jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mohamed S. El‐Attar | Sadeek A. Sadeek | Sherif M. Abd El‐Hamid | Hazem S. Elshafie
Source: International Journal of Molecular Sciences (article, 2022-07-20)
Field: Chemistry — Organic Chemistry

Spectroscopic Analyses and Antimicrobial Activity of Novel Ciprofloxacin and 7-Hydroxy-4-methylcoumarin, the Plant-Based Natural Benzopyrone Derivative Coumarin is highly distributed in nature, notably in higher plants. The biological features of coumarin include antibacterial, anticancer and antioxidant effects. It is well known that metal ions present in complexes accelerate the drug action and the efficacy of organic therapeutic agents. The main aim of the current study is the synthesis of different complexes of the interaction between ciprofloxacin hydrochloride (CIP) and coumarin derivative 7-hydroxy-4-methylcoumarin (HMC) with Zr(IV). The chelates of CIP with Zr(IV) were prepared and characterized by elemental analysis, melting point, conductance measurements, spectroscopic techniques involving IR, UV-Vis, <sup>1</sup>H NMR, and thermal behavior (TG-DTG) in the presence of HMC, dimethylformamide (DMF), pyridine (Py), and triethylamine (Et<sub>3</sub>N). Results of molar conductivity tests showed that the new synthesized complexes are electrolytes with a 1:1 or 1:2 electrolyte ratio, with the chloride ions functioning as counter ions. According to IR spectra, CIP acts as a neutral bidentate ligand with Zr(IV) through one carboxylato oxygen and the carbonyl group, HMC as a monodentate through the carbonyl group, and DMF through the oxygen atom of the carbonyl group and the N atom of Py and Et<sub>3</sub>N. The thermal behavior of the complexes was carefully investigated using TG and DTG techniques. TG findings signal that water molecules are found as hydrated and coordinated. The thermal decomposition mechanisms proposed for CIP, HMC, and Zr(IV) complexes are discussed and the activation energies (E<sub>a</sub>), Gibbs free energies (∆G*), entropies (∆S*), and enthalpies (∆H*) of thermal decomposition reactions have been calculated using Coats-Redfern (CR) and Horowitz-Metzeger (HM) methods. The studied complexes were tested against some human pathogens and phytopathogens, including three Gram-positive bacteria (<i>Bacillus subtilis</i>, <i>B. cereus</i>, <i>Brevibacterium otitidis</i>) and three Gram-negative bacteria (<i>Escherichia</i><i>coli</i>, <i>Pseudomonas aeruginosa</i> and <i>Klebsiella pneumoniae</i>), and compared to the free CIP and HMC parent compounds. Antimicrobial ; Ciprofloxacin ; Derivative (finance) ; Natural compound ; Biology ; Chemistry ; Stereochemistry ; Microbiology ; Traditional medicine ; Antibiotics ; Medicine ; Business ; Engineering ; Biochemical engineering Synthesis and biological activity ; Bioactive Compounds and Antitumor Agents ; Essential Oils and Antimicrobial Activity
Authors: Isabela Sales | Dinis O. Abranches | Tânia E. Sintra | Silvana Mattedi | Mara G. Freire | João A. P. Coutinho | Simão P. Pinho
Source: Fluid Phase Equilibria (article, 2022-07-19)
Field: Chemistry — Organic Chemistry

Selection of hydrotropes for enhancing the solubility of artemisinin in aqueous solutions Chemistry ; Solubility ; Solvatochromism ; Artemisinin ; Solvent ; Aqueous solution ; Solvation ; Organic chemistry Surfactants and Colloidal Systems ; Crystallization and Solubility Studies ; Analytical Chemistry and Chromatography
Authors: Erich Hellemann | Jennifer L. Walker | Mitchell A. Lesko | Dakshayini G. Chandrashekarappa | Martin C. Schmidt | Allyson F. O’Donnell | Jacob D. Durrant
Source: PLoS Computational Biology (article, 2022-03-02)
Field: Materials Science — Materials Chemistry

Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics Glucose is central to many biological processes, serving as an energy source and a building block for biosynthesis. After glucose enters the cell, hexokinases convert it to glucose-6-phosphate (Glc-6P) for use in anaerobic fermentation, aerobic oxidative phosphorylation, and the pentose-phosphate pathway. We here describe a genetic screen in Saccharomyces cerevisiae that generated a novel spontaneous mutation in hexokinase-2, hxk2G238V, that confers resistance to the toxic glucose analog 2-deoxyglucose (2DG). Wild-type hexokinases convert 2DG to 2-deoxyglucose-6-phosphate (2DG-6P), but 2DG-6P cannot support downstream glycolysis, resulting in a cellular starvation-like response. Curiously, though the hxk2G238V mutation encodes a loss-of-function allele, the affected amino acid does not interact directly with bound glucose, 2DG, or ATP. Molecular dynamics simulations suggest that Hxk2G238V impedes sugar binding by altering the protein dynamics of the glucose-binding cleft, as well as the large-scale domain-closure motions required for catalysis. These findings shed new light on Hxk2 dynamics and highlight how allosteric changes can influence catalysis, providing new structural insights into this critical regulator of carbohydrate metabolism. Given that hexokinases are upregulated in some cancers and that 2DG and its derivatives have been studied in anti-cancer trials, the present work also provides insights that may apply to cancer biology and drug resistance. Hexokinase ; Biochemistry ; Glycolysis ; Allosteric regulation ; Biology ; Saccharomyces cerevisiae ; Pentose phosphate pathway ; Mutant ; Mutation ; Glucose 6-phosphate ; Cell biology ; Enzyme ; Yeast ; Gene Enzyme Structure and Function ; Metabolism, Diabetes, and Cancer ; Biochemical and Molecular Research
Authors: Han‐Yue Zhang
Source: Chemical Science (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

A small-molecule organic ferroelectric with piezoelectric voltage coefficient larger than that of lead zirconate titanate and polyvinylidene difluoride Piezoelectric materials that generate electricity when deforming are ideal for many implantable medical sensing devices. In modern piezoelectric materials, inorganic ceramics and polymers are two important branches, represented by lead zirconate titanate (PZT) and polyvinylidene difluoride (PVDF). However, PVDF is a nondegradable plastic with poor crystallinity and a large coercive field, and PZT suffers from high sintering temperature and toxic heavy element. Here, we successfully design a metal-free small-molecule ferroelectric, 3,3-difluorocyclobutanammonium hydrochloride ((3,3-DFCBA)Cl), which has high piezoelectric voltage coefficients <i>g</i> <sub>33</sub> (437.2 × 10<sup>-3</sup> V m N<sup>-1</sup>) and <i>g</i> <sub>31</sub> (586.2 × 10<sup>-3</sup> V m N<sup>-1</sup>), a large electrostriction coefficient <i>Q</i> <sub>33</sub> (about 4.29 m<sup>4</sup> C<sup>-2</sup>) and low acoustic impedance <i>z</i> <sub>0</sub> (2.25 × 10<sup>6</sup> kg s<sup>-1</sup> m<sup>-2</sup>), significantly outperforming PZT (<i>g</i> <sub>33</sub> = 34 × 10<sup>-3</sup> V m N<sup>-1</sup> and <i>z</i> <sub>0</sub> = 2.54 × 10<sup>7</sup> kg s<sup>-1</sup> m<sup>-2</sup>) and PVDF (<i>g</i> <sub>33</sub> = 286.7 × 10<sup>-3</sup> V m N<sup>-1</sup>, <i>g</i> <sub>31</sub> = 185.9 × 10<sup>-3</sup> V m N<sup>-1</sup>, <i>Q</i> <sub>33</sub> = 1.3 m<sup>4</sup> C<sup>-2</sup>, and <i>z</i> <sub>0</sub> = 3.69 × 10<sup>6</sup> kg s<sup>-1</sup> m<sup>-2</sup>). Such a low acoustic impedance matches that of the body (1.38-1.99 × 10<sup>6</sup> kg s<sup>-1</sup> m<sup>-2</sup>) reasonably well, making it attractive as next-generation biocompatible piezoelectric devices for health monitoring and "disposable" invasive medical ultrasound imaging. Lead zirconate titanate ; Piezoelectricity ; Ferroelectricity ; Materials science ; Polyvinylidene fluoride ; Difluoride ; Zirconate ; Titanate ; Composite material ; Chemical engineering ; Chemistry ; Inorganic chemistry ; Optoelectronics ; Polymer ; Ceramic Ferroelectric and Piezoelectric Materials ; Acoustic Wave Resonator Technologies ; Perovskite Materials and Applications
Authors: Liang Xu | Xueting Long | Jiaxing He | Lingxiu Liu | Fangyuan Kang | Ziqi Deng | Jieyu Wu | Xiaofang Jiang | Jianguo Wang | Qichun Zhang
Source: Journal of Materials Chemistry C (article, 2022-10-11)
Field: Materials Science — Materials Chemistry

Aggregation effects on the one- and two-photon excited fluorescence performance of regioisomeric anthraquinone-substituted perylenediimide The isomerism effect on the aggregate emission properties of perylene diimide derivatives is studied. Banking on their bright emission, a cellular imaging test based on their nanoparticles is also conducted. Perylene ; Aggregation-induced emission ; Diimide ; Fluorescence ; Materials science ; Anthraquinone ; Excited state ; Photochemistry ; Anthracene ; Aggregate (composite) ; Nanoparticle ; Optoelectronics ; Nanotechnology ; Organic chemistry ; Optics ; Atomic physics ; Chemistry Luminescence and Fluorescent Materials ; Photochromic and Fluorescence Chemistry ; Nanoplatforms for cancer theranostics
Authors: Mojtaba Ghodsi | Morteza Mohammadzaheri | Payam Soltani | Hamidreza Ziaifar
Source: Journal of Magnetism and Magnetic Materials (article, 2022-05-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A new active anti-vibration system using a magnetostrictive bimetal actuator This paper introduces a new vibration reduction system using a magnetostrictive (Fe-Ga alloy) bimetal actuator. The proposed method (i) uses a magnetostrictive bimetal actuator instead of prevalent single material ones that need an auxiliary temperature control system and (ii) utilises a novel disturbance rejection control scheme that eliminates an unknown disturbance, without needing knowledge of its dynamics. In experiments, the vibration source is demonstrated as an unbalanced motor attached to the tip of a cantilever beam, resembling a beam-like element subject to ambiance vibrations. In the first step, the fundamental of this anti-vibration system is introduced and described. Then, analytical and data-driven modelling for the combination of the beam, the motor, and the bimetal is reported. These follow by model validation and impulse response analysis. Then, the proposed control system is introduced in detail. Experimental results indicate that the control system results in 33.6% decrease in beam vibration amplitude. Furthermore, the presented method in this paper can be employed as a design guideline for future applications. Bimetal ; Vibration ; Actuator ; Magnetostriction ; Active vibration control ; Materials science ; Beam (structure) ; Vibration control ; Cantilever ; Computer science ; Control theory (sociology) ; Impulse (physics) ; Acoustics ; Structural engineering ; Engineering ; Physics ; Composite material ; Control (management) Magnetic Properties and Applications ; Aeroelasticity and Vibration Control ; Shape Memory Alloy Transformations
Authors: Ya-Chi Liu | Yi‐Chung Dzeng | Chao-Cheng Ting
Source: IEEE Nanotechnology Magazine (article, 2022-06-14)
Field: Materials Science — Materials Chemistry

Nitrogen Vacancy-Centered Diamond Qubit: The fabrication, design, and application in quantum computing Quantum computing has gained enormous attention from both academia and industry for its capability in handling problems that challenge the limit of classical computation. It is expected to shine in areas such as artificial intelligence, financial technology, drug development, and chemical reaction modeling. The quantum bit, or qubit, is the essential unit of quantum computers (QCs), and there are different types of implementations of the qubit, such as superconductor-based qubits, trapped ion qubits, quantum dot qubits, photonic qubits, topological qubits, and nitrogen vacancy (NV) diamond qubits, which are known to be able to function at room temperature with high longevity. In this article, NV-centered diamond fabrication, qubit structure, bit control, entanglement, and decoherence, as well as the pros and cons, are briefly introduced. At the end, the status of the commercialization of NV diamond QCs and the benchmark of different types of qubits are summarized. Qubit ; Quantum computer ; Quantum entanglement ; Quantum teleportation ; Diamond ; Quantum decoherence ; Cluster state ; Quantum technology ; Physics ; Nanotechnology ; Quantum mechanics ; Topology (electrical circuits) ; Quantum ; Quantum network ; Materials science ; Open quantum system ; Electrical engineering ; Engineering Diamond and Carbon-based Materials Research ; Electronic and Structural Properties of Oxides ; Semiconductor materials and devices
Authors: Guangmao Li | Zhihua Yang | Shilie Pan
Source: Science China Materials (article, 2022-11-08)
Field: Materials Science — Electronic, Optical and Magnetic Materials

LiAlS2: A promising infrared frequency-conversion material with ultrawide band gap and high laser-induced damage threshold Materials science ; Band gap ; Infrared ; Laser ; Optoelectronics ; Second-harmonic generation ; Refractive index ; Dispersion (optics) ; Far-infrared laser ; Absorption (acoustics) ; Optics Crystal Structures and Properties ; Nonlinear Optical Materials Research ; Solid-state spectroscopy and crystallography
Authors: Donya Esmaeilpour | Jens Broscheit | Sergey Shityakov
Source: International Journal of Molecular Sciences (review, 2022-11-04)
Field: Materials Science — Biomaterials

Cyclodextrin-Based Polymeric Materials Bound to Corona Protein for Theranostic Applications Cyclodextrins (CDs) are cyclic oligosaccharide structures that could be used for theranostic applications in personalized medicine. These compounds have been widely utilized not only for enhancing drug solubility, stability, and bioavailability but also for controlled and targeted delivery of small molecules. These compounds can be complexed with various biomolecules, such as peptides or proteins, via host-guest interactions. CDs are amphiphilic compounds with water-hating holes and water-absorbing surfaces. Architectures of CDs allow the drawing and preparation of CD-based polymers (CDbPs) with optimal pharmacokinetic and pharmacodynamic properties. These polymers can be cloaked with protein corona consisting of adsorbed plasma or extracellular proteins to improve nanoparticle biodistribution and half-life. Besides, CDs have become famous in applications ranging from biomedicine to environmental sciences. In this review, we emphasize ongoing research in biomedical fields using CD-based centered, pendant, and terminated polymers and their interactions with protein corona for theranostic applications. Overall, a perusal of information concerning this novel approach in biomedicine will help to implement this methodology based on host-guest interaction to improve therapeutic and diagnostic strategies. Nanotechnology ; Biomolecule ; Amphiphile ; Biomedicine ; Dendrimer ; Nanomedicine ; Chemistry ; Polymer ; Small molecule ; Drug delivery ; Nanoparticle ; Cyclodextrin ; Biodistribution ; Combinatorial chemistry ; Materials science ; Organic chemistry ; Copolymer ; Bioinformatics ; Biochemistry Nanoparticle-Based Drug Delivery ; Polymer Surface Interaction Studies ; Advanced Polymer Synthesis and Characterization
Authors: Marko Antonijević | Edina Avdović | Dušica Simijonović | Žiko Milanović | Ana Amić | Zoran Marković
Source: International Journal of Molecular Sciences (article, 2022-01-01)
Field: Chemistry — Organic Chemistry

Radical Scavenging Activity and Pharmacokinetic Properties of Coumarin–Hydroxybenzohydrazide Hybrids Free radicals often interact with vital proteins, violating their structure and inhibiting their activity. In previous studies, synthesis, characterisation, and the antioxidative properties of the five different coumarin derivatives have been investigated. In the tests of potential toxicity, all compounds exhibited low toxicity with significant antioxidative potential at the same time. In this paper, the radical scavenging activity of the abovementioned coumarin derivatives towards ten different radical species was investigated. It was found that all investigated compounds show good radical scavenging ability, with results that are in correlation with the results published in the previous study. Three additional mechanisms of radical scavenging activity were investigated. It was found that all three mechanisms are thermodynamically plausible and in competition. Interestingly, it was found that products of the Double Hydrogen Atom Transfer (DHAT) mechanism, a biradical species in triplet spin state, are in some cases more stable than singlet spin state analogues. This unexpected trend can be explained by spin delocalisation over the hydrazide bridge and phenolic part of the molecule with a low probability of spin pairing. Besides radical-scavenging activity, the pharmacokinetic and drug-likeness of the coumarin hybrids were investigated. It was found that they exhibit good membrane and skin permeability and potential interactions with P-450 enzymes. Furthermore, it was found that investigated compounds satisfy all criteria of the drug-likeness tests, suggesting they possess a good preference for being used as potential drugs. Chemistry ; Scavenging ; Radical ; Coumarin ; Singlet state ; Membrane permeability ; Molecule ; Photochemistry ; Stereochemistry ; Computational chemistry ; Antioxidant ; Organic chemistry ; Membrane ; Biochemistry ; Excited state Free Radicals and Antioxidants ; Photochemistry and Electron Transfer Studies ; Electron Spin Resonance Studies
Authors: Luke T. Richardson | Elizabeth K. Neumann | Richard M. Caprioli | Jeffrey M. Spraggins | Touradj Solouki
Source: Analytical Chemistry (article, 2022-03-28)
Field: Chemistry — Spectroscopy

Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments Because of their diverse functionalities in cells, lipids are of primary importance when characterizing molecular profiles of physiological and disease states. Imaging mass spectrometry (IMS) provides the spatial distributions of lipid populations in tissues. Referenced Kendrick mass defect (RKMD) analysis is an effective mass spectrometry (MS) data analysis tool for classification and annotation of lipids. Herein, we extend the capabilities of RKMD analysis and demonstrate an integrated method for lipid annotation and chemical structure-based filtering for IMS datasets. Annotation of lipid features with lipid molecular class, radyl carbon chain length, and degree of unsaturation allows image reconstruction and visualization based on each structural characteristic. We show a proof-of-concept application of the method to a computationally generated IMS dataset and validate that the RKMD method is highly specific for lipid components in the presence of confounding background ions. Moreover, we demonstrate an application of the RKMD-based annotation and filtering to matrix-assisted laser desorption/ionization (MALDI) IMS lipidomic data from human kidney tissue analysis. Mass spectrometry imaging ; Chemistry ; Lipidomics ; Degree of unsaturation ; Annotation ; Mass spectrometry ; Computational biology ; Matrix-assisted laser desorption/ionization ; Chromatography ; Pattern recognition (psychology) ; Artificial intelligence ; Computer science ; Biochemistry ; Desorption Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Ning Zhu | Fanyi Dong | Guobang Shi | Xingzhen Lao | Heng Zheng
Source: Scientific Data (article, 2022-04-25)
Field: Chemistry — Spectroscopy

HORDB a comprehensive database of peptide hormones Peptide hormones (also known as hormone peptides and polypeptide hormones) are hormones composed of peptides and are signal transduction molecules produced by a class of multicellular organisms. It plays an important role in the physiological and behavioral regulation of animals and humans as well as in the growth of plants. In order to promote the research on peptide hormones, we constructed HORDB database. The database currently has a total of 6024 entries, including 5729 peptide hormones, 40 peptide drugs and 255 marketed pharmaceutical preparations information. Each entry provided comprehensive information related to the peptide, including general information, sequence, activity, structure, physical information and literature information. We also added information on IC<sub>50</sub>, EC<sub>50</sub>, ED<sub>50</sub>, target, and whether or not the blood-brain barrier was crossed to the activity information note. In addition, HORDB integrates search and sequence analysis to facilitate user browsing and data analysis. We believe that the peptide hormones information collected by HORDB will promote the design and discovery of peptide hormones, All data are hosted and available in figshare https://doi.org/10.6084/m9.figshare.c.5522241 . Hormone ; Peptide ; Database ; Computational biology ; Biology ; Bioinformatics ; Computer science ; Endocrinology ; Biochemistry Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Receptor Mechanisms and Signaling
Authors: Kazuki Okazawa | Yuta Tsuji | Keita Kurino | Masataka Yoshida | Yoshifumi Amamoto | Kazunari Yoshizawa
Source: ACS Omega (article, 2022-11-30)
Field: Materials Science — Materials Chemistry

Exploring the Optimal Alloy for Nitrogen Activation by Combining Bayesian Optimization with Density Functional Theory Calculations Binary alloy catalysts have the potential to exhibit higher activity than monometallic catalysts in nitrogen activation reactions. However, owing to the multiple possible combinations of metal elements constituting binary alloys, an exhaustive search for the optimal combination is difficult. In this study, we searched for the optimal binary alloy catalyst for nitrogen activation reactions using a combination of Bayesian optimization and density functional theory calculations. The optimal alloy catalyst proposed by Bayesian optimization had a surface energy of ∼0.2 eV/Å<sup>2</sup> and resulted in a low reaction heat for the dissociation of the N≡N bond. We demonstrated that the search for such binary alloy catalysts using Bayesian optimization is more efficient than random search. Density functional theory ; Bayesian optimization ; Alloy ; Catalysis ; Binary number ; Bayesian probability ; Materials science ; Dissociation (chemistry) ; Chemistry ; Thermodynamics ; Computational chemistry ; Mathematical optimization ; Computer science ; Mathematics ; Physical chemistry ; Physics ; Metallurgy ; Artificial intelligence ; Organic chemistry Machine Learning in Materials Science ; Ammonia Synthesis and Nitrogen Reduction ; Catalytic Processes in Materials Science