induced Dissociation And Electron Transfer Dissociation Of N-Glycopeptides: Gathering Orthogonal Connectivity Information From A Single Mass- Selected Precursor Ion Population, Venkata Kolli, Katherine N. Schumacher, Eric Dodds

Department of Chemistry: Faculty Publications

Glycopeptide-level mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses are commonly performed to establish site-specific protein glycosylation profiles that are of central importance to gaining structure-function insights on glycoproteins. Confoundingly, the complete characterization of glycopeptide connectivity usually requires the acquisition of multiple MS/MS fragmentation spectra. Complementary ion fragmentation techniques such as collision-induced dissociation (CID) and electron transfer dissociation (ETD) are often applied in concert to address this need. While structurally informative, the requirement for acquisition of two MS/MS spectra per analyte places considerable limitations upon the breadth and depth of large-scale glycoproteomic inquiry. Here, a previously developed method of …

Investigating Stress Response Across Integrated Biological Systems, Alice A. Han

Graduate Theses, Dissertations, and Problem Reports (ETD)

The impact that a stressor has on a living system, whether it is on a cellular, organ, or even a whole organism level, can affect the overall health of the system. Monitoring the biochemical response resulting from a stressful experience offers insight into the numerous potential outcomes ranging on the spectrum of survival and death. Accessing this information not only provides a heightened understanding of the biochemical adaptions that occur, but also allows for the development of prediction models (to assess prospective influences of the stressor) or potential therapeutic treatments (to alleviate adverse effects) using measurable, quantifiable, and comparable metrics. …

Separation Of Transition And Heavy Metals Using Stationary Phase Gradients And Chelation Thin Layer Chromatography / Evaluation Of The Effectiveness Of Pogil-Pcl Workshops, Stacy L. Stegall

Theses and Dissertations

Gradient surfaces exhibit a variation in functionality along the length of the surface. One method for preparing gradients is controlled-rate infusion (CRI). In Part 1 of this work, CRI was used to prepare gradients for the purpose of separating transition and heavy metals. Initial work on this project was focused on controlling the retention of the metal ions by varying the number of amine groups, aminoalkoxysilane concentration, and the infusion time. The retention factors of four metal ions varied predictably with increasing number of amine groups, increasing aminoalkoxysilane concentration, and increasing infusion time, producing small but useful changes in the …

Polyol Induced Partitioning Of Essential Oils In Aqueous Organic Solvent Mixtures, Thomas Delmastro

Seton Hall University Dissertations and Theses (ETDs)

Polyol Induced Extraction (PIE) was developed and patented at Seton Hall University by Drs. John R. Sowa Jr., Wyatt R. Murphy, and Mithilesh Deshpande. It was originally discovered and implemented as a method to recycle and reuse waste acetonitrile during the production shortage in 2008. Through the use of PIE, a solvent mixture containing acetonitrile and water can be separated by employing a polyol mass separating agent, which induces a phase separation. The system is separated into its corresponding aqueous and organic phases, with the organic phase being a highly purified organic liquid. Based on the successful experimental results that …

The Investigation Of The Electrical Control Of Hemimicelles And Admicelles On Gold For Analyte Preconcentration, Dheyaa Hussein Al-Karawi

Masters Theses & Specialist Projects

Hemimicelles and admicelles are well-investigated wonders in modern science; they are surfactant monolayers and surface adsorbed micelles, respectively. Capacitance measurements for monitoring the formation of dodecyl sulfate (DS) surfactant monolayer on positively charged gold substrates (planar gold) and the adsorbance of 2-naphthol onto DS surfactant monolayer were performed. The investigation of the electrical control of DS at various concentrations (4, 6, 16, and 32 mM) below and above the critical micelle concentration (CMC= 8 mM) on gold surfaces for analyte preconcentration, prior to chromatographic analysis, is presented. Charged ionic surfactants, such as DS, drawn to a surface of opposite charge …

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 …

Mida Boronates Are Hydrolysed Fast And Slow By Two Different Mechanisms, Jorge A. Gonzalez, O. Maduka Ogba, Gregory F. Morehouse, Nicholas Rosson, Kendall N. Houk, Andrew G. Leach, Paul H.-Y. Cheong, Martin D. Burke, Guy C. Lloyd-Jones

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

MIDA boronates (N-methylimidodiacetic boronic acid esters) serve as an increasingly general platform for building-block-based small molecule construction, largely due to the dramatic and general rate differences with which they are hydrolysed under various basic conditions. Yet the mechanistic underpinnings of these rate differences have remained unclear, hindering efforts to address current limitations of this chemistry. Here we show that there are two distinct mechanisms for this hydrolysis: one is base-mediated and the other neutral. The former can proceed more than three orders of magnitude faster, and involves rate-limiting attack at a MIDA carbonyl carbon by hydroxide. The alternative ‘neutral’ hydrolysis …

Staphylococcal Nuclease And Ubiquitin Local Folding Energies And Rates Using Peps-Hdx-Esi-Ms, Julie Rhee

Chemistry & Biochemistry Undergraduate Honors Theses

In this study, Protein Equilibrium Population Snapshot Hydrogen-Deuterium Exchange Electrospray Ionization Mass Spectrometry (PEPS-HDX-ESI-MS) was applied to study the local regions of model proteins, staphylococcal nuclease and ubiquitin. The hydrogen deuterium exchange (HDX) has become a key technique for studying the structural and dynamic aspects of proteins in solution. This technique creates a rapid exchange between all of the exchangeable hydrogen ions with deuterium when the protein is exposed to a solvent. The PEPS method is an equilibrium-based method used to determine the populations of the closed native and open denatured states of a protein. By combining the applications of …

Facilitating Conceptual Learning In Quantitative Chemistry, Sarah R. Johnson

Electronic Theses and Dissertations

Traditional chemistry laboratory courses have a manual consisting of “step-by-step” experiments; instructions are given to complete experiments, requiring minimal information/concepts processing to be successful. This experience leaves students unprepared for the real-world, where critical thinking skills are needed to conduct research. This study focused on building analytical techniques, conceptual knowledge, and critical thinking skills used to solve research problems. A new quantitative chemistry laboratory manual was developed to transition students from traditional to inquiry-based experiments, requiring analytical method development. Data showed students having less difficulty using the new manual (0.8281 average difficulty) on method development exam questions and experiments, compared …

Ruthenium-Catalyzed Amination Of Secondary Alcohols Using Borrowing Hydrogen Methodology, Kostiantyn O. Marichev, James M. Takacs

Department of Chemistry: Faculty Publications

A new ruthenium complex catalyzes the amination of primary and secondary alcohols and the regioselective mono- and sequential diamination of diols via the borrowing hydrogen pathway. Several variations on new intra- and intermolecular cyclizations of aminoalcohols, diols and diamines lead to heterocyclic ring systems.

Αβ-Peptide Mimics Of Z-Domain Peptides, Samuel H. Gellman, James W. Checco

Department of Chemistry: Faculty Publications

Described are αβ-peptide mimics of Z-domain scaffold pep tides, methods of making them, and methods of using them. The αβ-peptide mimics include B-amino acid residues and, optionally, disulfide bonds to stabilize the conformation of the mimics. The compounds may be truncated as compared to conventional Z-domain scaffold peptides and are resistant to proteolytic degradation due to the presence off-amino acid residues. The mimics can be made so as to bind selectively to a desired target.

Hlarp7 C-Terminal Domain Contains An Xrrm That Binds The 3' Hairpin Of 7sk Rna, Catherine D. Eichhorn, Rahul Chug, Juli Feigon

Department of Chemistry: Faculty Publications

The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal Lamodule binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear.We report the solution NMR structure of the hLARP7 CTD and …

Analytic Ab Initio-Based Molecular Interaction Potential For The Bro·H2O Complex, Ross D. Hoehn, Sachin D. Yeole, Sabre Kais, Joseph S. Francisco

Department of Chemistry: Faculty Publications

Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrO·H₂O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrO·H₂O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES …

Ring Closures And The Hammond Postulate, Charles A. Kingsbury

Department of Chemistry: Faculty Publications

This work reports an investigation of ring closure processes in relation to the Hammond postulate. Calculations favor the importance of thermodynamics, not kinetics, as the basis for the Hammond postulate. A kinetically rapid, but thermodynamically unfavorable reaction is shown to resemble product. The ease of ring closure to three-membered rings, compared to four-membered rings, is thought to be associated with conformational mobility and perhaps vibrations coupled to the reaction coordinate motion in the case of four-membered rings.

Live, Attenuated Vaccines And Methods Of Making And Using, Jiantao Guo, Qingsheng Li, Wei Niu, Yue Li, Nanxi Wang

Department of Chemistry: Faculty Publications

A live, attenuated HIV vaccine is provided, and methods of making a atenuated HIV vaccine are provided.

Processes And Reagents For Making Daryliodonium Salts, Stephen Dimagno

Department of Chemistry: Faculty Publications

This invention relates to processes and reagents for making diaryliodonium salts, which are useful for the preparation of fluorinated and radiofluorinated aromatic compounds.

Mutagenesis-Based Active-Site Characterization Of The Diabetes Drug Target Mitoneet, Lisa Mickley

Williams Honors College, Honors Research Projects

This project investigates the cluster stability of an outer mitochondrial membrane protein mitoNEET under mutational stress and drug binding analysis. MitoNEET is a part of a class of proteins that coordinate an Fe-S molecule into its tertiary structure. This protein is believed to facilitate the oxidative capacity of the electron transport chain by reversible loss of its coordinated Fe-S molecule. The research of this paper uses site directed protein mutagenesis to selectively alter the three cysteine, one histidine cluster coordination into more common coordination patterns such as two cysteine, two histidine or four cysteine. The ultimate goal is to optimize …

Signature Of Coexistence Of Superconductivity And Ferromagnetism In Two-Dimensional Nbse2 Triggered By Surface Molecular Adsorption, Xiaojiao Zhu, Yuqiao Guo, Hao Cheng, Jun Dai, Xingda An, Jiyin Zhao, Kangzhen Tian, Shiqiang Wei, Xiao Cheng Zeng, Changzheng Wu, Yi Xie

Department of Chemistry: Faculty Publications

Ferromagnetism is usually deemed incompatible with superconductivity. Consequently, the coexistence of superconductivity and ferromagnetism is usually observed only in elegantly designed multi-ingredient structures in which the two competing electronic states originate from separate structural components. Here we report the use of surface molecular adsorption to induce ferromagnetism in two-dimensional superconducting NbSe₂, representing the freestanding case of the coexistence of superconductivity and ferromagnetism in one two-dimensional nanomaterial. Surface-structural modulation of the ultrathin superconducting NbSe₂ by polar reductive hydrazine molecules triggers a slight elongation of the covalent Nb–Se bond, which weakens the covalent interaction and enhances the ionicity of …

Engineering Escherichia Coli For High‑Yield Geraniol Production With Biotransformation Of Geranyl Acetate To Geraniol Under Fed‑Batch Culture, Wei Liu, Xin Xu, Rubing Zhang, Tao Cheng, Yujin Cao, Xiaoxiao Li, Jiantao Guo, Huizhou Liu, Mo Xian

Department of Chemistry: Faculty Publications

Background: Geraniol is an acyclic monoterpene alcohol, which exhibits good prospect as a gasoline alternative. Geraniol is naturally encountered in plants at low concentrations and an attractive target for microbial engineering. Geraniol has been heterologously produced in Escherichia coli, but the low titer hinders its industrial applications. Moreover, bioconversion of geraniol by E. coli remains largely unknown.

Results: Recombinant overexpression of Ocimum basilicum geraniol synthase, Abies grandis geranyl diphosphate synthase, and a heterotic mevalonate pathway in E. coli BL21 (DE3) enabled the production of up to 68.6 ± 3 mg/L geraniol in shake flasks. Initial fed-batch fermentation only increased geraniol …

Highly Porous Zirconium Metal−Organic Frameworks With Β‑Uh3‑Like Topology Based On Elongated Tetrahedral Linkers, Xin Zhang, Xu Zhang, Jacob A. Johnson, Yu-Sheng Chen, Jian Zhang

Department of Chemistry: Faculty Publications

Two non-interpenetrated zirconium metal−organic frameworks (Zr-MOFs), NPF-200 and NPF-201, were synthesized via the assembly of elongated tetrahedral linkers with Zr₆ and Zr₈ clusters. They represent the first examples of MOFs to have the β-UH₃-like, 4,12,12T1 topology. Upon activation, NPF-200 exhibits the largest BET surface area (5463 m²g⁻¹) and void volume (81.6%) among all MOFs formed from tetrahedral ligands. Composed of negative-charged boron-centered tetrahedral linkers, NPF-201 is an anionic Zr-MOF which selectively uptakes photoactive [Ru(bpy)₃]²⁺for heterogeneous photo-oxidation of thioanisole.

Additional supporting information files are attached below.

Close Encounters With Creative Chemical Thinking: An Outreach Presentation Using Movie Clips About The Elemental Composition Of Aliens And Extraterrestrial Minerals, Mark A. Griep, Marjorie L. Mikasen

Department of Chemistry: Faculty Publications

To introduce more chemistry into a middle and high school bioengineering camp experience, we developed an educational and entertaining presentation that examines the chemistry in movies about aliens and minerals from outer space. Our goal was to help the campers to think creatively about the bioengineering projects they are doing and about its chemistry. After watching each movie clip, we explain whether the chemistry in the clip is real or fake, and then describe the real chemistry that inspired it. The chemical touchstone for the presentation is the periodic table. First, the campers learn that aliens in five movies are …

Flexble Robotic Actuators, Aaron D. Mazzeo, Stephen A. Morin, Robert F. Shepherd, George M. Whitesides, William B. Kalb

Department of Chemistry: Faculty Publications

Some embodiments of the disclosed subject matter includes a laminated robotic actuator. The laminated robotic actuator includes a strain-limiting layer comprising a flexible, non extensible material in the form of a sheet or thin film, a flexible inflatable layer in the form of a thin film or sheet in facing relationship with the Strain-limiting layer, wherein the inflatable layer is selectively adhered to the strain-limiting layer, and wherein a portion of an un-adhered region between the strain-limiting layer and the inflatable layer defines a pressurizable channel, and at least one fluid inlet in fluid communication with the pressurizable channel. The …

Forensic Chemical Analysis Of Synthetic Cathinones Using Portable Mass Spectrometric Instrumentation, Caitlin N. Cain

Undergraduate Research Posters

Forensic laboratories face issues with large backlogs on evidence needing to be analyzed is due to two reasons: budgeting issues and the emergence of designer drugs. Currently, forensic laboratory directors cite that there are a shortage of scientists to deal with the yearly increase in caseloads. Additionally, designer drugs like synthetic cathinones, commonly known as “bath salts,” have increased the backlog due to the changing chemical compositions and misidentification as other compounds. Therefore, the use of a portable mass spectrometer for on-site forensic chemical analysis of synthetic cathinones would reduce the backlog of suspected controlled substances in forensic chemistry laboratories. …

The Development Of Colorimetric Assays To Determine The Identity And Frequency Of Specific Nucleobases In Dna Oligomers, Elizabeth Marie Thomas

Theses and Dissertations--Chemistry

Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this dissertation, …

Bis(Spirolactam) 1,3-Double-Armed Calix[4]Arene Compounds And Their Application As Extractants For The Determination Of Heavy Metal Ions, Fintan Kelleher, Mary Deasy, James Ward, Li Li, Fiona Regan

Articles

A number of double-armed calix[4]arene compounds, with proline-derived spirolactam ligating groups on the lower rim, have been synthesised and investigated as extractants of toxic heavy metal ions from aqueous solution. Pedersen’s extraction technique was employed to determine the capability of these new 1,3-distal derived calix[4]arene spiroalactams to extract selected heavy metal ions (e.g. Pb²⁺, Cd²⁺, Zn²⁺, Cu²⁺, Ni²⁺, Co²⁺) from an aqueous phase into an organic phase. The percentage extraction was calculated using UV-vis spectroscopy. All of the compounds synthesised demonstrated good selectivity for the heavy metals selected …

Effect Of Surface Omniphobicity On Drying By Forced Convection, Madani A. Khan, Jeffrey Alston, Andrew Guenthner

STAR Program Research Presentations

Low energy surfaces can strongly repel both oil and water. Recently these surfaces have been fabricated on various substrates including fabric, aluminum, stainless steel and many other materials. In this experiment we explore the use of low energy surface deposition on aluminum alloy, stainless steel and silicon substrates, to enhance the drying rate of liquids removed from the surface by forced convection. We control surface roughness by substrate abrasion and by the growth of Al₂O₃ nanograss to enhance liquid repellence by use of a hierarchical texture. Liquid repellence of the substrates is measured by contact angles of …

Synthesis And Flammability Testing Of Epoxy Functionalized Phosphorous-Based Flame Retardants, Vladimir Benin, Xuemei Cui, Alexander Morgan, Karl Seiwert

Chemistry Faculty Publications

Several potential new phosphorus-containing flame retardant molecules were evaluated for heat release reduction potential by incorporation of the molecules into a polyurethane, generated from methylene diphenyl diisocyanate and 1,3-propane diol. The heat release reduction potential of these substances was evaluated 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 to qualitatively evaluate their potential reactivity into the polyurethane prior to heat release testing. The functionality of the flame retardants was epoxide based that would potentially react with the diol during polyurethane synthesis. Flammability testing …

The Best Of Both Worlds: Building On The Copus And Rtop Observation Protocols To Easily And Reliably Measure Various Levels Of Reformed Instructional Practice, Travis J. Lund, Matthew Pilarz, Jonathan B. Velasco, Devasmita Chakraverty, Kaitlyn Rosploch, Molly Undersander, Marilyne Stains

Department of Chemistry: Faculty Publications

Researchers, university administrators, and faculty members are increasingly interested in measuring and describing instructional practices provided in science, technology, engineering, and mathematics (STEM) courses at the college level. Specifically, there is keen interest in comparing instructional practices between courses, monitoring changes over time, and mapping observed practices to research-based teaching. While increasingly common observation protocols (Reformed Teaching Observation Protocol [RTOP] and Classroom Observation Protocol in Undergraduate STEM [COPUS]) at the postsecondary level help achieve some of these goals, they also suffer from weaknesses that limit their applicability. In this study, we leverage the strengths of these protocols to provide an …