Chemistry & Biochemistry Research Works
Permanent URI for this collectionhttp://hdl.handle.net/1903/15
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Item Acyclic Cucurbit[n]uril Bearing Alkyl Sulfate Ionic Groups - Electronic Supporting Data(Beilstein Journal of Organic Chemistry, 2025-01-09) Akakpo, Christian; Zavalij, Peter Y.; Isaacs, LyleThis dataset contains the electronic data files that support the publication.Item Quantifying modeling uncertainties in seismic analysis of dams: Insights from an international benchmark study(Wiley, 2023-12-19) Hariri-Ardebili, Mohammad AminAdvances in nonlinear dynamic analysis of dams have not completely resolved concerns over modeling confidence and analysis accuracy. Verification and validation offer accuracy assessment, but uncertainties persist during performance evaluation due to both epistemic (modeling) and aleatory (parametric) sources. Epistemic uncertainties arise from simplifications and modeling techniques. This paper addresses epistemic uncertainties in a gravity dam seismic analysis using data from the International Comnission on Large Dams (ICOLD) benchmark study. While the benchmark formulation included the finite element model of the dam, mechanical material properties, and dynamic loads, participants retained the flexibility to opt for best-practice modeling assumptions, simplifications, and other specifics. Notable response variability emerged, particularly in crack profiles and damage predictions. This study examines sources of variability, quantifying modeling uncertainty for the benchmark problem. More specifically, the modeling variability is quantified using the logarithmic standard deviation, also known as dispersion. This metric enables its incorporation into other seismic risk assessment and fragility studies. Under relatively low-intensity motion (peak ground acceleration [PGA] of 0.18 g in this case), modeling dispersion of 0.45, 0.30, 0.32, and 0.30 were calculated for the maximum dynamic crest displacement, maximum hydrodynamic pressure at the heel, heel and crest maximum acceleration, respectively. Additionally, the dispersion of the failure PGA was determined to be 0.7. Findings underscore the need for systematic seismic response modeling in dam engineering to enhance prediction accuracy. A better understanding of the sources and magnitudes of modeling uncertainties can help improve the reliability of dam seismic analysis and contribute to the development of more effective risk assessment and mitigation strategies.Item Comments regarding “Seismic damage analysis due to near-fault multipulse ground motion” by Guan Chen, Jiashu Yang, Ruohan Wang, Kaiqi Li, Yong Liu, Michael Beer; Earthquake Engineering & Structural Dynamics, 2023(Wiley, 2023-11-27) Hariri-Ardebili, Mohammad AminThis discussion is based on the paper by Chen et al. in 2023 (hereafter referred to as “the original paper/authors”). In their study, the original authors conducted a series of analyses using nonpulse, single-pulse, and multipulse ground motion records, evaluating their impact on a frame structure, a slope, and a gravity dam. Their key finding suggests that multipulse ground motion leads to more severe structural damage compared to nonpulse and single-pulse ground motions. However, it is important to note that the seismic damage analysis of the gravity dam in this paper does not adhere to state-of-the-practice recommendations. Consequently, drawing a definitive conclusion regarding the influence and importance of multipulse ground motion records on the seismic response of concrete dams requires further justification. This necessitates the incorporation of high-fidelity numerical models and probabilistic performance evaluation. We will discuss the significance of modeling assumptions, specifically addressing the dam–rock dynamic interaction in crack propagation and failure in dams.Item Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation(Springer Nature, 2023-11-08) Lemma, Betsegaw; Zhang, Di; Vamisetti, Ganga B.; Wentz, Bryan G.; Suga, Hiroaki; Brik, Ashraf; Lubkowski, Jacek; Fushman, DavidPost-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide's affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.Item Structural modulation and spin glassiness upon oxidation in oxygen storage material LnFeMnO4+x for Ln = Y, Lu, and Yb(AIP, 2023-06-12) Li, Tianyu; Liou, Sz-Chian; Hong, Stephanie J.; Zhang, Qiang; Mandujano, H. Cein; Rodriguez, Efrain E.The mixed valence multiferroic LnFe2+Fe3+O4 (where Ln = Y, Lu, and Yb) can reversibly uptake oxygen into its lattice, which is evidenced by a crystallographic phase transition along with the appearance of structural modulations. In this study, we show that the Mn-substituted version of this multiferroic can also be readily oxidized to LnFe3+Mn3+O4.5 revealing similar oxygen storage behavior. Through neutron, electron, and synchrotron x-ray diffraction studies, we observe a structural modulation that we attribute to a displacement wave in the fully oxidized compound. This wave exhibits commensurability with a wavevector q = (−2/7, 1/7, 0). Bond valence summation analysis of plausible interstitial oxygen positions suggests that oxygen insertion likely occurs at the middle of the Fe/Mn–O bipyramid layers. The structural modulation of LnFeMnO4.5 is two-dimensional, propagates along the ab-plane, and is highly symmetric as 12 identical modulation vectors are observed in the diffraction patterns. The nature of the lanthanide, Ln3+, does not seem to influence such modulations since we observe identical satellite reflections for all three samples of Ln = Y, Lu, and Yb. Both LnFeMnO4 and LnFeMnO4.5 display spin glassy behavior with 2D short-range magnetic ordering being observed in LnFeMnO4. Analysis of the neutron diffraction data reveals a correlation length of ∼10 nm. Upon oxidation to LnFeMnO4.5, the short-range magnetic order is significantly suppressed.Item Polymerization Reactions and Modifications of Polymers by Ionizing Radiation(MDPI, 2020-11-30) Ashfaq, Aiysha; Clochard, Marie-Claude; Coqueret, Xavier; Dispenza, Clelia; Driscoll, Mark S.; Ulański, Piotr; Al-Sheikhly, MohamadIonizing radiation has become the most effective way to modify natural and synthetic polymers through crosslinking, degradation, and graft polymerization. This review will include an in-depth analysis of radiation chemistry mechanisms and the kinetics of the radiation-induced C-centered free radical, anion, and cation polymerization, and grafting. It also presents sections on radiation modifications of synthetic and natural polymers. For decades, low linear energy transfer (LLET) ionizing radiation, such as gamma rays, X-rays, and up to 10 MeV electron beams, has been the primary tool to produce many products through polymerization reactions. Photons and electrons interaction with polymers display various mechanisms. While the interactions of gamma ray and X-ray photons are mainly through the photoelectric effect, Compton scattering, and pair-production, the interactions of the high-energy electrons take place through coulombic interactions. Despite the type of radiation used on materials, photons or high energy electrons, in both cases ions and electrons are produced. The interactions between electrons and monomers takes place within less than a nanosecond. Depending on the dose rate (dose is defined as the absorbed radiation energy per unit mass), the kinetic chain length of the propagation can be controlled, hence allowing for some control over the degree of polymerization. When polymers are submitted to high-energy radiation in the bulk, contrasting behaviors are observed with a dominant effect of cross-linking or chain scission, depending on the chemical nature and physical characteristics of the material. Polymers in solution are subject to indirect effects resulting from the radiolysis of the medium. Likewise, for radiation-induced polymerization, depending on the dose rate, the free radicals generated on polymer chains can undergo various reactions, such as inter/intramolecular combination or inter/intramolecular disproportionation, b-scission. These reactions lead to structural or functional polymer modifications. In the presence of oxygen, playing on irradiation dose-rates, one can favor crosslinking reactions or promotes degradations through oxidations. The competition between the crosslinking reactions of C-centered free radicals and their reactions with oxygen is described through fundamental mechanism formalisms. The fundamentals of polymerization reactions are herein presented to meet industrial needs for various polymer materials produced or degraded by irradiation. Notably, the medical and industrial applications of polymers are endless and thus it is vital to investigate the effects of sterilization dose and dose rate on various polymers and copolymers with different molecular structures and morphologies. The presence or absence of various functional groups, degree of crystallinity, irradiation temperature, etc. all greatly affect the radiation chemistry of the irradiated polymers. Over the past decade, grafting new chemical functionalities on solid polymers by radiation-induced polymerization (also called RIG for Radiation-Induced Grafting) has been widely exploited to develop innovative materials in coherence with actual societal expectations. These novel materials respond not only to health emergencies but also to carbon-free energy needs (e.g., hydrogen fuel cells, piezoelectricity, etc.) and environmental concerns with the development of numerous specific adsorbents of chemical hazards and pollutants. The modification of polymers through RIG is durable as it covalently bonds the functional monomers. As radiation penetration depths can be varied, this technique can be used to modify polymer surface or bulk. The many parameters influencing RIG that control the yield of the grafting process are discussed in this review. These include monomer reactivity, irradiation dose, solvent, presence of inhibitor of homopolymerization, grafting temperature, etc. Today, the general knowledge of RIG can be applied to any solid polymer and may predict, to some extent, the grafting location. A special focus is on how ionizing radiation sources (ion and electron beams, UVs) may be chosen or mixed to combine both solid polymer nanostructuration and RIG. LLET ionizing radiation has also been extensively used to synthesize hydrogel and nanogel for drug delivery systems and other advanced applications. In particular, nanogels can either be produced by radiation-induced polymerization and simultaneous crosslinking of hydrophilic monomers in “nanocompartments”, i.e., within the aqueous phase of inverse micelles, or by intramolecular crosslinking of suitable water-soluble polymers. The radiolytically produced oxidizing species from water, •OH radicals, can easily abstract H-atoms from the backbone of the dissolved polymers (or can add to the unsaturated bonds) leading to the formation of C-centered radicals. These C-centered free radicals can undergo two main competitive reactions; intramolecular and intermolecular crosslinking. When produced by electron beam irradiation, higher temperatures, dose rates within the pulse, and pulse repetition rates favour intramolecular crosslinking over intermolecular crosslinking, thus enabling a better control of particle size and size distribution. For other water-soluble biopolymers such as polysaccharides, proteins, DNA and RNA, the abstraction of H atoms or the addition to the unsaturation by •OH can lead to the direct scission of the backbone, double, or single strand breaks of these polymers.Item Potentiometric Carbon Quantum Dots-Based Screen-Printed Arrays for Nano-Tracing Gemifloxacin as a Model Fluoroquinolone Implicated in Antimicrobial Resistance(MDPI, 2020-12-30) Ayad, Miriam F.; Trabik, Yossra A.; Abdelrahman, Mona H.; Fares, Nermine V.; Magdy, NancyAntimicrobial resistance (AMR) is a neglected issue that poses a serious global threat to public health, causing long-term negative consequences at both humanitarian and economic levels. Herein, we report an unprecedented economic fabrication method of seven potentiometric screen-printed sensors for the ultra-trace determination of gemifloxacin (GEMI) as a model of the fluoroquinolones antibiotics deeply involved in the growing AMR problem. Sensors were constructed by depositing homemade carbon ink on a recycled X-ray sheet, patterned using stencils printed with an office printer in simple, cost-effective steps requiring no sophisticated equipment. Four sensors were modified using carbon quantum dots (CQDs) synthesized from dextrose through a single-step method. Sensors exhibited a linear response in the concentration ranges 10−5–10−2 M (sensors 1, 3 and 4), 10−6–10−3 M (sensor 2) and 10−6–10−2 M (sensors 5, 6 and 7). LOD allowed tracing of the target drug at a nano-molar level down to 210 nM. GEMI was successfully determined in pharmaceutical formulations and different water samples without any pretreatment steps with satisfactory recovery (96.93–105.28% with SD values < 3). All sensors revealed a long lifetime of up to several months and are considered promising tools for monitoring water quality and efficiency of water treatment measures.Item Intracellular Delivery of Active Proteins by Polyphosphazene Polymers(MDPI, 2021-02-10) Qamar, Bareera; Solomon, Melani; Marin, Alexander; Fuerst, Thomas R.; Andrianov, Alexander K.; Muro, SilviaAchieving intracellular delivery of protein therapeutics within cells remains a significant challenge. Although custom formulations are available for some protein therapeutics, the development of non-toxic delivery systems that can incorporate a variety of active protein cargo and maintain their stability, is a topic of great relevance. This study utilized ionic polyphosphazenes (PZ) that can assemble into supramolecular complexes through non-covalent interactions with different types of protein cargo. We tested a PEGylated graft copolymer (PZ-PEG) and a pyrrolidone containing linear derivative (PZ-PYR) for their ability to intracellularly deliver FITC-avidin, a model protein. In endothelial cells, PZ-PYR/protein exhibited both faster internalization and higher uptake levels than PZ-PEG/protein, while in cancer cells both polymers achieved similar uptake levels over time, although the internalization rate was slower for PZ-PYR/protein. Uptake was mediated by endocytosis through multiple mechanisms, PZ-PEG/avidin colocalized more profusely with endo-lysosomes, and PZ-PYR/avidin achieved greater cytosolic delivery. Consequently, a PZ-PYR-delivered anti-F-actin antibody was able to bind to cytosolic actin filaments without needing cell permeabilization. Similarly, a cell-impermeable Bax-BH3 peptide known to induce apoptosis, decreased cell viability when complexed with PZ-PYR, demonstrating endo-lysosomal escape. These biodegradable PZs were non-toxic to cells and represent a promising platform for drug delivery of protein therapeutics.Item Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies(MDPI, 2021-09-14) Olenginski, Lukasz T.; Taiwo, Kehinde M.; LeBlanc, Regan M.; Dayie, Theodore K.RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.Item On the Mechanism and Kinetics of Synthesizing Polymer Nanogels by Ionizing Radiation-Induced Intramolecular Crosslinking of Macromolecules(MDPI, 2021-10-22) Ashfaq, Aiysha; An, Jung-Chul; Ulański, Piotr; Al-Sheikhly, MohamadNanogels—internally crosslinked macromolecules—have a growing palette of potential applications, including as drug, gene or radioisotope nanocarriers and as in vivo signaling molecules in modern diagnostics and therapy. This has triggered considerable interest in developing new methods for their synthesis. The procedure based on intramolecular crosslinking of polymer radicals generated by pulses of ionizing radiation has many advantages. The substrates needed are usually simple biocompatible polymers and water. This eliminates the use of monomers, chemical crosslinking agents, initiators, surfactants, etc., thus limiting potential problems with the biocompatibility of products. This review summarizes the basics of this method, providing background information on relevant aspects of polymer solution thermodynamics, radiolysis of aqueous solutions, generation and reactions of polymer radicals, and the non-trivial kinetics and mechanism of crosslinking, focusing on the main factors influencing the outcomes of the radiation synthesis of nanogels: molecular weight of the starting polymer, its concentration, irradiation mode, absorbed dose of ionizing radiation and temperature. The most important techniques used to perform the synthesis, to study the kinetics and mechanism of the involved reactions, and to assess the physicochemical properties of the formed nanogels are presented. Two select important cases, the synthesis of nanogels based on polyvinylpyrrolidone (PVP) and/or poly(acrylic acid) (PAA), are discussed in more detail. Examples of recent application studies on radiation-synthesized PVP and PAA nanogels in transporting drugs across the blood–brain barrier and as targeted radioisotope carriers in nanoradiotherapy are briefly described.
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