Analytical Chemistry Commons^™

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.

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 …

High Initial Reversible Capacity And Long Life Of Ternary Sno2‑Co‑Carbon Nanocomposite Anodes For Lithium‑Ion Batteries, Pan Deng, Jing Yang, Shengyang Li, Tian-E Fan, Hong-Hui Wu, Yun Mou, Hui Huang, Qiaobao Zhang, Dong-Liang Peng, Baihua Qu

Department of Chemistry: Faculty Publications

The two major limitations in the application of SnO₂ for lithium-ion battery (LIB) anodes are the large volume variations of SnO₂ during repeated lithiation/delithiation processes and a large irreversible capacity loss during the first cycle, which can lead to a rapid capacity fade and unsatisfactory initial Coulombic efficiency (ICE). To overcome these limitations, we developed composites of ultrafine SnO₂ nanoparticles and in situ formed Co(CoSn) nanocrystals embedded in an N-doped carbon matrix using a Co-based metal–organic framework (ZIF-67). The formed Co additives and structural advantages of the carbon-confined SnO₂/ Co nanocomposite effectively inhibited Sn coarsening …

Spheroid-3d And Monolayer-2d Intestinal Electrochemical Biosensor For Toxicity/Viability Testing: Applications In Drug Screening, Food Safety, And Environmental Pollutant Analysis, Evangelia Flampouri, Shahzad Imar, Kieran O'Connell, Baljit Singh

Articles

The rise of three-dimensional cell culture systems that provide in vivo-like environments for pharmaco-toxicological models has prompted the need for simple and robust viability assays suitable for complex cell architectural structures. This study addresses that challenge with the development of an in vitro enzyme based electrochemical sensor for viability/cytotoxicity assessment of two-dimensional (2D) monolayer and three-dimensional (3D) spheroid culture formats. The biosensor measures the cell viability/toxicity via electrochemical monitoring of the enzymatic activity of nonspecific esterases of viable cells, through the hydrolysis of 1-naphthyl acetate to 1-naphthol. The proposed sensor demonstrated strong correlation (r = 0.979) with viable …

Highly Stable And Efficient All-Inorganic Lead-Free Perovskite Solar Cells With Native-Oxide Passivation, Min Chen, Ming-Gang Ju, Hector F. Garces, Alexander D. Carl, Luis K. Ono, Zafer Hawash, Yi Zhang, Tianyi Shen, Yabing Qi, Ronald L. Grimm, Domenico Pacifici, Xiao Cheng Zeng, Yuanyuan Zhou, Nitin P. Padture

Department of Chemistry: Faculty Publications

There has been an urgent need to eliminate toxic lead from the prevailing halide perovskite solar cells (PSCs), but the current lead-free PSCs are still plagued with the critical issues of low efficiency and poor stability. This is primarily due to their inadequate photovoltaic properties and chemical stability. Herein we demonstrate the use of the lead-free, allinorganic cesium tin-germanium triiodide (CsSn_0.5Ge_0.5I₃) solid-solution perovskite as the light absorber in PSCs, delivering promising efficiency of up to 7.11%. More importantly, these PSCs show very high stability, with less than 10% decay in efficiency after 500 h …

Urease Is An Essential Component Of The Acid Response Network Of Staphylococcus Aureus And Is Required For A Persistent Murine Kidney Infection, Chunyi Zhou, Fatema Bhinderwala, Mckenzie K. Lehman, Vinai C. Thomas, Sujata S. Chaudhari, Kelsey J. Yamada, Kirk W. Foster, Robert Powers, Tammy Kielian, Paul D. Fey

Department of Chemistry: Faculty Publications

Staphylococcus aureus causes acute and chronic infections resulting in significant morbidity. Urease, an enzyme that generates NH₃ and CO₂ from urea, is key to pH homeostasis in bacterial pathogens under acidic stress and nitrogen limitation. However, the function of urease in S. aureus niche colonization and nitrogen metabolism has not been extensively studied. We discovered that urease is essential for pH homeostasis and viability in urea-rich environments under weak acid stress. The regulation of urease transcription by CcpA, Agr, and CodY was identified in this study, implying a complex network that controls urease expression in response to changes …

Machine Learning Enabled Prediction Of Mechanical Properties Of Tungsten Disulfide Monolayer, Xinyu Wang, Dan Han, Yang Hong, Haiyi Sun, Jingzhi Zhang, Jingchao Zhang

Department of Chemistry: Faculty Publications

One of two-dimensional transition metal dichalcogenide materials, tungsten disulfide (WS₂), has aroused much research interest, and its mechanical properties play an important role in a practical application. Here the mechanical properties of h-WS₂ and t-WS₂ monolayers in the armchair and zigzag directions are evaluated by utilizing the molecular dynamics (MD) simulations and machine learning (ML) technique. We mainly focus on the effects of chirality, system size, temperature, strain rate, and random vacancy defect on mechanical properties, including fracture strain, fracture strength, and Young’s modulus. We find that the mechanical properties of h-WS₂ surpass those of …

Insights Into Gemcitabine Resistance And The Potential For Therapeutic Monitoring, Teklab Gebregiworgis, Fatema Bhinderwala, Vinee Purohit, Nina V. Chaika, Pankaj K. Singh, Robert Powers

Department of Chemistry: Faculty Publications

Introduction—Gemcitabine is an important component of pancreatic cancer clinical management. Unfortunately, acquired gemcitabine resistance is widespread and there are limitations to predicting and monitoring therapeutic outcomes.

Objective—To investigate the potential of metabolomics to differentiate pancreatic cancer cells that develops resistance or respond to gemcitabine treatment.

Results—We applied 1D ¹H and 2D ¹H-¹³C HSQC NMR methods to profile the metabolic signature of pancreatic cancer cells. ¹³C₆-glucose labeling identified thirty key metabolites uniquely altered between wild-type and gemcitabine-resistant cells upon gemcitabine treatment. Gemcitabine resistance was observed to reprogram glucose metabolism and to enhance the pyrimidine …

Detailed Characterization Of The Solution Kinetics And Thermodynamics Of Biotin, Biocytin And Haba Binding To Avidin And Streptavidin, Roberto F. Delgadillo, Timothy C. Mueser, Kathia Zaleta-Rivera, Katie A. Carnes, Jose Gonzalez-Valdez, Lawrence J. Parkhurst

Department of Chemistry: Faculty Publications

The high affinity (K_D ~ 10⁻¹⁵ M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (10⁹ M^-1s^-1) but recent single molecule and surface binding studies indicate that they are slower than expected (10⁵ to 10⁷ M^-1s^-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic …

Xflow: An Algorithm For Extracting Ion Chromatograms, Mathew M. Gutierrez, Rob Smith

Graduate Student Theses, Dissertations, & Professional Papers

Abstract: Mass spectrometry is a fundamental tool for modern proteomics. The increasing availability of mass spectrometry data paired with the increasing sensitivity and fidelity of the instruments necessitates new and more potent analytical methods. To that end, we have created and present XFlow, a feature detection algorithm for extracting ion chromatograms from MS1 LC-MS data. XFlow is a parameter-free procedurally agnostic feature detection algorithm that utilizes the latent properties of ion chromatograms to resolve them from the surrounding noise present in MS1 data. XFlow is designed to function on either profile or centroided data across different resolutions and instruments. This …

The Inductive Effect In Organic Chemistry, Charles A. Kingsbury

Department of Chemistry: Faculty Publications

The subtle difference between the successive polarization model and the flow of electrons through sigma bonds is explored, as well as the alternating charge model of Pople and the pervasive field model. The present paper is concerned with the ability of alkyl groups to serve as sigma inductive electron donors.

Electrocaloric Effect In Ferroelectric Ceramics With Point Defects, Ming Wu, Qingshan Zhu, Jianting Li, Dongsheng Song, Honghui Wu, Mengyao Guo, Jinghui Gao, Yang Bai, Yujun Feng, Stephen J. Pennycoock, Xiaojie Lou

Department of Chemistry: Faculty Publications

The electrocaloric effect has drawn much attention due to its potential application in cooling devices. A negative electrocaloric effect is predicted to be induced in defect-doped ferroelectrics by computational results [A. Grunebohm and T. Nishimatsu, Phys. Rev. B 93, 134101 (2016) and Ma et al., Phys. Rev. B 94, 094113 (2016)], but it need to be confirmed by experimental results. In this work, we prepared a 1mol. % Mn-doped Pb(Zr_0.2,Ti_0.8)O₃ ceramics (Pb((Zr_0.2,Ti_0.8)_0.99,Mn_0.01)O₃), and the electrocaloric effect of the defect-containing ferroelectric ceramics has …

In Situ Monitoring Of Linear Rgd-Peptide Bioconjugation With Nanoscale Polymer Brushes, Evmorfia Psarra, Ulla Konig, Martin Muller, Eva Bittrich, Klaus-Jochen Eichhorn, Petra B. Welzel, Manfred Stamm, Petra Uhlmann

Department of Chemistry: Faculty Publications

Bioinspired materials mimicking the native extracellular matrix environment are promising for biotechnological applications. Particularly, modular biosurface engineering based on the functionalization of stimuli-responsive polymer brushes with peptide sequences can be used for the development of smart surfaces with biomimetic cues. The key aspect of this study is the in situ monitoring and analytical verification of the biofunctionalization process on the basis of three complementary analytical techniques. In situ spectroscopic ellipsometry was used to quantify the amount of chemisorbed GRGDS at both the homopolymer poly(acrylic acid) (PAA) brush and the binary poly(N-isopropylacrylamide) (PNIPAAm)− PAA brushes, which was finally confirmed …

Catalytic Mechanism Of Amyloid-Β Peptide Degradation By Insulin Degrading Enzyme: Insights From Qm/Mm Mp2 Calculation, Rui Lai, Wei-Jen Tang, Hui Li

Department of Chemistry: Faculty Publications

Insulin degrading enzyme (IDE), a metalloprotease that degrades amyloid-β (Aβ) peptides and insulin, is associated with Alzheimer’s disease and diabetes. The mechanism of IDE catalyzed degrading of Aβ peptides, which is of fundamental importance in the design of therapeutic methods for Alzheimer’s disease, has not been fully understood. In this work, combined quantum mechanics and molecular mechanics (QM/MM) style Møller-Plesset second order perturbation theory (MP2) geometry optimization calculations are performed to investigate the catalytic mechanism of the Aβ40 Phe19-Phe20 peptide bond cleavage by human IDE. The analyses using QM/MM MP2 optimization suggest that a …

Molecular Insights Into Organic Particulate Formation, Manoj Kumar, Emily Burrell, Jason C. Hansen, Joseph S. Francisco

Department of Chemistry: Faculty Publications

Carboxylic acids have been detected in particles collected in various regions of the world. Here, we use experiments and Born–Oppenheimer molecular dynamics simulations to better understand the mechanism of particle formation from gas phase mixtures of formic acid (HCOOH), (CH₃)₃N, and water vapor. A flow reaction cell coupled to two scanning mobility particle sizers has been used to measure particle size, absolute number of particles and kinetics of particle formation. Experimental results show that the addition of (CH₃)₃N to a mixture of HCOOH and water vapor results in a dramatic increase in …

In-Situ-Investigation Of Enzyme Immobilization On Polymer Brushes, Meike Koenig, Ulla König, Klaus-Jochen Eichhorn, Martin Muller, Manfred Stamm, Petra Uhlmann

Department of Chemistry: Faculty Publications

Herein, we report on the use of a combined setup of quartz-crystal microbalance, with dissipation monitoring and spectroscopic ellipsometry, to comprehensively investigate the covalent immobilization of an enzyme to a polymer layer. All steps of the covalent reaction of the model enzyme glucose oxidase with the poly(acrylic acid) brush by carbodiimide chemistry, were monitored in-situ. Data were analyzed using optical and viscoelastic modeling. A nearly complete collapse of the polymer chains was found upon activation of the carboxylic acid groups with N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide and N-Hydroxysuccinimide. The reaction with the amine groups of the enzyme occurs simultaneously with re-hydration of the …

Development Of A Microcolumn One-Site Immunometric Assay For A Protein Biomarker: Analysis Of Alpha1-Acid Glycoprotein In Serum, Chenhua Zhang, Shae Lott, William Clarke, David S. Hage

Department of Chemistry: Faculty Publications

A one-site immunometric assay based on affinity microcolumns was developed for the analysis of alpha₁-acid glycoprotein (AGP) as a model protein biomarker. In this assay, a sample containing AGP was incubated with an excess amount of a labeled binding agent, such as fluorescein-labeled anti-AGP antibodies or F_ab fragments. The excess binding agent was removed by passing this mixture through a microcolumn that contained an immobilized form of AGP, while the signal was measured for the binding agent-AGP complex in the non-retained fraction. Theoretical and practical factors were both considered in selecting the concentration of labeled binding agent, …

Nmr Metabolomics Protocols For Drug Discovery, Fatema Bhinderwala, Robert Powers

Department of Chemistry: Faculty Publications

Drug discovery is an extremely difficult and challenging endeavor with a very high failure rate. The task of identifying a drug that is safe, selective and effective is a daunting proposition because disease biology is complex and highly variable across patients. Metabolomics enables the discovery of disease biomarkers, which provides insights into the molecular and metabolic basis of disease and may be used to assess treatment prognosis and outcome. In this regard, metabolomics has evolved to become an important component of the drug discovery process to resolve efficacy and toxicity issues, and as a tool for precision medicine. A detailed …

Reversible Mechanical Deformations Of Soft Microchannel Networks For Sensing In Soft Robotic Systems, Abhiteja Konda, Donghee Lee, Taesun You, Xiaoyan Wang, Sangjin Ryu, Stephen Morin

Department of Chemistry: Faculty Publications

Microfluidics has enabled numerous applications in, for example, analytical chemistry, medical diagnostics, microelectronics, and soft robotics. In most of these applications, the geometries of the microchannels are of fixed dimensions that (ideally) remain invariant during operation. In soft robotics, however, the geometries of the microchannels contained in soft actuation systems are inherently dynamic, and the specific dimensions are expected to change during operation, and, by extension, the fluid transport properties of the system are variable. If this characteristic is not properly considered, or if methods are not developed to control it, the progress of soft robotic devices with distributed fluid …

Design Of Single-Molecule Multiferroics For Efficient Ultrahigh-Density Nonvolatile Memories, Qing Yang, Tingting Zhong, Zhengyuan Tu, Lin Zhu, Menghao Wu, Xiao Cheng Zeng

Department of Chemistry: Faculty Publications

It is known that an isolated single-molecule magnet tends to become super- paramagnetic even at an ultralow temperature of a few Kelvin due to the low spin switching barrier. Herein, single-molecule ferroelectrics/multiferroics is proposed, as the ultimate size limit of memory, such that every molecule can store 1 bit data. The primary strategy is to identify polar molecules that possess bistable states, moderate switching barriers, and polarizations fixed along the vertical direction for high-density perpendicular recording. First- principles computation shows that several selected magnetic metal porphyrin molecules possess buckled structures with switchable vertical polarizations that are robust at ambient conditions. …

Mass Spectrometry And Nuclear Magnetic Resonance In The Chemometric Analysis Of Cellular Metabolism, Eli Riekeberg

Department of Chemistry: Dissertations, Theses, and Student Research

The development and awareness of Machine Learning and “big data” has led to a growing interest in applying these methods to bioanalytical research. Methods such as Mass Spectrometry (MS), and Nuclear Magnetic Resonance (NMR) can now obtain tens of thousands to millions of data points from a single sample, due to fundamental instrumental advances and ever-increasing resolution. Simple pairwise comparisons on datasets of this magnitude can obfuscate more complex underlying trends, and does a disservice to the richness of information contained within. This necessitates the need for multivariate approaches that can more fully take advantage of the complexity of these …

‘Cassette’-Ises (In Situ Enzymatic Screening) Identifies Complementary Chiral Scaffolds For Hydrolytic Kinetic Resolution Across A Range Of Epoxides, Sangeeta Dey, Douglas R. Powell, Chunhua Hu, David B. Berkowitz

Department of Chemistry: Faculty Publications

‘Cassette’-ISES (In Situ Enzymatic Screening) Identifies Complementary Chiral Scaffolds for Hydrolytic Kinetic Resolution Across a Range of Epoxides

A new ‘Cassette’-In Situ Enzymatic Screen (ISES) for combinatorial catalysis is introduced. This allows the experimentalist to obtain an information-rich readout, in real time, providing an estimate of the sense and magnitude of enantioselectivity across more than one substrate. In its first iteration, the screen identified Co^III-salen catalysts with β-pinene- and α-naphthylalanine-derived chiral scaffolds with broad, yet complementary, substrate specificities.

Guanidinium Compounds, Stephen Dimagno, Bao Hu

Department of Chemistry: Faculty Publications

The present application provides , inter alia , chemical com pounds useful as synthesis intermediates , said compounds comprising one or more guanidinium moieties and a hyper valent iodine atom . Methods for making these compounds are also provided.

Radioiodinated Compounds, Stephen Dimagno, Bao Hu

Department of Chemistry: Faculty Publications

This disclosure relates to reagents and methods useful in the synthesis of aryl iodines ,for example , in the preparation of iodine labeled radiotracers . The reagents and methods provided herein may be used to access a broad range of compounds , including aromatic compounds , heteroaromatic compounds , amino acids , nucleotides , and synthetic com pounds .

The Effects Of Cold Plasma Treatment On Sweet Basil (Ocimum Basilicum), Sauvelson Auguste

Seton Hall University Dissertations and Theses (ETDs)

The study discussed herein looks both to continue and to expand upon previous work conducted here at Seton Hall University, which investigated the effect of cold plasma processing on sweet basil and their essential oils. It was found that the application of cold plasma treatment increases plant growth and eugenol concentration, which is an essential oil component and one of the potential natural antioxidants used in food preservation. In this study, we considered methods for increasing the production and harvesting of plants that produce essential oils such as sweet basil (Ocimum basilicum). The study also incorporated more controls …

Nmr Structural Investigation Of Chlamydial Protein Complex And Lysine Glycomimetic For Drug Design, Abigael Chebichiy Songok

LSU Doctoral Dissertations

Research and design of drugs for treatment against microbial infections require the study of pathogenic proteins involved during infection and replication. Drugs can be designed to interfere with the interaction network of these pathogenic proteins and inhibit the infection process. Determination of the structure and ligands of the target proteins in microbes is essential for designing mechanistic-based drugs. Two Chlamydia proteins involved in host cell invasion were investigated in this study. The goal is to identify amino acids involved at the binding interface of Chlamydia chaperon proteins Scc1 and Scc4 by solution NMR spectroscopy. This information will give a lead …