Chemistry Commons^™

Reaction Mechanism Between Small-Sized Ce Clusters And Water Molecules: An Ab Initio Investigation On CeN+H2O, Rulong Zhou, Yang Yang, Seema Pande, Bingyan Qu, Dongdong Li, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Reactions of small-sized cerium clusters Ce_n (n = 1–3) with a single water molecule are systematically investigated theoretically. The ground state structures of the Ce_n/H₂O complex and the reaction pathways between Ce_n + H₂O are predicted. Our results show the size-dependent reactivity of small-sized Ce clusters. The calculated reaction energies and reaction barriers indicate that the reactivity between Ce_n and water becomes higher with increasing cluster size. The predicted reaction pathways show that the single Ce atom and the Ce₂ and Ce₃ clusters can all easily react with H …

Coherent Vibrational And Dissociation Dynamics Of Polyatomic Radical Cations, Katharine M. Tibbetts

Chemistry Publications

The ultrafast dynamics of polyatomic radical cat- ions contribute to important processes including energy transfer in photovoltaics, electron transfer in photocataly- sis, radiation-induced DNA damage, and chemical reac- tions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of polyatomic radical cations following elec- tron removal, which arises from excess electronic excita- tion of the molecule during the ionization process. This Concept article introduces the reader to how the pump- probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can overcome this challenge to capture coherent vibrational dynamics on the …

Probing Coherent Vibrations Of Organic Phosphonate Radical Cations With Femtosecond Time-Resolved Mass Spectrometry, Derrick Ampadu Boateng, Mi'kayla D. Word, Katharine M. Tibbetts

Chemistry Publications

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs (732 ± 28 cm−1) oscillations with a weak feature at 610–650 cm−1, while DIMP exhibits bimodal oscillations with a period of ∼55 fs …

Multifaceted Water Dynamics In Spherical Nanocages, M. Von Domaros, D. Bratko, B. Kirchner, G. Hummer, A. Luzar

Chemistry Publications

We present a new method to study position- dependent, anisotropic diffusion tensors inside spherically confined systems—a geometry that is common to many chemical nanoreactors. We use this method to elucidate the surprisingly rich solvent dynamics of confined water. The spatial variation of the strongly anisotropic diffusion predicted by the model agrees with the results of explicit molecular dynamics simulations. The same approach can be directly transferred to the transport of solutes to and from reaction sites located at nanoreactor interfaces. We com- plement our study by a detailed analysis of wa- ter hydrogen bond kinetics, which is intimately coupled to …

Molecular Polarizability In Open Ensemble Simulations Of Aqueous Nanoconfinements Under Electric Field, F. Moucka, S. Zamfir, D. Bratko, A. Luzar

Chemistry Publications

Molecular polarization at aqueous interfaces involves fast degrees of freedom that are often averaged-out in atomistic-modeling approaches. The resulting effective interactions depend on a specific environment, making explicit account of molecular polarizability particularly important in solutions with pronounced anisotropic perturbations, including solid/liquid interfaces and external fields. Our work concerns polarizability effects in nanoscale confinements under electric field, open to an unperturbed bulk environment. We model aqueous molecules and ions in hydrophobic pores using the Gaussian-charge-on-spring BK3-AH representation. This involves nontrivial methodology devel- opments in expanded ensemble Monte Carlo simulations for open systems with long-ranged multibody interactions and necessitates further improvements …

Role Of Water On The Rotational Dynamics Of The Organic Methylammonium Cation: A First Principles Analysis, Ross D. Hoehn, Joseph S. Francisco, Sabre Kais, Ali Kachmar

Department of Chemistry: Faculty Publications

Understanding the degradation mechanisms of lead-halide perovskites (CH₃NH₃PbI₃) under exposure to liquid/aerosol water is an essential problem within the photovoltaic community. Herein we investigate both the static and the dynamic properties of the methylammonuim cation (MA) as it coordinates with invading water molecules (MA.(H₂O)_n, n = 1, 2, 3, 4) using both stationary state quantum mechanics and first principle molecular dynamics simulations. Various solvation structures of MA were characterized by their stabilization energies, dipoles, and Maximally-Localized Wannier Function (MLWF) centers. Calculation – and analysis – of vibrational shifts in the …

Structural Basis Of 7sk Rna 5′ Γ-Phosphate Methylation And Retention By Mepce, Yuan Yang, Catherine D. Eichhorn, Yaqiang Wang, Duilio Cascio, Juli Feigon

Department of Chemistry: Faculty Publications

Among RNA 5′-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second non-enzymatic role as a core component of the 7SK RNP that is an essential regulator of RNA transcription. We report 2.0 and 2.1 Å X-ray crystal structures of human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5′ hairpin-single-stranded RNA region, explaining MePCE specificity for 7SK and U6. The structures reveal SAH and …

Molecular Insights Into Cage Occupancy Of Hydrogen Hydrate: A Computational Study, Rui Ma, Hong Zhong, Jinxiang Liu, Jie Zhong, Youguo Yan, Jun Zhang, Jiafang Xu

Department of Chemistry: Faculty Publications

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

Biosensor For The Oxidative Stress Biomarker Glutathione Based On Sam Of Cobalt Phthalocyanine On A Thioctic Acid Modified Gold Electrode, Mohammed Nooredeen Abbas, Ayman Ali Saeed, Mounir Ben Ali, Abdelhamid Errachid, Nadia Zine, Abdullatif Baraket, Baljit Singh

Articles

Self-assembled monolayer (SAM) of cobalt teraaminophthalocyanine (CoTAPc) was developed on thioctic acid (TA) dithiol modified gold electrode and electrochemically evaluated as a glutathione (GSH) selective biosensor. The CoTAPc-TA-Au modified electrode was developed by the covalent immobilization of the CoTAPc as the electrochemical mediator onto previously prepared gold electrode modified with TA (TA-Au) via amid bond formation with the carboxylic group of TA, producing well-organized SAM of the mediator. For comparison, another electrode modified with 3-mercaptopropionic acid (MPA) as a monothiol linker instead of TA was similarly prepared. The electrode surface modification was characterized using SEM, AFM, CV, and EIS. The …

Fluorescent Behavior Of Esculetin, Yukun Tu, Mark Muyskens

Summer Research

Esculetin is a member of coumarin family, more importantly, as well as one of the big three natural coumarins that have most academic publications. The adjacent -OHs on 6 and 7 positions gives esculetin intriguing hydrogen bonding mechanism, and the deprotonation the excited state of esculetin resembles both scopoletin and umbelliferone, which makes us eager to dive into esculetin’s chemistry

Determining Binding Constants Of Nickel(Ll) And Various Amine Ligands In A Competing Solution, Ryan Storteboom, Douglas A. Vander Griend

Summer Research

• Determining binding constants of Ni(II) and various amine ligands can provide valuable insight into what chemical species form in a competing solution.
• As a ligand is titrated into a Ni(II) solution, the color of the solution will shift.
• The titration is preformed in UV-Vis spectrometer to measure and record this shift in color.
• SIVVU, a computer program designed for analyzing these color shifts, is then used to determine the molar absorptivity and concentration profiles. From these SIVVU can calculate the binding constants of the different Ni(II) and the ligand species.

Discovering Chemical Structure With Linus Pauling, Jin H. Kim

Natural Sciences Student Research Presentations

This poster for the Natural Sciences Poster Session provides a brief history and description of structural chemistry, the science dealing with the molecular structure of chemical substances, with a focus on Linus Pauling, the only scientist to have received two unshared Nobel Prizes.

Radium Dial Watches, Zainab Alzoubi

Natural Sciences Student Research Presentations

This slide presentation for the Natural Sciences Poster Session at Parkland College summarizes the history of radium dial watches, including the Radium Girls, and explores whether radium dial watches might still be dangerous.

Organizing 6, 5-Carbon Nanotubes On Dna Origami Arrays, Kathryn A. Pitton

Theses, Dissertations and Capstones

Carbon nanotubes¹ are cylindrical carbon molecules and can be considered to be composed of one atom thick sheets of carbon called graphene. They have been at the forefront of nanochemistry due to their strength and multiple properties such as absorption, fluorescence, semiconduction, and light scattering capability. DNA Origami (DO)² has emerged as a novel domain for molecular design, resulting in the generation of numerous one, two, and three-dimensional structures that have provided platforms for the organization of organic species and inorganic nanoparticles through simple modifications. The use of DNA Origami to control the placement of single walled carbon …

Electrochemical Reduction Of Artemisinin: Chromatographic Identification Of Bulk Electrolysis Products, Faja Ombwayo, Zahilis Mazzochette, Amos Mugweru

College of Science & Mathematics Departmental Research

Artemisinin is a naturally occurring sesquiterpene lactone with an endo-peroxide bond. This drug is used for treatment of many diseases including malaria. The reduction of this molecule on an electrode surface was carried out by cyclic voltammetry as well as amperometry. Cyclic voltammetry of artemisinin generated one prominent peak wave at -1.0 V and another, smaller one at -0.3 V vs Ag/AgCl reference electrode. The bulk electrolysis of artemisinin on a carbon electrode generated two other irreversible peak waves at around -0.7 and -0.1 V. The concentration of the products was dependent on the time of electrolysis. LC-MS was used …

Brush-Arm Star Polymer Imaging Agents And Uses Thereof, Jeremiah A. Johnson, Hung Vanthanh Nguyen, Andrzej Rajca

Department of Chemistry: Faculty Publications

Disclosed are methods, compositions, reagents, systems, and kits to prepare nitroxide-functionalized brush-arm star polymer organic radical contrast agent (BASP-ORCA) as well as compositions and uses thereof. Various embodiments show that BASP-ORCA display unprecedented per-nitrox-ide and per-molecule transverse relaxivities for organic radical contrast agents, exceptional stability, high water solubility, low in vitro and in vivo toxicity, and long blood compartment half-life. These materials have the potential to be adopted for tumor imaging using clinical high-field ¹H MRI techniques.

Growth Of Carbon Dioxide Whiskers, Avinash Kumar Both, Chin Li Cheung

Department of Chemistry: Faculty Publications

We report the growth of carbon dioxide (CO₂) whiskers at low temperatures (–70 °C to –65 °C) and moderate pressure (4.4 to 1.0 bar). Their axial growth was assessed by optical video analysis. The identities of these whiskers were confirmed as CO₂ solids by Raman spectroscopy. A vapor– solid growth mechanism was proposed based on the influence of the relative humidity on the growth.

Role Of Water On The Rotational Dynamics Of The Organic Methylammonium Cation: A First Principles Analysis, Ross D. Hoehn, Joseph S. Francisco, Sabre Kais, Ali Kachmar

Department of Chemistry: Faculty Publications

Understanding the degradation mechanisms of lead-halide perovskites (CH₃NH₃PbI₃) under exposure to liquid/aerosol water is an essential problem within the photovoltaic community. Herein we investigate both the static and the dynamic properties of the methylammonuim cation (MA) as it coordinates with invading water molecules (MA.(H₂O)_n, n = 1, 2, 3, 4) using both stationary state quantum mechanics and first principle molecular dynamics simulations. Various solvation structures of MA were characterized by their stabilization energies, dipoles, and Maximally-Localized Wannier Function (MLWF) centers. Calculation – and analysis – of vibrational shifts in the …

Indole Reverses Intrinsic Antibiotic Resistance By Activating A Novel Dual-Function Importer, Yan Wang, Tian Tian, Jingjing Zhang, Xin Jin, Huan Yue, Xiao-Hua Zhang, Liangcheng Du, Fan Bai

Department of Chemistry: Faculty Publications

Bacterial antibiotic resistance modulation by small signaling molecules is an emerging mechanism that has been increasingly reported in recent years. Several studies indicate that indole, an interkingdom signaling molecule, increases bacterial antibiotic resistance. However, the mechanism through which indole reduces antibiotic resistance is largely unknown. In this study, we demonstrated a novel mechanism for indole-mediated reversal of intrinsic antibiotic resistance in Lysobacter. This reversal was facilitated by a novel BtuD-associated dual-function importer that can transfer both vitamin B₁₂ and antibiotics. Indole stimulated btuD overexpression and promoted efficient absorption of extracellular vitamin B₁₂; meanwhile, the weak selectivity …

Rapid-Scan Epr And Imaging, Yilin Shi

Electronic Theses and Dissertations

EPR imaging at low frequency is a powerful tool to obtain important biological information in vivo in a non-invasive way. Properties of nitroxide and trityl radical imaging reagents have been studied. Developments in rapid scan imaging techniques are reported that improve efficiency of experiments and user-friendliness of software.

Relaxation and signal-to-noise ratio (S/N) in pulse experiments on trityl radicals were measured at frequencies between 400 MHz and 1.5 GHz. Relaxation time increases as the frequency increases and the radical concentration decreases. Since relaxation time is a sensitive and accurate measure of oxygen pressure, this study provides criteria for the selection …

In-Quest Of Biomarkers For Alzheimer’S Disease And Pharmacokinetic Profile Of Anticancer Agents Using Lc-Ms In Human Plasma, Chandana Mannem

ETD Archive

In this dissertation work, a semi-quantitative assay using a lipidomics approach and an absolute quantitative assay using liquid chromatography-mass spectrometry techniques were developed (LC-MS). In the lipidomics approach, ultra-high pressure liquid chromatography in tandem with quadrupole time of flight (UHPLC-QTOF) mass spectrometry was used to profile, compare and quantitate the human plasma lipids in Alzheimer’s disease subjects (AD) and normal cognitive controls (NCCs). The purpose of this study is to identify potential plasma lipid markers of AD and to explore the relationships between AD and lipid pathways in humans by using bioinformatic tools. The plasma samples of study subjects were …

The Periodical Winter 2019, Southern Adventist University

the Periodical – Chemistry Department Newsletter

Volume 6, issue 1 of the Periodical includes articles about Professor Loren Barnhurst's departure from the university, an alumni spotlight, general department news, at a pictorial listing of 2018-2019 Chemistry graduates.

Fabrication And In-Situ Cross-Linking Of Carboxylic Acid-Functionalized Poly(Ester Amide) Scaffolds For Tissue Engineering, Kai Cao, Derek S. Flegg, Shigang Lin, Francois Lagugne-Labarthet, Kibret Mequanint, Elizabeth Gillies

Chemistry Publications

Three-dimensional (3D) scaffolds are important tools for tissue engineering, and should ideally provide both biochemical cues and biomechanical support for cells. Poly(ester amide)s (PEAs) have emerged as promising materials for the preparation of tissue engineering scaffolds and the pendant side chains of residues such as ʟ-lysine and ʟ-aspartic acid can provide sites for the conjugation of biochemical signals. However, it has been challenging to combine scaffold morphological stability with the presentation of reactive groups on PEA scaffolds. We describe here a new approach involving the functionalization of a ʟ-lysine-containing PEA with maleic anhydride to simultaneously introduce cross-linkable alkenes and carboxylic …

Triggering Depolymerization: Progress And Opportunities For Self-Immolative Polymers, Rebecca Yardley, Amir Rabiee Kenaree, Elizabeth Gillies

Chemistry Publications

Polymers that depolymerize end-to-end upon cleavage of their backbones or end-caps, often referred to as “self-immolative” polymers (SIPs), have garnered significant interest in recent years. They can be distinguished from other degradable and stimuli-responsive polymers by their ability to provide amplified responses to stimuli, as a single bond cleavage event is translated into the release of many small molecules through a cascade of reactions. Here, the synthesis and properties of the major classes of SIPs including poly(benzyl carbamate)s, poly(benzyl carbonate)s, polyphthalaldehydes, polyglyoxylates, polyglyoxylamides, poly(olefin sulfone)s, and poly(benzyl ether)s are presented. In addition, their advantages and limitations as well as their …

Thermo-Responsive And Covalently Cross-Linkable Hydrogels For Intra-Articular Drug Delivery, Andy Prince, Ian J. Villamagna, Aneta Borecki, Frank Beier, John R. De Bruyn, Mark Hurtig, Elizabeth Gillies

Chemistry Publications

The local delivery of drugs to joints is a recognized strategy in the treatment of osteoarthritis. Hydrogels, particularly those that can be injected as liquids but undergo gelation in the joint, are promising platforms for intra-articular drug delivery. However, their properties must be carefully designed and tuned to achieve sustained drug release, which has been a challenge with previous hydrogels. We describe here the use of a combination of non-covalent thermal gelation and covalent cross-linking with poly(caprolactone-co-lactide)(PCLA)-poly(ethylene glycol)(PEG)-PCLA triblock copolymers to achieve hydrogels with sustained drug release in joints. The hybrid cross-linking approach afforded higher viscoelastic and compression …

Polyglyoxylamides: Tuning Structure And Properties Of Self- Immolative Polymers, Quinton E.A. Sirianni, Amir Rabiee Kenaree, Elizabeth Gillies

Chemistry Publications

Self-immolative polymers (SIPs) are a class of stimuli-responsive materials that undergo controlled end-to-end depolymerization in response to stimuli. Their unique degradation and amplification properties have made them of interest for a diverse array of applications including sensors, vehicles for controlled release, and transient objects. Thus far, a limited number of SIP backbones exists, each with its own advantages and limitations. We report here the preparation and study of polyglyoxylamides (PGAms) as a new class of SIPs. PGAms were synthesized by simple post-polymerization modifications of poly(ethyl glyoxylate) (PEtG). While retaining the important stimuli-responsive depolymerization properties of polyglyoxylates, PGAms exhibited much different …

Reactivity Of Molybdenum And Tungsten Sulfido Complexes With First-Series Transition Metals, Khalil Mudarmah

ETD Archive

Ammonium tetrathiomolybdate (ATTM) is an important compound in bioinorganic chemistry, with medicinal applications. Metal complexes of sulfur-containing ligands have been widely used as building block in biology and inorganic chemistry. This project aims to increase the number of Mo-S and W-S complexes that may contribute to fields such as bioinorganic and medicinal chemistry, by the preparation of heterometallic complexes containing both Mo or S and a metal of the first transition series. The homobimetallic complex anion salts (Et4N)2[Mo2(S)2(μ-S)2(edt)2] (1) and (Et4N)2[W2(S)2(μ-S)2(edt)2] (2) have been prepared from ATTM and ammonium tetrathiotungstate (ATTW) in order to start our work. The overnight treatment …

Development Of An Spr Method To Monitor The Chemical Interaction Of Dna With A Small Reactive Molecule: Peroxynitrite As An Example, Divya Sharma

ETD Archive

Peroxynitrite is an anion with the formula ONOO-. It is an unstable structural isomer of nitrate, NO3-. Although its conjugate acid (ONOOH) is highly reactive, it is quite relatively stable in basic solutions. Generation of peroxynitrite in-vivo occurs through the diffusion-controlled reaction between superoxide anion and nitric oxide free radical. It is a strong oxidizing and nitrating agent, and its formation has been correlated with many pathological conditions. Because of its oxidizing properties, peroxynitrite can damage a wide array of molecules in cells, including DNA and proteins. Reactions of peroxynitrite with DNA, proteins, and lipids, trigger a wide array of …

Development Of An Spr Method To Monitor The Chemical Interaction Of Dna With A Small Reactive Molecule: Peroxynitrite As An Example, Divya Sharma

ETD Archive

Peroxynitrite is an anion with the formula ONOO-. It is an unstable structural isomer of nitrate, NO3-. Although its conjugate acid (ONOOH) is highly reactive, it is quite relatively stable in basic solutions. Generation of peroxynitrite in-vivo occurs through the diffusion-controlled reaction between superoxide anion and nitric oxide free radical. It is a strong oxidizing and nitrating agent, and its formation has been correlated with many pathological conditions. Because of its oxidizing properties, peroxynitrite can damage a wide array of molecules in cells, including DNA and proteins. Reactions of peroxynitrite with DNA, proteins, and lipids, trigger a wide array of …

Liquid Chromatography - Mass Spectrometric Analysis Of Clinicallyand Pharmacologically Relevant Molecules, Raghavi Kakarla

ETD Archive

Liquid Chromatography-Mass Spectrometry is an advanced analytical technique that offers high sensitivity and specificity and has been increasingly used for analysis of a wide variety of compounds including clinically and pharmacologically relevant molecules. In this dissertation we describe qualitative and quantitative liquid chromatographic mass spectrometric methods to analyze both small molecules and larger macromolecules that provide useful insights into diagnosis and management of several diseases. An LCMS(/MS) analytical method includes extraction of analytes of interest from the matrix followed by liquid chromatographic separation and mass spectrometric detection. Chapter I describes pre-analytical workflows and sample pretreatment techniques and theories underlying LC-MS …